GEM*: A molecular electronic density-based force field for molecular dynamics simulations

Journal of Chemical Theory and Computation

Volumn 10, Issue 4, 2014, Pages 1361-1365

  Duke, Robert E ^a   Starovoytov, Oleg N ^a   Piquemal, Jean Philip ^b,c   Cisneros, G Andrés ^a  

^a WAYNE STATE UNIVERSITY   (United States)

^b SORBONNE UNIVERSITÉ   (France)

^c LABORATOIRE DE CHIMIE THÉORIQUE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84898414089     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct500050p     Document Type: Article

References (71)

1. Case, D. A.; Cheatham, T. E., III; Darden, T. A.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufirev, A.; Simmerling, C.; Wang, B.; Woods, R. J. J. Comput. Chem. 2005, 26, 1668-1688
2. Jorgensen, W. L.; Tirado-Rives, J. J. Comput. Chem. 2005, 26, 1669-1700
3. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhoff, G.; Mark, A. E.; Berensen, H. J. C. J. Comput. Chem. 2005, 26, 1701-1718
4. Christen, M.; Hünenberger, P. H.; Bakowies, D.; Baron, R.; Brúgl, R.; Geerke, D. P.; Heinz, T. N.; Kastenholz, M. A.; Kräutler, V.; Oostenbrink, C.; Peter, C.; Trzesniak, D.; van Gunsteren, W. F. J. Comput. Chem. 2005, 26, 1719-1751
5. MacKerrell, A. D., Jr.; Brooks, B.; Brooks, C. L., III; Roux, N. B.; Won, Y.; Karplus, M. In CHARMM: The Energy Function and Its Parametrization with an Overview of the Program" in Encyclopedia of Computational Chemistry; Schleyer, P., Ed.; John Wiley & Sons Ltd.: New York, 1998; pp 271-277.
6. Salomon-Ferrer, R.; Case, D. A.; Walker, R. C. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2013, 3, 198-210
7. Stone, A. J. The Theory of Intermolecular Forces; Oxford University Press: Oxford, U.K., 2000.
8. Hermida-Ramón, J. M.; Brdarski, S.; Karlström, G.; Berg, U. J. Comput. Chem. 2003, 24, 161-176
9. Gresh, N.; Cisneros, G. A.; Darden, T. A.; Piquemal, J.-P. J. Chem. Theory Comput. 2007, 3, 1960-1986
10. Ponder, J. W.; Wu, C.; Ren, P.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. A., Jr.; Head-Gordon, M.; Clark, G. N. I.; Johnson, M. E.; Head-Gordon, T. J. Phys. Chem. B 2010, 114, 2549-2564
11. Day, P. N.; Jensen, J. H.; Gordon, M. S.; Webb, S. P.; Stevens, W. J.; Krauss, M.; Garmer, D.; Basch, H.; Cohen, D. J. Chem. Phys. 1996, 105, 1968-1986
12. Xie, W.; Gao, J. J. Chem. Theory Comput. 2007, 3, 1890-1900
13. Xie, W.; Orozco, M.; Truhlar, D. G.; Gao, J. J. Chem. Theory Comput. 2009, 5, 459-467
14. Shaik, M. S.; Liem, S. Y.; Popelier, t.; Paul, L. A. ″. P. j.. j. y... v... n... p...,.
15. Price, S. In Reviews in Computational Chemistry; Lipkowitz, K.; Boyd, D. B., Eds.; VCH Publishers: New York, 1999; Vol. 14.
16. Popelier, P. Atoms in Molecules: An Introduction; Prentice Hall: Harlow, England, 2000.
17. Kosov, D. S.; Popelier, P. L. A. J. Phys. Chem. A 2000, 104, 7339-7345
18. Popelier, P. L. A.; Joubert, L.; Kosov, D. S. J. Phys. Chem. A 2001, 105, 8254-8261
19. Popelier, P. L. A.; Kosov, D. S. J. Chem. Phys. 2001, 114, 6539-6547
20. Freitag, M. A.; Gordon, M. S.; Jensen, J. H.; Stevens, W. J. J. Chem. Phys. 2000, 112, 7300-7306
21. Kairys, V.; Jensen, J. H. Chem. Phys. Lett. 1999, 315, 140-144
22. Piquemal, J.-P.; Gresh, N.; Giessner-Prettre, C. J. Phys. Chem. A 2003, 107, 10353-10359
23. Cisneros, G. A.; Tholander, S. N.-I.; Parisel, O.; Darden, T. A.; Elking, D.; Perera, L.; Piquemal, J.-P. Int. J. Quantum Chem. 2008, 108, 1905-1912
24. Wang, B.; Truhlar, D. G. J. Chem. Theory Comput. 2010, 6, 3330-3342
25. Stone, A. J. J. Phys. Chem. A 2011, 115, 7017-7027
26. Wheatley, R. Mol. Phys. 2011, 7, 761-777
27. Gavezzotti, A. J. Phys. Chem. B 2002, 106, 4145-4154
28. Eckhardt, C. J.; Gavezzotti, A. J. Phys. Chem. B 2007, 111, 3430-3437
29. Volkov, A.; Coppens, P. J. Comput. Chem. 2004, 25, 921-934
30. Coppens, P.; Volkov, A. Acta Crystallogr., Sect. A 2004, 60, 357-364
31. Paricaud, P.; Predota, M.; Chialvo, A. A.; Cummings, P. T. J. Chem. Phys. 2005, 122, 244511
32. Giese, T. J.; Chen, H.; Dissanayake, T.; Giambasu, G. M.; Heldenbrand, H.; Huang, M.; Kuechler, E. R.; Lee, T.-S.; Panteva, M. T.; Radak, B. K.; York, D. M. J. Chem. Theory Comput. 2013, 9, 1417-1427
33. Hu, H.; Lu, Z.; Elstner, M.; Hermans, J.; Yang, W. J. Phys. Chem. A 2007, 111, 5685-5691
34. Cisneros, G. A.; Piquemal, J. P.; Darden, T. A. J. Chem. Phys. 2005, 123, 044109
35. Piquemal, J. P.; Cisneros, G. A.; Reinhardt, P.; Gresh, N.; Darden, T. A. J. Chem. Phys. 2006, 124, 104101
36. Cisneros, G. A.; Piquemal, J. P.; Darden, T. A. J. Chem. Phys. 2006, 125, 184101
37. Boys, S. F.; Shavit, I. In A Fundamental Calculation of the Energy Surface for the System of Three Hydrogen Atoms; WIS-AF-13, AD212985, NTIS: Springfield, VA, 1959.
38. Dunlap, B. I.; Connolly, J. W. D.; Sabin, J. R. J. Chem. Phys. 1979, 71, 4993-4999
39. Köster, A. M.; Calaminici, P.; Gómez, Z.; Reveles, U. Density Functional Theory Calculation of Transition Metal Clusters. In Reviews of Modern Quantum Chemistry, A Celebration of the Contribution of Robert G. Parr; Sen, K., Ed.; World Scientific: Singapore, 2002; pp 1439-1475.
40. Kitaura, K.; Morokuma, K. Int. J. Quantum Chem. 1976, 10, 325-340
41. Bagus, P. S.; Hermann, K.; Bauschlicher, C. W., Jr. J. Chem. Phys. 1984, 80, 4378-4386
42. Stevens, W. J.; Fink, W. H. Chem. Phys. Lett. 1987, 139, 15-22
43. Jeziorski, B.; Moszynski, R.; Szalewicz, K. Chem. Rev. 1994, 94, 1887-1930
44. Glendening, E. D. J. Am. Chem. Soc. 1994, 118, 2473-2482
45. Mo, Y.; Gao, J.; Peyerimhoff, S. D. J. Chem. Phys. 2000, 112, 5530-5538
46. Heßelmann, A.; Jansen, G.; Schütz, M. J. Chem. Phys. 2005, 122, 14103-14120
47. Piquemal, J.-P.; Marquez, A.; Parisel, O.; Giessner-Prettre, C. J. Comput. Chem. 2005, 26, 1052-1062
48. Khaliullin, R. Z.; Head-Gordon, M.; Bell, A. T. J. Chem. Phys. 2006, 124, 204105
49. Lu, Z.; Zhou, N.; Wu, Q.; Zhang, Y. J. Chem. Theory Comput. 2011, 7, 4038-4049
50. Cisneros, G. A.; Piquemal, J. P.; Darden, T. A. J. Phys. Chem. B 2006, 110, 11571-11581
51. Chaudret, R.; Ulmer, S.; van Severen, M.-C.; Gresh, N.; Parisel, O.; Cisneros, G. A.; Darden, T. A.; Piquemal, J.-P. AIP Conf. Proc. 2009, 1102, 185-192
52. Essmann, U.; Perera, L.; Berkowitz, M.; Darden, T. A.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593
53. York, D.; Yang, W. J. Chem. Phys. 1994, 101, 3298-3300
54. Darden, T. A. Dual bases in crystallographic computing. In International Tables of Chrystallography; Shmueli, U., Ed.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 2007; Vol. B.
55. Ren, P.; Ponder, J. W. J. Phys. Chem. B 2003, 107, 5933-5947
56. Ren, P.; Ponder, J. W. J. Comput. Chem. 2002, 23, 1497-1506
57. Ren, P.; Wu, C.; Ponder, J. W. J. Chem. Theory Comput. 2011, 7, 3143-3161
58. Wheatley, R. J.; Price, S. L. Mol. Phys. 1990, 69, 507-533
59. Domene, C.; Fowler, P. W.; Wilson, M.; Madden, P.; Wheatley, R. J. Chem. Phys. Lett. 2001, 333, 403-412
60. Thole, B. Chem. Phys. 1981, 59, 341-350
61. Cisneros, G. A. J. Chem. Theory Comput. 2012, 12, 5072-5080
62. Andzelm, J.; Wimmer, E. J. Chem. Phys. 1992, 96, 1280-1303
63. Godbout, N.; Andzelm, J. DGauss, versions 2.0, 2.1, 2.3, 4.0; Computational Chemistry List, Ltd.: Columbus, OH, 1999. The file that contains the A1, A2, and P1 auxiliary basis sets can be obtained from the CCL WWW site at http://www.ccl.net/cca/data/basis-sets/DGauss/basis.v3.html.
64. Stone, A. J. J. Chem. Theory Comput. 2005, 1, 1128-1132
65. Temelso, B.; Archer, K. A.; Shields, G. C. J. Phys. Chem. A 2011, 115, 12034-12046
66. Babin, V.; Medders, G. R.; Paesani, F. J. Phys. Chem. Lett. 2012, 3, 3765-3769
67. Babin, V.; Leforestier, C.; Paesani, F. J. Chem. Theory Comput. 2013, 9, 5395-5403
68. Ewald, P. Ann. Phys. 1921, 64, 253-287
69. Soper, A. Chem. Phys. 2000, 258, 121-137
70. Burger, S. K.; Cisneros, G. A. J. Comput. Chem. 2013, 34, 2313-2319
71. Lipparini, F.; Lagardère, L.; Stamm, B.; Cancès, E.; Schnieders, M.; Ren, P.; Maday, Y.; Piquemal, J. J. Chem. Theory Comput. 2014, accepted; DOI: 10.1021/ct401096t.