Biochemistry I
Lecture 2
January 16, 2013
Lecture 2: Molecular Forces, Water & Hydrogen Bonds
Assigned Reading: Ch 2.1 - 2.6 (Horton), Ch 2.1, 2.4 (Nelson & Cox)
Key Terms:

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





Interactions:
o Electrostatics
o van der Waals
o Entropy
Polar bonds
Electronegativity
Polar solvents
Water structure
Hydrogen bond (donor & acceptor)
Hydrophobic (nonpolar) compounds.
Hydrophilic (polar) compounds.
Interaction of salts with water.
Amphipathic or amphiphilic compounds.
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Pre-lecture Question:
Formaldehyde is a planer molecule.
H
C
i) What are the atomic orbitals of the carbon atom?
ii) What are the atomic orbitals of the oxygen?
H
2A. Molecular interactions:
i) Electrostatics: The force between two charged particles is:
qq
1 2
 o  8.854 10 12 C 2 / N  m 2
4 Dr 2
0
The force depends on the distance between the two charges and the
dielectric constant (D) of the media. A high dielectric constant, such
as that found in water, is important because the forces between
charges are attenuated, reducing charge interactions, except at short
distance.
F
1
1
H
O
C
H
O
Biochemistry I
Lecture 2
January 16, 2013
ii) van der Waals (induced dipole-induced dipole, induced dipoledipole, dipole-dipole) – an electrostatic interaction that does not
involve formal charges. Charges may be temporary (induced
dipole) or permanent (dipole).
Boiling points of hydrocarbons:
butane:
-0.5o C
isobutane:
-11.7o C
C C
Same number of carbons, why the
difference?
C
iii) Entropy - this isn't a force, but is important
in interactions, particularly non-polar
(hydrophobic) interactions.
2B. Polar bonds & Molecules
A bond is considered to be polar if there is a
significant difference in the
electronegativities of the participating atoms:
1
H
2.1
3
Li
1.0
2
He
4
Be
1.5
5
B
2.0
6
C
2.5
7
N
3.0
8
O
3.5
9
F
4.0
10
Ne
The dipole moment, μ, is defined by the
following equation:    qr .
All atoms
Polar molecule: A molecule is considered
polar if it is has a permanent dipole moment
associated with it.
2
C
C
C
C
C
Biochemistry I
Lecture 2
2C. Structure of Water
i.
ii.
iii.
iv.
v.
vi.
vii.
Oxygen has the following electronic configuration: 1s22s22p4.
In water, the 2s and the three 2p orbitals form four sp3 hybrid
orbitals.
These orbitals are tetrahedral in their orientation; however, the
ideal bond angle of 109° is distorted to 104.5° by electron
repulsion between the full orbitals.
The orbitals are populated such that two orbitals are filled and
two contain one electron each.
The filled orbitals cannot form bonds and are called lone pairs of
electrons.
The half-filled orbitals participate in the formation of a sigma
bond between oxygen and hydrogen.
"Bent" water molecule generates a permanent dipole moment,
making water a polar solvent.
2D. Hydrogen Bonds
i) Formation of H-bonds is primarily an electrostatic attraction between:
 Electropositive hydrogen, attached to an electronegative atom is the
hydrogen bond donor (i.e. NH)
 Electronegative hydrogen bond acceptor (e.g. the lone pairs of
oxygen in the case of water, or C=O group of an amide).
ii) Typical length: 2.7 Å between electronegative atoms.
iii) Typical angle: 180° ± 20°
iv)Typical energy: 20 kJ/mole.
Biochemical Significance of Hydrogen Bonds in Water:
i). In ice, the hydrogen bonds cause the
formation of cavities in the ice,
lowering the density of the solid.
ii) In liquid water, the hydrogen bonds
persist, and are transient, generating
small short-lived (nsec) clusters of "ice"
in liquid water.
iii) Hydrogen bonds are present over a
wide temperature range.
iv) The hydrogen bonds in water allow
water to absorb heat without a large
increase in temperature, giving
water a high heat capacity.
2E. Solvation – It is all about reaching the lowest energy.
ΔG=ΔH-TΔS
ΔH:
ΔS:
3
January 16, 2013
Biochemistry I
Lecture 2
January 16, 2013
i) Solvation of ions: Interaction by electrostatic forces.
qq
1 2
 o  8.854 10 12 C 2 / N  m 2
4 Dr 2
0
The dielectric constant is proportional to the dipole moment of the solvent, as the
dipole moment increases, D, increases:
Compound Dielectric C. (D) Dipole Moment ( )
Water
79
1.85
Methanol
32
1.66
Benzene
2
0.00
F
1
A large dipole moment means that the solvent molecules can interact favorably
with charged solute molecules.
ii) Hydrophilic (polar) compounds
(e.g. methanol):
H3C
O
H
iii) Hydrophobic (apolar) compounds
(e.g. methane).
http://chem.ps.uci.edu/~kcjanda/Group/Re
search_hydrates.html
iv)
Amphipathic
(or
amphiphilic)
compounds are both polar (usually
charged) and have a substantial nonpolar
section (e.g. fatty acids). These can form
micelles if the nonpolar part is sufficiently
large. Micelles are aggregates of
amphipathic molecules that sequester the
nonpolar part on the inside, much like the
inside of an orange.
4
O
O