Intramolecular force fields

Raman intensities of the molecular vibrations as well as of their crystal components have been calculated by means of a bond polarizibility model based on two different intramolecular force fields ([87], the UBFF after Scott et al. [78] and the GVFF after Eysel [83]). Vibrational spectra have also been calculated using velocity autocorrelation functions in MD simulations with respect to the symmetry of intramolecular vibrations [82]. 

Jorgensen et al. has developed a series of united atom intermolecular potential functions based on multiple Monte Carlo simulations of small molecules [10-23]. Careful optimisation of these functions has been possible by fitting to the thermodynamic properties of the materials studied. Combining these OPLS functions (Optimised Potentials for Liquid Simulation) with the AMBER intramolecular force field provides a powerful united-atom force field [24] which has been used in bulk simulations of liquid crystals [25-27],... 

The partial solution of Eq.(27) for the configurational space can be conceived as a stepwise process. The fluctuations around the transient configuration X(n) = (Rs(n), Rm (n)) contain—pell-mell— vibrations driven by the intramolecular force field, librations and cage vibration modes of molecules as a whole. The transient configuration evolving in a different time scale contains diffusion terms for liquid environments. 

In the majority of cases the force associated with the MM interactions is composed of a Coulombic term (typically a long-range correction is applied), non-Coulombic forces (Lennard-Jones 6-12 type potentials are the most commonly used formulation), and intramolecular force field contributions. The QM/MM coupling is composed of the Coulombic interactions with all core (Ni) and layer (N2) atoms plus non-Coulombic forces with all atoms in the layer region (N2). As the latter contributions correspond to the coupling terms in the core and layer regions, no violation of momentum conservation occurs. 

It should also be frankly acknowledged here that there are a variety of theoretical challenges associated with these problems that are not highlighted at all in this chapter. These range from formulation questions involving quantum versus classical issues in calculating rates (see, for example, Chapter 16) to the quantum chemical electronic structure issues of solute intramolecular force fields. These and other difficulties certainly impede the theoretical ability to confidently predict VET rates and mechanisms, but not the desire to try. 

In these calculations a slightly different intramolecular force field for D20 has been used (69), designed to exactly match the experimental liquid frequencies, the effect on the computed relaxation time is rather small, yielding an almost equal time, within numerical accuracy. 

FUERZA procedure for evaluation of intramolecular force fields... 

This procedure [170] consists of the calculation of intermolecular and intramolecular force fields using DFT calculations, the construction and minimization (in energy) of a simulation box containing the material of interest with parameters as obtained from the previous DFT calculations, the heating and equilibration process which includes recalculations of the force fields until a self-consistent force field with the required condition of pressure and temperature is obtained. 

J. M. Seminario, Calculation of Intramolecular Force Fields from Second-Derivative Tensors, Int. J. Quantum Chem. 30, 1271 1996. 

The molecular distortion from a perfect D4d symmetry was discussed by Pawley, Rinaldi and Kurittu by means of a constrained refinement of experimental data and by theoretical calculations which made use of intermolecular and intramolecular force fields available at that time [84, 85]. 

Simple classical intramolecular force fields are usually constructed in terms of the valence coordinates e.g. ... 

Geometrical distortion of the substrate by the enzyme is unlikely to be a significant factor in catalysis. The intermolecular forces of binding are generally too weak and flexible to distort the substrate. The intermolecular force field cannot overcome the intramolecular force field of the substrate. 

In a series of papers, Stock and coworkers have combined the quasiclassi-cal techniques used in the description of gas phase reactions with biomolecular force fields used in molecular dynamics (MD) simulations. This leads to nonequilibrium MD simulations, which mimic the laser excitation of the molecules by nonequilibrium phase-space initial condition for the solute and the solvent atoms. This approach is based on the following assumptions. Firstly, it is assumed that an empirical force field at least provides a qualitative modeling of the process. This is because the initial relaxation appears to be an ultrafast and generic process and because it can be expected that the strong interaction with the polar solvent smoothes out many details of the intramolecular force field. Secondly, quantum-mechanical effects are only included via the nonequilibrium initial conditions of the classical simulations. This means that the method represents a short-time approximation of quantum mechanics. 

Levin IW, Pearce RAR (1975) Intramolecular force field calculations methods and applications. In Durig JR (ed) Vibrational spectra and structm-e, Vol 4, Elsevier, Amsterdam,... 

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