Conformational analysis global energy minimum

The APME has thus far been tested on a disaccharide rt-i,-Rha/>-(l > 2)-a-L-Rhap-OMe.155 160 In addition to a global energy minimum at Ip = 0°, the analysis uncovered the existence of a weak local minimum at P 160° corresponding to anti-T conformer. The latter was not found by either the MD or LD molecular simulations, which showed the existence of two minima distributed at around 40° around P = 0° angle. The main APME minimum is a broader one encompassing both MD minima. It is difficult to ascertain whether the differences in the experimental GDO parameters (1.2-fold) for the two rings are due to the transitions between the minima identified by the MD or if these are due to the admixture of the anti-4 conformer suggested by the APME analysis. 

The analysis of crystal structures of 33 small molecules as pure compounds and as protein-bound compounds showed considerable differences in their conformations.Both conformations are also different from the global energy minimum conformation, and the degree of deformation depends on the number of bonds around which free rotation exists. Interrelations between different structures... 

Conformational Analysis of Flexible Molecules Location of the Global Minimum Energy Conformation by the Simulated Annealing Method. 

Either MM or QM can be used to carry out energy minimization. For example, a molecule can be drawn and its crude coordinates can be submitted for geometry optimization. The modeling software would systematically shift the atoms until the calculated energy was minimized. However, there is no way to know that this local minimum is the lowest possible (global) minimum. The method of conformational analysis systematically puts the molecule into all possible shapes and, in recent times, minimizes the energy at each increment of change. 

S. R. Wilson, W. Cui, J. W. Moskowitz, and K. E. Schmidt, Tetrahedron Lett. 29(35), 4373 (1988), Conformational Analysis of Flexible Molecules Location of the Global Minimum Energy Conformation by the Simulated Annealing Method. 

Crystallographic data on over 1000 steroids or steroid related compounds provide information concerning preferred conformation, relative stabilities, and substituent influence on the interactive potential of steroid hormones. Conformational analysis of these data and comparison with ab-initio and empirical energy calculations indicate that the conformations observed in the solid state are at or near global minimum energy conformations and provide a useful basis for empirical models of structure-function relationships. 

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