Conformations conformational analysis

Conformational analysis is the study of the energetics of different conformations. Many reactions depend on a molecule s ability to twist into a particular conformation conformational analysis can help to predict which conformations are favored and which reactions are more likely to take place. We will apply conformational analysis to propane and butane first, and later to some interesting cycloalkanes. 

Clearly, there is a need for computational tools that generate ensembles of conformations and a substantial step toward the understanding of the physical, chemical or biological, and pharmacological properties of a molecule to study or to analyze its possible conformations. Conformational analysis tries to correlate conformational changes of a molecule with the influence on its properties. 

Studies of Equilibria, Configuration and Conformation. - Conformational analysis of trihalo- triphospholanes (29) by low-temperature P NMR spectroscopy revealed the presence of two conformers. The ylidyl substituent of the chlorophosphine (94) exerts a strong influence on the P-Cl bond. The ylidyl chlorophosphines (94 R = R2N) are covalent in benzene but become more or less ionic in dichloromethane solution. The solvent dependent dissociation equilibrium can be followed by P NMR spectroscopy. In the case of an enamine-derived ylidyl chlorophosphine, the equilibrium shifts almost completely from the covalent to the ionic side within a rather narrow range of solvent composition, from 20 to 70% (vol) of dichloromethane. ... 

Conformational analysis is the study of how conformational factors affect the structure of a molecule and its properties. In this chapter we ll examine the conformations of various alkanes and cycloalkanes, focusing most of our attention on three of them ethane butaney and cyclohexane. You will see that even simple organic molecules can exist in many conformations. Conformational analysis will help us to visualize organic molecules in 3D and to better understand their structure and properties. 

There can be more than one staggered and one eclipsed conformation conformational analysis of butane... 

These 3D models describe a fixed conformation. The only permissible motions of this model are 3D translations and rotations of the molecule as a whole. The relative mobility of parts of an individual molecule can also be described on the basis of its 3D coordinates (see Three-dimensional Structure Generation Automation). It requires the specification of so-called rotatable bonds to record permissible or feasible changes of the conformation. Conformational analysis programs use such a model as their internal problem representation. Partially flexible ring systems require additional sophistication to be modeled adequately using this approach. 

Neuhaus D and Williamson M 1989 The Nuclear Overhauser Effect in Structural and Conformational Analysis (New York VCH)... 

Piela L, Kostrowicki J and Scheraga H A 1989 The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method J. Phys. Chem. 93 3339... 

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... 

M. Robb, M. Garavelli, M. Olivucci, and F, Bernardi, in Reviews in Computational Chemistry, K. Lipkowitz and D. Boyd, eds., Vol. 15, John Wiley Sons, New York, 2000, pp. 87-146. M. Olivucci, M, Robb, and F. Bernardi, in Conformational analysis of molecules in excited states, Wiley-VCH, New York, 2000, pp. 297-366. 

M. Oobatake and G.M. Crippen, Residue-residue potential function for conformational analysis of proteins, J.Phys. Chem. 85 (1981), 1187-1197. 

Obtaining an Ensemble of Conformations What is Conformational Analysis ... 

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. 

The physical, chemical cind biological properties of a molecule often depend critically upo the three-dimensional structures, or conformations, that it can adopt. Conformational analysi is the study of the conformations of a molecule and their influence on its properties. Th development of modem conformational analysis is often attributed to D H R Bcirton, wh showed in 1950 that the reactivity of substituted cyclohexanes wcis influenced by th equatoricil or axial nature of the substituents [Beirton 1950]. An equcilly important reaso for the development of conformatiorml analysis at that time Wcis the introduction c analytic il techniques such as infreired spectroscopy, NMR and X-ray crystaillograph] which actucilly enabled the conformation to be determined. 

As we have discussed, a common strategy in conformational analysis is to perform two-stage process involving first, the generation of a large number of minimum enerj... 

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. 

Gilson M K and B Honig 1988. Calculation of the Total Electrostatic Energy of a Macromoleculai System Solvation Energies, Binding Energies and Conformational Analysis. Proteins Structure Function and Genetics 4 7-18. 

R and M M Hann 2000. The In Silico World of Virtual Libraries. Drug Discovery Today 5 326-336. R and I D Kuntz 1990. Conformational Analysis of Flexible Ligands in Macromolecular eptor Sites. Journal of Computational Chemistry 13 730-748. 

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