Noncovalent interactions

Chemistry is much more than the making and breaking of covalent bonds! Many important chemical interactions in biological systems are noncovalent in nature.

The presence of noncovalent interactions in biological polymers accounts for the process of denaturation of DNA, RNA, and proteins.

This is why some biological polymers are so unstable in dilute solution and denature on glass surfaces, at high and low pH, or at low and high temperatures.

Charge - charge interactions

A charge-charge (electrostatic) interaction is non-directional. You are familiar with this type of interaction from general chemistry. It is very strong at short ranges and depends heavily on the dielectric constant of the immediate environment.

equation: F (force) = k(qq/er²) q = the charge;
r = distance between the charges;
e = dielectric constant of the medium

the force is higher in a lower dielectric medium

What is an example of a high dielectric medium? (water = 78.54)
What is an example of a low dielectric medium? (hydrocarbons like n-pentane = 1.84)

Why the difference? Polarity of the solvent (some of the electrical force "used" to align polar solvent molecules acts against thermal motion)

Remember this when we discuss protein folding! Free energy is the ability to do work, and work is F x Dr (a force acting over a distance)

Permanent dipoles (energy --> 1/r² for charge-dipole; 1/r³ for dipole-dipole)

A permanent dipole occurs when charge polarizations in a molecule do not vectorally cancel out H
compare carbon dioxide and ammonia O=C=O vs.

van der Waals interactions (energy --> 1/r⁶ for two induced dipoles)

The van der Waals interactions (also called London or dispersion forces) are very weak ionic interactions that result from temporary dipoles, which can give rise to attractive interactions.

Pentane remains liquid at room temperature due to these forces.

Benzene molecules stack because of these forces

Hydrogen bonds

Hydrogen bonds - represent electrostatic attractions resulting from the (permanent) uneven distribution of electrons in bonds. These bonds are very pronounced in water.

Half-life of H bond in water = 10 sec! This type of bonding is strongly directional (-21 kJ/mol).

The rule of thumb for hydrogen bonds is that they occur when hydrogen is attached to small, highly electronegative atoms (such as oxygen, nitrogen, sulfur)

Summary of energies:

van der Waals = - 10 kJ/mol
electrostatic = - 15 kJ/mol
H-bond = - 21 kJ/mol
C-C = -350 kJ/mol
Properties of water (including ionization) Why is water so unusual? It has a freezing point of 0 C; a boiling point of 100C. It has a high viscosity, high surface tension, high dielectric constant, and is a good solvent for polar or ionic substances (like dissolves like).

		water 	n-pentane

mol. wt.	18	72.2   (daltons)
density	        0.997	0.626  (g/ml)
b.p.	        100	36.1   (oC)
e		78.5	1.84  
viscosity	0.0089	0.0023 (g/cm/sec)
surface tension	72	17     (dyne/cm)