Systematic study of the boundary composition in poisson boltzmann calculations

Journal of Computational Chemistry

Volumn 28, Issue 16, 2007, Pages 2538-2544

  Kar, Parimal ^a   Wei, Yanjie ^a   Hansmann, Ulrich H E ^a,b   Höfinger, Siegfried ^a  

^a MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

^b FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

Continuum electrostatics; Implicit solvation models; Poisson boltzmann; Polarizable continuum model; Solvation

Indexed keywords

CONTINUUM ELECTROSTATICS; IMPLICIT SOLVATION MODELS; POISSON BOLTZMANN; POLARIZABLE CONTINUUM MODELS;

BOLTZMANN EQUATION; BOUNDARY CONDITIONS; CONVERGENCE OF NUMERICAL METHODS; DENSITY FUNCTIONAL THEORY; FINITE DIFFERENCE METHOD; QUANTUM THEORY; SOLVENTS;

POISSON DISTRIBUTION;

SOLVENT;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; ELECTRICITY; QUANTUM THEORY; STATISTICAL DISTRIBUTION; THERMODYNAMICS;

COMPUTER SIMULATION; ELECTROSTATICS; MODELS, CHEMICAL; QUANTUM THEORY; SOLVENTS; STATISTICAL DISTRIBUTIONS; THERMODYNAMICS;

EID: 35948937280     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20698     Document Type: Article

References (39)

1. Tomasi, J.; Persico, M. Chem Rev 1994, 94, 2027.
2. Cramer, C. J.; Truhlar, D. G. Chem Rev 1999, 99, 2161.
3. Tomasi, J.; Mennucci, B.; Cammi, R. Chem Rev 2005, 105, 2999.
4. Roux, B.; Simonson, T. Biophys Chem 1999, 78, 1.
5. Rinaldi, D.; Ruiz-López, M. F., Rivail, J. L. J Chem Phys 1983, 78, 834.
6. Warwicker, J.; Watson, H. C. J Mol Biol 1982, 157, 671.
7. Honig, B.; Nicholls, A. Science 1995, 268, 1144.
8. Luo, R.; David, L.; Gilson, M. K. J Comput Chem 2002, 23, 1244.
9. Baker, N. A.; Sept, D.; Joseph; S.; Holst, M. J.; McCammon, J. A. Proc Natl Acad Sci USA 2001, 98, 10037.
10. Bashford, D.; Karplus, M. Biochemistry-US 1990, 29, 10219.
11. Tironi, I.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. J Chem Phys 1995, 102, 5451.
12. Zauhar, R. J.; Morgan, R. S. J Mol Biol 1985, 186, 815.
13. Juffer, A. H.; Botta, E. F. F.; van Keulen, B. A. M.; van der Ploeg, A.; Berendsen, H. J. C. J Comput Phys 1991, 97, 144.
14. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J Am Chem Soc 1990, 112, 6127.
15. Onufriev, A.; Bashford, D.; Case, D. A. J Phys Chem B 2000, 104, 3712.
16. Curutchet, C.; Orozco, M.; Luque, J. F.; Mennucci, B.; Tomasi, J. J Comput Chem 2006, 27, 1769.
17. Carlson, H. A.; Jorgensen, W. L. J Phys Chem 1995, 99, 10667.
18. Connolly, M. L. J Am Chem Soc 1985, 107, 1118. Available at: http://www.netsci.org/Science/Compchem/featurel4e.html
19. Lii, J.-H.; Allinger, N. L. J Am Chem Soc 1989, 111, 8576.
20. Aqvist, J. J Phys Chem 1990, 94, 8021.
21. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J Am Chem Soc 1984, 196, 765.
22. Halgren, T. J Am Chem Soc 1992, 114, 7827.
23. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, Q.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E, III. Acc Chem Res 2000, 33, 889.
24. Page, C. S.; Bates, P. A. J Comput Chem 2006, 27, 1990.
25. Becke, A. D. J Chem Phys 1997, 107, 8554.
26. Sadlej, A. J. Theor Chim Acta 1991, 79, 123.
27. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne; P. E. Nucleic Acids Res 2000, 28, 235.
28. Akiyama, Y.; Onizuka, K.; Noguchi, T.; Ando, M. In Proceedings of the 9th Genome Informatics Workshop (GIW'98); Universal Academy Press, 1998, p 131-140. Available at: http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl.
29. Vorobjev, Y. N.; Hermans, J. Biophys J 1997, 73, 722.
30. Sanner, M. F.; Olson, A. J.; Spehner, J.-C. In the Proceedings of the 11th ACM Symposium Computational Geometry, Vancouver, British Columbia, 1995, p C6-C7.
31. Hayryan, S.; Hu, C-K.; Skřivánek, J.; Hayryan, E.; Pokorný, I. J Comput Chem 2005, 26, 334.
32. Schaftenaar, G.; Noordik, J. H. J Comput Aid Mol Des 2000, 14, 123.
33. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
34. Höfinger, S. Modelling Molecular Structure and Reactivity in Biological Systems; Royal Society of Chemistry Publishing, Cambridge, UK, 2006, p 151.
35. Höfinger, S. J Comput Chem 2005, 26, 1148.
36. Marshall, N. J.; Grail, B. M. J Pept Sci 2000, 6, 186.
37. Ren, P.; Ponder, J. W. J Phys Chem B 2003, 107, 5933.
38. Gaussian 03, Revision B.05, Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian, Inc., Wallingford, CT, 2004.
39. Roos, B. O.; Wildmark, P.-O. Eds. European Summerschool in Quantum Chemistry, Book II; University of Lund, Lund University, 2000, p. 561.