The carbon adjacent to a carbonyl; in amino acids, the chiral stereocenter in all amino acids except glycine.
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α-Hydrogen
Hydrogen atoms connected to α-carbons adjacent to carbonyls.
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α-State
A magnetic state seen in NMR spectroscopy in which nuclei have magnetic moments that are aligned with an incident magnetic field, thus having lower energy.
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Absolute conformation
The exact spatial arrangement of atoms or groups in a chiral molecule around a single chiral atom, designated by (R) or (S).
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Acetal
A functional group that contains a carbon atom bonded to two −OR groups, an alkyl chain, and a hydrogen atom.
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Achiral
A molecule that either does not contain a chiral center or contains chiral centers and a plane of symmetry; as such, it has a superimposable mirror image.
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Acid dissociation constant (Ka)
A measurement of the strength of an acid in solution; the higher the Ka, the lower the pKa and the stronger the acid.
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Affinity chromatography
A special type of column chromatography in which a column is customized to bind a substance of interest.
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Aldehyde
A functional group containing a carbonyl and a hydrogen (RCOH); always found at the end of a chain.
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Aldol condensation
A reaction in which an aldehyde or ketone acts as both the electrophile and nucleophile, resulting in the formation of a carbon- carbon bond in a new molecule called an aldol.
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Alkane
A simple hydrocarbon molecule with the formula CnH2n+2.
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Amide
A functional group containing a carbonyl and an amino group (RCONR2).
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Amino acids
Dipolar compounds that contain an amine and a carboxylic acid attached to a single carbon (the α-carbon); the building blocks of peptides.
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Amphoteric
Describes molecules that can act as both acids and bases.
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Angle strain
Increased energy that results when bond angles deviate from their ideal values.
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Anhydride
A functional group containing two carbonyls separated by an oxygen atom (RCOOCOR); often the condensation dimer of a carboxylic acid.
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Anti conformation
A type of staggered conformation in which the two largest groups are antiperiplanar to each other; the most energetically favorable conformation.
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Antibonding orbital
A higher-energy, less stable orbital that results from the overlap of wave functions with opposite signs.
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Antiperiplanar
A conformation in which substituents are in the same plane, but on opposite sides of a bond.
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Axial
Describes groups on a cyclic molecule that are perpendicular to the plane of the molecule, pointing straight up or down.
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Azimuthal quantum number (l)
Describes the subshell in which an electron is found; possible values range from 0 to n − 1, with l \= 0 representing the s subshell, l \= 1 representing p, l \= 2 representing d, and l \= 3 representing f.
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β-lactam
Four-membered cyclic amides that are more reactive to hydrolysis than linear amides or larger cyclic amides; often used as the backbone for antibiotics.
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β-state
A magnetic state seen in NMR spectroscopy in which nuclei have been irradiated with radio-frequency pulses to bring them to a higher-energy state.
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Bonding orbital
A lower-energy, more stable orbital that results from the overlap of wave functions with the same sign.
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Carbonyl
A double bond between a carbon and an oxygen.
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Carboxylic acid
A functional group that contains a carbonyl and a hydroxyl group on the same carbon (RCOOH).
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Carboxylic acid derivative
A compound that can be created from a carboxylic acid by nucleophilic acyl substitution; includes anhydrides, esters, amides, and others.
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Chemical properties
Characteristics of compounds that change chemical composition during a reaction; determine how a molecule will react with other molecules.
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Chemical shift (δ)
An arbitrary variable used to plot NMR spectra; measured in parts per million (ppm).
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Chemoselectivity
A reaction's preference for one location over another within a molecule.
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Chiral
A molecule or carbon atom bonded to four different groups and without a plane of symmetry; thus, it is not superimposable on its mirror image and has an enantiomer.
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Chiral center
Atoms that are chiral within a molecule.
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Chromatography
A tool used to separate compounds based on how strongly they adhere to a stationary phase or travel with a mobile phase.
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Cis
A molecule in which the two substituents are on the same side of an immovable bond.
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Cis-trans isomers
Diastereomers with different arrangements of substituents around an immovable bond.
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Column chromatography
A type of chromatography that uses a column filled with silica or alumina beads as an adsorbent, allowing for separation; uses gravity to move the solvent and compounds down the column.
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Condensation reaction
A reaction that combines two molecules into one, with the loss of a small molecule.
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Configuration
The spatial arrangement of the atoms or groups in a molecule.
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Configurational isomers
Isomers that can only interconvert by breaking bonds; include enantiomers, diastereomers, and cis-trans isomers.
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Conformational isomers
Isomers that are the same molecule, just at different points in their natural rotation about a σ bond.
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Conjugation
Alternating single and multiple bonds that create a system of parallel unhybridized p-orbitals; thus, electrons can be shared between these orbitals, forming electron clouds above and below the plane of the molecule and stabilizing the molecule.
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Constitutional isomers
Molecules that have the same molecular formulas but different connectivity; also called structural isomers.
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Coordinate covalent bond
A covalent bond in which both electrons in the bond come from the same starting atom.
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Coupling
In NMR spectroscopy, a phenomenon that occurs when there are protons in such close proximity to each other that their magnetic moments affect each other's appearance in the NMR spectrum by subdividing the peak into subpeaks; also called splitting.
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Coupling constant (J)
The magnitude of splitting in NMR spectroscopy, measured in hertz.
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Covalent
One of two types of chemical bonds in which electrons are shared between atoms.
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Cyanohydrin
A functional group containing a nitrile (−C≡N) and a hydroxyl group.
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d-orbital
An atomic orbital that is composed of four symmetrical lobes and contains two nodes.
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Decarboxylation
The complete loss of a carboxyl group as carbon dioxide.
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Deprotection
Reversion of a protecting group to its original functional group.
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Deprotonation
The removal of a hydrogen cation (H+) from a molecule.
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Deshielding
The phenomenon of atoms pulling electron density away from surrounding atoms; in NMR spectroscopy, pulls a group further downfield on the spectrum.
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Developing chamber
A beaker with a lid or wide-mouthed jar used in thin-layer chromatography.
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Dialcohols
Alcohols with two hydroxyl groups that are commonly used as protecting groups for aldehyde or ketone carbonyls; also called diols.
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Diastereomers
Non-mirror-image configurational isomers that differ at at least one-but not all-chiral carbons; have different chemical and physical properties.
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Distillate
The liquid evaporated, condensed, and collected during distillation.
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Distillation
A separation and purification technique that takes advantage of differences in boiling point to separate two liquids by vaporization and condensation.
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Doublet
Two peaks of identical intensity in an NMR spectrum that are equally spaced around the true chemical shift of a group of protons; it results from splitting by another hydrogen.
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Downfield
Movement toward the left in an NMR spectrum.
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Electron-donating
Describes groups that push additional electron density toward another atom; stabilizes positive charges and destabilizes negative charges while decreasing acidity.
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Electron-withdrawing
Describes groups that pull electron density away from another atom; stabilizes negative charges and destabilizes positive charges while increasing acidity.
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Electrophile
"Electron-loving" atoms with a positive charge or positive polarization that can accept an electron pair when forming new bonds with a nucleophile.
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Eluent
The solvent used in chromatography, after it has passed through the stationary phase.
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Elute
To displace with solvent, as in thin-layer chromatography.
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Enantiomers
Nonsuperimposable mirror images of a chiral molecule; have all the same physical and chemical properties except for rotation of plane-polarized light and reactions in a chiral environment.
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Enol
The resonance form of a carbonyl that has a carbon-carbon double bond (ene) and an alcohol (-ol).
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Equatorial
Describes groups on a cyclic molecule that are in the plane of the molecule.
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Ester
A functional group containing a carbonyl and an alkoxy group (RCOOR).
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Extraction
The transfer of a dissolved compound from a starting solvent into a solvent in which the product is more soluble.
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Fingerprint region
In an IR spectrum, the region of 1500 to 400 cm−1 where more complex vibration patterns, caused by the motion of the molecule as a whole, can be seen; it is characteristic of each individual molecule.
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Fischer esterification
The formation of an ester from a carboxylic acid and an alcohol in acidic conditions.
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Fischer projection
A system to represent three-dimensional molecules in which horizontal lines indicate bonds that project out from the plane of the page (wedges) and vertical lines indicate bonds going into the plane of the page (dashes); points of intersection represent carbon atoms.
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Flash column chromatography
A technique that speeds up column chromatography by forcing the solvent through the column by increasing pressure with a nonreactive gas.
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Fractional distillation
A modified form of distillation used to separate two liquids with similar boiling points (less than 25°C apart); uses a fractionation column, which contains inert materials onto which the liquids can condense and reflux back into the reaction vial, allowing more refined separation.
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Fraction
A volume of eluted fluid from column chromatography; each fraction contains different compounds that are collected as they leave the column.
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Gabriel (malonic-ester) synthesis
A method of synthesizing amino acids that uses potassium phthalimide and diethyl bromomalonate followed by an alkyl halide; two substitution reactions are followed by hydrolysis and decarboxylation.
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Gas chromatography (GC)
A type of chromatography used to separate vaporizable compounds; the stationary phase is a crushed metal or polymer, and the mobile phase is a nonreactive gas.
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Gauche conformation
A type of staggered conformation in which the two largest groups are 60° apart.
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Geminal diol
A functional group with two hydroxyl groups on the same carbon; also called a hydrate.
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Hemiacetal
A functional group that contains a carbon atom bonded to one −OR group, one −OH group, an alkyl chain, and a hydrogen atom.
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Hemiketal
A functional group that contains a carbon atom bonded to one −OR group, one −OH group, and two alkyl chains.
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Heterolysis
Cleavage of a bond in which both electrons are given to the same atom.
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High-performance liquid chromatography (HPLC)
A form of chromatography in which a small sample is put into a column that can be manipulated with sophisticated solvent gradients to allow very refined separation and characterization; formerly called high-pressure liquid chromatography.
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Highest occupied molecular orbital (HOMO)
The highest-energy molecular orbital containing electrons; in UV spectroscopy, electrons are excited from the HOMO to the LUMO.
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Hydride reagent
Reducing reagents containing hydride anions (H-).
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Hydrogen bonding
An intermolecular force that results from the extreme polarity of the bonds when hydrogen atoms are attached to highly electronegative atoms (N, O, or F).
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Hydrolysis
The breaking of a molecule using water.
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Hydroxyl group
An -OH group; seen in alcohols, hemiacetals and hemiketals, carboxylic acids, water, and other compounds.
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Hydroxyquinone
A compound containing a quinone (conjugated ring with carbonyls) and a hydroxyl group.
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Imine
A double bond between a carbon and a nitrogen.
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Immiscible
Describes two solvents that will not mix with or dissolve each other.
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Induction
The pull of electron density across sigma bonds.
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Infrared (IR) spectroscopy
A technique that measures molecular vibrations at different frequencies, from which specific bonds can be determined; functional groups can be inferred based on this information.
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Inorganic phosphate (Pi)
Derived from phosphoric acid, the molecule that forms high-energy bonds for energy transfer in nucleotide triphosphates like ATP; also used for enzyme regulation.
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Ion-exchange chromatography
A special type of column chromatography in which the beads in the column are coated with charged substances so that they attract or bind compounds with an opposite charge.
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Ionic
One of two types of chemical bonds in which electrons are transferred from one atom to another.
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Isomers
Molecules with the same molecular formula but different chemical structures.
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Jones oxidation
An oxidation reaction in which primary alcohols are oxidized to carboxylic acids and secondary alcohols are oxidized to ketones; requires CrO3 dissolved with dilute sulfuric acid in acetone.
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Ketal
A functional group that contains a carbon atom bonded to two −OR groups and two alkyl chains.
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Ketone
A functional group containing a carbonyl with two alkyl groups (RCOR); always found within a chain.
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