Organic Chemistry 1

Question 1

What effect does multiple bonding have on bond energy and bond length?

Answer 1

Multiple bonding decreases bond length.

Multiple bonding increases bond energy.

Question 2

What effect does multiple bonding have on rigidity in molecular structure?

Answer 2

• Multiple bonding increases rigidity in molecular structure.
• Single bonds can rotate, but double and triple bonds can’t.
• Even partial double bonds like those found in the peptide bond prevents free rotation.

Question 3

What are isomers?

Answer 3

Same molecular formula, different structural formula.

“Same in writing, different in drawing…”

Question 4

What are positional structural isomers?

Answer 4

Positional isomers: structural isomers that have the same functional groups positioned differently.

Question 5

What are functional structural isomers?

Answer 5

Functional isomers: structural isomers that have different functional groups.

Question 6

What are constitutional isomers?

Answer 6

Structural (constitutional) isomers have the same molecular formula, but different connectivity.

Question 7

What are geometric isomers?

Answer 7

Geometric isomers have the same molecular formula, same connectivity, but have different orientation across a double bond.

When both sides of the double bond contains the same 2 groups, then cis and trans is used.

Cis = same side, Trans = opposite sides.

When different groups are attached to either side, Z and E is used.

Z is when the higher priority groups (ranked according to the Cahn-Ingold-Prelog rules) are orientated on the same side across the double bond. Zusammen is the German word for together.

E is when the higher priority groups are orientated on different sides across the double bond. Entgegen is the German word for opposed.

Question 8

What are stereoisomers?

Answer 8

• Stereoisomers have the same molecular formula, same connectivity, but have different 3-D arrangements across one or more asymmetric (chiral) centers.
• Chiral center is any atom with 4 different entities attached to it.
• You can’t have stereoisomers if you don’t have a chiral center.

Stereoisomers have the same chemical properties.

In rings, it is easier to assign stereoisomers as cis/trans rather than R or S. Cis is having the same groups on the same side of the ring.
Trans is having the same groups on different sides of the ring.

Question 9

What are enantiomers?

Answer 9

Enantiomers are mirror images of each other.

That means ALL chiral centers in one enantiomer is reversed in the other.

Enantiomers have the same physical properties.

Question 10

What are diastereoisomers?

Answer 10

Diastereomers - more than one chiral center, inversion of stereochemistry on some but not all of its chiral centers.

For examples, diastereomers would have stereochemistries of
(R)-(R) vs (R)-(S).
Another example of diastereomers would be (R)-(R)-(S)-(R) vs (R)-(R)-(R)-(R).

Diastereomers have different physical properties.

Question 11

Meso compounds

Answer 11

• Meso compounds may have chiral centers, but as a molecule, they are achiral and optically inactive.
• Meso compounds reduce the total number of stereoisomers.

A compound will have a total of 2^{#chiral centers}stereoisomers if it is not meso.

Question 12

Diastereomers vs Stereoisomers

Question 13

What are D and L regarding stereoisomers?

Answer 13

Note: in biological molecules, people use D and L for R and S, respectively.

Caution: D and L (absolute configurations) are NOT the same as d and l (relative configuration). Read the section below on rotation of polarized of light for more details.

Question 14

conformational isomers

Answer 14

• Conformational isomers have the same molecular formula, same connectivity, same stereochemistry, but can rotate about a single bond to switch between different conformations.
• Technically, conformational isomers are not really isomers because you don’t have to break any bonds to convert from one conformation to another. They are more accurately called conformers.

Conformers about a single bond

Eclipsed

• Syn-periplanar: highest torsional strain, most unstable, bulky groups eclipse each other.
• Anticlinal eclipsed: high torsional strain, unstable, bulky groups eclipse hydrogens.

Staggered

• Gauche: low torsional strain, stable, bulky groups 60° staggered.
• Anti: lowest torsional strain, most stable, bulky groups 180° staggered.

Single bonds will rotate such that it achieves the most stable conformation.

Question 15

Newman Projection Models

Question 16

Cyclohexane: Chair, Twist Boat, Boat Conformations

Answer 16

• Chair: most stable, everything is staggered.
• Twist boat: less stable, things are not completely eclipsed.
• Boat: least stable, everything is eclipsed.

Hexose rings will twist and turn to achieve the most stable conformation.

Question 17

**Cyclohexane: Axial vs Equatorial **

in chair and boat conformations

Answer 17

Steric interactions

• Axial: most unstable because the axial groups are orientated with a high degree of clashing.
• Equatorial: most stable because the equatorial groups are orientated away from one another.

Bulky groups like to be in the equatorial position.

Question 18

Torsional strain

Answer 18

the strain due to eclipsing of groups across a single bond

Question 19

Conformation stability

Answer 19

Most stable conformation: completely staggered (chair), with bulky groups in the equatorial position.

Least stable conformation: completely eclipsed (boat), with bulky groups in the axial position.

Question 20

polarization of light, specific rotation

Answer 20

• Light is an electromagnetic wave..Electromagnetic waves are waves of electric and magnetic fields (in phase, but perpendicular to each other and also to the direction of propagation).
• Normal light has the EM fields in all directions (in a 360° circle perpendicular to the direction of propagation).
• Polarized light has EM fields all in one direction.
• Specific rotation: chiral molecules containing a single enantiomer will rotate polarized light (to varying degrees) either to the left or to the right. This is why chiral molecules are said to be “optically active”.
• Left rotation: (-) or l or levorotatory.
• Right rotation: (+) or d or dextrorotatory.
• Caution: (+) or (-) does NOT correspond to R/S configurations.
• Caution: d and l is NOT the same as D and L. The upper case letters denote absolute configurations in sugars.

Question 21

absolute and relative configuration

(Assigning R and S)

Answer 21

Steps in assigning (R) and (S) - refer to figure.

• a. Is the carbon center chiral? For our molecule, the answer is yes because 4 different groups are attached to the carbon atom.
• b. Assign priorities according to the Cahn-Ingold-Prelog rules (see below).
• c. Turn the molecule such that the lowest priority group is at the back.
• d. Rotate from the 1st to 2nd to 3rd priority group like a steering wheel. It’s (R) if you end up turning right, and it’s (S) if you end up turning left.note: if you’re good at visualizing stuff, you do this much faster by skipping step c.

Absolute configuration is the (R) or (S) that’s labeled on the chiral centers.

Relative configuration is always defined in relationship to another chiral center. The direction that a molecule rotates plane-polarized light is the prime example of relative configuration.

Question 22

conventions for writing R and S forms

Answer 22

If only 1 chiral center

• (R/S)-molecule, where R/S is the absolute configuration and molecule is the name of the compound.
• For example, (R)-2-hydroxyl-propanal.

If more than 1 chiral center

• (#R/S, #R/S)-molecule, where # is the carbon number (in ascending order), R/S is the absolute configuration, and molecule is the name of the compound.
• For example, (2R,3S)-2,3,4-hydroxyl-butanal.

Question 23

conventions for writing E and Z forms

Answer 23

If only 1 double bond

• (E/Z)-molecule, where E/Z is the geometric configuration across the double bond, and molecule is the name of the compound.
• For example, (Z)-2-chloro-2-butene. (see geometric isomer figure)

If more than 1 double bond

• (#E/Z, #E/Z)-molecule, where # is the carbon number (the smaller one in the double bond, in ascending order), and molecule is the name of the compound.

Question 24

Cahn-Ingold-Prelog rules for assigning priority

Answer 24

Start with shell 1, which is the atoms directly bonded to the chiral carbon.

• The atom with the higher MW has greater priority.If atoms are the same, look at next shell.

Shell 2, which are the atoms adjacent around shell 1 atoms.

• The atom with the higher MW has greater priority.
• If same atoms, the more # of the high MW species, or the more bonds to the high MW species wins.
• For example, -CHO will have higher priority than -CH2OH because the aldehyde has a double bond to oxygen.
• For example, -CH(OH)2 will have higher priority than -CH2OH because the diol has 2 oxygens while the alcohol only has 1.

What about -CH(OH)2 vs. CH2F?

Ans: It doesn’t matter how many oxygens there are, because fluorine has greater molecular weight. So fluorine has higher priority.

If by now, everything is still the same, go to shell 3 and repeat the procedure.

Question 25

racemic mixtures

separation of enantiomers by biological means

Answer 25

• Racemic mixtures contain equal amounts of both enantiomers. Another name for racemic mixtures is racemate.
• Racemic mixtures do not rotate polarized light, so they are optically inactive.

Separation of enantiomers

• Convert enantiomers to diastereomers.
• Separation of diastereomers.
• Convert diastereomers back to enantiomers.

Separation of enantiomers by biological means

• Enzymes are highly specific and can differentiate between enantiomers.
• For example, if an enzyme digests or modifies all L-amino acids, then you’d be able to use that enzyme to separate a D/L racemic mixture.
• In nature, all proteins are made up of L-amino acids.

Question 26

Aliphatic - alkanes

physical properties

Answer 26

• Hydrophobic.
• London Dispersion Forces present only.
• Lower boiling points than compounds the same size but with functional groups
• Very long alkanes can have very high boiling points due to the sum of all the dispersion forces.

A useful reference is that heptane, the 7 membered alkane, has the same boiling point as water.

Question 27

Aliphatic - alkanes: important reactions

Answer 27

combustion

• Complete combustion of alkanes:
  alkane or cycloalkane + O2 → CO2 + H2O
• Complete combustion of anything:
  fuel + oxygen → carbon dioxide + water

substitution reactions with halogens, etc.

• Alkane + halogen + free radical initiator → alkyl halide
• Free radical initiators = hν (UV light) or peroxides.
• Substitution occurs via a free radical mechanism - see below.

Question 28

Aliphatic - alkanes: stability principles

Answer 28

stability of free radicals; chain reaction mechanism; inhibition

• The more substituted the radical, the more stable it is.
• Stability: 3° > 2° > 1° > methyl.

Substitution will occur preferentially at the more substituted carbon atom

Question 29

Radical Chain

Answer 29

The free radical chain reaction is dependent on the presence of free radicals. Therefore, anything that inhibits free radicals will inhibit this reaction. One example is antioxidants, which eats up free radicals and therefore inhibits the free radical chain reaction.

Question 30

Ring Strain (alkanes)

Answer 30

Cyclopropane has the highest ring strain.Cyclobutane has the second highest ring strain.Cyclohexane has the lowest ring strain.Any ring with greater or equal to 14 carbon atoms has the next lowest ring strain.Stick with the above rule and you can answer any questions comparing ring strain. The MCAT will not require you to make weird ring strain comparisions, for example between cyclopropane and cycloheptane.Ring strain consists of Angle (Baeyer) strain and Torsional strain.

Angle (Baeyer) strain is caused by deviation from the ideal sp3tetrahedral bond angle of 109.5°Torsional strain is caused by the molecule having eclipsedconformations instead of staggered ones.Cyclopropane has both angle (Baeyer) strain and torsional strain.Cyclohexane, in the chair conformation, has no angle (Baeyer) or torsional strain.You’ll frequently see people write Bayer strain instead of Baeyer strain. They mean the same thing.

Question 32

Bicycle molecules

Answer 32

Bicyclic molecules have more ring strain than monocyclic molecules. Except for spiro bicyclics, which have similar ring strain as their monocyclic counterparts.