Stereochemistry

Assuming that the all reactants are present, inorganic reactions are chiefly governed by temperature, that is, temperature is critical to determining whether or not a particular reaction will proceed. In biological reactions, however, the shape of the molecules becomes the critical factor. Small changes in the shape or alignment of molecules can determine whether or not a reaction will proceed. In fact, one of the critical roles of enzymes in biochemistry is to lower the temperature requirements for chemical reactions. Assuming the proper enzymes are present, biological temperatures are usually sufficient to allow reactions to proceed. This leaves the stereochemistry of molecules as the controlling factor in biological and organic (molecules and compounds with Carbon) reactions (assuming all the reactants are present) is the shape and alignment of the reacting molecules.

The molecular geometry around any atom is depends upon the number of bonds to other atoms and the presence or absence of lone pairs of electrons associated with the atom.

The chemical formula of a molecule is only a simple representation of the order of arrangement of atoms. It does not show the three-dimensional structure of the molecule. It is usually left up to the reader to translate the chemical formula into its geometric arrangement. For example, the chemical formula for methane is CH₄. This formula indicates that a central carbon atom is bonded to four hydrogen atoms (C-H). In order to convert this formula into the three dimensional molecular array for methane, one must know that when a carbon atom has four single bonds to four atoms, each of the bonds points towards a different corner of a tetrahedron, as shown in Figure 1. In the figure, the solid wedge shaped bonds are coming out of the paper and the dotted wedges are going into the paper.

Another way to visualize a carbon atom with four single bonds is to consider the central carbon atom at the center of a pyramid, also shown in Figure 1. At each point in the pyramid is located a hydrogen atom that is bonded to you. One hydrogen or pyramid point is directly above your head. One is in front of you, one point is behind you to your right, and another behind you to your left. These three hydrogen atoms or points are all on a level below the one you are on. The three dimensional arrangement of each carbon atom with four single bonds is always the same and the angle between any two bonds is 109.5°.