Hydrogen Bonding

Jianing LiDepartment of Chemistry

Columbia UniversityMarch 10th , 2007

Let’s do a puzzle first:It’s a compound containing two elementsM.p.=0 °C, B.p=100 °CIt’s odorless, tasteless, clear in liquid stateIt’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 pointWater is attracted to itself

surface tensionThe answer is :

Hydrogen bond

H bond in complex molecules

Question: What holds the two DNA strands together?

Hydrogen Hydrogen Bond!!Bond!!

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 bondsHydrogen: attached directly to one of the most electronegative elementsElectronegative 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/atoms/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->SpartanFile->NewDraw the moleculeSetup->Calculation->Setup->SubmitDisplay->OutputMethod: Hatree FockBasis 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

H

H

O

H

HO

H

Practice Exercise #3:

Calculate the Energy of Stability of the DNA base pairs