Physical Chemistry of Reactions

The fundamentals of thermodynamics, equilibria, and kinetics are essential to structural dynamics and indeed, to dynamics in all disciplines. These topics are presented in depth in textbooks of physical chemistry. The authors define important terms and concepts in thermodynamics and kinetics and offer some examples specific to structural dynamics. In marked contrast to thermodynamics, the concepts of time and reaction rate are central to kinetics. The underlying framework to understand reaction rates is known as transition state theory. In the absence of an enzyme, the uncatalyzed reaction typically occurs via a single transition state of high free energy with few or no transient, short-lived intermediates. In contrast, an enzyme-catalyzed reaction breaks up the overall reaction into a series of sequential intermediates and elementary steps along the reaction coordinate. These intermediates are separated by transition states, each of whose free energy is substantially reduced from that of the sole transition state in the uncatalyzed reaction.