Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method

Journal of Computational Chemistry

Volumn 23, Issue 6, 2002, Pages 610-624

  Ferré, Nicolas ^a   Assfeld, Xavier ^a   Rivail, Jean Louis ^a  

^a UNIVERSITÉ DE LORRAINE   (France)

Author keywords

Ab initio; Biomolecule; DFT; Hybrid force field; Macromolecular system; Post Hartree Fock; QM MM method; Strictly localized bond orbitals

Indexed keywords

EID: 0037197652     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.10058     Document Type: Article

References (64)

1. 1 Gao, J. ; Thompson, M., Eds. ACS Symposium: Combined Quantum Mechanical and Molecular Mechanical Methods 712 ; American Chemical Society: Washington, DC, 1998.
2. 2 Monard, G. ; Merz, K., Jr. Acc Chem Res 1999, 32, 904.
3. 3 Warshel, A. ; Levitt, M. J Mol Biol 1976, 103, 227.
4. 4 Field, M. ; Bash, P. ; Karplus, M. J Comp Chem 1990, 11, 700.
5. 5 Harrison, M. ; Burton, N. ; Hillier, I. ; Gould, I. Chem Commun 1996, 24, 2769.
6. 6 Ranganathan, S. ; Gready, J. J Phys Chem B 1997, 101, 5614.
7. 7 Bentzien, J. ; Muller, R. ; Florián, J. ; Warshel, A. J Phys Chem B 1998, 102, 2293.
8. 8 Cummins, P. ; Gready, J. J Phys Chem B 2000, 104, 4503.
9. 9 Mulholland, A. ; Lyne, P. ; Karplus, M. J Am Chem Soc 2000, 122, 534.
10. 10 Matsubara, T. ; Maseras, F. ; Koga, N. ; Morokuma, K. J Phys Chem 1996, 100, 2573.
11. 11 Woo, T. ; Margl, P. ; Blöchl, P. ; Ziegler, T. J Phys Chem B 1997, 101, 7877.
12. 12 Amara, P. ; Volbeda, A. ; Fontecilla–Camps, J. ; Field, M. J Am Chem Soc 1999, 121, 4468.
13. 13 Sierka, M. ; Sauer, J. J Chem Phys 2000, 112, 6983.
14. 14 de Vries, A. ; Sherwood, P. ; Collins, S. ; Rigby, A. ; Rigutto, M. ; Karmer, G. J Phys Chem B 1999, 103, 6133.
15. 15 Dapprich, S. ; Komáromi, I. ; Suzie Byun, K. ; Morokuma, K. ; Frisch, M. J Mol Struct (Theochem) 1999, 461–462, 1.
16. 16 Eichinger, M. ; Tavan, P. ; Hutter, J. ; Parrinello, M. J Chem Phys 1999, 110, 10452.
17. 17 Lyne, P. ; Hodoscek, M. ; Karplus, M. J Phys Chem A 1999, 103, 3462.
18. 18 Woo, T. ; Margl, P. ; Deng, L. ; Cavallo, L. ; Ziegler, T. Catal Today 1999, 50, 479.
19. 19 Antes, I. ; Thiel, W. J Phys Chem A 1999, 103, 9290.
20. 20 Zhang, Y. ; Lee, T.‐S. ; Yang, W. J Chem Phys 1999, 110, 46.
21. 21 Zhang, Y. ; Liu, H. ; Yang, W. J Chem Phys 2000, 112, 3483.
22. 22 Woo, T. ; Pioda, G. ; Röthlisberger, U. ; Togni, A. Organometallics 2000, 19, 2144.
23. 23 Poteau, R. ; Ortega, I. ; Alary, F. ; Ramirez Solis, A. ; Barthelat, J.‐C. ; Daudey, J.‐P. J Phys Chem A 2001, 105, 198.
24. 24 Poteau, R. ; Alary, F. ; Abou El Makarim, H. ; Heully, J.‐L. ; Barthelat, J.‐C. ; Daudey, J.‐P. J Chem Phys A 2001, 105, 206.
25. 25 Hong, G. ; Strajbl, M. ; Wesolowski, T. ; Warshel, A. J Comp Chem 2000, 21, 1554.
26. 26 Théry, V. ; Rinaldi, D. ; Rivail, J. ; Maigret, B. ; Ferenczy, G. J Comp Chem 1994, 15, 269.
27. 27 Monard, G. ; Loos, M. ; Théry, V. ; Baka, K. ; Rivail, J. Int J Quantum Chem 1996, 58, 153.
28. 28 Antonczak, S. ; Monard, G. ; Ruiz–López, M. ; Rivail, J. J Am Chem Soc 1998, 120, 8825.
29. 29 Assfeld, X. ; Rivail, J. Chem Phys Lett 1996, 263, 100.
30. 30 Assfeld, X. ; Ferré, N. ; Rivail, J. In ACS Symposium: Combined Quantum Mechanical and Molecular Mechanical Methods ; American Chemical Society: Washington, DC, 1998, p. 234, 712.
31. 31 Gao, J. ; Amara, P. ; Alhambra, C. ; Field, M. J Phys Chem A 1998, 102, 4714.
32. 32 Náray–Szabó, G. ; Surján, P. Chem Phys Lett 1983, 96, 499.
33. 33 Ferenczy, G. ; Rivail, J.‐L. ; Surján, P. ; Náray–Szabó, G. J Comp Chem 1992, 13, 830.
34. 34 Náray–Szabó, G. Comput Chem 2000, 24, 287.
35. 35 Philipp, D. ; Friesner, R. A. J Comp Chem 1999, 20, 1468.
36. 36 Murphy, R. ; Philipp, D. ; Friesner, R. Chem Phys Lett 2000, 321, 113.
37. 37 Kairys, V. ; Jensen, J. H. J Phys Chem A 2000, 104, 6656.
38. 38 Huzinaga, S. ; Cantu, A. J Chem Phys 1971, 55, 5543.
39. 39 McWeeny, R. Proc R Soc A 1959, 253, 242.
40. 40 Reuter, N. ; Dejaegere, A. ; Maigret, B. ; Karplus, M. J Chem Phys 2000, 104, 1720.
41. 41 Ferré, N. ; Assfeld, X. ; Rivail, J.‐L. Application of the LSCF Method to Ionized States. To be submitted.
42. 42 Löwdin, P. J Chem Phys 1950, 18, 365.
43. 43 Szabo, A. ; Ostlund, N. Modern Quantum Chemistry ; McGraw‐Hill: New York, 1982.
44. 44 As long as the occupied orbitals are not mixed with the virtual ones.
45. 45 Pople, J. ; Krishnan, R. ; Schlegel, H. ; Binkley, J. Int J Quantum Chem Quantum Chem Symp 1979, 13, 225.
46. 46 Foster, J. ; Boys, S. Rev Mod Phys 1960, 32, 300.
47. 47 Edminston, C. ; Ruedenberg, K. Rev Mod Phys 1963, 35, 457.
48. 48 Pipek, J. ; Mezey, P. J Chem Phys 1989, 90, 4916.
49. 49 Weinstein, H. ; Pauncz, R. ; Cohen, M. In Advances in Atomic and Molecular Physics, Vol. 7 ; Academic Press: New York, 1971, p. 97.
50. 50 Sironi, M. ; Famulari, A. Theor Chem Acc 2000, 103, 417.
51. 51 Liu, S. ; Pérez–Jordá, J. ; Yang, W. J Chem Phys 2000, 112, 1634.
52. 52 One has to understand “exact” as “obtained without the LSCF scheme.”
53. 53 Schlegel, H. ; Frisch, M. Int J Quantum Chem 1995, 54, 83.
54. 54 Hall, R. ; Hindle, S. ; Burton, N. ; Hillier, I. J Comp Chem 2000, 21, 1433.
55. 55 Frisch, M. ; Trucks, G. ; Schlegel, H. ; Scuseria, G. ; Robb, M. ; Cheeseman, J. ; Zakrzewski, V. ; Montgomery, J., Jr. ; Stratmann, R. ; Burant, J. ; Dapprich, S. ; Millam, J. ; Daniels, A. ; Kudin, K. ; Strain, M. ; Farkas, O. ; Tomasi, J. ; Barone, V. ; Cossi, M. ; Cammi, R. ; Mennucci, B. ; Pomelli, C. ; Adamo, C. ; Clifford, S. ; Ochterski, J. ; Petersson, G. ; Ayala, P. ; Cui, Q. ; Morokuma, K. ; Malick, D. ; Rabuck, A. ; Raghavachari, K. ; Foresman, J. ; Cioslowski, J. ; Ortiz, J. ; Baboul, A. ; Stefanov, B. ; Liu, G. ; Liashenko, A. ; Piskorz, P. ; Komaromi, I. ; Gomperts, R. ; Martin, R. ; Fox, D. ; Keith, T. ; Al‐Laham, M. ; Peng, C. ; Nanayakkara, A. ; Gonzales, C. ; Challacombe, M. ; Gill, P. ; Johnson, B. ; Chen, W. ; Wong, M. ; Andres, J. ; Gonzales, C. ; Head–Gordon, M. ; Replogle, E. ; Pople, J. Gaussian 98, Revision A.9 ; Gaussian, Inc.: Pittsburgh, PA, 1998.
56. 56 Cornell, W. ; Cieplak, P. ; Bayly, C. ; Gould, I. ; Merz, K., Jr. ; Ferguson, D. ; Spellmeyer, D. ; Fox, T. ; Cladwell, J. ; Kollman, P. J Am Chem Soc 1995, 117, 5179.
57. 57 Mayo, S. ; Olafson, B. ; Goddard, W., III. J Phys Chem 1990, 94, 8897.
58. 58 Rappé, A. ; Casewit, C. ; Colwell, K. ; Goddard, W., III ; Skiff, W. J Am Chem Soc 1992, 114, 10024.
59. 59 Rivail, J.‐L. Eléments de Chimie Quantique à l'Usage des Chimistes ; InterEditions/CNRS Editions: Paris, 1994.
60. 60 More strictly, it could be linked to the following expression: E ∝ (Z X · Z Y − Z X · 1) where Z X stands for the nuclear charge of the atom X.
61. 61 It is possible to increase the accuracy of the frontier bond potential to reach errors in frontier bond lengths of less than 1 pm, but in this case, the transferability of the potential with respect to the basis set is lost. We should note that using effective group pseudopotentials 23 to describe the frontier atoms, the pseudopotential is only valid for the basis set it derived from.
62. 62 Németh, K. ; Coulaud, O. ; Monard, G. ; Ángyán, J. J Chem Phys 2000, 113, 5598.
63. 63 Zhu, C. ; Byrd, R. ; Lu, P. ; Nocedal, J. L‐BFGS‐B: A Limited Memory FORTRAN Code for Solving Bound Constrained Optimization Problems Tech. rep. NAM‐11, EECS Department, Northwestern University, 1994.
64. 64 Byrd, R. ; Lu, P. ; Nocedal, J. ; Zhu, C. SIAM J Sci Comput 1995, 5, 1190.