Molecular mechanics minimization

Focuses on force field calculations for understanding the dynamic properties of proteins and nucleic acids. Provides a useful introduction to several computational techniques, including molecular mechanics minimization and molecular dynamics. Includes discussions of research involving structural changes and short time scale dynamics of these biomolecules, and the influence of solvent in these processes. 

The adsorption of the modifier-substrate complex onto Pt (111) surface was investigated using the Soiids-Docking module of the Insightll package. This module determines the conformations of the adsorbed molecules by a combined approach of high temperature molecular dynanuc simulations with molecular mechanics minimization. All the calculated structures were visualized on a Silicon Graphics workstation. 

In order to integrate the NMR distance constraint data into a molecular mechanics minimization routine, we have chosen a smooth approximation of the above function... 

A last point that should be raised with regard to validation is that any comparison between theory and experiment must proceed in a consistent fashion. Consider molecular geometries. Chemists typically visualize molecules as having structure . Thus, for example, single-crystal X-ray diffractometry can be used to determine a molecular structure, and at the end of a molecular mechanics minimization one has a molecular structure, but is it strictly valid to compare them ... 

Klahn M, Braun-Sand S, Rosta E, Warshel A (2005) On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions. J. Phys. Chem. B 109 15645-15650... 

Zamai et al. from the same company have also published data on sequence-directed peptide inhibitors [80]. They used the model of big ET-1 which they proposed on the basis of computerized structure prediction, molecular mechanics minimization and molecular dynamics [81]. The effect of the sequence-directed inhibitors on the in vitro chymotrypsin-catalyzed hydrolysis of big ET-1 was investigated as a strategy for inhibiting formation of endothelin. 

Molecular mechanics minimization and molecular dynamics were chosen to examine the possible conformations for the two acyl enzymes and conclusions were drawn from the time evolution of the two systems. The starting point was a crystal structure of phenylethaneboronic acid bound to alpha-chymotrypsin. QUANTA/CHARMM (Brooks et al, 1983) was employed for the calculations. Ninety-five water molecules from the X-ray structure were included. Distance monitoring and the creation ofH-bonds were the main criteria for differentiating between the two molecules. Both acyl enzymes have their ketone carbonyls H-bonded to Gly-216 NH. Both start with their ester carbonyl in the oxyanion hole (H-bonded to Ser-195 and to Gly-193). The R-acyl enzyme looses both of these hydrogen bonds during the simulation. Attack of water on the R-species should, thus, be less frequently successful. Values for differences in energy were not used because of a small... 

Adding one water molecule to the ion pair and molecular mechanics minimization of the whole molecule. The optimized structure resulted in an arrangement in which the water molecule is located at the polar edge of the molecule. 

Use ChemOffice Net to answer Problem 15.42. (Do not run the molecular-mechanics minimization.)... 

MM Molecular Mechanics Minimization of the molecular electronic energy,... 

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