Calculation and Application of Molecular Interaction Fields

In this chapter, I will first describe how MIFs are computed and then give selected examples of how MIFs can be applied. MIFs will be described primarily with reference to their calculation with the GRID program [10]. Other programs may be used to compute MIFs these have different energy functions and parame-trizations. 

The starting point for a MIF calculation is provided by the atomic coordinates of the target molecule. These may have been determined experimentally or theoretically. In many calculations of MIFs, the target is treated as a rigid structure. How- 

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I 2 Calculation and Application of Molecular Interaction Fields Acknowledgments... 

Wade, R. C. Calculation and application of molecular interaction fields. In Molecular Interaction Fields (Mannhold, R., Kubinyi, H., Folkers, G. Eds), In Methods and Principles in Medicinal Chemistry (Cruciani, G Ed.), Vol. 27, Wiley-VCH Weinheim, 2006, pp. 27-42. 

In summary, the two problem areas of state-of-the-art mobility calculations are the neglect of inelasticity of molecular collisions, especially with respect to rotation, and poor quality or absence of force fields for ion-molecule interactions. However, the impossibility of rigorously solving the Schrodinger equation for polyatomic molecules has stimulated rather than precluded continuous improvement and application of approximate quantum chemistry methods. 

Several other related aspects of TCFs can be mentioned, but will not be covered here to concentrate instead on calculational methods and applications of collisional TCFs. An earlier alternative approach in terms of superoperators [18] suggests ways of extending the formalism to include phenomena where the total energy is not conserved due to interactions with external fields or media. It has led to different TCFs which however have not been used in calculations. Information-theory concepts can be combined with TCFs [10] to develop useful expressions for collisional problems [19]. Collisional TCFs can also be expressed as overlaps of time-dependent transition amplitude functions that satisfy differential equations and behave like wavepackets. This approach to the calculation of TCFs was developed for Raman scattering [20] and has more recently been extended using collisional TCFs for general interactions of photons with molecules [21] and for systems coupled to an environment [22-25]. This approach has so far been only applied to the interaction of photons with molecular systems. Flux-flux TCFs [26-28] have been applied to reactive collision and molecular dynamics problems, but their connection to collisional TCFs have not yet been studied. 

Abstract It is well known that solvents can modify the frequency and intensity of the solute spectral bands, the thermodynamics and kinetics of chemical reactions, the strength of molecular interactions or the fate of solute excited states. The theoretical study of solvent effects is quite complicated since the presence of the solvent introduces additional difficulties with respect to the smdy of analogous problems in gas phase. The mean field approximation (MFA) is used for many of the most employed solvent effect theories as it permits to reduce the computational cost associated to the smdy of processes in solution. In this chapter we revise the performance of ASEP/MD, a quanmm mechanics/molecular mechanics method developed in our laboratory that makes use of this approximation. It permits to combine state of the art calculations of the solute electron distribution with a detailed, microscopic, description of the solvent. As examples of application of the method we smdy solvent effects on the absorption spectra of some molecules involved in photoisomerization processes of biological systems. 

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