Hydrogen Bonding
Jianing Li
Department of Chemistry
Columbia University
March 10th , 2007
Let’s do a puzzle first:
It’s a compound containing two
elements
M.p.=0 °C, B.p=100 °C
It’s odorless, tasteless, clear in liquid
state
It’s the essential to life
It’s dihydrogen oxide
(water)
A Special Molecule: H2O
Two Special properties of H2O
In the state of liquid
under room
temperature
 boiling point
Water is attracted
to itself
 surface tension
The answer is :
Hydrogen bond
H bond in complex molecules
Hydrogen
Question: What holds the two DNA strands
Bond!!
together?
Where does H bond come from?
Why F, O and N?
Electronegativity:
Electronegativity is the tendency of an atom in a molecule
to attract shared electrons to itself. An electronegative atom
pulls more of the electron density from the bond towards
itself.
The origin of hydrogen bonds
Hydrogen: attached directly
to one of the most
electronegative elements
Electronegative elements:
not only significantly
negative charged, but also
has at least one "active"
lone pair.
Electrons: contained in a
relatively small volume of
space which therefore has
a high density of negative
charge.
http://www.chemguide.co.uk/a
toms/bonding/hbond.html
Look back to the water
• Most properties that water
displays is a result of the
attraction that different
molecules of water have for
each other.
• Water is cohesive, or attracted to itself. The high cohesion of
water is the reason for it’s high surface tension.
• Water has a high boiling point (relative to other molecules its
size). The large network of hydrogen bonds found in water causes
the water molecules to “like” to be near one another in the liquid
phase. It takes a lot of energy to force the molecules apart from
each other into the gas phase.
What hydrogen bonds help to do?
Multiple hydrogen bonds
hold the two strands of the DNA double helix
together
hold polypeptides together in such secondary
structures as the alpha helix and the beta
conformation
help enzymes bind to their substrates
help antibodies bind to their antigen
help transcription factors bind to each other and
DNA ……
Let’s have a qualitative idea
Bond length: X-H...Y system: X-H distance
is typically ~1.1 Å, whereas H...Y distance
is ~ 1.6 to 2.0 Å.
The length of hydrogen bonds depends on
bond strength, temperature, and pressure.
The bond strength itself is dependent on
temperature, pressure, bond angle, and
environment (usually characterized by local
dielectric constant). The typical length of a
hydrogen bond in water is 1.97 Å (197 pm).
Let’s have a qualitative idea
Bond energy: Hydrogen bonds can
vary in strength from very weak (1-2
kJ mol−1) to extremely strong (40 kJ
mol−1), as in the ion HF2−. Typical
values include:
O—H--:N (29 kJ/mol)
O—H--:O (21 kJ/mol)
N—H--:N (13 kJ/mol)
N—H--:O (8 kJ/mol)
Chemical Bond or not?
hydrogen bonds are chemical bonds?
The typical hydrogen bond is stronger
than van der Waals forces, but
weaker than covalent or ionic bonds.
Hydrogen bonds are not chemical
bonds
Question #1: Water complex
Question #2: DNA Base Pairs
Use Spartan to Calculate H bond
Insert the USB key -> Lab Apps>Spartan
File->New
Draw the molecule
Setup->Calculation->Setup->Submit
Display->Output
Method: Hatree Fock
Basis Set: 3-21G**
Click the box of charge calculation
Practice Exercise #1:
Why no hydrogen bond in H2S?
How does the electonegativity
affect to the H bond?
Comparison of the hydrogen bonds
in H2O and H2S: Dipole, charge
distribution
Practice Exercise #2:
Calculate the
number of water
molecules in the
most stable water
complex in gas state.
Bond Energy=E(water complex) -E(free water)*n
Example:
n=2,
Bond Energy=E(complex of 2 water molecules) -E(free water)*2
H
O
O
H
H
H
H
H
O
Practice Exercise #3:
Calculate the
Energy of Stability
of the DNA base
pairs