Molecular mechanics, conformation

In this molecule only the bond between the steroid skeleton and the aziridine moiety can rotate freely. A molecular mechanics conformational analysis resulted in two low energy conformations (Fig. 9.4, see p. 264), both of which had almost identical potential energy, as calculated in the Tripos force field [10]. 

Molecular graphics, molecular mechanics, conformational search (for applicatons in inorganic chemistry see[4])... 

D. M. Ferguson, W. A. Glauser, and D. J. Raber,/. Comput. Chem., 10(7), 903 (1989). Molecular Mechanics Conformational Analysis of Cyclononane Using the RIPS Method and Comparison with Quantum-Mechanical Calculations. 

It is on this expression that the whole field of molecular mechanics, conformational calculations, and molecular dynamics... 

Relative shape descriptors are defined in terms of a reference structure, which may be an experimental X-ray or NMR structure. Similarly, we can use a molecular mechanics conformational energy minimum as the initial structure for a dynamics simulation. The reference can also be a target conformation with desired shape features—for example, being maximally compact i -aie or... 

A number of issues need to be addressed before this method will become a routine tool applicable to problems as the conformational equilibrium of protein kinase. E.g. the accuracy of the force field, especially the combination of Poisson-Boltzmann forces and molecular mechanics force field, remains to be assessed. The energy surface for the opening of the two kinase domains in Pig. 2 indicates that intramolecular noncovalent energies are overestimated compared to the interaction with solvent. 

I. Pettersson, T. Liljefors, Molecular mechanics calculated conformational energies of organic molecules a comparison of force fields, in Reviews in Computational Chemistry, Vbl. 9,... 

The book is organised so that some of the techniques discussed in later chapters refer to material discussed earlier, though I have tried to make each chapter as independent of the ofhers as possible. Some readers may therefore be pleased to know that it is not essential to completely digest the chapters on quantum mechanics and molecular mechanics in order to read about methods for searching conformational space Readers with experience in one or more areas may, of course, wish to be more selective. 

Ferguson D M and D J Raber 1989. A New Approach to Probing Conformational Space with Molecular Mechanics Random Incremental Pulse Search, journal of the American Chemical Society 111 4371-4378. 

Traditionally, molecular mechanics has not been the method of choice for predicting transition structures. However, since it is the only method viable for many large molecules, some elforts have been made to predict transition structures. Since the bonds are explicitly defined in molecular mechanics methods, it is not possible to simply find a point that is an energy maximum, except for conformational intermediates. 

The level of theory necessary for computing PES s depends on how those results are to be used. Molecular mechanics calculations are often used for examining possible conformers of a molecule. Semiempiricial calculations can give a qualitative picture of a reaction surface. Ah initio methods must often be used for quantitatively correct reaction surfaces. Note that size consistent methods must be used for the most accurate results. The specific recommendations given in Chapter 18 are equally applicable to PES calculations. 

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