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organic chemistry glossary > odds & ends > home      

Organic Chemistry Glossary

 

achiral: A molecule that's superimposable on its mir ror image. Achiral molecules do not rotate plane-polarized light.

acid: A proton donor or an electron pair acceptor.

alcohol: A molecule containing a hydroxyl (OH) group. Also a functional group.

aldehyde: A molecule containing a terminal carbonyl (CHO) group. Also a functional group.

alkane:A molecule containing only C-H and C-C single bonds.

alkene:A molecule containing one or more carbon-carbon double bonds. Also a functional group.

alkyne:A molecule containing one or more carbon-carbon triple bonds. Also a functional group.

allylic carbon: An sp3 carbon adjacent to a double bond.

amide: A molecule containing a carbonyl group attached to a nitrogen (-CONR2). Also a functional group.

amine: A molecule containing an isolated nitrogen = (NR3). Also a functional group.

anion: A negatively charged atom or molecule.

anti addition: A reaction in which th= e two groups of a reagent X-Y add on opposite faces of a carbon-carbon bond.

anti conformation: A type of staggered conformation in which the two big groups are opposite of each other in a Newman projection.

anti-aromatic: A highly unstable planar ring system with 4n pi electrons.

anti-periplanar (a.k.a. anticoplanar): The conformation in which a hydrogen and a leaving group are in the same plane and on opposite sides of a carbon-carbon single bond. The conformation required for E2 elimination.

aprotic solvents: Solvents that do not contain O-H or N-H bonds.

aromatic: A planar ring system that contains uninterrupted p orbitals around the ring and a total of 4n+2 pi electrons. Aromatic compounds are unusually stable compounds.

aryl: An aromatic group as a substituent.

axial bond: A bond perpendicular to the equator of the ring (up or down), typically in a chair cyclohexane.

base: A proton acceptor or an electron pair donor.

benzyl group: A benzene ring plus a methylene (CH2) unit (C6H5—CH2).

benzylic position: The position of a carbon attached to a benzene ring.

benzyne: A highly reactive intermediate. A benzene ring with a triple bond.

bicyclic: A molecule with two rings that share at least two carbons.

Brønsted acid: A proton donor.

Brønsted base: A proton acceptor.

carbanion: A negatively charged carbon atom.

carbene: A reactive intermediate, characterized by a neutral, electron-deficient carbon center with two substituents (R2C:).

carbocation: A positively charged carbon.

carbonyl group: A carbon double bonded to oxygen (C=O).

carboxylic acid:A molecule containing a carboxyl (COOH) group.Also a functional group.

cation: A positively charged molecule or atom.

chair conformation: Typically, the most stable cyclohexane conformation. Looks like a chair.

chemical shift: The location of an NMR peak relative to the standard tetramethylsilane (TMS), given in units of parts per million (ppm).

chiral center: A carbon or other atom with four nonidentical substituents.

chiral molecule: A molecule that's not superimposable on its mirror image. Chiral molecules rotate plane-polarized light.

cis: Two identical substituents on the same side of a double bond or ring.

configuration: The three-dimensional orientation of atoms around a chiral center. It’s given the designation R or S.

conformation: The instantaneous spatial arrangements of atoms. Conformations can change by rotation around single bonds.

conjugate acid: The acid that results from protonation of a base.

conjugate base: The base that results from the deprotonation of an acid.

conjugated double bonds: Double bonds separated by one carbon-carbon single bond. Alternating double bonds.

constitutional isomers: Molecules with the same molecular formula but with atoms attached in different ways.

coupling protons: Protons that interact with each other and split the NMR peak into a certain number of lines following the n+1 rule.

coupling constant: The distance between two neighboring lines in an NMR peak (given in units of Hz).

covalent bond: Bond in which the two electrons are shared between the two atoms.

dehydrohalogenation: Loss of a hydrohalic acid (like HBr, HCl, and so on) to form a double bond.

delta value (a.k.a. d value): The chemical shift.  The location of an NMR peak relative to the standard tetramethylsilane (TMS), given in units of parts per million (ppm).

diastereomers: Stereoisomers that are not mirror images of each other.

Diels-Alder reaction: A reaction that brings together a diene and a dienophile to form bicyclic molecules and rings.

diene: A molecule that contains two alternating double bonds.  A reactant in the Diels-Alder reaction.

dienophile: A reactant in the Diels-Alder reaction that contains a double bond.  Dienophiles are often substituted with electron-withdrawing groups.

dipole moment: A measure of the separation of charge in a bond or molecule.

doublet: Describes an NMR signal split into two peaks.

eclipsed conformation: Conformation about a carbon-carbon single bond in which all of the bonds off of two adjacent carbons are aligned with each other (0o apart when viewed in a Newman projection).

E isomer: Stereoisomer in which the two highest priority groups are on opposite sides= of a ring or double bond.

E1 elimination reaction: A reaction that eliminates a hydrohalic acid (like HCl, HBr, etc) to form an alkene.  A first order reaction that goes through a carbocation mechanism.

E2 elimination reaction: A reaction that eliminates a hydrohalic acid (like HCl, HBr, etc) to form an alkene. A second order reaction that occurs in single step, in which the double bond is formed as the hydrohalic acid is eliminated.

electronegativity: A term describing the electron piggishness of an atom. More technically, a measure of the tendency of an atom to attract the electrons in a covalent bond to itself. 

electrophile: Electron lover. A molecule that can accept a lone pair of electrons (a Lewis acid).

enantiomers: Molecules that are nonsuperimposable mirror ima= ges of each other.

equatorial: The bonds in a chair cyclohexane that are oriented along the equator of the ring.

ester: A molecule containing a carbonyl group adjacent to an oxygen (RCOOR').  Also a functional group.

ether: A molecule containing oxygen singly-bonded to two carbon atoms.  Also a functional group.  Ether often refers to diethyl ether. 

fingerprint region: Region of an IR spectrum below 1,500 cm-1. The fingerprint region of the IR spectrum is often complex and difficult to interpret. 

functional group: A reactivity center.

gauche conformation: A type of staggered conformation in which two big groups are next to each other

halide: A member of the VIIA column of the periodic table (like F, Cl, Br, I, etc).  Or a molecule that contains one of these atoms.  Also a functional group. 

Hückel's rule: A rule that states that completely conjugated planar rings with 4n+2 pi electrons are aromatic.

hybrid orbitals: Orbitals formed from mixing together atomic orbitals, like the spx orbitals, which result from mixing s and p orbitals.

hyperconjugation: Weak interaction (electron donation) between sigma bonds with p orbitals.  Hyperconjugation explains why alkyl substituents stabilize carbocations.

inductive effects: Electron donation or withdrawal by electropositive or electronegative atoms through the sigma bond framework.

intermediate: Any species formed in a reaction on the way to making the product. Typically, intermediates are unstable.

ionic bond: Bond in which the electrons are unshared between two atoms.

IR spectrosco py: An instrumental technique that measures IR light absorption by molecules.  Can be used to determine functional groups in an unknown molecule. 

isolated double bonds: Double bonds separated by more than one carbon-carbon single bond.

J value: The coupling constant between two peaks in an NMR signal.   Given in units of Hz. 

ketone: A compound that contains a carbonyl group attached to two carbons.   Also a functional group.

kinetic product: The product that forms the fastest. (This product has the lowest energy of activation.)

kinetics: The study of reaction rates.

Lewis acid:An electron pair acceptor.

Lewis base:An electron pair donor.

Markovniknov’s rule: A rule that states that electrophiles add to the less highly substituted carbon of a carbon-carbon double bond (or the carbon with the most hydrogen atoms).

mass spectrometry: An instrumental technique involving the ionization of molecules into fragments.  Can be used to determine the molecular weights of unknown molecules.

meso compounds: Molecules that have chiral centers but are achiral as a result of one or more planes of symmetry in the molecule.

meta: Describes the positions of two substituents on a benzene ring that are separated by one carbon.

meta-directing substituent: Any substituent on an aromatic ring that directs in coming electrophiles to the meta position.

molecular ion: The fragment in a mass spectrum that corresponds to the cation radical (M+)of the molecule. The molecular ion gives the molecular mass of the molecule.

molecular orbital theory: Model for depict ing the location of electrons that allows electrons to delocalize across the entire molecule. A more accurate but less user-friendly theory than the valence-bond model.

multistep synthesis: Synthesis of a compound that takes several steps to achieve.

n+1 rule: Rule for predicting the coupling for a proton = in 1H NMR spectroscopy. An NMR signal will split into n+1 peaks, where n is the number of equivalent adjacent protons.

natural product: A compound produced by a living organism.

nitrile: A compound contain a cyano group: a carbon triply-bonded to a nitrogen (CN).  Also a functional group

NMR: Nuclear magnetic resonance sprectroscopy.  A technique th at measures radiofrequency light absorption by molecules.  A powerful structure-determining method. 

node: A region in an orbital with zero electron density.

nucleophile: Nucleus lover. A molecule with the ability to donate a lone pair of electrons (a Lewis base)

nucleophilicity: A measure of the reactivity of a nucleophile in a nucleophilic substitution reaction.

organic compound: Carbon-containing compound.

optically active: Rotates plane-polarized light.

orbital: The region of space in which an electron is confined (the electron “apartment”).

ortho: Describes the positions of two substituents on a benzene ring that are on adjacent carbons.

ortho-para director: An aromatic substituent that directs incoming electrophiles to the ortho or para positions.

para: Describes the poitions of two substituents on a benzene ring that are separated by two carbons.

phenyl ring: A benzene ring as a substituent. Abbreviated Ph.

pi bond (a.k.a. p bond): A bond with electron density above and below the two atoms, but not directly between the two atoms. Found in double and triple bonds.

pKa:The scale for defining a molecule's acidity (pKa =-log Ka).

plane-polarized light: Light that oscillates in a single plane.

plane of symmetry: A plane cutting through a molecule in which both halves are mirror images of each other.

protic solvent: A solvent that contains O-H or N-H bonds.

proton: An H+ ion. Also a positively-charged nuclear particle.

R group: Abbreviation given to an unimportant part of a molecule.  Indicates Rest of molecule.

racemic mixture: A 50:50 mixture of two enantiomers.  Racemic mixtures are optically inactive (don't rotate plane-polarized light).

radical: An atom or molecule with an unpaired electron.

resonance structures: Structures used to better depict the location of pi and nonbonding electrons on a molecule. A molecule looks like a hybrid of all resonance structures.

s-cis conformation:  A conformation in which the two double bonds of a conjugated diene are on the same side of the carbon-carbon single bond that connects them. The required conformation for the Diels-Alder reaction.

s-trans conformation: The conformation in which the two double bonds of a conjugated diene are on opposite sided of the carbon-carbon single bond that connects them.

sigma bond (a.k.a. s bond): A bond in which electrons are located between the nuclei of the bonding atoms.  Single bonds are sigma bonds.

singlet: Describes an NMR signal consisting of only one peak.

SN1 reaction: A first order substitution reaction that goes through a carbocation intermediate.

SN2 reaction: A second order substitution reaction that takes place in one step and has no intermediates.

sp: A hybrid orbital made by mixing one s orbital and one p orbital.

sp2: A hybrid orbital made by mixing one s orbital and two p orbitals.

sp3: A hybrid orbital made by mixing one s orbital and three p orbitals.

staggered conformation: Conformation about a carbon-carbon single bond in which bonds off of one carbon are at a maximum distance apart from bonds coming off of an adjacent carbon (60odg apart when viewed in a Newman projection).

stereochemistry: Study of molecules in three dimensions.

stereoisomers: Molecules that have the same atom connectivity, but different orientations = of those atoms in three-dimensional space.

steric hindrance: Term referring to the way that atoms can shield a site by getting in the way of approach of a reactant.

substituent: A piece that sticks off of the main carbon chain or ring.

syn addition: A reaction in which two groups of a reagent X-Y add on the same face of a carbon-carbon double bond.

tautomers: Molecules that differ in the placement of a hydrogen and double bonds and are easily interconvertible. Keto and enol forms are tautomers.

thermodynamics: Study of the energies of molecules.

thermodynamic product: The reaction product with the lowest energy..

thiol:A molecule containing an SH group.  Also a functional group.

transition state: The highest point on the energy hill that takes one species into another.

triplet: Describes an NMR signal split into three peaks.

Z isomer: Isomer in which the two highest-priority substituents are on the same side of a double bond or ring.

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