Structure simulation models using pair potentials

The simulation of structures using pair potential methods gives important information, including unit cell dimensions, atomic positions and details of atomic motion including lattice vibrations (phonon modes). Further analysis permits the calculation of heat capacities, the dependence of volume with temperature and the prediction of vibrational spectra, such as IR and neutron spectroscopies. Codes that perform such periodic structure energy minimisation using pair potential models include METAPOCS, THBREL and GULP (Table 4.1). All have been used successfully to model framework structures. 

One of the further refinements which seems desirable is to modify Eq. (9) so that it has wiggles (damped oscillatory behavior). Wiggles are expected in any realistic MM-level pair potential as a consequence of the molecular structure of the solvent (2,3,10,11,21,22) they would be found even for two hard sphere solute particles in a hard-sphere liquid or for two H2I80 solute molecules in ordinary liquid HpO, and are found in simulation studies of solutions based on BO-level models. In ionic solutions in a polar solvent another source of wiggles, evidenced in Fig. 2, may be associated with an oscillatory nonlocal dielectric function e(r). ( 36) These various studies may be used to guide the introduction of wiggles into Eq. (9) in a realistic way. 

In principle, the expressions for pair potentials, osmotic pressure and second virial coefficients could be used as input parameters in computer simulations. The objective of performing such simulations is to clarify physical mechanisms and to provide a deeper insight into phenomena of interest, especially under those conditions where structural or thermodynamic parameters of the studied system cannot be accessed easily by experiment. The nature of the intermolecular forces responsible for protein self-assembly and phase behaviour under variation of solution conditions, including temperature, pH and ionic strength, has been explored using this kind of modelling approach (Dickinson and Krishna, 2001 Rosch and Errington, 2007 Blanch et al., 2002). 

Atomistic simulations have also been performed on pyroxenes and pyroxenoids by Catlow et al. (1982) and predict the stable Mg end member to have the diopside structure and the stable Ca end member the wol-lastonite structure, as observed. However, only pair potentials were employed in this study, and Post and Burnham (1986) have found that diopside structures are poorly described within such a model. It would clearly be of interest to repeat the simulations using the three-body silicate potentials, which have yielded accurate Si-O-Si angles in quartz (Catlow et al., 1985). 

However, before proceeding with the description of simulation data, we would like to comment the theoretical background. Similarly to the previous example, in order to obtain the pair correlation function of matrix spheres we solve the common Ornstein-Zernike equation complemented by the PY closure. Next, we would like to consider the adsorption of a hard sphere fluid in a microporous environment provided by a disordered matrix of permeable species. The fluid to be adsorbed is considered at density pj = pj-Of. The equilibrium between an adsorbed fluid and its bulk counterpart (i.e., in the absence of the matrix) occurs at constant chemical potential. However, in the theoretical procedure we need to choose the value for the fluid density first, and calculate the chemical potential afterwards. The ROZ equations, (22) and (23), are applied to decribe the fluid-matrix and fluid-fluid correlations. These correlations are considered by using the PY closure, such that the ROZ equations take the Madden-Glandt form as in the previous example. The structural properties in terms of the pair correlation functions (the fluid-matrix function is of special interest for models with permeabihty) cannot represent the only issue to investigate. Moreover, to perform comparisons of the structure under different conditions we need to calculate the adsorption isotherms pf jSpf). The chemical potential of a... 

Although FEP is mostly useful for binding type of simulations rather than chemical reactions, it can be valuable for reduction potential and pKa calculations, which are of interest from many perspectives. For example, prediction of reliable pKa values of key groups can be used as a criterion for establishing a reliable microscopic model for complex systems. Technically, FEP calculation with QM/MM potentials is complicated by the fact that QM potentials are non-seperable [78], When the species subject to perturbation (A B) differ mainly in electronic structure but similar in nuclear connectivity (e.g., an oxidation-reduction pair), we find it is beneficial to use the same set of nuclear geometry for the two states [78], i.e., the coupling potential function has the form,... 

In this article, we have presented a series of LD and MD simulations for ice Ih using a variety of water potentials and the results were compared with INS measured DOS. Neutron measurements were shown to provide unique information on the fundamental intramolecular and intermolecular modes, some of which cannot be obtained from the standard IR and Raman techniques. A full knowledge of the intermolecular vibrations as modulated by the molecule s environment in the lattice systems is necessary for a complete analysis of the dynamics of these ice structures. Equipped with the precise knowledge of the structural information obtained by the diffraction measurements [81,82], one can model the system rigorously with suitable force fields or potential functions. The extensive simulation results show that classic pair-wise potentials were unsuccessful in reproducing the measured DOS for ice Ih. 

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