MCAT Organic Chemistry - COMPLETE

International Union of Pure and Applied Chemistry (IUPAC)

simplies chemical naming; unambiguous relationship between the name and structure of a compound; no two compounds have the same name

parent chain

Longest Carbon Chain Containing the Highest-Order Functional Group

Numbering

highest priority functional group/substituted carbons with the lowest number; assign substituents the number of carbon they are attached to

heteroatoms

atoms besides carbon and hydrogen, like oxygen, nitrogen, phosphorus, or halogens

Substituents

functional groups that are not part of the parent chain; assign the number of carbon they are attached to; numeric and hyphenated prefixes are ignored while alphabetising

carbon chain substituents

end with -yl

n- means normal

multiple - prefixes di-, tri-, tetra-, etc. directly before substituents

Alkanes

simple hydrocarbon molecules with the formula C_nH_(2n+2); saturated - only single bonds

name is the Greek root describing the number of carbons followed by –ane

Alkyl halides

indicated by a prefix: fluoro–, chloro–, bromo–, or iodo–; number the carbon

alkenes

simple hydrocarbon molecules with the formula C_nH_2n; unsaturated - at least one double bond

ends with -ene; number starting carbon of bond before parent or before suffix; number of multiple bonds prefix added to suffix

alkynes

simple hydrocarbon molecules with the formula C_nH(_2n-2); unsaturated - at least one triple bond

end with -yne; number starting carbon of bond before parent or before suffix; number of multiple bonds prefix added to suffix

Alcohol/hydroxyl group

―OH

ends with alykl parent suffix - e + ol; higher priority than alkyl chains - number each before suffix; if no priority, hydroxy- substituent; often have common names - name of alkyl group + alcohol

diol/glycol

alcohol with two hydroxyl groups

entire hydrocarbon + -diol; number each hydroxyl group

geminal diols/hydrates

diols with hydroxyl groups on the same carbon

not commonly seen because they spontaneously dehydrate to produce carbonyl compounds

vicinal diols

diols with hydroxyl groups on adjacent carbon

carbonyl group

―C=O

chain-terminating substituents

appear in the end of carbon chains

Aldehyde

carbonyl group found at the end of the carbon chain

parent alkane - e + al; do not include number if on carbon 1; if not priority, oxo- prefix

common names: formaldehyde; acetaldehyde; propionaldehyde

aldose sugars

Ketone

carbonyl group somewhere in the middle of the carbon chain

parent alkane - e + al; always include number; also alkyl groups in alphabetical order + ketone, if not priority, oxo-/keto- prefix

common names; acetone (2-propanone; smallest ketone)

ketose sugars

carbon names adjacent to carbonyl

adjacent to the

carbonyl carbon is indicated by alpha (α), then beta (β), gamma (γ), and delta (δ)

both sides of ketone

Carboxylic (organic) acids/carboxyl group

contain both a carbonyl group (C=O) and a hydroxyl group (―OH) on a terminal carbon; also written (COOH); highest priority functional group

parent alkane - e + -oic acid

common names: formic acid, acetic acid, propionic acid

Esters

COOR; hydroxyl group is replaced with an alkoxy group

name of parent acid - -oic acid + -oate; if not priority, alkoxycarbonyl- prefix

aloxy group

-OR, where R is a hydrocarbon chain

amide

CONR, hydroxyl group is replaced by an amino group; complex—the amino nitrogen can be bonded to zero, one, or two alkyl groups

name of parent acid - -oic acid + -amide; substituents attached to nitrogen are labeled with N-; if not priority; carbamoyl-/amido- prefix

amino group

a substituent group containing nitrogen

anhydride

In the formation of an anhydride from two carboxylic acid molecules, one water molecule is removed; symmetric if 2 same acid, asymmetric if 2 different acids; cyclic if intramolecular reaction of dicarboxylic acid

name of parent acid - acid + anhydride

Order of priority

Carboxylic acid > anhydride > ester > amide > aldehyde > ketone > alcohol > alkene or alkyne > alkane

isomers

compounds with the same molecular formula but different structures; same molecular weights

relative term

structural/constitutional isomers

do not have the same connectivity; least similar; vary in physical and chemical properties

stereoisomers

have the same connectivity/structural backbone

For any molecule with n chiral centers, there are 2n possible stereoisomers

conformational isomers/conformers

type of stereoisomer, do not require bond breaking to interconvert, differ in rotation around single bonds; interconversion barrier may be easy to overcome at room temperature but not at low temps.

configurational isomer

type of stereoisomer, requires bond breaking to interconvert

diastereomers

type of configurational isomer, molecules with 2+ stereogenic centers that differ at some, but not all, of them; any stereoisomer that is NOT an enantiomer

optically active

enantiomers

type of configurational isomer, nonsuperimposable mirror images

optically active

cis-trans isomers (formerly geometric)

type of diastereomers, differ in arrangement around an immovable bond

physical properties

observable with no change in composition of matter

ex. melting point, boiling point, solubility, odor, color, density.

chemical properties

reactivity of molecule, resulting in change in composition; generally attributable to functional groups in the molecule.

Newman projection

molecule is visualized along a line extending through a carbon–carbon bond axis

staggered conformation

no overlap of atoms along the line of sight

anti conformation

type of staggered conformation; the two largest groups are antiperiplanar (in the same plane, but on opposite sides) to each other; lowest energy state

gauche conformation

type of staggered conformation; when the two largest groups are 60° apart

(also means unsophisticated or awkward)

eclipsed conformation

overlap of atoms along the line of sight; the two largest groups are 120° apart or on top of each other

totally eclipsed conformation

two largest groups directly overlap each other with 0° separation, synperiplanar (in the same plane, on the same side) ; highest energy state

ring strain

a type of instability that exists when bonds in a molecule form angles that are abnormal

arises from three factors: angle strain, torsional strain, and nonbonded/steric strain

Angle strain

when bond angles deviate from their ideal values by being stretched or compressed

Torsional strain

when cyclic molecules must assume conformations that have eclipsed or gauche interactions

Nonbonded/steric strain/van der Waals repulsion

when nonadjacent atoms or groups compete for the same space

flagpole interactions

steric interactions that occur between substituents attached to adjacent carbon atoms in cyclic organic compounds

axial equatorial orientations alternate around the ring

ideal cyclobutane conformation

puckered

ideal cyclopentane conformation

envelope

cyclohexane conformations

chair (most stable)

boat

twist/skew-boat

axial

substituents that are perpendicular to the plane of the ring; sticking up/down

equatorial

parallel to the plane of the ring; sticking out

chair flip

one chair form is converted to another; all axial and equatorial groups switch

bulkiest groups favor equatorial position to reduce flagpole interactions

half-chair conformation

half-chair, half-planar cyclohexane, highest energy level

cis ring

largest groups on same side (up/down) of the ring

trans ring

largest groups on opposite side (up/down) of the ring

optical isomers

another term for configurational isomers due to the fact they can rotate polarised light

chiral

mirror image cannot be superimposed on the original object; molecule lacks an internal plane of symmetry

from Greek word for hand

achiral

mirror image can be superimposed on the original object; molecule has at least one internal plane of symmetry

chiral center

carbon with four different substituents

optical activity

rotation of plane-polarized light by a chiral molecule

specific rotation

the unique angle an optically active compounds rotates polarised light

[α] = α_obs/cl

where [α] is specific rotation in degrees, α_obs is the observed rotation in degrees, c is the concentration in g/mL, and l is the path length in dm

dextrorotary (d-/(+))

compound that rotates the plane of polarised light to the right/clockwise

levorotatory (l-/(−))

compound that rotates the plane of polarised light to the left/counterclockwise

racemic mixture

when dextrorotary and levorotary enantiomers are present in equal concentration; rotations cancel and no optical activity is observed

can be separated by reacting with another compound’s enantiomer → makes diastereomers with different physical properties

cis isomer

simple substituents over a double bond on same side

trans isomer

simple substituents over a double bond on opposite sides

meso compound

a molecule with chiral centers that has an internal plane of symmetry

not optically active

configuration

spatial arrangement of atoms/groups in a molecule

relative configuration

configuration in relation to another chiral molecule

absolute conformation

exact spatial arrangement of atoms/groups in a molecule, independent of other molecules

Cahn–Ingold–Prelog priority rules

priority is assigned based on the atom bonded to the double-bonded carbons: the higher the atomic number, the higher the priority. If the atomic numbers are equal, priority is determined by the next atoms outward; again, whichever group contains the atom with the highest atomic number is given top priority. If a tie remains, the atoms in this group are compared one-by-one in descending atomic number order until the tie is broken.

E/Z nomenclature

compounds with polysubstituted double bonds

Z (zusammen) - together
E (entgegen) - opposite

R/S forms

used for chiral (stereogenic) centers in molecules

1. assign priority

2. Arrange in space so lowest priority is in the back/invert the stereochemistry (remember to switch assignment at end)

3. Draw a circle number substituents in numerical order

4. Assign R/S

5. Write the name

R configuration

rectus/right, clockwise from high to low priority

S configuration

sinister/left, counterclockwise from high to low priority

Fischer projection

horizontal lines = wedges, vertical lines = dashes

1. determine order of substituents and direction - designation is opposite

2. Swap the lowest priority group onto vertical axis, then switch the other two - designation is same

principal quantum number, n

corresponds to the energy level of a given electron in an atom and is essentially a measure of size; the smaller the number, the closer the shell is to the nucleus, and the lower its energy; 1 to ∞

azimuthal quantum number, l

corresponds to subshells; ranges from 0 to n−1; 0, 1, 2, and 3 correspond to the s, p, d, and f subshells; energy increases as the azimuthal quantum number increases

magnetic quantum number, m_l

corresponds to orbitals; ranges from −l to +l

orbital

describes the probability of finding an electron in a given region of space

s-orbital

spherical and symmetrical, centered around the nucleus

p-orbital

composed of two lobes located symmetrically about the nucleus and contains a node at the nucleus; ‘dumbbell’; three different orientations, along the x-, y-, or z-axis.

node

an area where the probability of finding an electron is zero

d-orbital

composed of four symmetrical lobes, the fifth looks like a donut wrapped around the center of a p-orbital, and contains two nodes; rare in org. chem.

spin quantum number, m_s

correspond sto electrons; ±½

molecular orbitals

two atomic orbitals combine, obtained mathematically by adding or subtracting the wave functions of the atomic orbitals

bonding orbital

signs of wave functions are the same; lower energy, more stable; likely to find electrons between atoms

antibonding orbital

signs of wave functions are different; higher energy, less stable; unlikely to find electrons between atoms

sigma (σ) bond

bonding molecular orbital is formed by head-to-head or tail-to-tail overlap

single bonds

σ bonds, accommodating two electrons; free rotation; longest bond

pi (π) bond

two p-orbitals line up in a parallel (side-by-side) fashion and their electron clouds overlap in a bonding orbital ;cannot exist independently of a σ bond

double bond

One π bond on top of an existing σ bond; hinders rotation; medium length bond

triple bond

A σ bond and two π bonds; hinders rotation; shortest bond

orbital hybridization

new orbital shapes formed by mixing different types of orbitals on one atom; a way of making all of the bonds to a central atom equivalent to each other

s-character

the percent of s-orbitals mixing into a hybrid orbital

ex. sp³ has 25%