9. Organic Chemistry Basics

What to know for organic chemistry questions:

1. Nomenclature

2. Structure/Behavior

3. Key Reactions

4. Lab Techniques

Alkanes

Simple hydrocarbons composed of only single bonds

How to name alkanes:

1. Identify/name longest chain (parent chain)

2. Label substituents so they have the lowest numbers

3. Name substituents with -yl suffix

   1. Di, tri, tetra for multiple of the same substituents

4. Iso and cyclo count towards alphabet

   If multiple paths, use one with MORE substituents

Functional Group

Group of atoms/bonds responsible for a characteristic set of behaviors (Alcohols, amines, etc.)

Naming with functional groups:

Find parent chain but chain molecule ending to functional group’s specific ending
If more than 2 functional groups, pick highest priority

Functional Group Naming Priorities:

Carboxylic Acid > Ester > Acid Chloride > Amide > Aldehyde > Ketone > Alcohol > Thiol > Amine > Alkyne > Alkene > Alkane

Alkyl halides and ethers are lower than alkane

Resonance

Equivalent structures in which electrons are delocalized

Electron Delocalization

Result of resonance that affects chemical properties and contribute to a molecule’s stability

Common Structures with Resonance on MCAT

Carboxylate anion, Peptide Bond

Conjugation

Form of resonance when three or more adjacent p-orbitals align (conjugated double bonds); π system

How to tell if a molecule is conjugated?

Alternating sigma and pi bonds

What spectrum are conjugated systems detected by?

UV-VIS (utilizes low EM energy)

Aromatic Compounds

Conjugated, cyclic, planar molecules that follow Huckel’s Rule (4n+2)

How to tell if a compound is aromatic?

Has a conjugated system, is planar, and followed 4n+2 (if it follows 4n rule, it is antiaromatic)

Benzene

Pyridine

Pyrimidine

Purine

Imidazole

Pyrrole

Borazine

Heterocycles

Aromatic rings containing atoms other than carbon

What is pyridine found in?

NiacinWha

What purine and pyrimidine found in?

Nucleic acids

How does resonance affect bond lengths?

Causes bonds to be intermediates of double and single bonds

Heat of Hydrogenation

How much energy would be released upon adding hydrogens to double bonds; Exothermic

Heat of Hydrogenation =

ΔH^o bonds broken - ΔH^o bonds formed

(ΔH^o x # of pi bonds, negative)

Why does benzene have a lower heat of hydrogenation than cyclohexene?

Benzene is resonance stabilized, so it has lower internal energy to begin with (more stable)

Heat of Hydrogenation Trend

1. Decreases with resonance stability

2. Decreases with more substituents (mono vs di vs tri-substituted)

3. Cis is higher than trans

Why is phenol more acidic than a regular alcohol?

If the phenol loses a hydrogen, there is resonance stability so it is more likely to donate a proton.

Structural/Constitutional Isomers

Same molecular formula but different structure (way their constituents are connected)

Should have different names but same # atoms

Stereochemistry

How molecules are arranged in space

Functional Isomers

Structural isomers with different functional groups

How to tell if two molecules are structural isomers?

Make sure there is different connectivity of substituents BUT have same formula (count # of molecules)

Tautomers

• Structural Isomers that interconvert with each other, in equilibrium

  • Keto-enol tautomerism

Keto-enol Tautomerism

Keto formed favored, enol form is a double bond and hydroxyl group with a enolate ion intermediate for reactions

Resonance vs. Tautomers

Resonance are the SAME structures with delocalized electrons

Tautomers are DIFFERENT structures due to breaking/forming bonds

Examples of Tautomers

1. Keto and enol

2. Enamine and imine

3. Lactams and lactims

4. Amids and amidic acids

Stereoisomers

Molecules with one pattern of connectivity have different spatial arrangement

3 ways Stereochemistry occurs:

1. Arrangement of single bonds (rotation)

2. Orientation (cis or trans) across double bond

3. Orientation at chiral center (R/S, d/l system)

Can double bonds be rotated?

No, they are locked in either cis or trans; rotating would break bond

Newman projections

Visualize orientation around a single bond; front carbon is a dot, back carbon is a circle

Eclipsed (close) vs. Staggered

Eclipsed is more unstable and higher energy due to torsional strain

Staggered Newman Subsets

1. Anti

2. Gauche

Eclipsed Newman Subsets

1. Eclipsed

2. Totally eclipsed

Anti Newman

Most stable, least torsional strain; maximum separation of 180^o

Gauche Newman

Staggered but closer together with 60^o separation

Eclipsed Newman

Contain overlapping orbitals (not the bulkiest ones)

Totally Eclipsed

Bulky groups overlap each other

What type of isomer does rotating around a single bond generate?

Conformational isomers

Which Newman projection orientation has the highest PE?

Total eclipsed because there is the most torsional strain

What is the ideal bond angle?

Tetrahedral, sp3 109.5^o angle

Conformational Isomers of Cyclohexanes

Boat, twist-boat, and chair; cyclohexane alternates but chair is most stable

Why does cyclohexane have isomers?

To resolve steric, torsional, and angle strain

Angle strain

Angle between single-bonded carbons deviates from 109.5

Torsional Strain

Eclipsing substituents on neighboring atoms (Newman)

Steric Strain

Substituents (including hydrogen) are too close together

What orientation in the chair do bulky substituents go on?

The equatorial orientation, where repulsions are minimum

Cis cycloalkane

Two substituents that point up or down together

Trans cycloalkane

Two substituents up and down

Can free rotation around C-C bond occur in cycloalkane?

No, there is too much strain in a cyclic molecule.

Cis double bond

Both substituents are on the same side of a double bond

Trans double bond

Substituents are on opposite sides (diagonal) of a double bond

How are fatty acids often described?

Cis or trans (for unsaturated because they contain double bonds)

Which fatty acids contain double bonds?

Unsaturated fatty acids (saturated only have single bonds)

Which unsaturated fatty acids are naturally occuring?

Cis because it prevents them from evenly stacking (trans causing health problems because of stacking)

E-Z Classification of Double Bonds

Based on Cahn-Ingold-Prelog (highest) priority of substituents on the double bond (Z or E)

Z-Isomers

Highest priority substituents are on the same side of double bond

E-Isomers

Highest priority substituents are on opposite sides of double bond

All cis-isomers are __-isomers and all trans-isomers are __-isomers

Z; E

Cahn-Ingold-Prelog Rule

E and Z classification based on atomic weights of substituents or the atomic weight of the atoms attached to substituents if the same

Chiral Centers (Stereocenter)

Atoms connected to an sp³ carbon with four unique groups; non-superimposable on mirror image

Are all stereocenters chiral centers?

No, a stereocenter can be achiral (like a E/Z double bond); BUT a chiral center is ALWAYS a stereocenter

Maximum number of stereoisomers =

2ⁿ, n = number of stereocenters

Chiral (enantiomers) vs. achiral molecules

Achiral molecules have a plane of symmetry and CAN be superimposed while enantiomers can not

Meso Compounds

Molecules that MUST have multiple stereocenters (usually 2) with a plane of symmetry, causing them to be achiral

Specific Rotation (l or d), [a]

Solutions of chiral compounds rotate planes of polarized light at unique angles (because of a mix)

Dextrorotary (d)

Clockwise (+) rotation of polarized light

Levorotary (l)

Counterclockwise (-) rotation of polarized light

What are most amino acids’ specific rotations?

Levorotatory (l); except for Cysteine

Cysteine’s R/S Configuration

R (due to thiol -SH group); all other amino acids are S

Specific Rotation Formula [a] =

a/cl

a = observed rotation (degrees)

c = concentration (g/mL)

l = length of tube (dm)

Racemic Mixture

50:50 mixture of stereoisomers; no rotation of light because +[a] and -[a] cancels out

Amino Acid Chirality

All amino acids are chiral except for glycine

% Enantiomeric Excess =

[a]_observed/[a]_pure

Only how much one exceeds the other (otherwise would be racemic)

R/S System

Follows Cahn-Ingold Rule to determine absolute configuration of stereocenters

How to determine R/S:

1. Assign substituent priority based off atomic weight

2. Draw lowest substituent in the back

3. Order of substituents 1-4 is left to right = R, right to left is S

   If lowest priority is in the front, true orientation is opposite

Enantiomers and Diastereomers

Distinctions between two isomers of the same molecule (all stereocenters orientation different or some the same)

Enantiomers

Non-superimposable mirror images; all stereocenters are orientated differently

Diastereomers

Not all stereocenters are orientated differently (some are the same); NOT mirror images

Vinyl Group

Group attached directly to double bond

Allylic Group

Group attached adjacent to double bond

Geminal Groups (usually diols)

Groups on the same carbon

Vicinal Groups

Groups on adjacent carbons