Potential energy calculations, molecular structure determination

A correct calculation of solvation thermodynamics and solution structure is conceivable only in terms of the methods of statistical physics, in particular, the computer experiment schemes, including, in the first place, the molecular dynamics (MD) and the Monte-Carlo (MC) methods [10]. By means of the MD method Newton s classic equations of motion are solved numerically with the aid of a computer assuming that the potential energy of molecular interaction is known. In this manner, the motion of molecules of the liquid may be observed , the phase trajectories found and then the values of the necessary functions are averaged over time and determined. This method permits both the equilibrium and the kinetical properties of the system to be calculated. 

A series of Monte Carlo computer simulation studies of the structure and properties of molecular liquids and solutions have recently been carried out in this Laboratory.The calculations employ the canonical ensemble Monte Carlo-Metropolis method based on analytical pairwise potential functions representative of ab initio quantum mechanical calculations of the intennolecular interactions. A number of thermodynamic properties including internal energies and radial distribution functions were determined and are reported herein. The results are analyzed for the structure of the statistical state of the systems by means of quasicomponent distribution functions for coordination number and binding energy. Significant molecular structures contributing to the statistical state of each system are identified and displayed in stereographic form. 

Only the structures of di- and trisulfane have been determined experimentally. For a number of other sulfanes structural information is available from theoretical calculations using either density functional theory or ab initio molecular orbital theory. In all cases the unbranched chain has been confirmed as the most stable structure but these chains can exist as different ro-tamers and, in some cases, as enantiomers. However, by theoretical methods information about the structures and stabilities of additional isomeric sul-fane molecules with branched sulfur chains and cluster-like structures was obtained which were identified as local minima on the potential energy hypersurface (see later). 

Currently, a wide variety of methods exists for calculating the molecular structure of large liquid crystal molecules which make use of pre-determined functional forms for the interactions in a molecule and semi-empirical information to parametrise the potentials. In general the interaction terms represent the energy cost of distorting bonds and bond angles from equilibrium. These can be expressed as... 

Because of the large number of chemicals of actual and potential concern, the difficulties and cost of experimental determinations, and scientific interest in elucidating the fundamental molecular determinants of physical-chemical properties, considerable effort has been devoted to generating quantitative structure-property relationships (QSPRs). This concept of structure-property relationships or structure-activity relationships (QSARs) is based on observations of linear free-energy relationships, and usually takes the form of a plot or regression of the property of interest as a function of an appropriate molecular descriptor which can be calculated using only a knowledge of molecular structure or a readily accessible molecular property. 

One of the important electrochemical interfaces is that between water and liquid mercury. The potential energy functions for modeling liquid metals are, in general, more complex than those suitable for modeling sohds or simple molecular liquids, because the electronic structure of the metal plays an important role in the determination of its structure." However, based on the X-ray structure of liquid mercury, which shows a similarity with the solid a-mercury structure, Heinzinger and co-workers presented a water/Hg potential that is similar in form to the water/Pt potential described earlier. This potential was based on quantum mechanical calculations of the adsorption of a water molecule on a cluster of mercury atoms. ... 

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