Vibrational spectroscopy, static

The cross-section in Eq. (1 illustrates another distinguishing feature of inelastic neutron scattering for vibrational spectroscopy, i.e., the absence of dipole and polarizability selection rules. In contrast, it is believed that in optical and inelastic electron surface spectroscopies that a vibrating molecule must possess a net component of a static or induced dipole moment perpendicular to a metal surface in order for the vibrational transition to be observed ( 7,8). This is because dipole moment changes of the vibrating molecule parallel to the surface are canceled by an equal image moment induced in the metal. 

Our purpose here is to review spectroscopic approaches, optical and vibrational, applied to the determination of enzyme structure and dynamics. We focus on hydride transfer reactions in protein catalysis. Vibrational spectroscopy is especially useful in the study of the molecular mechanism of enzymes because it is structurally specific and is of high resolution bond distortions as small as 0.01-0.001 A can be discerned by vibrational spectroscopy. It is at this level of atomic resolution that enzyme induced bond distortions usually manifest themselves. In addition, both enthalpic and entropic factors can be characterized by vibrational spectroscopy, sometimes in quantitative terms. Although most of the chapter is concerned with the structures of static protein-ligand complexes, the dynamics of how these complexes are formed and depleted has recently become a viable topic for scientific... 

As far as crystalline structures are concerned, X-ray and/or neutron diffraction methods and vibrational spectroscopy are complementary. The former can determine with accuracy the structure of the rigid framework but have some difficulties in locating protonic species, particularly if they are (statically or dynamically) disordered and if their concentration is low. The latter are well-suited for the identification of protonic entities and their types of association, the investigation of some structural details such as different crystallographic sites, (non)equivalent molecules, protonation sites, A-H and A... B distances and the nature and degree of structural disorder. 

The applications of quantum-based MD which we present throughout this chapter in the context of infrared vibrational spectroscopy and collision-induced dissociation rely on Bom-Oppenheimer MD simulations, briefly outlined below. Within Bom-Oppenheimer MD, the static (time-independent) Schrodinger equation is solved at each step of the dynamics, i.e., for each configuratirai of the nuclei ... 

The main limitations of the theoretical harmonic approach (referred to in the remainder of the text as static harmonic ) to vibrational spectroscopy are ... 

Gregoriou, V.G., Rodman, S.E., Nair, B.R., and Hammond, P.T. (2006) Studying the Viscoelastic Behavior of Liquid Crystalhne Polyurethanes Using Static and Dynamic FTIR Spectroscopy, in Vibrational Spectroscopy of Biological and Polymeric Materials (eds V.G. Gregoriou and M.S. Braiman), CRC Press, Taylor Francis, Boca Raton, FL, USA, Ch. 1. 

Vidal F, Busson B, Tadjeddine A, Peremans A. 2003. Effect of a static electric field on the vibrational and electronic properties of a compressed CO adlayer on Pt(l 10) in nonaqueous electrolyte as probed by infia ed reflection-absorption spectroscopy and infi ared-visible sum-fi equency generation spectroscopy. J Chem Phys 119 12492-12498. 

The term exp(-2k2c ) in (6-9) accounts for the disorder of the solid. Static disorder arises if atoms of the same coordination shell have slightly different distances to the central atom. Amorphous solids, for instance, possess large static disorder. Dynamic disorder, on the other hand, is caused by lattice vibrations of the atoms, as explained in Appendix 1. Dynamic disorder becomes much less important at lower temperatures, and it is therefore an important advantage to measure spectra at cryogenic temperatures, especially if a sample consists of highly dispersed particles. The same argument holds in X-ray and electron diffraction, as well as in Mossbauer spectroscopy. 

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