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The Molecular Modeling Workbook for Organic Chemistry - Hehre J.W.

Hehre J.W., Shusterman J.A. The Molecular Modeling Workbook for Organic Chemistry - Wavefunction, 1998. - 307 p.
Download (direct link): molecularmodelingworkbook1998.djvu
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"Zwitterion" and "non-zwitterion" isomers are related by the shift of a
proton, and are known as tautomers.
To what extent do zwitterions bear "full" + and - charges? Compare atomic
charges in the zwitterionic and non-zwitterionic forms of glycine. What
is the total charge on -NH3 in the zwitterionic form? What is the total
charge on -C02? Are these charges much greater than those on -NH2 and -
C02H, respectively, in the non-zwitterionic form of glycine? Is the
dipole moment for zwitterionic glycine much greater than that for the
non-zwitterionic tautomer? Display electrostatic potential maps for both
zwitterionic and non-zwitterionic glycine. Which shows the greater charge
separation?
Which form of glycine, zwitterionic or non-zwitterionic, is the lower-
energy species in the gas phase? Rationalize your observation. Does the
ordering or the difference in tautomer stabilities change in going to an
aqueous environment? Structures, atomic charges and electrostatic
potential maps for both zwitterionic and non-zwitterionic forms of
glycine surrounded by 20 water molecules are available. Which is the
lower energy form? Has solvation had a greater effect on atomic charges
and electrostatic potentials for the zwitterionic or non-zwitterionic
form? Account for your observation.
224 Chapter 16 Biological Chemistry
Amino Acid Sidechains
The 20 natural amino acids differ from each other by the nature of their
sidechains. Differences involve overall size, hydrophobic or hydrophilic
character and, perhaps most importantly, ionization state. While the
sidechains are normally written in terms of "neutral" structures, some
may also exist in either protonated or deprotonated forms depending on
pH.
A selection of amino acids (acid A, acid B,...) terminated at both ends
by amide functionality, i.e., MeNHCO-CHR-NHCOMe, are provided. These are
given in the ionization states found at neutral pH. For each, first
identify the amino acid, and then the ionization state (neutral,
protonated or deprotonated). Next compare electrostatic potential maps
among the different amino acids. Which amino acids would prefer
hydrophobic environments? Hydrophilic environments? Explain your
reasoning.
The X-ray crystal structures of proteins show that highly polar and/or
charged amino acids usually congregate on the exterior regions while less
polar, uncharged amino acids congregate in interior regions. Explain. For
each of the amino acids above, indicate a preference for interior or
exterior regions.

Each amino acid is characterized by an "isoelectric point", the pH at
which it exists in neutral form. Differences in isoelectric points may be
exploited to separate amino acids in what is termed an electrophoresis
experiment.

Electrostatic potential map for acid A shows positively and negatively-
charged regions (in red and blue, respectively) and neutral regions (in
green). The former would prefer hydrophilic environments while the latter
would prefer hydrophobic environments.
Chapter 16 Biological Chemistry 225
Amino Acid Conformation
The structures of amino acids incorporated into polypeptides and proteins
may be characterized by a pair of dihedral angles involving the so-called
a carbon for each amino acid.
0 R Q
II o I v II '/w'c--[|'w'
H
A set of low-energy conformers has been provided for alanine (R=CH3)
tetramer (terminated at both ends by amide functionality). For each
conformer, identify each of the a carbons and measure the o and \|/
dihedral angles (see table below).
a carbon O ?
c, C13N1C1C2 NjCiQNs
c4 C2N2C4C5 n2c4c5n3
c7 c5N3c7c8 n3c7c8n4
N10 C8N4C10C11 N4C10C11N5
Make a plot of \|/ (vertical axis) vs. o (horizontal axis) with \|/=0,
o=0 in the middle and ranging from -180 to 180 for both variables. Put
a point on your plot for each dihedral angle (in each conformer). You
have constructed what is now known as a Ramachandran plot.
Are the points randomly scattered, or are they clustered in certain
regions of the plot? If the latter, see if you can see any common
structural motifs (see also Chapter 16, Problem 9).
16 Biological Chemistry
Amide Bonds
The backbone of polypeptides and, more generally, proteins is made up of
a linear sequence of amino acids.
Two of the three single bonds involved in each unit are flexible, and
their detailed conformation dictates overall polypeptide structures and
(ultimately) function. The amide bond is generally assumed to be rigid.
Why? (See also Chapter 10, Problem 1.)
Examine the geometry of formamide. Is the CN bond shorter than expected
for a normal single bond (in methylamine), and closer to that expected
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