Biochemistry I

2: Water & Hydrogen Bonds

Reading in Campbell: Chapter 2.1-2.2.

Chime display of a water cluster.

2.1 Structure and Polar Nature of Water

1. Electronic Structure of Water
1. Oxygen has the following electronic configuration: 1s²2s²2p⁴.
2. The 2s and 2p orbitals form four sp³ hybrid orbitals.
3. These orbitals are tetrahedral in shape (ideal bond angle of 109°, distorted to 104.5°).
4. The orbitals are populated such that two orbitals are filled and two contain one electron. This distribution is a consequence of Hund's rule: when two electrons are populating two orbitals of equal energy then each orbital will contain one electron.
5. The filled orbitals cannot form bonds and are called lone pairs of electrons.
6. The half-filled orbitals participate in the formation of a sigma bond between oxygen and hydrogen.

2. Solvation

1. Hydrophobic (apolar) compounds (e.g. hexane).
2. Hydrophilic (polar) compounds (e.g. sodium ion, ethanol).
3. Amphipathic (or amphiphilic) compounds are both polar and nonpolar (e.g. fatty acids).
4. Solvation of ions: forces between two charged particles:



The force depends on the distance between the two charges and the dielectric constant (D) of the media.

Compound	Dielectric Constant	Dipole Moment (m )
Formamide	110	3.37
Water	79	1.85
Methanol	32	1.66
Benzene	2	0.00

The dipole moment reflects the charge distribution of a molecule. It is defined by the following equation:


A larger dipole moment means that the solvent molecules can interact favorably with charged solute molecules, thus screening their charges. Consequently, a high dipole moment usually implies a high dielectric constant. A high dielectric constant, such as that found in water, is important because the forces between charges are attenuated.

1. Characteristics of H-Bonds
1. Formation of H-bonds is primarily an electrostatic attraction between:
   Electropositive hydrogen bond donor (i.e. hydrogen)
   Electronegative hydrogen bond acceptor (e.g. the lone pair electrons of oxygen in the case of water)
2. Typical length: 1.8Å (from hydrogen to oxygen, 2.7 Å from nitrogen to oxygen)
3. Typical angle: 180° ± 20°
4. Typical energy: 20 kJ/mole (in a vacuum)
5. Facilitates rapid proton diffusion in aqueous media
2. Significance of hydrogen bonds
   1. Solvent properties of water.
   2. Responsible for the low density of ice.
   3. Ice-like structure is present up to the boiling point.
      (DH_sublimation = 47 kJ/mol; DH_fusion = 7 kJ/mol). Radial density functions show that tetrahedral geometry is present over a wide temperature range.
   4. Responsible for the high boiling point of water.
   5. Heat capacity (C_p=dQ/dT=dH/dT): This is important for temperature regulation in organisms.
   6. Play an important role in recognition at the molecular level- most (all) hydrogen bonds must be satisfied in these interactions.

1. Water, itself
2. Ethanol
3. Hexane
4. Soap (micelles)
5. Cations

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