Problems in molecular modeling

One problem in molecular modelling calculations is that large powers of 10 tend to appear in all the calculated quantities. Thus, for example, molecules have... 

Lipton, M Still, W. C. The multiple minimum problem in molecular modeling. Tree searching internal coordinate conformational space. J. Comp. Chem. 1988, 9, 343-355. 

FIGURE 5.2 Matrix representation of a fundamental problem in molecular modeling of geochemical systems. More accurate calculations are computationally more demanding, but larger model systems are needed to account for all the components in a geochemical system. Judicious use of each method can generate accurate and realistic molecular simulations. 

M. Lipton and W. C. Still,/, Comput. Chem., 9(4), 343 (1988). The Multiple Minimum Problem in Molecular Modeling. Tree Searching Internal Coordinate Conformational Space. 

In this chapter we shall consider four important problems in molecular modelling. First, we discuss the problem of calculating free energies. We then consider continuum solvent models, which enable the effects of the solvent to be incorporated into a calculation without requiring the solvent molecules to be represented explicitly. Third, we shall consider the simulation of chemical reactions, including the important technique of ab initio molecular djmamics. Finally, we consider how to study the natiure of defects in solid-state materials. 

Of course, the fact that every problem presents molecular models raises natural questions about the accuracy and meaning of these models. Molecular models are not derived from experiments, but rather from computer calculations. Thus, there will be some differences between modeling data and experimental data, and one must occasionally interpret these data in different ways. 

The aim of the series is to present the latest fundamental material for research chemists, lecturers and students across the breadth of the subject, reaching into the various applications of theoretical techniques and modelling. The series concentrates on teaching the fundamentals of chemical structure, symmetry, bonding, reactivity, reaction mechanism, solid-state chemistry and applications in molecular modelling. It will emphasize the transfer of theoretical ideas and results to practical situations so as to demonstrate the role of theory in the solution of chemical problems in the laboratory and in industry. 

For a good review of the cyclobutadiene problem, see Carpenter BK (1988) In Liotta D (ed) Advances in molecular modelling. JAI Press Inc., Greenwich, CT... 

Look for this logo in the chapter and go to OrganicChemistryNow at http //now.brookscole.com/hornback2 for tutorials, simulations, problems, and molecular models. 

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