The single water molecule

The contours of the total electron density in the HOH plane of the water molecule, as obtained from sophisticated quantum chemical calculations, are shown in Fig. 2.2 and indicate a shape not far from sphericaL The water molecule has a dipole moment of approximately 

Dynamics Three normai modes of vibration of the Isolated water molecule 

Properties of Water in the Gaseous Phase 1.2.1. The single water molecule 

In order to understand the properties of liquid water and its role in biological systems, one must be familiar with the basic properties of a single water molecule. 

This particular geometry has been established by a number of experiments utilizing a variety of methods as well as by theoretical calculations. For most of our studies of the properties of liquid water, we can assume that a water molecule has a rigid geometry with a fixed bond length and a fixed bond angle. 

This simplified model is not sufficient for studying properties that are affected by the vibrations of a single water molecule, or by the dissociation of the molecule into charged ions H+ and OH . 

In this book we shall not discuss dissociation of a water molecule into either the ions H or OH or to the neutral components hydrogen or oxygen. However, it is important to have an idea of the order of magnitude of the energies involved in the formation of a water molecule. 

An important characteristic feature of the charge distribution in a water molecule follows from the hybridization of the Is and the Ip orbitals of the oxygen atom. As a result of this hybridization, two lobes of charge are created by the unshared electron pairs (or lone-pair electrons) which are symmetrically located above and below the molecular plane. These two directions, together with the two O-H directions, give rise to the tetrahedral geometry which is one of the most prominent structural features of the water molecule, and is probably the one responsible for the particular mode of packing of the molecules in the liquid and solid states. 

---

We have made the following approximate calculation to estimate protein-water interactions by a less cumbersome procedure it is assumed that the protein molecule has a unique fixed structure determined by x-ray crystallography and interactions are calculated between the protein and a single water molecule in the absence of other solvent molecules. Using this simple system, one may consider all positions and orientations of the single water molecule relative to the protein in a step-wise manner. We present here the result of this calculation for the crystal of bovine pancreatic trypsin inhibitor (BPTI). The calculated energy, mapped in three dimensions, is a highly informative description of the crystal s solvent space. 

As a result of use of a stationary protein backbone, sharpness of maxima of the simulated density is exaggerated therefore, the ranges of thermal motion of crystallographic and simulated waters are in reasonable agreement. The single water molecule entirely surrounded by protein has both lowest thermal parameter and narrowest distribution of simulated density. 

At this stage, we have a solid starting point for any theoretical work. The internal PF can be calculated from the available data on the single water molecule. Unfortunately, the configurational integral is an extremely complicated function. To evaluate this, we need to make further approximations. In fact, even for simple liquids such as argon, there is no way of writing the... 

Figure 2.1 The single water molecule and its average geometry. Reproduced from Finney (2004) with kind permission of The Royal Society.

The first group of these studies concentrated on the characterization of the geometrical and energetic parameters of different hydrated complexes. The global minimum on the potential surface of the products of intermolecular interactions between the single water molecule and the above-mentioned... 

---