Structural Biochemistry/Organic Chemistry/Organic Chemistry Terms

Organic Chemistry Terms

Enantiomers: Two molecules that are mirror images of each other. They are non-superimposable.

Diastereomers: Two molecules that are not enantiomers. Thus, they are not mirror images of each other and non-superimposable.

Epimers: Two molecules that differ in configuration of only one stereocenter.

Stereoisomerism: same structure, but different spatial arrangements

Covalent bonding: formed by sharing of electrons

Ionic bonding: based on electrostatic attraction of two ions with opposite charges

Ionization potential (IP): energy to remove an electron from an atom

Electron affinity (EA): energy released when electron attaches itself to an atom

Net energy input - IP + EA

Pauli's exclusion principle: no orbital may be occupied by more than two electrons.

Hund's rule: degenerate orbitals, s.a. p orbitals, are first occupied by one e- each, all of these e- having the same spin

Aufbau principle: process of adding e- one by one to the orbital sequence

Energy splitting: energy by which the bonding level drops and anti-bonding level is raised

Constitutional or structural isomers: molecules with same molecular formula, but differ in the sequence in which the atoms are held together

Delocalize: tendency of e- to spread out

Chemical Thermodynamics: deals with changes in energy that take place when processes s.a. chemical reaction occurs; controls the extent to which a reaction goes to completion

Chemical Kinetics: concerns the velocity or rate at which the concentration of reaction and products change; describes the speed at which a reaction goes to completion

Reaction Mechanism: step-by-step explanation in molecular terms of how reactants are transformed into products; a mechanism involves the sequence of the breaking and forming of bonds and the identities of any intermediate molecules

Nucleophile ("nucleus-loving"): a species (generally electron rich) which reacts with species that are electron poor (i.e. nuclei)

Electrophile ("electron-loving"): a species (generally electron poor) which reacts with species that are electron rich (has unshared  electron pair(s))

Diasteromers: stereoisomers that are not mirror images.

Enantiomers: stereoisomers that are non-superimposable mirror images. They have same melting point, boiling point, refractive index, and same solubility properties.

Pyrolysis: when both C-H bonds and C-C bonds rupture

Bronstead-Lowry acid: proton donor

Bronstead-Lowry base: proton acceptor

Lewis acid: accepts electron pair

Lewis base: donates electron pair

Coulomb's Law: opposite charges attract (electrons to protons); like charges repel (- repel -; + repel +)

Node: region of space where the probability of finding the electron is zero; corresponds to where the wave function has a value of 0

3 Factors that control rate of chemical reactions: energy of activation, temperature, and concentration of reactants

Eclipse conformation: aligned; high energy

Staggered conformation: most stable, furthest away from each other; low energy

"Saturated": all bonds in alkanes are single bonds, all C atoms are sp3 hybridized

"Unsaturated": an organic molecule that contains a carbon-carbon double bond or triple bond.

"Hydrocarbons": only contain H and C

Hash: below the plane

Wedge: above the plane

Hyperconjugation: neighboring C-H bonds can overlap with partially filled p-orbitals; a stabilizing factor. Also, it explains the origin of inductive electron release by alkyl groups.

Petroleum "cracking": generates carbon free radicals catalytically

Radical chain mechanism: initiation step, propagation step (2), termination step (several)

Synthetic Organic Chemistry: science of producing more useful, structurally complex molecules from less structurally complex molecules by successive chemical reaction pathways

Ring strain: eclipsing strain + angle strain

Cycloalkanes: restricted rotation; Cn2n; may be eclipsing + angle strain; cis-trans isomerism

Cyclopropane: one rigid, planar conformation; full eclipsing of bonds; lots of eclipsing strain; lots of angle strain

Cyclobutanes : prefer a "folded conformation"; some angle strain; some eclipsing strain; no specific arrangement; no easily predictable preferred conformation

Cyclopentanes : prefer an "envelope conformation"; no angle strain; minor eclipsing strain; no specific arrangement of bonds; no easily predictable preferred conformation

Cyclohexanes : prefer a "chair conformation"; no angle strain or eclipsing strain; boat and twist boat are minor conformers; chair conformation has: 6 axial bond + 6 equatorial bonds, all bonds are staggered, substituted cyclohexanes have one preferred chair conformation

Halogenation : radical reaction in which a hydrogen atom in an alkane is replaced by halogen

Monosubstitued cyclohexanes : replace one H of cyclohexane by a methyl

Racemic mixture : an equal mixture of 2 enantiomers

Nucleophile substitution : nucleophiles-compounds with an unshared electron pair

Solvolysis : cleavage by solvent

Inductive effect : an effect which spreads out or concentrates electron density due to differences in electronegativity between 2 atoms; a transmissive through-bond phenomenon

Oxidation : an increase in number of bonds from C to a more electronegative element

Spectroscopy : the study of light energy absorption and emission by molecules; a technique for analyzing molecules based on how they absorb radiation. For identification: NMR, IR, UV, and MS.

Quanta : discrete package that organic molecules absorb energy in

Excitation : the absorbed energy produces motion

Chiral center : an atom that contains four different groups that are bonded to it. In order for a molecule to be chiral a chiral center must be present.

Conjugated systems : two double bonds that are separated by a single bond in between. The p-orbitals of the two double bonds overlap with each other across a sigma bond or a single bond.

Steric hindrance: A hindrance that prevents or slows a reaction due to the spatial arrangement of the molecules in the structure. The arrangement of molecules would be arranged in such a way as to block the site of attack.