1. Hydrogen Bonding Jianing Li Department of Chemistry Columbia University March 10 th, 2007

2. 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)

3. A Special Molecule: H 2 O

4. Two Special properties of H 2 O In the state of liquid under room temperature  boiling point Water is attracted to itself  surface tension The answer is : Hydrogen bond

5. H bond in complex molecules Question: What holds the two DNA strands together?

6. Where does H bond come from? Why F, O and N?

7. 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.

8. 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

9. 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.

10. 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 ……

11. 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).

12. 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 HF 2 −. 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)

13. 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.van der Waals forcescovalentionic bonds Hydrogen bonds are not chemical bonds

14. Question #1: Water complex

15. Question #2: DNA Base Pairs

16. 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

17. Practice Exercise #1: Why no hydrogen bond in H 2 S? How does the electonegativity affect to the H bond? Comparison of the hydrogen bonds in H 2 O and H 2 S: Dipole, charge distribution

18. Practice Exercise #2: Calculate the number of water molecules in the most stable water complex in gas state.

19. Example: n=2,

20. Practice Exercise #3: Calculate the Energy of Stability of the DNA base pairs