Optimization of the OPLS-AA force field for long hydrocarbons

Journal of Chemical Theory and Computation

Volumn 8, Issue 4, 2012, Pages 1459-1470

  Siu, Shirley W I ^a,b   Pluhackova, Kristyna ^a   Böckmann, Rainer A ^a  

^a UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

^b UNIVERSITY OF MACAU   (Macao)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84859561660     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct200908r     Document Type: Article

References (55)

1. Tuteja, A.; Choi, W.; Ma, M.; Mabry, J. M.; Mazzella, S. A.; Rutledge, G. C.; McKinley, G. H.; Cohen, R. E. Science 2007, 318, 1618-1622
2. Mitsuhashi, R.; Suzuki, Y.; Yamanari, Y.; Mitamura, H.; Kambe, T.; Ikeda, N.; Okamoto, H.; Fujiwara, A.; Yamaji, M.; Kawasaki, N.; Maniwa, Y.; Kubozono, Y. Nature 2010, 464, 76-79
3. Ryckaert, J. P.; Bellemans, A. Chem. Phys. Lett. 1975, 30, 123-125
4. Ryckaert, J. P.; Bellemans, A. Faraday Discuss. 1978, 66, 95-106
5. Jorgensen, W. L.; Madura, J. D.; Swenson, C. J. J. Am. Chem. Soc. 1984, 106, 6638-6646
6. Berger, O.; Edholm, O.; Jähnig, F. Biophys. J. 1997, 72, 2002-2013
7. Toxvaerd, S. J. Chem. Phys. 1990, 93, 4290-4295
8. Ungerer, P.; Beauvais, C.; Delhommelle, J.; Boutin, A.; Rousseau, B.; Fuchs, A. H. J. Chem. Phys. 2000, 112, 5499-5510
9. Kaminski, G.; Duffy, E. M.; Matsui, T.; Jorgensen, W. L. J. Phys. Chem. 1994, 98, 13077-13082
10. Price, M. L. P.; Ostrovsky, D.; Jorgensen, W. L. J. Comput. Chem. 2001, 22, 1340-1352
11. Chang, J.; Sandler, S. I. J. Chem. Phys. 2004, 121, 7474-7483
12. Schuler, L. D.; Daura, X.; van Gunsteren, W. F. J. Comput. Chem. 2001, 22, 1205-1218
13. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236
14. Thomas, L. L.; Christakis, T. J.; Jorgensen, W. L. J. Phys. Chem. B 2006, 110, 21198-21204
15. Haynes, W. M. CRC Handbook of Chemistry and Physics, 91st ed.; Taylor and Francis Group, LLC: Boca Raton, FL, 2010-2011.
16. Kahn, K.; Bruice, T. C. J. Comput. Chem. 2002, 23, 977-996
17. Egberts, E.; Marrink, S.-J.; Berendsen, H. J. C. Eur. Biophys. J. 1994, 22, 423-436
18. Møller, C.; Plesset, M. S. Phys. Rev. 1934, 46, 618-622
19. Kendall, R. A.; Dunning, T. H.; Harrison, R. J. J. Chem. Phys. 1992, 96, 6796-6806
20. Klauda, J. B.; Brooks, B. R.; MacKerell, A. D., Jr.; Venable, R. M.; Pastor, R. W. J. Phys. Chem. B 2005, 109, 5300-5311
21. Schaftenaar, G.; Noordik, J. H. J. Comput.-Aided Mol. Design 2000, 14, 123-134
22. Ahlrichs, R.; Bär, M.; Häser, M.; Horn, H.; Kölmel, C. Chem. Phys. Lett. 1989, 162, 165
23. Helgaker, T.; Jorgensen, P.; Olsen, J. Molecular Electronic-Structure Theory; John Wiley & Sons Ltd.: New York, 2002.
24. Jurečka, P.; Hobza, P. Chem. Phys. Lett. 2002, 365, 89-94
25. Werner, H.-J; Knowles, P. J.; Knizia, G; Manby, F. R.; Schütz, M.; Celani, P.; Korona, T.; Lindh, R.; Mitrushenkov, A.; Rauhut, G.; Shamasundar, K. R.; Adler, T. B.; Amos, R. D.; Bernhardsson, A.; Berning, A.; Cooper, D. L.; Deegan, M. J. O.; Dobbin, A. J.; Eckert, F.; Goll, E.; Hampel, C.; Hesselmann, A.; Hetzer, G.; Hrenar, T.; Jansen, G.; Köppl, C.; Liu, Y.; Lloyd, A. W.; Mata, R. A.; May, A. J.; McNicholas, S. J.; Meyer, W.; Mura, M. E.; Nicklass, A.; O'Neill, D. P.; Palmieri, P.; Pflüger, K.; Pitzer, R.; Reiher, M.; Shiozaki, T.; Stoll, H.; Stone, A. J.; Tarroni, R.; Thorsteinsson, T.; Wang, M.; Wolf, A. MOLPRO, a package of ab initio programs, version 2010.1; www.molpro.net, 2010.
26. Apol, E.; Apostolov, R.; Berendsen, H. J. C.; van Buuren, A.; Bjelkmar, P.; van Drunen, R.; Feenstra, A.; Groenhof, G.; Kasson, P.; Larsson, P.; Meulenhoff, P.; Murtola, T.; Pall, S.; Pronk, S.; Schulz, R.; Shirts, M.; Sijbers, A.; Tieleman, P.; Hess, B.; van der Spoel, D.; Lindahl, E. GROMACS User Manual, version 4.5.4; Royal Institute of Technology and Uppsala University: Stockholm and Uppsala, Sweden, 2010.
27. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435-447
28. Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. J. Comput. Chem. 2004, 25, 1656-1676
29. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463-1472
30. van der Spoel, D.; van Maaren, P. J. J. Chem. Theory Comput. 2006, 2, 1-11
31. Allen, M. P.; Tildesley, D. J. Computer Simulations of Liquids; Clarendon: Oxford, U.K., 1987.
32. Bussi, G.; Donadio, D.; Parrinello, M. J. Chem. Phys. 2007, 126, 014101
33. Klauda, J. B.; Venable, R. M.; Freites, J. A.; O'Connor, J.; Tobias, D. J.; Mondragon-Ramirez, C.; Vorobyov, I.; MacKerell, A. D., Jr.; Pastor, R. W. J. Phys. Chem. B 2010, 114, 7830-7843
34. Poger, D.; Mark, A. E. J. Chem. Theory Comput. 2010, 6, 325-336
35. Yeh, I.-C.; Hummer, G. J. Phys. Chem. B 2004, 108, 15873-15879
36. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem. 1987, 91, 6269-6271
37. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Imprey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
38. Sun, Y.; Kollman, P. A. J. Comput. Chem. 1995, 16, 1164-1169
39. Yaws, C. L. Chemical Properties Handbook; McGraw-Hill: New York, 1999.
40. Yaws, C. L. Yaws' Handbook of Physical Properties for Hydrocarbons and Chemicals, 2008; http://www.knovel.com/web/portal/browse/display?-EXT-KNOVEL- DISPLAY-bookid=2147 (accessed February 26, 2012),.
41. Yaws, C. L. Yaws' Thermophysical Properties of Chemicals and Hydrocarbons, 2010; http://www.knovel.com/web/portal/browse/display?-EXT-KNOVEL- DISPLAY-bookid=2906 (accessed February 26, 2012).
42. Casal, H. L.; Mantsch, H. H. J. Mol. Struct. 1989, 192, 41-45
43. Holler, F.; Callis, J. B. J. Phys. Chem. 1989, 93, 2053-2058
44. McCall, D. W.; Douglass, D. C.; Anderson, E. W. Phys. Fluids 1959, 2, 87-91
45. Tofts, P. S.; Lloyd, D.; Clark, C. A.; Barker, G. J.; Parker, G. J. M.; McConville, P.; Baldock, C.; Pope, J. M. Magn. Reson. Med. 2000, 43, 368-374
46. Yaws, C. L. Yaws' Transport Properties of Chemicals and Hydrocarbons, 2010; http://www.knovel.com/web/portal/browse/display?-EXT-KNOVEL-DISPLAY- bookid=2905 (accessed February 26, 2012),.
47. Ivanciuc, O.; Ivanciuc, T.; Filip, P. A.; Cabrol-Bass, D. J. Chem. Inf. Comput. Sci. 1999, 39, 515-524
48. Shirts, M. R.; Pande, V. S. J. Chem. Phys. 2005, 122, 134508
49. Ben-Naim, A.; Marcus, Y. J. Chem. Phys. 1984, 81, 2016-2027
50. Michielan, L.; Bacilieri, M.; Kaseda, C.; Moro, S. Bioorg. Med. Chem. 2008, 16, 5733-5742
51. Briggs, J.; Chung, H.; Caffrey, M. J. Phys. II (France) 1996, 6, 723-751
52. Borne, J.; Nylander, T.; Khan, A. Langmuir 2000, 16, 10044-10054
53. Marrink, S. J.; Mark, A. E. J. Phys. Chem. B 2001, 105, 6122-6127
54. Marrink, S. J.; Risselada, H. J.; Yefimov, S.; Tieleman, D.; de Vries, A. H. J. Phys. Chem. B 2007, 111, 7812-7824
55. Unruh, T.; Smuda, C.; Busch, S.; Neuhaus, J.; Petry, W. J. Chem. Phys. 2008, 129, 121106