Overview of the Biological System Under Study

Abstract

Biophysical chemistry is a method of simplifying and abstracting from the natural biological system. The foundation theory in biophysical chemistry is the study of the interaction of electromagnetic fields with light and matter. This theory is called quantum electrodynamics and unifies the treatment of electrons and electromagnetic fields (see Appendix B). Today, quantum electrodynamics or QED is the best (most accurate) abstraction we have to describe the natural system of chemical interactions in the Universe. It is sufficient to explain all chemical behavior. Therefore the whole of chemistry and biology rests upon its ample foundation stones. Unfortunately as an abstraction, QED is not practical for daily use because it is computationally intractable. We will allude to QED but will not explore it in any great depth in this volume. Instead we will be more concerned with building our chemical biology upon simpler and more accessible abstractions of electronic structure. The most commonly applied abstraction of QED is the Schrödinger equation, which treats the electronic structure as if it were a wave. Again, theoretically such a treatment should allow us to understand chemical biology ab initio (from first principles) but is unfortunately too complex and must itself be replaced by a less complete but more accessible abstraction, molecular orbital theory (MO). Molecular orbital theory is grounded in quantum theory and as a greatly simplified abstraction is very useful in understanding the structure and properties of molecules. Unfortunately as the size of the molecular system being modeled grows, MO theory suffers severe computational constraints and is most useful qualitatively.