Physical science {chemistry} can study analytical, biochemical, physical, general, and organic chemistry.
Chemistry {inorganic chemistry} can be about substances, reactions, acids, bases, oxidations, reductions, and phases.
Moles {mole, chemistry}| is mass, in grams, divided by molecular weight, in atomic mass units. Substance mass, in grams, is moles multiplied by substance molecular weight, in atomic mass units.
An alchemic substance {philosopher's stone}| can control nature by strengthening essence in each thing.
Physical and chemical tests {chemical test} {property test} can reveal chemicals present.
process
To identify chemical, test the following properties in sequence.
Check color. Check odor.
For state, find solid crystal group, liquid viscosity, or gas nature. Check melting or boiling point.
For solubility, check in water, organic solvent, base, bicarbonate, hydrochloric acid, and sulfuric acid, which protonates O, N, and S.
For combustion, use Beilstein test for halides, ignition test for highly unsaturated or aromatic organic chemicals, and flame test for metals.
process: chemical tests
Use chemical tests for chemical groups.
Sodium iodide in acetone detects halides.
Ferrous hydroxide detects nitro- groups.
Bayer test or bromine in carbon tetrachloride detects double bonds.
Tollen's test detects aldehydes.
Iodoform, dinitrophenylhydrazine, and chromic-acid tests detect aldehydes and ketones.
Sodium bicarbonate, silver nitrate, and neutralization with base, on pH paper or in meter, detect carboxylic acid.
Sodium hydroxide, ferric chloride, and bromine water detect phenols.
Hinsberg test and nitrous acid detect amines.
Acetyl chloride, Lucas test, and chromic acid detect alcohols.
Ferric hydroamate or hydrolysis with base detects esters.
process: spectroscopy
Spectroscopy detects cyano- groups. Infrared spectroscopy detects chemical bonds. Ultraviolet-visible spectroscopy detects aromatic chemical groups. Nuclear magnetic resonance (NMR) detects electron densities. Mass spectroscopy detects elements.
Chemical names {chemical naming} have formats.
name from formula
Chemical name comes from chemical formula. In general, write name for each symbol in formula in same sequence as in formula, in order of increasing electronegativity.
To write correct symbol names, first check formula for complex ions.
Then check for atom or ion valences or charges.
Write first atom or ion name.
If molecule is ionic, and metal ion can have more than one valence number, write metal-ion valence in roman numerals in parentheses.
For covalent molecules, if number of attached oxygens or other atoms is one, write "mono-". If two, write "di-". If three, write "tri-". If four, write "tetra-". If five, write "penta-". If six, write "hexa-".
If molecule is ionic, write second-ion root. If molecule is covalent, write root of atom with attached oxygens or other atoms.
Always add "-ide" to root.
For example, the ionic compound FeCl2 [2 is subscript] is iron (II) chloride. The covalent compound SO2 [2 is subscript] is sulfur dioxide.
Acid names {acid naming} have the following rules. If anion name ends in "-ide", start with "hydro-", add anion root, and then add "-ic acid", as in hydrochloric acid. If anion name ends in "-ate", start with anion root and then add "-ic acid", as in sulfuric acid. If anion name ends in "-ite", start with anion root and then add "-ous acid", as in sulfurous acid.
Polyatomic ion names {complex ion naming} can have five parts.
hydrogen
If ion has one hydrogen, begin name with "hydrogen". For two hydrogens, begin with "dihydrogen". For three hydrogens, begin with "trihydrogen".
oxygen
If ion central atom can attach oxygen in more than two ways, use prefix "per-" for ion with the most oxygen atoms or prefix "hypo-" for ion with the least oxygen atoms.
root
Then use central atom root. Root for C is carbon-. Root for N is nitr-. Root for O is ox-. Root for P is phosph-. Root for S is sulf-. Root for Cl is chlor-. Root for Mn is mangan-.
oxygen suffix
If ion central atom can attach oxygen in at least two ways, add "-ite" to root for ion with fewer oxygens or add "-ate" to root for ion with more oxygens.
ion
Then add the word "ion".
example
ClO4- [4 is subscript and - is superscript] is perchlorate ion, ClO3- [3 is subscript and - is superscript] is chlorate ion, ClO2- [2 is subscript and - is superscript] is chlorite ion, and ClO- [- is superscript] is hypochlorite ion.
CO3-- [3 is subscript and -- is superscript] is carbonate ion.
NO3- [3 is subscript and - is superscript] is nitrate ion and NO2- [2 is subscript and - is superscript] is nitrite ion.
O2-- [2 is subscript and -- is superscript] is peroxide ion.
PO4--- [4 is subscript and --- is superscript] is phosphate ion.
SO3-- [3 is subscript and -- is superscript] is sulfite ion. SO4-- [4 is subscript and -- is superscript] is sulfate ion.
MnO4- [4 is subscript and - is superscript] is permanganate ion.
special
Polyatomic ions can have special names. NH4+ [4 is subscript and + is superscript] is ammonium ion. OH- [- is superscript] is hydroxide ion. CN- [- is superscript] is cyanide ion. C2H3O2- [2 and 3 are subscripts and - is superscript] is acetate ion. HCO3- [3 is subscript and - is superscript] is bicarbonate ion.
Find chemical formulas {chemical formula} {formula, chemistry} using percent composition. For each element, divide percent composition by atomic mass units, to find number of elements per molecular weight. Then divide smallest number into others. If all answers are close to whole numbers, use whole numbers as subscripts in chemical formula. If answers are not all whole numbers, multiply answers by two, then three, then four, and so on, until answers are whole numbers. Then use whole numbers as subscripts in chemical formula.
Chemical formula comes from chemical name {formula from name}. Because molecule has zero total charge, sum of ion charges and atom valences must equal zero. First, write atom or complex-ion symbols in same sequence as in name. Remember or look up ion or atom charges or valence. For atoms or complex ions, assign number subscripts so sum, of charge or valence times subscript, adds to zero.
Ion names follow rules {simple ion naming}. If cation has one atom, use atom name followed by the word ion. For example, Na+ [+ is superscript] is sodium ion. If anion has one atom, use atom root followed by "-ide". For example, O2- [2 is subscript and - is superscript] is oxide ion.
Material properties {material property, chemical} {chemical property} are hardness, strength, color, melting temperature, vaporizing temperature, tensile strength, malleability, ductility, adhesiveness, cohesiveness, and elasticity.
attraction to other substances {adhesiveness}.
attraction to itself {cohesiveness}.
wire-forming ease {ductility}|.
Materials have ability to return to original shape after stretching, compressing, or twisting {elasticity, material}|.
rolling-flat ease {malleability}|.
Substances {element}| can have only one atom type. Hydrogen is H2 [2 is subscript]. Nitrogen is N2 [2 is subscript]. Oxygen is O2 [2 is subscript]. Fluorine is F2 [2 is subscript]. Chlorine is Cl2 [2 is subscript]. Bromine is Br2 [2 is subscript]. Iodine is I2 [2 is subscript].
Elements, such as carbon and sulfur, can have several physical forms {allotrope}|.
Hitting light nuclei with heavy ions {cold fusion, element} makes elements 107, 108, 109, 111, and 112 [discovered from 1980 to 1996].
Lead is stable at 82 protons and 126 neutrons {magic mountain}.
Solid elements {boron} can polymerize, form rings, and be in white borates.
Elements {chlorine} can be gas, be reactive, and make hydrochloric acid. Chlorine makes chlorates, such as bleach, with oxygen.
Elements {fluorine} can be reactive gas that forms strong polar covalent bonds with non-metals and forms ionic bonds to metals.
Elements {hydrogen} can form polar covalent bonds with non-metals, making clear liquid acids. Hydrogen forms hydrides with strongly reducing metals. Hydrogen gas is mild reducing agent and reacts slowly. Chemical reactions involving hydrogen ion and hydride ion are fast.
Elements {nitrogen} can be inert gas. Ammonia is in basic fertilizer. Nitrous oxide is anesthetic. Nitrogen-nitrogen double-bond diazo compounds are solid dyes.
Elements {oxygen} can be gas and be oxidizer but be unreactive at low temperature. Ozone is powerful oxidizer. Two oxygens make the oxidizer peroxide ion. Oxygen combines with hydrogen to make water.
Elements {phosphorus, element} can have atomic number 15, with 15 protons and 15 electrons. Hennig Brand discovered phosphorus [1669]. Phosphorus means "bearer of light" in Greek.
properties
Phosphorus is non-metal, waxy, white or red, and solid. Atomic weight is 30.97, so phosphorus has 16 neutrons. Boiling point is 277 C. Melting point is 44 C. Density at 25 C is 1.82 g/cm^3.
reactions
Phosphorus is reactive and makes phosphates with oxygen. Red phosphorus is not as reactive as white. White is very reactive and catches fire in air at 35 C. At temperatures below 35 C, white phosphorus glows in air. For safety, phosphorus must be in water. Phosphorus is toxic and can damage nose and jaw cartilage and bones.
sources
Heating calcium phosphate with carbon and silicon dioxide produces phosphorus. Yearly amount is several million tons. Phosphorus is also in fluoroapatite, which is calcium, fluorine, and phosphate.
purposes
Phosphorus mainly makes phosphoric acid. Phosphoric acid is for fertilizers, which must have phosphate.
comparison
Phosphorus chemistry is similar to nitrogen chemistry.
Elements {silicon, element} can form silicates with oxygen to make sand, asbestos, mica, glass, and quartz. Etching it makes semiconductor circuits.
Elements {sulfur, element} can make sulfates and sulfites with oxygen, as well as sulfoxides for detergents. Hydrogen-sulfide gas has rotten-egg smell, as does carbon disulfide.
Most elements {metal, element}| are solid at room temperature, melt at high temperature, are gray to white in color, shine if polished, conduct electricity and heat, are malleable, are ductile, are dense, and tend to lose electrons in chemical reactions. The most-metallic elements are in periodic-table lower left. Elemental metals can bind to themselves in pure metals or alloys. They can bind to non-metals to make salts.
Few elements {semimetal} {metalloid}| are soft and crumbly solids or hard and brittle solids, have low melting temperature, are fairly shiny, are gray or colorless, are semiconducting, are not malleable, are not ductile, are rocklike, and have medium density.
Elements {non-metal}| can be colorless gases or colored soft solids, have low melting point, have no shine, have no conductivity, have low density, and tend to gain electrons in chemical reactions. The most-non-metallic elements are in periodic-table top right.
Radium compounds glow in the dark {radioactive element}|. Uranium and plutonium compounds are fuels for nuclear reactors.
Nuclei {transuranium element}| {transuranic element} can be heavier than uranium.
Hitting heavy nuclei with neutrons makes elements 93, 94, 99, and 100 [discovered by 1958].
Hitting heavy nuclei with alpha particles makes elements 95, 96, 97, 98, and 101 [discovered by 1958].
Hitting heavy nuclei with light-element ions, such as boron-5, makes elements 102 to 106 [discovered from 1958 to 1974].
Light-element ions can hit and split nuclei of elements above 106.
Hitting light nuclei with heavy ions {cold fusion, light nucleus} makes elements 107, 108, 109, 111, and 112 [discovered from 1980 to 1996].
Hitting light nuclei with heavy ions, such as calcium-48, makes elements 110 and 113 to 118 [discovered from 1994 on].
stability
At 114 is stable region, in which element lasts longer, especially element with 184 neutrons. Lead is also stable at 82 protons and 126 neutrons, at magic mountain.
Nature has 10,000 different inorganic and 10^11 different organic compounds {molecule}|. People know properties of 10^9 molecules.
color
Metal complexes can have metal ions with d orbitals, which chemically bind other molecules at smaller energy levels than s or p orbitals, lowering energy levels to visible light range, from ultraviolet for s and p orbitals. Iron compounds are red. Cobalt compounds are blue. Nickel compounds are green. Copper compounds are blue or green. Lead compounds are white. Silver compounds are black.
Organic molecules can have conjugated double bonds, which spread electron-orbital energies and lower energy levels to visible-light range, from ultraviolet for single bonds. Organic dyes and indicators have long carbon sequences and have lowest light frequencies, from red to blue.
diameter
Molecules have diameters from 10^-8 centimeters to 10^-5 centimeter. In periodic-table rows, right-most atom is half left-most-atom diameter. Last-row atom diameter is much greater than first-row atom diameter.
electrical property
Atom diameter and proton number determine electrical properties. Diameter changes have more effect than proton-number changes. Noble gases have lowest electron affinity and highest ionization energy, because electron shells are full. Elements in top-right periodic table have highest electron affinity and highest ionization energy, because they have relatively small diameter and relatively large proton number.
Substances {compound, chemistry}| can have different atoms bound together.
In molecules, atom atomic-weight sum is molecule mass {molecular weight}| {formula mass} {molecular mass}, in atomic mass units.
In compounds, element percentage {percent composition} is atomic mass, in atomic mass units, multiplied by number of atoms, divided by molecular weight, in atomic mass units.
High-temperature superconductors {strange metal state} {bad metal} can have impurities.
Ions {complex ion} can have more than one atom. Complex ions typically have central positive atom {mononuclear atom}. Mononuclear atom binds to negative atom ligands. Ligands can chelate to central atom at two or more sites.
properties
Central atom can have high charge, small radius, and filled or half-filled d orbitals. Central atom can have low charge, large radius, and odd number of d-orbital electrons. If central atom has higher positive charge, greater atomic weight, and/or more electrons in d orbitals, complex ion is more stable. d orbitals are most stable when they are half full or have 3, 6, or 8 electrons.
types
Heme has iron as central atom. Chlorophyll has magnesium as central atom. Vitamin B12 has cobalt as central atom.
In covalent compounds, ionization potential is inversely proportional to half the distance {effective atomic radius} between two covalently bound nuclei. Effective atomic radius ranges from 0.037 nanometers to 0.3 nanometers.
In gases, atoms have potential energies, which range from -0.9 eV to +3.6 eV, to attract additional electrons {electron affinity}. Atom electronegativity directly correlates with electron affinity.
Atomic nuclei attract electrons in shared orbitals {electronegativity}. Electronegativity is proportional to sum of ionization potential and electron affinity.
energy
For two bonded atoms, electronegativity difference is proportional to square root of bond-energy ionic bonding part {partial ionic character}, which ranges from 0.8 eV to 4.0 eV.
bonds
If both atoms have high electronegativity, they have covalent bonding. If both atoms have low electronegativity, they have metallic bonding. If one atom has high electronegativity and one atom has low electronegativity, they have ionic bonding.
location
Atom with higher electronegativity has higher probability of containing bonding electrons, and lower probability of containing antibonding electrons, than other atom.
To remove outermost electron, gas atoms require energy {ionization potential} {ionization energy}, which ranges from 4 eV to 24 eV.
Dots can represent electrons in molecule electron structures {Lewis structure}. Atoms, except hydrogen with two dots, have eight dots, to represent electrons in outer shell. Two dots are at atom right, bottom, left, or top. If two atoms bond, two dots are between them. If two atoms have double bond, four dots are between them.
Molecules {radical, molecule}| {free radical} can have no charge but have only one unpaired electron in outer orbital. Peroxides have oxygen free radicals. When peroxide or double-bonded carbon binds to carbon, carbon atom can have free radical.
Two non-metal-atom electrons {unshared pair} can be in non-bonding outer-shell orbital.
Atoms have number {valence, atom}| of outer-shell electrons, or missing outer-shell electrons, needed to complete outer shell.
Atom rotational, vibrational, and translational energy modes have same energy {energy partition} {partition of energy, chemistry}. If energy is different, rotation or vibration gains or loses energy to neighboring rotations and vibrations and returns to equilibrium.
Molecular groups can rotate around single bonds {rotation, bond}. Double bonds, triple bonds, and bonds with resonance have no rotation.
types
Because spherical molecules are symmetric in all three space directions, spherical molecules have no net rotation. Spin around axis leaves molecule the same. Spherical molecules cannot rotate around axis that does not go through center.
Linear molecules can spin around axis perpendicular to chemical bond, so linear molecules can have net rotation. Because linear molecules are symmetric in one space direction, linear molecules have no net rotation around line between nuclei, because spin around that axis leaves molecule the same.
Molecules that are not spherical or linear have no symmetry axis and can rotate around three mutually perpendicular space dimensions.
Molecule bonds can have different vibration types {vibration, molecule}.
types
Vibrations can stretch and compress chemical bonds along line between nuclei. Vibrations can widen and narrow angle between two bonds.
number
Molecules with no bonds cannot vibrate.
Molecules with one bond have one vibration type, bond compressing and stretching.
Molecules with two bonds can have four vibration modes. One bond can stretch, as the other compresses. Both bonds can stretch and compress at same time. Angle between bonds can narrow and widen. One bond can move downward perpendicular to bond plane, while one moves upward perpendicular to bond plane.
symmetry
Molecule symmetries can make two vibration modes indistinguishable and decrease total number of vibration modes.
Compounds {binary compound} {diatomic compound} can have two different elements. Hydrofluoric acid, for glass etching, is HF. The strong acid hydrochloric acid is HCl.
Table salt is NaCl. Sodium fluoride toothpaste compound is NaF. Sodium-bromide stomach soother is NaBr. Sodium iodide iodizing salt is NaI. Potassium chloride salt substitute is KCl.
Poisonous colorless odorless carbon monoxide gas is CO. The poisonous gas nitric oxide is NO. Calcium oxide, lime fertilizer, is CaO. Bronze green color, cupric oxide, is CuO. The solid used in flat stovetops, magnesium oxide, is MgO.
Compounds {triatomic compound} can have three atoms.
Water is H2O [2 is subscript].
Colorless odorless carbon dioxide gas, from burning, is CO2 [2 is subscript].
Inefficient burning makes nitrogen dioxide gas, NO2 [2 is subscript]. The colorless anesthetic gas nitrous oxide is N2O [2 is subscript].
Gas with rotten egg smell, hydrogen sulfide, is H2S [2 is subscript]. The irritating gas for preserving food and for refrigeration, sulfur dioxide, is SO2 [2 is subscript].
Lye or sodium hydroxide strong base is NaOH. The strong base potassium hydroxide is KOH. Milk of magnesia or magnesium hydroxide antacid is MgOH. Slaked lime mortar, calcium hydroxide, is CaOH.
Potash or potassium oxide fertilizer is K2O [2 is subscript].
Calcium chloride drying agent is CaCl2 [2 is subscript], for icy roads.
Black silver tarnish, silver oxide, is Ag2O [2 is subscript].
Hydrogen cyanide poisonous gas is HCN. Silicon-oxide glass is SiO2 [2 is subscript].
Black car-battery-terminal coating, lead oxide, is PbO2 [2 is subscript].
Bleach or sodium hypochlorite is NaClO.
Compounds {polyatomic compound} can have more than three atoms.
organic
Natural gas or methane is CH4 [4 is subscript]. Artificial gas or propane is C3H8 [3 and 8 are subscripts]. Lighter fluid or butane is C4H10 [4 and 10 are subscripts].
Carbon tetrachloride solvent is CCl4 [4 is subscript]. Chloroform anesthetic is CH3Cl [3 is subscript].
The strong base-forming gas ammonia is NH3 [3 is subscript].
Hydrogen peroxide disinfectant is H2O2 [2 is subscript].
iron
Rust or iron oxide is Fe2O3 [2 and 3 are subscripts]. Magnetite iron ore, iron (II) oxide, is FeO. Hematite iron ore, iron (III) oxide, is Fe2O3 [2 and 3 are subscripts].
calcium
Limestone, chalk, and the cement ingredient calcium carbonate is CaCO3 [3 is subscript]. Calcium phosphate bone mineral is Ca3(PO4)2 [3 and 2 are subscripts]. Plaster of paris or calcium sulfate is CaSO4 [4 is subscript].
sodium
Baking soda or sodium bicarbonate is NaHCO3 [3 is subscript]. Soda ash or sodium carbonate is Na2CO3 [2 and 3 are subscripts]. The fixer for photographic solutions, sodium thiosulfate, is NaHSO4 [4 is subscript].
alkali metals
The gunpowder and meat-curing salt saltpeter or potassium nitrate is KNO3 [3 is subscript].
The manic-depressive treatment lithium carbonate is Li2CO3 [2 and 3 are subscripts]. Lithium dialkylamides remove protons in chemical reactions.
Magnesium hydroxide antacid is Mg(OH)2 [2 is subscript]. The laxative, tanning, and dyeing compound Epsom salts or magnesium sulfate is MgSO4 [4 is subscript].
The compound used for GI tract x-rays, barium sulfate, is BaSO4 [4 is subscript].
boron
The compound used in heatproof glass, boron oxide, is B2O3 [2 and 3 are subscripts]. Boron nitride abrasive is BN3 [3 is subscript]. Borax detergent ingredient is B(C2H2O2)3 [2 and 3 are subscripts]. The abrasive carborundum or boron carbide is BC3 [3 is subscript].
aluminum
The treatment for canker sores, and compound for water purification, alum, aluminum potassium sulfate, is AlK(SO4)2 [4 and 2 are subscripts]. The white layer coating aluminum is aluminum oxide, Al2O3 [2 and 3 are subscripts], used in ceramics and abrasives. Aluminum hydroxide antacid is Al(OH)3 [3 is subscript].
copper
The blue compound copper sulfate is CuSO4 [4 is subscript]. The green compound copper chloride is CuCl2 [2 is subscript].
silver
Silver nitrate silver-plating salt is AgNO3 [3 is subscript].
The white layer coating aluminum is aluminum oxide or Al2O3 {alumina} [2 and 3 are subscripts], used in ceramics and abrasives.
Transparent brittle materials {glass}| can have different-length bonds and low thermal expansion. Sand is silicon dioxide. To make glass, melted sand receives small amounts of soda and lime at 2700 F. Melted sand is clear solid but is not crystalline. Glass does not melt at one temperature but becomes more fluid over temperature range. People can cut, blow, shape, and mold hot glass. Drawing molten glass through shaped boats floating in melted glass makes glass sheets. The glass cools slightly and then vertical rollers make it have equal thickness.
Compounds {halide} can contain fluorine, chlorine, bromine, or iodine.
Molecules {metal complex} can have metal ions with d orbitals, which chemically bind other molecules at smaller energy levels than s or p orbitals, lowering energy levels to visible-light range from ultraviolet-light range. Iron compounds are red. Cobalt compounds are blue. Nickel compounds are green. Copper compounds are blue or green. Lead compounds are white. Silver compounds are black.
Nitrogen burns at 800 F to make nitrogen oxides {nitrogen compound}. Cyanuric acid oxidizes nitrogen oxides to carbon dioxide, water, and nitrogen gas.
Ions {phosphate ion}, (PO4)-3 [4 is subscript and -3 is superscript], can have phosphorus and oxygen.
bone
Bone is calcium phosphate, Ca3(PO4)2 [3, 4, and 2 are subscripts]. 20% of skeleton is calcium phosphate. Teeth have calcium phosphate.
energy
Phosphate bonds in adenosine monophosphate (AMP), adenosine diphosphate (ADP), and adenosine triphosphate (ATP) store energy.
detergent
Detergents can have phosphates, because phosphate softens water. Many places ban phosphate detergents, because they cause lakes and rivers to have too many algae and other plants, which makes less oxygen in water and kills animal life.
Water {water, molecule} relates to anhydrous, hydrate, efflorescence, deliquescence, hygroscopic, and desiccant.
phases
Water can exist in 13 crystalline phases and five amorphous phases. Water can be high-density amorphous ice at 10 K to 65 K or low-density amorphous ice at 65 K to 125 K. Amorphous ice is in interstellar space. Space amorphous ice can flow with UV light and allows carbon dioxide, carbon monoxide, methanol, and ammonia formation. Cubic ice forms at 135 K to 200 K. Hexagonal ice forms from 200 K to 273 K.
ice surface
Ice has liquid water at surface, several molecules thick, with less structure than solid, because water interacts with air. Ice with impurities has thicker layer. Ice has a liquid surface layer even if it is tens of degrees below freezing. Water-surface-layer charge separation, on ice crystals moving upward and hail falling downward, causes lightning.
Most substances have no adhering water {anhydrous}|.
Solid can absorb water from air and become solution {deliquescence}|.
Chemicals {desiccant}| that can take up water can keep other chemicals dry.
Hydrates can give water to air {efflorescence, water}|.
Substances {hydrate}|, with dissolved ions, can adhere to water.
Compounds can absorb water from air {hygroscopic}|.
Water {hard water}| can have mostly calcium and magnesium ions.
Water {soft water}| can have mostly sodium and potassium ions.
Molecule atoms have stable electrical attractions {bonding, molecule}| {chemical bond}.
electrons
Only outermost electrons participate in chemical bonds, because they can contact another atom.
electrons: stability
Atoms have potential energy. Bonding lowers potential energy. Because radius is less, filled outer-electron shells have lower potential energy than unfilled.
electrons: types
Bonding types result from competition between weak bonds with low activation energy and strong bonds with large activation energy. Single covalent bond overlaps sigma orbitals. Double covalent bond overlaps sigma orbitals and pi orbitals. Triple covalent bond overlaps sigma orbitals and two pi orbitals.
electrons: bond order
Bonding order is 1sigma bonding, 1sigma antibonding, 2sigma bonding, 2sigma antibonding, 2sigma bonding, 2pi bonding, 2pi antibonding, 2sigma antibonding, 3sigma bonding, 3sigma antibonding, 3sigma bonding, 3sigma antibonding, 3pi bonding, 3pi antibonding, and so on.
bond length
Bonded atom pairs always have same average distance between nuclei. Bond length has lowest potential energy.
bond strength
Non-polar covalent bonds are stronger than polar, ionic, or metallic bonds, because atoms share electrons more equally and attractive force between electrons and nuclei is higher, making bond length less. Multiple bonds have shorter bond lengths, because nucleus shielding is more.
Ionic bonds are stronger if ions have more charges and larger sizes.
Metal alloys make stronger metallic bonds, because rapid electron transfer maximizes shell filling.
bond angle
Average angle between two bonds is always the same.
Similar-size non-metals can form covalent bonds {catenation}.
Metals can bind to anion and be soluble {chelation}|. Chelometric titration can measure all metals, except sodium, potassium, and lithium. Disodium EDTA at pH 4 to pH 5 chelates metals. Metal is Lewis acid, and ligand is Lewis base. Eriochrome Black T is indicator and goes from red to blue. Adding magnesium EDTA can measure calcium. EGTA titrates calcium. Xylenol is indicator for acid titrations with EDTA.
Atoms can make numbers {combining capacity} of covalent bonds or can become ions.
Compounds with alternating single and double bonds {conjugation, bond}| have electron resonance.
Molecule electrons can move among connected p orbitals and spread electron orbitals {delocalization}|, which lowers potential energy by minimizing electron repulsions.
Repulsions among electrons in different adjacent orbitals can change orbital shapes {hybridization, bonding}| {hybrid orbital theory}, to make same-shape orbitals. Orbital hybridization can happen if excited states are available.
shape
Hybrid orbitals have ellipsoid shapes. Shape is between s and p orbital shape. Electrons are mostly on one atom side.
types
Four adjacent orbitals make four hybrid orbitals and tetrahedron shape {sp3 hybridization}. Three adjacent orbitals make three hybrid orbitals and triangle shape {sp2 hybridization}, with one unaffected p orbital in pi bond. Two nearby orbitals make two hybrid orbitals and line shape {sp hybridization}, with two unaffected p orbitals in pi bonds.
Atoms or molecules {ligand}| can covalently or ionically bond to central atom, in different configurations depending on orbitals.
number
Central atom can bind coordination number of ligands. Central atom can have six ligands, at octahedron corners {octahedral}, at two d, one s, and three p orbitals. Cubic ligand arrangement has six bonds, at cube corners, at two d, one s, and three p orbitals. Central atom can have four ligands {square planar}, at square corners, at two d, one s, and three p orbitals. Tetrahedral ligand arrangement has four ligands, at tetrahedron corners, at one s and three p orbitals.
central atom
Metal ions have five d orbitals. z^2 and x^2 - y^2 orbitals point along axes and have higher energy. Electrostatic repulsion causes xy, yz, and xz orbitals to point between axes and have lower energy. If field is weak, energy difference is small, and all electrons go to all five d orbitals, with parallel spins, as in Hund's rule. If field is strong, metal d-orbital energy differences are large, spins pair, and electrons stay in the three lower-energy d orbitals.
Minimum potential energy is when molecule atoms, except hydrogen, have eight electrons, in four orbitals, in outer shell {octet rule}.
Hybrid bonding orbitals can represent alternative electron-arrangement averages, such as single and double bond interchanges {resonance, bonding}|.
delocalization
Molecule electron orbitals spread when electrons move between connected p orbitals, lowering potential energy by minimizing electron repulsions.
aromatic compounds
Benzene and other aromatic compounds, which have five-member or six-member carbon and nitrogen rings with alternating single and double bonds, have electron resonance.
conjugation
Compounds with alternating single and double bonds have electron resonance.
carboxyl group
If an atom single-bonds to an atom type and double-bonds to same atom type, so bonds can interchange, as in carboxyl ion -COO- or guanidium ion -CNN-, compound has electron resonance.
Electrons between two atomic nuclei reduce electric repulsion {shielding}|, by reducing nucleus apparent positive charge.
Weak electrical attractions {van der Waals force} are between charges induced on neighboring molecules by electronegative atoms. Van der Waals forces are at distances less than 0.25 nanometers. Higher-atomic-weight atoms make stronger van der Waals forces.
Bonding theories {molecular orbital theory} (MO) can use molecular electron orbitals. Bonding orbitals have electrons between nuclei, which causes shielding. Antibonding orbitals have electrons beyond nuclei, with no shielding. Only these two wave-interference types result in net amplitude and so are the only bonding types.
number
Number of occupied bonding orbitals compared to number of occupied antibonding orbitals gives total bond number. If antibonding equals bonding, no bond forms.
strength
Bond strength depends on atomic-orbital overlap, which is greatest for identical orbitals. If electronegativity difference between atoms is great, bonding and antibonding orbitals are similar in energy, because shielding is minimal.
errors
Molecular orbital theory weights ionic effects too heavily.
Bonding theory {valence-bond theory} involves electric interactions between atoms. Molecular orbitals only form between valence electrons, because only valence electrons can contact outside world and valence electrons are least bound. Other electrons are too tightly bound. However, valence-bond theory weights ionic effects too lightly.
Enough energy {bond energy} {energy, bond} can break bonds. Bond breaks at 40,000 to 260,000 calories per mole. Because shell is full, atoms in chemical bonds have lower energy and are more stable than isolated atoms. Symmetries in covalent chemical bonds make energy lower by minimizing electron repulsions.
Electrons can induce electric dipoles and cause electrical attractions {London energy} between atoms. London energy is at distance less than 0.6 nanometers.
Atoms {ion}| can donate electrons to or accept electrons from other atoms, so atom becomes positive or negative.
Atoms with strong electric forces can gain several electrons to fill shell {anion}|.
Atoms with strong electric forces can lose several electrons to make empty shell {cation}|.
One covalent sigma bond {single bond}| can be between two atomic nuclei.
One sigma and one pi bond {double bond}| can be between two atomic nuclei.
One sigma and two pi bonds {triple bond}| can be between two atomic nuclei.
Molecular orbitals {antibonding orbital} can be difference between two atomic orbitals that have quantum-wave destructive interference. Antibonding orbitals have electrons beyond nuclei. No shielding makes positively charged nuclei repel. Outside electrons pull positively charged nuclei apart.
Molecular orbitals {bonding orbital} can be sums of atomic orbitals that have quantum-wave constructive interference. Bonding orbitals have electrons between nuclei. Shielding reduces repulsion of positively charged nuclei. Between electrons pull positively charged nuclei together.
Most atomic and molecular orbitals {non-bonding orbital} have no sharing, overlap, or quantum-wave interference.
Chemically bonded hydrogen atom near chemically bonded nitrogen, oxygen, or fluorine atom forms electric dipole {hydrogen bond}|. Nitrogen, oxygen, or fluorine unshared-electron pairs attract hydrogen nuclei. Only nitrogen, oxygen, and fluorine atoms are small enough for unshared-electron pairs to get close enough to hydrogen nucleus.
strength
Electric attraction is one-tenth covalent-bond strength.
time
Hydrogen bonds break and reform in 10^-11 seconds.
forms
Hydrogen bonds can have two configurations. Oxygen atom, hydrogen atom, and atom bonded to hydrogen can be in straight line. This hydrogen-bond type is stronger. Water has many strong-type hydrogen bonds.
At hydrogen, angle of nitrogen, oxygen, or fluorine atom and atom bonded to hydrogen angle can be 109 degrees, as in tetrahedral configuration. This hydrogen-bond type is weaker.
multiplication
Hydrogen bond polarizes atom bonded to hydrogen atom. Polarization aligns other atoms and causes more hydrogen bonding.
Atoms can donate electrons to or accept electrons from other atoms, so one atom becomes positively charged and other atom becomes negatively charged, and opposite ion charges attract {ionic bonding}|. Anions with strong electric forces can gain electrons to fill shell. Cations with strong electric forces can lose electrons to empty shell.
Metal atoms exchange outer electrons to try to fill outer shell {metallic bonding}|. Mercury is liquid, because it has weak metallic bonds.
Two atoms can share two electrons {covalent bond}|, which spend most time between the atomic nuclei and share a bonding orbital. Molecular electron orbitals fill with electrons using same rules as for filling atomic electron orbitals. Bonding orbitals fill before antibonding orbitals. Covalent bonding fills both atoms' outer shells.
antibonding
Shared electrons can spend most time outside the atomic nuclei on line between nuclei, in antibonding orbitals. Outside electrons pull nuclei apart and so oppose covalent chemical bonding. Net bond number equals (bonding electrons - antibonding electrons) / 2.
factor
Atoms with weak electric forces make covalent bonds. Atoms with weak electric forces can gain electrons to complete shell. Atoms with weak electric forces can lose electrons to empty shell.
Two different-electronegativity atoms can bind by sharing electrons, and one atom attracts shared electrons more {polar bond}| {polar covalent bonding}.
Covalent chemical bonds {sigma bond}| {sigma bonding orbital} can overlap atom s orbital and other-atom 1s or 2s orbital, 1p or 2p orbital, or s-p hybrid orbital, with constructive interference and electrons between nuclei. Sigma bonding orbitals are symmetric around line joining the atomic nuclei. Atom s orbital can overlap other-atom 1s or 2s orbital, 1p or 2p orbital, or s-p hybrid orbital {sigma antibonding orbital}, with destructive interference and electrons not between nuclei.
Covalent chemical bonds {pi bond}| {pi bonding orbital} can overlap atom 2p orbitals, so shared electrons are between nuclei but in two regions, one above and one below line between atomic nuclei. Atom 2p orbital can overlap other-atom 2p orbital {pi antibonding orbital}, with destructive interference and electrons not between nuclei.
Molecule atoms can make and break chemical bonds {chemical reaction, inorganic}|. Chemical reactions make reactant molecules into product molecules. Chemical reactions typically release energy as heat.
energy release
Molecules have energy levels, with Boltzmann energy distribution. Reactants have higher ground-state potential energy and/or more widely spaced energy levels. If there is reaction path, molecules tend to become products, which have lower ground-state potential energy and/or less widely spaced energy levels. Potential-energy difference becomes kinetic energy and so heat. Products and heat have higher entropy than reactants.
reaction rate
Chemical-reaction rate depends on activation energy to go from reactants to products. Reaction rate depends on forward and backward chemical-reaction rates.
mass
Balanced chemical equations allow knowing reactant or product amounts from reactant or product amounts. Ratio between unknown reactant or product coefficient and known reactant or product coefficient equals ratio between unknown reactant or product moles and known reactant or product moles.
Reaction diagrams {Börn-Haber cycle} can show how molecule chemical properties relate to atomic chemical-property combinations.
Reaching chemical-reaction transition state requires energy {activation energy}| (Ea). Transition state has potential energy that is higher than reactant potential energy and is higher than product potential energy. For drugs, activation energy equals site-atom attached-hydrogen effective activation-energy sum.
Chemicals {catalyst}| can increase reaction rate, but chemical reaction does not alter them.
amount
Reaction needs only small catalyst amount, because reaction reuses catalyst. However, catalysts can break down, have dirt or product coatings, or have surface damage.
processes
Catalysts reduce energy needed to start reaction. Catalysts allow transition state with lower activation energy, make molecule easier to attack, allow leaving group to leave easier, make attacking group attack better, orient molecules for optimum bond stretching, provide functional groups for forces or transfer, or line up reactant molecules.
types
Enzymes are protein catalysts.
Acids and bases are catalysts {homogeneous catalyst}. Basic catalysts cause isomerization, halogenation, or condensation. Acid catalysts cause tautomerism, solvolysis, or inversion. Neutral catalysts polarize solvent.
types: solid
Solid catalysts {heterogeneous catalyst} provide structured surfaces. Ceramic or metal catalysts are for industrial processes. Surface chemistry is for catalysis, corrosion, membranes, surface tension, and electrodes.
If molecule collision energy with surface is same as surface thermal-vibration energy, surface can absorb molecule and collision energy. Molecule-absorption rate depends on collision energy. Electrode surfaces have an ion layer, covered by an opposite-charge ion layer.
Catalytic surfaces must not bind too strongly or too weakly. Collision rate is not important, because absorption surface is large. Activation energy is small and not determining factor for surface catalysts.
As atoms bind to catalyst, catalyst surfaces orient molecules and dissociate molecular bonds. Then new bond can form by collision or reorientation. Molecules on catalysts can move depending on impurities, defects, and crystal planes. Movement allows reaction atom transfer.
types: gas and metals
Gas molecules chemisorb on metals, because metal absorption area is much greater than gas collision area, so entropy decreases. How saturated surface is affects absorption. If concentration is high or time on surface is long, absorption is less. Because neighboring sites move, they affect absorption sites.
Metals bind oxygen strongest, then acetylene, ethylene, carbon monoxide, hydrogen, carbon dioxide, and nitrogen. Platinum, iron, vanadium, and chromium can adsorb all these substances. Manganese and copper can adsorb some. Magnesium and lithium only absorb oxygen. Iron, nickel, platinum, and silver surfaces are catalysts for hydrogenations and dehydrogenations.
Nickel oxide, zinc oxide, and magnesium oxide are catalysts for oxidations and dehydrogenations, because they are semiconducting. Metal sulfides are catalysts for desulfurations, because they are semiconducting. Aluminum oxide, silicon oxide, and magnesium oxide are catalysts for dehydrations, because they are insulators. Phosphoric acid and sulfuric acid are catalysts for polymerizations, isomerizations, alkylations, and dealkylations {cracking, petroleum}.
Chemical reaction starts when outside energy stretches, twists, or compresses molecule chemical bonds {initiation, reaction}.
energy
Energy typically comes from heat or light. Light adds electric energy and affects electrons directly. Heat makes molecules move faster with more kinetic energy, causing more and higher-energy molecule collisions.
size
In large molecules, collision is less likely to disrupt bond, because collision is more likely to hit other bonds.
shape
Molecule shape determines if collision affects bond. If collision is along bond line, bond disruption is more than if collision is from side.
charge
Bond disruption is greater if colliding atoms have opposite electric charges. Bond disruption is greater if colliding atoms have same electric-charge absolute value.
Light can cause chemical reaction {photoactivation}, as in photosynthesis.
Chemical bond is stable state with relatively low potential energy. See Figure 1. Collision, heat, or radiation can stretch, twist, or compress chemical bond to maximum extent {transition state}| {activated complex}, as molecule electrical attractions resist chemical-bond disruption. Transition state has greatest disruption, highest potential energy, and maximum separation. See Figure 2. If it can become new conformation or molecule, transition state is hybrid of stable chemical states before and after chemical reaction.
From transition state, molecules can go back to original states or become new conformations or molecules, with equal probability. See Figure 3.
After displacement from equilibrium, system returns to equilibrium and sum of all work done by forces during displacement and return equals zero {principle of virtual work} {virtual work principle}.
Chemical reactions proceed over time {reaction rate}|.
rate
Reaction goes in two directions at once, from reactants to products {forward reaction} and products to reactants {reverse reaction}. Backward reaction rate divides into forward reaction rate to find overall rate.
half-life
Reactant amount eventually reaches half original amount {half-life, reactant}: half-life = C * (1 / c^(n - 1)), where C is constant, c is concentration, and n is reaction order.
factors
Reaction rate depends on temperature, pressure, reactant concentrations, catalysts, states, and reactant physical forms: rate constant = (collision frequency) * e^(-E / (R*T)), where R is gas constant, T is temperature, and E is activation energy. If reactant concentration is in excess, concentration stays constant during reaction.
process
Reactants and products have initial, intermediate, and final concentrations. Reactions destroy reactants and makes products.
process: mechanism
Reaction rate depends on reaction mechanism. Reaction mechanism can depend on zeroth, first, second, or third reactant-concentration power {order, reaction}.
Reaction rate can be constant {zero-order reaction}.
Reaction rate can depend on one reactant concentration or pressure {first-order reaction}. First-order reaction uses linear equation: rate = dC / dt = k * C0 where dC is concentration change, dt is time change, k is rate constant, and C0 is concentration. ln(C / C0) = -k*t, where C is concentration, C0 is initial concentration, k is rate constant, and t is time. Find final and intermediate product or reactant concentrations from initial concentration, rate constant, and time: Cf = Ci * e^(k*t), where Cf is final concentration, Ci is initial concentration, k is rate constant, and t is time.
Reaction rate can depend on two reactant concentrations or pressures {second-order reaction}. Second-order reaction uses quadratic equation.
process: temperature
Reaction rate depends directly on temperature. Reaction rate is faster with higher temperature. 10-K increase doubles reaction rate.
process: form
Reactant physical form affects reaction rate. Greater surface area, lower viscosity, and higher solvent polarity increase reaction rate. If surfaces must touch for reaction, rate depends on contact area.
process: state
Reactant gas, liquid, or solid physical state affects reaction rate.
process: rate constant
Physical factors that affect reaction rate are temperature, catalyst, physical form, and physical state. All physical factors are in one constant {rate constant}. People know rate constants for many chemical reactions.
process: rate-limiting
In chemical-reaction series, in which previous-reaction products are next-reaction reactants, one reaction {rate-limiting reaction} is slowest.
process: ions
Ionic reactions are fast if both reactants have opposite charge. Large ions and high-charge ions increase reaction rate. Increased ionic strength increases rate, if ions have opposite charge, but otherwise slows reaction rate. Solvents with high dielectric constants, like water, reduce repulsions and attractions between reactants and slow reaction rates.
Acid-base reactions are ionic, and reaction rate increases with more acid or base. Ions can modify reaction by forming weak acids and bases.
In ionic solutions, higher ionic strength, more polar solvent, and greater ion charge causes high collision rate and short contact time, so reaction rate is higher.
process: non-polar
In non-polar solutions, higher viscosity makes contact longer and collision rate lower, so reaction rate is lower.
Chemical-reaction equation {chemical equation} uses molecule chemical formulas and special symbols. Reactant formulas are on left, and product formulas are on right.
direction
Horizontal arrow pointing right separates reactants from products. Delta symbol means to add heat. hv symbol means to add light.
terms
Plus signs separate molecules.
symbols
Up arrow (^) at formula right indicates that reaction produces gas. Down arrow at formula right indicates that reaction precipitates solid. The letter s at formula right means that reagent is solid. The letter l at formula right means that reagent is liquid. The letter g at formula right means that reagent is gas. The letters aq at formula right mean that reagent is aqueous.
balance
Atoms on chemical-reaction left must also be on right, so both sides have same atom numbers and types {conservation of mass, chemical equation}.
Before chemical reaction, chemicals {reactant}| {reagent} exist.
If chemical reaction has more than one reactant, one reactant {limiting reagent}| depletes first as reaction proceeds. Find limiting reagent from balanced chemical reaction, using the following rule. If first-reactant coefficient to second-reactant coefficient ratio is larger than first-reactant moles to second-reactant moles ratio, second reactant is limiting reagent.
After chemical reaction, new chemicals {product, reaction}| exist.
Relative reactant and product masses have relations {stoichiometry}|.
If written chemical reaction has one product or reactant missing, calculations {balancing chemical equation} can find missing product or reactant. If written chemical reaction has one coefficient missing, calculations can find missing coefficient.
First, find all missing atoms, because each atom on left must also be on right.
Using found atoms, write positively charged atom symbol first and negatively charged atom symbol second.
Use naming-formula rules to find candidate molecule, using number subscripts for symbols if necessary.
Write equation using candidate molecule.
Add coefficients to reactants and products to make atom numbers equal on both sides. To find coefficients, first balance metal-atom coefficients, then balance non-metal-atom coefficients, except H and O, then balance hydrogen coefficients, and finally balance oxygen coefficients. If chemical equation is not yet balanced, double metal-atom coefficients, then balance non-metal-atom coefficients, except H and O, then balance hydrogen coefficients, and finally balance oxygen coefficients.
In chemical reactions, total mass {conservation of mass, reaction}, total charge {conservation of charge}, and total energy {conservation of energy, reaction} stay constant. Sum of reactant charges equals sum of product charges. Total reactant mass equals total product mass. Reactant energy equals product energy plus heat.
In chemical reactions, formed or used gas volumes relate by whole-number ratios {combining volumes law} {law of combining volumes} {Guy-Lussac law} {law of Guy-Lussac}.
In reaction series, in which previous-reaction products are next-reaction reactants, total change over series equals sum of reaction changes {Hess' law} {Hess law}.
Chemical-reaction product amount {yield, reaction}| never equals maximum theoretical product amount, because reactions are inefficient. Calculating reaction efficiency {percent yield} uses the balanced chemical reaction. Percent yield equals ratio between product moles and limiting-reagent moles, expressed as percentage.
Knowing chemical equation and reactant and product concentrations at equilibrium allows reaction-constant calculation {equilibrium constant}|. Equilibrium constant is product of product concentrations, each raised to power of its chemical-equation coefficient, divided by product of reactant concentrations, each raised to power of its chemical-equation coefficient. For example, in chemical equation 2 A + 3 B -> C + 4 D, equilibrium constant K = ([A]^2 * [B]^3) / ([C] * [D]^4). Chemical reaction aX + bY -> cZ + dW equilibrium constant is K = (X^a * Y^b) / (Z^c * W^d).
tables
People know many reaction equilibrium constants, at specific temperatures. Dissociating acids and bases have equilibrium dissociation constants. Dissolving salt in water or other solvent has equilibrium solubility constant.
irreversible
Equilibrium constant greater than 10^9 means reaction is irreversible.
product concentrations
Equilibrium constant and initial reactant concentrations result in product concentration at equilibrium. First, use chemical equation to make equilibrium-constant equation with correct exponents. In equilibrium-constant equation, replace product concentration with x if coefficient is 1, replace with 2*x if coefficient is 2, replace with 3*x if coefficient is 3, and so on. If coefficient is 1, replace reactant concentration with its initial concentration minus x. Replace with 2 * (initial concentration minus x) if coefficient is 2. Replace with 3 * (initial concentration minus x) if coefficient is 3, and so on. For example, for chemical equation 2 A + 3 B -> C + 4 D, equilibrium constant K = ([A]^2 * [B]^3) / ([C] * [D]^4). To find A concentration: K = ((2*x)^2 * B^3) / (C * D^4). Use equilibrium constant value from table of constants. Solve for x.
Product concentration is x times its coefficient in chemical equation. Reactant concentration is (initial concentration minus x) times its coefficient in chemical equation.
partition functions
Reactant and product partition functions can find chemical-reaction equilibrium constant.
After reaction, reactant and product amounts stay constant {equilibrium, reaction}|. At equilibrium, total-energy change is zero, free-energy change is zero, substance change is zero, all chemical potentials are equal, and all forces are equal. Product concentrations and reactant concentrations have equilibrium-constant ratio.
rates
At equilibrium, forward and backward reaction rates are equal. Product-formation rate equals reactant-formation rate. Amounts do not change, so reaction is complete.
factors
Equilibrium concentrations and amounts do not depend on catalyst or factors affecting reaction rate. Equilibrium concentrations depend only on energies and entropies.
factors: temperature
If reaction requires heat, temperature increase makes more product.
factors: pressure
If gas is reactant, pressure increase makes more product. If temperature increases, system acts to reduce pressure and so return to equilibrium.
factors: amount
Adding more reactants changes them to products, until equilibrium reestablishes. Adding more products turns them into reactants, until equilibrium reestablishes. Increasing reactant concentration, or removing product, increases product.
Substances have chemical reactivity {activity, chemical} {chemical activity}| {chemical potential, reactivity}. Chemical activity expresses true concentration or pressure. Substance concentration relative to other concentrations depends on chemical potential. Solids and pure liquids, including water, have chemical activity one. Metal activities, in decreasing order, are Li, K, Ba, Sr, Ca, Na, Mg, Al, Mn, Zn, Cr, Fe, Cd, Co, Ni, Sn, Pb, H, Cu, Ag, Pd, Hg, Pt, and Au. Non-metal activities, in decreasing order, are F, Cl, Br, and I.
Chemical potential difference {affinity, reaction}| from reactants to products is chemical-reaction driving force.
Substance partial pressure {fugacity}|, relative to other partial pressures, depends on chemical potential.
Methods can control reaction {reaction control}. In non-polar solution, if activation energy is low, diffusion controls reaction. In ionic solutions, if activation energy is high and is late in reaction, use vibration at frequency similar to rotation frequencies to control reaction, because bonds are short. In ionic solutions, if activation energy is high and is early in reaction, use translational energy to control reaction, because bonds are long.
Lasers can initiate photolytic reactions {flash photolysis}.
Mixing chambers and controlled reactant flows control reaction {flow technique}.
Molecule streams {molecular beam} can hit other molecules at precise speeds and orientations.
Temperature can change equilibrium {relaxation method, chemistry}, if reaction requires heat.
Reactions have different forms {reaction types}: chain, synthesis, decomposition, substitution, metathesis, nucleophilic, electrophilic, and molecular rearrangement.
Phosphoric acid and sulfuric acid are catalysts for carbon-chain dealkylations {cracking, dealkylation}| {dealkylation}. Petroleum separation uses phosphoric acid, sulfuric acid, silicon oxide, and aluminum oxide. Silicon oxide and aluminum oxide build branched hydrocarbons. Olefins form on platinum with silicon oxide, followed by isomerization, ring formation, splitting, and hydrogenation.
Two chemicals can bind to make something with different properties than original chemicals {hypergolic}. For example, hydrazine and nitrogen tetroxide react when in contact to make nitrous oxide and water: N2H2 + NO4 -> 3 NO + H2O [where 2 and 4 are subscripts].
Pressure can cause luminescence {triboluminescence}.
Product can be reactant, which can make more product {chain reaction, chemistry}|. Reaction rate continually increases, until system physically disrupts.
One reactant can make two products {decomposition reaction}. Decomposition includes hydrolysis and dehydration reactions.
Chemical can attack negatively charged group {electrophilic reaction}.
Two compounds can make two new compounds {double replacement reaction} {metathesis reaction}. Acid-base reactions have metathesis. Metal compounds can catalyze carbon-carbon double-bond changes.
One reactant can change to same chemical in different configuration {molecular rearrangement}.
Chemical can attack positively charged group {nucleophilic reaction}.
Element and compound can make another element and another compound {single replacement reaction} {substitution reaction, inorganic}. Metal-atom to metal-ion oxidation has substitution.
Two reactants can make one product {synthesis reaction}. Synthesis includes polymerization, hydration, and oxidation reactions, like rusting and combustion.
Energy transfer can involve permanent change that cannot reverse {irreversible reaction}, because heat is made.
Energy transfer can have no friction or other opposing changes {reversible reaction}. In reversible reactions, external and internal temperatures and pressures are approximately the same. In reversible processes, system and surroundings are always in equilibrium. Reversible processes approximate slow energy transfer with small force and minimal resistance.
In reactions {spontaneous reaction}, activation energy can be less than difference in potential energy between transition state and products.
Chemical reactions can release or absorb thermal energy {heat of reaction}|.
Chemical reactions {endothermic reaction} absorb energy if product potential energy is higher than reactant potential energy. Endothermic reactions make complex molecules and require high temperature or strong light at specific frequency.
Chemical reactions {exothermic reaction} release energy {heat, reaction} if reactant potential energy is higher than product potential energy.
Reactions {monomolecular reaction} can have one reactant, as in SN1 and E1 reactions. Molecule vibrations and rotations can cause molecule to decay to new state, as in gas decays, Type I nucleophilic substitutions, Type I eliminations, dissolution, and state changes.
Reactions {bimolecular reaction} can have two reactants, as in SN2 and E2 reactions. Molecule collisions can form transition states and can transfer energy or functional groups, as in isomerizations, Type II nucleophilic substitutions, Type II eliminations, enzyme reactions, syntheses, and dimerizations.
Reactions {termolecular reaction} can have three reactants, as in enzymatic reactions.
Chemicals {acid, chemistry} can accept electron pairs or donate protons. Acids donate protons {Brönsted acid}, accept electron pairs {Lewis acid}, or add hydrogen ions to water when they dissolve. Acids {polyprotic acid} can donate more than one proton.
properties
Acids taste sour, are colorless, and are corrosive.
production
Dissolving non-metallic oxide in water makes acid.
factors
For diatomic acids, acidity increases with negative-ion atomic weight. Acidity increases with increasing number of no-hydrogen oxygens around central atom.
acids
Common acids are nitric acid, sulfuric acid, hydrochloric acid, hydrofluoric acid, carbonic acid, phosphoric acid, formic acid, acetic acid, and other carboxylic acids.
Solution acidity {acidity}| is negative logarithm of hydrogen-ion concentration: pH = -log(H+). pH can range from 0 to 14. Pure water has dissociation constant K = 10^-7, so pK is 7, and pH is 7. Pure water is neither acid nor base. 1 M hydrochloric acid has pH 0. Lemon juice has pH 2. Soda water has pH 4. Coffee has pH 5. Urine and rain have pH 6. Water has pH 7. Bicarbonate of soda has pH 8. Milk of magnesia has pH 10. Cleaning ammonia has pH 11. 1 M sodium hydroxide has pH 14.
Chemicals {amphiprotic} can either donate or accept proton.
Molecules {amphoteric} can have both acidic and basic groups.
Chemicals {base, chemistry}| can donate electron pairs or accept protons. Bases accept protons {Brönsted base}, donate electron pairs {Lewis base}, or donate hydroxide ions to water when they dissolve. Bases taste bitter, are colorless, are slippery, and are caustic. Dissolving metal oxide in water makes base. Bases include sodium hydroxide, potassium hydroxide, ammonium hydroxide, magnesium hydroxide, calcium hydroxide, and aluminum hydroxide.
To keep solution pH constant {buffer}|, add weak acid or base and soluble salt with same anion. Weak-acid anion acts as weak base. Weak-base anion acts as weak acid. Adding acid or base to solution causes weak base or acid to neutralize added acid or base. However, adding too much acid or base can overwhelm weak acid or base. Weak-acid or base concentration to soluble-salt concentration ratio, and anion dissociation constant, determine buffer pH. Citrate buffer has pH near 5. Bicarbonate buffer has pH near 6. Phosphate buffer has pH near 7. Tris buffer has pH from 4 to 8.
Bases {caustic, base}| can react with organic matter.
After base accepts proton, it becomes weak acid {conjugate acid}.
After acid donates proton, it becomes weak base {conjugate base}.
Acids {corrosive}| can react with metals and inorganic materials.
Solutes dissolve in solvent {dissociation, chemistry}|. Buffer, weak-acid, or weak-base solution has low dissociation. Dissociation constant equals hydrogen ion concentration times anion concentration divided by acid concentration. Water dissociation constant = 10^-14, so hydrogen ion = 10^-7 M. Water ionization is more if temperature is more.
Weak acids have hydrogen ion and anion {hydrolysis}|. Salts with anion react with water to associate some hydrogen ion and form weak bases. Weak bases have hydroxide ion and cation. Salts with cation react with water to associate some hydroxide ion and form weak acids.
Hydrogen ions in water bind to water molecules electrically to make positively charged ion {hydronium ion}: H+ + H2O -> H3O+ [2 and 3 are subscripts, and + is superscript].
Weak acids or bases {indicator, acidity}| with conjugated double bonds can change electronic structure and color at different pH. At pH 1, malachite green changes from yellow to green. At pH 2, thymol blue changes from red to yellow. At pH 4, bromphenol blue changes from yellow to blue. At pH 4, methyl orange changes from red to yellow. At pH 4.5, bromcresol green changes from yellow to blue. At pH 5, methyl red changes from red to yellow. At pH 7, bromthymol blue changes from yellow to purple. At pH 7.4, phenol red changes from yellow to red. At pH 9, phenolphthalein changes from clear to red. At pH 9, thymol blue changes from yellow to blue. At pH 10, thymolphthalein changes from clear to blue. At pH 11, alizarin yellow R changes from yellow to red.
Acid and base reactions make water, metal anions, and non-metal cations {acid-base reaction, inorganic} {neutralization}|. Neutralization reactions involve proton transfer. Acid and base neutralize each other, because metal anions and non-metal cations are not very acidic or basic.
As concentration decreases, ionized-acid percentage increases {Ostwald's dilution law} {Ostwald dilution law}.
In acid-base reactions, anion and cation can attract electrically to form compounds {salt}|.
Oxidizing agent and reducing agent react to make reduced molecule and oxidized molecule, respectively, by transferring one or more electrons {redox reaction, inorganic} {oxidation-reduction reaction}.
equilibrium constant
Find redox-reaction equilibrium constant from balanced equation. From balanced equation, separate reduction and oxidation half-reactions. Find half-reaction standard potentials and total potential. Note number of electrons transferred. Equilibrium constant equals exponential of standard potential V times number of electrons transferred n times one faraday F, divided by gas constant k times temperature T: exp(V*n*F/k*T).
Molecules can lose electrons {oxidation}. Losing electrons increases positive charge.
Molecules can gain electrons {reduction}|. Gaining electrons decreases positive charge.
If all electrons shared in chemical bonds go to the more-electronegative atom, each atom has resultant charge {oxidation number}|. Oxidation number is number of electrons added to, or subtracted from, outer shell to make full shell. In molecules, atoms with higher electronegativity tend to gain electrons from atoms with lower electronegativity.
metals
Metals have positive oxidation numbers, because they lose electrons and empty outer shell. Metals are reducers, because they themselves oxidize.
non-metals
Oxygen and fluorine have negative oxidation numbers, because they gain electrons to fill outer shell. Oxygen and fluorine are oxidizers, because they themselves reduce.
hydrogen
Hydrogen can gain or lose one electron, making oxidation number +1 or -1.
others
Atoms can have several oxidation numbers, because they can fill or empty outer shell in different ways, through orbital hybridization.
functional group
Functional-group oxidation number is atom oxidation-number sum.
Metal oxidation states in acids and bases show specific relations {Frost diagram}.
Slow metal ionization {rusting} {corrosion}| can use oxidation, from oxygen in air or acidic water. Metal impurities make circuit from impurity to metal. Corrosion rate depends on exposed area. Aluminum oxide covers aluminum and prevents further corrosion.
Zinc coatings {anodized}| protect metal, because zinc corrodes first.
Because it is electron source, magnesium can prevent corrosion by returning electrons to metal {cathode protection}.
Galvanic cells {battery, redox}| can connect to make electric current by solution chemical reactions. Batteries {dry cell battery} can use paste. Batteries {wet cell battery} can use liquid solution.
voltage
Metals used for electrodes depend on battery solution. Metal combinations make different battery voltages across electrodes. Typical voltage is one volt to three volts.
series
Electrochemical cells can connect in series, so cell voltages add. Automobile batteries use lead plates and sulfuric acid solution.
recharging
Some batteries can recharge by applied electric voltage and current.
additives
Battery additives are useless.
Some batteries {primary cell}| cannot recharge.
Some batteries {secondary cell} can recharge.
battery {storage cell}|.
Current flows from battery negative terminal through circuit and power-using device {load, circuit} to positive terminal and then solution.
Electric voltage can electrolyze or electroplate material {electrolysis}|. Electrolysis uses potential to drive electrochemical reaction. Electric current can split solute molecules into two ions. Mass deposited in electroplating, or split in electrolysis, is proportional to total charge transfer. Mass deposited in electroplating, or split in electrolysis, is proportional to atomic weight to ion charge ratio {chemical equivalent}.
calculation
Find material electrolyzed or electroplated, or charge needed to electrolyze or electroplate material amount, from balanced equation. From balanced equation, separate reduction and oxidation half-reactions. Note number of electrons transferred. Moles of electrons used are coulombs divided by 96,500 Coulombs. Coulombs used is current amperes times seconds. Ratio of electrolyzed or electroplated product coefficient to transferred-electron number is ratio of electrolyzed or electroplated product moles to electrons-used moles.
potential
Nernst potential is minimum voltage needed to reverse spontaneous reaction at given conditions. Concentration gradient at electrode surface can make overpotential. Total needed potential {decomposition potential} includes Nernst potential, overpotential, and electrical-resistance potential.
activation energy
Temperature, current-to-area ratio, electrode surface, and electrode type affect reaction activation energy.
types: constant current
Constant-current electrolysis is for metals with reduction potential greater than hydrogen and for potential greater than hydrogen decomposition potential. Hydrogen ions in high-acidity solution carry constant current, because they are much more numerous than metal ions. Substrate keeps hydrogen gas low, so gas does not cover hydrogen electrode. Constant current times time makes total charge.
types: constant voltage
Constant-voltage electrolysis keeps potential high enough to lower metal-ion concentration to optimum level but low enough to stop hydrogen-gas evolution or other-metal deposition. In this method, current decreases over time.
types: controlled potential
Controlled-potential electrolysis uses third electrode (SCE) as reference to keep oxidation potential at cathode constant, keep current high enough, and prevent unwanted reactions. Current decreases over time exponentially. Cathode potential determines decomposition potential, so, as metal deposits, ion concentration goes down, and decomposition potential goes up.
In electrolysis, material moles formed or reacted is electron moles divided by metal or other ion charge {equivalent, chemistry}|.
In oxidation-reduction reactions, electrons transfer. Electron transfer requires voltage {potential, reaction}. Oxidation-reduction half-reactions have potentials. Total oxidation-reduction reaction potential is sum of half-reaction potentials.
level
Electronegative atoms have high reduction potentials.
calculation
Cell standard potential depends on half-reaction potentials and balanced equation. From balanced equation, separate reduction and oxidation half-reactions. Tables have half-reaction reduction potentials at 25 C. Subtract reduction potential for oxidation half-reaction from reduction potential for reduction half-reaction to find chemical-reaction potential.
spontaneity
If oxidation-reduction chemical-reaction potential is greater than zero, chemical reaction is spontaneous. If reduction potential is more than oxidation potential, ionization potential is higher, hydration energy is lower, and sublimation energy is more.
equilibrium
When oxidation-reduction reaction is complete, potential is zero.
Half-cell reduction-reaction voltage depends on oxidized and reduced concentrations, temperature, and number of electrons transferred {Nernst equation}. V = V0 - R * T / (n * ln([Co] - [Cr])), where V is reaction potential, V0 equals standard unit cell potential, R is gas constant, T is temperature, n is number of electrons transferred, Co is oxidized-ion concentration, and Cr is reduced-ion concentration.
Activation energy comes from electric field and from temperature.
valence charge
Electrode voltage is V = V0 + R * T * ln(K / (z * F)), where V is voltage, V0 is standard potential, R is gas constant, T is temperature, K is equilibrium constant, z is absolute value of transferred charge {valence charge}, and F is 1 Faraday. Therefore, exp(-V / (R*T)) = K / (z * F) and K = z * F * exp(-V / (R*T)). Standard potential is at concentration 1 M, pressure 1 atmosphere, and temperature 25 C. Solids have concentration = 1. Voltage is always positive. If V > 0, reaction is spontaneous. At equilibrium, voltage = 0 and current = 0.
Molecules {oxidizing agent}| can gain electrons from another molecule. Oxygen, halogens, permanganates, and chromates are oxidizing agents.
Molecules {reducing agent}| can lose electrons to another molecule. Small, light metals are reducing agents.
Redox reactions can be in solutions {cell, redox reaction}|. Conducting plates can be in two connected half-cells. Current from one electrode goes through wire to other electrode and then through solution.
potential
Metal and metal ion have potential difference, because electrons and ions separate. If potential > 0, metal favors reduction. If potential < 0, metal favors metal oxidation.
Nernst equation
If electrode voltage is > 0, reaction is spontaneous. At equilibrium, voltage = 0 and current = 0.
tables
Tables can show reduction-half-reaction potentials. Hydrogen electrode has standard potential 0 V.
diffusion
In fast reactions, diffusion controls reaction rate. Moving electrode or stirring solution minimizes diffusion effects.
salt bridge
Agar and potassium-chloride salt bridge can connect half-cells.
membrane
Membranes that block and allow ion flows can have potential difference, because membrane sides have different ion concentrations. Membrane-permeable ion diffuses through until electrostatic repulsion from higher-concentration side stops ion flow.
Redox reaction has two parts {half-reaction}| {half-cell} that interact, reducing-agent oxidation and oxidizing-agent reduction. Cell redox reactions oxidize reducing agent and reduce oxidizing agent. For example, half-reaction for hydrogen electrode is 2 H+ + 2 e- [+ and - are superscripts] <-> 1 H2 [2 is subscript].
Potential difference produced by open circuit {electromotive force}| (emf) is voltage that can make electricity.
Devices that make electric current have resistance force {back electromotive force}| to current. Maximum battery power has battery back electromotive force equal to circuit resistance.
Voltage applied to cells {electrolytic cell}| can force current through cell and cause reverse redox reaction. In electrolytic cells, cathode is electron source, and anode is electron sink. Applying voltage and current can split molecules by electrolysis. For example, water can form hydrogen and oxygen. Aluminum salts can make aluminum.
Spontaneous redox reaction in cells {galvanic cell}| can make current. In galvanic cells, anode oxidizes and is negative, while cathode reduces and is positive. Metal or metal-oxide electrode can be in solution {wet cell} or paste {dry cell}. Different metal or metal oxide can be in same solution or paste, or another solution or paste connected to first by conductor, to make two coupled cells and a battery. Metal reacts with solution to make ions. Metal anode loses electrons and becomes positive. Metal cathode gains electrons and becomes negative. Electrodes have potential difference.
battery types
Batteries can have nickel and cadmium in acid solution. Edison cells have nickel oxide and iron electrodes in alkaline solution. Batteries can have lead and lead oxide in acid solution.
Galvanic cells {fuel cell}| can have continuous fuel supply. Fuel cells make electric current by oxidizing hydrides or other substances. Fuel cells are efficient, cool, and clean.
Electrolysis can put metal on conducting surfaces {electroplating}|. In silver plating, gold plating, and zinc plating, metal derives from salt solution. Electric current adds electrons to change ion to metal at electrode.
In electrolytic cells, oxidation is at positively charged electrode {anode, cell}|. In galvanic cells, reduction is at positively charged electrode.
In electrolytic cells, reduction is at negatively charged electrode {cathode, cell}|. In galvanic cells, oxidation is at negatively charged electrode.
Substance can be solid at low temperature, liquid at intermediate temperature, and gas at high temperature {phase, chemistry}|. States or phases have different relations between material volume, temperature, and potential energy.
free energy
Current phase has lowest free energy for temperature. Potential energy depends on distance between molecules. Entropy depends on molecule number and temperature.
phases: solid
Solid phase has lowest volume and smallest potential energy, because average distance between molecules is smallest. Solids have low chemical potential. Low temperature makes material solid, because decrease in potential energy is higher than decrease in entropy. Solid phase has most order, because it has patterned crystal structure and temperature is lowest. Solid phase has least randomness and lowest entropy. Solids can have several crystal forms and so different solid phases.
phases: gas
Gas phase has highest volume and greatest potential energy, because average distance between molecules is greatest. Gases have high chemical potential. High temperature makes material gas, because increase in entropy is higher than increase in potential energy. Gas phase has least order, because all molecules are independent, with no physical structure, and temperature is highest. Gas phase has greatest randomness and highest entropy.
phases: liquid
Compared to solid, liquid phase has more volume and more potential energy, as distance between molecules becomes more. Intermediate temperature makes material liquid, because entropy change is similar to potential energy change. Liquid phase has less order than solid phase, because crystal structure breaks down into fluid structure, and temperature is more.
factors
Temperature, pressure, phase number, and substance amounts, concentrations, and pressures affect chemical systems.
factors: independence
Some factors relate to others, and some are independent. Available phases are independent, because substances can go to all phases.
factors: temperature
Temperature can freely vary, must be the same throughout system, and does not depend on other factors.
factors: pressure
Pressure can freely vary, must be the same throughout system, and does not depend on other factors.
factors: substances
Number of independent components is number of substances minus one. Because total percentage must be 100%, because sum of mole fractions must equal one, one substance's percentage is dependent.
factors: number
With no equilibria in system, number of independent factors is (c - 1) * p + 2, where c is component number, and p is phase number.
factors: equilibrium
Substance amounts in two phases in contact at phase boundary typically are in equilibrium. Chemical potentials of both phases must be equal. Number of equilibria is c * (p - 1), where c is component number, and p is phase number.
factors: degrees of freedom
Factor number and equilibria number determine how many factors {degrees of freedom, equilibrium} can freely change in chemical systems. Degrees of freedom equal free-variable number v minus equilibria number e {phase rule, components}: v - e. Degrees of freedom total: c - p + 2 = 1 + 1 + (c - 1) * p - c * (p - 1), where c is component number, and p is phase number.
factors: equilibrium and ions
If chemical systems have ions, electrical neutrality requires adding one more equilibrium to chemical system.
factors: equilibrium and initial state
Knowing chemical-system initial state fixes one more factor and adds one more equilibrium.
factors: equilibrium and field
If force field is present in chemical system, it adds one more phase to chemical system.
factors: equilibrium and phases
Two immiscible substances can make two heterogeneous phases, even if both are liquids, because they have boundary. Both components are in equilibrium. Heterogeneous phase is mixture and has several components, several phases, and several equilibria.
Two miscible substances can combine to make only one homogeneous phase, with no boundary, because they mix and so are not in equilibrium. Homogeneous phase counts as one component and one phase.
phase change
Physical systems tend to go to lowest potential energy and greatest entropy. Electrical forces push or pull atoms and change potential energy to kinetic energy. Friction opposes electrical forces, so kinetic energy tends to become heat. Physical systems tend toward most randomness and lowest physical order and so greatest entropy. Number of molecules freed from order relates to average random kinetic energy and so temperature.
phase change: free energy
Total available energy is free energy and is energy from order breakdown plus potential energy. Physical systems tend to go to lowest free energy. Lowest free energy is optimum between lowering potential energy and raising entropy.
phase change: temperature
System has same average random translational kinetic energy throughout. Temperature stays constant during phase change from gas to liquid, or liquid to solid, because all heat energy removed is potential energy, which kept molecules apart, not kinetic energy. Temperature stays constant during phase change from solid to liquid or from liquid to gas, because added kinetic energy from heat becomes potential energy that makes molecules farther apart.
Substances can bind onto solid surfaces {adsorption}|.
Equal gas volumes at same temperature and pressure contain same number of molecules {Avogadro's hypothesis} {Avogadro hypothesis}. At standard temperature and pressure, number is one mole {Avogadro's number}, which is 6*10^23 molecules.
Particles in suspension move randomly in all directions with many velocities {Brownian motion}|. Brownian motion depends on time.
cause
Fluid-molecule collisions cause fluid random motions and microscopic-particle oscillations. Particles travel short average distance, through mean free path, before next collision. Collision frequency varies inversely with mean free path.
examples
Telephone errors have bursts, with random intervals between errors. Brownian-motion zerosets, or random Cantor sets with fractal dimension between zero and one, can model them.
examples: random walk
Processes {random walk} can take same-length steps in all directions. Average distance from origin is square root of step number. Return to origin is probable. Random walk can be along a line or have more dimensions.
comparison
Brownian motion is neither fractal nor self-similar.
Materials have ability to conduct electricity {conductivity}|.
conductor
Conductor molecules can have half-filled electron energy level, so electrons can jump to same energy level in neighboring molecules. Metallic crystals are conductors.
semiconductor
Semiconductor molecules can have energy level filled with electrons and slightly higher empty energy level, so electrons can jump into neighboring molecules at normal temperatures. Covalently bonded crystals are semiconductors.
insulator
Insulator molecules can have energy level filled with electrons and much higher empty energy level, so electrons cannot jump into neighboring molecules at normal temperatures. Ionic crystals and hydrogen-bonded crystals like ice, hydrogen fluoride, and proteins are insulators. Insulators are typically transparent.
In inorganic ionic crystals, a number {coordination number} of other atoms surround each atom. Eight opposite-charge atoms surround each atom, if atoms have equal size. Six opposite-charge atoms surround each atom, if atoms have unequal size. Four opposite-charge atoms surround each atom, if atoms have very unequal size.
Substance solid, liquid, and gas phases can all be present at triple point at high temperature {critical temperature}| and high pressure {critical pressure}.
At critical temperature and pressure, substance solid, liquid, and gas phases are all present {triple point} {criticality, phase}|. At high pressure and temperature, gas and liquid can be one phase, dense gas or gaseous liquid.
If substance releases into another substance, released substance tends to flow {diffusion}| throughout other substance, until released substance evenly distributes.
cause
Random molecule elastic collisions cause diffusion. Diffusion decreases system order. Gases tend to expand as molecules collide. Expansion rate depends on molecule velocity and size and on barriers to motion.
spectrum
In media, introduced foreign substance diffuses outward over time depending on number {spectral dimension} of medium-particle nearest neighbors. For ink in water, ink volume V increases as time t to 3/2 power: V = t^1.5.
For most solids, heat capacity per mole is constant {Dulong and Petit law} {law of Dulong and Petit}.
Molecular collisions cause gas to flow through container holes {effusion}|.
Two phases can have no net flow between them {equilibrium between phases}. At boiling-point or melting-point temperature, both phases, liquid/gas or solid/liquid, respectively, have same free energy and are in equilibrium. If temperature decreases, substance becomes denser, because entropy change is small but potential-energy change is large. If temperature increases, substance becomes less dense, because entropy change is large but potential-energy change is small.
Different pure fluids can come from fluid mixture by controlling pressure, vaporizing mixture at increasing temperatures, and cooling and condensing each vapor {fractionation}|.
Work that gas can do equals heat energy in gas {gas law} {ideal gas law, work}: P*V = n*R*T, where P is pressure, V is volume, n is moles, R is gas constant, and T is absolute temperature. Pressure times gas volume is work that gas can do. Product of gas moles and absolute temperature and gas constant is gas heat energy.
volume
Volume {molar volume} of one mole of ideal gas at standard temperature of 25 C and standard pressure of one atmosphere is 22.4 liters.
ideal gas
Ideal gas law assumes that molecules have elastic collisions, have no volume, and have no forces among them. At low pressure, real gas has less pressure than ideal gas, because molecules attract each other. At high pressure, real gas has higher pressure than ideal gas, because molecules repulse each other.
modifications
Ideal-gas-law modifications {van der Waals equation} {virial equation} account for molecule sizes and interactions.
Gas diffusion rate is inversely proportional to gas-density square root {Graham's law} {Graham law}.
Expanding gas can cool if temperature is below maximum temperature {Joule-Thompson inversion temperature}.
Vapor at critical point has white glow {opalescence, glow}|.
Degrees of freedom d are free-variable number n minus equilibria number e {phase rule, degrees of freedom}: d = n - e.
Melting solids along a moving band {zone melting}| can make impurities remain in melted part and pure part solidify behind moving band.
Gases and liquids {fluid}| are similar in flow properties. Van der Waals forces between molecules can cause cohesion, adhesion, adsorption, and surface tension. More polarized materials have increased molecule van-der-Waals forces, so cohesion and surface tension are greater, and adhesion is smaller.
Matter {gas phase} can have low density, flow, be compressible, have no local or global order, and expand to fill volume.
energy
Gases have high kinetic energy. Molecules have speed 500 meters per second. Electric forces between molecules have little effect.
distances
Molecules are 20 nanometers apart. Gases have distances between molecules that are five to ten times more than distances in solids and liquids. Gases are like spaces of vacancies with some positions filled.
size
Gas-molecule diameter is 0.5 nanometers.
relations
If gas volume increases while temperature stays the same, pressure decreases, and entropy and potential energy increase. If gas temperature increases while pressure stays the same, volume increases, and entropy and potential energy increase.
Temperature and pressure depend on kinetic energy, and volume and entropy depend on potential energy. If total energy is constant, P/V = S/T, where P is pressure change, V is volume change, S is entropy change, and T is temperature change. Potential energy increases when entropy increases, and entropy increases when potential energy increases.
Matter {liquid phase} can be dense, flow, have local order several atoms wide, have long-range disorder between local-order regions, have no expansion to fill volume, have less than 3% compression, have translational kinetic energy, and have molecule interactions.
types
Liquids can be molten salts, metallic liquids, hydrogen-bonded liquids, or van der Waals bonded liquids.
cohesion
Cohesive forces can be ionic, dipoles, ions and dipoles, dipoles and induced dipoles, or London forces between neutral atoms. Internal forces can be repulsive if compression is high.
melting
Melting is similar to reaching elastic limit in solid under stress.
At high temperature, materials can exist as ionized gas {plasma phase}|, as substance vaporizes and loses electrons.
High-density proton plasmas {Wigner solid} can act like liquids.
Matter {solid phase}| can be firm, be incompressible, have local and global order, have no flow, and have no expansion to fill volume.
crystal
Most solids are crystals. Crystals can be cubes, prisms, rhomboids, parallelepipeds, hexagons, or diamonds.
types
Elements {molecular elemental solid} can have molecules bound by weak van der Waals forces. Metal elements {metallic elemental solid} have atoms bound with metallic bonds. Non-metal elements {non-metallic network elemental solid} have each atom covalently bound to four or less atoms, in covalent-bond crystal lattices. Salts {ionic solid} can have ionic bonds between ions. Salts {polar solid} can have dipole-dipole bonds between polar molecules.
oscillations
Solid molecules vibrate and rotate but do not translate to new positions. Solids can transmit pressure in force direction but cannot cause pressure.
Solids can have no regular structure {amorphous solid}|, such as glass.
Almost all solids have regular molecule, ion, or atom arrays {crystal}|.
types
Crystals {cubic crystal} can have eight atoms around small atom, three perpendicular four-fold same-length axes, and five crystal classes.
Crystals {rhomboid crystal} can have twelve atoms around similar size atom with every third layer directly above another.
Crystals {rhombohedral crystal} can have one three-fold axis, with one axis perpendicular to the other two but with different length, and two axes with same length at 120-degree angle to perpendicular axis, and make five crystal classes.
Crystals {hexagonal crystal} {hexagon crystal} can have twelve atoms around similar size atom with alternate layers directly above each other.
Crystals {tetrahedral crystal} {tetrahedron crystal} can have four large ions around each small ion.
Crystals {octahedral crystal} {octahedron crystal} can have six large ions around each small ion.
Crystals {triangular crystal} can have three large ions around each small ion.
Crystals {planar crystal} can have two large ions around each small ion.
symmetry
Only one, two, three, four, or six rotational symmetries can fill all space with no gaps or overlaps, so only seven crystal types are common.
packing
The more similar in size atoms or ions are, the more atoms or ions can surround one atom or ion. Number of atoms or ions surrounding one atom also depends on ion charge or covalent-bond number.
lattice
Crystals have lattice structure. Including crystal type and lattice type, 32 crystal classes exist. 14 unit cell and 32 crystal class translations and transformations make 234 possible crystal shapes.
crystal growth
Crystals grow at dislocations, because binding molecules can contact two surface atoms. Impurities, long bond lengths during fast growth, and screw dislocations can cause dislocations and irregularities.
Small crystal faces grow fastest by deposition. Large crystal faces can adsorb other materials.
Crystal surfaces are never flat but are lumpy. Perfect crystals cannot grow.
Diagrams {Miller index} can show crystal planes, using three perpendicular axes. Crystal vertices are one unit length or less apart. Coordinate reciprocals indicate planes through vertices. Putting origin at one vertex and using coordinates for other vertices indicates edges. If plane is parallel to axis, coordinate reciprocal is zero.
Crystal growth can be along one axis {dendritic growth}, because heat leaves best at tips, so deposition is easiest there.
Unit cells can undergo translation and reflection {glide plane}.
Unit cells can undergo translation and turn around axis {screw axis} 0, 180, 120, 90, 72, or 60 degrees.
Crystals {clathrate} can be so open that they can hold small molecules inside, without bonding. Examples are very-cold-water forms and very-cold methane and hydrogen gas mixtures.
Metal crystals {metal crystal} can have hexagonal close packing, face-centered cubic close packing, or body-centered cubic close packing.
Substances {polymorphic solid} can have more than one crystal form.
Crystals {liquid crystal}| {dynamic scattering liquid crystal} (LCD) can have regularity in only one or two dimensions, allowing unit cells to slide past each other in third dimension. Liquid crystals are anisotropic, flow in sheets or steps, and are asymmetric molecules. Numbers can display electronically using reflected or transmitted light, as electric field makes crystal tinted, and no electric field makes crystal transparent.
Liquid crystals {nematic crystal} can have linear crystals with regularity in only one dimension, are like threads with no planes, orient, and are not periodic.
Liquid crystals {smectic crystal} can have planar crystals with regularity in two dimensions, orient, and are not periodic.
Missing atoms, extra atoms, or different atom types {crystal defect} alter regular crystal structure.
Crystal defects {dislocation, crystal} can displace unit cells from usual positions. Inserted atoms wedged into lattice can cause dislocations {edge dislocation}. Dislocations {screw dislocation} can be around axis to make helical unit-cell arrangements. Dislocations in crystals affect brittleness, ductility, and other mechanical crystal properties. Alloys lack dislocations and so do not slide, because odd atoms move to lowest free-energy positions.
Crystal ions can move to interstitial places and so leave vacancies {Frenkel defect}.
Different molecules or atoms {impurity}| can be in crystals.
Extra ions {interstitial ion} can be in ionic crystals.
In ionic crystal, cations and anions can be missing {Schottky defect}.
Ions can be missing from ionic crystals {vacancy}|.
Crystals have repeating atom groups {unit cell}. Crystals have lattice structure.
Only 14 possible arrangements {Bravais lattice} of identical spheres can make unit cells {space lattice}. Three are cubic, two monoclinic, four orthorhombic, two tetragonal, one triclinic, one hexagonal, and one rhombohedral.
Using half-unit circles as atoms, in a 3 x 4 surface area make two-dimensional figures: squares; triangles, hexagons, and rhombuses; centered rectangles; rectangles, and oblique figures.
From most symmetric to least symmetric two-dimensional space lattices (see Figure 1).
Square: Cell is a unit-length-side square, as in the first figure above. The two axes have equal length, both axes are mirror planes, and both axes have 90-degree rotation symmetry. Atoms are at corners. Cell has 90-degree rotation symmetry and two planes with mirror symmetry. Atoms have 4 atoms 1 unit away and 4 atoms SQR(2) away. Density is 12/12 = 1.
Hexagonal: Cell is a unit-length-side triangle with angles 60 degrees, a rhombus with angles 60 and 120 degrees, and a hexagon, as in the second figure above. The two axes have equal length, both axes are mirror planes, and both axes have 60-degree rotation symmetry. Atoms are at corners. Rhombus has 180-degree rotation symmetry and two planes with mirror symmetry. Triangle has 60-degree rotation symmetry and no planes with mirror symmetry. Atoms have 6 atoms 1 unit away. Density is ~13/12 > 1.
Centered rectangular: Cell is a parallelogram with angles not 30, 45, 60, 90, or 120 degrees, short diagonal unit length, and a rectangle with two sides greater than unit length and two side greater than that, as in the third figure above. The two axes have unequal length, one axis is a mirror plane, and both axes have 180-degree rotation symmetry. Atoms are at corners. Cell has 180-degree rotation symmetry and two planes with mirror symmetry. Corner atoms have 4 atoms 1 unit away, 2 atoms farther away, and 2 atoms even farther away, and central atoms have 4 atoms 1 unit away and 4 atoms farther away. Density is ~10/12 < 1.
Rectangular: Cell is a rectangle, as in the fourth figure above. The two axes have unequal length, both axes are mirror planes, and both axes have 180-degree rotation symmetry. Atoms are at corners. Cell has 180-degree rotation symmetry and two planes with mirror symmetry. Atoms have 2 atoms 1 unit away, 2 atoms farther away, and 4 atoms even farther away. Density is 6/12 = 0.5.
Oblique: Cell is a parallelogram with angles not 30, 45, 60, 90, or 120 degrees, as in fifth figure above. The two axes have unequal length, no axes are mirror planes, and both axes have 180-degree rotation symmetry. Atoms are at corners. Cell has 180-degree rotation symmetry and no planes with mirror symmetry. Each atom has 2 atoms 1 unit away, 2 atoms farther away, 2 atoms even farther away, and 2 atoms much farther away. Density is <6/12 < 0.5.
From most symmetric to least symmetric three-dimensional space lattices:
Isometric crystal: Cubic cell base is a square with angles 90 degrees, and height is perpendicular to base. All faces are squares. All axes have equal length. Atoms are at corners, can be in body center, and can be in face centers (three Bravais lattices). Point-group symmetry has three rotations by 90 degrees. For corners only, each atom has 4 atoms around in a plane and 2 atoms (above and below) along the perpendicular, total 6. For face-centered, corner atoms have 8 atoms around in a plane and 2 atoms (above and below) along the perpendicular, and centered atoms have 4 atoms around in a plane and 2 atoms (above and below) along the perpendicular. For body-centered, corner atoms have 4 atoms around in a plane, 2 atoms (above and below) along the perpendicular, and 4 atoms along diagonals, and centered atoms have 8 atoms along diagonals.
Hexagonal crystal: Cell base is a parallelogram with angles 120 and 60 degrees, and height is perpendicular to base. Two faces are parallelograms, and four faces are rectangles. Parallelogram axes have equal length, and height has any length. Atoms are at corners (one Bravais lattice). Point-group symmetry has one rotation by 60 degrees. Each atom has 6 atoms around in a plane and 2 atoms (above and below) along the perpendicular, total 8.
Tetragonal crystal: Cell base is a square, and height is perpendicular to base. Four faces are rectangles, and two faces are squares. Square axes have equal lengths, and height is not equal to square-side length. Atoms are at corners, and can be in body center (two Bravais lattices). Point-group symmetry has one rotation by 90 degrees. For corners only, each atom has 4 atoms around in a plane and 2 atoms (above and below) along the perpendicular, total 6. For body-centered, corner atoms have 4 atoms around in a plane, 2 atoms (above and below) along the perpendicular, and 4 atoms along diagonals, and centered atoms have 8 atoms along diagonals.
Rhombohedral crystal: Trigonal-point-group cell base is a rhombus, and height is not perpendicular to base. All faces are rhombuses. All axes have equal lengths. Atoms are at corners (one Bravais lattice). Point-group symmetry has one rotation by 120 degrees. Each atom has 4 atoms around in a plane and 2 atoms (above and below) along the perpendicular, total 6.
Orthorhombic crystal: Cell base is a rectangle, and height is perpendicular to base. All faces are rectangles. All axes have unequal lengths. Atoms are at corners, can be in body center, can be in base-face centers, and can be in all face centers (four Bravais lattices). Point-group symmetry has three rotations by 180 degrees and two mirror planes. For corners only, each atom has 4 atoms around in a plane and 2 atoms (above and below) along the perpendicular, total 6. For base-face-centered, corner atoms have 8 atoms around in a plane and 2 atoms (above and below) along the perpendicular, and centered atoms have 4 atoms around in a plane and 2 atoms (above and below) along the perpendicular. For all-face-centered, corner atoms have 8 atoms around in a plane and 2 atoms (above and below) along the perpendicular, and centered atoms have 4 atoms around in a plane, 4 atoms along diagonals, and 2 atoms (above and below) along the perpendicular. For body-centered, corner atoms have 4 atoms around in a plane, 2 atoms (above and below) along the perpendicular, and 4 atoms along diagonals, and centered atoms have 8 atoms along diagonals.
Monoclinic crystal: Cell base is a parallelogram, and height is perpendicular to base. Two faces are parallelograms, and four faces are rectangles. The three axes have unequal length. Atoms are at corners and can be in face centers (two Bravais lattices). Point-group symmetry has one rotation by 180 degrees and one mirror plane. For corners only, each atom has 4 atoms around in a plane and 2 atoms (above and below) along the perpendicular, total 6. For face-centered, corner atoms have 8 atoms around in a plane and 2 atoms (above and below) along the perpendicular, and centered atoms have 4 atoms around in a plane and 2 atoms (above and below) along the perpendicular.
Triclinic crystal: Cell base is a parallelogram, and height is not perpendicular to base. All faces are parallelograms. All axes have unequal lengths. Atoms are at corners (one Bravais lattice). There are no point-group symmetries. Each atom has 4 atoms around in a plane and 2 atoms (above and below) along the perpendicular, total 6.
Lattices {primitive lattice} can have atoms at unit-cell corners.
Lattices {body-centered lattice} can have one or two atoms at unit-cell centers. Lattices {body-centered cubic close packing} can have atoms in cube centers, with identical atoms at cube corners.
Lattices {face-centered lattice} can have one atom in unit-cell face. Unit cells with different atoms {face-centered cubic close packing} can have atoms in cube centers and in cubic-unit-cell face centers.
Unit-cells {cubic close packing} can be cubic. Twelve identical atoms surround each atom, and every third layer is directly above another.
Unit cells {hexagonal close packing} can be hexagonal. Twelve identical atoms surround each atom, and alternate layers are directly above each other.
Unit crystals can have same structure after rotation around axis, reflection across axis, inversion through central point, translation along axis, or any combination {symmetry, crystal}. Nature has six symmetry groups: isometric, hexagonal, tetragonal, orthorhombic, monoclinic, and triclinic.
Symmetry groups {hexagonal} can have rotation by 60 degrees. Hexagonal crystals have one six-fold axis, with one axis perpendicular to the other two axes but with different length, and two axes with same length at 60-degree angle to perpendicular axis, and makes seven crystal classes.
Symmetry groups {cubic symmetry group} {isometric symmetry group} can have rotation by 90 degrees, reflection, and inversion.
Symmetry groups {monoclinic symmetry group} can have rotation by 90 degrees. Crystals {monoclinic crystal}| can have one two-fold axis, two perpendicular same-length axes, and one non-perpendicular different-length axis, to make three crystal classes.
Symmetry groups {orthorhombic symmetry group} can have rotation by 180 degrees and reflection. Crystals {orthorhombic crystal} can have three two-fold axes, which are all perpendicular but have different lengths, to make three crystal classes.
Symmetry groups {tetragonal symmetry group} can have rotation by 90 degrees. Crystals {tetragonal crystal} can have one four-fold axis and three perpendicular axes but only two with same length, to make seven crystal classes.
Symmetry groups {triclinic symmetry group} can have rotation by 120 degrees. Crystals {triclinic crystal}| can have three axes, all not perpendicular but all of same length, to make two crystal classes.
Substances can mix with other substances {mixture}|. Mixed-substance chemical potential is less than pure-substance chemical potential, because mixtures have more disorder.
Liquid can be suspension in gas {aerosol}|, like dust and fog.
Liquid can be suspension in liquid {emulsion, mixture}|, like mayonnaise, cheese, and shaken salad dressing.
Liquid can be colloid in another liquid {sol, mixture}|, like india ink.
Gas can be suspension in liquid {foam}|, like whipped cream and foam rubber.
Solid can be colloid in liquid {gel}|, like jelly.
Mixing two substances can make one phase or solution {homogeneous phase}, with no boundaries.
Two substances can mix {heterogeneous phase} but have boundaries between different regions.
Mixtures {colloid}| with particle diameters 1 to 100 nanometers are translucent or opaque, separable by fine membranes, and settle slowly. Solutions can have many small particles, which attract an opposite-charge ion layer, which then attract an ion layer. Layers prevent good precipitation. Hydrophilic colloids are viscous, hard to coagulate, and gel-like. Hydrophobic colloids are sols, make curds, and are easy to coagulate.
Mixtures {suspension}| can have particles with diameter greater than 100 nanometers, be translucent or opaque, be separable by coarse membranes, and settle quickly.
Solvent molecules can surround solute molecules, to make one phase {solution, chemistry}|. Liquid solutions are transparent, because they are one phase with no surfaces for light reflection. To find solution substance concentration, divide substance moles by volume in liters of solution, not just solvent.
Membrane allows solvent molecules to pass but not solute molecules. If membrane separates solution from another solution, solvent passes into solution with higher solute concentration, because more solvent molecules hit membrane on side with less solute and pass through to other side {osmosis}|.
For example, solvent can be water, with many solute molecules inside membrane bag. See Figure 1.
pressure
Osmosis increases solvent amount on membrane side with higher solute concentration, causing extra pressure on that membrane side. The osmotic pressure resists further osmosis, because number of solvent molecules hitting both membrane sides becomes equal.
For example, water passes into bag, making bag bigger and stretching it. Membrane is under pressure. The extra water inside causes higher pressure inside, meaning more water molecules hit membrane inside. See Figure 2.
chemical potential
Mixtures have higher chemical potential than pure liquids, so pure liquid goes from pure-liquid membrane side to mixture membrane side, raises liquid level on mixture side, and lowers chemical potential. Chemical-potential decrease generates osmotic pressure, which tries to bring system into equilibrium.
small solutes
Membrane can allow small solute molecules and ions to pass through, but not large solute molecules. Small molecules diffuse through membrane, tending to make small-solute molecule concentrations equal on both membrane sides.
Osmosis increases solvent amount on membrane side with higher concentration, causing extra pressure {osmotic pressure}| on membrane from that side. The extra pressure resists further osmosis, as number of solvent molecules hitting both sides becomes same.
Solvents can have electronegative atoms {polarity}|.
types
Polar solvents include water, ethyl alcohol, and methyl alcohol. Acetone is slightly polar. Benzene is non-polar.
solution
Like dissolves like. Polar solvents can dissolve in each other. Non-polar solvents can dissolve in each other. Sticky non-polar solids are harder to dissolve in non-polar solvents, because they do not break up. Acetone, methyl alcohol, ethyl ether, and ethyl alcohol are soluble in water. Benzene, carbon tetrachloride, chloroform, hexane, cyclohexane, methylene chloride, toluene, and xylene are insoluble in water.
Solid can dissolve in water to make ion solutes {electrolyte}|.
Two liquids {immiscible liquids}| can be unable to dissolve in each other, like benzene and water.
Two liquids {miscible liquids}| can dissolve in each other, like alcohol and water.
Material true concentration or partial pressure {partial molar quantity} depends on other-substance concentrations or partial pressures, because having different substances contributes more disorder to system. Substances interact, because system has total pressure, temperature, and concentration.
Material true concentration or partial pressure {chemical potential, solution}| {free energy per mole} depends on partial molar quantity, because having different substances contributes more disorder to system. Substances interact, because system has total pressure, temperature, and concentration that distribute among substances. Substance partial molar Gibbs free energy is partial derivative of free energy with substance moles, if temperature, pressure, and other-substance amounts are constant.
Gas solubility in liquid is proportional to partial pressure of gas in contact with liquid {Henry's law} {Henry law}.
Gases in mixtures independently contribute pressure {partial pressure} to total gas pressure {law of partial pressures}.
Solute-vapor partial pressure above solution equals solute mole fraction times pure-solute vapor pressure {Raoult's law} {Raoult law}.
Pure substances have molar quantities, but mixtures have partial molar quantities, which depend on material moles divided by total moles, the mole fraction. Solution properties {colligative property}|, such as partial pressures, boiling point elevation, freezing point depression, osmotic pressure, solubility, volatility, and surface tension, can depend on solute mole fraction. Partial molar quantities are interdependent, because mole fraction total must be one.
Solutions have higher boiling point than pure solvent {boiling point elevation}|, because solute molecules are heavier than solvent molecules and have lower volatility. If liquid includes impurities that are less volatile than liquid, liquid boils only at higher temperature. Salt in water raises boiling temperature. Mixture boiling point is higher, because mixtures are more random, so difference between liquid and gas is less. Immiscible substances lower boiling point, because both vapor pressures add to increase pressure. In boiling-point elevation, temperature change dT equals constant k times molality M: dT = K*M. People know constants for solutes and solvents.
Solutions have lower freezing point than pure solvent {freezing point depression}|, because solute molecules are impurities in solvent crystals and so make crystals harder to form. In freezing-point depression, temperature change dT equals constant k times molality M: dT = K*M. People know constants for solutes and solvents.
Solid solute molecules can crystallize and separate from liquid solvent molecules {precipitation from solution}|.
causes
Decreasing solubility causes precipitation. Solubility decreases by cooling. Solubility decreases by adding organic non-polar solvents, such as acetone and ethanol, to water solution.
polarity
Solubility decreases by neutralizing solution to reduce acidity and polarity. Adding concentrated ammonium sulfate usually causes precipitation from aqueous solution. Molecules precipitate best at isoelectric points, because they have least polarization there.
types
Precipitates {lyophobic}, like sulfur and metal salts, can be small pellet-like precipitates, with molecules that reject water and adsorb ions. Precipitates {lyophilic}, like starch and gelatin, can be large curd-like precipitates, with molecules that adsorb water.
Crystals can precipitate from solution {fractional crystallization}, by evaporating solvent, by cooling solution, or by adding another solvent to solution.
At temperature, a number of solute grams can dissolve in 100 milliliters of solvent {solubility}|. If solubility is greater than one percent, solute can dissolve well in solvent {soluble}.
water solubility
Compounds have solubility in water {aqueous solubility}. Nitrates, acetates, chlorides, bromides, most iodides, most sulfates, sodium salts, potassium salts, and ammonium salts are soluble in water.
Hydroxides except sodium hydroxide and potassium hydroxide; sulfides except sodium sulfide, magnesium sulfide, and aluminum sulfide; arsenates except sodium arsenate and potassium arsenate; carbonates except sodium carbonate and potassium carbonate; and phosphates except sodium phosphate and potassium phosphate are insoluble in water.
precipitation
Solubility is maximum concentration before precipitation from solvent. For precipitation, concentration product {solubility product} must be greater than equilibrium constant.
factors
Solute solubility in solvent depends on solute polarity, size, and surroundableness and solvent polarity, size, and surroundability.
factors: temperature
Higher temperature increases solubility, because increased random motion breaks up and mixes solute and solvent more.
factors: concentration
Low concentration increases solubility, because solvent molecules can better surround solute molecules, with less solute molecules near other solute molecules.
factors: stirring
Stirring increases solubility, because more motion mixes solute and solvent more.
factors: ions
More hydrogen ion increases solubility in polar solvent, by increasing polarity. More ions increase solubility in polar solvent, by increasing polarity.
Ionic solutes with large ions and large charges are harder to dissolve. Ionic solutes with small ions and charges of +1 or -1 are easier to dissolve. Large ions with charge +1 or -1 dissolve better than small ions with charge +2, -2, +3, -3, or greater. Salts with small volume, especially hydrogen ions and acids, increase solubility by allowing more shielding. Higher-charge salts increase solubility more, because they shield better. Salts that form metal-ion complexes increase solubility, by more shielding.
factors: common ion
Low concentration of ion common to two solutes increases solubility, because solvent molecules can better surround solute molecules, with less solute molecules near other solute molecules. Common ion provides more molecules for collision. Solubility decreases if common ion is present in large amounts, because the other ion must then be at low concentration to equal solubility product.
factors: diverse ion
Solubility increases if diverse ion is present, because charges have more shielding and polarity increases.
factors: polarity
Similar-polarity molecules dissolve each other best, because electrical attractions for similar molecules are stronger.
factors: size
Small molecules dissolve better, because solvent molecules can better surround solute molecules.
factors: shape
Spherical molecules dissolve better than elongated ones, because solvent molecules can better surround spherical molecules.
When water molecules surround ions, energy {energy of hydration} {hydration energy}| releases. Small atoms have more hydration than large ones, because water surrounds them better.
Solvent molecules can surround other-substance {solute} molecules.
Solubility can decrease by adding salt with common ion and higher solubility, to make higher concentration and force solute out of solution {common ion effect}.
Ions in solution increase polarity and increase solubility {Debye-Hückel law}.
Substance {solvent, chemistry}| molecules can surround solute molecules.
Solvent is usually water {aqueous solution}.
Solvent can be alcohol {tincture}|.
Solid can dissolve in another solid {alloy}|, as in steel, bronze, and brass. Steel is carbon in iron. Bronze is tin in copper. Brass is zinc in copper.
Liquid can dissolve solid {amalgam}|, as metals can dissolve in mercury.
Solutions have ratio {concentration}| of solute mass or volume to total solution or solvent mass or volume.
Concentration {molal} can measure number of solute moles dissolved in one solution kilogram.
Concentration {molar, concentration} (M) can measure number of solute moles dissolved in one solution liter.
Concentration {mole fraction} can measure number of solute moles dissolved in one solution mole.
Concentration {normal, concentration} (N) can measure number of solute-ion equivalents dissolved in one solution liter.
Concentration {parts per million} (ppm) can measure number of solute milligrams dissolved in one solution liter.
Concentration {percent solution} can measure number of solute grams or milliliters dissolved in 100 solution grams or milliliters.
Solutions {dilute solution}| can have low concentration.
Solutions {concentrated solution} can have high concentration.
Solutions {saturated solution}| can have maximum concentration, at temperature, if dissolved solute is in contact with solid solute.
At a temperature, if no solid is present and solution has no crystallization, solution can have concentration higher than saturated concentration {supersaturated}|.
Chemistry {organic chemistry} can be about molecules with carbon. About 100,000,000,000 carbon-based molecules {organic molecule, chemistry} exist.
In plastics, such as divinylbenzene, covalent or hydrogen bonds can link two polymer chains {cross-linking, plastic}|.
Functional group or molecule can attract to negatively charged atom {electrophile}|. Electrophiles, from strongest to least strong, are hydrogen ion, positive halide ion, and carbon. Charged electrophiles are stronger than uncharged ones.
Chemical symbolism {Fischer projection} can show bond direction.
Functional group or molecule can attract to positively charged atom {nucleophile}|. Nucleophile order, from strongest to least strong, is organic base, base, amine, alcohol, and halide. Charged nucleophiles are stronger than uncharged nucleophiles.
Rules {Sequence Rule} can show nature of symmetry axes and chirality planes.
Large substituents can interfere with rotations and slightly alter bond angles {steric hindrance}|.
Organic molecules have three-dimensional arrangements {conformation, molecule}|. Carbon-chain substituents can have alternate forms {carbon chain conformation}.
Carbon-chain substituents can align {eclipsed form}. Eclipsed form has more hindrance, more potential energy, and less probability.
Carbon-chain substituents can alternate position {staggered form}. Staggered form has less hindrance, lower potential energy, and more probability.
The two highest-priority groups can be on same double-bond side {cis, orientation}|, designated by prefix Z.
The two highest-priority groups can be on opposite double-bond sides {trans, orientation}|, designated by prefix E.
In six-carbon rings with only single bonds, carbons have single bonds to two substituents. Whole ring {ring configuration} can look like a chair {chair configuration} or boat {boat configuration}.
If adjacent carbons have one substituent and one hydrogen atom, substituents can both be axial or equatorial {trans, ring} or can be one axial and one equatorial {cis, ring}. Single bonds between carbon atoms allow rotation. Because ring bond rotation must change two single bonds simultaneously, bond rotation cannot change cis to trans, or trans to cis.
Bonds {axial bond} to substituents can point perpendicular to rings.
Bonds {equatorial bond} to substituents can point parallel to rings. Large substituents tend to be equatorial.
Molecules {isomer}| with same atoms can have different chemical and physical arrangements. Isomers {structural isomer} can have different chemical bonds among chain atoms. Isomers {functional isomer} can have different chemical bonds among substituents.
To distinguish and name isomer, give atom with highest atomic number highest priority. For atoms with same atomic number, use atomic mass to assign priority. If two or more atoms are the same, go outward from chiral atom, applying same rules to farther atoms. Treat double bonds like two single bonds with atoms.
Isomers {conformational isomer} can have same chemical bonds, but rotations around single bonds make different spatial relations.
Isomers {diastereomer}| that are not mirror images can be unable to superimpose.
Double bonds between two carbon atoms make all bonds lie on one plane. The four single bonds can have different isomers {geometric isomer}. The two highest-priority groups can be on opposite double-bond sides {trans, double bond}, with prefix E. The two highest-priority groups can be on same double-bond side {cis, double bond}, with prefix Z.
Structural isomers can transfer proton between two non-equivalent sites {tautomerism}|. Aldol and ketol exhibit tautomerism.
Isomers {stereoisomer}| {optical isomer} can have right-handed and left-handed structures that single-bond four different substituents to carbon atom. Stereoisomers are asymmetric molecules, such as enantiomer, racemic, diastereomer, and meso compound. The D and L system {glyceraldehyde} designates stereoisomers relative to (+)-glyceraldehyde {D-glyceraldehyde} and (-)-glyceraldehyde {L-glyceraldehyde}.
For R-S systems {Cahn-Ingold-Prelog system} {CIP system}, at asymmetric carbon atom, place lowest-atomic-number bound atom straight-behind the plane, with the three other atoms facing observer. Mark highest-atomic-number atom and next highest. For atoms with same atomic number, use atomic mass. If two or more atoms are the same, go outward from chiral atom, applying same rules to farther atoms. Double bonds, triple bonds, and aromatic rings are like two or three bonds with atoms. If highest to next highest goes clockwise, compound is R or Rectus. If highest to next highest goes counterclockwise, compound is S or Sinister.
Isomers {meso compound}| have asymmetric carbon but also have symmetry plane that cancels optical rotation.
Two isomers {enantiomer}| {enantiomorph} can be mirror images.
Mixtures {racemic mixture} can have equal enantiomer amounts.
Reactions {racemization}| can change one enantiomer into the other.
Stereoisomers can rotate plane-polarized light clockwise {dextrorotatory} (+), as measured by degrees in polarimeter.
Stereoisomers can rotate plane-polarized light counterclockwise {levorotatory} (-), as measured by degrees in polarimeter.
Molecules {hydrocarbon}| can have only carbon and hydrogen.
Carbon atoms in sequences or rings can attach hydrocarbon chains or rings {side chain, hydrocarbon} {hydrocarbon side chain}.
Carbon atoms in sequences or rings can attach atoms or atom groups {substituent group}|.
Carbon atoms {carbon}| can attach carbons to make sequences or rings.
non-metals
Carbon forms covalent bonds with non-metals. Carbon and chlorine make the volatile liquids carbon tetrachloride and chloroform. Carbon and fluorine make the liquid refrigerant Freon and the solid fluorocarbon Teflon. Carbon and oxygen make carbon monoxide gas and carbon dioxide gas. Carbon and nitrogen make cyanide ion with triple bond between nitrogen and carbon, nitrile compounds with triple bond between nitrogen and carbon, imine compounds with double bond between nitrogen and carbon, and amine compounds with single bond between nitrogen and carbon.
Carbon atoms {primary carbon} can attach to only one other carbon atom.
Carbon atoms {secondary carbon} can attach to two other carbon atoms.
Carbon atoms {tertiary carbon} can attach to three other carbon atoms.
Carbon atoms {carbanion} can gain unshared electron pairs and have only three bonds, to become electrophiles. Carbanions can be in organic bases.
Carbon atoms {carbocation} {carbonium ion} can lose electron pairs and have only three bonds, to become nucleophiles. Carbocations are more in polar solvents. Carbocations are more at tertiary carbons than at secondary or primary carbons.
Aliphatic hydrocarbons can be chains {alkane}| or rings {cycloalkane}. Small alkanes have one carbon {methane}, two carbons {ethane}, three carbons {propane}, four carbons {butane}, five carbons {pentane}, six carbons {hexane}, seven carbons {heptane}, or eight carbons {octane}.
branching
Alkanes {n-alkane} can have no branches. Alkanes {iso-alkane} can branch at second carbon. Alkanes {neo-alkane} can have two single-carbon side-chain methyl groups on second carbon. Alkanes can have functional group on second carbon {sec-}. Alkanes can have functional group and carbon side chain on second carbon {tert-}.
properties
Alkanes are colorless, odorless, not polar, not reactive, not acidic, not basic, and oxidizable. If alkane has one to four carbons, it is gas. If alkane has five to nineteen carbons, it is liquid. If alkane has more than nineteen carbons, it is waxy solid.
Hydrocarbons {aliphatic}| can have only single bonds.
Alkanes {alkyl group} can attach to carbon chains as side chains.
Alkanes can have single-carbon side chains {methyl group}.
Mixtures {naphtha} can have alkanes with four to ten carbons.
Mixtures {kerosene} can have alkanes with nine to fifteen carbons.
Mixtures {diesel fuel} can have alkanes with fifteen to twenty-five carbons.
Mixtures {lubricating oil} can have alkanes with more than 20 carbons.
Mixtures {asphalt} can have alkanes with more than 30 carbons.
Hydrocarbons {alkene}| {olefin} can have at least one double bond. Small alkenes have two carbons {ethylene} {ethene} or three carbons {propylene} {propene}. Alkenes are colorless, odorless, reactive, not polar, not acidic, not basic, and oxidizable or reducible. Alkenes with two to four carbons are gases. Alkenes with more than four carbons are liquids.
Alkanes can attach halides {alkyl halide}. Alkyl halides are colorful, smell powerful and bad, are very reactive, are polar, are not acidic or basic, and are not oxidizable or reducible. Alkyl halides are liquids, except for methyl halide gases. Alkyl halides are heavier than water.
Alkene substituents {allyl} can have three carbons and double bond at far end from carbon chain.
Ethylenes {vinyl group} can be side chains.
Hydrocarbons {alkyne}| can have at least one triple bond. The smallest alkyne has two carbons {acetylene} {ethyne}. Alkynes are colorless, odorless, reactive, not polar, not acidic, not basic, and oxidizable or reducible. Alkynes are gases.
C2H2 [2 is subscript] {carbene} is like methylene and has singlet or triplet spin states.
Hydrocarbons {aromatic compound}| {aryl compound} can have planar ring of six carbons, five carbons and one nitrogen or oxygen, or four carbons and one nitrogen or oxygen.
properties
Aromatics are colorless, have gasoline-like smell, are not polar, and are not acidic or basic. Rings are not oxidizable or reducible and are unreactive.
resonance
Ring has resonating single and double bonds, which delocalize electrons into two rings, one above and one below planar ring.
substituents
Hydroxyl, ether, ester, amine, alkyl, halide, and phenyl groups donate electrons to aromatic rings. Nitro, cyanide, carboxyl, aldehyde, ketone, sulfoxide, and hydrogen groups take electrons from aromatic rings, as do ammonium ion and primary amine ion.
ring number
Aromatic compounds can have three aromatic rings {anthracene}, four aromatic rings {tetracene}, five aromatic rings {pentacene}, and so on {polyacene} {acene}.
ring number: phase
Aromatic compounds with one ring are liquids. Aromatic compounds with more than one ring are solids.
examples
Explosive aryls include TNT and picric acid. Aryls include vanillin, toluidine, indole, cholesterol, and menthol.
Aromatic compounds {naphthalene} can have two aromatic rings.
Six-carbon aromatics {benzene} can have no side chains. Benzene can be functional group {phenyl-}. Compound can have methylbenzene functional group {benzyl-}. Benzene rings can have same side chains at opposite carbons {para-, benzene ring}, on adjacent carbons {ortho-, benzene ring}, or separated by one carbon {meta-, benzene ring}.
Benzene rings {anisole} can have methyl ether side chain.
Benzene rings {cresol} can have hydroxyl side chain and adjacent methyl side chain.
Benzene rings {cumene} can have isopropyl side chain.
Benzene rings {aniline} can have amine side chain, as in dyes, indicators, and pigments. Aniline can have positive ion {anilinium}.
Benzene rings {phenol} can have hydroxyl side group, as in dyes, indicators, and detergents {alkylphenol}.
Benzene rings {styrene} can have ethene side chain.
Benzene rings {thymol} can have hydroxyl side group, adjacent isopropyl side chain, and opposite methyl side chain.
Benzene rings {toluene} can have methyl side chain.
Benzene rings {xylene} can have two methyl side chains.
Organic compounds {alcohol, chemical}| can have carbon atom single-bonded to hydroxyl group: -C-O-H. Alcohols are colorless, have pungent and sweet odor, are reactive, are polar, are basic or acidic, and are oxidizable and reducible. Alcohols with less than twenty carbons are liquids. Alcohols dissolve in water if they have less than six carbons. Carbon atom with two hydroxyl side chains is unstable and reverts to aldehyde or ketone.
Organic compounds can have carbon atom single-bonded to oxygen atom single-bonded to hydrogen atom {hydroxyl group}: -O-H.
Sodium or magnesium metal can remove hydrogen atom from alcohol oxygen atom to make hydrogen gas and ion {alkoxide ion} with charge -1: -C-O- [last - is superscript].
Sulfuric or hydrobromic acid can add hydrogen atom to alcohol oxygen atom to make unstable ion {alkyloxonium ion} {oxonium ion} with charge +1: -C-O+H2 [+ is superscript, and 2 is subscript].
Alcohols {ethylene glycol} can have two carbons, each with one hydroxyl group.
Alcohols {glycerol, alcohol} can have three carbons, each with one hydroxyl group.
Organic compounds {amine, organic}| can have carbon atom single-bonded to nitrogen atom: -C-N-. Amines are colorful, have pungent powerful odor, are slightly reactive, are polar, and are not oxidizable or reducible. Amines are liquids, except for ammonia gas. Amines are slightly basic if they have zero or one alkyl group, highly basic if they have two or three alkyl groups, and even more highly basic if alkyl group has double bond.
Amines {azide}| can have only three nitrogens.
A nitrogen atom can single-bond to a carbon atom and double-bond to a nitrogen atom, with only hydrogens on other bonds, in resonating structures {diazonium ion}.
A carbon atom can bind to three nitrogens, including one double bond, with only hydrogens bonded to nitrogens, in resonating structures {guanidium ion}.
Amines {piperidine} can have one non-aromatic ring with five carbons and one nitrogen atom.
Amines {pyrrolidine} can have one non-aromatic ring with four carbons and one nitrogen atom.
One carbon atom can double-bond to one nitrogen atom single-bonded to another carbon atom {Schiff base}: C=N-C.
Ketones and aldehydes have carbon atom double-bonded to oxygen atom {carbonyl}. Aldehydes and ketones are colorless, have sweet odor, are polar, are not acidic or basic, are oxidizable to carboxylic acids, and are reducible to alcohols. Carbonyls are reactive. Aldehydes are more reactive than ketones. Aldehydes and ketones are liquids unless they have more than twenty carbons. Small aldehydes and ketones dissolve in water.
Aldehydes and ketones can be substituents {oxy-}.
In aldehyde or ketone carbonyl groups, carbon has slight positive charge and oxygen has slight negative charge. Aldehyde or ketone can hybridize to have positive carbon atom and negative oxygen atom {enolate ion}, with single bond between carbon and oxygen.
If aldehyde or ketone carbonyl carbon attaches to another carbon, the double bond can move between the carbons, and hydrogen atom from second carbon can move to oxygen {keto-enol isomerism}.
Carbonyl can be at carbon-chain end {aldehyde}|: -C=O.
The smallest aldehyde {methanal} {formaldehyde, carbonyl} has one carbon atom.
Aldehydes {ethanal} {acetylaldehyde} can have two carbon atoms.
Other aldehydes {benzaldehyde} or ketones are in camphor, citral, vanillin, cinnamon, and almonds.
Carbonyl can be in carbon-chain middle {ketone}|: =C=O.
The smallest ketone {propanone} {methyl methyl ketone} {acetone} has three carbons.
Ketones {lactone} can have rings with five carbon atoms and one oxygen atom. One carbon atom double-bonds to an oxygen atom outside ring.
Organic compounds {carboxylic acid}| can have terminal carbon atom double-bonded to oxygen atom and single-bonded to hydroxyl group.
properties
Carboxylic acids are colorless, have strong and bad odor, are reactive, are polar, are acidic, and are reducible to aldehydes. Carboxylic acids are liquids if they have less than twelve carbons.
types
Small carboxylic acids have one carbon {methanoic acid} {formic acid}, two carbons {ethanoic acid} {acetic acid}, three carbons {propanoic acid} {propionic acid}, four carbons {butanoic acid} {butyric acid}, five carbons {pentanoic acid} {valeric acid}, or six carbons {hexanoic acid} {caproic acid}.
types: saturated fatty acids
Larger carboxylic acids have twelve carbons {lauric acid}, fourteen carbons {myristic acid}, sixteen carbons {palmitic acid}, eighteen carbons {stearic acid}, or twenty carbons {arachidic acid}.
types: unsaturated fatty acids
Fatty acids can have double bonds in carbon chain. First double bond is at ninth carbon, second is at twelfth carbon, and third is at fifteenth carbon. Sixteen carbons can have one double bond {palmitoleic acid}. Eighteen carbons can have one double bond {oleic acid}. Eighteen carbons can have two double bonds {linoleic acid}. Eighteen carbons can have three double bonds {linolenic acid}. More double bonds increase fatty-acid liquidity.
derivatives
Carboxylic-acid derivatives substitute nucleophile for carboxylic-acid hydroxyl group. Nucleophile can be ether to make ester, amine to make amide, carboxylic acid to make anhydride, or halide to make acyl halide.
Carboxylic acids can be substituents {acyl-}.
Carboxylic acids dissolve in water and lose proton to make ion {carboxyl ion}. Carboxyl ion has resonance between single and double bonds to oxygens.
Carboxylic acids have salt forms {carboxylate}, which use suffix -ate, as in sodium citrate.
Long fatty acids can add sodium ion to make sodium salt {soap}|.
Carboxylic acids {carbonic acid} can have one carbon, three oxygens, and two hydrogens.
Carboxylic acids {dicarboxylic acid} can have carboxyl groups on both ends. Small dicarboxylic acids have two carbons {oxalic acid}, three carbons {malonic acid}, four carbons {succinic acid}, five carbons {glutaric acid}, or six carbons {adipic acid}.
Propanoic acid {lactic acid} can have hydroxyl group on second carbon.
Organic molecules {limonene} can be skin irritants.
Benzene rings {phthalic acid} can have adjacent carboxyl group. Phthalates can affect body hormone levels.
Propanoic acid {pyruvic acid} can have ketone on second carbon.
Benzoic acid {salicylic acid} can have a hydroxyl group in para- position.
large dicarboxylic acid {tartaric acid} {cream of tartar, acid}.
Branched carbon chain can have three carboxyl groups {tricarboxylic acid}, such as citric acid.
Carboxylic-acid nucleophile can substitute for carboxylic-acid hydroxyl group. Organic compounds {acid anhydride} can have last carbon in carbon chain double-bonded to oxygen atom and single-bonded to carboxylic acid. Acid anhydrides are colorless, smell bad like carboxylic acids, are highly reactive, are polar, are not acidic, are not basic, are not oxidizable or reducible, dissolve slightly in water, and are liquids unless more than six carbons.
Acid anhydrides {imide}| can be amides.
Organic compounds {acyl halide} can have last carbon in carbon chain double-bonded to oxygen atom and single-bonded to halogen. Acyl halides are colorful, have harsh and pungent and bad odor, are highly reactive, are polar, are not acidic, are not basic, are not oxidizable or reducible, dissolve slightly in water, and are liquids unless more than six carbons.
Organic compounds {amide}| can have last carbon in carbon chain double-bonded to oxygen atom and single-bonded to amino group. Amides include urea, phenobarbitol, and caffeine.
properties
Amides are colorful, have harsh and pungent and bad odor, are slightly reactive, are polar, are not acidic, are not basic, are not oxidizable or reducible, dissolve slightly in water, and are liquids unless more than six carbons.
bond
Amide bonds resonate, because double bond between carbon and oxygen can shift to nitrogen, making nitrogen positive, carbon positive, oxygen negative, and bond planar.
Nitrogen makes organic compounds {nitrogen compounds}. Organic compounds {nitro organic compounds} can have nitrogen atom double-bonded to oxygen atom and single-bonded to another oxygen atom: -O-N=O.
Nitrogen compounds {cyanide} can have carbon atom triple-bonded to nitrogen atom and single-bonded to hydrogen atom.
Nitrogen compounds {hydrazine} can have two nitrogens and six hydrogens, with double bonds.
Nitrogen aromatic compounds {imidazole} can have three carbons and two nitrogens, separated by carbon atom, in ring.
Nitrogen compounds {imine}| can have nitrogen-carbon double bond.
Nitrogen compounds {nitrile}| can have carbon atom double-bonded to nitrogen atom, -C=N-. Nitrile side chains {isonitrile} have carbon on end and nitrogen double-bonded to another carbon: C-N=C-. Isonitriles usually smell strong and bad.
One nitrogen atom can double-bond to two oxygen atoms, so nitrogen has positive charge {nitronium ion}: O=N+=O.
One carbon atom can double-bond to one nitrogen atom single-bonded to hydroxyl {oxime}: -C=N-OH.
Nitrogen aromatic compounds {pyridine} can have five carbon atoms and one nitrogen atom in ring.
Nitrogen aromatic compounds {pyrimidine, nitrogen} can have four carbons and two nitrogens, separated by carbon atom, in ring.
Nitrogen aromatic compounds {pyrrole} can have four carbon atoms and one nitrogen atom in ring.
Organic compounds {ester}| can have carbon-chain last carbon double-bonded to oxygen atom and single-bonded to alkoxyl group.
properties
Esters are colorless, smell good and sweet, are reactive, are polar, are not acidic, are not basic, are not oxidizable or reducible, and dissolve somewhat in water. Esters are liquid unless more than six carbons.
derivatives
A phosphate group {phosphate ester} can replace carboxylic-acid hydroxyl group. A sulfate group {sulfate ester} can replace carboxylic-acid hydroxyl group. Alkylbenzene-sulfonic-acid sodium salt detergent is sulfate ester. A sulfhydryl group {thioester} can replace carboxylic-acid hydroxyl group. Thioesters are more reactive than esters. Thioesters can ionize as thiolate ion to make weak base.
Carbon atom at carbon-chain end can have hydroxyl group and ether side chain {hemiacetal}. Carbon atom at carbon-chain end can have two ether side chains {acetal}.
Carbon atom in carbon-chain middle can have hydroxyl group and ether side chain {hemiketal}. Carbon atom in carbon-chain middle can have two ether side chains {ketal}.
Oxygen atom single-bonded to carbon atom {alkoxyl group}, -O-C, can attach to carbon atom.
Organic compounds {epoxy} {oxirane} can have a ring with two carbons and one oxygen.
Organic compounds {ether, chemical}| can have an oxygen atom single-bonded between two carbons: -C-O-C-. Ethers are colorless, have pungent and sweet odor, are slightly reactive, are non-polar, are not basic or acidic, and are oxidizable or reducible. Ethers can dissolve in water if small. Polybrominated diphenyl ethers are flame-retardant chemicals.
Ether rings {dioxane} can have four carbons and two opposite-side oxygens, with no double bonds. Dioxane can dissolve in water.
Ether rings {oxazole} can have, oxygen, carbon, nitrogen, and two carbons.
Phenol can have carbon atom single-bonded to benzene {R group}, which is single-bonded to hydroxyl {phenyl}, -R-CH2-O-H [2 is subscript].
Aromatic compounds {furan} can have four carbon atoms and one oxygen atom in ring. Tetrahydrofuran can dissolve in water.
Aromatic compounds {pyran} can have five carbon atoms and one oxygen atom in ring.
Organic compounds {sulfur organic compound} can have carbon atom single-bonded to sulfur. Perhaps, mercaptan vials or rings can open if people are in danger. Bad smells repulse attackers. Splashing some on attackers is a mark hard to remove.
Organic compounds {sulfide} can have sulfur bonded between two carbons, -C-S-C-.
Two thiols can react to eliminate hydrogens from sulfurs and make sulfur-sulfur bond {disulfide bond}.
Three carbons can bond to one sulfur to give sulfur positive charge {sulfonium ion}.
Compounds {thioether} similar to ethers have sulfur atom instead of oxygen atom.
Sulfhydryl groups can replace carboxylic-acid hydroxyl groups to make thioesters. Thioesters are more reactive than esters. Thioesters can ionize {thiolate ion} to make weak bases.
Alkylbenzene-sulfonic-acid sodium salt is sulfate ester {detergent}|.
Organic compounds can have carbon atom single-bonded to sulfur atom, which is single-bonded to hydrogen atom {sulfhydryl group}, -S-H.
Sulfhydryls {thiol} {mercaptan} are similar to alcohols, but sulfur replaces oxygen. Hydrogen sulfide has rotten-egg smell. Beta-mercaptoethanol has bad smell. Thiols can be side chains. Thiols are colorless, have bad odor, are reactive, can be more acidic than alcohols or can be basic, and are oxidizable and reducible.
Molecules {polymer}| can link repeated subunits into sequence. Carbohydrates, proteins, and nucleic acids are polymers.
mass
Polymers have masses of 10,000 to 100,000 dalton. Masses have normal distribution, skewed toward lower masses. Centrifugation or light scattering can indicate mass.
osmotic pressure
Polymer osmotic pressure is higher than ideal solution pressure, because polymers are large molecules.
colloid
Polymers make colloids, because molecules are long.
viscosity
Polymer viscosity depends on molecule size and shape. Shape has four parameters: moments in three spatial dimensions and orientation.
Polymers {plastic, chemistry}| can have hydrocarbon subunits. Thermoplastics melt if heated. Thermosetting plastics do not melt if heated. Plastics can have covalent or hydrogen bonds that cross-link polymer chains.
types
Nitrocellulose was first plastic [1879] and comes from cellulose. It was in the first billiard balls and then in dental plates and Celluloid shirt collars. Nitrocellulose is in combs, brushes, eyeglass frames, film negatives, and car lacquer.
Cellulose acetate was second plastic invented, comes from cellulose, coats fabric-covered airplanes, is in model airplane glue, and is in nail polish, mixed with acetone.
Polyethylene comes from ethylene.
Polystyrene comes from styrene.
Polyvinyl chloride or PVC comes from vinyl chloride.
Acrylic comes from acrylonitrile.
Polyester comes from ethylene glycol and propylene glycol.
Nylon comes from amide.
Polymers {elastomer} can stretch and then resume shape, because normally they are contracted chains. Elastic polymers have cis double bonds, to allow stretching.
Nitrocellulose {cellophane} can be for wrapping.
Nitrocellulose {rayon} can be fibers.
Rayon and cellophane have basic units {viscose}.
Organic molecules have carbon chemical reactions {chemical reaction, organic}.
Organic molecules can have acid-base reactions {acid-base reaction, organic}.
acidity
Bonds from highest to lowest acidity are H-Br, H-Cl, H-F, H-S-, H-O-, H-N-, and H-C-. From highest to lowest acidity, compounds are inorganic acids, carboxylic acids, alkylammonium ion, thiol, phenol, and alcohol.
basicity
From highest to lowest basicity, organic and inorganic compounds are -NH2- [2 is subscript and last - is superscript] or nitride, -R-O- [last - is superscript] or alkoxide, -O-H, -S-H, -Cl, NH3 [3 is subscript] or ammonia, and H2O [2 is subscript] or water.
neutral
Ketones, aldehydes, alkenes, and alkanes are neither acids nor bases.
Lewis
Lewis bases can attack double bond between carbons to make negatively charged carbanion. Lewis acids can attack double bond between carbons to make positively charged carbonium ion.
Organic reactions {addition reaction} can bind substituents to double bond to make two single bonds.
For double bond between two carbons, carbons have two other constituents. Molecule is planar, with constituent angles of 120 degrees. See Figure 1.
Electrophile, typically hydrogen ion, slowly attacks double-bond electrons to make carbocation. In addition reactions, hydrogen atom binds to primary carbon, by Markownikoff's rule. See Figure 2.
Then nucleophile quickly adds to the other tertiary or secondary carbon, which is more polar than primary carbon atoms. See Figure 3.
conformation
Conformation is typically cis, but is trans for two similar substituents.
polarity
Terminal carbon double bonds are not sufficiently polar for attack, but internal double bonds are polar enough for attack.
alkenes
Alkenes have double bonds between carbons. Alkene + water -> alcohol. Alkene + ammonia -> amine. Alkene + halogen acid -> alkyl halide. Alkene + hydrogen gas -> single bond. Alkene + halogen gas -> alkyl halide, on both carbons with trans conformation.
Oxidation-reduction reactions {Belousov-Zhabotinskii reaction} {Belosov-Zhabotinski reaction} (B-Z reaction) (BZ reaction) using sodium bromate, malonic acid, sulfuric acid, and cerium ions, and involving twenty-one reaction steps, can produce spatial patterns in dishes, after delays.
As shown by ferroin indicator, cerium-ion catalysts change oxidation state, blue and magenta, or do not change oxidation state, yellow and clear, to make concentric circles or spirals. Concentrations oscillate with period {limit cycle, concentration}.
feedback
Oscillation happens only far from chemical equilibrium and requires feedback.
diffusion
Spatial patterns require diffusion.
chemical patterns
Non-linear multiple-reaction kinetics and feedback, through diffusion or direct chemical addition, can form temporal and spatial patterns far from equilibrium. Patterns require flows and feedback. Reaction far from equilibrium between high-concentration species typically affects low-concentration catalytic compound, which can have two different oxidation states or shift easily between acid and base. Reaction rates oscillate.
Chemical-pattern formation depends on dissipative structure theory. Turing [1952: The Chemical Basis of Morphogenesis] invented chemical and biological spatial-pattern-formation theory. Belousov and Zhabotinskii [1958, 1964] discovered oscillating chemical reaction, and Noyes [1972] analyzed mechanism {oregonator model}.
Continuous-flow stirred-tank reactor (CSTR) studies oscillating systems over time. Continuous-flow unstirred reactor (CFUR) studies oscillating systems over space.
Substitution into benzene rings {benzene ring reaction} replaces a hydrogen on a ring carbon with nitro, sulfoxy, halogen, or other nucleophilic substituent.
process
Strong acid, such as iron (III) chloride or aluminum chloride, can slowly polarize benzene-ring carbon atom to make carbocation. Carbocation resonates at attacked-carbon ortho carbon and para carbon. Nucleophile quickly adds to attacked carbon, and hydrogen ion leaves.
process: already substituted
If benzene ring already has one nitro, sulfoxyl, halogen, or other nucleophilic substituent, substituted nucleophile substituent has positive charge.
If benzene ring already has one nitro, sulfoxyl, halogen, or other nucleophilic substituent, electron-donating nucleophilic substituent quickly adds to substituted-carbon ortho carbon or para carbon.
If benzene ring already has one nitro, sulfoxyl, halogen, or other nucleophilic substituent, and bromine or strong acid polarizes carbon atom to make carbocation, electron-withdrawing nucleophile can slowly add to substituted-carbon meta carbon.
resonances
Meta carbon and substituted carbon have three resonance structures. Substituted carbon and ortho or para carbons have four resonance structures.
Carboxylic acid and ester can combine to make longer carbon chain {carbon chain reaction}, if negatively charged nucleophile is present. Negatively charged nucleophile can create carbanion on carboxylic-acid second carbon. Carbanion can attack ester. Negative charge migrates to ester double-bonded oxygen. First ester carbon bonds to first carboxyl carbon. Carboxyl reforms as nucleophile leaves, leaving new carbon-carbon single bond.
To add carbon atom to carbon chain {condensation reaction, organic}, aldehyde or ester combines with alcohol, to make new carbon-carbon single bond and water molecule.
Cyanide and alkyl chloride can react to lengthen alkyl carbon chain by adding cyanide carbon {cyanide reaction}. Reaction releases nitrogen and chloride.
Organic reactions {electrophilic addition reaction} can add electrophilic substituent to carbonyl group.
carbonyl
Carbonyl groups have double bond between carbon and oxygen. Carbonyl groups are planar, with two substituents on carbon and none on oxygen. Bond angles are 120 degrees. See Figure 1.
process
Hydrogen ion attacks carbonyl oxygen and adds to it, making positive charge. Double bond does not break. See Figure 2.
Then positive charge migrates to carbonyl carbon to make carbocation. See Figure 3.
Then water or alcohol adds to carbon. See Figure 4. Hydrogen at carbonyl oxygen and hydrogen at nucleophile leave and combine to make hydrogen gas.
In alcohols, amines, or alkyl halides, organic reactions {elimination reaction} can make two substituents leave adjacent carbon atoms and form double bond. Acid or base starts reaction.
acid and alcohol
For example, compound can be alcohol. See Figure 1.
Acid pulls off nucleophile, and hydrogen atom leaves. See Figure 2. Double bond forms, and then acid reforms. See Figure 3.
base and alcohol
For example, compound can be alcohol. See Figure 4. Base pulls hydrogen atom from carbon with no substituent. See Figure 5. Nucleophile leaves other carbon. Double bond forms, and base reforms. See Figure 6.
E1 elimination
Secondary or tertiary carbon carbocation can form slowly, and then double bond forms quickly {E1 elimination}. Secondary or tertiary carbon is more polar than primary carbon. Acid or base starts this elimination type.
E2 elimination
Molecule can slowly push substituent from primary carbon, because primary carbons have no large substituents and low polarization. Bond breaks, and double bond quickly forms {E2 elimination}. See Figure 7, Figure 8, and Figure 9.
base
If strong base is present and reactant is alcohol or alkyl halide, mechanism favors eliminations over substitutions, because base can strongly attract hydrogen atom. If reactant is amine or carboxylic-acid derivative and nucleophile is neutral or acidic, substitution happens more than elimination.
Free radical can attack double bond between carbons {free radical reaction}, to make neutral atom with odd-numbered electron configuration at carbon atom.
Aryl or alkyl group single-bonded to magnesium halide can react with carbonyl-group carbon to lengthen aryl-group or alkyl-group carbon chain by adding carbonyl-group carbon atom {Grignard reagent reaction}.
In addition reactions, hydrogen atom binds to primary carbon {Markownikoff's rule} {Markownikoff rule}.
Organic reactions {nucleophilic addition reaction} can add nucleophilic substituent to carbonyl group.
nucleophilic attack
Water molecule, alcohol, hydride ion, carbide ion, ammonia molecule, or amine nucleophile can attack carbonyl carbon.
carbonyl
Carbonyl groups have double bond between carbon and oxygen. Carbonyl groups are planar, with two substituents on carbon and none on oxygen. Bond angles are 120 degrees. See Figure 1.
hydrogen
Water molecule, alcohol, or hydride ion attacks carbonyl carbon to make tetrahedral carbocation. Carbocation and negatively charged oxygen resonate with double-bonded carbon and oxygen. See Figure 2. If carbonyl carbon is not single-bonded to carbon atom, carbonyl oxygen adds hydrogen atom. See Figure 3. If carbonyl carbon is single-bonded to carbon atom, hydrogen from second carbon can migrate to oxygen to make alcohol and carbanion, or stay at second carbon to make carbocation and oxygen ion, by tautomerism. See Figure 4.
carbide
Carbide ion attacks carbonyl carbon. See Figure 5. Carbide negative charge migrates to oxygen. See Figure 6. Double bond forms between carbonyl carbon and carbide carbon. See Figure 7. Positively charged hydrogen ion from acid adds to negatively charged oxygen to make hydroxyl and one bond between carbons. See Figure 8. Carbide reacts with carbonyl to make new carbon-carbon single bond at tetrahedral carbon {condensation reaction, nucleophilic}.
nitrogen
Ammonia or amine attacks carbon. See Figure 9, Figure 10, Figure 11, and Figure 12. Double bond forms between carbonyl carbon and amine nitrogen atom. Oxygen leaves with two hydrogens, to make water. See Figure 13.
After initiation, molecule {plasticizer} can better link polymer subunits by covalent bonds.
Carbon chains can extend {polymerization}| by attaching a subunit to chain end and then repeating. Organisms use energy, inorganic nutrients, and organic nutrients to make molecules {precursor, biology} that polymerize to make biological polymers.
reactions
Polymers can form using addition reactions with acids, bases, radicals, or ions. Polymers can form using condensation reactions, in which water molecule leaves as bond forms between carbon atom and carbon or oxygen atom.
process
Polymerization has three steps.
Sulfuric acid, strong inorganic or organic base, or organic-peroxide radical makes carbocation, carbanion, or free radical, respectively, in subunit and then double bond breaks {initiation, polymerization}.
Carbocation, carbanion, or free radical, respectively, attacks other-subunit double bond, in addition reactions, to make one bond from first carbon to first subunit carbon. Plasticizer molecule helps covalently bond subunits.
Added base terminates acid reaction, added acid terminates base reaction, or two free radicals react to make terminal bond {termination}.
Organic reactions {proton transfer reaction} can involve hydrogen-ion migration.
Organic compounds can oxidize or reduce {redox reaction, organic}. Organic compounds, from most to least oxidized, are carboxylic acid, ketone and aldehyde, alcohol, alkene, and alkane. Organic compounds can oxidize to higher oxidation with potassium chromate, potassium permanganate, ozone, or oxygen. Organic compounds can reduce to lower oxidation with sodium metal, magnesium metal, zinc metal, sodium thiosulfate, acids, and hydrogen gas. If no water is present, lithium aluminum hydride or sodium borohydride can reduce aldehydes and ketones to alkoxides.
Organic reactions {substitution reaction, organic} can substitute nucleophiles. In reactant, two carbons share one bond, and secondary or tertiary carbon has small and weak nucleophile. See Figure 1.
substitution type 1
Bigger and stronger nucleophile can substitute for weaker and smaller nucleophile, at rate that depends on reactant concentration {substitution type 1} (SN1).
In slow step, polar solvent separates substituent from molecule, making secondary or tertiary carbocation. Secondary or tertiary carbons have more polarity, have larger substituents, and prevent pushing more, compared to primary carbons. See Figure 2.
In fast step, other substituent substitutes for separated substituent, helped by polar solvent. See Figure 3. SN1 reactions are not stereospecific, because pull can be from any side.
For example, hydroxyl or cyanide substitutes for halide. Amine substitutes for hydroxyl.
substitution type 2
In reactant, two carbons share one bond, and primary carbon has large and strong nucleophile. See Figure 4.
Weak and small nucleophile can substitute for bigger and stronger nucleophile, with rate that depends on two reactant concentrations {substitution type 2} (SN2).
First, electric repulsions from second molecule push away substituent from first molecule, giving intermediate state. Intermediate state is planar, because five substituents attach to carbon. See Figure 5.
Old substituent leaves, helped by non-polar solvent. SN2 reactions have stereospecific product, because pushing can be from one side only. See Figure 6.
To make carboxylic-acid derivatives, nucleophile attaches to carboxyl carbon to make tetrahedral carbon {tetrahedral carbonyl addition compound}. Nucleophiles from strongest to least strong are hydroxyl, amine, alkoxyl, halide, and carboxyl. Acid catalyst can attack carboxyl double bond. Then old nucleophile leaves as carboxyl reforms.
Functional groups can attack tetrahedral carbon from one side {Walder inversion}. The new functional group pushes off opposite functional group and binds, causing tetrahedron inversion.
Ethers can form by substitution reaction {Williamson synthesis}.
Biological chemistry {biochemistry}| is about carbohydrates, proteins, nucleic acids, and lipids.
Molecules {carbohydrate}| can have only carbons, oxygens, and hydrogens, with one oxygen atom attached to each carbon. Carbohydrates have alcohol side chains, except for one carbonyl side chain.
Pancreatic amylase in small intestine digests polysaccharides. Polysaccharides are 98% absorbed. Intestine absorbs fructose passively but transports glucose and galactose across membrane actively {absorption, food} {food absorption}.
If carbohydrate in diet is low, fats provide energy, and acetyl-CoA builds up in cells.
Alpha and beta rings are equivalent {anomer}.
Sugars can link by ether bonds {glycosidic bond}. In glycosidic bonds, carbonyl-carbon hydroxyl leaves with hydrogen atom from other-sugar hydroxyl, forming water. Then other-sugar hydroxyl oxygen binds to carbonyl carbon. First-sugar carbonyl is on either first or second carbon. Other-sugar carbon is fourth or sixth carbon. Glycosidic bonds break by hydrolysis.
Sugar substitutes {artificial sweetener} include saccharin, cyclamate, aspartame, and mannitol.
Connective tissue, skin, cornea, and bone have saccharides {chondroitin sulfate}. Chondroitinase cleaves and dissolves extracellular-matrix chondroitin.
Plants have molecules {fiber, nutrition}| that people cannot digest into smaller molecules and/or absorb across intestinal wall into blood.
solubility
Some fiber {insoluble fiber} {crude fiber} does not absorb water. Other fiber {soluble fiber} {dietary fiber} can absorb water.
bond
Cellulose is crude fiber. Lignin, hemicellulose, and pectin are dietary fiber. Cellulose, lignin, hemicellulose, pectin, and inulin have glycosidic bonds that are not the same as for starch and glycogen. Human intestine cannot break them down.
sources
Soluble fiber is in fruit, oats, barley, beans, peas, lentils, peanuts, and some vegetables. Insoluble fiber is in fruits, grains, nuts, and vegetables. Starchy vegetables have low fiber.
functions
Insoluble fiber adds bulk and maintains regular bowel movements. Soluble fiber increases bile-acid secretion. Soluble fiber absorbs water. Soluble fiber affects blood sugar and cholesterol levels.
Three-carbon monosaccharides {glycerol, saccharide} can have alcohol group at each carbon.
Extracellular proteins {glycoprotein}| have saccharides bound to asparagine, serine, threonine, and lysine. Egg-white ovalbumin, egg-white avidin, mucoprotein, collagen, eye-lens protein, basement-membrane protein, ribonuclease, pepsin, cholinesterase, chorionic gonadotropin, follicle-stimulating hormone, thyroid-stimulating hormone, fibrinogen, gamma-globulin, blood-group proteins, and fish-blood antifreeze protein are glycoproteins.
Animal-cell coats and ground substance have glycosphingolipids, acid mucopolysaccharide, and glycoprotein, which are soft, flexible, and adhesive and are for cell recognition and growth inhibition.
Arterial wall has carbohydrate blood-coagulation blocker {heparin}.
Acid mucopolysaccharides, mucins, and mucoprotein make fluid {mucus}|. Mucus keeps inner body surfaces slippery or sticky. Mouth mucus is antibacterial.
Seeds and fruit have chemicals {psoralen} sensitive to light. Light makes them react with DNA.
To enter TCA cycle, pyruvate {pyruvate} first converts to acetyl-CoA. NAD+ attaches acetyl to CoA by thioester bond and makes carbon dioxide and two NADH, in irreversible reaction. Process uses free enzymes in inner mitochondria. ATP inhibition regulates reaction. Arsenate can poison reaction.
Pigments {pigment compounds} are chlorophyll, carotenoid, xanthophyll, and physobilin. Light oxidizes pigments. Donated electron adds to NADP+. Electron-transport chain and oxidative phosphorylation make ATP and oxygen.
Chlorophyll a {chlorophyll}| absorbs orange light, and chlorophyll b absorbs red light, making plants green.
Yellow, red, or purple pigments {carotenoid} absorb at different wavelengths.
Carotenoid {physobilin} absorbs blue or red.
Carotenoid {xanthophyll} absorbs yellow.
Monosaccharides can form polymers {polysaccharide}|, with glycosidic bonds between units. Polysaccharides are not water-soluble and are not sweet.
Seaweed carbohydrate can make gel {agar}|.
Unbranched polysaccharides {cellulose}| in plant cell walls have linked glucose molecules.
Short polysaccharides {dextran} {dextrin}| of 5 to 15 carbons are for energy.
Short polysaccharides {dextrose}| of 5 to 15 carbons are for energy.
Branched polysaccharides {glycogen}| in animals link glucoses and store energy.
Carbohydrates {gum arabic} can be gum.
Polysaccharides {hemicellulose} can link pentose molecules and be in gum.
Linear soluble polymers {hyaluronic acid} can surround egg cell and have disaccharide units.
Carbohydrates {inulin} can be fructose polymers.
Carbohydrates {lignin} can be in tree and grass cell walls. Lignin is hard and woody. It remains when enzymes turn cellulose into sugar.
Two-carbon to ten-carbon polysaccharides {oligosaccharide} can be for energy.
Glucose chains {pectin, polymer}| can be in unripe fruit and be thickeners or gels.
Mouth amylases {ptyalin} can make polysaccharides into dextrin.
In plants, polysaccharides {starch, plant}| can link glucose molecules and store energy. Starches can be unbranched and helical {amylose} or branched {amylopectin}.
Two delta-aminolevulinic acids make porphobilinogen ring, which becomes tetrapyrrole, which makes molecules {porphyrin}|. Porphyrin can make heme. Chlorophyll has porphyrin ring, as does cytochrome oxidase. If bad metabolism causes porphyrin to have no metal inside, porphyrin goes to skin, bones, and teeth, where light makes free radicals {porphyria}.
Iron-containing ring structure {heme} can derive from succinyl-CoA of TCA cycle. Two delta-aminolevulinic acids make porphobilinogen ring, which becomes tetrapyrrole, which makes porphyrin. Porphyrin can make heme. Heme breakdown product is bilirubin, excreted in urine.
Glucose and galactose {hexose} have six carbons. One amino group can bind at glucose second carbon {glucosamine}. Glucosamine is in insect chitin. One amino group can bind to galactose {galactosamine}. Galactosamine is in glycolipids and chondroitin sulfate. One amino group can bind to aldehyde sugars at first carbon {muramic acid} {neuraminic acid}. Muramic acid and neuraminic acid make cell walls.
Sucrose has one glycosidic bond between fructose and glucose, from second carbon to first carbon {invert sugar}|, to make acetal or ketal.
Carbohydrates {monosaccharide}| can have three to seven carbons and one carbonyl group, as in glucose, fructose, mannose, maltose, and galactose. Monosaccharides {triose} can have three carbons, such as glyceraldehyde. Monosaccharides {tetrose} can have four carbons. Monosaccharides {pentose} can have five carbons, such as ribose. Monosaccharides (hexose) can have six carbons. Aldehyde hexoses are glucose, mannose, and galactose. Ketone hexoses include fructose, in honey and fruit. Monosaccharides {heptose} can have seven carbons.
Sugar aldehyde or ketone group can reduce to alcohol group {reduced sugar}|, to make glycerol, inositol, sorbital, and mannitol.
Carbohydrates {sugar}| can be disaccharides. Glycosidic bonds link two monosaccharides. Sucrose, in sugar cane, sugar beets, and corn syrup, has fructose and glucose. Maltose, in malt, has two glucoses.
Lactose, in milk, has galactose and glucose. Lactase gene, for lactose digestion, can stay active after infancy. Regulatory-region mutations happened in Funnel Beaker culture of Sweden and Holland [-4000 to -3000], in Nilo-Saharan peoples of Kenya and Tanzania [-4800 to -700], in Beja people of northeast Sudan [-4800 to -700], and in Afro-Asiatic peoples of north Kenya [-4800 to -700].
Carbohydrates have reactions {carbohydrate reactions}. Mitochondria have citric acid cycle (Krebs cycle). Cytoplasm and mitochondria have gluconeogenesis. Cytoplasm has glycolysis. Mitochondria have oxidative phosphorylation. Cytoplasm has pentose phosphate pathway. Mitochondria have respiratory chain.
organs
Brains use glucose and do not store fat or glycogen. Muscle stores glycogen and uses glucose when active. Heart muscle uses ketone bodies. Liver puts glucose into blood and regulates glucose blood level.
Reactions {anaerobic} can require no oxygen.
TCA cycle uses oxygen {aerobic respiration} to make carbon dioxide.
Acetyl-CoA reactions {Claissen condensation} can lengthen carbon chains by branching. Acetyl-CoA ketone, CH3-CO-S-CoA [3 is subscript], can lose hydrogen when CoA leaves, CH3-CO-, and separate charges to make (C-H2)-(C+O) [2 is subscript and - and + are superscripts]. Ketone carbon is positive, and methyl carbon is negative. Separated charges attack dicarboxylic acid, HOOC-CH2-COOH [2 is subscript], to add ketone, HOOC-(CH2C-H2C+O)-COOH [2 is subscript and + and - are superscripts]. Adding water molecule neutralizes carbon and makes branched carbon chain, HOOC-CHCH2COOH-COOH [2 is subscript], as hydrogen gas leaves.
Reactions {reverse aldol condensation} {condensation reaction, carbohydrate} can lengthen carbon chains by two carbons.
ketol-enol
Proton can transfer from -CO-CH2OH ketol last carbon to next-to-last carbon, to make enol double bond between carbons and alcohol on next-to-last carbon: -COH=CHOH. Enol can add water molecule to make separated charges: -(H2OC+OH)-(C-HOH) [2 is subscript and + and - are superscripts]. Last carbon becomes negative, and next-to-last carbon becomes positive.
aldol
Enol with separated charges can attack aldol, -CHOH-CHO, carbonyl double bond to single-bond carbonyl carbon and carbanion: -CHOH-(C-OH)-CHOH-(H2OC+OH)- [2 is subscript and + and - are superscripts]. Positive charge is still on next-to-last enol carbon, and negative charge is on last aldol carbon.
proton transfer
Water leaves, and proton transfers from positive charge to carbanion and makes atoms neutral: -CHOH-CHOH-CHOH-CHOH-.
Glucose can convert to ethanol and carbon dioxide, using no oxygen {fermentation}|. Glucose converts to pyruvate. Pyruvate converts to acetaldehyde by losing carbon dioxide. Acetaldehyde reduces to ethanol using NADH. Berzelius described fermentation [1837].
Glucose can convert to pyruvate and then to lactic acid {glycolysis}| {Embden-Meyerhof pathway}. Glycolysis makes more ATP than it uses and is anaerobic, requiring no oxygen. Glycolysis enzymes float free in cytoplasm. In first part, glucose becomes glyceraldehyde-3-phosphate by adding two ATPs to ends and splitting into two molecules. In second part, glyceraldehyde-3-phosphate becomes pyruvate and makes four ATPs. Pyruvate makes lactic acid by adding NADH.
Isocitrate makes glyoxalate, and glyoxalate makes malate {glyoxalate cycle}, if acetyl-CoA is present. Glyoxysomes make succinate, which is precursor for fatty-acid synthesis.
Glucose-6-phosphate becomes 6-phosphogluconate by oxidation {phosphogluconate pathway} {pentose phosphate pathway} {hexose monophosphate shunt}. Aldehyde becomes carboxyl. NAD+ becomes NADPH. 6-phosphogluconate makes pentoses, such as ribose-5-phosphate, for nucleotides. Hexose monophosphate shunt in reverse makes hexoses from pentoses for extra energy. Pentose phosphate pathway is in photosynthesis dark reaction.
Sugars can isomerize by keto-enol tautomerism at carbonyl {isomerization}|.
By isomerization {keto-enol isomerization}, enol can become ketol, and ketol can become enol. Keto-enol isomerization must polarize, with lysine, cysteine, or serine.
At cysteine, aldehyde can oxidize to carboxylic acid using two NAD+ {oxidation, carbohydrate}. R-CHO -> R-CHOH-S-cys + 2 NAD+ -> R-CO-S-cys + 2 NADH -> R-COOH. Sugars can oxidize to makes acids: ascorbic acid, gluconic acid, uronic acid, and phytic acid {oxidized sugar}. Sugar aldehyde or ketone group can reduce to alcohol group to make glycerol, inositol, sorbital, and mannitol reduced sugars. Glycerol and inositol bind fatty acids. Sorbital and mannitol are food additives.
Hydrogen-ion transfer provides energy to convert ADP to ATP {phosphorylation}. ADP makes ATP {oxidative phosphorylation}, using hydrogen-ion gradient set up by respiratory chain in mitochondria inner membrane. Channels through membrane allow hydrogen ions to flow past ATPase, which uses electric and flow energy to phosphorylate ADP. ADP controls process by controlling coupling between FAD+ to FADH2 [2 is subscript] and NAD+ to NADH, by folding inner membrane more or less. Arsenate or dinitrophenol destroys pH gradient. Oligomycin binds to ATPase.
Carbon dioxide, water, and sunlight can make oxygen and glucose {photosynthesis}|.
process
First, light reacts with water, NADP+, and ADP to make oxygen, NADPH, H+, and ATP {light phase}. Light oxidizes pigments, to release electron. Donated electron adds to NADP+. Electron transport chain and oxidative phosphorylation make ATP and oxygen. Then carbon dioxide, NADPH, H+, and ATP make glucose, NADP+, and ADP {dark phase}, with no light required.
pigments
Chlorophyll a absorbs orange light, and chlorophyll b absorbs red light, making plant green. Yellow, red, or purple carotenoid pigments absorb at different wavelengths. Xanthophyll carotenoid absorbs yellow. Physobilin carotenoid absorbs blue or red.
Older system absorbs light at 710 nanometers and makes ATP but no oxygen. Newer system absorbs light at 680 nanometers and makes oxygen.
bacteria
Nitrogen-fixing bacteria use photosynthesis to make nitrogen into ammonia. Nitrate-fixing bacteria use photosynthesis to make ammonia. Sulfur bacteria use photosynthesis to make sulfates.
NADH and NADPH from glycolysis, TCA cycle, and other oxidations reduce oxygen to water in mitochondria {respiration, metabolism}. Hydrogen ions increase inside mitochondria and make pH gradient across mitochondrial membrane.
respiratory chain
Aerobic reduction reactions {respiratory chain} make the following compounds: FMNH2 [2 is subscript], ferrous iron, coenzyme Q, cytochrome b, iron-sulfur bond, cytochrome c, cytochrome c1, cytochrome a, cytochrome a3, and water from oxygen.
phosphorylation
Oxidative phosphorylation links to respiratory chain at three places: coenzyme Q reduction, cytochrome c reduction to cytochrome c1, and oxygen reduction to water. At the three steps, respiratory chain places hydrogen ions on mitochondria inner-membrane outside.
poisons
Hydrogen cyanide, carbon monoxide, and hydrogen sulfide inhibit oxygen reduction to water.
Fruit can increase sugar and decrease complex carbohydrates {ripening}|. After picking, starch builds up, and sugar breaks down. Ethylene can ripen fruit.
Citrate and ATP can make acetyl-CoA. Acetyl-CoA enters cycles {TCA cycle} {tricarboxylic acid cycle} {citric acid cycle} {Krebs cycle} and becomes two carbon dioxides and four NADH hydrogens. TCA cycle makes citrate, isocitrate, alpha-ketoglutarate, succinyl-CoA, succinate, fumarate, malate, oxaloacetate, and citrate again. These are mostly three-carbon carboxylic acids. Pyruvate, carbon dioxide, and ATP can make oxaloacetate and malate, which can enter cycle.
purpose
NADH hydrogens are for reduction reactions.
aerobic
TCA cycle uses oxygen to make carbon dioxide.
Acetyl compounds {acetyl-CoA} can enter lipid chain, go to TCA cycle, or become pyruvate. Acetyl-CoA breaks down to water and carbon dioxide. Pyruvate can become acetyl-CoA. Amino acids can make acetyl-CoA. Fatty acids can become acetyl-CoA.
Last carbon can have aldehyde functional group and next-to-last carbon can have alcohol functional group, -CHOH-CHO {aldol}. Aldol and ketol have tautomerism. Aldol can transfer two protons to last carbon to make ketol, -CHO-CHOH. Ketol can transfer two protons to next-to-last carbon to make aldol.
Carbohydrates have carbonyl group {carbonyl group}. First carbon can have aldehyde group {aldose}. Second carbon can have ketone group {ketose}. In water, ketone oxygen can substitute for hydroxyl on next-to-last carbon, to make five-carbon ring {furanose}. Furanose is hemiketal. In water, aldehyde oxygen can substitute for hydroxyl on next-to-last carbon to make six-carbon ring {pyranose}. Pyranose is hemiacetal.
anomer
Carbonyl carbon can be axial {alpha-glycosidic bond} or equatorial {beta-glycosidic bond} to sugar ring. Oxygen can be on right {alpha ring} or left {beta ring}. Alpha and beta rings have similar properties.
Proton can transfer from ketol last carbon to next-to-last carbon to make alkene double bond between carbons and alcohol on next-to-last carbon, -COH=CHOH {enol}. Enol can add water molecule to make separated charges, -(H2OC+OH)-(C-HOH) [2 is subscript and + and - are superscripts].
Ketone can be at next-to-last carbon and alcohol on last carbon, -CO-CH2OH [2 is subscript] {ketol}. Aldol and ketol exhibit tautomerism. Ketol can transfer two protons to next-to-last carbon to make aldol, -CHOH-CHO. Aldol can transfer two protons to last carbon to make ketol.
Fats, oils, fatty acids, steroids, and terpenes {lipid}| are complex hydrocarbons. Terpenes and steroids are simple lipids. Fatty-acid-based lipids are complex lipids. Lipids are for insulation and energy storage. Cell membranes and hormones have lipids. Most lipids are insoluble in water. Lipids can have polar ends and be soluble in water. Lipids contain 2.25 times more energy, by mass, than do carbohydrates or proteins, because they can oxidize more.
lipid disease
Lipids can make gall bladder contract {gall bladder disease}. Gallstones can block bile-salt flow. Cystic fibrosis is inherited low ability to digest fat.
Fatty acids can break down {fatty-acid oxidation} {beta-oxidation} in mitochondria.
functions
Fat tissue hydrolyzes and esterifies fat and oil if body needs energy. Muscle uses fatty acids when resting.
process
In fat cells, lipase binds to triglyceride to split glycerol from fatty acid. Blood serum albumin carries fatty acids to tissues. In tissues, ATP adds CoA to fatty-acid carboxyl end to make acetyl group. Process repeatedly removes acetyl group, with two carbons, from fatty-acid end. Unsaturated bonds become trans, not cis, isomers.
products
Fatty-acid oxidation makes ATP, NADH, acetyl-CoA, and water. Camels store fat in humps, not water.
factors
B vitamins and pantothenic acid affect fat breakdown and synthesis.
Enzymes {lipase} can catabolize triglycerides.
Molecules {emulsifier}, with polar and non-polar ends, can bind non-polar end to fat molecule and dissolve polar end in water {emulsification}|, to make micelles.
Acetyl-CoA added to another acetyl-CoA makes carboxylic acid, and then fatty-acid chain adds two-carbon acetyl-CoA {fatty-acid synthesis}. Cytoplasm has fatty-acid synthesis.
Air oxidizes fats {rancid}|.
Strong hydroxide can break triglyceride into glycerol and fatty-acid salts, both of which can dissolve in water {saponification}|.
If carbohydrate level is too low, cell makes acetyl-CoA. Acetone, acetoacetate, and beta-hydroxybutyrate {ketone body} accumulate.
Carboxylic acids {fatty acid}| can have long hydrocarbon chains. Fatty acids have even numbers of carbons, from 12 to 20. Liver regulates fatty acids in blood.
Sphingosine, ceramide, sphingomyelin, and cerebroside {cell-surface lipid} determine blood group, direct development, make organ structures, confer immunity, and signal cancer.
Blood has triglyceride globular micelles {chylomicron}. Non-polar ends are inside, and polar ends, which dissolve in water, are on surface. Lipids digest slowest. Intestine absorbs 95% of lipids.
Triglycerides {phosphoglyceride} can have fatty acids replaced by phosphates. Cell-membrane phosphatidic acid, lecithin or phosphatidyl choline, and cephalin or phosphatidyl ethanolamine are phosphoglycerides.
Ether group can replace triglyceride fatty acid {plasmalogen}.
CDP, serine, ethanolamine, or choline can replace phosphatidic-acid phosphate group to make other lipids {sphingolipid}. Palmitic acid, in CoA form, adds serine to replace CoA and then reduces to sphingosine. Acyl CoA can bind to sphingosine to make ceramide. CDP-choline can bind to ceramide to make sphingomyelin. UDP-sugar can bind to ceramide to make cerebroside. Sialic acid can bind to cerebroside to make ganglioside. Ganglioside is in synapses and nerve receptors.
Cell-surface lipids {sulfatide} can determine blood group, direct development, structure organs, confer immunity, and signal cancer.
Lipids {triglyceride}| {triacylglycerol} can combine three fatty acids and one glycerol. Glycerol can attach fatty acid at each alcohol. Triglycerides {fat, biochemistry} can have three saturated fatty acids. Triglycerides {oil, biochemistry} can have three unsaturated fatty acids.
synthesis
Dihydroxyacetone phosphate reduces to glycerol-3-phosphate, in glycolysis pathway. Acetyl-CoA binds to two glycerol-3-phosphate hydroxyls, to make phosphatidic acid. Replacing phosphatidic acid phosphate group with fatty acid makes triglyceride.
Fatty-acid esters {wax, lipid} can have long chain alcohols or sterols. Carnauba wax is hard and lustrous and is for floor, car, and furniture. Candelilla wax is brown and is for records, floor, and candles. Bayberry wax is for candles. Beeswax is for cosmetics, candles, polishes, crayons, and artificial flowers. Wool wax is purified lanolin for ointments, cosmetics, and soaps.
Petroleum wax is odorless, tasteless, and inactive. Paraffin is hard petroleum wax for paper coatings. Petroleum jelly is soft petroleum wax for medicine.
Four-carbon alkenes {butadiene} can have two double bonds. Butadiene can single bond a side chain to second carbon. Butadiene can attach a methyl group to make isoprene. Butadiene can attach tertiary carbon to make neoprene.
Butadiene {isoprene}| can attach methyl-group side chain. Polymers can be isoprene chains, with fifth carbon attached to second carbon. Rubber is natural isoprene polymer.
Butadiene {neoprene} can single bond a tertiary-carbon side chain on second carbon.
Organic molecules {terpene}| can use isoprene structure. Monoterpenes are geranium, lemon, mint, turpentine, camphor, and caraway. Linear polyterpenes are rubber and gutta-percha. Fat-soluble terpenes are vitamin A, vitamin E, vitamin K, and carotene. Polyprenols are coenzyme Q, bactoprenol or dolichol hydrogen carrier, and phytol in chlorophyll. Squalene makes cholesterol. Rubber and gutta-percha are terpenes.
Proteins {lipoprotein}| can carry lipids in blood. Serum albumin carries short-chain fatty acids in blood.
Lipoproteins {high-density lipoprotein}| (HDL) can carry phospholipids.
Lipoproteins {low-density lipoprotein}| (LDL) can carry cholesterol.
Lipoproteins {very low-density lipoprotein}| (VLDL) can carry triglycerides.
Hydrocarbon chains {mono-unsaturated hydrocarbon}| {monounsaturated hydrocarbon} can have one double bond and no triple bonds.
Hydrocarbon chains {polyunsaturated hydrocarbon}| can have more than one double bond.
Hydrocarbon chains {saturated hydrocarbon}| can have no double or triple bonds between carbons and hold maximum hydrogens.
Cholesterol is the fundamental structure in many hormones {steroid hormone}|.
biology
Steroids induce enzymes to increase glucose usage and start stress response. Sex steroids and glucocorticoid hormones have neuron receptors.
types
Ergosterol makes vitamin D.
Bile acids emulsify and absorb lipids in small intestine.
Male sex-hormone androgens include testosterone and androstenol. Female sex-hormone estrogens include estrone, estradiol, and progesterone.
Adrenocorticosteroids, such as corticosterone and aldosterone, control body water amount. Cortisone reduces inflammation.
Digitoxin affects heart rate.
Lipids {cholesterol}| can have quadruple aromatic carbon rings. Cholesterol is the fundamental structure in steroid hormones. Plants have no cholesterol, which is only in animals.
process
Acetate becomes acetyl-CoA and acetoacetyl-CoA. Added water makes 3-hydroxy-3-methyl-glutaryl CoA, which reduces to mevalonate when CoA leaves. ATP adds three phosphates to alcohol oxygens to reduce mevalonate to activated isoprene isopentyl pyrophosphate. Isoprenes cyclically add to make squalene. Squalene epoxide makes cholesterol. Adding functional groups to ring carbons makes other steroids from cholesterol.
Lipids {sterol}| can have quadruple aromatic carbon rings. Plant sterols {phytosterol} include campesterol, sitosterol, and stigmasterol. Animal sterols {zoosterols} include cholesterol.
Lipids {stanol}| can be saturated sterols. Stanols can add fatty acids to make stanol esters.
Polymers {nucleic acid}| can have nucleotides connected by phosphodiester bonds. Nucleic acids are 10% of body dry weight.
structure
Phosphodiester-bond phosphate groups link pentose fifth carbon to next-pentose third carbon, called 5' to 3' linkage. Nucleotide nitrogenous bases are perpendicular to phosphodiester bond chain. Nucleotide ribose rings are parallel to phosphodiester bond chain. Phosphodiester bonds have no rotation. Nucleic acids have no branches.
information
Molecules encode genetic information in base sequences and replicate using strands as templates. DNA bases are adenine A, guanine G, cytosine C, and thymine T. DNA codes instructions for replication, transcription, and translation, to initiate and grow tissues and organs during development, to react to cell environment during development and in life, and to cycle over hours, days, months, and years.
Repressors typically form at constant rate {constitutive synthesis}.
If A hydrogen-bonds to T by conventional Watson-Crick pairing, another T can hydrogen-bond to A {Hoogsteen pairing}. If G hydrogen-bonds to C by conventional Watson-Crick pairing, another C can hydrogen-bond to G.
Bacteriophage, plasmids, and chromosomes have mobile genetic elements {replicon}.
Mutations {nonsense mutation} can make stop codons from non-stop codons.
Pyrimidine can substitute for pyrimidine, or purine can substitute for purine {transition, nucleotide}.
Pyrimidine can substitute for purine, or vice versa {transversion}.
DNA has two linear polynucleotide strands hydrogen-bonded together to form twisted ladder shape {double helix}|.
hydrogen bonds
Nitrogenous bases adenine and thymine in DNA or uracil in RNA can link by two hydrogen bonds, on aromatic-ring side away from pentose and phosphate, if aromatic-ring planes are parallel, with one inverted. Nitrogenous bases cytosine and guanine can link by three hydrogen bonds, on aromatic-ring side away from pentose and phosphate, if aromatic-ring planes are parallel, with one inverted.
ladder
Strands are pentose sugars and phosphodiester bonds and make ladder sides. Strand bonds have opposite direction. Nitrogenous-base and hydrogen-bond-link planar aromatic rings are ladder rungs. Because tetrahedral chemical bonds form at angle, ladder twists and is helical.
Ribose sugar (RNA) or deoxyribose sugar (DNA), phosphate group, and nitrogenous-base adenine, guanine, cytosine, and thymine in DNA or uracil in RNA can link to other bases with phosphodiester bonds to make sequences {base sequence} {DNA sequence}.
Two adjacent nucleic-acid polymers {anti-parallel strands} can have opposite bond direction.
Hydrogen bonding between adenine and thymine in DNA or uracil in RNA, or between guanine and cytosine {base pairing}, links two DNA strands or DNA and RNA strands.
Hydrogen bonds can form between adenines and thymines in DNA or uracils in RNA, and between cytosines and guanines {complementary bases}.
polymer chain {strand, DNA}.
Topoisomerase and gyrase affect DNA coiling and can add to or subtract from helix angle {supercoiling}. Circular DNA has negative supercoiling.
Molecules {effector} can help RNA polymerase bind to DNA or help DNA strands separate.
Histone H1 connects DNA beads {nucleosome}. Nucleosomes have 200 bases, two H2A histones, two H2B histones, two H3 histones, two H4 histones, and other regulatory proteins.
Proteins {catabolite activator protein} (CAP) can bind to cAMP to form cAMP-CAP complexes, which bind to promoter for gene that breaks down lactose and galactose. If glucose is low, cAMP builds up.
Enzymes {modification enzyme} can methylate DNA at special sites.
Enzymes {topoisomerase} {gyrase} can affect DNA coiling and can add to or subtract from helix angle for supercoiling.
Cells can copy DNA double helices {replication, DNA}| {DNA replication}.
separation
Replication protein uses ATP to separate DNA nucleotide chains, by breaking hydrogen bonds between nitrogenous bases, so DNA unwinds. Replication protein starts at one DNA location and separates chains in both directions simultaneously. Single-strand binding protein keeps DNA strands apart.
pairing
RNA primer binds to operon first part and provides starting molecule to which DNA polymerase can add paired deoxyribonucleotides. Free deoxyribonucleotides hydrogen-bond with DNA-strand deoxyribonucleotides: A and T, or C and G.
linking
DNA polymerase links deoxyribonucleotides by phosphodiester bonds between pentoses, at rate 10 nucleotides per second. Pyrophosphate leaves. Copying error rate is only 10^-9. Exonuclease checks new strand at new deoxyribonucleotide pairs to see if deoxyribonucleotides paired correctly. Exonuclease removes wrongly paired nucleotides. Second exonuclease checks if double helix is correct and unwinds DNA if DNA double helix is not correct.
ligating
DNA ligase joins DNA strand ends. Both new strands link from ribose fifth carbon to next-ribose third carbon. One strand is continuous. One strand has Okazeki fragments. DNA ligase connects Okazeki fragments.
result
Replication makes two double helices, each with one strand of old double helix and one new strand {semiconservative replication, DNA}.
Replication protein uses ATP to separate DNA nucleotide chains, by breaking hydrogen bonds between nitrogenous bases {replication fork}, and so unwinds DNA.
Enzymes {replication protein} can use ATP to separate DNA nucleotide chains, by breaking hydrogen bonds between nitrogenous bases, and so unwind DNA.
Enzyme {single-strand binding protein} keeps DNA strands apart.
RNA primer binds to operon first part and provides a starting molecule for enzymes {DNA polymerase} that synthesize DNA from existing nucleic acid. It adds paired deoxyribonucleotides to DNA template strand and links them to make new strand.
Enzymes {DNA ligase} can join DNA strand ends and can rejoin broken DNA.
One strand forms in 1000-nucleotide segments {Okazeki fragment}. DNA ligase connects Okazeki fragments.
DNA, enzymes, and energy can make RNA {transcription, DNA}| {DNA transcription}.
process: strand separation
RNA polymerase binds to DNA double helix locations {promoter, DNA}. RNA polymerase separates DNA strands for one complete double-helix turn, little more than three nucleotides. RNA polymerase separates two deoxyribonucleotide chains by breaking hydrogen bonds, starting at one double-helix point and going in one direction only. Transcription uses DNA strand lying in third carbon to fifth carbon direction. Direction that chains separate is opposite to chain phosphodiester-bond direction.
process: polymerase
Eukaryotic 5.8S, 18S, and 28S rRNA use RNA polymerase I. Eukaryotic mRNA and snRNA use RNA polymerase II. Eukaryotic 5S rRNA and tRNA use RNA polymerase III. RNA types have different promoters. RNA polymerase does not need primer.
process: matching
Free ribonucleotides in solution hydrogen-bond to matching chain deoxyribonucleotides. Adenine and thymine hydrogen-bond. Adenine and uracil hydrogen-bond. Guanine and cytosine hydrogen-bond. Error rate is 10^-4 to 10^-5.
process: linking
Using phosphodiester bonds, RNA polymerase links ribonucleotides to make RNA sequence. Phosphodiester bonds invert compared to original-DNA-strand phosphodiester bonds. Nucleotides link at rate 50 nucleotides per second.
process: termination
RNA transcription terminates just after poly-uracil region, using RNA chain-terminating proteins. Using rho protein, region near tRNA end curves around to hydrogen bond with itself using paired A and U or C and G ribonucleotides to make a hairpin loop.
process: separation
RNA polymerase leaves DNA, and RNA separates from DNA. Double helix reforms.
product
Transcription makes one rRNA, tRNA, or mRNA strand. In higher animals, mRNA intron regions can make protein, and exons do not. Introns can be separate or overlap.
blocking
Actinomycin can block transcription by sliding between and separating guanines and cytosines. Mushroom poisons block RNA polymerase from making histone protein.
DNA
DNA operons have gene for repressor, promoter where RNA polymerase binds, operator where repressor can bind and inducer can remove repressor, and one or more genes, typically in that order. RNA or protein binding at regulatory regions controls RNA amount.
DNA: repressor
Repressor prevents RNA polymerase from binding at promoter, because operator is next to promoter. Bacteriophage lambda has repressor-gene {cro gene} repressor. Cro and other repressors typically are dimers that have alpha-helix binding in DNA-helix major groove. Repressors can affect several transcriptions {trans-acting control}.
DNA: promoter
Promoters affect downstream transcription {cis-acting control}. Catabolite activator protein binds to cAMP to make cAMP-CAP complexes, which bind to promoter for lactose and galactose breakdown genes. If glucose is low, cAMP builds up.
Enzymes {RNA polymerase} can bind to DNA double-helix promoters.
Three nucleotides {termination sequence} end transcription.
Special enzymes {nuclease} can modify free-floating RNA. Nuclease adds methyl groups to nucleotides. Nucleases make other modified bases, such as inosine. In eukaryotes, nuclease adds adenines to mRNA 3' end to stabilize RNA and protect 3' end. In eukaryotes, nuclease adds nucleotides to mRNA to protect 5' end.
Endonuclease can split long RNA into functional pieces. For example, nuclease divides chain that contains all rRNA types into different ribosomal RNAs. Photolyase restores UV-induced dimers, using light.
Using enzymes {rho protein}, region near tRNA end curves around to hydrogen bond with itself, using paired A and U or C and G ribonucleotides.
Proteins induced from other sites control RNA transcription {transcriptional control}.
E. coli tryptophan operon (trp) has five genes, but, if tryptophan is at high levels, only short transcription {leader, DNA} can happen {attenuation}. Leader makes hairpin that stops transcription. If tryptophan is low, full operon transcribes, because different hairpin has few tryptophans.
mRNA, rRNA, and tRNA together can make protein {translation, RNA}| {RNA translation}.
template
mRNA nucleotide sequence codes for protein. mRNA is 2% of all RNA.
process
AUG or GUG codon, which codes for methionine, always starts mRNA. mRNA attaches to both smaller ribosome rRNA and larger ribosome rRNA. Ribosomes have two slots, one {peptidyl site} for current amino acid and one {aminoacyl site} for amino acid to add. Three mRNA nucleotides are in slots and lie in 5' carbon to 3' carbon direction.
process: tRNA
tRNA has amino acid on one side tip and three nucleotides on other side tip. Nucleotide tip can be complementary to three mRNA nucleotides in one slot. tRNA with complementary tip hydrogen-bonds its three tip nucleotides to the three slot nucleotides and brings one amino acid into ribosome slot. Streptomycin prevents tRNA attachment to first site.
process: peptide bonding
When amino acids are in both slots, ribosomal enzymes and GTP-protein complex join both amino acids by one peptide bond. Amino acid adds to protein chain in one second.
process: shift
Then ATP shifts both amino acids one slot. Messenger RNA also slides over one slot, leaving one slot empty. Diphtheria toxin inhibits translocation enzyme.
process: repeat
Empty slot fills with tRNA, amino acid comes in, and enzymes make peptide bond.
process: termination
The last three mRNA nucleotides are UAG, UAA, or UGA and do not pair with any tRNA tip, so slot stays empty and terminates mRNA coding. Puromycin terminates amino-acid chain early.
process: release
Enzyme releases protein and mRNA from ribosome.
modification
Enzymes can modify free-floating proteins after translation. Enzymes can remove formyl group from methionine. Enzymes can remove amino acids from amino end. Enzymes can form disulfide bonds. Enzymes can add hydroxyl to side chain. Enzymes can add sugar. Enzymes can add phosphate. Enzymes can split protein into functional parts.
Three DNA or RNA nucleotides {codon} can code for amino acids. Up to six codons can code for same amino acid. Codons coding for same amino acid have same first two bases. Coding redundancy can minimize errors. Codons are the same for all species, except for mitochondria. Mitochondrial DNA uses different genetic code for different groups.
Before initiation sites, mRNA has a purine-rich ribosome-binding site {Shine-Dalgarno sequence}, which matches rRNA molecule site. With extra ribosomal proteins, some bind to Shine-Dalgarno site and prevent or slow protein synthesis.
mRNA sites control translation rate and protein synthesis {translational control}.
Genes {suppressor gene} can make tRNA with an anticodon that matches stop codon but adds an amino acid. If DNA mutation makes a stop codon, such tRNAs allow cell to continue reading mRNA. Suppressor genes suppress such mutations.
Bases A, C, G, and T can attach to N-(2-aminoethyl)-glycine {peptide nucleic acid} (PNA). PNAs have no electric charge, are more stable, and bind better to DNA or RNA than oligonucleotides do.
triplex
If PNA is all C or T and so is homopyrimidine, PNA strand can lie in double-stranded-DNA major groove and bind to double-stranded DNA {PNA-DNA triplex}. Two PNA strands can push away a DNA strand, which forms a loop, and make a triple-strand {triplex invasion}. PNA strand can bind to DNA strand, displacing but not removing other DNA strand {duplex invasion}. Two PNA strands can bind to opposite DNA-strand regions, displacing but not removing DNA strands {double duplex invasion}.
DNA {TNA} can have different sugar than ribose.
DNA {xDNA} can be less likely to mutate.
Combining adenosine and three phosphate groups {adenosine triphosphate} (ATP) can carry energy in phosphate bonds. Magnesium or calcium ions attach to phosphate to make ATP have neutral charge. ATP decreases noradrenaline release from adrenergic nerves and acetycholine release from cholinergic nerves.
Combining guanine and three phosphate groups {guanidine triphosphate} (GTP) can carry energy in phosphate bonds. Magnesium or calcium ions attach to phosphate to make ATP have neutral charge.
Organic molecules {nucleotide}| can have a nitrogenous base and a phosphate group bound to a pentose sugar.
location
Mitochondria have nucleotide synthesis.
types
Nitrogenous base determines nucleotide type: purine or pyrimidine. Molecule can contain ribose sugar (RNA) or deoxyribose sugar (DNA). Nucleotides make RNA, DNA, ATP, NAD, FAD, CoA, and cyclic AMP.
nucleic acid
Nucleotides can link to other bases with phosphodiester bonds. Adenine, guanine, cytosine, and thymine are in DNA. Adenine, guanine, cytosine, and uracil are in RNA.
history
Levene and Bass isolated uridylic acid [1931].
Ribonucleotides make higher nucleotides by adding hydrogen atom using NADPH {deoxyribonucleotide} (DNA). Adenylate makes deoxyadenylate. Guanidylate makes deoxyguanidylate. Cytodylate makes deoxycytodylate. Uridylate makes deoxyuridylate. Deoxyuridylate methylation makes thymidylate. Thymine deoxyribonucleotide is stable and is in DNA, instead of uracil deoxyribonucleotide. Uracil ribonucleotide is in RNA, rather than thymine ribonucleotide, because thymine ribonucleotide easily changes into cytosine, but uracil ribonucleotide does not change.
Nucleotides {ribonucleotide} can have hydroxyl group at pentose-sugar second carbon.
Adenine and guanine {purine}| are double-ring nitrogenous bases synthesized from glycine, aspartate, glutamine, carbon dioxide, or methyl groups. Purine breaks down to urate.
Cytosine, thymine, and uracil {pyrimidine, nucleic acid}| are single-ring nitrogenous bases synthesized from carbamoyl phosphate and aspartate, which make carbamylaspartate, which becomes dihydroorotate, which NAD+ oxidizes to orotic acid, making pyrimidine ring. Orotic-acid nitrogen binds to ribose-ring first carbon by pyrophosphate, to make uridylate. Uridylate transamination can make cytidylate.
Nucleotides {nucleoside} can lose a phosphate group.
Nitrogen-containing molecules {base, nucleic acid} {nitrogenous base} can be purine or pyrimidine: adenine, guanine, cytosine, thymine in DNA, or uracil in RNA.
Rather than uracil, similar nucleotides {thymine} can be in DNA, because cytosine can deaminate to become uracil and so change DNA template too easily. If DNA cytosine deaminates, enzymes remove new uracils and replace with cytosine to repair chain.
Bonding uracil and three phosphate groups {uridine triphosphate} (UTP) can carry energy in phosphate bonds. Magnesium or calcium ions attach to phosphates, so ATPs have neutral charge.
Nucleic acids {ribonucleic acid}| (RNA) can have ribonuceotides. Hydroxyl groups at pentose-sugar second carbons make RNA chains unable to lie anti-parallel to each other for more than several bases, so RNA cannot make double helices. RNA can double back on itself to make hairpin loops, with short double strand at neck.
types
Ribose-nucleotide nucleic acid is for protein translation (mRNA), codon translation (tRNA), protein-synthesis sites (rRNA), and intron excision from RNA (snRNA). Specific 22-nucleotide fragments of RNA have regulatory activity.
genes
E. coli has 50 to 200 RNA genes, as do other organisms. Over 95 percent of eukaryotic RNA encodes rRNA, mRNA, and tRNA, not proteins.
RNA {messenger RNA}| (mRNA) can hold information for making proteins. mRNA is 5% of RNA and has short life. mRNA is ribonucleotide chain copied from gene.
Two or three globular RNAs {ribosomal RNA}| (rRNA) can make ribosomes for protein synthesis. rRNA is 80% of RNA. rRNA has three or four long-lived types. Ribosomes look like snowmen, with two main rRNA globules beside each other. Globular rRNAs have two adjacent binding sites for tRNAs and mRNA. Ribosomes use many proteins.
RNA {transfer RNA}| (tRNA) can transfer amino acids from cytoplasm to ribosomes, to make protein chains. tRNA is 15% of RNA.
structure
tRNA is 75 bases long and has three-leaf-clover shape. tRNA has modified bases in three locations to make tRNA hydrophobic and curve back on itself. Middle-clover-leaf tip has three ribonucleotides, which differ for different amino acids. Clover-stem tip has three ribonucleotides that bind an amino acid. Different tRNAs bind different amino acids. There are more than 40 different tRNAs.
number
Different tRNA amounts differ greatly. Low amounts can limit protein production.
codon
RNA has three-nucleotide codons. tRNA has three tip nucleotides {anticodon}. Anticodon binds to first two codon nucleotides exactly but can bind inexactly to third codon nucleotide {wobble}.
mitochondria
Mitochondria have only 22 tRNAs and use only first two codon bases.
Polypeptides {protein, peptide}| {polypeptide} are 50% of body solids. Polypeptide has 5 to 4000 amino acids.
nitrogen
Protein is the only nitrogen source in diet. Nitrogen leaves body as urea in urine.
metabolism
Conjugated protein can bind to another molecule. Peptide-bond breaking, phosphorylation, dephosphorylation, amidation, methylation, and glycosylation alter protein structure and function.
structure
Protein has four structure levels: primary, secondary, tertiary, and quaternary.
functions
Most proteins are enzymes. Proteins are also for transport, structure, storage, hormones, movement, toxins, protection, and clotting. Proteins maintain water balance, because soluble cell proteins cause higher water pressure inside cell, by osmosis. Proteins buffer water solution inside cells, because soluble proteins have weak acid and weak base groups.
functions: storage
Proteins {storage protein} can be for storage. Ferritin stores iron. Casein stores carbohydrate. Ovalbumin stores fat and carbohydrate.
functions: structures
Fibrous proteins {structural protein} are for body structure.
Alpha-keratin is in skin, hair, wool, horn, and nails. Alpha-keratin has three to seven amino acid chains in bundle, cross-linked by disulfide bonds, which then bundle again.
Scales, claws, beaks, silk, and feathers have beta-keratin. Beta-keratin is mostly glycine, alanine, and serine.
Collagen covers organs and bones. Collagen has three amino-acid chains twisted into left-handed helix. It is mostly glycine, alanine, proline, and hydroxyproline. It has lysine-bond cross-links. Boiled collagen is gelatin.
Elastin is in ligaments and stretchable connective tissue such as blood vessel walls.
Resilin is in flea-leg ligaments, fly-wing ligaments, and cicada-song vibrating tissue.
Glycoprotein is in membranes and cell walls.
Mucoprotein is in membranes and cell walls.
Wing joints have resilen, which is elastic.
Insect skeletons have sclerotin.
Viruses have protein coats.
functions: transport
Proteins {transport protein} can transport small molecules {protein transport}.
Ceruloplasmin carries copper.
Ferritin carries iron.
Hemoglobin carries oxygen and carbon dioxide.
Lipoprotein carries fats and cholesterol.
Myoglobin carries oxygen and carbon dioxide.
Serum albumin carries fatty acids and many other substances.
Proteins can also carry calcium and heavy metals.
Cell has 30,000 organelles {proteasome}| that are 100 times bigger than proteins, are tubes, and have proteases that fragment poorly folded or poorly working proteins. Cytoplasm free proteases split protein fragments into amino acids.
enzymes
E1 enzyme activates ubiquitin, which can bind to E2 enzyme, which can then bind to E3 enzyme. E3 enzyme has various possible F-box regions that recognize different protein-end regions. E2-E3 complex (SCF complex) can bind protein at F-box, attach ubiquitins to protein, and release.
proteasome
If several ubiquitins attach to protein, ubiquitin chain attaches to proteasome and activates enzymes that unfold protein and pull protein chain into proteasome tube.
First amino acids can make sequence {signal sequence} that lets protein go through membrane channels.
Amino-acid catabolysis makes energy {amino-acid oxidation}. Liver mitochondria have amino-acid oxidation. Protein-hormone, purine, pyrimidine, vitamin, and porphyrin metabolism involves amino-acid oxidation. Transamination, to make alpha-ketoacid, or deamination, through oxidation by NAD+ to make carbohydrate, removes amino group. Oxidation removes amino acid side chains. Oxidized amino acids become pyruvate, acetyl-CoA, alpha-ketoglutarate, succinyl-CoA, fumarate, or oxaloacetate, for use in TCA cycle.
After release through membranes, membrane-protein complex {calcium pump} restores calcium ions to inside membrane.
Protein chains can have cross connections {cross-linking, protein}|. Two nearby cysteines, which form a spontaneous disulfide bond, can have strong cross-linking. Protein side chains can form hydrogen bonds with oxygens on other amino acids, such as glycine, cysteine, tyrosine, serine, threonine, asparagine, and glutamine.
Proteins above 37 C can lose three-dimensional structure {denaturation, protein}|. If protein has less than 100 amino acids, folding is subcritical after denaturation. If protein has more than 100 amino acids, folding is critical after denaturation.
Proteins can catalyze reactions {enzymatic reaction}|.
types
Enzymes can catalyze hydrogen-ion interactions. They can catalyze anion and cation formation. They can catalyze chelation. They can catalyze charge-transfer coupling. They can catalyze organic-acid formation and breakdown. They can catalyze proton abstractions. They can catalyze Schiff-base reactions.
They can catalyze configuration inversion.
They can catalyze phosphate transfer. They can catalyze pyrophosphate incorporation. Adenylate cyclase can catalyze cAMP-mediated reactions. They {guanylate cyclase} can catalyze cGMP-mediated reactions. They can catalyze transfers.
They can catalyze oxidation. They can catalyze reduction.
They can catalyze metal-bridge formation. They can catalyze metal binding.
They can catalyze acetylation. They can catalyze acylation.
They can catalyze free-radical reactions.
They can catalyze ring breaking and forming.
They metabolize amines, amides, aldehydes, histidines, imidazoles, ketones, nitroxides, oxides, serines, thiols, and thiol esters. They metabolize lipoproteins, carbohydrates, membranes, ion channels, enzyme proteins, lipids, and nucleic acids.
process
Enzymatic reactions can involve active-site directed agents, induced fit, steric effects, and molecular vibrations.
process: reversible
In enzyme-catalyzed chemical reaction, substrate and enzyme quickly and reversibly bind together to make transition state {enzyme-substrate complex}. The reversible reaction has forward and backward reaction rates {Michaelis-Menten rate equation, enzymatic reaction}.
process: irreversible
Transition state slowly and irreversibly separates to reform enzyme and make product. The irreversible reaction has only forward reaction rate.
process: overall
Reaction first part reaches equilibrium quickly, and intermediate concentration quickly becomes constant {steady state, equilibrium}. At steady state, intermediate concentration change over time is zero, free-enzyme concentration is much less than substrate concentration, and intermediate concentration equals total enzyme concentration.
d[ES]/dt = 0 = f1*[E]*[S] - b1*[ES] - f2*[ES]. [E] = [ET] - [ES]. [E] << [S], so [ES] = [ET]. [ES] is enzyme-substrate-complex concentration. [ET] is total-enzyme concentration. [E] is enzyme concentration. f1 is reversible-reaction forward rate. b1 is reversible-reaction backward rate. f2 is irreversible-reaction forward rate.
process: rate
Substrate depletion rate equals product creation rate: product amount divided by time in seconds. Rate is reaction velocity. Rate depends on forward rate, of making product from intermediate, times intermediate concentration.
Reaction rate can be constant {constitutive reaction rate}. Reaction rate can depend on another-molecule concentration {induced reaction rate}.
Product formation rate depends on maximum possible rate, substrate concentration, and forward and back reaction rate constants.
Maximum velocity depends on enzyme concentration and rate constant. Maximum rate {maximum velocity} {Vmax} equals forward reaction rate times total enzyme concentration.
Rate constant for whole Michaelis-Menten equation depends on all three rates: Km = (b1 + f2) / f1. Reaction velocity v depends on rate constant Km, substrate concentration S, and maximum velocity Vmax: v = (Vmax * [S]) / (Km + [S]).
After formation, proteins spontaneously rotate around single bonds, under electric forces, to make three-dimensional structures {protein folding}|.
process: forces
Amino-acid side chains have polarity. Amino acids can be more polarized, dissolve in water, and tend to be at protein surface. Electric forces are greatest at protein surface, where water interacts with amino-acid side chains. Protein ends polarize and are always at protein surface.
Amino acids can be non-polar and tend to be in protein interior. Protein middle has no water, and side chains there interact among themselves.
process: time
It takes 0.2 second to fold protein.
process: misfolding
One-third of proteins misfold {misfolding, protein}. Rotenone pesticide increases misfolding.
structure
In protein structure, all torques equal zero, and all angular accelerations equal zero. Peptide bonds have no rotation. Typically, all amino acids contribute to structure.
structure: globular
Protein typically becomes globular, because amino-acid chain folds back on itself. Globular proteins have 3.5 to 7.5 loops, with 16 to 24 amino acids each. Loop almost touches ends. Loop goes in same direction as alpha helix coil. Loop follows right-hand rule, with loop going around fingers and thumb in forward-motion direction along sequence.
structure: peptide bond
Peptide bond has N[H2]-Calpha[HR]-Ccarboxy[O]-N[H]-Calpha[HR]-Ccarboxy[O] (2 is subscript).
Bond lengths are the following. C-C for sp^3 = 0.1524 nanometers. C-H for sp^3 = 0.1090 nanometers. C-S = 0.1810 nanometers. S-S = 0.2036 nanometers. C-O peptide bond = 0.123 nanometers. N-H peptide bond = 0.100 nm. Calpha-N = 0.146 nanometers. Calpha-Csidechain = 0.153 nanometers. Calpha-Hsidechain = 0.100 nanometers. Calpha-Ccarboxy = 0.152 nanometers. C-N peptide bond = 0.132 nanometers. Ccarboxy-Cnextalpha = 0.243 nanometers. N-Cnextcarboxy = 0.246 nanometers. Calpha-Nnext = 0.241 nanometers. Ccarboxy-Cnextcarboxy = 0.372 nanometers. N-Nnext = 0.368 nanometers. Calpha-Cnextalpha = 0.381 nanometer.
Bond angles in degrees are the following. C-C-C for sp^3 = 113.0, C-C-H for sp^3 = 109.3, H-C-H for sp^3 = 107.2, C-S-C = 100.4, and C-S-S = 104.5.
Distance between alpha carbons can be 0.381 nanometers {beta sheet, protein}, 0.250 nanometers {alpha helix, protein}, 0.090 nanometers {beta turn, protein}, or random {random coil, protein}.
Protein structure descriptions can use phi angle around N-Calpha axis and psi angle around Calpha-C axis, at all Calphas. One angle has highest probability.
Right-handed alpha helix has phi angle = -57 degrees and psi angle = -47 degrees. Range can be -180 to +180 degrees. Normal range is -180 to +60 degrees. -120 degrees is normal. For proline, angle is always 0 or 110 degrees.
Beta sheet has phi angle -120 and psi angle +120. Range can be -180 to +180 degrees. Normal range is -60 to +120 degrees. Normal is 0 degrees.
technique
To study protein folding, place start position for first amino acid nonexistent alpha carbon at 0,0,0. Pick phi angle. Make new k-axis vector be N-Calpha bond. New i-axis direction is from k-axis line to Ccarboxy. j axis is cross product of k with i. Pick psi angle. Make k-axis vector be Calpha-Ccarboxy bond. New i axis is direction from bond to previous N. j axis is cross product of k with i.
Translate polar coordinates to Cartesian coordinates as necessary. Use many known structures to get actual side-chain coordinates from actual values. Use these to find conditional probabilities for amino acids and nearest, second nearest, and so on, amino acid, to make large table. Do not use alpha helix, beta sheet, or beta turn for values. Just find best parameter set and number.
Transition state slowly and irreversibly separates to reform enzyme and make product {Michaelis-Menten rate equation, enzyme}. The irreversible reaction has only forward reaction rate.
Amide bonds {peptide bond}| can form between amino-acid carboxyl groups and amino-acid amino groups. Peptide bonds resonate, are planar, have no rotation, and have hydrogen in trans configuration to oxygen. Peptide bonds do not allow branching.
Trypsin in stomach acid normally cleaves proteins, using water. If body water is low, trypsin ligates amino acids, forming water {plastein reaction}.
Cell-membrane proteins {sodium-potassium pump} can use one-third of all ATP, keep cell volume constant, make membrane excitability possible, and drive amino-acid and sugar active transport. If sodium is present, ATPase phosphorylates. Conformational change carries sodium ion from cell inside to outside, and potassium ion from outside to cell inside, against concentration gradients. Digitalis affects sodium-potassium pumps.
In muscle and microtubule contraction {muscle contraction}|, protein slides along another protein by grabbing and pulling, using ATP.
process
Calcium ions are in muscle-cell sarcoplasmic reticulum. Calcium-ion release initiates sliding. If calcium ion is present, tropomyosin goes into actin helix groove, and calcium opens binding sites, so actin can bind. Then ATPase globule tilts 45 degrees, pulling actin along. Then actin releases. After contraction, tissue elasticity passively returns muscle to normal length.
myosin
Myosin has four light chains and two long alpha-helix chains, which make two beads at myosin end. Beads are ATPases, connect actin to myosin, and are where calcium ions act. Three thick myosins surround each thin actin.
actin
Actin is globular protein that polymerizes into globule helix. Six thin actin proteins surround each thick myosin protein.
tropomyosin
Tropomyosin molecule helically wraps around actin.
troponin
Troponin molecule has binding sites for calcium, tropomyosin, and actin.
Transverse tubules are adjacent to sarcoplasmic reticulum at structures {triad junction}.
Muscle fibers have fine-tube {tubule} networks on cell surfaces and insides.
Skeletal muscle has parallel protein filaments {myofibril} lined up along elongated muscle-cell axis. Dark A bands have overlapping actin and myosin. Light I bands have actin, tropomysin, and troponin.
Repeating units {sarcomere} can have alternating dark A bands and light I bands. Dark Z line is in light I-band middle, where actins connect. Light H zone is in dark A-band middle and has thick myosin. Light H zone has middle dark M line, where myosins meet.
Proteins can have hydrogen bonds between every fourth peptide bond, with hydrogen-bond plane parallel to helical axis and side chains perpendicular to helical axis {alpha helix, protein structure}. Big or charged amino acids disrupt alpha helix. Proline stops alpha helix, because it is imino acid and does not make regular peptide bond.
Proteins can have hydrogen bonds between amino-acid chains lying in opposite directions, with side chains perpendicular to hydrogen bonds {beta sheet, protein structure}. Large amino acids interfere with hydrogen bonding and disrupt beta sheets.
The charged amino acids serine, isoleucine, and proline can make amino-acid-chain turn {beta turn, protein structure}. Proline is imino acid and makes irregular peptide bond at different angle.
Proteins {fibrous protein} can be elongated amino-acid chains. Fibrous proteins are for structure.
Proteins {globular protein} can have polar side chains on surface and non-polar side chains inside, with sharp bends at proline, serine, or isoleucine. Most proteins, such as enzymes, are globular.
Proteins {oligomer} can have multiple amino-acid chains.
Amino acid sequence {primary structure} determines protein properties.
Amino-acid-sequence three-dimensional alignment can be irregular, alpha helix, beta sheet, or beta turn {secondary structure} {conformation, protein}. Heat or chemicals can disrupt secondary structure and change protein conformation {denaturation, protein structure}.
Overall amino-acid-chain shape can be globular or fibrous {tertiary structure}.
Protein oligomers can have multiple amino-acid chains {quaternary structure}. Hydrogen bonds hold chains together. Hemoglobin has two "alpha" chains and two "beta" chains.
Carbon atoms can attach to carboxyl group and amino group {amino acid}|. The carbon atom also attaches to hydrogen atom and functional group {side chain, amino acid}. Cells can have 150 different amino acids.
asymmetry
Central carbon is asymmetric, because it has four different groups. It can rotate light clockwise (R) or counterclockwise (L).
groups
Amino acids have groups. Alkyl amino acids are glycine, alanine, valine, leucine, and isoleucine. Aromatic amino acids are phenylalanine, tryptophan, and tyrosine. Sulfur amino acids are cysteine, which is thiol, and methionine, which is thioether. Hydroxyl amino acids are the alcohols serine and threonine and the phenol tyrosine. Acidic amino acids have charge -1 in solution: aspartic acid and glutamic acid. Amide amino acids are asparagine and glutamine.
Lysine and arginine, which have amino group, are basic amino acids and have charge +1 in solution. Histidine is basic amino acid, is secondary amine, has aryl ring with two nitrogens, has charge +0.5 in solution, and has smaller charge in solution because it is weak base.
Imino acid is proline, which is secondary amine. Non-polar amino acids are alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, and proline.
polymerization
Amino acids can polymerize to make protein. Twenty different amino acids are in protein. Proteins have only L-amino acids, not R-amino acids. Amino acids that are fewest in proteins are methionine, then histidine, and then tryptophan. Methionine is first amino acid in protein chain. Free amino acid to dipeptide ratio is 10:1.
absorption
Intestine absorbs 92% of amino acids.
types
Delta-aminolevulinic acid comes from glycine and succinyl-CoA. Epinephrine comes from tyrosine. Melanin comes from tyrosine. Phenylalanine makes tyrosine. Serotonin comes from tryptophan. Amino acids can make folic acid, S-adenosylmethionine, thyroxine, histamine, sphingosine, and NAD+. Amino acids can lose amino group to become carboxylic acids in TCA cycle. Carboxylic acids in TCA cycle can gain amino group to become amino acids. Amino acids can break down to ammonia and urea.
Fibrinogen, thrombin, and blood-factor proteins participate in blood clotting {blood clotting}|.
Proteins {conjugated protein} can bind to other molecules.
Cysteine can bind to another cysteine {cystine} by disulfide bond.
Glutamic acid {glutamate, protein} builds purines and pyrimidines.
Cell proteins {heat-shock protein} can increase during stress. HSP40 carries newly folded amino-acid chains. HSP60 chaperone covers proteins as they fold, to prevent partly folded proteins from hitting others, and binds to misfolded intermediates to restart folding. HSP70 holds ATP, but when ATP leaves, it binds peptide and so aids protein conformation and assembly. HSP90, such as gp96, organizes proteins from other chaperones into receptors and other multiprotein structures. HSP70 and HSP90 carry antigens to antigen-presenting-cell CD91 receptors.
Small proteins {interferon}| can bind to plasma membranes and can protect against viruses that degrade mRNA and block protein-synthesis initiation. After viral-gene expression starts, interferon can stop all viral-gene expression {interferon response}. In humans, viruses that make long double-stranded RNAs trigger PKR enzyme production, which stops mRNA translation to protein. RNAse L breaks down mRNA. Interferon cytokine secreted by virus-infected cells enhances both these responses.
Alpha-keratin {keratin}| is in skin, hair, wool, horn, and nails. Alpha-keratin has three to seven amino acid chains in bundle, cross-linked by disulfide bonds, which then bundle again. Scales, claws, beaks, silk, and feathers have beta-keratin. Beta-keratin is mostly glycine, alanine, and serine.
Amino acids can link by peptide bonds {peptide}|. Peptides do not branch. Peptides are transmitters and hormones.
Proteins {protein hormone}, such as insulin, growth hormone, and adrenocorticotropin, can be hormones.
Protofibrils {protofibril} are soluble, have 4 to 30 misfolded proteins that clump together, and do not break down quickly enough in disease, later forming fibrils and {amyloid} plaque.
Urea processing uses the following steps {urea cycle}. Ammonia builds up in cells from various deaminations. Ammonia is toxic, because it blocks TCA cycle. In mitochondria, ammonia reacts with two ATP, carbon dioxide, and water molecule to make one carbamyl phosphate. In cytoplasm, carbamyl phosphate reacts with ornithine to make citrulline. Citrulline diffuses to cytosol and reacts with aspartic acid, which splits to give arginine and fumarate. Water reacts with arginine to make nitrogen compounds {urea}| {ornithine}. Urea is not toxic, can cross membranes, and excretes in urine.
Proteins, such as snake venoms, can be poisons {toxin}|. Bacteria make diphtheria toxin. Cobra venom and banded kait venom bind to acetylcholine receptor. Tetanus toxin and black-widow-spider toxin affect acetylcholine vesicle release. Tetanus toxin prevents glycine release. Benzodiazepines, phencyclidine, and strychnine are toxins. Poisons can stay inside cells {endotoxin} or secrete to outside {exotoxin}. LAL chemical, from horseshoe crab blood, tests for endotoxins in drugs and implants.
Botulinus toxin {botulism}| affects acetylcholine vesicle release.
Proteins {enzyme}| can be catalysts. Enzyme and ribozyme catalysts regulate biochemical reactions. Coenzymes can bind to or assist enzymes.
history
Schwann discovered pepsin [1825], which cuts proteins. Robiquet and Boutron discovered emulsin [1830]. Leuchs discovered ptyalin [1831]. Payen and Persoz discovered amylase [1833], which cuts starches. Corvisart discovered trypsin [1856], which cuts proteins. Kuhne invented the word enzyme [1878]. Bertrand discovered need for coenzymes [1897]. Arthur Harden and William John Young discovered coenzyme for zymase [1906]. Henri studied enzyme kinetics and proposed enzyme-substrate complex [1903]. Barger and Stedman discovered that physostigmine inhibited cholinesterase [1923], which metabolizes choline. Jones and Perkins discovered ribonuclease [1923], which cuts RNA. Enzymes are proteins [1925]. Briggs and Haldane used steady state for enzyme kinetics [1925]. Sumner discovered urease [1926], which metabolizes urea. Stedman discovered acetylcholinesterase [1932], which metabolizes acetylcholine. Aeschlimann discovered that neostigmine inhibited cholinesterase [1931]. Hellerman hypothesized need for thiol groups in enzymes, as did Bersin and Logemann [1933]. Hellerman hypothesized need for metal bridges in enzymes [1937]. Mann and Keilin discovered that sulfanilamide inhibited carbonic anhydrase [1940]. Sanger and Tuppy found insulin amino-acid sequence [1951]. Sutherland discovered cyclic AMP in animal cells [1956]. Koshland hypothesized enzyme conformation changes upon binding [1958]. Kendrew used x-ray crystallography on myoglobin [1958]. Merrifield developed solid-phase peptide synthesis and built insulin and ribonuclease [1963].
types
Chymotrypsin, cytochrome, diastase, flavin, lipase, lysozyme, nuclease, RNA polymerase, thermolysin, and DNA polymerase are enzymes.
transition states
About 100,000,000 transition-state shapes exist for enzymes.
In competitive inhibition, inhibitor shape can be similar to substrate shape, so inhibitor can bind to enzyme at substrate site {active site}.
In non-competitive inhibition, inhibitors can bind to enzymes at other sites {allosteric site} to alter active sites.
Molecules {coenzyme}| can bind to enzymes to activate them. Michaelis and Wollman discovered that free radicals formed from alpha-tocopherol [1950]. Lipmann isolated coenzyme A [1945]. Mitchell, Snell, and Williams isolated folic acid [1941]. O'Kane and Gunsalus isolated lipoic acid [1948]. Metals can be coenzymes [1930]. Jansen and Donath isolated thiamine [1926]. Fildes hypothesized that molecules similar to natural substrates or coenzymes compete and are therapeutic. Methotrexate treats leukemia (Farber) [1946].
Post-transcription, enzymes {proteolytic enzyme} can cleave terminal amino acids and break peptide chains into pieces: proteinase, peptidase, pepsin, trypsin, chymotrypsin, carboxypeptidase, amino peptidase, dipeptidase, endopeptidase, and exopeptidase.
Reagents {substrate} can bind to enzymes at active sites.
Enzyme precursors {zymogen} can split or react to create enzymes.
Molecules {inhibitor} can bind to enzyme to reduce reaction rate {enzyme inhibition}.
Inhibitor shape can be similar to substrate shape, so inhibitor can bind to enzyme at active site {competitive inhibition}.
Inhibitor can bind to enzyme at allosteric site to alter active site {non-competitive inhibition}.
Inhibitor can bind directly to enzyme-substrate complex to change activation energy {uncompetitive inhibition}.
Heat-shock proteins {foldase}, such as HSP60, envelope proteins as they fold to prevent partly folded proteins from hitting others.
Heat-shock proteins {chaperone} bind to misfolded intermediates to restart folding.
Molecules {ubiquitin, protein}| can bind misfolded proteins and go to proteosomes to break peptide bonds.
Proteins can be for protection {immunity}|. Antigen binding to beta-lymphocyte surface triggers process that creates plasma cells. Plasma cells specialize to make antibody to antigen.
Antigens can enter body. Immunoglobulin proteins {antibody}| bind antigens, so body can remove foreign molecules. Antibodies bind to antigens by hydrogen bonds, van der Waals forces, and ionic bonds. Antibody-connecting subunits can cross plasma membrane and bind to cells.
structure
Antibodies have three subunits. Two subunits can bind to one antigen each. One subunit connects two binding subunits to make Y-shaped structure. Antibodies have two light protein chains and two heavy protein chains, linked by disulfide bonds. Light chains are at Y tips. All antibodies have kappa or lambda light chain but different heavy-chain constant regions. Heavy chains are in arms and base of Y. Light and heavy chains have variable end and constant end. Several hundred genes code variable regions, making millions of different antibodies. About 100,000,000 different antibody shapes can exist.
precipitation
When one antibody binds to two antigens, complex becomes insoluble. Bound molecules precipitate from solution, and then cell phagocytes eat them.
Five proteins {immunoglobin}| affect immunity. IgA is in secretions. Immune system makes IgM first. IgG increases as IgM decreases. IgE is for allergies. IgD is another immunoglobin.
Large molecules {antigen}| can enter body from outside.
Antigens have regions {epitope}| where other molecules can bind.
Small molecules {hapten} can bind to epitope.
Protein groups {complement, protein} can lyse cells if antibodies bind to cells.
Genes {joint gene} {J gene} can code for connections between light and heavy chains.
Parasites {virus, organism} can have DNA or RNA surrounded by protein.
nucleic acid
Virus has nucleic acid 4 to 250 genes long. Nucleic acid can be RNA or DNA, single or double-stranded.
injection
Protein coat has sites that attach to cell membrane. After attachment, protein coat contracts to inject nucleic acid into cell.
replication
After injection, viral genes can transcribe. Proteins from those viral genes prevent host-cell DNA transcription. Then cells transcribe viral genes whose proteins replicate virus and protect viral DNA from attack. Enzyme protects from attack by methylating sites that are vulnerable to attack by cell nucleases.
protein coat
After rod-like-virus nucleic acid replicates, nucleic acid binds protein-subunit disks at a site and then adds more subunit disks as nucleic acid folds into helix inside.
After sphere-like-virus nucleic acid replicates in cell, cell makes protein spheres, and enzyme inserts nucleic acid into protein sphere. One cell can make up to 200 viruses.
types
After assembly, virus can lyse cell and let viruses out to attack more cells. Virus can allow cell to remain packed with viruses, without bursting.
Viruses have protein coats {capsid}, with identical subunits hydrogen-bonded into symmetric structures. Special capsid proteins recognize cells by binding to cell-membrane proteins. After attachment, virus nucleic acid enters cell by injection through cell membrane, using energy from ATP.
Nucleic acids {bacteriophage}| can act like viruses in bacterial cells. It is DNA or RNA that has protein coat. It tries to enter cell from outside and then integrate into chromosome. Bacteriophages replicate in cell along with chromosome.
Viruses {RNA virus} can have RNA instead of DNA. RNA viruses can use RNA-directed RNA polymerase for direct RNA replication. RNA viruses can use RNA-directed DNA polymerase to make DNA from RNA and then make viral RNA from DNA. RNA viruses include polio, colds, foot-in-mouth disease, rabies, cancer retrovirus, and human immune deficiency virus.
Viruses {Sendai virus} can alter membranes and allow two cells to fuse, even if they are from different species.
Carbon transfers among many forms {carbon cycle, Earth}.
ocean
Rivers remove land sediments, and calcium carbonate enters sea. Carbonate buffers sea and is in equilibrium with carbon dioxide in air. Carbonates can becomes shells or skeletons. Eaten shells and skeletons later sink and dissolve. Carbonates can remain in sponges, algae, and coral reefs. Algae reefs began 2,000,000,000 years ago. Animal reefs began 600,000,000 years ago. Reefs collapsed 530,000,000; 350,000,000; 225,000,000; and 65,000,000 years ago.
organisms
Autotroph organisms get carbon from carbon dioxide. Heterotroph organisms get carbon from glucose.
cells
Photosynthetic cells convert carbon dioxide and water to glucose. Cells break down glucose to carbon dioxide and water for energy.
carbon
Carbon atoms can bond to carbon atoms and other non-metals, with single and multiple bonds, to make rings, chains, and branching chains. Many polarities and charge structures are possible. Carbon covalent bonding provides stability, alterability, and variety in organic molecules.
Cells make nitrogen into nitrate or ammonia, then make nitrate or ammonia into amino acids, then break down amino acids to ammonia and urea, and then break down ammonia and urea to nitrate and nitrite {nitrogen cycle, biochemistry}. Nitrogen-fixing bacteria {chemolithotroph} change nitrogen gas to ammonia. Nitrate-making bacteria make nitrate from ammonia.
Cells reduce oxygen and hydrogen donors to water, and then oxidize water to oxygen {oxygen cycle}. Aerobe organisms use oxygen as electron acceptors to cause reduction. Obligate-anaerobe organisms use sugar as electron acceptor to cause reduction. Facultative-aerobe organisms use either oxygen or sugar but prefer oxygen as electron acceptor to cause reduction. Anaerobe organisms do not use oxygen.
Water is both inside and outside cells {water cycle, biochemistry}. Water is 70% of human body weight. Cell water has phosphate buffer and is at pH 6.8. Cell proteins make high osmotic pressure. Intercellular fluid has bicarbonate buffer and is at pH 7.2. Osmotic pressure is low outside cells.
Cells change light energy into chemical-bond energy {energy cycle, cells}. Cells make glucose and can make ATP high-energy bonds. Cells diffuse ATP to all cell parts. Cells use ATP to phosphorylate other compounds. Cells use ATP to make acetyl-CoA for making carbon-carbon bonds. Cells use high-energy compounds to synthesize molecules, cause movement, send electrical signals, or generate heat. Cells break down synthesized molecules, dissipate electric energy, and make energy into heat through friction.
reduced molecule
Cells use ATP to make NADH, NADPH, and FADH2 [2 is subscript] electron acceptors and hydrogen donors. Reduced molecules, which can oxidize to release energy, store energy for biochemical reactions. Oxidation-reduction reactions are reversible. NAD can add one hydrogen atom to make reduced NADH. Phosphated NADP can reduce to NADPH. FAD can add two hydrogens to make reduced FADH2 [2 is subscript].
Adenosine triphosphate (ATP) transfers energy {ATP cycle}. Cells cannot store ATP. ATP cannot cross membranes.
functions
ATP actively transports, contracts muscle, phosphorylates molecules, makes thioester with acetyl-CoA, makes enols, and makes guanidiene.
metabolism
ATP can break down to adenosine monophosphate (AMP) and pyrophosphate. ATP can break down to adenosine diphosphate (ADP) and orthophosphate. Orthophosphate transfers to arginine or creatinine. Cells regenerate ATP by ADP and orthophosphate oxidation, in respiration pathway or glycolysis pathway.
acidity
At high pH, energy in ATP is less, because electron repulsion is less.
concentration
If ATP concentration increases, energy in ATP is less, because dissociation is less.
magnesium
Magnesium binds to ATP phosphates. If magnesium increases, energy in ATP decreases, because magnesium blocks charges more.
Basic organism energy flow {basal metabolism rate}| sustains life. People have energy-use rate while completely resting, typically 1600 calories per day. Human rate averages 1000 calories per kilogram per hour. Rate is proportional to body surface and body weight. Whole-body average energy flow is 20% to 50% higher than basal metabolism rate.
gender
Rate is higher in males. Rate increases in pregnancy and lactation, up to three times more.
hormones
Thyroid and growth hormones affect basal metabolism rate.
factors
Rate increases in fever. Rate lowers during fasting.
isothermal
Metabolism typically is in isothermal environments, like sea or warm-blooded animals.
warm-bloodedness
Warm-blooded animals use up to ten times more energy than cold-blooded animals. Warm-blooded animals can live in wider temperature ranges and move faster. Temperature constancy requires muscle movement to heat tissues. Temperature constancy requires mechanisms to cool tissues. Brain controls temperature. Parents must keep eggs and babies warm. Temperature control turns off during sleep. Warm-bloodedness can be at different temperatures in different conditions. Food quantity must be more. Senses must find food. Memory must remember food locations. Planning must improved for better food strategies. Chewing must be more efficient. Breathing passage alters to allow breathing while eating.
Bonds {phosphate bond}| can store energy for biochemical reactions. Phosphate bonding is reversible. Molecules {adenosine monophosphate} (AMP) can have one nucleotide and one phosphate. Molecules {adenosine diphosphate} (ADP) can have one nucleotide and two phosphates. Adenosine triphosphate (ATP) has one nucleotide and three phosphates.
Cells use energy in different ways {troph}. Organisms {phototroph} can use sunlight for energy. Non-sulfur purple bacteria {photoorganotroph} are photosynthetic. Organisms {chemotroph} can use energy-containing molecules and oxidation-reduction reactions for energy. Organisms {lithotroph} can use water, hydrogen sulfide, sulfur, ammonia, hydrogen, or ferrous compounds as electron donors to cause oxidation. Organisms {organotroph} can use glucose and other organic electron donors to cause oxidation.
Files {MOL File} with file extension .mol can describe molecule atoms and connections.
Files {PDB File} from Brookhaven Protein Databank with file extension .pdb can contain XYZ coordinates for all protein atoms, as well as hydrogen bonding information.
Files {SD File} with file extension .sd or .sdf can describe molecule atoms and connections, in two dimensions.
Files {TGF File} with file extension .tgf can describe molecule atoms and connections, in three dimensions.
Files {XYZ File} with file extension .xyz can describe molecule atoms and connections, in three dimensions.
Compounds {drug, chemistry} {drug-like compound} can metabolize with biological molecule.
size
Drugs have molecular weight 200 to 700.
side effects
Drugs must have few side effects.
absorption
Body can absorb drugs.
distribution
Drugs can go to body organs and/or tissues.
metabolism
Drugs have chemical reactions at sites. Drugs have orientation at receptor site. Drugs can sterically interact with receptor site.
excretion
Drugs do not excrete too quickly.
solubility
Drugs have solubility, partition coefficients, diffusivity, and ionization degree.
variation
Drugs can vary using different salts, esters, and side groups for different sizes and surface areas.
form
Drugs can be solutions, suspensions, capsules, or tablets. They can be oral, subcutaneous, intravenous, inhaled, or patch.
history
In England, William Morton [? to 1868] used inhaled ether [1846] during surgery on October 16 (Ether Day). inhaled chloroform [1850]. inhaled nitrous oxide and oxygen [1868]. hypodermic syringe [1868]. intravenous morphine [1868]. chloral hydrate [1869]. inhaled nitrous oxide and oxygen followed by chloroform or ether [1876]. paraldehyde [1882]. cocaine [1884]. sulfones [1888]. ethyl p-aminobenzoate [1890]. Novocaine is procaine hydrochloride. Phenacetin comes from aniline by hydroxylation and conjugation [1890 to 1899]. aspirin [1899]. Anti-pyrine came from quinine [1900]. urethane [1900].
Organizations regulated by the Food and Drug Administration (FDA) are required to comply with Good Laboratory Practices {good laboratory practices} (GLP). GLP compliance requires organizations to have administrative policies, written procedures, competent personnel, and trained personnel. As part of GLP compliance, software products used in regulated organizations should comply with FDA regulations and document how compliance was achieved.
Code of Federal Regulations (CFR), Title 21, Chapter I, Part 11
Specific functions, electronic records, and auditing of software systems are required to be compliant with Code of Federal Regulations (CFR), Title 21, Chapter I, Part 11, Electronic Records; Electronic Signatures Final Rule (FDA CFR21 Part 11).
FDA CFR21 Part 11 requires accurate, reliable, and consistent software.
FDA CFR21 Part 11 does not necessarily require encryption.
FDA CFR21 Part 11 requires versioning of data and audit records.
FDA CFR21 Part 11 requires data to be entered in specific fields before processing.
FDA CFR21 Part 11 requires auditing.
FDA CFR21 Part 11 requires electronic signatures.
FDA CFR21 Part 11 has installation requirements. All necessary software components must be successfully installed and a report generated.
FDA CFR21 Part 11 has logon and logoff requirements. Systems limit access to only authorized persons, by checking user name and password. After a specific time period, automatic logoff occurs.
FDA CFR21 Part 11 has security requirements for data and audit record management, with file and operating system permissions. Attempts at unauthorized use are sent by electronic mail to the Administrator. User and user groups have privileges to files, directories, and functions. Systems can detect invalid or altered records. Auditing of user events detects creation, modification, and deletion of files, using checksums.
FDA CFR21 Part 11 requires instrument maintenance logs.
FDA CFR21 Part 11 has requirements for reporting data, parameters, and auditing information.
Drugs have absorption, distribution, metabolism, and excretion {ADME}.
Pharmacokinetics (PK) is about absorption, distribution, metabolism, and excretion {ADME/PK profile}.
Drug Metabolism and PharmacoKinetics {DMPK}.
Inactive chemicals {excipient}, such as solvent or powder, can carry active drugs.
Plasma proteins {human serum albumin} (HSA) can carry other molecules.
Drugs {pharmacodynamic drug, complex} can make complexes but not cause chemical reactions or conformational changes.
Drugs have absorption, distribution, metabolism, and elimination {pharmacodynamics} (PD).
Population genotypes can identify SNPs affecting drug metabolism {pharmacogenomics}.
Absorption, distribution, metabolism, and elimination affect drugs {pharmacokinetics} (PK).
High-enough concentration {potency}| causes biologic response.
Drugs {prodrug} can require metabolization to transport or be active.
Drugs can cause birth defects {teratogenicity}|, by acting on development processes.
Drug can damage tissues {toxicity}|.
Foreign compounds {xenobiotics} are vapors, alcohol, drugs, pollutants, solvents, food toxins, pesticides, and pyrolysis products. Pyrolysis products come from charring fat or protein.
Drugs have activity {drug, activity}, depending on structures and other factors.
Activity is half maximum at a concentration {IC50}.
Mopac quantum-mechanical calculation can find activation energy {initial activation energy} (Ea0).
Structure can associate with physicochemical property {property-activity relationship}.
Measured activity equals physicochemical-variable function {quantitative structure-activity relationship} (QSAR). QSAR relates activity magnitude, such as tissue concentration, to compound physico-chemical or structural property magnitudes, such as carbon-atom numbers. QSAR (3D-QSAR) can be in three dimensions.
Activity equals physicochemical-variable function {structure-activity relationship} (SAR).
Structures and properties have relation {structure-property correlation} (SPC).
Systems {Corey Pauling Koltun} (CPK) can display space-filling compound models.
Molecule alignments can adjust {field-fit procedure}.
Indexes {kappa index, drug} can depend on molecular shape and flexibility.
Network mappings {Kohonen topology-preserving mapping} can retain topology.
Calculations {Morgan algorithm} can make unique numberings for connection tables.
Strings {SMILES} can uniquely describe three-dimensional structure.
Searches {substructure searching} can use connectivity-table parts as search criteria.
Topological indexes {Tanimoto index} can represent graphs as numbers.
Indexes {topological index} can represent graphs as numbers.
Indexes {valence molecular-connectivity index} can use valence to indicate connectivity.
Sums {branching index} over all bonds, of inverse of square root of end-atom-valence product, can measure branching amount.
Indexes {molecular connectivity index} can depend on branching.
Normal-distribution outlier tests {Dixon's Q-test, drug} {Dixon Q-test, drug} can measure smallest and largest difference ratio.
Normal-distribution outlier tests {Grubbs' s-test, drug} {Grubbs s-test, drug} can compare absolute value, of difference between mean and value, divided by standard deviation, to T-distribution value.
Rules {Active Analog Approach} can align molecule activities by analogous structures.
Rules can align molecule activities by structural group {active pharmaceutical ingredient} (API).
Non-parametric methods {alternating conditional expectations} (ACE) can analyze activity.
Input "neuron" layer can hold physico-chemical properties and feed to middle layer using sigmoidal function {transfer function} with weights for outputs. Middle-layer "neurons" feed to one output {artificial neural network} (ANN).
Mathematical tools {chemometrics} applied to structure-activity relationships can find correlations and regression, recognize patterns, classify compounds and properties, design experiments for random screening and measuring, and validate results.
Quantum mechanics can pair with empirical approaches {computer-assisted metabolism prediction} (CAMP).
Cell arrays can pool more than one sample in cells, which allows fewer cells. Methods {deconvolution} can track sample pooling.
convolution
Convolution puts each sample into several cells, in regular pattern. Testing looks for one effect. Some cells show effect, but most do not. If sample causes effect, all cells with that sample show effect. Cells that contain that sample form pattern, so pattern indicates sample name.
deconvolution
Deconvolution uses convolution method and resulting cell pattern to find sample name. For example, for 100-cell array, 10 samples can feed into 90 cells, each cell receiving two samples. Ten cells have control samples. See Figure 1. Samples are in 18 cells. If testing shows that all 18 have activity over threshold, then that sample is effective.
If sample interactions cause effect, deconvolution can find interactions. If testing shows that only one cell has activity over threshold, those two samples must interact to be effective.
Combining quantum mechanics and physico-chemical properties {empirical-quantum chemical} {combined empirical/quantum chemical approach} can predict chemical behavior.
Models {Korzekwa-Jones model} can be for P-450 hydrogen abstraction and depend on difference between radical free energy and hydrogenated-atom free energy, as well as radical ionization potential and constant additive term.
Steric effects and van der Waals forces can cause fields {Lennard-Jones potential}.
Plots {loading plot} can use variable weights.
Semiempiric methods {modified neglect of differential overlap} (MNDO) can ignore overlap.
Molecule-modeling programs {molecular modeling}, such as Alchemy III and SYBYL from Tripos, can use electrostatics or quantum mechanics.
Non-parametric methods {non-linear partial least-squares, drug} (NPLS) can find least squares.
Response-surface methods {non-parametric method}, such as ACE, NPLS, and MARS, can be non-parametric.
IF/THEN statement sets {rule induction system, drug} can make output from input.
Graphs {score plot} can plot compound activities.
In multidimensional property space, compound clusters make classes separated by distance {cluster analysis} (CA). CA reduces unimportant variables. Substructure, topological index, physico-chemical property, calculated physico-chemical property, or hydrophobicity can determine classes.
Using discrete or continuous data and embedded data can put compounds into groups by activity level {cluster significance analysis} (CSA). CSA locates small clusters in large spaces.
Methods {Cone and Hodgkin similarity index} can measure molecular similarity.
Models {discriminant-regression model} (DIREM) can locate small clusters in large spaces.
Methods {distance-b program} (EVE) can locate small clusters in large spaces.
Unsupervised methods {hierarchical cluster analysis} (HCA) can measure distances between all points and make point vs. distance dendograms.
Structures can cluster in large databases by rating different compounds by similarity {Jarvis-Patrick method}.
Supervised methods {k-nearest neighbor} (k-NN) can calculate new-object distances from all other objects, to locate small clusters in large spaces.
Processes {partitioning} can merge individuals into groups or split whole into clusters.
Values {similarity measure} can compare distances.
Methods {single class discrimination} (SCD) can locate small clusters in large spaces.
Classifications {supervised method} can use already known patterns and clusters.
Activity and descriptor correlation vectors {trend vector analysis} can rank compound similarity.
Hierarchical methods {Ward's clustering method} {Ward clustering method} can agglomerate compounds to find clustering.
Supervised methods {Soft Independent Modeling of Class Analogies} (SIMCA) can use region-boundary or envelope models, to locate small clusters in large spaces.
Clustering methods {class analogy} can be SIMCA methods.
Distance measures {city-block distance} between structure-space points can be the same as Manhattan distance.
Distance measures {Manhattan distance} between structure-space points can be the same as city-block distance.
Distance measures {Minkowski distance} between structure-space points can be the same as Lp-metric.
Distance measures {Lp-metric} between structure-space points can be the same as Minkowski distance.
Structure-space points have distances {Mahalanobis distance}.
Hierarchical methods {centroid linkage} that agglomerate compounds can find clustering.
Hierarchical methods {complete linkage} that agglomerate compounds can find clustering.
Hierarchical methods {single linkage} that agglomerate compounds can find clustering.
Processes have factors {factor analysis}. Physico-chemical or structural properties describe compounds and have components {descriptor, factor} {X-variable, factor} {X descriptor, factor}. Chemical activities relate to variables {response variable}.
Methods {canonical factor analysis} can be for factor analysis.
Methods {centroid method} can be for factor analysis.
QSAR {combinatoric QSAR} can find similarities using different descriptor combinations.
Moments of inertia, and dipole and quadrupole moments, can be descriptors to calculate molecular moments {Comparative Molecular Moment Analysis} (CoMMA). CoMMA depends on shapes and charges.
Properties and structures have relations {Correlation Analysis}.
Factor-analysis methods {correspondence analysis} {correspondence factor analysis} (CFA) can use variable frequencies relative to activities, finds chi-square values, and finds principal components.
Principal components {disjoint principal component} (DPP) can be independent.
Thresholds {eigenvalue-one criterion} can be how many components have eigenvalues greater than one.
Unsupervised linear methods {eigenvector projection} can find factors.
Models {Evolutionary Programming} (EP) can add and subtract randomly selected variables, with crossing-over, and evaluate for "fitness" or best fit.
Methods {evolving factor analysis} (EVA) can analyze ordered data.
Methods {percentage of explained variance} {explained variance percentage} can indicate number of components required to reach 90% of total variance.
Parameters and descriptors can linearly relate to free energy {extrathermodynamic approach}.
Factor-analysis methods {free energy perturbation} (FEP) can use free-energy changes.
Binary descriptors can note molecule-substructure presence or absence {Free-Wilson approach}.
Linear property sets can have different values, change values by crossing-over between related such genes, and have random change {Genetic Function Algorithm} (GFA), to select best fit.
Values {Hammett sigma value} can relate to electronic and electrostatic properties.
Activity, partition coefficients for hydrophobicity, ionization degree, and molecular size relate {Hansch equation}.
Variables {latent variable} can be linear-descriptor combination.
Supervised methods {linear discriminant analysis} (LDA), in which boundary surface minimizes region variance and maximizes variance between regions, can put compounds into groups by activity level.
log K = k1 * sigma + k2 {linear free energy equation, drug} (LFE).
Supervised methods {linear learning machine} (LLM) can divide n-dimensional space into regions, using discriminant function.
Factor-analysis methods {maximum-likelihood method} can find factors.
Metric or non-metric methods {multidimensional scaling} (MDS) can analyze similarity or dissimilarity matrices to find dimension number and place objects in proper relative positions.
Non-parametric methods {multivariate adaptive regression spline} (MARS) can find factors.
Models {Mutation and Selection Uncover Models} (MUSEUM) can add and subtract randomly selected variables, with no crossing-over, and evaluate for "fitness" or best fit.
Unsupervised linear methods {non-linear iterative partial least-squares} (NIPALS) can represent data as product of score matrix, for original observations, and loading-matrix transform, for original factors.
Topological mappings {non-linear mapping} (NLM) can be factor-analysis methods in which linear-variable combinations make two or three new variables.
Information about compound physico-chemical properties can predict compound chemical or physiological behavior in vitro and in vivo {predictive computational model}.
Variables {principal component} (PC) can be linear-descriptor combinations. Unsupervised linear method {principal component analysis, factor} (PCA) represents data as product of score matrix, for original observations, and loading-matrix transform, for original factors. PCA is factor-analysis method in which linear variable combinations make two or three new variables. PCA reduces unimportant variables.
Singular-value decomposition (SVD) can find best singular values for predicting {principal component regression} (PCR). SVD projects regression to latent structures.
Modified PCA {principal factor analysis} can find principal factors.
Methods {Procrustes analysis} can identify descriptor sets for describing similarity.
Methods {QR algorithm} can diagonalize matrices.
Unsupervised linear methods {rank annihilation} can find factors.
Residual variance approaches constancy {Scree-test, drug}, and plotted slope levels off {Scree-plot}, depending on component number.
In unsupervised linear methods {singular value decomposition, drug} (SVD), correlation matrix is product of score, eigenvalue, and loading matrices, with diagonalization using QR algorithm.
Factor-analysis methods {spectral mapping analysis} (SMA) can first take data logarithm to eliminate outliers and then subtract means from rows and columns, to leave only variation, showing which variables are important and how much.
Spaces {structure space} can have two or three principal components.
Methods {target-transformation factor analysis} can rotate features to match known pattern, such as hypothesis or signature.
Factors and response variable have relations {Unsupervised Method}, without using factor information or predetermined models.
Designs {factorial design} can try to ensure design-space sampling, if position varies.
Designs {fractional factorial design} can try to ensure design-space sampling, if position varies.
Three-level designs {response surface method} (RSM) can have three factors that quantify relationships among responses and factors. RSM includes MLR, OLS, PCR, and PLS linear designs; non-linear regression analysis (NLR); and non-parametric methods, such as ACE, NPLS, and MARS.
isomer-enumeration method {Cayley tree structure}.
Isomer-enumeration methods {CONGEN program} can be successors to DENDRAL.
Isomer-enumeration methods {DENDRAL program} can be forerunners of CONGEN.
isomer-enumeration method {Henze and Blair recursion formulas}.
Isomer-enumeration methods {Polya's enumeration theorem} {Polya enumeration theorem} can use group theory.
Electron orbitals {molecular orbital} can be for whole molecule.
Analyses {ab initio analysis} can use all electrons.
Adding atomic orbitals can approximate molecular orbitals {linear combinations of atomic orbitals} (LCAO).
Semiempiric methods {perturbative configuration interaction using localized orbitals} (PCILO) can use perturbations.
Analyses {semiempiric} can use valence electrons and parameterize core electrons.
Sigma electrons can contribute {simple delta index, drug}.
Factors, properties, or structures {regressor} can contribute to response values {regression, regressor} {Regression Analysis}.
Regression can project to latent structures {canonical correlation} (CC), to put compounds in classes.
Regression {continuum regression} (CR) can project to latent structures, to put compounds in classes.
Variance-covariance matrix {correlation matrix, drug} can scale to normalize data.
Regression can project to latent structures {kernel algorithm}, to put compounds in classes.
Methods {matrix diagonalization, drug} can simplify data variance-covariance matrix.
Parametric methods {non-linear regression} (NLR) can find descriptor coefficients by non-linear regression.
Regression can project to latent structures {ridge regression} (RR), to put compounds in classes.
Methods {Spearman rank correlation coefficient} can measure molecular similarity.
Complete, symmetric, square matrix {variance-covariance matrix} uses property values and structure values.
Regression can project to latent structures {adaptive least-squares} {ALS algorithm}, to put compounds in classes.
Methods {classical least-squares, drug} (CLS) can be the same as ordinary least-squares analysis.
Partial least-squares {Comparative Molecular Field Analysis} (CoMFA) can analyze grid around site atom and find grid-point electrostatic and steric interactions, to make sampled-point descriptors.
Compounds have different classes with different weights {fuzzy adaptive least-squares} (FALS).
Methods {Generating Optimal Linear PLS Estimations} (GOLPE) can use PLS and D-optimal design to select variables, and cross-validates.
Fitting methods {inverse least-squares} (ILS) can find regression line.
Methods {least-squares regression, drug} can be the same as ordinary least-squares analysis.
Methods {linear least-squares regression, drug} can be the same as ordinary least-squares analysis.
Partial least-squares methods {matrix bidiagonalization method, drug} can simplify data variance-covariance matrix.
Regression can project to latent structures {multi-block PLS}, to put compounds in classes.
Methods {multiple least-squares regression, drug} can be the same as ordinary least-squares analysis.
Methods {multiple linear regression} (MLR) can measure linear component dependence on physico-chemical or structural properties and finds descriptor coefficients.
Methods {multivariate least-squares regression, drug} can be the same as ordinary least-squares analysis.
Methods {non-least-squares} (NLS) can detect non-linear relationships.
Fitting methods {ordinary least-squares} (OLS) can find descriptor coefficients.
Methods {partial least-squares} (PLS) can use least-squares to find independent variables and dependencies among variables. It projects regression to latent structures. It maximizes latent-variable and observable covariation. It diagonalizes the matrix.
Methods {SAMPLS algorithm} can apply PLS to trend vector analysis.
Estimates {best linear unbiased estimator} (BLUE) can give smallest variance among estimators.
Error measures {standard error} can be square root of MSE.
SSE, SSR, or SST {sum of squares of differences} {squares of differences sum}.
SSE / (observation number + factor number - 1) {mean square error} (MSE).
Errors or residuals can cause sum {SSE} of squares of differences between observed and predicted responses.
Regression can cause sum {SSR} of squares of differences between observed and mean.
Sum {SST} of squares of differences between predicted and mean makes total: SST = SSE + SSR.
Drugs have tests {drug experiment}.
experimental design
Samples can test properties and activities. Experiment uses numbers and sample types from population, as well as methods and instruments. Three-level design assigns three levels (-1,0,1) to each factor to determine how responses vary with factors or variables, for making mechanistic physico-chemical models, using physical chemical properties as factors, or empirical polynomial models, using arbitrary variables as factors. Three-level mixture design determines whether factor is useful or significant or not. Two-level design assigns two levels (0,1) to each factor to determine whether factor is useful or significant, for screening, searching, or filtering.
kinetics
Experiments can read samples multiple times over time to find reaction rate or inhibition constant.
Biological reaction series can makes protocols {assay, experiment}. Protocol or method series use reagents to identify compounds, genes, proteins, or quantities.
Methods {protocol, experiment}| can run experiments. Experiments can perform steps or tasks on samples: prepare samples, mix with reagents, hybridize, wash, detect, and analyze.
Samples can be read more than once {replication, sample}.
In screening, calculated results translate into given ranges {scoring}, like high, medium, or low.
three-level design {Box-Behnken design}.
Experimental designs {CARSO approach} can be for random compound screening in experiment series.
three-level design {central composite design}.
Experimental designs {Craig plot} can be for random compound screening in experiment series.
Test-set selection methods {D-optimal design} can try to ensure design-space sampling, if positions vary, and can account for excluded volumes.
Experiment designs {sequential optimization} can use steps toward optimum.
Experimental designs {Topliss tree} can be for random compound screening in experiment series.
Experiments {dose response curve} can read samples at different concentrations and fit IC50 curves.
Experiments {ELISA} can back-calculate sample concentration, using reference curve.
Automated assays {High-Throughput Screening} (HTS) can test many diverse compounds against enzymes or cell targets, to identify possible new drugs.
More than one sample can be in wells {pooling} in screening experiment. Samples mix in plate wells according to patterns, so system measures all samples the same number of times. Total well number is fewer than with one sample per well.
Experiments {ratio experiment} can read samples twice, for agonist vs. antagonist, to determine activity ratios.
Automated assays {screening} {high-throughput screening} can identify promising compounds from compound libraries.
users and groups
Roles (types of users) have a set of privileges. Users have roles.
inventory
Inventory database has sample IDs.
experiment type: ELISA
Plate has high and low controls (averages), dose-response titration (IC50), and replicated samples (averages of % inhibition); Fit the result into the standard curve for a first estimate IC50, and back calculate the concentration of an expressed protein by using a standard reference curve on each plate. Look for the well that has a result which falls on the linear portion of the standard curve.
experiment type: ratio
Each plate is read twice, first reading the growth of a specific protein, and second measuring the survival of various cells (or agonist vs. antagonist receptors). % inhibitions are calculated for each of these readings, and then the ratio. Sort on any of the three results. Since plates are carried from one reader station to the next, they may get out of order, may be put into the reader backwards, or may get dropped, so data system should be able to deal with all of these problems. This is a case of 'multiple data points per well'.
experiment type: dose response, multiple calculations
Several different models calculate, fit, and display the IC50 curves simultaneously, like straight line regression and 4-parameter curve fitting, with constant high and low inflection points. Then register one or more, with model name, parameters, and comments.
experiment type: titration
From each daughter plate, 3 to 4 assay plates at different concentrations are made. An activity value is calculated for each well, as well as the activity changes as a function of concentration.
experiment type: titration and dose response across plates
A single 96 well plate is filled with 48 samples in duplicate. The plate is then copied across 8 other plates at different concentrations. The result from the 9 plates is used to calculate a dose response curve and IC50.
experiment type: no controls on data plates
All controls (high, low, reference, dose-response curve) are on one or more reference plates, interspersed throughout the runset. Calculate a 'curve' for the standards on the reference plates, by plate sequence or time. Could use controls only on nearest reference plate.
experiment type: whole plant experiment
Growth of different plant species at time intervals, with qualitative and quantitative (Scores) results. At the end of the experiment, a report of the changes over time. A ''score' is based on observing the well and is a coded value that means something like 'severe yellowing of stem' or "intense chlorosis of stem" with more than one score per well.
experiment type: colormetric assay
Inhibition makes well white, but experiment failure makes "milky white". A scientist can see the difference, but the automated reader can be fooled. so scientist marks specific wells as bogus BEFORE the results are read into the data system.
experiment type: kinetics
Each well is read multiple times over time and the calculated value is based on the multiple raw values. All raw data is saved or only the final derived value. Plot of the timed values.
experiment type: Ki values
Dose response experiment, with a ligand of known activity value and concentration recorded. The IC50, and further calculations based on IC50, ligand activity, and ligand concentration are saved for each sample.
experiment type: pooling and replicates
Pooled plates have replicated mixtures. Same as HTS and REP, but with a reference to mixture in Inventory.
experiment type: non-plate based experiments
Row of tubes, lawn format, and so on.
variable group
A candidate variable group is selected or built. The group should take account of the dimension variables to be used for the RFM upload and for the layout. The group should take account of the layout actual and placeholder values. The group should have clauclations from raw data and places to mark data invalid or promotable. The group might have a Review check.
layout
A candidate layout for the Well table is developed. The layout should have an actual concentration, actual well types for High/Low/Data/Reference wells, and placeholders for the sample IDs. The dimension, calculation, and set variables should work with the layout.
calculations
Candidate calculations are selected or made for the calculation variables of the variable group. The calculations need to follow the default or nondefault rules for calcs, especially for parent-child relations, performance, and using ASSOC, MATCHALL, and CONDITION= correctly.
reader file and format
An actual or realistic reader file is available from such an experiment, and the reader file sections are made and tested, and the sections assigned to variables of the variable group. Ordinals are assigned to Row and Column variables, along with dimensions that match the variable group and layout.
protocols and templates
Protocol assays or attributes might be added to the protocol. (Sections or templates might be built for the protocol display.) A protocol is selected or made, which contains the variable group, layout(s), and RFM formats, plus any required fields.
dictionaries and terms
Dictionary terms and dictionaries might be added for use in the protocol.
result tables
Result tables are selected or made, together with the result maps from the variable group to the result table(s).
experiments
The completed protocol is used to start an experiment, the layout and the RFM format are added, then the reader file(s) are selected. Any placeholders in the layout must be filled in. (Assembler). The experiment is calculated and stored.
analysis
The experiment is analyzed to determine if any data is invalid or questionable, and a recalculation and store occurs. A rule might be used for automatic checking for bad controls, dropped plates, and so on. The analysis might include a mod to a calc formula, data, or a change of model for a curve.
decision
The experiment is analyzed to determine if any samples are worthy of further experimentation. Such samples are marked for further testing. A score might be assigned based on rules.
review and/or release
A review is made (typically by a higher authority) of the results. That such a review has been made is noted somewhere. Perhaps the data is allowed to be used or seen by other workgroups, or is sent to corporate database.
browsing
Other persons at a company want to see a summary of the validated results, in a set format for all researchers, to avoid duplication and error.
Blood drug amount {bioavailability} relates to dose.
Brain-compartment drug concentration to blood-compartment drug concentration makes ratios {Blood-Brain Barrier penetration}.
Drug diffusion calculations {diffusivity} can measure drug-diffusion ease.
Distribution and elimination can combine {disposition, drug}.
Drugs have different concentrations in various body tissues {distribution, drug}.
Excretion {elimination, drug} uses urine and feces.
Ingested drugs affect intestinal-wall cells {enterocyte}.
Bile goes back to GI tract for recycling {enterohepatic cycling} (EHC).
Liver removes drugs from blood {intrinsic clearance} (CL).
Compounds above 500 to 700 cannot diffuse across lipid membrane {molecular weight theory}.
Percentage of orally administered drug in general blood circulation, or in urinary excretion, compares to intravenous administration {absolute oral bioavailability} {oral bioavailability}.
A vein {portal vein} carries blood to liver from GI tract.
Active or passive transport carries drug from intestine to portal vein {absorption, drug}.
Compounds absorbed from intestine {human intestinal absorption} (HIA) go to portal vein.
Intestines have contents travel rate {motility}.
Acidic or neutral drugs can diffuse across GI-tract lipid membrane, but basic drugs cannot diffuse {pH partition theory}.
Drug goes from intestine to portal vein {predicted fraction of human absorption} (Fa). Fraction is in percent.
Compounds can have good solubility in lipids {lipophilicity}.
Values {Fujita-Hansch pi value} can relate to lipophilicity.
Octanol/water partition coefficient logarithms {log P} can measure lipophilicity.
Hydrophobicity measures {molecular lipophilicity potential} (MLP) can calculate lipophilicity surface.
Lipophilic compounds can diffuse across lipid membrane {octanol-buffer partition coefficient theory}.
On brain-capillary endothelial-cell insides, proteins {P-glycoprotein} can prevent high-lipophilicity drugs from crossing BBB.
Drugs must get to sites {transport, drug} {drug transport}.
Diffusion carries molecules across membranes {passive transport}.
Drug breakdown by oxidation {drug metabolism} is mainly in liver.
Compounds can have an added group {adduct}.
Drug can inhibit or induce another drug {drug-drug interaction}.
Proteins {flavoprotein} can bind FAD or FMN.
Molecules {glutathione} (GSH) can participate in phase II conjugations.
Phase I oxidations, Phase II conjugations, and transport into bile reduce drug in hepatic blood {hepatic first-pass elimination} (HFPE).
Iron compounds {iron-oxene} {iron-oxenoid} can contain free oxygen atoms.
Drug metabolism makes products {metabolite}.
Nitrosoalkanes irreversibly bind to reduced heme intermediates of CYP450 enzymes {metabolite intermediate complexation}.
Compounds or forces can mutate genes {mutagenicity}.
Metabolism percentage {regioselectivity} categorizes sites as major, minor, or unobservable. Rate constant differences among sites cause metabolic-site regioselectivity.
Drugs can affect targets {selectivity, drug} and other sites.
Substrates {agonist} can bind to receptors and cause biologic response.
Substrates {antagonist, chemistry} can bind to receptor but cause no biologic response.
Hydrogen atoms can bind to carbon atoms {acetylation}.
Amino acids can bind to carboxylic-acid groups {amino acid conjugation}, on anti-inflammatory, hypolipidaemic, diuretic, and analgesic drugs.
Enzymes can change drugs to make them toxic {bioactivation}.
Drug metabolism has oxidations and reductions {biotransformation}.
Two charges can exchange {charge-transfer coupling} in reactions.
Molecules can attach small molecule {conjugation, molecule}.
Processes can make rings {cyclization}.
Glucuronic acid allows glucuronide formation {glucuronic acid conjugation}.
Molecules can conjugate with glutathione {glutathione conjugation} to form mercapturic acid.
Atoms {hydrogen bond acceptor} (HBA) can add hydrogen atom.
Atoms {hydrogen bond donor} (HBD) can release hydrogen atom.
Hydrogen atoms can abstract {hydrogen transfer}.
Hydrogen atoms can bind to oxygen atom {hydroxylation}.
Enzymes can change conformation to allow substrate binding {induced fit}.
Drugs can form complexes with receptors and then cause chemical or conformational changes {intrinsic activity, drug}.
Drug metabolism has oxidation or reduction {Phase I enzyme reaction}.
Drug metabolism has conjugation with small molecules {Phase II enzyme reaction}.
Hydrogen atoms removed from molecules {proton abstraction} can make water.
After ATP activates sulfate, sulfotransferase makes sulfate esters {sulfate conjugation}.
nucleophosphate energy compound {guanidine diphosphate} (GDP).
Energy molecules {uridine diphosphate} (UDP) can participate in phase II reactions.
Enzymes {adenylate cyclase} {adenylcyclase} can alter cAMP.
Enzymes {carboxylesterase} can catalyze phase I reactions.
Enzymes {cytochrome P-450} catalyze phase I reactions 3A4, 2D6, 2C9, 1A2, and 2E1.
Enzymes {epoxide hydratase} {epoxide hydrolase} can oxidize olefins and aromatics to make epoxide or oxirane metabolites. It can produce carcinogens.
Enzymes {glucuronyl-transferase} can catalyze phase II reactions, adding glucuronide to drugs.
Enzymes {glutathione-S-transferase}, in liver-cell cytoplasm, can catalyze phase II reactions to conjugate compounds to glutathione.
Enzymes {microsomal flavoprotein mono-oxygenase} can oxidize nitrogen or sulfur organics.
Enzymes {microsomal hydroxylase} can catabolize many compounds, mostly by oxidation, in endoplasmic reticulum.
Enzymes {mixed-function oxidase} (MFO) can catabolize many compounds, mostly by oxidation, in endoplasmic reticulum.
Enzymes {phospholipase A2} can catabolize lipids.
Enzymes {phospholipase C} can catabolize lipids.
Enzymes {protein kinase} can catabolize proteins.
Enzymes {uridine diphosphoglucose transferase} {uridine-diphosphate-glucuronosyl-transferase} (UDP-GT) (UGT) can catalyze phase II reactions, adding glucuronide to drugs.
Chemicals can inhibit drugs {drug inhibition}. Inhibitor has binding constant.
Inhibitor can bind to non-active site {allosteric non-competitive inhibition}.
Drugs {entry inhibitor} can prevent viruses from entering cells.
Drugs {integrase inhibitor} can prevent virus DNA from inserting into host DNA.
Drugs {maturation inhibitor} can block gag-protein protease receptor, so gag protein is not split, and HIV virus coat is not made. PA-457 comes from betulinic acid from Taiwan herb, plane trees, and birch trees.
Metabolized compounds can bind to enzymes {mechanism-based inhibition}.
Drugs {protease inhibitor} can inhibit protease enzymes.
Most-reactive electron {highest occupied molecular orbital} (HOMO) can be in electron-rich nucleophilic molecules.
Most-reactive electron {lowest unoccupied molecular orbital} (LUMO) can be in electron-poor electrophilic molecules.
Total metabolism has rate {absolute metabolism rate}.
Reaction rate typically depends on concentration and temperature {enzyme kinetics}.
Metabolism rate at site has estimated ease {lability}.
Enzymes have binding constants {Michaelis-Menten constant} (Km).
Sites {labile site} can have high metabolism rate and low activation energy.
Sites {moderate site} can have intermediate metabolism rate and activation energy.
Sites {stable site} can have low metabolism rate and high activation energy.
Active compounds have small clusters {asymmetric set} in compound space.
Automated assays {biological screening} can identify promising compounds from compound libraries.
Active compounds have small clusters {embedded set} in compound space.
Sample collections {inventory, sample} {sample inventory} can be ready for testing, stored in plate wells.
From many compounds, processes {lead finding} {lead generation} {lead selection} can identify compounds that have significant chemical activity.
Processes {lead optimization} can efficiently identify structure-activity relationships for generated leads.
Sample points {outlier} can be far from expected values.
Samples can go to further testing {promotion}.
Drug-receptor geometry {drug structure} is a physico-chemical property and can be quantitative.
structure-activity relationships
Drugs have structure-activity relationships (SAR), which can be quantitative (QSAR). Drugs have property-activity relationships.
activity
Drug activity equals physicochemical-variable function. Drug activity relates to concentration, partition coefficient, or product formation. Stages have probabilities. Drug activity is proportional to concentration product, complexing probability, changing probability, and partitioning probability.
activity: complex formation
Drugs form complexes with receptors {intrinsic activity, complex}. Drugs {chemotherapeutic drug} can cause chemical reactions or conformational changes. Drugs {pharmacodynamic drug, complexes} can make complexes but do not change conformation or cause reactions.
Complex-formation probability is formation-reaction equilibrium constant. Equilibrium constant depends on both equilibrium type and substituent electronic influence on reaction center. log(K) = k1 * sigma + k2 {linear free energy equation, structure} (LFE). log(1 / concentration) = k1 * sigma + k2. Electronic influences are universal and have tables of values. Equilibrium type results from multiple regression analysis of simultaneous equations.
activity: partitioning
If hydrophobicity affects drug structure, partition coefficient affects activity. log(K) = k3 * pi + k1 * sigma + k2 and log(1 / concentration) = k3 * pi + k1 * sigma + k2. Partition coefficients are universal and have tables of values.
activity: transport
Drugs have to get to target site. Drug transport involves diffusion, active transport, adsorption, binding to serum proteins, or membrane interactions. Mechanisms that oppose drug transport are excretion, metabolism, and localization in fat. Excretion is faster for hydrophilic. Metabolism is faster for hydrophobic. Localization in fat is faster for hydrophobic. Drug transport affects drug activity. log(K) = k3 * pi + k1 * sigma + k2 - k4 * pi^2. log(1 / concentration) = k3 * pi + k1 * sigma + k2 - k4 * pi^2. Drug transport factors are universal and have tables of values.
structure
Molecule structure depends on atom types, atom numbers, chemical bonds, spatial relations, and atom locations. Features are either present or absent, with no interactions.
structure: molecular connectivity indices
Kier and Hall used features such as electrotopologic state index, valence, molecular shape and flexibility {kappa index, structure}, branching, unsaturation, cyclization, and heteroatom position. They found molecular connectivity indices, based on Randic's branching index, calculated from hydrogen-suppressed chemical graph or skeleton structure. For example, atoms can have number of sigma electrons contributed {simple delta index, structure} or number of valence electrons {valence delta}.
structure: molecular orbital
Quantum-mechanical structure description uses molecular orbital (MO) theory. Molecular orbitals depend on electron location and energy. Total conformation energy gives probability. MO typically ignores solvents.
Highest occupied molecular orbital gives the most-reactive electron for electron-rich nucleophilic molecules. Lowest unoccupied molecular orbital gives the most-reactive electron for electron-poor electrophilic molecules.
MO can test reaction paths and find thermodynamic information, by checking energies in different configurations.
Molecular orbitals can be linear combinations of atomic orbitals (LCAO). Atomic-orbital contribution probability is linear-coefficient squared, and point charge is probability sum.
structure: interactions
Comparative Molecular Field Analysis (CoMFA) uses partial least-squares to analyze grid around site atom and find grid-point hydrophobic, electrostatic, and steric interactions.
structure: ab initio
Ab initio analysis uses electron locations to find charges, electrostatic potentials, dipole moments, ionization energies, electron affinity, and activation energies. Semiempiric analysis uses only valence electrons and parameterizes core electrons. Modified neglect of differential overlap (MNDO) ignores overlaps. Perturbative configuration interaction using localized orbitals (PCILO) uses perturbations. Varying bond angles, bond lengths, and torsion angles can find minimum energy and preferred conformation.
structure: axial-equatorial configuration
Non-conjugated-ring substituent positions can be in ring plane {equatorial configuration} or perpendicular {axial configuration}.
structure: branching
Carbon chain can have fork {branching}.
structure: ionization degree
Molecule can have charge {degree of ionization} {ionization degree}.
structure: dipole moment
Opposite charges can separate by distance.
structure: electrostatic potential
Electric potential energy comes from electric field.
structure: molecular similarity
Molecules can be similar in 3D atomic configuration, atom pairs, chemical graphs, electron densities, field potentials, molecular fragments, molecular properties, molecular surfaces, steric volumes, or topological/information theory indexes.
structure: orientation
Molecule spatial alignment is at receptor site.
structure: radical
Atoms can have one electron in outer orbital.
structure: singlet or triplet state
Orbital state can have paired electrons {singlet state}. Orbital state can have unpaired electrons {triplet state}.
Connection tables number non-hydrogen atoms, name atomic elements, name atom number to which they connect, and name atom types {Chemical Abstracts Service} (CAS).
Molecules can be vectors, including chemical activity, in abstract space {Chemical Descriptor Space} (CDS).
Base compounds {building block} can attach one to four small molecules {combinatorial chemistry} to add functional groups and make compound libraries with molecular weights 300 to 750.
Tables {connection table} can describe three-dimensional structures.
Matrices {connectivity matrix} can graph molecular connections.
Electrostatic fields make potentials {Coulombic potential}.
Polar solute can cross lipid membrane if hydrogen bonds to water break {desolvation}. Polar solute with fewer hydrogen bonds to water and lower hydrogen-bonding potentials can diffuse more easily.
Indexes {electrotopologic state index} can depend on topology structures.
Molecular markers {encoding tag} can track combinatorial-chemistry molecules.
Molecule atoms {hetero} can be not carbon C or hydrogen H. Hetero can refer to solvent, non-solvent, water, ion, or ligand atoms.
Compounds {heterocyclic compound} can have rings with atoms other than carbon.
Molecular regions can repel water {hydrophobicity}.
Cytochrome P450 has types {isoform}.
Combinatorial chemistry makes compound permutations {library of compounds}.
Tables {nearest neighbor table} can rank different compounds by similarity.
Superimposed molecules show constants across diverse molecules and so identify sites and reactions {pharmacophore}.
Molecules have atomic properties, functional groups, and molecular properties {similarity matrix}.
Oxygen can have positive charge {superoxide anion}.
Possible compound permutations can be in database {virtual compound library}.
Strings {Wiswesser line notation} (WLN) can uniquely describe three-dimensional structure.
X-ray crystallography patterns {X-ray structure} can indicate atom positions.
Methods {validation methods} can check structure-activity relationship correlations, predictions, and designs.
Validation methods {bootstrapping validation method} can use only internal data.
Methods {cross-validated correlation coefficient} can validate and predict data.
For all data subsets, algorithms {cross-validation} (CV) can remove one data subset and calculate remainder.
Other data can pair with model to predict activity {external validation}.
Validation methods {Fisher F-test} can use F test.
Validation methods {fitness function} (FIT) can measure fit.
cross-validation method {jackknife validation method, drug}.
Methods {lack-of-fit} (LOF) can measure fit.
cross-validation method {leave-groups-out, drug} (LGO).
cross-validation method {leave-one-out, drug} (LOO).
Methods {predictive residual sum of squares, drug} (PRESS) can measure fit.
cross-validation method {scrambling dependent Y-values, drug}.
Methods {standard deviation method, drug} (sPRESS) can measure fit.
Methods {standard error of predictions, drug} (SDEP) can measure fit.
Methods {standard error of regression, drug} can measure fit.
Chemistry {analytical chemistry} can have analyses. Chemistry techniques are chromatography, conductivity, diffraction, electrolysis, gas pressure, gravimetry, potentiometry, radioactivity, reflectance, resonance, spectrophotometry, spectroscopy, titrimetry, and volumetry.
error types
Error types are measured-value and true-value difference {absolute error}, absolute-error average {mean error}, measured value as percent of true value {relative error, analysis}, and absolute error divided by true value {percent error}. Bad or uncalibrated instruments, careless or suspect operations, incomplete reactions, co-reactions, and material impurities cause error {determinate error}. Errors {indeterminate error} can be random.
Burning {ashing}| requires 400 C to 700 C in furnace, followed by dissolving sample in hydrochloric acid. Lead, zinc, cobalt, antimony, chromium, molybdenum, strontium, and iron evaporate at 500 C. Low-temperature ashing uses microwaves to make oxygen radicals and oxidizes sample at less than 100 C. Oxygen combustion can find carbon and hydrogen amounts. Ascarite absorbs carbon dioxide. Dehydrite absorbs water.
Computer analysis of measurements from many points can display 3D images {Computerized Tomography} (CT) (CAT) from MRI, x-rays, and PET.
Boiling and then condensing liquid {distillation}| can remove impurities.
Frequency spectrum {hyperfine structure, molecule} indicates molecular-orbital type.
In Kjeldahl digestion, nitrogen {nitrogen analysis} makes ammonium sulfate, using potassium sulfate, sulfuric acid, and mercury, copper, or selenium catalyst. Adding sodium hydroxide ends reaction. Distilling into hydrochloric acid finishes analysis.
Experimenters can study surfaces {surface analysis} by low-energy electron diffraction, reflected-light polarization {ellipsometry}, high-curvature electron emission {field-emission microscopy}, edge helium-atom ionization {field-ionization microscopy}, and crystal-hole atom ionization with mass spectroscopy {atom-probe field-ionization microscopy}.
Analysis {chemical analysis} can be qualitative or quantitative. Analysis method depends on speed, cost, instrument availability, and required results.
Analysis {ultramicroanalysis} can be on very small samples, less than 1 milligram.
Analysis {microanalysis} can be on small samples, 1 to 10 milligram or less than 50 microliter.
Analysis {semimicro analysis} can be on medium samples, 10 milligram to 100 milligram or 50 microliter to 100 microliter.
Analysis {macroanalysis} can be on large samples, greater than 100 milligram or 100 microliter.
Analysis {qualitative analysis}| can be about which atoms and molecules are reactants and products, how fast reactions are, or how easy reactions are.
Analysis {quantitative analysis}| can measure reactant and product amounts.
Quantitative analysis tests candidate compounds {sample, chemistry}. Time, randomness, proper conditions, amount needed, and number needed affect sampling. Storing and preserving samples depends on temperature, pressure, dust, gas, evaporation, leakage, light, preservatives, and container material.
Sample parts {constituent, sample} {sample constituent} can be more than 1% {major constituent}, 0.1% to 1% {minor constituent}, or less than 0.1% {trace constituent}.
Samples {sample preparation} can have ashing, centrifugation, chromatography, crystallization, dissolution, distillation, drying, oxidation, precipitation, and reduction.
Apparatus {laboratory equipment} includes glassware and metalware. Apron. Balance. Beaker. Bunsen burner. Cover slip. Crucible. Dissecting needle. Dropper. Dropper bottle. Flask. Forceps. Funnel. Goggles. Graduated cylinder. Lens paper. Petri dish. Pipet or pipette. Razor blade. Ring. Ring stand. Scalpel. Scissors. Slide. Stirring rod. Test tube. Test tube holder. Test tube rack. Thermometer. Thistle tube. Tongs. Watch glass. Wire gauze.
Laboratory heating devices {Bunsen burner}| can provide hot steady smokeless flame. Bunsen burners have short, vertical metal tube, connected to gas source. Tube has perforations at bottom to admit air. Michael Faraday designed Bunsen burner, but the German chemist Robert Wilhelm Bunsen modified it [1855].
Containers {container} can be glass or ceramic. Borosilicate glass, called Pyrex or Kimax, has yellow tinge, melts at high temperature, and resists rapid temperature change. Soft glass has green tinge, and alkali attacks it. Porcelain is inert. Teflon is inert and has high melting point.
Recorders, transducers, alarms, specialized quality-control devices, and test instruments {controller device} can monitor and control chemical processes.
Containers {crucible}| used for heating to high temperature are Gooch, sintered, and porcelain filter.
Machines {dessicator}| {vacuum dessicator} can be for drying.
Paper {filter paper}| can be ashless for burning.
Ovens {furnace, chemistry}| can be for ashing and ignition, up to 1200 C.
Technical grade or commercial grade is lowest grade {grade, chemical} {chemical grade}. U.S.P. is safe for humans. Reagent grade or A.C.S. is high quality. Primary standard is highest quality.
Covered areas {hood}| can conduct fumes to outside building.
Flasks {Kjeldahl flask} can be for digestion and dissolving, with no splattering or bumping.
Furnaces {oven, chemistry} can be for drying.
Bottles {wash bottle} can have spouts for rinsing.
High-speed spinning {centrifugation}| can separate substances by density or particle size. Solid pellet can form at tube end. Sucrose solutions or cesium chloride have a density gradient.
mass
Centrifugation can find molecule mass. Terminal-velocity sedimentation rate through medium depends directly on particle molecular weight. Machine reaches sedimentation rate when molecule cross-sectional size and viscosity balance centrifugal force. Sedimentation rate also depends on temperature and solvent.
polymer
Polymer sedimentation rate depends on volume divided by acceleration. In density gradient, centrifugal force balances polymer diffusion at equilibrium density.
Terminal velocity {sedimentation rate} through medium depends directly on particle molecular weight. Machine reaches sedimentation rate when molecule cross-sectional size and viscosity balance centrifugal force. Sedimentation rate also depends on temperature and solvent. Polymer sedimentation rate depends on volume divided by acceleration.
Two phases in contact, one moving and one stationary, dissolve solute with different solubilities or adsorb solute at different rates {chromatography}|.
purposes
Chromatography is non-destructive, separates mixtures into groups, and can be quantitative.
phases
Stationary phase is starch or diatomaceous earth on columns or plates {chromatograph}. Solid substrate saturates with solvent. Moving phase is solvent at constant pH and salt concentration.
process
Solute in solution starts at saturated-substrate edge. Solvent flows through saturated substrate. Molecules transfer back and forth between mobile and stationary phases.
Depending on relative solubility, molecules spend different times in phases. Molecules that are more soluble in moving phase than in stationary phase move faster. Molecule polarity, size, shape, and charge in solution affect movement rate. Smaller compounds elute faster.
diffusion
Molecules diffuse, so peaks can be wide if flow rate is slow and time is long.
types
Gas or liquid mixtures can separate using gas chromatography, liquid chromatography, supercritical fluid chromatography, or capillary electrophoresis.
At constant pH and salt concentration, liquid or gas solvent {moving phase} flows through stationary phase.
Solvents {eluant} can flow past solid and carry molecules to analyze.
Column efficiency {height equivalent of theoretical plate} (HETP) is column length divided by theoretical plate number, which depends on retention volume divided by baseline peak width. High volume means good resolution, so small HETP is good. HETP depends on sideways diffusion, longitudinal diffusion {band spread}, mass transfer from phase to phase, and flow rate, which depend on viscosity. Optimum flow rate keeps diffusion minimal. Equations {von Deemster equation} can relate these quantities.
Starch or diatomaceous earth {stationary phase} on column or plate chromatographs has solvent at constant pH and salt concentration.
Fluid chromatography {supercritical fluid chromatography} {supercritical fluid extraction} can use carbon dioxide or water above critical point, to analyze labile and low-volatility compounds.
Plots {total ion chromatogram} (TIC) can show retention time versus ion amount.
Molecules in solution, at constant pH and salt concentration, can bind to substrate, coenzyme, or inhibitor attached to agarose resin, as solution flows past resin {affinity chromatography}. After solution passes through resin, solvent at different pH and salt concentration passes through, to remove molecules from resin.
Chromatography {column chromatography} can use column with stationary solid adsorbent, such as cellulose, and moving liquid solvent.
Chromatography {gas-liquid chromatography} (GLC) can use stationary liquid phase and moving gas phase.
purpose
GLC can separate high-volatility substances, such as molecules with carbon, nitrogen, and hydrogen atoms, and determine amounts, with no decomposition. GLC needs only small sample.
process: column
Columns are polyester, silicone polymer, or diatomaceous earth, with varying mesh sizes. Mesh size determines surface area. Columns are 1 to 3 meters long.
process: solvent
Solvent saturates column material. Inert, thermally stable liquids with low vapor pressure can be solvents. Typical solvents are naphthalene or anthracene. Squalene is for non-polar molecules. Amides are for polar molecules.
process: solution
Solution starts at column end.
process: gas
Inert helium or nitrogen gas, at high pressure, is mobile phase.
process: flow
Volatile molecules in solution can separate between gas and liquid phases. More-volatile molecules spend more time in moving gas phase and move faster. High flow-rate minimizes diffusion. Heating makes molecules more volatile. Temperature is 25 C to 150 C. Lower temperature gives better resolution.
volume
Gas volumes {retention volume} elute samples.
time
Columns take time {retention time, column} to elute samples. Retention time depends on number of carbons. Bigger molecules are slower. First sample takes minimum time {dead time}.
detection
To detect sample, use Wheatstone bridge to measure conduction {thermal conductivity} (TCD).
Ionize in flame {flame ionization} (FID), if sample is solid or liquid organic but not carbonyl.
Measure decrease in electron flow {electron capture} (ECD) for halogens, oxygen, nitrogen, and sulfur compounds but not for hydrocarbons, amines, or ketones.
Chromatography {gas-solid chromatography} (GSC) can separate and determine amount, using alumina, silica, charcoal, zeolite, or polymer beads like Porapak as solid.
Liquid-liquid chromatography {high-pressure liquid chromatography} (HPLC) can use high pressure. The 100-atmosphere pressure requires special packing materials, such as Zipax or Coracil bonded beads, with porous-material coatings. Beads can have different sizes. Solvent, pH, ionic strength, and temperature affect HPLC.
purposes
HPLC separates molecules with low vapor pressure and high molecular mass or easily decomposed materials, such as nucleic acids, amino acids, bile acids, drugs, pesticides, herbicides, surfactants, and anti-oxidants. It is fast, is sensitive, and has high resolution.
Molecules or ions in solution can exchange with molecules or ions bound to polymer resin, at constant pH and salt concentration, as solution flows past resin {ion-exchange chromatography}. After solution passes through resin, solvent at different pH and salt concentration, or different solvent, passes through resin to remove bound molecules or ions.
ion types
Polystyrene or CM-cellulose sulfonated groups bind hydrogen ions or sodium ions {cation exchange}. DEAE-cellulose amine groups bind anions {anion exchange}. Anion-exchange resins, such as DEAE Sephadex, can have surface depressions for size separation.
clay
Besides polymer resins, ion-exchange chromatography can use clays, as in water softening, or sodium aluminum silicate zeolites.
chemical activity
Debye-Hückel theory relates potential-energy and chemical-potential lowering to ion solubility. Low chemical potential means solution is more random and more soluble. Ions in solution have more potential energy than uncharged molecules. Ion chemical potential depends on molecule concentration, size, and charge. Other ions go faster or slower as they pass charge. Opposite-charge counterions surround ions, making ions closer together than in random arrangements and lowering potential energy and chemical potential. Counterions shield ions and reduce effective charge, lowering potential energy and chemical potential.
chemical activity: solvent polarization
Solvent has dielectric constant and polarization. Polarization decreases attraction between ions, lowering potential energy and chemical potential. Water lowers chemical potential most, because it has highest dielectric constant.
chemical activity: factors
Lower concentration, higher temperature, higher solvent dielectric constant, lower ion charge, and larger ion size cause lower chemical potential, because potential energy is lower.
chemical activity: field
External electric field increases chemical potential. Negative voltage decreases positive-ion chemical potential, because ions have less-directed motion. Low chemical potential makes low current. Electric field can come from two different ion concentrations or two different phases. At equilibrium, potentials are equal in all phases.
Chromatography {liquid-solid chromatography} {adsorption chromatography} can separate non-polar molecules with different steric or spatial configurations. Adsorption chromatography can separate large amounts. Solid phase is silica, calcium carbonate, charcoal, or alumina, which all adsorb liquid solvents well. Eluant solvent flows past solid, carrying molecules to analyze. Bigger molecules and more polar molecules adsorb better and move slower. Second eluant can elute high-polarity molecules that stay in solid.
Liquid-liquid chromatography {paper chromatography} can separate barbiturates, antibiotics, amino acids, hormones, indoles, and ions. Paper chromatography is cheap, fast, and sensitive. Paper is stationary phase and saturates with solvent. Paper draws mobile phase along by capillary action. Fluorescent dyes stain separated molecules. Ninhydrin stains amino acids.
Chromatography {liquid-liquid chromatography} {partition chromatography} can be for polar molecules. It has high resolution, uses small batches, is more reproducible, and uses lower concentration than adsorption chromatography. Stationary phase is deactivated silica gel, diatomaceous earth, or cellulose, which absorb water. Organic solvents, such as octanol, slightly soluble in water are mobile phase. Solute has relative concentrations in octanol and water. Polarity, hydrogen bonding, and molecule size affect partition. Concentration ratio {partition coefficient} determines mobility.
Solid-liquid chromatography {thin-layer chromatography} can separate amino acids, food colorings, drugs, sugars, dyes, insecticides, ions, and salts. It is cheap, fast, and sensitive. Stationary phase is silica or alumina layer on glass plate. Solvent typically is strong acid or base.
To precipitate salt {crystallization}|, reduce salt solubility. Slow precipitation makes larger crystals, because they can form and reform. Crystals have fewer impurities, because area is smaller. Maintaining low supersaturation, keeping pH low, holding temperature high, and using the most-dilute precipitating agents promotes slow crystallization. After precipitation, add excess agent, lower temperature, and raise pH to ensure complete precipitation. Precipitated crystals adsorb ions. Timed washing can remove impurities. Water washing can dissolve crystal or make colloid. Washing with volatile reagent or with solution with common ion does not dissolve crystal or make colloid.
Other salts can also precipitate {coprecipitation}, trapping or occluding solvent-molecule impurities. Using optimum conditions for reducing solubility minimizes trapped and occluded molecules. Re-precipitation can remove more impurities.
To prevent colloid formation, solutions do not move {Ostwald ripening} while crystals start to form.
X-rays {x-ray crystallography}| {x-ray diffraction} can find atom positions and electron densities. X-rays have wavelength 0.1 nanometers, the same as atom spacing in crystals. Crystal planes reflect x-rays. Large ions polarize easily. Small ions have large field. Cations are less polarizable than anions, because positive charge holds electrons better. Transition metals have bigger fields.
process
Powder rotates for instrument to check all interplanar distances and make one line for each plane, on film. Alternatively, one crystal rotates for instrument to make differing intensity-point patterns, on film.
Interference pattern can calculate spacing between crystal planes: path-length difference = 2 * d * sin(A) {Bragg condition}, where d is distance between planes, and A is angle.
Compounds can dissolve {dissolution, compound}| in fluids. Solid or liquid solute in liquid solvent tends to break into molecules through collisions with surrounding solvent molecules. Solubility depends on melting point and fusion enthalpy. If both are low, solute is easy to disrupt and dissolve, and solubility is high. Solubility is low if chemical potential is high, because solute order is high.
flux
Inorganic compounds can fuse with acid flux, such as hydrochloric acid, nitric acid, or dry perchloric acid. Inorganic compounds can fuse with base flux, such as sodium carbonate. Ratio is 1:10 to 1:20. Flux and compound melt in crucible for 30 minutes until clear, and then cool and dissolve in dilute acid or water.
digestion
Organic materials can dissolve by oxidizing in boiling acid {wet digestion}: nitric and sulfuric acids, or nitric, perchloric, and sulfuric acids.
Adding solvent that does not dissolve well to mixture, and letting mixture and solvent separate, puts solute in new solvent {extraction}|. Extraction solvent can be ammonium chloride, acetic acid, or other salt. In two solvents, equilibrium solute-concentration ratio equals solute-solubility ratio {distribution coefficient}.
Techniques {conductivity measurement} {conductance measurement} can measure total electrolytes in solution.
purposes
Conductivity can detect bath and electrolyte acidity, scrubbing-tank basicity, and water, soil, milk, biological tissue, and ion-exchange-chromatography ions. Conductivity is fast, accurate, and non-destructive.
AC current
AC current prevents decomposition. Low frequency is for high resistance, and high frequency is for low resistance, to keep capacitance low.
ions
Conductivity in solutions depends on solute-ion transport. If ion charge is low, velocity is high, and conductivity is high. Proton goes from water molecule to water molecule directly and so is fast. Big ions have small hydration and small effective size. Ion hydration and ionic interactions affect conductivity.
ions: electrolyte
Strong electrolytes slightly reduce conductivity as concentration increases, because there are more collisions. Weak electrolytes have low molar conductivity, because they do not dissociate. Weak electrolyte causes more variation.
standard
Potassium chloride is standard.
solvent
Solvent-ion collisions affect solute-ion velocity through solvent.
solvent: viscosity
Higher viscosity makes more-random flow and resists conduction.
temperature
High temperature increases conductance.
Techniques {coulometry} can measure charge that has flowed, by weighing metal or gas produced by electrolysis. 1 Faraday = 96487 Coulomb = 1 mole of electrons.
Instruments {coulometer} can have silver anode and platinum cathode in silver perchlorate solution, in series with cell to test. Deposited silver weight indicates total charge that flowed.
Two platinum electrodes can be in iodine and potassium iodide solution. Titration with reducing agent finds iodide-concentration change.
Two platinum electrodes in potassium sulfate solution can produce hydrogen and oxygen gas.
Opposite-charge ions {counterion} surround ions. Opposite charges attract and make ions closer together than in random arrangements, lowering potential energy and chemical potential. Counterions shield ions and reduce effective charge, lowering potential energy and chemical potential.
Potential-energy and chemical-potential lowering depend on ion solubility {Debye-Hückel theory}.
Electric current can reduce metal ion to make metal, separating metal from solution or mixture, for weighing {electrogravimetry}.
Voltage can separate charged molecules in solution {electrophoresis}|. Electrophoresis can use pH gradient.
purposes
Electrophoresis can separate nucleic acids and peptides by size and charge.
process
Solution at constant, buffered pH is in paper or gel. Voltage applied across paper or gel moves charged molecules. The most-highly-charged molecules move most. Molecular size and shape also affect movement.
gel
Gel can be polyacrylamide {polyacrylamide gel electrophoresis} (PAGE). Gel can be agarose sugar, which can have different concentrations to separate different size ranges. Thinner gels allow more resistance and so more voltage compared to current.
detergent
During electrophoresis {SDS-gel electrophoresis}, detergent can coat molecules. Molecules then have same shape and charge, so only molecule size determines separation.
pH
During electrophoresis {zone electrophoresis} {moving boundary electrophoresis}, solution pH can change as solution moves. During electrophoresis {disc electrophoresis}, solution pH in gels can change over time in one direction. During electrophoresis {slab electrophoresis}, solution pH in gels can change over time in two directions.
Iodine in potassium iodide solution is oxidizing agent {iodimetry}. I3- [3 is subscript and - is superscript] ion is at pH 6 to 8. Starch is indicator.
Iodide ion is reducing agent {iodometry}. Sodium thiosulfate titrates iodine. Starch is indicator.
Ion solutions have charge concentration {ionic strength} depending on ion charge and concentration: I = 0.5 * z1^2 * c1 + 0.5 * z2^2 * c2, where z = charge and c = concentration.
pH gradient across solution can move molecules to minimum-charge point {isoelectric point} {isoelectric focusing}.
Charge separation at electrode makes voltage {overvoltage} above standard potential.
Oxidation or reduction voltage change {oxidation-reduction titration} can indicate compound amount. Indicator oxidation increases voltage, by millivolts. Indicator reduction decreases voltage. Indicators and samples can change color.
types
Potassium permanganate is oxidizing agent, which standardizes with sodium oxalate or iron (II) sulfate. Potassium chromate is standard oxidizing agent. Cerium +4 ion in acid is standard oxidizing agent, with ferroin as indicator.
Thiosulfate is reducing agent, which oxygen in water does not oxidize and which standardizes with perchloric acid. Fe+2 ion titrates cerium, chromium, and vanadium ions, with ferroin as indicator. Tin (II) chloride reduces iron.
reactions
Carbon dioxide or acid removes sodium sulfate and sulfur dioxide reducing agents. Acid removes metals like zinc and lead. Phenol removes bromine and chlorine. Hydrazine boiling removes permanganate and peroxide.
Measuring galvanic-cell potential {potentiometry} can find ion concentration.
purposes
Potentiometry measures body-fluid, column-effluent, waste-water, pool, detergent, silver-thiocyanate solution, iodide, bromide, chloride, calcium, nitrate, copper, lead, sulfate, aluminum, phosphate, metal-plating cyanide wastes, bleach-chlorine, paper-bleach, water-pollution, and sewage ions. Titration by potentiometer is accurate.
Potentiometry is for redox reactions, precipitations, acid-base reactions, complexing, or indicators. pH meters and ion detectors use direct potentiometry or potential change followed by titration.
potentiometer
Potentiometers measure voltage at zero current, to eliminate internal resistance. Potentiometer has reference electrode and indicator electrode. Circuit has equal and opposite voltage.
Exact-voltage cells {Weston cell} can calibrate potentiometers.
At halfway to equilibrium, potential equals sample potential. At equivalence, potential is half sum of sample potential and titration ions, if valences are equal. Otherwise, it is weighted average. On graph, steepest slope is equivalence point.
potentiometer: reference electrode
Reference electrodes can change voltage by salt-bridge ion-flow-rate change, temperature change, pH change, electrical-resistance change, and mercury, potassium, or chloride sample contamination.
potentiometer: indicator electrode
Indicator electrodes are for redox reactions. Indicator electrodes must be rapid and exact. If both molecules are ions, electrodes are platinum. If ions are strong reducing agents, electrodes are gold. Strong reducing agents are chromium, titanium, or vanadium. If system uses metal and ion, and metal does not react in water, electrodes are gold. Silver, cadmium, mercury, and copper do not react in water. If system uses metal and low-solubility salt, electrodes are gold. Hydrogen electrode is for pH.
Voltage can determine solution metal concentration {voltametry}.
Techniques {polarography} can measure solution concentration, by diffusion-controlled oxidation or reduction at electrode surface. Voltage relates to metal-ion concentration.
purposes
Polarography measures transition metal ions, inorganic ions, water and blood oxygen levels, and ion resonance in organic compounds, aldehydes, acids, ketones, nitrogen compounds, and halides. Inorganic ions are sulfide, oxide, hydroxide, and chromate. Polarography is sensitive, with ion concentrations from 0.01 M to 0.000001 M.
process
A small electrode receives potential that depletes ions near it. With no stirring, electrode and solution have a concentration gradient. Polarized electrodes block ion flow, so nearby ion concentration is due only to ion diffusion from solution. Diffusion rate depends on concentration, if concentration gradient is constant. Potassium chloride minimizes electrostatic effects. Impurities and capacitances can cause other currents.
types
In electrodes {dropping mercury electrode} (DME), mercury can oxidize, removing oxygen gas from solution. Dropping mercury electrodes, rotating disk electrodes, or ring-disk electrodes remove surface layer.
Polarography methods {amperometry} can measure oxidation or reduction by titration, instead of directly.
Metals {electrode}| can contact solutions. Corrosion, electrolysis, electroplating, and batteries involve electrodes.
oxidation
At anode, ions enter solution, so anode is negative, and solution is positive. Oxidation is at anode surface, and reduction is at cathode surface. Opposite charges surround electrode charges, and solution ions solvate, with high attraction at surfaces. Charge gradient is higher for higher concentration and higher ion mobility. Higher temperature reduces attraction, by breaking up surface layer. Applied electric force reduces attraction.
current
Ion formation or discharge rate is current density, which is 0 at equilibrium. Ion far from electrode feels net force. At 10^-7 meters, ion sees widely distributed charges, as it enters ion layer around electrode and feels constant voltage. When ion reaches electrode surface, voltage changes rapidly to opposite sign. Finally, ion reaches electrode pure metal.
At high current, potential can be constant, such as at hydrogen electrode or calomel electrode. If high overvoltage causes high current density, diffusion can be too slow, and electrode can become polarized. Adding extra potential or moving electrodes reduces polarization. Solution friction causes slower cation flow than electron flow, causes ohmic resistance, and decreases current. Power generation maximizes if concentration polarization is just below limiting current.
Reference electrodes {calomel electrode} can use mercury and saturated mercury chloride. Potassium chloride reduces variation with temperature and can be salt bridge.
Electrodes {glass electrode} can pair with calomel electrodes or silver/silver chloride electrodes. Glass electrodes have silver and silver chloride in 0.1 M hydrochloric acid, in thin glass membrane. Temperature, acidity, and sodium contamination affect it. It requires storage in 0.1 M potassium chloride. It requires cleaning.
Reference electrodes {hydrogen electrode} can use platinum electrodes, with hydrogen gas at one atmosphere and hydrogen ion at one-molar concentration. Hydrogen electrodes can have platinum-surface changes and can vary hydrogen-gas pressure and hydrogen-ion concentration, so they are hard to control.
Silver and silver chloride reference electrode {silver electrode} has saturated silver chloride on silver surrounded by saturated potassium-chloride solution as salt bridge. It is stable at high temperature. It can be internal reference for glass electrode.
Membrane that allows smaller particles to pass but not larger ones can separate larger substances from smaller ones {filtration}|. Filtering {ultrafiltration} can use pressure and membranes with smaller pores.
Porous-material membranes allow small solute and solvent molecules to pass {dialysis}| but stop larger molecules, such as proteins, starches, and nucleic acids. For example, cellophane membranes allow molecules less than 1000 daltons to pass.
purpose
Dialysis dilutes impurities from solutions. Dialysis concentrates large-molecule solutions.
dilution
For example, on one membrane side is salt and large-molecule solution. On other side is water. Net ion flow enters water, because concentration is higher on salt side, so more ions reach membrane each second from concentrated side. Net water flow enters salt solution, because water concentration is higher on water side, so more water molecules reach membrane each second from water side.
concentration
On one membrane side is large-molecule solution. On other side is concentrated-salt solution. Net salt-ion flow enters large-molecule solution, because concentration is higher on salt side, so more ions reach membrane each second from salt side. Net water flow enters salt solution, because water concentration is higher on large-molecule side, so more water molecules reach membrane each second from large-molecule side.
Molecules can separate by size, using agarose, Sephadex, or Biogel beads {gel filtration}. Beads have surface depressions. Same-size or smaller-size molecules stay in depressions and slow, but larger molecules flow past and so exit faster.
Porous-material sheets {membrane, filter}| allow smaller solute and solvent molecules to pass through but stop larger molecules, such as proteins, starches, and nucleic acids.
Techniques {actinometry} can measure incident radiation using a thermopile.
For solution light absorbance, molecule and solvent extinction coefficient A times solution light-path length L times molecule concentration c equals logarithm of transmitted-light percent T {Beers law} {Beer-Lambert law}: A*L*c = log(T). Molecule and solvent extinction coefficient is molar absorptivity. Outer-shell electron transitions are at ultraviolet and visible wavelengths. People know substance extinction coefficients and molar absorptivities, which depend on outer-shell electron-transition energies and probabilities. If molar absorptivity is high, sensitivity is high. Method can also use integrated absorption coefficient or oscillator strength.
Reaction vibrations and rotations can make light {chemiluminescence}.
Molecule structures {chromophore} determine color. For example, retinal visual pigment molecules have chromophore group. Hydroxyl, amine, and halogen groups do not make UV or visible light, but they can affect nearby-chromophore intensity or wavelength. However, groups separated by two single bonds do not affect each other.
Techniques {densitometry} can use UV or visible light to measure absorbance. Absorbance is linear with concentration. Densitometry measures staining in gels.
Absorbed light can re-emit at lower frequency {fluorescence}|.
purpose
Re-emission can measure concentration. Fluorescent dyes can bind to molecules to trace them. Fluorescence is 100 times more accurate than UV-visible methods and is more sensitive. Fluorescence has no interference, because instrument can choose band.
cause
Molecules with rigid co-planar structures, like anthracene and naphthalene, have fluorescence. Electrons can jump to high orbital, fall back to lower excited orbital by short vibration-induced jumps, and then fall to lowest band by spontaneous emission, giving visible light. Lowest band can have vibrational levels. Fluorescence is fast.
compounds
Substances, such as amino acids tyrosine, phenylalanine, and tryptophan, can absorb ultraviolet light and emit visible light.
concentration
If concentration is less than 0.01 M, Beer's law applies.
factors
Solvent, pH, molecule interactions, and temperature affect fluorescence. Higher temperatures cause less intensity, because more jump types are possible. Nitrates quench fluorescence.
phosphorescence
Excited electrons can fall from excited singlet to triplet and then from triplet to singlet ground state if heavy atom collision is available to change angular momentum. In solids, process is slow, so phosphorescence lasts several seconds.
Visible-light detectors {fluorimetry} can be at right angles to exciting radiation from mercury or xenon arc lamps.
Techniques {nephelometry} can measure light scattered at right angles to light path. At dilute concentrations, absorbance is directly proportional to scattering coefficient, path length, and concentration, as in Beer's law. Particle sizes, particle shapes, solution pH, temperature, and mixing can change scattering. Scattering is more if wavelength is less, so UV light causes more scattering. Nephelometry is 10 times more sensitive than turbidimetry.
Techniques {phosphorescence}| can use absorbed-light re-emission. Orbital ground state is singlet with spins paired. Lower excited orbital state is triplet with spins parallel. Higher excited orbital state is singlet with spins paired. Electron can fall from excited singlet to triplet if heavy atom is available to change angular momentum. Electron can fall from triplet to singlet ground state if heavy atom is available to change angular momentum. Electron fall requires heavy-atom collision. In gas, process is fast. In liquids, process is moderate. In solids, process is slow, so phosphorescence lasts several seconds. Electron-gun TV screens and fluorescent lights have phosphor coatings.
fluorescence
Fluorescence uses ultraviolet light to put electrons in high orbitals, from which they fall back to lower excited orbitals, by short vibration-induced jumps, from which they fall to lowest band by spontaneous emission, giving visible light. Fluorescence does not require collisions because momentum does not change, so fluorescence is fast.
Techniques {reflectance analysis} can compare surface refractive-index differences. Reflectance tests paint, fabric, paper, plaster, drugs, glass, food, and ink. Integrating sphere or ellipsoid mirror receives reflected light.
Reflectance {specular reflectance} can be mirror-like. Reflectance {diffuse reflectance} can be from rough surfaces, which have absorption and scattering.
Methods {turbidimetry} can measure light that passes through suspension compared to total light. Suspensions scatter light. Turbidimetry measures air and water particle pollution, finds wine and drug clarity, measures clear-fluid protein, measures bacteria counts, finds sulfur and sulfate levels, and measures plastic polymerization amount.
Methods {x-ray fluorescence} can detect all elements with mass greater than atomic number 12, by bombardment with x-rays. It can find trace elements in ore, blood, art, alloys, soils, and cultural artifacts. Secondary x-rays come from lithium chloride, sodium chloride, or ammonium dihydrogen phosphate. X-rays can excite inner electrons. Proportional counter with pulse-rate analyzer counts only pulses of specific energy ranges. Spectrum identifies atom. Voltage, matrix, wavelength, time, and absorption affect non-linear measurement.
Precipitation {precipitation test} uses tungstic acid, TCA, or barium hydroxide and zinc sulfate. Precipitation with silver ion tests for chloride, bromide, iodide, and thiocyanate ion, with chromate ion and ferric alum as indicators. Weak-acid anion dye, like fluorescein, can bind to precipitate.
Solution can precipitate into large lumps {coagulation}|. Stirring to separate colloidal particles, adding diverse ion to break layers, heating to break layers, and reducing concentration to make ions closer together hinder coagulation.
Cold temperature or organic solvent can precipitate solid from solution {gravimetry}. Precipitate dries in oven to remove water and burn filter paper off, before weighing. Organic precipitates can chelate. Ignition can make oxides or -ate compounds, for easier weighing.
Electromagnetism and radio waves can determine molecule electron configuration {electron spin resonance} (ESR). Unpaired electrons are in free radicals, transition-metal-complex d orbitals, and triplet-state molecules. Unpaired electrons can change spin state.
process
In molecules, net proton spin in nearby atomic nuclei causes magnetic field around electrons to differ. Applying magnetic field and shining microwaves resonates molecule unpaired electron spins, at specific frequencies. Frequency spectrum {hyperfine structure, frequency} can indicate molecular-orbital type.
intensity
Intensity increases as temperature increases, until numbers of ground-state and excited-state molecules are equal.
Techniques {nuclear magnetic resonance} (NMR) {magnetic resonance imaging} (MRI) can measure electron density around hydrogen nuclei and other nuclei that have magnetic fields.
purposes
NMR can detect proton transfers and isomer interconversions. Sample size is 0.1 ml to 0.4 ml. Accuracy is 1/10^8. MRI {functional MRI} (fMRI) can scan body or brain for regions where increased glucose containing oxygen-15 indicates high cellular activity. Blood-oxygen-level dependent (BOLD) method uses blood flow and volume increase with increased metabolism.
theory: spin
Atomic nuclei with odd atomic number or odd atomic mass number have an unpaired proton or neutron and so net spin. Hydrogen and nitrogen have atomic numbers 1 and 7, respectively, and have net spin. Radioactive elements carbon-11, nitrogen-13, and oxygen-15 have net spin.
theory: magnetic field
Charges with net spin make magnetic fields. Proton magnetic moment is small compared to electron magnetic moment, because proton mass is much larger. Applying strong 14000-gauss magnetic field aligns atomic-nucleus protons parallel or anti-parallel with field, because altering proton spin angle requires large torque. Spin and spin angle to applied magnetic field have quanta.
theory: microwave radiation
Parallel and anti-parallel alignments have energy difference at microwave energy levels. Applying microwave radiation can flip protons from parallel to anti-parallel, or vice versa. Microwave wavelength needed to flip indicates nucleus and neighboring-nuclei atomic mass.
theory: neighbor shielding
In molecules, neighboring atoms affect proton magnetic fields. More electrons near atomic nucleus shield it from outside magnetic fields, requiring more microwave energy to change field alignment. Different functional groups attached to hydrogen atom provide more or less shielding. Shielding from lowest to highest is methyl -CH3 [3 is subscript], methylene -CH2 [2 is subscript], methyne -CH, amine -NH2 [2 is subscript], and hydroxyl -OH. Polar molecules have greatest shielding, and non-polar molecules have smallest shielding. Trimethylsilane (TMS) is NMR standard compound, because it has silicon atom surrounded by three methyl groups and so minimum electron shielding.
theory: energy
Total energy of microwave frequency that changes alignment indicates number of hydrogens, or other magnetic nuclei, with same electron environment. For example, TMS has nine protons with same electron environment and has relative total energy nine. Frequency variations around microwave frequency can change alignment. Frequency-variation number indicates number of non-equivalent protons that affect shielding electrons. For example, TMS has zero variations, because all protons are equivalent.
theory: width
Peak width is greater for slow transitions, when inverse of time {relaxation time} in excited state is more, because transverse relaxation gives energy to neighboring nuclei. Transverse relaxation is rapid in solids, so proton NMR does not use solids. Longitudinal relaxation makes heat.
MRI {diffusion tensor imaging} (DTI) can measure water diffusion in tissues.
Ultraviolet, visible, or infrared absorption can determine chemical-bond concentrations {spectroscopy}|.
dipole
Molecules with permanent electric dipole moment have rotational spectra. Molecules with changing dipole moment have vibrational spectra, unless symmetry cancels dipole-moment change. Electronic transitions always cause vibrations through recoil.
Doppler effects
Spectral lines broaden by Doppler shifts. Shift is more if wavelength is bigger, because relativistic effects are greater. Shift is more if temperature is high, because molecular-speed range is wider. Shift is less if mass is more, because same-temperature velocities are lower.
Spectral lines broaden {lifetime broadening} by time {lifetime}| in excited state, because short lifetime means large energy. Lifetime can shorten by stimulated emission by other radiation or by electric-field vibration. Higher frequencies cause faster emission, because they have more energy available. Lifetime can shorten by collisions, because they carry energy away.
Light from lamp containing heavy metal can pass through heavy metals in solution in flame, so metal atoms absorb light to measure metal concentration {atomic absorption spectroscopy} {absorption flame spectroscopy}. Atomic absorption measures percent absorption. For atomic absorption, concentration can be 10 to 100 parts per million.
Metals in solution in flame emit light at strong emission wavelength lines, which can measure calcium, sodium, potassium, and low-molecular-mass-metal concentration {atomic emission spectroscopy} {emission flame spectroscopy}. Sample can be in graphite furnace, carbon-rod analyzer, boat, cup, or atomizer. Premixing is in mixing chamber or by baffles. Flame temperature is low enough not to ionize atoms. Flame excites electrons. Atomic emission detects emission-line intensity. For atomic emission, concentration must be 1%.
Techniques {emission spectroscopy} can detect emitted light. Emission spectroscopy can measure amounts of 80 metallic and metalloid elements in minerals, paint, air pollution, water pollution, and oil. Emission spectroscopy produces spectra in UV-visible range. AC spark is more intense and quantifiable. Laser can measure tiny impurities. Quartz tube with microwave coil can make inductively coupled plasmas.
problems
Emission spectroscopy has matrix effects and non-linear results. Emission spectroscopy detects the most-intense spectrum lines, which are also the most wandering. Emission spectroscopy is destructive, because DC arc ionizes metal atoms.
Spectroscopy {infrared spectroscopy} (IR) can detect functional groups and chemical-bond types. IR is simple, is cheap, uses infrared wavelengths 1 micrometer to 20 micrometers, and has narrow absorption bands. Infrared light source is Nernst glower or nichrome wire. Infrared light detector is thermocouple, thermister, or bolometer. Sodium-chloride prisms or reflection gratings select wavelength. Double beam allows scanning.
solvent
Solids, liquids, and gases have concentration 0.1% to 10%. Water absorbs infrared light, so it cannot be solvent. Carbon disulfide solvent is for wavelengths 7.5 micrometers to 16 micrometers. Carbon tetrachloride solvent is for wavelengths 2.5 micrometers to 7.5 micrometers.
container
Sodium chloride or potassium chloride windows hold sample. Path length is 0.1 millimeters to 1.0 millimeter.
theory
Organic-molecule functional groups have chemical bonds with rotations and vibrations. Rotations and vibrations have energies in infrared-light range. IR typically measures vibrations, rather than rotations, because vibrations have higher energies and frequencies. Rotations appear superimposed on vibrational spectral lines and make wider vibrational bands.
theory: dipole moment
The greater the dipole moment, the greater the infrared frequency. The longest chemical bonds and most-polarized functional groups have highest frequencies. Chemical-bond frequencies from highest to lowest are N-H, O-H, C-H, C=O, C=C, C-O, C-C, and H-H.
theory: rotations
Molecule rotation states depend on molecular symmetries. Spherical molecules have no rotational states. Linear molecules have one state, if they are symmetric along axis. Linear molecules with asymmetry have two states. Asymmetric molecules have three states, one for each axis.
Massive molecules have long dipole and have close rotational energy levels. Molecules with large bond distance have long dipole.
theory: vibrations
Chemical bond has stretching vibration. Two same-atom chemical bonds have bending vibrations. Vibrations involve simple harmonic motion, along bond axis or around bond angle. Vibrations give information about bond rigidity and bond-breaking energies. Strong bonds and long bond distances have more energy and make close energy levels. The most-polarized bonds have longest wavelength.
Bond bending is easier than bond stretching, because forces are less, so bending-vibration frequencies are less than stretching-vibration frequencies.
One bond has one less vibrational state, because rotation around bond makes vibrations cancel, because they have all directions. Homonuclear diatomic molecules have no stretching or bending vibrations, because they have no dipole. Heteronuclear diatomic molecules have only stretching vibrations along one bond.
Molecules with three atoms can have bending vibrations. n atoms can have 3*n vibrational states {degrees of freedom, atom}: three for translations and three or less for rotations. Pi-bond twisting is vibration.
problems
Vibrational energy levels get closer together nearer bond-dissociation energy. Liquids and solids have more vibration effects, because they have bonding and van der Waals forces.
Spectroscopy {mass spectroscopy} (MS) can find atomic and molecular mass. Mass spectroscopy is fast, reliable, expensive, and delicate.
sensitivity
Mass spectroscopy can detect masses from 1 to 400,000 daltons, at concentrations as low as 10^-12 M.
uses
Mass spectroscopy can find molecule functional groups by fragment mass differences. For example, methyl groups have mass 15, CO groups have mass 28, water has mass 18, ammonia has mass 17, and phenyl groups have mass 77.
Mass spectroscopy measures leak detection, blood gases, and tracers and analyzes petroleum, plastics, fertilizers, and insecticides. Mass spectroscopy can detect illegal drugs, impurities, pollutants, reaction products, and toxins in gases, liquids, and solids. Mass spectroscopy determines age, quantifies chemical composition, studies metabolism, detects molecular changes, and monitors chemicals. Mass spectroscopy can sequence peptides.
process
Mass spectroscopy measures mass-to-charge ratio of ionized atoms or molecules.
process: vaporization
A 350-C vacuum chamber heats sample to make gas, which expands into ionization chamber through pinhole.
process: ionization
70-eV electron beams ionize sample molecules to make ions with charge +1. Ionization can use proton transfer from ionized methane. Vaporized molecules can ionize {desorption, mass spectroscopy} by californium-252, secondary ions, lasers, high electric field on thin film, or electrospray from high-voltage needle.
process: electric field
Source positive charge repels positively charged ions into analyzer. Ions enter strong electric field and accelerate through slits to collimate.
process: magnetic field
Ions enter magnetic field and arc in semicircle. Typically, magnetic field or voltage sweeps. Big ions move slower and have big radius. Small ions move faster and have small radius.
process: detector
Ions hit surface with applied voltage, causing charge cascade {electron multiplier}. Ions make current, which can be as small as 10^-15 A. Detector measures ion energy and location. Location indicates ion mass. Energy, converted to electric current or light, indicates ion number.
process: types
Double-focusing mass spectroscopy separates masses first by radial electric field and then by radial magnetic field.
Sector detector uses electric field to focus ions, then magnetic field to spread ions. Larger masses need stronger fields to focus them on detector. Smaller masses need smaller field to bring them to detector. Detector plate converts collision energy into ions or electrons, detected as current, or photons, detected by photomultiplier.
Quadrupole mass filter uses four parallel plates or rods with constant direct-current electric field between two plates and varying radio-frequency electric field between two plates.
Ion traps use two parallel plates and ring electrode to trap ions that have mass range. Electric field increases to eject ions toward detector.
High-resolution detectors can measure dalton fractions. Fourier-transform ion-cyclotron resonance (FT-ICR) can trap ions between electrodes in a magnetic field. Radio-frequency electric field makes ions orbit. Orbiting ions create electromagnetic frequency measured by detector plates.
Time-of-flight (TOF) methods send ions accelerated to constant velocity across distance. Detector measures time and so mass.
Two-stage mass spectroscopy (MS/MS) can separate compound from mixture or separate compound constituents to analyze compound structure.
process: results
If electron-beam energy is high enough, sample has unique ion-fragment pattern {cracking, mass spectroscopy}. Highest-mass peak is original molecule with one electron missing. Pattern depends on chemical-bond strength, atoms, total molecular mass, and ionization potential. Chemical bonds break most easily where molecules branch. Double bonds can break. Saturated ring compounds break at side-chain alpha carbon. Carbonyls break so carbonyl ionizes. Aromatic compounds do not break.
process: isotopes
Isotopes cause peak doubling or tripling. Elements have definite peak-doubling or peak-tripling ratios. F, P, and I have no isotopes. 2H, 15N, and 18O [2, 15, and 18 are superscripts] have negligible amounts.
process: isotope ratios
First, find carbon number. 13C [13 is superscript] is 1.11% of total carbon, so first peak to second peak ratio shows carbon number. Next, find oxygen, sulfur, chlorine, and bromine numbers by isotope ratios. Find nitrogen number. If molecular mass is even, nitrogen number is 0 or even. If molecular mass is odd, nitrogen number is odd. You can also use compound spectra tables.
Spectroscopy {Mössbauer spectroscopy} can study number of s orbitals involved in bonding and study valences. Atomic nuclei absorb gamma rays and then emit them, causing crystal recoil and vibration, which causes Doppler shift in electronic-transition wavelengths. Holding crystal in crystal lattice can minimize recoil. Decay is slow. Line width is small.
Spectroscopy {Near Infrared Spectroscopy} (NIRS) can detect glucose and oxygen by infrared reflection.
Spectroscopy {Raman spectroscopy} can study plastics, waxes, pure organic molecules, complex ions, or non-spherical molecules, by polarizing non-polar bonds with UV or visible light and analyzing infrared radiation.
scattering
UV or visible light scatters from molecules to polarize them, with +2 or -2 total angular momentum. Rayleigh scattering is elastic, with unchanged wavelength. Raman scattering is inelastic, because it makes dipoles, so vibration and rotation energy levels affect it.
polarization
Polarization causes infrared-light emission or absorption at vibration or rotation energies. Raman-scattering vibrations are not infrared. Raman-scattering rotations are infrared. Raman lines can have lower frequency {Stokes line} or higher frequency {anti-Stokes line}.
Spectroscopy {UV-visible spectroscopy} can find solution substance concentrations by measuring visible or ultraviolet light absorbance.
purposes
UV-visible spectroscopy can detect functional groups, bonds, and spatial configurations and so identify molecules. It can find equilibrium point, pH, or pK by comparing absorbance at two wavelengths. UV-visible spectroscopy is simple and cheap.
purposes: visible
Visible light can detect colored molecules, in concentrations down to 0.01 M, using standard curve for calibration.
technique
Extinction coefficient or molar absorptivity depends on outer-shell-electron transition energies and probabilities. Tables show values for most substances. Method can also use integrated absorption coefficient or oscillator strength. If molar absorptivity is high, sensitivity is high. Wavelength is maximum-absorbance wavelength. Bandwidth is broad, because energy is low. Path length through solution is typically one centimeter. Air absorbs light of less than 200-nanometer wavelength, so UV light path has vacuum. Glass absorbs all UV light, so containers are quartz.
theory: transition metal
Transition-metal ions have incomplete d orbitals, with three at lower energy and two at higher energy, which have electronic transitions in visible light. Central transition-metal ions can have two sets of low-energy d orbitals, with no symmetry center from metal-ion bonding orbitals to ligand antibonding orbitals or from metal-ion antibonding orbitals to ligand antibonding orbitals. Then intensity is low, because vibrations can also cause such transitions. High intensity is if charges transfer from ligand to ion, or vice versa.
theory: double bonds
Ultraviolet light can detect molecules with carbon-oxygen double or triple bonds or with carbon-carbon conjugated bonds. Unconjugated double bonds involve UV light. Pi-bond electrons jump to antibonding pi orbital to make UV light.
If double bond conjugates, electron delocalization causes small jump and visible light. Intensity is high.
Indicator color changes are large, because proton gain or loss changes conjugation. More conjugation makes longer wavelengths.
Molecules with lone electron pairs can make UV or visible light by jumping to antibonding pi orbitals, typically forbidden visible-light transitions.
theory: no light
Closed-shell electrons and sigma-bond electrons do not give UV or visible light. Hydroxyl, amine, and halogen groups do not give UV or visible light, but they can affect intensity or shift chromophore wavelengths.
Techniques {x-ray absorption} can find heavy atoms among lighter atoms, such as crystal impurities, gasoline lead, broken bones, barium enemas, body iodide, and steel and plastic faults. Absorption depends on molecular mass, density, and thickness. X-rays can come from electrons that hit metal anode at 80,000 V. X-rays hit target, whose ionization energy allows high primary x-ray absorption {absorption edge} and which emits lower-energy x-rays {secondary x-ray}. Detection is by film.
Electronic transitions cause spectra if asymmetric electron-distribution changes cause transient dipole moments {allowed transition}. Then angular momentum change is +1 or -1. Radiation intensity depends on electronic transition probability. Electric dipoles give highest intensity, because they have allowed transitions.
Symmetric electron-distribution changes {forbidden transition} do not change angular momentum. Electric quadrupoles and magnetic dipoles give low intensity, because they have forbidden transitions.
Reaction with high-concentration titrant {titration}| can measure concentrations in acid-base reactions, precipitations, oxidation-reductions, and complexometric reactions.
complexometric reaction
Reactions {complexometric reaction} can make water-soluble chelate from metal ion and EDTA.
volume
Titrants are at high concentration, so volume used is small.
titrant
Hydrochloric acid is for base titration. Sodium hydroxide is for acid titration.
process
Find acid or base concentration by reacting solution volume with known-concentration base or acid volume, until solution is neutral. pH or voltage changes fast at beginning, then rate becomes small as amounts become almost equal, and then rate becomes rapid again if past titration point. Find concentration by converting volume to mass.
Indicators typically change color at second rapid-rise beginning. Titrating weak acid or base slowly changes pH at pK. When pH = pK, salt and acid or base are equal.
standardization
Sodium carbonate standardizes strong-acid titrant. Find first sodium-carbonate endpoint with phenolphthalein at pH 8.0 to 9.5. Find second endpoint with methyl red at pH 4 to 6. Boiling removes carbon dioxide.
Potassium hydrogen phthalate (KHP) standardizes strong-base titrant. Phenolphthalein is indicator.
oxidation-reduction
For oxidation-reduction reactions, moles times valence {equivalent} depends on charge. Valence divides into molecular weight {equivalent weight}.
back titration
Methods {back titration} can add excess titrant to sample and then find excess titrant by titrating with another titrant.
Sample milligrams can be equivalent to one-milliliter titrant {titer}. Total weight m is titer t times number n of titrant milliliters: m = t*n.
Titration measures concentrations in acid-base reactions, precipitations, oxidation-reductions, and complexometric reactions by reaction with high-concentration solution {titrant}.
Analytical balances weigh dry substances {weighing, analysis}|. First, find weighing-paper, weighing-bottle, or weighing-dish tare weight. Find sample and container weight. Subtract tare weight to find sample weight. Weighing is at constant temperature, usually 24 C. No finger oil and no air drafts can affect sample. Analytical balances are not for sodium hydroxide, hydrogen iodide, hydrogen bromide, iodine, or bromine, which are corrosive.
empty container or holder weight {tare}|.
Chemistry {industrial chemistry} can be about flows and heat.
industrial processes
Work needed depends on material viscosity, density, friction, pressure, and temperature. Work moves, compresses, mixes, separates, pumps, or conveys materials. Chemical-transport work uses blowers, compressors, pumps, pipes, and conveyors. Separations and purifications use adsorption, distillation, crystallization, chromatography, filtering, electrostatics, evaporation, absorption, solvent extraction, drying, leaching, flotation, gelling, zone melting, settling, centrifugation, and cycloning.
flow
Chemical processes involve material flow from containers into reaction vessels, heat or work added to, or subtracted from, reaction vessels to cause chemical reactions or separations, and product flow from reaction vessels into containers.
flow: measurement
Devices that measure flows include constriction devices {Venturi tube, flow} {orifice plate} {rotometer} {pitot tube}, velocity devices {magnetic flowmeter}, and displacement devices {turbine flowmeter} {wet test meter}.
flow: types
Chemical processes {plug-flow reactor} (PFR) can use amounts {plug, flow} at a time {batch processing, chemical} in reaction vessels. Chemical processes {continuous stirred tank reactor} (CSTR) can have continuous material flow {continuous processing} in reaction vessels.
flow: reaction rate
Flow rate, reaction-vessel size, reaction time allowed, temperature, and catalysts control chemical-reaction rates.
heat transfer
Heat is either generated or needed {heat transfer}. Heat transfers can recover wasted heat, add needed heat, or cool reaction vessels. Heat transfers can cause chemical reactions, change reaction rates, protect equipment, change flow rates, or separate materials. Heat transfers can use countercurrent heat exchangers.
Heat transfer typically uses a pipe system, in which cold fluid flows by warm fluid and warm fluid flows by cold fluid {countercurrent heat exchanger}.
Chemical processes involve heat and work controls {energy balance}. Volume changes, from pressure changes, and heat flows are the most-important factors in calculating energy balance.
Chemical processes involve control of input and output amounts, which are equal {material balance}. Input is reactants and catalysts. Output is products, wastes, residues, and leftover reactants. Chemical process must control flammable or explosive materials.
Chemistry includes analytical chemistry, biochemistry, inorganic chemistry, organic chemistry, and physical chemistry.
He lived 1783 to 1833, was chef to Talleyrand and Alexander I of Russia, and carved marzipan, fat, and sugar {pièce montée}.
He served courses from menu and used stock, at Ritz Hotel.
He began Alchemy and Hermetism or Hermetic philosophy.
Chenoboskion is on Nile River west bank in Upper Egypt.
Nature has interconvertible and mixable elements: earth or solid, fire or energy, air or gas, water or liquid. Metals relate to body parts. Gold represents longevity. Sulfur, as fire and spirit, and mercury, as water and soul, make minerals and metals. Gold has value, because it does not rust and does not change with heat, alkali, or acid. All metals can grow into gold. Philosophers Stone, Elixir of Life, or Red Tincture can change base metal into gold.
Epistemology
Using reason can make people like gods, by removing misconceptions {twelve madnesses} and perceiving the order of nature.
Metaphysics
God is beyond human conception.
Perhaps, she wrote, "One becomes two, two becomes three, and out of the third comes the one as the fourth."
He lived 100 to 150. Principles similar to alchemy arose in China from Taoism. Nature has interconvertible and mixable elements: water, fire, wood, gold, and earth.
He lived 410 to 485.
He was Gnostic, and he mentioned Mary the Jewess.
He lived 283 to 343 and was Taoist.
He lived 581 to 673.
He lived ? to 803.
Alchemists were astrologers, animists, philosophers, and healers. Major European alchemists were Roger Bacon, Albertus Magnus, Basil Valentine, and Paracelsus. Alchemists changed metal color, reduced, distilled, calcinated, sublimated, and cupellated. They used a still {alembic} and refluxing apparatus {kerostalsis}. Alchemists hoped to find gentle universal solvent {alkahest}.
He lived 1493 to 1541. He searched for substance {philosopher's stone, Paracelsus} that can control nature by strengthening essence of universe in all things. To mercury and sulfur, he added salt, for body, to have three primary substances {tria prima}.
He lived 1540 to 1616.
He lived 1604 to 1668 and formed sodium sulfate [1625].
He lived 1627 to 1691, invented Boyle's law, and found elements.
He lived 1635 to 1682 and invented a heat theory [1702], in which heat is a substance {phlogiston} {caloric fluid}.
He lived 1660 to 1734 and invented a heat theory [1702], in which heat is a substance {phlogiston, Stahl} {caloric fluid, Stahl}.
He lived 1728 to 1799 and discovered carbon dioxide [1754] and latent heat [1759 to 1763].
He lived 1733 to 1804 and discovered ammonia, carbon dioxide, carbon monoxide, nitrogen, nitrous oxide [1793], oxygen, and sulfur dioxide. For the greatest happiness of the greatest number, ruler and ruled interests must integrate, by forcing rulers to depend on ruled to stay in power.
He lived 1743 to 1794, invented definite-proportions law {constant-composition law}, and noted mass conservation.
He lived 1774 to 1836 and found Henry's gas-solubility law [1803].
He lived 1778 to 1850 and invented law of combining volumes and law of Guy-Lussac [1808].
He lived 1766 to 1844 and studied atomic theory, compounds, atomic weights, partial-pressure law, and color blindness.
He lived 1776 to 1856 and calculated Avogadro's number [1811].
He lived 1785 to 1838 and studied heat capacity and invented law of Dulong-Petit [1819].
He lived 1791 to 1820 and studied heat capacity and invented law of Dulong-Petit [1819].
He lived 1805 to 1869 and invented Graham's diffusion law [1829].
He lived 1791 to 1867 and invented Faraday's electrolysis laws [1831] and studied magnetic induction and diamagnetism.
He lived 1802 to 1850 and noted enthalpy changes [1840].
He lived 1814 to 1878, studied energy conservation [1841], and showed that living things use chemical processes for heat and power [1845]. Energy conservation is the only form in which axiom of causality is true.
He lived 1822 to 1888 and noted energy conservation [1850], studied gas kinetic theory, and invented virial theorem. Entropy always increases [1865].
He lived 1826 to 1910 and defined the mole [1858], found atomic weights, and invented molecular formulas.
He lived 1834 to 1907 and invented the periodic law and element periodic table [1869].
He lived 1844 to 1906 and studied entropy and probability [1871].
He lived 1839 to 1903 and studied vectors and thermodynamic equilibrium in many-particle systems.
He lived 1859 to 1927 and studied electrolytic ion solutions [1884].
He lived 1850 to 1936 and invented Le Chatelier's reaction-direction principle [1884].
He lived 1863 to 1922 and studied vaporization entropy. Vaporization entropy is approximately 87 Joules/Kelvin per mole for most liquids {Trouton's rule} [1884].
He lived 1830 to 1901 and invented Raoult's vapor-pressure law [1886].
He lived 1854 to 1919 and studied element emission lines, making Rydberg formula [1888].
He lived 1853 to 1932, studied chemical equilibrium [1900], reaction rates, and color, and invented Ostwald process for nitric acid [1902].
He lived 1887 to 1915 and found atomic numbers [1912].
He lived 1877 to 1945 and studied isotopes [1913].
He lived 1879 to 1947 and discussed acids as proton transfers [1923].
He lived 1875 to 1946 and discussed acids as electron pair acceptors and invented Lewis structures [1923].
He lived 1896 to 1997 and invented Hund's orbital electron-spin rule [1925].
He lived 1898 to 1964 and studied chain reactions [1933].
He lived 1901 to 1994 and studied electronegativity [1932] and protein structure [1951].
He lived 1824 to 1887, discovered spectra absorption lines [1859], and discovered cesium and rubidium.
He lived 1811 to 1899, improved Bunsen burner [1860], and discovered cesium and rubidium. He discovered hydrated-iron-oxide antidote for arsenic poisoning.
Fenn lived 1917 to ?. Tanaka lived 1959 to ?. They invented matrix assisted laser absorption ionization (MALDI) for mass spectroscopy [1949 to 1954]. It works with Time-of-Flight TOF detectors.
He lived 1852 to 1911 and studied stereochemistry and diamond structure [1874].
He lived 1852 to 1919 and studied enzymes and carbohydrate chemistry [1874 to 1906].
He lived 1931 to ?.
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Date Modified: 2022.0225