MCAT Study Guide Ochem Ch. 3 – Structure 2017-08-15T06:45:05+00:00

I.          3.7  BONDING IN ORGANIC MOLECULES

A.     Hybridization

A mathematical combination of atomic orbitals centered on the same atom to produce a set of composite (hybrid) orbitals

B.     sp hybridization can be determined by attached groups + lone pairs

spx hybrid orbital s character p character # of attached atoms + # of lone pairs Bond angles Molecular geometry
sp 50% 50% 2 180º Linear
sp2 33% 67% 3 120º Trigonal planar
sp3 25% 75% 4 109.5º Tetrahedral

C.    Sigma bonds (σ bonds)

1.     Consists of 2 e-s that are localized between 2 nuclei

2.     Formed by end-to-end overlap of 1 hybridization orbital

3.     There is only ever 1 σ bond in a multiple bond (others are  π bonds)

D.    Pi bonds (π bonds)

1.     Composed of 2 e-s that are localized to the region that lies on opposite sides of the plane formed by the 2 bonded nuclei (not directly between, like the σ bond)

2.     Formed by alignment of 2 unhybridized p orbitals

II.          3.2  STRUCTURAL FORMULAS

A.     Saturated

Molecules with no double or triple bonds (no π bonds)

1.     H atoms = 2(C atoms) + 2

B.     Unsaturated

At least 1 π bond or a ring

C.    Degree of unsaturation (aka index of hydrogen deficiency):

1.     (2n + 2 – x)/2 → n = C atoms, x = H atoms

2.     Halogens are treated like Hs

3.     Oxygens are ignored

 

III.          3.3  BOND LENGTH AND DISSOCIATION ENERGY

A.     BDE (bond dissociation energy)

Energy required to break a bond homolytically

1.     1 electron per bond broken goes to each fragment of the molecule

2.     These fragments are now radicals

3.     *Not to be confused with heterolytic bond cleavage (dissociation), where both electrons go to one fragment, forming a cation and an anion

C – C C = C C ≡ C C – O C = O  C ≡ O
BDE 83 144 200 86 191 256
r in (Ǟ) 1.54 1.34 1.2 1.43 1.2 1.13

*r is bond length

The greater s character, the shorter the bond

 

IV.          3.4  ISOMERISM → very important!

A.     Constitutional isomers

Compounds that have the same molecular formula but whose atoms are connected together differently

B.     Conformational isomers

Compounds that have the same molecular formula and the same atomic connectivity, but differ only in rotation about a single σ bond)

1.     For saturated hydrocarbons, there are multiple orientations (conformational isomers):

a)     Staggered – more stable than eclipsed due to electronic repulsion

(1)   Anti-conformation (antistaggered)– most stable staggered form, where the two largest groups are 180º apart

(2)   Gauche conformation – usually less stable staggered form, where two largest groups are 60º apart

(a)   Can be more stable if the close R groups can form intramolecular H-bonds with each other

b)     Eclipsed – less stable than staggered

c)     Infinite other conformations that are less important

2.     Cyclohexane conformations:

a)     Chair conformation most stable; if functional groups, they are more stable in the equatorial (as opposed to axial) position

b)     Boat position less stable

C.    Stereoisomers

Compounds that have the same molecular formula and atomic connectivity, but differ in spatial arrangements of atoms

D.    Chirality

A property of a molecule that cannot be superimposed on its mirror image

1.     Achiral – molecules that have a plane of symmetry and can be superimposed on their mirror images

2.     Chiral center – an atom (usually carbon) with 4 different groups attached to it

a)     These carbons are called stereocenter, stereogenic center, or asymmetric center

3.     # of stereoisomers = 2n → n = chiral centers

 E.     Absolute Stereocenter Configuration

1.     Cahn-Ingold-Prelog rules are arbitrary rules to assign absolute configuration to a stereocenter:

a)     1:  Priority is assigned according to increasing atomic number. If isotopes are present, the higher-weight isotopes gets priority. If 2 identical atoms are attached to the stereocenter, the next atoms in the chains are compared until a difference is found

b)     2:  A multiple bond is counted as 2 single bonds (instead of saying a carbon is double bound to an oxygen, you’d say a carbon is bound to two oxygen)

c)     3:  Once priorities have been assigned, the molecule is rotated so that the lowest priority group points directly away from the viewer. Then trace a path from highest priority to lowest

(1)   Clockwise path = R configuration (R for “right”)

(2)   Counterclockwise path =  S configuration (S sounds like “left”)

F.     Enantiomers

Stereoisomers that are non-superimposable mirror images (“en” is almost but not the same, as “an” →  they are mirror images of each other)

1.     Properties:

a)     Same melting point, boiling point, dipole moment, dielectric constant

b)     Different optical activity – see below

G.    Optical activity

1.     Optically active – a compound that rotates the plane of polarized light

2.     Dextrorotary (d or +) – rotates plane-polarized light clockwise (right)

3.     Levorotary (l, or -) – rotates a plane-polarized light counterclockwise (left)

4.     A pair of enantiomers will rotate plane-polarized light with equal magnitude but in opposite directions!

a)     A 50-50 mix of antiomers (racemic mixture) will not rotate at all

b)     Configuration of isomer is not related to direction of optical rotation

H.    Diastereomers

1.     Stereoisomers that are not enantiomers (non-superimposable non-mirror images)

a)     These have to have > 1 stereocenters (or else they’d be enantiomers)

I.       Epimers

1.     Subclass of diastereomers that differ in their absolute configuration at a single chiral center (D-glucose vs D-galactose)

a)     The prefix D on the sugars refers to the orientation of the -OH group on the highest numbered chiral center (C-5)

b)     When the -OH is on the left, is is L-sugar

c)     When the -OH is on the right, it is a D-sugar

J.      Anomers (think α-nomers)

1.     Epimers that for as a result of ring closure (sugar chemistry)

a)     EX:  α-D-   glucopyranose and β-D-glucopyranose

2.     Remember,  α looks like a fish in the sea (down) and β (bird) is in the sky (up)

K.     Meso Compounds

1.     Compounds with > 1 stereocenters that have an internal plane of symmetry in the compound

2.     This reduces the amount of stereoisomers to 3 instead of 4 (compare to diastereomer section)

3.     Not optically active! The mirror images cancel each other out

L.     Geometric Isomers

1.     Diastereomers that differ in orientation of substituents around a ring or double bond (no rotation with these)

a)     Ring:

(1)   Cis (same side) – less stable

(2)   Trans (opposite sides – more stable

b)     Double bonds:

(1)   Z (“zame” side) – most stable

(2)   E (opposite side) – less stable

M.    Summary of isomers

 

XI.          1.11  PHYSICAL PROPERTIES OF HYDROCARBONS

A.     Melting point and boiling point

Indicates how well molecules interact with each other

1.     Interactions are primarily due to London dispersion forces (attractive force due to temporary dipoles due to asymmetric electron distribution

2.     These forces must be overcome to go solid → liquid or liquid → gas (melting, boiling)

3.     Branching inhibits these forces by reducing surface area available for intermolecular interaction

4.     MW increases the surface are for these forces to interact,

5.     RULES:

a)     Branching decreases MP and BP

b)     MW increases MP and BP

c)     H-bonding increases MP and BP (Must have N, O, or F!)

 

XII.          1.12:  THE ORGANIC CHEMIST’S TOOLBOX

A.     Reaction Intermediates

1.     These are stabilized in 2 ways:  inductive effects and resonance (see below)

2.     3 types

a)     Carbocations (carbonium)

(1)   positively charged species with full (+) charge on a C

b)     Alkyl radicals

(1)   1 unpaired electron

c)     Carbanions

(1)   Negatively charged species with full (-) charge localized on C

STABILITY CONTINUUM
Carbocations Ml
Alkyl radicals ethyl
Carbanions Methyl
More stable Less stable
Less reactive More reactive
Low energy High energy

 B.     Inductive Effects (σ bonds)

1.     Substituents surrounding a reaction intermediate can be thought of as either electron-donating or electron withdrawing groups

a)     Electron donating groups push e density away from themselves through σ bonds

(1)   These are less electronegative than carbon

b)     Electron-withdrawing groups pull es toward themselves through σ bonds

(1)   These are more electronegative than carbon

2.     Inductive effect – the stabilization of reaction intermediates by the sharing of es through σ bonds

3.     EX:  Why is trichloroacetic acid stronger than acetic acid?

a)     The Cl pull es towards themselves, making the O—H bond weaker (dissociates more easily)

b)     The conjugate base is very weak and stable

C.    Resonance Stabilization (π bonds)

1.     Conjugated system – a system containing 3 or more atoms that each bear a p orbital; these orbitals are aligned, creating the possibility of delocalizing electrons

a)     Localized es  – ones that are confined to 1 orbital between 2 atoms, or are a lone pair

b)     Delocalized es – e-s that are allowed to interact with orbitals on adjacent atoms

2.     3 Basic principles of resonance stabilization

a)     Resonance structures usually involve e-s that are one atom away from a pi bond or unhybridized p orbital

b)     Resonance structures of the lowest energy are the most important (3 criteria)

(1)   Resonance contributors in which the octet rule is satisfied are most important

(2)   Resonance structures that minimize separation of FC are best

(3)   (-) charge should be on most electronegative atom, and vice versa

c)     Resonance structures can never be drawn through atoms that are truly sp3 hybridized (4 σ bonds)

3.     EX

a)     Acidity of functional groups

(1)   Propanol, if it loses a proton, is not very stable; no resonance!

(2)   This makes the conjugate base (alkoxide ion) very strong (reactive)

(3)   Carboxylic acid, if it loses a proton, is stable due to resonance

(4)   This makes the conjugate base very weak (unreactive)

D.    Ring Strain

1.     Arises when bond angles between ring atoms deviate from the ideal angle predicted by hybridization of the atoms (cyclopropane and cyclobutane have high degrees strain)

2.     Deviation of the bond angles from the  normal 109º weakens the C—C bonds and increases reactivity

a)     Generally, C—C bonds are almost impossible to cleave via hydrogenation in a linear alkane, but are much easier to cleave an a cycloalkane with ring strain

MCAT Study Guide Ochem - Kim Matsumoto


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