engleski

An improvement of the overlapping spheres method for finding low-energy conformations: introduction of a moving center of interactions

The model of overlapping spheres (OS) for finding the low-energy conformations1-3 is based on the minimization (by steepest descent method) of the van der Waals excluded volume inside the sphere with radius Rv, centered at the geometrical center of molecule or a molecular segment. Starting from the initial (Ą§seedĄ¨) conformation, heavily distorted molecular structure is obtained, which after geometrical optimization by molecular mechanics method, yields a new conformation with usually lower energy than the energy of the Ą§seedĄ¨ conformation. As an improvement of the method, the center of sphere was situated at the point deffined as: _ _ xi = xi + (xij - xi) s n i = 1,2,3 (1) _ where xi , xij, s, and n is i-th coordinate (x, y, z) of geometrical center of the molekule, i-th Cartesian coordinate of sterically most crowded atom, length of step, and the number of steepest descent iterations, respectively. Step length, s, is usually put equal to 0.001 for nmax =1000, so the sphere moves smoothly from geometrical center of molecule to the center of the sterically most crowded atom. The sterically most crowded atom, j, is detected from the condition: N max ƒĂ 1/ [1+(rij ĄV ro)2] (2) i=1 where rij is distance between i-th and j-th atom, ro = 0.35 nm, and N is a total number of atoms in the molecule. Equations (1) and (2) were evaluated at every steepest descent iteration. The new algorithm was checked on branched alkanes and was proved more efficient than the original procedure (s = 0). The best results were obtained by increasing the Rv value for 0.1 nm (in the range of 0.3 to 0.6 nm) after every subsequent cycle of optimization.

molecular mechanics; conformational analysis; molecular volumes

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