Journal of Chemical Physics
Feedback | Help | Exit
The Journal of Chemical Physics
   
 
 
 
Previous Article
Relative energy of the high-(5T2g) and low-(1A1g) spin states of the ferrous complexes [Fe(L)(NHS4)]: CASPT2 versus density functional theory
High-level ab initio calculations using multiconfigurational perturbation theory [complete active space with second-order perturbation theory (CASPT2)] were performed on the transition energy between ...
Next Article
Solving the spin-boson model of strong dissipation with flexible random-deterministic scheme
The zero-temperature dynamics of the spin-boson model with strong dissipation has been a challenging problem for more than 20  years. To solve this and quantum dynamics of dissipative system...

Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface

J. Chem. Phys. 128, 034105 (2008); doi:10.1063/1.2816557

Published 16 January 2008

You are not logged in to this journal. Log in

Hao Hu, Zhenyu Lu, Jerry M. Parks, Steven K. Burger, and Weitao Yang
Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
To accurately determine the reaction path and its energetics for enzymatic and solution-phase reactions, we present a sequential sampling and optimization approach that greatly enhances the efficiency of the ab initio quantum mechanics/molecular mechanics minimum free-energy path (QM/MM-MFEP) method. In the QM/MM-MFEP method, the thermodynamics of a complex reaction system is described by the potential of mean force (PMF) surface of the quantum mechanical (QM) subsystem with a small number of degrees of freedom, somewhat like describing a reaction process in the gas phase. The main computational cost of the QM/MM-MFEP method comes from the statistical sampling of conformations of the molecular mechanical (MM) subsystem required for the calculation of the QM PMF and its gradient. In our new sequential sampling and optimization approach, we aim to reduce the amount of MM sampling while still retaining the accuracy of the results by first carrying out MM phase-space sampling and then optimizing the QM subsystem in the fixed-size ensemble of MM conformations. The resulting QM optimized structures are then used to obtain more accurate sampling of the MM subsystem. This process of sequential MM sampling and QM optimization is iterated until convergence. The use of a fixed-size, finite MM conformational ensemble enables the precise evaluation of the QM potential of mean force and its gradient within the ensemble, thus circumventing the challenges associated with statistical averaging and significantly speeding up the convergence of the optimization process. To further improve the accuracy of the QM/MM-MFEP method, the reaction path potential method developed by Lu and Yang [Z. Lu and W. Yang, J. Chem. Phys. 121, 89 (2004)] is employed to describe the QM/MM electrostatic interactions in an approximate yet accurate way with a computational cost that is comparable to classical MM simulations. The new method was successfully applied to two example reaction processes, the classical SN2 reaction of Cl−+CH3Cl in solution and the second proton transfer step of the reaction catalyzed by the enzyme 4-oxalocrotonate tautomerase. The activation free energies calculated with this new sequential sampling and optimization approach to the QM/MM-MFEP method agree well with results from other simulation approaches such as the umbrella sampling technique with direct QM/MM dynamics sampling, demonstrating the accuracy of the iterative QM/MM-MFEP method. ©2008 American Institute of Physics
History: Received 3 July 2007; accepted 31 October 2007; published 16 January 2008
Permalink: http://link.aip.org/link/?JCPSA6/128/034105/1
BUY THIS ARTICLE   (US$28)
Download HTML Download Sectioned HTML Download PDF (1120 kB) View Cart

KEYWORDS and PACS

Keywords
PACS
  • 82.60.Lf
    Thermodynamics of solutions (chemistry)
  • 82.20.Ej
    Quantum theory of reaction cross section in chemical kinetics
  • 82.30.Fi
    Ion-molecule, ion-ion, and charge-transfer chemical reactions
  • 82.30.Hk
    Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
  • YEAR: 2008

RELATED DATABASES


To view database links for this article,
you need to log in.
To view database links for this article,
you need to log in.

PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
Publisher:
AIP is a member of CrossRef AIP

REFERENCES (92)
View in Separate Window/Tab
For access to fully linked references, you need to log in. For access to fully linked references, you need to Log in.
  1. A. Warshel, Computer Modeling of Chemical Reactions in Enzymes and Solutions (Wiley & Sons, New York, 1991).
  2. A. Warshel and M. Levitt, J. Mol. Biol. 103, 227 (1976).
  3. J. -K. Hwang, G. King, S. Creighton, and A. Warshel, J. Am. Chem. Soc. 110, 5297 (1988).
  4. M. Strajbl, G. Hong, and A. Warshel, J. Phys. Chem. B 106, 13333 (2002).
  5. A. Warshel, Annu. Rev. Biophys. Biomol. Struct. 32, 425 (2003).
  6. A. Warshel, P. K. Sharma, M. Kato, Y. Xiang, H. Liu, and M. H. M. Olsson, Chem. Rev. 106, 3210 (2006).
  7. J. Chandrasekhar, S. F. Smith, and W. L. Jorgensen, J. Am. Chem. Soc. 107, 154 (1985).
  8. W. L. Jorgensen, Acc. Chem. Res. 22, 184 (1989).
  9. O. Acevedo and W. L. Jorgensen, J. Am. Chem. Soc. 128, 6141 (2006).
  10. M. J. Field, P. A. Bash, and M. Karplus, J. Comput. Chem. 11, 700 (1990).
  11. P. A. Bash, M. J. Field, R. C. Davenport, G. A. Petsko, D. Ringe, and M. Karplus, Biochemistry 30, 5826 (1991).
  12. Q. Cui and M. Karplus, J. Chem. Phys. 112, 1133 (2000).
  13. Q. Cui and M. Karplus, J. Phys. Chem. B 104, 3721 (2000).
  14. Q. Cui and M. Karplus, J. Am. Chem. Soc. 123, 2284 (2001).
  15. M. Garcia-Viloca, J. Gao, M. Karplus, and D. G. Truhlar, Science 303, 186 (2004).
  16. J. Gao and X. Xia, Science 258, 631 (1992).
  17. J. Gao and D. G. Truhlar, Annu. Rev. Phys. Chem. 53, 467 (2002).
  18. J. L. Gao, Curr. Opin. Struct. Biol. 13, 184 (2003).
  19. J. Gao, S. Ma, D. T. Major, K. Nam, J. Pu, and D. G. Truhlar, Chem. Rev. 106, 3188 (2006).
  20. H. Y. Liu, Y. K. Zhang, and W. T. Yang, J. Am. Chem. Soc. 122, 6560 (2000).
  21. Y. Zhang, H. Liu, and W. Yang, J. Chem. Phys. 112, 3483 (2000).
  22. H. Liu, M. Elstner, E. Kaxiras, T. Frauenheim, J. Hermans, and W. Yang, Proteins Struct. Funct. Genet. 44, 484 (2001).
  23. G. A. Cisneros, H. Y. Liu, Y. K. Zhang, and W. T. Yang, J. Am. Chem. Soc. 125, 10384 (2003).
  24. H. Liu, Z. Lu, G. A. Cisneros, and W. Yang, J. Chem. Phys. 121, 697 (2004).
  25. Z. Lu and W. Yang, J. Chem. Phys. 121, 89 (2004).
  26. H. Hu and W. Yang, J. Chem. Phys. 123, 041102 (2005).
  27. G. A. Cisneros, M. Wang, P. Silinski, M. C. Fitzgerald, and W. T. Yang, J. Phys. Chem. A 110, 700 (2006).
  28. P. Hu and Y. K. Zhang, J. Am. Chem. Soc. 128, 1272 (2006).
  29. L. H. Wang, X. Y. Yu, P. Hu, S. Broyde, and Y. K. Zhang, J. Am. Chem. Soc. 129, 4731 (2007).
  30. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23, 187 (1977).
  31. B. Kuhn and P. A. Kollman, J. Am. Chem. Soc. 122, 2586 (2000).
  32. U. C. Singh and P. A. Kollmann, J. Comput. Chem. 7, 718 (1986).
  33. M. J. Frisch, G. W. Trucks, et al.H. B. Schlegel, GAUSSIAN 03, Gaussian, Inc., Wallingford, CT, 2004.
  34. A. Shurki and A. Warshel, Adv. Protein Chem. 66, 249 (2003).
  35. T. Wesolowski and A. Warshel, J. Phys. Chem. 98, 5183 (1994).
  36. T. Wesolowski, R. P. Muller, and A. Warshel, J. Phys. Chem. 100, 15444 (1996).
  37. R. P. Muller and A. Warshel, J. Phys. Chem. 99, 17516 (1995).
  38. J. Bentzien, R. P. Muller, J. Florián, and A. Warshel, J. Phys. Chem. B 102, 2293 (1998).
  39. Y. Zhang, T. -S. Lee, and W. Yang, J. Chem. Phys. 110, 46 (1999).
  40. G. A. Cisneros, H. Y. Liu, Z. Y. Lu, and W. T. Yang, J. Chem. Phys. 122, 114502 (2005).
  41. M. Wang, Z. Lu, and W. Yang, J. Chem. Phys. 121, 101 (2004).
  42. G. A. Cisneros, M. Wang, P. Silinski, M. C. Fitzgerald, and W. Yang, Biochemistry 43, 6885 (2004).
  43. M. Wang, Z. Lu, and W. Yang, J. Chem. Phys. 124, 124516 (2006).
  44. S. L. Wang, P. Hu, and Y. K. Zhang, J. Phys. Chem. B 111, 3758 (2007).
  45. C. Corminboeuf, P. Hu, M. E. Tuckerman, and Y. K. Zhang, J. Am. Chem. Soc. 128, 4530 (2006).
  46. J. Kästner, H. M. Senn, S. Thiel, N. Otte, and W. Thiel, J. Chem. Theory Comput. 2, 452 (2006).
  47. M. Klahn, S. Braun-Sand, E. Rosta, and A. Warshel, J. Phys. Chem. B 109, 15645 (2005).
  48. G. A. Cisneros and W. T. Yang (unpublished).
  49. H. Hu, Z. Y. Lu, and W. T. Yang, J. Chem. Theory Comput. 3, 390 (2007).
  50. M. Nagaoka, N. Okuyama-Yoshida, and T. Yamabe, J. Phys. Chem. A 102, 8202 (1998).
  51. N. Okuyama-Yoshida, M. Nagaoka, and T. Yamabe, Int. J. Quantum Chem. 70, 95 (1998).
  52. N. Okuyama-Yoshida, K. Kataoka, M. Nagaoka, and T. Yamabe, J. Chem. Phys. 113, 3519 (2000).
  53. H. Hirao, Y. Nagae, and M. Nagaoka, Chem. Phys. Lett. 348, 350 (2001).
  54. P. Fleurat-Lessard and T. Ziegler, J. Chem. Phys. 123, 084101 (2005).
  55. S. -Y. Yang, I. Hristov, P. Fleurat-Lessard, and T. Ziegler, J. Phys. Chem. A 109, 197 (2005).
  56. G. Li and Q. Cui, J. Mol. Graph. Model. 24, 82 (2005).
  57. L. Maragliano, A. Fischer, E. Vanden-Eijnden, and G. Ciccotti, J. Chem. Phys. 125, 024106 (2006).
  58. M. Higashi, S. Hayashi, and S. Kato, J. Chem. Phys. 126, 144503 (2007).
  59. R. E. Miller, Optimization: Foundations and Applications (Wiley & Sons, New York, 2000).
  60. T. H. Rod and U. Ryde, J. Chem. Theory Comput. 1, 1240 (2005).
  61. A. Morita and S. Kato, J. Am. Chem. Soc. 119, 4021 (1997).
  62. R. G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules (Oxford University Press, Oxford, 1994).
  63. H. Hu, Z. Lu, and W. Yang, J. Chem. Theory Comput. 3, 1004 (2007).
  64. Z. Lu, H. Hu, and W. Yang (to be published).
  65. H. Jónsson, G. Mills, and K. W. Jacobsen, Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions, Classical and Quantum Dynamics in Condensed Phase Simulations, edited by B. J. Berne, G. Ciccotti, D. F. Coker (World Scientific, Singapore, 1998).
  66. P. Y. Ayala and H. B. Schlegel, J. Chem. Phys. 107, 375 (1997).
  67. S. K. Burger and W. Yang, J. Chem. Phys. 124, 054109 (2006).
  68. T. L. Hill, An Introduction to Statistical Thermodynamics (Dover, New York, 1987).
  69. J. Hermans and L. Wang, J. Am. Chem. Soc. 119, 2707 (1997).
  70. M. Strajbl, Y. Y. Sham, J. Villa, Z. T. Chu, and A. Warshel, J. Phys. Chem. B 104, 4578 (2000).
  71. C. L. Brooks III, M. Karplus, and B. M. Pettitt, Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics (Wiley & Sons, New York, 1988).
  72. H. Hu, M. Elstner, and J. Hermans, Proteins Struct. Funct. Genet. 50, 451 (2003).
  73. G. Mann, R. H. Yun, L. Nyland, J. Prins, J. Board, and J. Hermans, in Computational Methods for Macromolecules: Challenges and Applications—Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modelling, edited by T. Schlick and H. H. Gan (Springer, Berlin, 2002), p. 129.
  74. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
  75. A. D. MacKerell, B. Brooks, C. L. Brooks, L. Nilsson, B. Roux, Y. Won, and M. Karplus, in The Encyclopedia of Computational Chemistry, edited by P. v. R. Schleyer et al.. (Wiley & Sons, Chichester, 1998), Vol. 1, p. 271.
  76. M. E. Tuckerman, B. J. Berne, and G. J. Martyna, J. Chem. Phys. 97, 1990 (1992).
  77. T. Schlick, R. D. Skeel, A. T. Brünger, L. V. Kalé, J. A. Board, J. Hermans, and K. Schulten, J. Comput. Phys. 151, 9 (1999).
  78. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984).
  79. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).
  80. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 13, 1011 (1992).
  81. A. D. Becke, J. Chem. Phys. 98, 5648 (1993).
  82. C. Lee, W. Yang, and R. G. Parr, Phys. Rev. B 37, 785 (1988).
  83. M. Head-Gordon, J. A. Pople, and M. J. Frisch, Chem. Phys. Lett. 153, 503 (1988).
  84. D. J. McLennan, Aust. J. Chem. 31, 1897 (1978).
  85. P. A. Bash, M. J. Field, and M. Karplus, J. Am. Chem. Soc. 109, 8092 (1987).
  86. M. H. M. Olsson and A. Warshel, J. Am. Chem. Soc. 126, 15167 (2004).
  87. Y. R. Mo and J. L. Gao, J. Comput. Chem. 21, 1458 (2000).
  88. K. Ohmiya and S. Kato, Chem. Phys. Lett. 348, 75 (2001).
  89. A. Radzicka and R. Wolfenden, Science 267, 90 (1995).
  90. R. Wolfenden and M. J. Snider, Acc. Chem. Res. 34, 938 (2001).
  91. A. Warshel, J. Biol. Chem. 273, 27035 (1998).
  92. T. C. Bruice and P. Y. Bruice, J. Am. Chem. Soc. 127, 12478 (2005).

CITING ARTICLES
For access to citing articles, you need to log in.
For access to citing articles, you need to Log in.


Copyright © American Institute of Physics