Conformational analysis, molecular

Rastelli, G., Fanelli, F., Menziani, M.C., Cocchi, M. and De Benedetti, P.G. (1991) Conformational analysis, molecular modeling and quantitative structure-activity relationships studies of 2,4-diamino-6,7-dimethoxy-2-substituted quinazoline al-adrenergic antagonists. Journal of Molecular Structure (Theochem), 251, 307—318. 

Holzgrabe, U. and Hopfinger, A.J. (1996). Conformational Analysis, Molecular Shape Comparison, and Pharmacophore Identification of Different Allosteric Modulators of Muscarinic Receptors. J.Chem.lnfComput.ScL, 36,1018-1024. 

Waller, C.L., Wyrick, S.D., Kemp, W.E., Park, H.M. and Smith, FT. (1994). Conformational Analysis, Molecular Modeling, and Quantitative Structure-Activity Relationship Studies of Agents for the Inhibition of Astrocytic Chloride Transport. Pharm.Res., JJ, 47-53. 

Holzgrabe, U., Hopfinger, A.J., 1996. Conformational analysis, molecular shape comparison and pharmacophore identification of different allosteric modulators of muscarinic receptors. J. Chem. Inf. Comp. Sci. 36, 1018-1024. 

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. 

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. 

Shephard M J and Paddon-Row M N 1996 Conformational analysis of Cgg ball and chain molecules a molecular orbital study Aust. J. Chem. 49 395-403... 

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. 

There is a lot of confusion over the meaning of the terms theoretical chemistry, computational chemistry and molecular modelling. Indeed, many practitioners use all three labels to describe aspects of their research, as the occasion demands "Theoretical chemistry is often considered synonymous with quantum mechanics, whereas computational chemistry encompasses not only quantum mechanics but also molecular mechaiucs, minimisation, simulations, conformational analysis and other computer-based methods for understanding and predicting the behaviour of molecular systems. Molecular modellers use all of these methods and so we shall not concern ourselves with semantics but rather shall consider any theoretical or computational tecluiique that provides insight into the behaviour of molecular systems to be an example of molecular modelling. If a distinction has to be... 

Volumen and Hydratationswarme der lonen. Zeitschrift filr Physik 1 45-48. aan C M and K B Wiberg 1990. Determining Atom-Centred Monopoles from Molecular Electro-itic Potentials. The Need for High Sampling Density in Formamide Conformational Analysis. imal of Computational Chemistry 11 361-373. 

A R, D P Dolata and K Prout 1990. Automated Conformational Analysis and Structure Generation Algorithms for Molecular Perception. Journal of Chemical Information and Computer Science 30 316-324. 

S. Piofeta, Ji., Conformational Analysis of Aliphatic Amines by Quantum and Molecular Mechanical Methods, Pb.D. Dissertation, University of Georgia, 1978, available from University Microfilms International, Arm Arbor, Mich. 

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... 

---