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This introductory chapter provides information on some fundamental aspects of crystal structures and their diffraction of X-rays as a basis for the rest of the book. It describes electrons, atoms, molecules, and crystals scatter X-rays, leading to the observed diffraction pattern, and introduces concepts such as the reciprocal lattice, structure factors, Fourier transforms, Bragg's law for the geometry of diffraction, the phase problem encountered in crystallography, and the meaning of resolution and how it is related to the extent of the measured diffraction pattern.

In this chapter the theory of the static structure factor, which is closely related to the underlying fluid structure, is described. Different methods of calculating this quantity are presented, including perturbational approaches,, integral equations (including those based on the interaction site model), and computer simulations. Wherever possible the results of these calculations are compared with experimental data obtained from X-ray, neutron, and electron scattering. The range of fluids considered is broad, including simple inorganic species, polar and nonpolar organic liquids, water, and aqueous solutions. The effect of both temperature and pressure on the fluid structure is analysed and used to distinguish between competing molecular models. Quantum effects are considered where these are significant. The utility of Reverse Monte Carlo calculations and their particular limitations for molecular fluids are also discussed.

Phonons are introduced as an example of quasi-particles that can only exist in matter. Debye’s quantum model for heat capacity of solids and comparison with experimentin different temperature ranges is presented. The dispersion relations of lattice vibration (phonons) and quantization for chains of atoms presented, revealing the optical and acoustic modes; anharmonic effects are discussed. Crystal lattice structures and Brillouin zones are introduced. Phonon scattering and the Umklapp process described. The variation of the thermal conductivity of dielectrics with temperature is interpreted. X-ray scattering studies of phonon dispersion relations are described. Coupling between phonons with photons in polaritons is explained: Raman scattering studies of GaN used to exhibit the cross-over of their dispersion relations. The Mössbauer effect, a recoilless process, and its dependence on temperature are explained.

Biological processes take place in an aqueous environment, and the discovery and characterization of biological macromolecules is tightly interwoven with the development of physical chemistry and solution thermodynamics. Following a recap of calorimetry and fundamental thermodynamics relations, this chapter examines their extension to aqueous solutions and macromolecular hydration and solvation. The thermodynamics approach to analytical ultracentrifugation and small angle X-ray and neutron scattering is presented. Finally, work is discussed in which NMR and inelastic neutron scattering experiments have been used to explore a molecular dynamics interpretation of thermodynamic functions.

The statistical mechanics of atomic motion in gases and solids have convenient starting points. For gases it is the ideal gas limit where intermolecular interactions are disregarded. In solids, the equilibrium structure is pre-determined, the dynamics at normal temperature is characterized by small amplitude motions about this structure and the starting point for the description of such motions is the harmonic approximation that makes it possible to describe the system in terms of noninteracting normal modes (phonons). Liquids are considerably more difficult to describe on the atomic/molecular level: their densities are of the same order as those of the corresponding solids, however, they lack symmetry and rigidity and, with time, their particles execute large-scale motions. Expansion about a noninteracting particle picture is therefore not an option for liquids. On the other hand, with the exclusion of low molecular mass liquids such as hydrogen and helium, and of liquid metals where some properties are dominated by the conduction electrons, classical mechanics usually provides a reasonable approximation for liquids at and above room temperature. For such systems concepts from probability theory (see Section 1.1.1) will be seen to be quite useful. This chapter introduces the reader to basic concepts in the theory of classical liquids. It should be emphasized that the theory itself is general and can be applied to classical solids and gases as well, as exemplified by the derivation of the virial expansion is Section 5.6 below. We shall limit ourselves only to concepts and methods needed for the rest of our discussion of dynamical processes in such environments.