Organic Chemistry

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

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Alcohol

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-a compound that has a HC=O as a terminal group
-named by replacing the -e in the corresponding alkane with -al

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Aldehydes

Front 3

-compounds consisting of only carbons and hydrogens bonded with sigma bonds
-as chain length increases, boiling point, melting point, and density increase
-however, chain branching decreases both boiling and density

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Alkanes

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-compounds containing carbon-carbon double bonds
-the compound is named by replacing the -ane in the corresponding alakne with -ene

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Alkenes

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

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Alkynes

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-a compound that has a carbonyl group bonded to nitrogen
-named by dropping the -oic acid in the corresponding acid and adding -amide
-substituents attached to the nitrogen are listed following N-

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Amide

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

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Amine

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-a compound that has an COOH terminal group
-named by replacing the -e in the corresponding alkane with -oic acid

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Carboxylic Acid

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-a compound that has a COOR group
-named as alkyl or aryl alkanoates

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Ester

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-a compound that has an oxygen attached to two alkyl groups (R-O-R')
-the compound can be named alkoxyalkane or as an alkyl ether

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Ether

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-alkanes with halogen substituent
-the compound can be named as an alkyl halide

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Haloalkanes

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-a compound that has carbon double bonded to nitrogen

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Imine

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-a compound that has a nonterminal carbonyl group
-named by replacing the -e in the corresponding alkane with -one

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Ketone

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-a molecule that is not superimposable upon its mirror image
-it must have at least one central atom attached to four different atoms

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Chiral Molecules

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-molecule with multiple Chiral centers such as meso compound

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Achiral Molecules

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-stereoisomers that differ by rotation about one or more single bonds, usually represented using New projections

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Conformational Isomer

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-stereoisomers that are not mirror images of each other
-differ in their configurations in at least one chiral center and share the shame configuration in at least on chiral center
-they have the same chemical properties but different physical properties

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Diastereomers

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

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Enantiomers

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-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

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Geometric Isomers

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-a stereoisomer with an internal plane of symmetry
-optically inactive

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Meso Compounds

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-a mixture that contains equal amounts of the (+) and (-) enantiomers
-are not optically active

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Racemic Mixture

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

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Stereoisomers

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-compounds with the same molecular formula but different connectivity
-have different chemical and physical properties

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Structural Isomers

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-carbon adjacent to the carbon containing the functionality under consideration

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Alpha Carbon

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-atoms that can dissociate to form a stable species after accepting electron pairs
-weak bases are good candidates

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Leaving Group

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-a species that tends to donate electrons to another atom
-attracted to the positive charge
-with the same attacking atom (OH-, CH3O-) in aprotic solvents, nucleophile strength correlates to basicitiy
-in protic solvents and in situations where the attacking atom is different (OH-, SH-), strength correlates to size

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Nucleophile

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-a carbon atom bonded to two other carbon atoms

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Secondary Carbon

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-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

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SN1

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-bimolecular nucelophilic 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

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SN2

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-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

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Activating Substituents

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-cyclic, fully conjugated planar compound with 4n + 2(pi) electrons
-each atom in the compound must possess a p orbital in order to allow for maximum conjugation

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Aromatic Compound

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

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Benzyl

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-electron-withdrawing substituents already attached to the aromatic ring
-they decrease the ring's potential to react with other species
-with the exception of halogens (which are ortho/para directing), these species are meta

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Deactivating Substituents

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-the rule stating that in order for a ring to be aromatic, it must contain 4n + 2 conjugated pi electrons

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Huckel's Rule

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-the term used to describe benzene when it is used as a substituent

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Phenyl

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-describes a situation where the atomic connectivity remains unchanged while the electron distribution between the atoms changes

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Resonance

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-primary alcohols can be oxidized to aldehyde using PCC and further oxidized to carboxylic acids using KMnO4, Na2Cr2O7, or CrO7
-secondary alcohols can be oxidized to ketons using any of these oxidants

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Oxidation of Alcohols

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-the process by which the carbonyl oxygen of a ketone gets protonated to form an enol

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Enolization

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-isomers that can interconvert by exchanging the location of a proton

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Tautomers

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

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Hydrogen Bonding

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-an alkyl magnesium halide that is used to make carbon-carbon bonds
-the alkyl group has a negative charge and acts as a nucelophile attacking electrophilic carbons

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Grignard Reagent

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-an amino group attached to a carbon in a carbon-carbon double bond

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Enaminers

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-a nitrogen triple-bonded to a carbon

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Nitrile

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-an amine where the nitrogen atom is attached to one alkyl chain (H2NR)

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Primary Amine

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-an amine where the nitrogen atom is attached to two alkyl chains (HNR2)

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Secondary Amine

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-type of chromatography that is used to seperate nucleic acids based on size
-the agarose gel serves as the stationary phase and the nucleic acid serves as the mobile phase
-the negatively charged nucleic acids travel toward the anode
-smaller strands of nucleic acids travel faster than larger ones

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Agarose Gel Electrophoresis

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-a separation technique used to separate particles according to mass, shape, and density
-particles of greater mass and density settle near the bottom of the test tubes, while lighter compounds remain on top

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Centrifugation

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-a seperation technique that uses the retention time of a compound in the mobile phase as it travels through the secondary phase to separate compounds with different chemical properties

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Chromatography

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-a separation technique used to seperate liquids with different boiling points
-the mixture is heated slowly, and as the liquid with lower boiling point converts into its gaseous form, it passes through a condenser, where it cools back into its liquid form

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Distillation

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-a method used to separate a component in a mixture by exploiting its solubility properties
-two solvents are usually used (one aqueous and one organic), and the component of interest will be soluble in one phase, while the impurities will be soluble in the other solvent

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Extraction

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-a separation technique used to separate solids from liquids
-this technique utilizes a filter than allows liquids and small particles to pass through while retaining larger particles

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Filtration

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-type of chromatography used to separate proteins based on charge
-the stationary gel has an established pH gradient and the proteins (mobile phase) will travel to the point where the pH equals their isoelectric point

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Isoelectric Focusing

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

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Recrystallization

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-type of chromatography used to separate proteins based on mass
-SDS binds to proteins, giving them a large negative charge that cancels the effect of the charges from the individual amino acids
-lighter proteins travel faster than heavier ones

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SDS-PAGE

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-a separation technique used to separate a mixture of solids from impurities that have different vapor pressures
-the sample is heated under a vacuum
-as it sublimes directly into the gaseous phase, the gas is condensed on a cold surface

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Sublimination

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-sugar that contains an aldehyde group

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Aldose

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-cyclic sterioisomers that differ in configuration at the hemiacetal carbon (C1)
-in a six-membered ring, if the hydroxy group attached to C1 and the substituent attached to C5 are trans, the molecule is referred to as the alpha anomer
-if both groups are cis, then the molecule is referred to as the beta anomer
-note that C1 and C5 are carbons adjacent to the oxygen in the ring

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Anomers

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-isomers that differ in configuration at only one sterogenic center

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Epimers

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-the 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
-polysacccharides are held together

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Glycosidic Linkages

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-sugar that contains a ketone group

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Ketose

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-the smallest unit of carbohydrates
-e.g., glucose and fructose

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Monosaccharides

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-the conversion of an alpha anomer to a beta anomer that occurs when a sugar ring opens, rotates about the bond between C1 and C2, and closes

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Mutarotation

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-proteins that require a covalently bonded prosthetic group to function properly
-hemoglobin is an example of such proteins

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Conjugated Proteins

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-the point at which a compound is electrically neutral

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Isoelectric Point

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-the sequence of amino acids in apolypeptide, read from the N-terminus to the C-terminus

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Primary Structure of Proteins

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-different polypeptide chains, each referred to as a subunit, associate together to form a functional protein

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Quaternary Structure of Proteins

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-regularly repeating local structures such as alpha-helices and beta-pleated sheets often formed by hydrogen bonds between residues that are nearby on the chain

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Secondary Structure of Proteins

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-three-dimensional structure of a peptide that 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

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Tertiary Structure of Proteins

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-amphoteric compound with no net electric charge

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Zwitterion