Mcat Organic Chemistry Ii

Front 1

When is a bond formed?

Back 1

A bond is formed when a pair of electrons can lower their energy level by positioning themselves between two nuclei in such a ways to take advantage of the positive charge of both nuclei.
When the force between two objects is attractive and decreases with distance, the lowest PE level for those objects is when they are closest to each other.
Electrons are at their lowest energy level when they form a bond because they have minimized their distance form both nuclei.

Front 2

Are pi bonds or sigma bonds more reactive?

Back 2

Pi bonds.
The electrons in a pi bond are further from the nuclei than the electrons of a sigma bond, and therefore at a higher energy level, less stable, and form a weaker bond.
Less stability means more reactivity.

Front 3

How to figure out the type of hybrid orbital an atom forms

Back 3

Simply count the number of sigma bonds and lone pairs of electrons on that atom.
Match this number to the sum of the superscripts in a hybrid name.

Front 4

Delocalized electrons

Back 4

Result from pi bonds only
Molecules containg delocalized electrons can be represented by a combination of two or more Lewis structures called resonance structures.
An example is benzene.

Front 5

Chirality

Back 5

Chiral molecules differ from their reflections, while a chiral molecules are exactly the same as their reflections.
Any carbon is chiral when it is bonded to four different substituents.

Front 6

Observed rotation

Back 6

The direction and degree to which a compound rotates plane polarized light is given by its observed rotation.

Front 7

Optically inactive compounds

Back 7

Do no rotate plane-polarized light. There is no rotation of the plane of the electric field.
May be compounds with no chiral centers, or they may be chiral compounds containing equal amounts of both steroisomers. The latter is called a racemic mixture.

Front 8

Racemic mixture

Back 8

Chiral compounds containing equal amounts of both stereoisomers.
Racemic mixtures are optically inactive.

Front 9

Optically active compounds

Back 9

Chiral molecules can be separated from their mirror images by chemical means. The result is a compound containing molecules with no mirror image existing in the compound.
When plane-polarized light is projected through such a compound, the orientation of its electric field is rotated. Such a compound is optically active.
If the compound rotates plane-polarized light clockwise = + or d.
If it rotates counterclockwise = - or l.

Front 10

Stereoisomers

Back 10

Two molecules with the same molecular formula and the same bond to bond connectivity that are not the same compound are called stereoisomers.
There are two types of stereoisomers: enantiomers and diastereomers.

Front 11

Enantiomers

Back 11

Enantiomers are stereoisomers that have the same molecular formula, the same bond to bond connectivity, are mirror images f each other, but are not the same molecule.
When placed separately into a polarimeter, enantiomers rotate plane-polarized light in opposite directions to an equal degree.
The specific rotation of R-2-butanol is -13.52 degrees.
The specific rotation of S-2-butanol is +13.52 degrees.

Front 12

Diastereomers

Back 12

Have the same molecular formula, the same bond to bond connectivity, are NOT mirror images to each other, and are not the same compound.
One type of diastereomer is a geometric isomer (cis and trans)
Cis molecules have a dipole moment while trans molecules do not.

Front 13

Physical properties of geometric isomers

Back 13

Due to their dipole moement, cis molecules have stronger intermolecular forces leading to higher boiling points.
Due to their lower symmetry, however, cis molecules do not form crystals as readily, and thus have lower melting points.

Front 14

Combustion with alkanes

Back 14

Combustion takes place when alkanes are mixed with oxygen and energy is added.
Combustion of alkanes only takes place at high temperatures, such as inside the flame of a match.
Combustion of an alkane takes place when oxygen is added at high temperatures.

Front 15

Products of combustion of an alkane

Back 15

carbon dioxide, water, and heat

Front 16

Synthesis of an alkene

Back 16

Occurs via an elimination reaction.
One or two functional groups are eliminated or removed to form a double bond.
Dehydration of an alcohol or dehydrohalogenation are two possible mechanisms.

Front 17

Dehydration of an alcohol

Back 17

Is an E1 reaction where an alcohol forms an alkene in the presence of hot concentrated acid.
E1 means that the rate depends upon the concentration of only one species. In this case, it is the alcohol concentration.

Front 18

Dehydrohalogenation

Back 18

Forms an alkene
May proceed either by an E1 mechanism (absence of a strong base) or by an E2 mechanism (a high concentration of a strong, bulky base).
E1 is two steps, E2 is one step.

Front 19

Catalytic hydrogenation

Back 19

Hydrogenation is an example of an addition reaction.
Involves a heterogeneous catalyst.
Hydrogenation is an exothermic reaction with a high every of activation.
Syn addition of alkynes creates a cis alkene.

Front 20

Oxidation of alkenes

Back 20

May produce glycols (hydroxyl groups on adjacent carbons) or oxidation may cleave the alkene at the double bond as in ozonolysis.

Front 21

Markovnikov's rule

Back 21

The hydrogen will add to the least substituted carbon of the double bond.
When hydrogen halides (HF, HCl, HBr, HI) are added to alkenes, they follow this rule.

Front 22

anti-Markovnikov addition

Back 22

If peroxides (ROOR) are present, then bromine, not the hydrogen, will add to the least substituted carbon. This is called an anti-Markovnikov addition.
The other halogens will still follow Markovnikov's rule even in the presence of peroxides.

Front 23

Sn1 reaction

Back 23

Has 2 steps and has a rate that is dependent on only one of the reactants (the 1 in Sn1).
The first step is the rate-determining step, and is the formation of the carbocation.
The rate is directly proportional to the concentration of the substrate.
The second step is the nucleophile attacking the carbocation.
In an Sn1 reaction, the leaving group simply breaks away on its own to leave a carbocation behind.

Front 24

Sn2 reaction

Back 24

Occur in a single step.
The rate IS dependent on the concentration of the nucleophile AND the substrate.
A nucleophile attacks the intact substrate from behind the leaving group and knocks the leaving group free while bonding to the substrate.
The rate of Sn2 reactions decreases from methyl to secondary substrates. Sn2 reactions typically don't occur with tertiary substrates.

Front 25

Sn1 vs. Sn2

Back 25

"The nucleophile and the five S's"
Sn2 requires a strong nucleophile, while nucleophilic strength doesn't affect Sn1.
1. Sn2 requires a methyl, primary, or secondary substrate, while Sn1 requires a secondary or tertiary substrate. Sn2 reactions don't occur with a stercally hindered substrate.
2. A highly polar solvent increases the reaction rate of Sn1 by stabilizing the carbocation, but slows down Sn2 reactions by stabilizing the nucleophile.
3. The speed of an Sn2 reaction depends upon the concentration of the substrate and the nucleophile, while the speed of an Sn1 depends only on the substrate.
4. Sn2 inverts sterechemistry about the chiral center, while Sn1 creates a racemic mixture.
5. Sn2 never rearranges the carbon skeleton, but Sn1 may.

Front 26

Physical properties of alcohols

Back 26

Alcohols follow the same general trends as alkanes.
Boiling point goes up with molecular weight and down with branching.
Melting point also increases with molecular weight.
Boiling and melting points are much higher than alkanes due to hydrogen bonding.
Alcohols are more soluble in water than alkanes and alkenes.

Front 27

Alcohols as acids

Back 27

Since an alcohol can lose a proton, it can act like an acid.
However, alcohols are less acidic than water.
The order of acidity for alcohols from strongest to weakest is: methyl, primary, secondary, tertiary.
The most stable conjugate base will be the conjugate of the strongest acid (the most stable conjugate base will have the weakest negative charge).

Front 28

Alcohols usually behave as

Back 28

nucleophiles

Front 29

Oxidation of alcohols

Back 29

Primary and secondary alcohols can be oxidized.
Tertiary alcohols cannot be oxidized.

Oxidation = loss of hydrogen; addition of oxygen; addition of halogen.
Reduction = addition of hydrogen; loss of oxygen; loss of halogen.

Front 30

Ethers

Back 30

Ethers, other than epoxides, are relatively non-reactive.
They are polar.
Although they cannot hydrogen bond with themselves, they can hydrogen bond with compounds that contain a hydrogen attached to a N, O, or F atom.
Organic compounds tend to be much more soluble in ethers than alcohols because no hydrogen bonds need to be broken. These properties make ethers useful solvents.
(Ether is almost always the answer to solvent questions on the MCAT)

Front 31

carbonyl

Back 31

A carbonyl is a carbon double bonded to an oxygen.
The double bond is shorter and stronger than the double bond of an alkene.

Front 32

Whenever you see a carbonyl on the MCAT, think what two things?

Back 32

1. planar stereochemistry
2. partial positive charge on the carbon and partial negative charge on the oxygen.
The partial negative charge on the oxygen means that it is easily protonated.

Front 33

Physical properties of aldehydes and ketones

Back 33

Aldehydes and ketones are more polar and have higher boiling points than alkanes and alkenes of similar molecular weight.
However, they cannot hydrogen bond with each other, so they have lower boiling points than corresponding alcohols.
Aldehydes and ketones do accept hydrogen bonds with water and other compounds that can hydrogen bond, making them excellent solvents for these substances.
Aldehydes and ketones with up to four carbons are soluble in water.

Front 34

enolate ion

Back 34

Normally hydrogens are not easily removed from carbons because carbon anions are very strong bases and unstable.
However, alpha-carbon anions are stabilized by resonance. This anion is called an enolate ion (en from alkene and ol from alcohol).

Front 35

aldehydes vs. ketones (reactivity, acidity)

Back 35

Because alkyl groups are electron donating and a ketone has two alkyl groups attached to the carbonyl, the carbonyl carbon of the conjugate base of the ketone is less able to distribute negative charge and is slightly less stable than that of an aldehyde.
Thus aldehydes are slightly more acidic than ketones. This same property makes aldhydes more reactive than ketones.
Both aldehydes and ketones are less acidic than alcohols.
Any electron withdrawing groups attached to the alpha-carbon or the carbonyl tend to stabilize the conjugate base and thus increase acidity.

Front 36

enol tautomers

Back 36

Ketones and aldehydes exist at room temperature as enol tautomers.
Tautomerization involves a proton shift, in this case from the alpha-carbon position to the carbonyl oxygen position.
Both tautomers exist at room temperature, but the ketone or aldehyde tautomer is usually favored.
Tautomerization is a reaction at equilibrium, not a resonance (resonance structures' atoms don't move and neither resonance structure actually exists).

Front 37

acetals and ketals as blocking groups

Back 37

Because acetals and metals are unreactive toward bases, they are often used as blocking groups.
In other words, a base would typically act as a nucleophile to attack an aldehyde or ketone at the carbonyl carbon, the the aldehyde or ketone can be temporarily changed to an acetal or ketal to prevent it from reacting with a base.

Front 38

aldol condensation

Back 38

aldol condensation occurs when one aldehyde reacts with another, when one ketone reacts with another, or when an aldehyde reacts with a ketone.
The reaction is catalyzed by an acid or base.

Front 39

Halogenation

Back 39

Halogens add to ketones at the alpha carbon in the presence of a base or an acid.
When a base is used, it is difficult to prevent halogenation at more than one of the alpha positions. The base is also consumed by the reaction with water as a by-product, whereas the acid acts as a true catalyst and is not consumed.

Front 40

The Wittig Reaction

Back 40

Converts a ketone to an alkene.
A phosphorous ylide is used.

Front 41

Behavior of a carboxylic acid (for the MCAT)

Back 41

Look for carboxylic acid to behave as an acid or as the substrate in a nucleophilic substitution reaction.
Like any carbonyl compound, its stereochemistry makes it susceptible to nucleophiles.
When the hydroxyl group is protonated, the good leaving group water is formed, and substitution results.

Front 42

decarboxylation

Back 42

when a carboxylic acid loses a carbon dioxide, the reaction is called decarboxylation.

Front 43

acyl chlorides

Back 43

acyl chlorides are Bronsted-Lowry acids, and, just like aldehydes, they donate an alpha-hydrogen.
The electron withdrawing chlorine stabilizes the conjugate base more than the lone hydrogen of an aldehyde, making acyl chlorides significantly stronger acids than aldehydes.
Acid chlorides are the most reactive of the carboxylic acid derivatives because of the stability of the Cl- leaving group.

Front 44

alcohols react with carboxylic acid through nucleophilic substation to form

Back 44

esters.

A strong acid catalyzes the reaction by protonating the hydroxyl group on the carboxylic acid.

Front 45

amide formation

Back 45

amides are formed when an amine, acting as a nucleophile, substitutes at the carbonyl of a carboxylic acid or one of its derivatives.

Front 46

How many bonds can nitrogen make?

Back 46

Nitrogen can take three or four bonds.
When nitrogen takes four bonds it has a positive charge.
When you see nitrogen on the MCAT and it has only three bonds, you should draw in the lone pair of electrons immediately.

Front 47

Three important considerations when dealing with nitrogen containing compounds

Back 47

1. They may act as a Lewis base donating their lone pair of electrons.
2. They may act as a nucleophile where the lone pair of electrons attacks a positive charge.
3. Nitrogen can take on a fourth bond, becoming positively charged.

Front 48

Do ammonia and amines act as acids or bases? Strong or weak?

Back 48

Ammonia and amines act as weak bases by donating their lone pair of electrons.
Electron withdrawing substituents decrease the basicity of an amine, whereas electron donating substituents increase the basicity of an amine.

Front 49

Physical properties of amines and ammonia

Back 49

Amines and ammonia can hydrogen bond, which raises boiling point and increases solubility.
All amines can hydrogen bond with water, making the lower molecular weight amines very soluble in water.
Ammonia, primary amines, and secondary amines can hydrogen bond with each other.
Amines with comparable molecular weights have higher boiling points thank alkanes but lower than alcohols.

Front 50

Amines react with aldehydes and ketones to produce:

Back 50

Amines react with aldehydes and ketones losing water to produce imines and enamines.
The amine acts as a nucleophile, attacking the electron deficient carbonyl carbon of the ketones.
The ketone undergoes nucleophilc addition.

Front 51

Wolff-Kishner reduction

Back 51

The Wolff-Kishner reduction reduces a ketone or aldehyde by removing the oxygen and replacing it with two hydrogens.
You can do the same thing by adding hot acid in the presence of amalgamated zinc (zinc treated with mercury), but some ketones and aldehydes can't survive such a treatment. That's where the Wolff-Kishner reduction comes in.

Front 52

Are amino groups good leaving groups?

Back 52

As a leaving group, the amino group would be -NH2, so amino groups are very poor leaving groups.
However, an amino group can be converted to a quaternary ammonium salt, NR4-X, by repeated alkylations. The quaternary ammonium salt is an excellent leaving group.

Front 53

Is nitrous acid a strong or weak acid?

Back 53

Weak acid
A strong acid can dehydrate nitrous acid to produce nitrosonium ion and water.

Front 54

Can amides hydrogen bond?

Back 54

Amides with a hydrogen attached to the nitrogen are able to hydrogen bond to each other.

Front 55

NMR

Back 55

Refers to nuclear magnetic resonance spectroscopy.
The nucleus most commonly studied with nor is the hydrogen nucleus, but it is possible to study the nucleus of carbon-13 and other atoms as well.
In NMR, the frequency of the electromagnetic radiations is held constant while the magnetic field strength is varied.
Absent any electrons, all protons absorb electromagnetic energy from a constant strength magnetic field at the same frequency. However, hydrogen atoms within different compound experience unique surrounding electron densities and are also uniquely affected by the magnetic fields of other nearby protons.
The electrons shield the protons from the magnetic field.

Front 56

NMR spectrum

Back 56

A graph of the magnetic field strengths absorbed by the hydrogens of a specific compound at a single frequency.
The field strength is measured in parts per million, and, despite the decreasing numbers, increases from left to right.
The leftward direction is downfield and the rightward direction is called upfield.

Front 57

Unless otherwise indicated, NMR is concerned with?

Back 57

Hydrogens

Front 58

Reading an NMR spectrum

Back 58

Each peak represents chemically equivalent hydrogens.
Splitting of peaks is created by "neighboring hydrogens".
Each peak indicates one or a group of chemically equivalent hydrogens. Such hydrogens are said to be enantiotropic.
The area under a peak is proportional to the number of hydrogens represented by that peak. The more chemically equivalent hydrogens, the greater the area.
Lateral position is dictated by electron shielding. Electron-withdrawing groups tend to lower shielding and thus decrease the magnetic field strength at which resonance takes place. This means that hydrogens with less shielding tend to have peaks downfield or to the left.
Likewise, electron-donating groups tend to increase shielding and increase the required field strength for resonance.

Front 59

What is splitting, or spin-spin splitting, in regards to NMR spectrums?

Back 59

Splitting results from neighboring hydrogens that are not chemically equivalent.
The number of peaks due to splitting for a group of chemically equivalent hydrogens is given by the simple formula:
n+1, where n is the number of neighboring hydrogens that are NOT chemically equivalent.

Front 60

For proton NMR spectroscopy, follow what three steps?

Back 60

1. Identify chemically equivalent hydrogens.
2.Identify and count neighboring hydrogens that are not chemically equivalent. Use n+1 to figure the number of peaks created by splitting for the chemically equivalent hydrogens.
3. If necessary, identify electron withdrawing/donating groups near the chemically equivalent hydrogens. Withdrawing groups will move their signal to the left.

Also, aldehyde protons have a very distinctive shift at 9.5 ppm. Watch for it.

Front 61

Aldehyde protons have a very distinctive shift. What is it?

Back 61

9.5 ppm.

On the MCAT, watch for it.

Front 62

How does carbon NMR differ from hydrogen NMR?

Back 62

The nucleus must have an odd atomic or mass number to register on NMR, so carbon-13 is the only carbon isotope to register.
Treat carbon NMR the same way as proton NMR, except IGNORE SPLITTING.

Front 63

Mass spectrometry

Back 63

Gives the molecular weight, and, in the case of high resolution mass spectrometry, the molecular formula.
In mass spectrometry, the molecules of a sample are bombarded with electrons, causing them to break apart and to ionize.

Front 64

Chromatography

Back 64

Chromatography is the resolution, or separation, of a mixture by passing it over or through a matrix that adsorbs different compounds with different affinities, ultimately altering the rate at which they lose contact with the resolving matrix.
The mixture is usually dissolved into a solution to serve as the mobile phase, while the resolving matrix is often a solid surface.
the surface adsorbs compounds from the mixture, establishing the stationary phase.
The compounds in a mixture that have a greater affinity for the surface move more slowly.
The result of chromatography is the establishment of separate and distinct layers, one pertaining to each component of the mixture.

Front 65

Distillation

Back 65

Distillation is separation based upon vapor pressure.
A solution of two volatile liquids with boiling point differences of approximately 20 degrees celcius or more may be separated by slow boiling.
The compound with the lower boiling point, and thus higher vapor pressure, will boil off and can be captured and condensed in a cool tube.

Front 66

Crystallization

Back 66

Crystallization is based upon the principle that pure substances form crystals more easily than impure substances.