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Alcohol

A compound containing an -OH group. Compound is named by replacing the -e in the corresponding alkane with -ol.

Aldehyde

Compound with a HC=O as a terminal group. These are named by replacing the -e in the corresponding alkane with -al. (Formaldehyde, Acetaldehyde, Propionaldehyde).

Alkanes

Compounds with only carbon and hydrogen atoms with sigma bonds (single bonds). As chain length increases, boiling point, melting point, and density increase. However, chain branching decreases boiling point and density.

Alkenes

Compounds containing carbon-carbon double bonds. Named by replacing the -ane in the corresponding alkane with -ene.

Alkynes

Compounds containing carbon-carbon triple bonds. The compound is named by replacing the -ane in the corresponding alkane with -yne.

Amide

A compound that has a carbonyl group (C=O) bonded to nitrogen. They are named by dropping the -oic in the corresponding acid and adding -amide. Substituents attached to the nitrogen are listed following N-.

Amine

A compound in which a carbon is bonded to a nitrogen with a single bond. They are named by replacing the -e in the corresponding alkane with -amine. Substituent groups attached to the nitrogen can be named using the prefix N-.

Carboxylic Acid

A compound with a COOH terminal group. Compounds are named by replacing the -e in the corresponding alkane with -oic acid. Formic acid (methanoic acid), acetic acid (ethanoic acid) are common names for the simplest types.

Ester

Compound with a COOR group. They are named as alkyl or aryl alkanoates.

Ether

Compound with an oxygen attached to two alkyl groups (R-O-R'). Compound can be named either as an alkoxyalkane or as an alkyl ether.

Haloalkanes

Alkanes with a halogen substituent. Compound can be named either as a haloalkane or alkyl halide.

Imine

Compound with a carbon double-bonded to nitrogen (C=N).

Ketone

Compound with a nonterminal carbonyl group (R-C=O-R'). Ketones are named by replacing the -e in the corresponding alkane with -one.

Chiral Molecule

A molecule not superimposable on its mirror image. It must have at least one central atom with four different attached atoms. However a molecule with multiple centers may not fit into this category.

Conformational Isomer

Stereoisomers that differ by rotation about one or more ingle bonds, usually represented using Newman projections.

Diastereomers

Stereoisomers that are not mirror images of each other. Diastereomers differ in their configurations in at least one chiral center and share the same configuration in at least one chiral center. They have the same chemical properties but different physical properties.

Enantiomers

Nonsuperimposable stereoisomers that are mirror images of each other. Enantiomers differ in configuration at every chiral center but share the same chemical and physical properties in a nonstereospecific environment. Optical activity is different.

Geometric Isomers

Isomers that differ in the arrangement of substituents around a double bond. Geometric isomers are often differentiated using either the cis/trans notation for simple compounds or Z/E notation for more complex compounds, and can differ in their physical and chemical properties.

Meso Compound

A stereoisomer with an internal plane of symmetry. Meso compounds are optically inactive.

Racemic Mixture

A mixture that contains equal amounts of the (+) and (-) enantiomers. Racemic mixtures are not optically active.

Stereoisomers

Compounds with the same molecular formula and connectivity but different arrangements in space. Stereoisomers include geometric isomers, diastereomers, enantiomers, conformational isomers, and meso compounds.

Strucutral Isomers

Compounds with the same molecular formula but different connectivity. Structural isomers have different chemical and physical properties.

Alpha Carbon

The first carbon atom adjacent to the carbon attached to the targeted functional group.

Leaving Group

Atoms that can dissociate to form a stable species after accepting electron pairs. Weak bases tend to be good leaving groups.

Nucleophile

A species that tends to donate electrons to another atom. They are attracted to positive charge, a nucleus, (protons and neutrons). In protic solvents and situations with different attacking atoms, its strength correlates to size. In aprotic solvents with the same attacking atom, its strength corresponds to basicity.

Secondary Carbon

Carbon atom bonded to two other carbon atoms.

Sn1 Reactions

Unimolecular nucleophilic substitution reactions. Leaving group leaves, forming a carbocation that then reacts with a nucleophile. Reactivity increases from methyl to primary to secondary to tertiary with increasing carbocation stability.

Sn2 Reactions

Bimolecular nucleophilic substitution reactions occur through a concerted mechanism where the nucleophile attacks as the leaving group starts to leave. Reactivity increases from tertiary to secondary to primary with decreasing steric effects.

Activating Substituents

Activating substituents are electron-donating substituents already attached to the aromatic ring. They increase the ring's potential to react with other species. Activating species are ortho/para directing.

Aromatic Compound

Cyclic, fully conjugated planar compound with 4n+2∏ electrons. Each atom in the compound must possess a p orbital in order to allow for maximum conjugation.

Benzyl

The term used to describe toluene substituted at the methyl position when it is used as a substituent.

Deactivating Substituents

Electron-withdrawing substituents already attached to the aromatic ring. They decrease the ring's potential to react with other species. These are meta-directing, except ortho/para directing halogens.

Hückel's Rule

In order for a ring to be aromatic, it must contain 4n+2 conjugated electrons.

Phenyl

Term used to describe benzene when it is used as a substituent.

Resonance

Describes a situation where the atomic connectivity remains unchanged while the electron distribution between the atoms changes.

Oxidation of Alcohols

Primary alcohols can be oxidized to aldehydes using PCC and further oxidized to carboxylic acids using KMnO₄, Na₂Cr₂O₇, or CrO₃. Secondary alcohols can be oxidized to ketones using any of these oxidants.

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Enolization

Process by which the carbonyl oxygen of a ketone gets protonated to form an enol.

Tautomers

Isomers that can interconvert by exchanging the location of a proton.

Hydrogen Bonding

Strong intermolecular bond between a hydrogen atom bonded to an electronegative atom (like F, O, or N) and lone electron pairs on the F, O, or N atom.

Grignard Reagent

An alkyl magnesium halide used to make carbon-carbon bonds. Alkyl group in a Grignard reagent has a negative charge and acts as a nucleophile attacking electrophilic carbons.

Agarose Gel Electrophoresis

Type of Chromatography, used to separate nucleic acids based on size/length of chain. The media serves as the stationary phase and the nucleic acid as the mobile phase. Negatively charged nucleic acids travel toward the anode (positive end). Smaller strands travel faster than larger chains.

Centrifugation

Separation technique used to separate particles according to mass, shape and density. Greater mass and density settle near the bottom while lighter compounds remain on top. This is meant to simulate a gravitational pull.

Chromatography

Separation technique using retention time of a compound in the mobile phase as it travels through the stationary phase to separate compounds with different chemical properties.

Distillation

Separation technique exploiting different boiling points for liquid mixture. Mixture is heated slowly and as the liquid with the lower boiling point converts into its gaseous form, it passes through a condenser where it cools back to its liquid form.

Filtration

Separation technique separating solids from liquids. This utilizes a filter allowing liquids and small particles to pass through while retaining larger particles.

Extraction

Separation method exploiting solubility properties. Two solvents are usually used, one aqueous and one organic, and teh component of interest will be soluble in one phase while the impurities will be soluble in the other solvent.

Recrystallization

Separation technique used to purify particles of interest from a mixture of solids. Mixture is dissolved in saturating amounts in warm solvent. As the solution cools, the pure substance crystallizes while impurities remain in solution.

SDS-PAGE

Type of chromatography used to separate proteins based on mass. SDS binds to the proteins, giving them a negative charge cancelling the effect of charges from the individual amino acids. Lighter proteins travel faster than heavier ones.

Sublimation

Separation technique used to separate a mixture of solids from impurities that have different vapor pressures. As it sublimes directly into the gaseous phase, the gas is condensed on a cold surface.

Isoelectric Focusing

Type of chromatography used to separate proteins based on charge. Stationary gel has an established pH gradient and the mobile phase proteins will travel to the point where the pH equals their isoelectric point.

Aldose

Sugar containing an aldehyde group -CH=O

Anomers

Cyclic stereoisomers differing in configuration at the hemiacetal carbon (C1). In a 6-membered ring, if the hydroxy group attached to C1 and the substituent attached to C5 are trans, the molecule is referred to as the α anomer. If both groups are cis, the molecule is reffered to as ß anomer. C1 and C5 are carbons adjacent to the oxygen in the ring.

Epimers

Isomers differing in configuration at only one stereogenic center.

Glycosidic Center

Bond that forms when the hemiacetal group of one sugar reacts with a hydroxyl group on another sugar to form an acetal group in between the two sugars. Polysaccharides are held together by glycosidic linkages.

Ketose

Sugar containing a ketone group R-C=O-R'

Monosaccharides

Small unit of carbohydrates. Glucose and fructose are examples.

Mutarotations

Conversion of an α anomer to a ß anomer, occuring when a sugar ring opens, rotates about the bond between C1 and C2, and closes.

Conjugated Proteins

Proteins requiring a covalently bonded prosthetic group to function properly. Hemoglobin is an example.

Isoelectric Point

Point at which a compound is electrically neutral.

Primary Structure of Proteins

Sequence of amino acids in a polypeptide, read from N-Terminus to the C-Terminus.

Secondary Structure of Proteins

Regularly repeating local structures such as α-Helices and ß-pleated sheets often formed by hydrogen bonds between residues nearby on the chain.

Tertiary Structure of Proteins

Three-dimensional structure of a peptide, results from hydrophobic and hydrophilic interactions between residues far apart on the chain. Disulfide bonds and hydrogen bonds can also add to the tertiary structure of the protein.

Quaternary Structure of Proteins

Different polypeptide chains, each referred to as a subunit, associate together to form a functional protein.

Zwitterion

Amphoteric (reacts as acid or base) compound with no net electric charge.

Enamines

An amino group attached to a carbon in a carbon-carbon double bond.

Nitrile

Nitrogen triple-bonded to a carbon.

Primary Amine

An amine where the nitrogen atom is attached to one alkyl chain (H₂NR).

Secondary Amine

An amine where the nitrogen atom is attached to two alkyl chains (HNR₂).

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