Chem 313 Advanced Organic Chemistry for the Life Sciences 2010
Prof. John Sherman, Office: A243, 822-2305, [email protected]
Office Hours: open (call, e-mail, see me after class, make an appointment, or just pop by)
TA: Jon Freeman will run two tutorials per week. Day/time to be announced.
Text: No formal text. Use any introductory organic text.
Handouts: Some notes will be posted on the web and/or handed out. These will be mostly definitions
and other data. The majority of notes will be in-class.
A. Amino acids and peptides (3-4 weeks)
1. Amino acids-structure, acid/base properties
2. Reactions of amino acids
3. Peptides-structure determination, synthesis of
B. Carbohydrates (3-4 weeks)
1. Monosaccharides-structure, conformations (review)
2. Reactions of monosaccharides
3. Protecting groups
4. Glycoside couplings
5. Oligosaccharide structures
C. Organophosphate esters (1-2 weeks)
1. Acid/base properties, hydrolysis mechanisms, synthesis of
2. DNA/RNA synthesis
D. Pyridoxal phosphate and Thiamin (1-2 weeks)
1. Structure, function
2. Mechanisms of catalytic reactions
Breakdown: midterm 1: 10%; midterm 2: 15%; final: 50%; lab: 25%.
Note: It is necessary to pass both the lecture and the laboratory parts of the course
independently to pass the overall course! ! !
Goals: Survey the organic chemistry that is relevant to biomolecules. Delve into mechanisms to
understand why/how reactions go the way they do. Compare and contrast chemists’ and nature’s ways
of puttting molecules together.
Reviews: For any topic, you should review as needed. Read the relevant chapter or sections from your
old textbook. Any organic textbook will do; you can use textbooks from the library or google a topic.
For starters, review amino acids, stereochemistry, and acid/base chemistry.
1 Amino Acids and Peptides
Amino acids are difunctional compounds that contain both an amine and a carboxylic acid
functionality. The acid has the priority in naming. The carbons between the functional groups are
designated α, β, γ, δ, etc. starting from the carbonyl. Although there are 100s of naturally occurring
amino acids, and many more synthetic derivatives, there are 20 common amino acids, those that are
found in proteins. The 20 common amino acids are all α-amino acids. The 20 common amino acids
differ in their R group or side chain. They have common names, three letter codes, and one letter
codes. Glycine, Gly, or G, has no side chain (R = H). The 20 common amino acids are given on the
next page. You do not need to memorize specific amino acids.
2 20 Common Amino Acids and their 3- and 1-letter Codes
H 2 CO 2
Lysine Lys K
H 2 CO 2 Glycine Gly G
H2N CO2H Alanine Ala A
H2N CO2H Methionine Met M
H2N CO2H Valine Val V
H N CO H Leucine Leu L
2 2 H2N CO2H Cysteine Cys C
H2N CO 2 Serine Ser S
H 2 CO 2 Isoleucine Ile I
H 2 CO 2 Threonine Thr T
H 2 CO 2 OH
Arginine Arg R
H2N CO 2 Phenylalanine Phe F
H 2 CO 2 Tyrosine Tyr Y
H N CO H
2 2 Aspartic Acid Asp D
CO 2 OH
H N CO H H 2 CO 2 Histidine His H
2 2 Asparagine Asn N
H 2 CO 2
Glutamic acid Glu E H2N CO 2 Tryptophan Trp W
H 2 CO 2 Glutamine Gln Q
Proline Pro P
3 Chirality: Glycine is achiral. The other 19 common amino acids are chiral. Each contains a
stereogenic center at the alpha carbon. The 19 common amino acids are of the “L” configuration. This
means when drawn in a Fischer Projection (review if needed) with the most oxidiz2d carbon (CO H) at
the top, R groups on the bottom, and 2he NH /H are drawn horizontally, 2hen the NH is on the left it
is “L”. On the right would be “D”. D/L are conventions.
Fischer Projections: Vertical lines go into the page (dashes); horizontal lines come out of the page
(wedges). A switch of two substituents leads to the opposite configuration (R goes to S, S to R); two
switches and you are back to where you started. Careful rotation about a second-to top or bottom
vertical bond also yields the same configuration for that center. See below.
CHO CO H CO H
HO H H2N H H2N H
2 CH 3 CH 3
L-Glyceraldehyde L-Alanine (of "S" configuration)
L-Cysteine, "R" configuration
CO 2 CO H2
H N H HSH C2 NH 2
CH 2H H
Two switches or
rotation about C–CO H
D/L configurations do not correlate with d/l, +/–, which are real observables based on optical rotation.
The alpha carbon of cysteine has R configuration (review Cahn-Ingold-Prelog rules if needed), while
the other 18 common amino acids have “S” configuration; again, all 19 common amino acids are “L”
(Gly is achiral). Finally, two common amino acids, Threonine and Isoleucine, have a second
stereogenic center within their side chains; the other 17 have no stereogenic centers in their side
4 Acid-Base Properties of Amino Acids. Review of acid/base chemistry:
CH 3O H2 CH 3O 2 + H
pK = 4.74
CH 3O 2 H
K a = 1.8 x 10
CH CO H
pK a – log (1.8 x 10 ) = 4.74
K a 10 -4.74
CH C3 2
Ka pK a 4.74
If = 1, then = 1 = =
CH C3 H 2 H
pK CH 3O 2
If pH = 5.74, = 10 =
pH CH 3O H2
pKa 3 2
If pH = 3.74, = 0.1 =
CH 3O H2
At a pH equal to the aK of an acid, the acid and its conjugate base are present in equal amounts. When
the pH is one pH unit above the aK , there is 10 times more conjugate base present than conjugate
acid. At a pH two units above theapK , there is 100 times more conjugate base present than conjugate
acid. At a pH one unit below theapK , there is 10 times more conjugate acid present than conjugate
If HA has a pK of 5 and HB has a pK of 10, then HA is more acidic than HB, and B is more basic
– a a
than A . At a pH of 3, the predominant species are HA and HB. At pH 7, the predominant species are
A and HB. At pH 12, the predominant species are A and B .
5 Back to Amino Acids: All amino acids have an amino group (basic) and a carboxyl group (acidic).
Some have acidic or basic groups in their side chains. Simple amino acids, where the side chain is
neither acidic nor basic, exist as zwitterions in neutral aqueous solution; that is, they contain both
positive and negative charges. Tha pK of the carboxylic acid is about 2.3a and the pK the ammonium
is about 9.6. Why is tha pK of an amino acid so much lower than that of acetic acid (4.74)?
CO 2 CO 2
H3N H H 3 H + H
the acidic proton
pK a 2.3
the acidic proton
CO 2 CO 2
H N H H N H + H
Some side chains of amino acids contain acidic or basic graups. pK ’s of these groups are given below
(you do not need to memorize these).
AA pKaof Side Chain
Factors that might affect a reaction: (1) Sterics, (2) Electronics, (3) Hydrogen bonding, and (4)
Solvation. Review these concepts. Within Electronics, we have: induction, resonance (delocalization
of charge), hybridization, octets (atoms like to have full octets), and aromaticity (achieving aromaticity
accords stabilization). Review these concepts. Charges are not stable; reducing charge, even partially
or by spreading it around, will stabilize a compound.
The carboxylic acid of a typical α-amino acid is more acidic than a simple carboxylic acid because of
the inductive effect: the positive charge on the ammonium a few bonds away inductively withdraws
electron density from the carboxylate and thereby stabilizes the negative charge; the conjugate base is
thus stablized. Resonance and sterics do not come into play. Hydrogen bonding is possible, but it is
negligible in such a small molecule in water due to hydration (solvation by water).
6 Pyridinium is 5 pK unats more acidic than ammonium due to hybridization: the lone pair of pyridine is
sp while the lone pair of an amine is sp . An sp lone pair is held more tightly to the nucleus and thus
has less affinity for a proton. (The more s-character, the closer the orbital/electrons/charge are to the
nucleus. This is stabilizing for a negative charge, but destabilizing for a positive charge. The lone pair
of pyridine is held closer to the nucleus than in an amine, so pyridine’s lone pair is more stable, less
basic than the lone pair of an amine.) No octet is lost, no aromaticity is lost, there are no induction
issues. Resonance? Yes, but delocalization of the charge would break up the aromaticity somewhat and
lose octets, so this will be minor. (Six π electrons in a closed loop affords aromaticity, which gains a
benzene ring 36 kcal/mol of stabilization. For a protonated pyridine, there are six pi-electrons and six
p-orbitals in a closed loop for all resonance structures.)
Pyrrolium is 14 pK unias more acidic than ammonium due to a gain of aromaticity upon deprotonation
to become pyrrole. If pyrrole is protonated on its nitrogen, it loses aromaticity and has no resonance
structures. If it is protonated on its α-carbon, it loses aromaticity and has three resonance structures, all
of which lack an octet. It does protonate on its α-carbon over the N (and over the β-carbon), but
pyrrolium is very acidic.
Guanidiniums (e.g., Arg) have higher pK ’s thaa ammoniums due to delocalization of the positive
charge (resonance); the conjugate acid is stablized and is thus less acidic. There is about a 1/3 + charge
on each nitrogen. There will only be a small charge on the carbon due to a lost octet on the carbon
when it is charged: normally, it is preferable to put a + charge on the less electronegative atom. In
guanidinium, it is better to put a + charge on the more electronegative nitrogen (and maintain all
octets) than on the less electronegative carbon since the carbon will lose its octet. The hybridization on
carbon will be sp , but the nitrogens are each sp in one of three resonance structures and sp in two of3
three resonance structures: you can consider them sp , or in between sp and sp , or just consider
them effectively sp since the three nitrogens and the carbon are coplanar. In any case, the higher
basicity of guanidine compared to an amine is due to delocalization of the + charge in the conjugate
acid. If the hybridization is sp , that would reduce the basicity. Delocalization more than compensates
for any effect of hybridization on the pK in tais example. Although the hybridization of guanidinium
is an interesting question to consider, it is a good example of a concept that is too grey to be likely to
appear on an exam.
Phenols (e.g., Tyr) have markedly lower pK ’s thaa alcohols due to the delocalization of the negative
charge around the ring (resonance); the conjugate base is stablized. This breaks up the aromaticity
somewhat, but no octets are lost, so there is a net gain in stability of the conjugate base versus that of a
simple alkoxide. Hybridization: this is a bit complex, but there doesn’t seem to be a way to have much
net gain in stability for the conjugate base.
Imidazole (His side chain) is aromatic. Like pyridine, protonation does not disturb the aromaticity.
Also like pyridine, the lone pair on the nitrogen(s) is sp . An imidazolium should be a bit more stable
than a pyridinium from the standpoint of resonance between the nitrogens of the immidazolium, but
the extra nitrogen also inductively withdraws, and this likely leads to the overall very similar pK ’s of a
imidazolium and pyridinium.
Thiols (cysteine side chain): pK areamuch lower than alcohols due to lower charge density on anion.
The “hard” alkoxide anion has higher affinity for a “hard” proton.
7 Isoelectric point (pI): The pH at which the amino acid exists in solution predominantly as a neutral
species. For simple amino acids (those with no acidic or basic groups in their side chains), the pI =
(pKa1 + pKa2)/2. This is the average of tae two pK s.
CO 2 CO 2 CO 2
H N H H N H H N H
3 3 2
R R R
pK = 2.3 pKa= 9.7
2.3 + 9.7
pI = = 6.0
9.7 N B
The acidic form, A, predominates below pH 2.3. The basic form, B, predominates above pH 9.7. The
neutral form, N, predominates between pH 2.3 and 9.7, and is maximized at pH 6. A and N are in a 1:1
ratio at pH 2.3. N and B are in a 1:1 ratio at pH 9.7. Thus, the equilibrium arrows above imply species
present in equal amounts; all species are in equilibrium at all pH’s.
If there is a potential charge in the side chain, the pI is the average of the two pK s that yield a neutral
species. Techniques for characterization and separation such as Electrophoresis take advantage of the
different charges of the amino acids (and peptides and proteins) by effecting different mobility toward
8 the positive versus negative ends of electrodes. Thus, familiarity with charge states aids in separation
and characterization. Given all aK s of an amino acid, you should be able to calculate the pI.
Buffers: If amino acids are present in appreciable amounts, they can be used as buffers. They can
buffer at any pH that corresponds to one of theia pK ’s. Given tha pK ’s and amounts of species in
solution, the pH can be calculated. Likewise, given theapK ’s and the desired pH, the amounts of
species needed to create that buffer can be calculated. You should be able to perform simple buffer
calculations. Homework: given a solution of alanine at pH 9.00, draw the structure of the species
present in appreciable quantities and calculate the concentration of each of these species.
Synthesis of Amino Acids
Plants can make all 20 amino acids. Humans can make 10. These 10 are considered nonessential, while
the other 10 are essential for our diet. Only a few amino acids are made from scratch biosynthetically;
most are derived from a few main amino acids. For example glutamine is derived from glutamic acid.
We will look at some ways that nature makes amino acids when we discuss reactions of enzymes that
use PLP at the end of the course. Beyond that, we will leave amino acid biosynthesis to biochemistry
How do chemists synthesize amino acids? Again, many are derivatives from others, where the original
source is often natural (i.e., from microorganisms, gelatin, animal skin, etc.). Synthesis is required for
non-natural amino acids or for those that are not readily available in suitable quantities. Keys to
synthesizing an amino acid are of course (1) incorporating the amino and carboxyl groups in the
appropriate positions (e.g., α to each other), and (2) incorporating the appropriate chirality. There are
many ways to synthesize amino acids. Chem. Rev. 2007, 107, 4584-4671 is an 88 page review of just
catalytic asymmetric amino acid synthesis. That could be a whole course. We will discuss only two
Ester Hydrolysis: Before we get into the Gabriel Synthesis, let’s review a “simple” mechanism is
some detail. Esters can be hydrolyzed under basic conditions or under acidic conditions.
Under basic conditions (Saponification), the stable species are hydroxide, alkoxide, alcohol, and water;
any oxygen atom should be neutral or have a formal charge of –1 for any species, including
intermediates. H , CH3OH 2 H 3 will not be present in appreciable amounts. They are not stable.
Such species should be avoided in any mechanism under basic conditions. Oxygen atoms should not
have a +1 formal charge under basic conditions. The aK ’s of said species are below 0, whereas the pH
is around 10 or above. The ultimate product will be R2O , not RC2 H, unless of course there is an
The shortcut notation below is often used with nucleophilic reactions at cabonyls. It denotes formation
of and then collapse of a tetrahedral intermediate.
O O nuc R nuc
R OR' R OR' R OR'
nuc: nuc: + R'O
9 Esters are not very electrophilic, nor is water a very strong nucleophile. Under basic conditions, the
nucleophile is hydroxide. Upon attack by hydroxide, a tetrahedral intermediate forms. Might this
species lose its ROH proton? It could under these conditions, but that would yield a dianion, which
would not be very stable. No points would be taken off for such a species under these conditions.
Could the ROR be protonated before departure? Not likely under basic conditions; points would be
taken off for that. Is the shorthand formation/collapse of the tetrahedral intermediate acceptable? I’ll
use it in class to save time. I’d prefer to see details on exams, but it is acceptable. Show all bond-
making and bond-breaking, including protonations/deprotonations and use the appropriate proton or
Ester hydrolysis under basic conditions will not be reversible since the carboxylate is essentially non-
electrophilic with respect to alkoxide. (A carboxylate can react with a strong reducing agent such as
LAH, but that is another matter.) And again, virtually no carboxylic acid will be present. If an ester has
hydrogens on the α-carbon it may also undergo Claisen condensations under basic conditions.
Many reaction mechanisms entail one or more proton transfers. We will write these out at first, but
eventually, we may just say “H transfer.” It is usually not the same proton that is actually transferred
(thus the expression “proton transfer” is misleading), although this is possible, particularly in an
enzyme’s active site. The transfer may be internal, especially if 6-membered transition state is
possible, but the “transfer” is often inter-molecular. The solvent involved is usually not the same
molecule that removes and delivers the proton. There are typically heaps of protons and solvent
H H O OH H O OH
H O OH R OR' R O R'
R OR' H
H H H
Under acidic conditions, ester hydrolysis is reversible. The ratio of ester to acid is dependent on the
ratio of water to alcohol (and on the relative thermodynamic stabilities of the ester and acid). The
nucleophile is water, as no hydroxide, alkoxide, or oxygen with a formal charge of –1 will be present
in appreciable amounts (pH is around 3 or below). The ester must be protonated first to make it
electrophilic enough to react with water. Does it matter which lone pair of the ester carbonyl is
protonated? Well, they are non-equivalent, but no it doesn’t matter. You should challenge yourself
with such questions. Can the leaving group be an alkoxide? No, not under acidic conditions. For proton
transfers, I’d like to see details. A proton rarely actually transfers between atoms of a molecule; it is
usually a two step process.
Back to Amino Acid Synthesis: The Gabriel Synthesis involves addition of potassium phthalimide to
diethyl-2-bromomalonate. The ensuing diester is hydrolyzed to the diacid, then decarboxylated, then
further hydrolyzed: the imide is hydrolyzed to yield an amine (amino acid) and the diacid phthalic
acid. You should be comfortable with such a mechanism, which involves tautomerization. Use of the
10 Gabriel Synthesis yields a racemic product: the tautomerization following the decarboxylation entails
protonation at the α-carbon, which will occur 50:50 from each side. There are methods to resolve
(separate enantiomers) amino acids such as formation of diastereomers. Alternatively, homochiral (one
enantiomer only) amino acids are usually obtained from natural sources or from enantioselective
Gabriel Synthesis Overview
O O O
– KBr OEt
N K + EtO OEt N
Br SN2 OEt
O O O
potassium 1,2-benzenedicarboxylicimide +
(potassium phthalimide) Ester hydrolysisH3O , heat
CO 2 O O
hydrolysis decarboxylation OH
CO 2 N N
+ OH – CO2 OH
HO 2 NH 3 O O
There are many methods to create unusual homochiral amino acids. We will look at only one, and very
briefly at that. Chiral catalysts have been used to synthesize homochiral amino acids. Industrial
syntheses include those to make L-DOPA (used to treat Parkinson’s disease) and Aspartame (artificial
sweetener). The 2001 Nobel Prize in Chemistry was awarded in part for such work.
Enantiospecific amino acid synthesis using a chiral auxiliary. An enantiospecific process is one
where a starting enantiomer gives predominantly one enantiomeric product; the other starting
enantiomer will give the other enantiomeric product. A chiral auxiliary is a homochiral (one
enantiomer) helper molecule that is incorporated into an achiral molecule of interest, helps it achieve a
stereoselective process, and is then removed, thus leaving a new chiral molecule that is not racemic.
We’ll look at (1R,2S)-2-amino-1,2-diphenylethanol acting as a chiral auxiliary to effect enantiospecific
amino acid synthesis. In the first step, an SN2 reaction between the amine (which is more nucleophilic
than the alcohol) and the α-bromoester yields an intermediate that quickly cyclizes to a six-membered
ring; the low nucleophilicity of the alcohol is compensated by the intramolecularity of the reaction. In
the second step, a weak base mops up the acid produced and thus helps convert the remaining starting
material from an ammonium to an amine. The second step protects the amine as a carbamate (t-
butoxycarbonyl, t-Boc); the carbamate is not nucleophilic. Third step: sodium hexamethylsilazide is a
very strong base that is sterically hinde