Theoretical crystal structure prediction is still an unsolved and a very challenging problem in theoretical chemistry. A solution to the problem is very important for the development of intermolecular potentials, and therefore, for efficient computer-aided drug design. Two methods of global minimization, the diffusion equation method (DEM) and the distance scaling method (DSM), were applied to predict the crystal structures of the hexasulfur and benzene molecules. No knowledge about the systems other than the geometry of the molecules and the pairwise potentials was assumed; i.e., no assumptions were made about the space groups, cell dimensions, or the number of molecules in the unit cell. The crystal structures, known from experiment, were predicted correctly. To verify the power of the method, the problem of global minimization of the potential energy of crystals of both molecules was intentionally increased considerably in complexity: viz., the numbers of molecules in the unit cell were doubled (from 3 to 6 in the case of hexasulfur, and from 4 to 8 in the case of benzene), and the search for the global minimum was repeated; the method again located the global minimum for each molecule. These results demonstrate that the method is extremely powerful. Future work will be focused on crystal structure prediction of flexible molecules, using a new, much more powerful, Self-Consistent Basin-to-Deformed-Basin Mapping Method (SCBDBM). This new DEM/DSM-based global optimization method has been designed to significantly enhance the efficiency of deformational methods.
| Chiang, Chi-Tung; Shores, Kevin S; Freindorf, Marek et al. (2008) Size-restricted proton transfer within toluene-methanol cluster ions. J Phys Chem A 112:11559-65 |
| Kazmierkiewicz, Rajmund; Liwo, Adam; Scheraga, Harold A (2003) Addition of side chains to a known backbone with defined side-chain centroids. Biophys Chem 100:261-80 |
| Kazmierkiewicz, Rajmund; Liwo, Adam; Scheraga, Harold A (2002) Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method. J Comput Chem 23:715-23 |
| Liwo, Adam; Arlukowicz, Piotr; Czaplewski, Cezary et al. (2002) A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field. Proc Natl Acad Sci U S A 99:1937-42 |
| Scheraga, Harold A; Pillardy, Jaroslaw; Liwo, Adam et al. (2002) Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. J Comput Chem 23:28-34 |
| Scheraga, Harold A; Vila, Jorge A; Ripoll, Daniel R (2002) Helix-coil transitions re-visited. Biophys Chem 101-102:255-65 |
| Pillardy, J; Arnautova, Y A; Czaplewski, C et al. (2001) Conformation-family Monte Carlo: a new method for crystal structure prediction. Proc Natl Acad Sci U S A 98:12351-6 |
| Vila, J A; Ripoll, D R; Scheraga, H A (2001) Influence of lysine content and pH on the stability of alanine-based copolypeptides. Biopolymers 58:235-46 |
| Pillardy, J; Czaplewski, C; Liwo, A et al. (2001) Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc Natl Acad Sci U S A 98:2329-33 |
| Czaplewski, C; Rodziewicz-Motowidlo, S; Liwo, A et al. (2000) Molecular simulation study of cooperativity in hydrophobic association. Protein Sci 9:1235-45 |
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