Molecular associations, acids, computational

Significant progress in the optimization of VDW parameters was associated with the development of the OPLS force field [53]. In those efforts the approach of using Monte Carlo calculations on pure solvents to compute heats of vaporization and molecular volumes and then using that information to refine the VDW parameters was first developed and applied. Subsequently, developers of other force fields have used this same approach for optimization of biomolecular force fields [20,21]. Van der Waals parameters may also be optimized based on calculated heats of sublimation of crystals [68], as has been done for the optimization of some of the VDW parameters in the nucleic acid bases [18]. Alternative approaches to optimizing VDW parameters have been based primarily on the use of QM data. Quantum mechanical data contains detailed information on the electron distribution around a molecule, which, in principle, should be useful for the optimization of VDW... 

A theoretical approach is applied to elucidate the molecular conformations, associated flexibility, and dynamics of polylp-hydroxybenzoic acid) esters, pHB. Properties such as the radius of gyration and persistence length which are characteristic for the stiffness of a macromolecule are calculated on the basis of two different theoretical methods (a) Molecular dynamics and (b) the RIS model augmented by the more recent scheme for the matrix computations. The analysis of the results obtained by the latter method reflects a strong dependence on the choice of the structural parameters of the system. 

Nikolai B. Ulyanov studied mathematics in Moscow State University and worked on computational modeling of DNA bending as part of his Ph.D. project in the group of Dr. Victor Zhurkin in the Engelhardt Institute of Molecular Biology in Moscow. He was a postdoctoral fellow with Prof. Ramaswamy Sarma studying NMR spectroscopy of DNA at the State University of New York at Albany. Currently he is Associate Adjunct Professor at the University of California at San Francisco. His research interests focus on the structure and dynamics of nucleic acids, studied by computational methods and NMR. 

Peptides containing amino acids in which the a-proton has been replaced by a methyl group or other alkyl group (a,a-dialkyl amino acids) serve as the simplest example of helix mimetics. The severe restrictions of (p,v / space by an a-methyl amino acid to limit backbone conformations only to values associated with both a- and 310-heli-ces was discovered independently by Marshall and Bosshard (90) and by Burgess and Leach (171). These early predictions from molecular modeling have been confirmed by multiple studies, both computationally (172-175) and experimentally (176-183) in the subsequent 35 years. Numerous examples of the introduction of a-methyl amino acids into biologically... 

As was theoretically predicted by molecular computation and then experimentally verified, the trans-cis photoisomerization rate for the bound probe was found to be markedly inhibited, compared to that expected for the free probe in solution. The fluorescence-photochrome labeled probe was competitively displaced from the anti-TNP binding site in the presence of the picric acid hapten, and photoisomerization then commenced to produce the fluorescence-silent cis-stilbene diastereomer (Figure 10.14). The process of association and dissociation of a hapten-antibody complex was readily monitored by the fluorescence technique in the presence of both antibody-bound and free haptens. 

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