Energy conformational analysis

In the past few years, the experimental data has been frequently complemented with theoretical work (conformational analysis, energy minimization, shielding-effect calculations) and this certainly provided supplementary support to the method/reagent in-... 

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... 

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. 

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. 

K. Rasmussen, in G. Berthier and co-workers, eds., Eecture Notes in Chemisty, Vol. 27, Potential Energy Functions in Conformational Analysis, Springer-Vedag, Berlin, 1985. 

To extract the conformational properties of the molecule that is being studied, the conformational ensemble that was sampled and optimized must be analyzed. The analysis may focus on global properties, attempting to characterize features such as overall flexibility or to identify common trends in the conformation set. Alternatively, it may be used to identify a smaller subset of characteristic low energy conformations, which may be used to direct future drug development efforts. It should be stressed that the different conformational analysis tools can be applied to any collection of molecular conformations. These... 

MK Gilson, B Homg. Calculation of the total electrostatic energy of a macromolecular system Solution energies, binding energies, and conformational analysis. Proteins 4 7-18, 1988. 

Beginning with cycloheptane, which has four confomnations of similar energy, conformational analysis of cycloalkanes becomes more complicated. The sane fundamental principles apply to medium and large rings as apply to smaller ones—but there ar e more atoms and more bonds to consider and more confor-mational possibilities. 

Conformational analysis (Section 4.8) A means of assessing the energy of a substituted cycloalkane by totaling the steric interactions present in the molecule. 

---