Conformational analysis, molecular dynamics

Conformational study of glycal-type neuraminidase inhibitors has been undertaken by lorga and co-workers using a combined approach of conformational analysis, molecular dynamics and quantum chemistry. /hh couplings have been calculated for the resulting conformations by the use of several already published empirical equations and compared with the experimental ones. Several examples of nucleosides and carbohydrates whose structures were obtained with the help of Vrh couplings are given in Table 2. 

Anselmi et al. (02JCS(P2)1525), very recently published the conformational analysis and dynamics of cA/ rafts-4-methylcyclohexyl tetrahydro-pyranyl ethers (cf. Scheme 12) and compared their structures with the floral odors of the compounds. The cis isomer 40(cis), endowed with a main white flower note, has an bent, oval molecular shape. The trans derivatives 40(trans) and 41, exhibit different odors, possess an extended structure of cylindrical molecular shape. Brenna et al. (02CJC714) reexamined the configuration/conformation of rose oxide analogues. However, the conformational analysis provided poorer results than published previously (78JPC303) without even citing the previous paper. 

New applications, new methodologies, and new perspectives are offered in this second volume. We have arranged the contributions as follows. First are four chapters dealing with conformational analysis, molecular mechanics, and molecular dynamics. Following these are four chapters on quantum mechanically oriented topics and two chapters on quantitative structure-activity relationships (QSAR). Lastly, an essay focusing on pivotal papers and trends in the computational chemistry literature and an updated appendix on software for molecular modeling are presented. 

Molecular orbital and molecular mechanical calculations have been used to investigate the conformational preferences of the various eight-membered heterocycles, which consist of four low-energy conformational families categorized as the boat-chair, crown, boat, and chair forms (see Section 9.25.4.1). The predicted energy minimized conformations in vacuo can be compared to those observed in the solid state by x-ray diffraction analysis. Molecular dynamics calculations are used to simulate solution conformations which in turn can be compared to those determined experimentally by NMR spectral studies. 

Other methods which are applied to conformational analysis and to generating multiple conformations and which can be regarded as random or stochastic techniques, since they explore the conformational space in a non-deterministic fashion, arc genetic algorithms (GA) [137, 1381 simulation methods, such as molecular dynamics (MD) and Monte Carlo (MC) simulations 1139], as well as simulated annealing [140], All of those approaches and their application to generate ensembles of conformations arc discussed in Chapter II, Section 7.2 in the Handbook. 

A molecular dynamics simulation samples the phase space of a molecule (defined by the position of the atoms and their velocities) by integrating Newton s equations of motion. Because MD accounts for thermal motion, the molecules simulated may possess enough thermal energy to overcome potential barriers, which makes the technique suitable in principle for conformational analysis of especially large molecules. In the case of small molecules, other techniques such as systematic, random. Genetic Algorithm-based, or Monte Carlo searches may be better suited for effectively sampling conformational space. 

Fiber, R. Karplus, M. Multiple conformational states of proteins a molecular dynamics analysis of myoglobin. Science 235 318-321, 1987. 

A molecular dynamics simulation used for a conformational search can provide a quick assessment of low energy conformers suitable for further analysis. Plot the average potential energy of the molecule at each geometry. This plot may also suggest conformational changes in a molecule. 

In a different context, conformational analysis is essential for the analysis of molecular dynamics simulations. As discussed in Chapter 3, the direct output of a molecular dynamics simulation is a set of confonnations ( snapshots ) that were saved along the trajectory. These conformations are subsequently analyzed in order to extract information about the system. However, if, during a long simulation, the molecule moves from one... 

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