Before considering the dynamics of proteins and nucleic acids, it is necessary to review some of the structural and energetic properties of these molecules and their solvent surroundings. In the following sections, we sketch some important structural characteristics in simple physical terms. We also describe the interatomic forces that govern molecular structure and flexibility. This general discussion is far from complete. Some additional details are reviewed as necessary in discussing specific dynamic processes in later chapters. Fortunately, many comprehensive reviews of these structural topics are available; references to some of these are given in the following sections.

In considering structure at the level of atomic detail, it is essential to keep in mind the time scale of observation. In macromolecules, there will be subtle differences between any particular instantaneous structure (observed on a time scale that is shorter than the period of vibration of bond lengths) and the average structure that is seen by an X-ray diffraction study which observes average positions over many hours. This is an even more important issue in liquids. An instantaneous structure of liquid water, such as may be obtained from a Monte Carlo or molecular dynamics simulation, will be characterized by well-defined atomic positions. Discussions about this structure in terms of the extent of hydrogen bonding and the similarities to and differences from the structure of ice are possible. Experimentally, however, most methods look at properties averaged over times that are much longer than the characteristic times of rotational and translational diffusion.