MCAT Review OChem Notes (Full)
MCAT Review OChem Notes (Full)
MCAT Review OChem Notes (Full)
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C 4
N 5
O 6
F 7
S 6
P 5
Si 4
Cl 7
H and C
1
2 or 6
3 or 5
4
1
Typically found in
Hydrocarbon (alkane, alkene, alkyne), hydride. All organic compounds
contain hydrogen.
Alkane, alkene, alkyne, aromatic rings. All organic compounds contain
carbon.
Amine, amide, imine, hydrazone, oxime, nitro compound, diazo
compound, nitrile/cyanide, azide
Alcohol, ether, aldehyde, ketone, carboxylic acid, acyl halide, anhydride,
amide, ester, ozone
Fluoride
Thiol, sulfide, sulfate, sulfite
Phosphorous compound, phosphate, phosphite
Silane, silicon dioxide
Chloride, hypochlorite, chlorite, chlorate, perchlorate
Si
Cl
Resonance structures result from electrons not being fixed in position (that's why you "push"
electrons when drawing resonance structures).
When electrons are not fixed in position, they are delocalized electrons.
For all practical purposes, resonance and electron delocalization mean the same thing.
In ions, resonance and electron delocalization occurs to "distribute" the charge around.
In molecules, resonance and electron delocalization occurs in aromatic rings and conjugated
double bonds.
Multiple bonding
its effect on bond length and bond energies
Multiple bonding decreases bond length.
Multiple bonding increases bond energy.
rigidity in molecular structure
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.
structural isomers
Structural isomers have the same molecular formula, but different connectivity.
Positional isomers: structural isomers that have the same functional groups positioned
differently.
Constitutional isomers: structural isomers that have different functional groups.
geometric isomers
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 of 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.
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.
Enantiomers are mirror images of each other. That means ALL chiral centers in one
enantiomer is reversed in the other.
You can't have stereoisomers if you don't have a chiral center.
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).
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.
A compound will have a total of 2#chiral centers stereoisomers if it is not meso.
Meso compounds may have chiral centers, but as a molecule, they are achiral and optically
inactive.
Meso compounds reduce the total number of stereoisomers.
Stereoisomers have the same chemical properties.
Enantiomers have the same physical properties.
Diastereomers have different physical properties.
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.
conformational isomers
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.
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Absorption spectroscopy
infrared region
Every time you have a bond, the atoms in a bond have their
atomic orbitals merged together to form molecular orbitals.
Every time you have a molecular orbitals, you get bonding
molecular orbitals and non-bonding and/or anti-bonding
orbitals.
Normally, electrons sit in their bonding orbitals because it is
the most stable there. If bonding orbitals are full, then nonbonding orbitals are occupied.
Given enough energy (as in absorption), the electrons
transition from the bonding or non-bonding orbitals to the
anti-bonding orbitals.
If too much energy is absorbed, enough electrons escape the
bonding orbitals / enter the anti-bonding orbitals to break the
bond completely.
For UV absorption, we're not worried about breaking bonds.
We're only interested in the pi-electrons of double bonds
because their molecular orbital transitions result in UV
absorption.
Double bonds absorb UV because the pi electrons transition
from the bonding and non-bonding molecular orbitals to the
anti-bonding orbitals.
conjugated systems
Conjugated systems decreases the energy of electromagnetic
radiation that is absorbed.
The more conjugated double bonds there are, the longer the
wavelengths of absorbed radiation.
If there are enough conjugated double bonds, the molecule
will start to absorb in the visible region.
ionizes it? Ans: this "molecular ion" will be detected as the parent
peak, also called the molecular ion peak.
What if the electrons not only ionize but also fragment your
molecule? Ans: all the fragmented ions will be detected and
plotted in the mass spectra.
The faster (higher energy) the bombarding electron, the more
fragmentation.
The more fragmentation, the smaller the molecular ion peak.
These ions have a characteristic mass to charge ratio (m/e or m/z).
A magnetic field resolves (separates) the different m/z ions so they can
be individually detected and plotted on a spectrum.
The resulting spectrum plots Relative abundance vs. the m/z ratio.
The parent peak, or the molecular ion peak, is the peak that depicts the
ion of the molecule without fragmentation. It has the highest m/z ratio.
Peaks clustered really close to one another depicts isotopes.
The base peak is the tallest peak (most abundant species).
Mass spec is useful for:
Measuring the molecular weight of a molecule.
Identify the molecule by fragmentation patterns.
Identity heteroatoms by their characteristic isotope ratios.
NMR spectroscopy
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Organic phase
Solvent Nonpolar solvent
Solute Nonpolar solutes dissolve here
The organic phase does not always
float on top. Chloroform, for
Density
example, sinks below the aqueous
phase.
Aqueous phase
Water
Ionic and polar solutes
dissolve here
Water is usually denser than
other solvents, but some
organic solvents are even
denser.
Distillation
Separates liquids based on boiling point. The stuff with the lower boiling
point is boiled off and collected; the higher boiling point stuff remains
behind.
Simple distillation = done with a normal column = can separate two
liquids if the difference in boiling point is large.
Fractional distillation = done with a fractionating column = can separate
two liquids with smaller differences in boiling point.
Vacuum distillation = done under lower pressure (vacuum) = lowers the
boiling point for all liquid components so you don't have to crank up the
temperature so high (chemical might decompose).
Gas-liquid chromatography
Good if analyte can be promoted to gas phase.
Gas-liquid chromatography (GLC) is the same thing as gas
chromatography (GC).
The gas part is the mobile phase, the liquid part is the stationary
phase coated to the inside walls of the column.
Substrate equilibrates between mobile (gas) and stationary (liquid
coat) phase.
Those with greater affinity for the stationary phase comes out of
the column slower. Polar substrate has more affinity for polar
Hydrocarbons
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Aliphatic - alkanes
Description
nomenclature
#C
Name for straight chain
Name for cyclic
atoms
alkane
alkane
1
Methane
N/A
2
Ethane
N/A
3
Propane
Cyclopropane
4
Butane
Cyclobutane
5
Pentane
Cyclopentane
6
Hexane
Cyclohexane
7
Heptane
Cycloheptane
8
Octane
Cyclooctane
9
Nonane
Cyclononane
10
Decane
Cyclodecane
After Decane, there is Undecane (11), Dodecane (12), Tridecane
(13), Tetradecane (14), and so forth for eleven membered alkanes
upwards.
physical properties
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.
Important reactions
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 = h (UV light) or peroxides.
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Description
nomenclature
Prefix: hydroxyl, hydroxy.
Suffix: -ol, alcohol.
physical properties
Hydrogen bonding.
Higher boiling point than the same compound without the alcohol group.
Water soluble as long as molecule does not contain a long hydrophobic region.
infrared absorption of OH group: 3300 cm-1 and broad due to hydrogen bonding.
Important reactions
substitution reactions: SN1 or SN2, depending on alcohol and derived alkyl halide
R-OH + HX <--> R-X + H2O
Factors that favor sn1: stable carbocation, tertiary carbon center, protic solvent.
Factors that favor sn2: unstable carbocation, primary carbon center, aprotic (but polar) solvent.
All substitution reactions need a good leaving group.
SN1 = unimolecular reaction, intermediate carbocation formed.
protection of alcohols: the best protecting group for alcohol is the trimethylsilyl group.
To protect, add Cl-SiMe3 to R-OH.
The alcohol gets "capped" into R-O-SiMe3.
To deprotect, add F-.
reactions with SOCl2 and PBr3
R-OH + SOCl2 --> R-Cl (by products: SO2 + HCl)
R-OH + PBr3 --> R-Br (by products: H3PO3, R3PO3, HBr)
preparation of mesylates and tosylates
Formation of mesylates and tosylates are also reactions that involve inorganic esters.
In biochemistry DNA/RNA polymerization, the 3'-OH alcohol group attacks the 5'-phosphate to form an
inorganic ester linkage (phosphodiester linkage of DNA/RNA backbone).
General principles
hydrogen bonding: hydrogen bonding in alcohols give them a higher boiling point than their corresponding
alkanes.
acidity of alcohols compared to other classes of oxygen-containing compounds: lower pKa = more acidic.
Compound
COOH (carboxylic acids)
ArOH (phenols)
H2O (water)
pKa
5
10
16
ROH (alcohols)
15
-CH2(CO)-R (alpha hydrogen in aldehydes and ketones) 20
-CH2(CO)-OR (alpha hydrogen in esters)
25
effect of chain branching on physical properties: going from straight chain to branched alkane (with same #
carbons) = molecules can not pack as well = more fluidity = harder to freeze = lower freezing/melting point.
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Description
nomenclature
Aldehyde suffix: -al, -aldehyde.
Ketone prefix: keto-, oxo-.
Ketone suffix: -one, ketone.
physical properties
C=O bond is polar, with the carbon partially positive and oxygen
partially negative.
Dipole-dipole interactions give these molecules higher boiling points
than their corresponding alkanes, but not as high as the corresponding
alcohols or carboxylic acids.
infrared absorption of C=O bond: 1700 cm-1
Important reactions
nucleophilic addition reactions at C=O bond
acetal, hemiacetal
Grignard reagents are just like organometallic reagents, they produce R-.
R-X + Mg -> R-Mg-X
R-Mg-X + C=O -> R-C-OH
General principles
effect of substituents on reactivity of C=O; steric hindrance: bulky groups on
either side of C=O blocks access to the electrophilic carbon, so reactivity goes
down.
acidity of alpha H; carbanions
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Description
nomenclature
Suffix: -oic acid, carboxylic acid, -dioic acid.
physical properties and solubility
High boiling point due to hydrogen bonding.
Soluble in water.
infrared absorption
C=O at 1700 cm-1
-OH at 3100 cm-1
Important reactions
carboxyl group reactions
nucleophilic attack
reactions at 2 position
halogenation: RCOOH + X2 -> halogenation at the alpha carbon (2
position).
General principles
H bonding: COOH has high boiling point because of H bonding.
dimerization: Hydrogen bonding causes dimerization of carboxylic
acids.
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Acid Derivatives
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Description
nomenclature:
suffix
example
ethanoyl chloride
ethanoic anhydride
Anhydrides
-oic anhydride
N-methyl ethanamide
Amides
-amide
methyl ethanoate
Esters
-oate
physical properties
C=O bond is polar, so there are dipole-dipole interactions.
No hydrogen bond exists in acid chlorides, anhydrides, or esters
unless there is an -OH group somewhere.
Amides can hydrogen bond because of the N-H group. In fact,
hydrogen bonding involving the amide backbone of polypeptides
form the secondary structure of proteins.
Amides have higher boiling points than the other acid derivatives.
Important reactions
preparation of acid derivatives
Carboxylic acid + SOCl2 Acid chloride.
Carboxylic acid + carboxylic acid + heat Anhydride.
Acid chloride + carboxylic acid + base Anhydride.
Acid chloride + alcohol + base Ester.
Acid chloride + amine Amide.
Acid chloride + water Carboxylic acid.
General principles
relative reactivity of acid derivatives: Acid chloride > Anhydride >
Esters > Amides
Acid halides are the most reactive derivatives because halides are
very good leaving groups.
Amides are the most stable derivatives because NR2- is a terrible
leaving group. Also, the C-N bond has a partial double bond
characteristic. Proteins are made of peptide bonds, and they are
very stable.
steric effects: bulky groups around the C=O group helps protect the
carbon center from nucleophilic attack.
electronic effects: groups that can redistribute and stabilize negative
charges are good leaving groups. For example, the anhydride has a good
leaving group - the carboxylate ion - because the COO- can redistribute
the negative charge to both oxygens via resonance.
strain (e.g., beta-lactams)
Amides have a double bond characteristic between the carbon and
nitrogen. This means that the C-N bond can not rotate.
Normally, the sigma bonds in a ring rotate as to achieve the most
stable conformation, but this can't occur for the C-N bond if the
ring contains an amide.
Because of C-N bond in an amide can not rotate, rings that contain
amides have higher strain.
An example of this is the beta-lactam, which is basically a 4
membered ring with 1 amide in it.
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Description; nomenclature
Important reactions
decarboxylation
General principles
acidity of alpha hydrogen and beta-keto ester
Any hydrogen alpha to (adjacent to) a carbonyl group is more acidic than a
regular hydrogen. The alpha hydrogen of a beta-keto ester is even more
acidic because it's adjacent to 2 carbonyl groups.
The reason for the acidity is the stabilization of the deprotonated species by
the enolate ion resonance structures.
keto-enol tautomerism
Amines
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Description
nomenclature
Prefix: aminoFor example, 2-aminopropanoic acid.
Suffix: -amine.
For example, propanamine.
3 amines can be chiral. But they are always racemic because of spontaneous inversions
at room temperature.
Even protonated 3 amines undergo inversion because the proton comes on and off in
an acid-base equilibrium.
4 amines can be chiral and they stay chiral because they don't undergo inversion.
infrared absorption
primary amines = R-NH2 = 2 N-H bonds = 2 peaks around 3300 cm-1.
secondary amines = R2-NH = 1 N-H bonds = 1 peak around 3300 cm-1.
tertiary amines = R3-N = no N-H bonds = 0 peak around 3300 cm-1.
Major reactions
amide formation
OH-).
reactions with nitrous acid
Ar-NH2 + HONO Ar-N2+ + H2O + OHnitrous acid = HNO2 = HONO
The reason why the nitrogen in nitrous acid can be attacked is the following:
amine + methyl iodide exhaustive methylation of the amine elimination with the
methylated amine as leaving group.
Unlike E1 reactions where the more substituted double bond is formed (Zaitsev),
Hofmann elimination forms the less substituted double bond (Hofmann).
The nitrogen of the amine donates its lone electron pair to the adjacent carbonium ion
(carbocation).
effect of substituents on basicity of aromatic amines
Aromatic amines are weaker bases than aliphatic amines. This is because the amine
donates its electron density to the aromatic ring. Also, the amine forms stable resonance
structures with the aromatic ring, which is absent once the amine becomes protonated.
Electron donating groups on the aromatic amine increase the basicity of aromatic
amines. This is because the electron donating groups contribute to the electron density
on the nitrogen.
Electron withdrawing groups on the aromatic amine decrease the basicity of aromatic
amines. This is because the electron withdrawing groups steal electron density from the
amines. This is because the electron withdrawing groups steal electron density from the
nitrogen.
Anything ortho to the amine, no matter whether it is electron donating or withdrawing,
will decrease the basicity of the aromatic amine. This is because of the ortho effect,
which is basically sterics. The protonated amine will have a greater steric interaction
with the ortho group, so it will be less stable.
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Description
nomenclature and classification, common names
nomenclature
Carbohydrate = Sugars, monosaccharides, disaccharides, polysaccharides
Prefix:
Deoxy = it has an -H in place of an -OH at a certain position.
D/L = absolute configuration = assigned based on the chirality of the
carbon atom furthest from the carbonyl group.
/ = anomeric configuration.
Suffix: all sugars end in -ose.
classification
aldose = sugars with an aldehyde group.
ketose = sugars with a ketone group.
pyranose = sugars in a 6 membered ring structure = hexagon shaped. For
example, glucopyranose = glucose in a 6 membered ring.
furanose = sugars in a 5 membered ring structure = pentagon shaped. For
example, fructofuranose = fructose in a 5 membered ring.
#ose = sugar with # carbon atoms. For example, hexose = sugar with 6
carbons. Another example: aldopentose = a five-carbon sugar with an aldehyde
group.
In order to be classified as a carbohydrate, a molecule must have:
at least a 3 carbon backbone.
an aldehyde or ketone group.
at least 2 hydroxyl groups.
common names
The sugar that make up RNA is ribose, and for DNA it is deoxyribose (More
precisely it's 2'-deoxyribose because the difference is at the 2 carbon).
Sucrose is a disaccharide made from -glucose and -fructose joined at the
hydroxyl groups on the anomeric carbons (making acetals). Sucrose is table
sugar, the sugar we buy in stores.
Glycogen = same as starch, but with additional 1-6 linkages for branching.
absolute configuration
The chiral carbon furthest from the carbonyl group determines the absolute
configuration L or D of the sugar.
If in the fischer projection, the OH group on the chiral carbon furthest from the
carbonyl is pointing left, then it's L. If it's pointing right, then it's D.
Note: L and D are enantiomers, not epimers. So, every chiral carbon center inverts.
It's just that you assign L and D based on the chiral carbon furthest from the
carbonyl.
cyclic structure and conformations of hexoses
Anomers = different configuration in the chiral, anomeric carbon when the molecule
is in the cyclic form.
Anomers are simply a special type of epimers.
Epimers are simply a special type of diastereomers.
Don't confuse with enantiomers (D/L configuration), in which everything changes
configuration.
Reactions of Monosaccharides
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Description
absolute configuration at the alpha position
Reactions
peptide linkage
General principles
primary structure of proteins
Primary structure = sequence.
The primary structure of proteins is read from the N-terminus to
the C-terminus.
secondary structure of proteins
Secondary structure = repetitive motifs formed by backbone
interactions.
Backbone interactions = hydrogen bonding between the NH and
C=O
The two most common secondary structures are helices and
pleated sheets.
The helix is right-handed, with the R groups sticking outward.
In sheets, R groups stick out above and below the sheet.
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Description; structure
steroids
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Description
structure of phosphoric acids (anhydrides and esters)
Important reactions
Wittig reaction