Computer-assisted energy calculation

The article presented here indicates the fast growing number of contributions to the area of conformational properties of peptides. Despite considerable progress in the understanding of limited aspects there is still quite a way to go. It became evident in this review that theoretical prediction and experimental results are occasionally incompatible, and more data have to be collected. But molecular modeling and computer-assisted energy calculation prove to be useful when it comes to designing model experiments. 

An alternative metlrod of solution to these analytical procedures, which is particularly useful in computer-assisted calculations, is the finite-difference technique. The Fourier equation describes the accumulation of heat in a thin slice of the heated solid, between the values x and x + dx, resulting from the flow of heat tlirough the solid. The accumulation of heat in the layer is the difference between the flux of energy into the layer at x = x, J and the flux out of the layer at x = x + dx, Jx +Ox- Therefore the accumulation of heat in the layer may be written as... 

B. Kuhn, O. Donini, S. Huo, J. Wang, and P. A. Kollman, MM-PBSA applied to computer-assisted ligand design, in Free Energy Calculations in Rational Drug Design, M. R. Reddy and M. D. Erion, eds., Kluwer/Plenum Press, New York (2001), pp. 243-251. 

The goal of the present study was to develop a computer-based cubic section model of the substrate binding domain of HLADH. It was considered that the Jones cubic section model could be refined by use of computer assisted substrate overlay in combination with kinetic data on a wide variety of substrates. As in the Jones approach we used the alcohol products as the surrogate substrate structures. Thus, we determined the low energy conformation of alcohols produced from ketones that have been reported to be reduced by HLADH and for which comparative kinetic data vs cyclohexanol could be calculated. As well, we determined the preferred conformations of all alcohols that would have been produced from ketones subjected to but failing to undergo HLADH reduction. These calculations utilised molecular mechanics (MACROMODEL) and yielded accurate co-ordinates for ali atoms in each alcohol. Where enantiomeric or stereoisomeric alcohols were produced or capable of production, the co-ordinates of each were calculated. 

At the same time, many theoretical calculations have been carried out over the last two decades to find new polynitrogens. Computational studies have been able to assist and encourage experimental work to find and identify unknown polynitrogens by providing information about molecular structures and kinetic stabilities on the potential energy surface with respect to N2. Many hypothetical structures of polynitrogens (from N4 to N60) have been predicted by quantum-mechanical calculations, which have led to the... 

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