Abstract
A new approach is proposed for enclosing all stationary states, including saddle points of all orders, of a potential energy surface based on the αBB deterministic branch and bound global optimization algorithm. This method is based on rigorous optimization methods and offers a theoretical guarentee of enclosing all solutions to the equation ∇V=0. This method is applied to the ECEPP/3 (Empirical Conformational Energy Program for Peptides) potential energy surfaces of unsolvated and solvated tetra-alanine. By analyzing the topography of the potential energy surfaces, we calculate reaction pathways, transition rate matrices, time-evolution of occupation probabilities, and rate disconnectivity graphs, and we identify appropriate criteria for the selection of a reaction coordinate.
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References
Westerberg, K.M. and Floudas, C.A. (1999),J. Chem. Phys. 110(18):9259.
Maranas, C.D. and Floudas, C.A. (1995), J. Global Opt. 7 143
Andoulakis, I.P., Maranas, C.D. and Floudas, C.A. (1995), J. Global Opt. 7(4): 337.
Adjiman, C. and Floudas, C.A. (1996),J. Global Opt. 9: 23.
Adjiman, C., Dallwig, S., Floudas, C.A. and Neumaier, A. (1998), Computers and Chem. Eng. 22(9): 1137.
Adjiman, C., Androulakis, I.P. and Floudas, C.A. (1998), Computers and Chem. Eng. 22(9): 1159.
Jarrold, M.F. (1994), in Clusters of Atoms and Molecules, H. Haberland (ed.). Springer, Berlin, Chap. 2.7, 163.
Kunz R.E. and Berry, R.S. (1995),J. Chem. Phys. 103(5): 1904.
Becker, O.M. and Karplus, M. (1997), J. Chem. Phys. 106(4): 1495.
Czerminski, R. and Elber, R. (1990),J. Chem. Phys. 92(9): 5580.
Némethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S. and Scheraga, H.A. (1992), J. Phys. Chem. 96: 6472.
Tsai, C.J. and Jordan, K.D. (1993), J. Phys. Chem. 97: 11227.
Cerjan, C.J. and Miller, W.H. (1981),J. Chem. Phys. 75(6): 2800.
Simons, J., Jorgensen, P., Taylor, H. and Ozment, J. (1983), J. Phys. Chem. 87: 2745.
Banerjee, A., Adams, N., Simons, J., Shepard, R. (1985), J. Phys. Chem. 89: 52.
O'Neal, D., Taylor, H. and Simons, J. (1984), J. Phys. Chem. 88:1510.
Culot, P., Dive, G., Nguyen, V.H. and Ghuysen, J.M. (1992), Theor. Chim. Acta 82:189.
Augspurger, J.D. and Scheraga, H.A. (1987), J. Phys. Chem. 91: 4105.
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Westerberg, K., Floudas, C. Dynamics of Peptide Folding: Transition States and Reaction Pathways of Solvated and Unsolvated Tetra-Alanine. Journal of Global Optimization 15, 261–297 (1999). https://doi.org/10.1023/A:1008341702093
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DOI: https://doi.org/10.1023/A:1008341702093