Hybrid ab initio Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems

Journal of Chemical Physics

Volumn 128, Issue 1, 2008, Pages

  Hodak, Miroslav ^a   Lu, Wenchang ^b   Bernholc, J ^b  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULES; COPPER; DENSITY FUNCTIONAL THEORY; MOLECULAR DYNAMICS; PROTEINS; SOLVATION;

LIQUID WATER SYSTEM; SOLVATION SHELLS;

BIOLOGICAL SYSTEMS;

COPPER; HYDROGEN; WATER;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; PRION; QUANTUM THEORY; THERMODYNAMICS;

COMPUTER SIMULATION; COPPER; HYDROGEN; PRIONS; QUANTUM THEORY; THERMODYNAMICS; WATER;

EID: 38049006405     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2814165     Document Type: Article

References (80)

1. P. Hohenberg and W. Kohn, Phys. Rev. PRVBAK 0096-8269 10.1103/PhysRev.136.B864 136, B864 (1964).
2. W. Kohn and L. J. Sham, Phys. Rev. PRVAAH 0096-8250 10.1103/PhysRev.140. A1133 140, A1133 (1965).
3. J. Tomasi and M. Persico, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 10.1021/cr00031a013 94, 2027 (1994).
4. J. L. Rivail and D. Rinald, Liquid State Quantum Chemistry: Computational Applications of The Polarizable Continuum Models (World Scientific, Singapore, 1995).
5. C. J. Cramer and D. G. Truhlar, Continuum Solvation Models (Kluwer, Dordrecht, 1996).
6. J. Fattebert and F. Gygi, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.10069 23, 662 (2002).
7. D. Begue, P. Carbonniere, V. Barone, and C. Pouchan, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/j.cplett.2005.09.099 416, 206 (2005).
8. L. Guimarães, H. Avelino de Abreu, and H. Duarte, Chem. Phys. CMPHC2 0301-0104 10.1016/j.chemphys.2006.12.023 333, 10 (2007).
9. P. Bonifassi, P. Ray, and J. Leszczynski, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/j.cplett.2006.09.082 431, 321 (2006).
10. R. Zhou and B. Berne, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.142430099 99, 12777 (2002).
11. Y. M. Rhee, E. J. Sorin, G. Jayachandran, E. Lindahl, and V. S. Pande, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0307898101 101, 6456 (2004).
12. S. Miertus, E. Scrocco, and J. Tomasi, Chem. Phys. CMPHC2 0301-0104 10.1016/0301-0104(81)85090-2 55, 117 (1981).
13. R. Cammi and J. Tomasi, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540161202 16, 1449 (1995).
14. A. Warshel and M. Levitt, J. Mol. Biol. JMOBAK 0022-2836 10.1016/0022-2836(76)90311-9 102, 227 (1976).
15. U. C. Singh and P. A. Kollmann, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540070604 7, 718 (1986).
16. M. J. Field, P. A. Bash, and M. Karplus, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540110605 11, 700 (1990).
17. T. Kerdcharoen and K. Morokuma, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/S0009-2614(02)00210-5 355, 257 (2002).
18. L. Thomas, Proc. Cambridge Philos. Soc. PCPSA4 0068-6735 23, 542 (1927).
19. E. Fermi, Rend. Accad. Naz. Lincei ZZZZZZ 0392-7881 6, 602 (1927).
20. E. Fermi, Z. Phys. ZEPYAA 0044-3328 10.1007/BF01351576 48, 73 (1928).
21. C. von Weizsacker, Z. Phys. ZEPYAA 0044-3328 10.1007/BF01337700 96, 431 (1934).
22. R. O. Jones and O. Gunnarsson, Rev. Mod. Phys. RMPHAT 0034-6861 10.1103/RevModPhys.61.689 61, 689 (1989).
23. Y. Wang and E. Carter, Orbital Free Kinetic Energy Density Functional Theory (Kluwer, Dordrecht, 2000), Chap., pp. 117-184.
24. A. E. DePristo and J. D. Kress, Phys. Rev. A PLRAAN 1050-2947 10.1103/PhysRevA.35.438 35, 438 (1987).
25. A. J. Thakkar, Phys. Rev. A PLRAAN 1050-2947 10.1103/PhysRevA.46.6920 46, 6920 (1992).
26. P. I. Plindov and S. K. Pogrebnya, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/0009-2614(88)87061-1 143, 535 (1988).
27. J. P. Perdew, Phys. Lett. A PYLAAG 0375-9601 10.1016/0375-9601(92)91058-Y 165, 79 (1992).
28. H. Lee, C. Lee, and R. Parr, Phys. Rev. A PLRAAN 1050-2947 10.1103/PhysRevA.44.768 44, 768 (1991).
29. D. Lacks and R. Gordon, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.466274 100, 4446 (1994).
30. A. D. Becke, Phys. Rev. A PLRAAN 1050-2947 10.1103/PhysRevA.38.3098 38, 3098 (1988).
31. J. A. Alonso and L. A. Girifalco, Phys. Rev. B PLRBAQ 0556-2805 10.1103/PhysRevB.17.3735 17, 3735 (1978).
32. E. Chacón, J. E. Alvarellos, and P. Tarazona, Phys. Rev. B PRBMDO 0163-1829 10.1103/PhysRevB.32.7868 32, 7868 (1985).
33. E. Smargiassi and P. A. Madden, Phys. Rev. B PRBMDO 0163-1829 10.1103/PhysRevB.49.5220 49, 5220 (1994).
34. Y. A. Wang, N. Govind, and E. A. Carter, Phys. Rev. B PRBMDO 0163-1829 10.1103/PhysRevB.58.13465 58, 13465 (1998).
35. Y. A. Wang, N. Govind, and E. A. Carter, Phys. Rev. B PRBMDO 0163-1829 10.1103/PhysRevB.60.16350 60, 16350 (1999).
36. R. Gordon and Y. Kim, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1677649 61, 3122 (1972).
37. Y. Kim and R. Gordon, Phys. Rev. B PLRBAQ 0556-2805 10.1103/PhysRevB.9. 3548 9, 3548 (1974).
38. T. Wesolowski and A. Warshel, J. Phys.: Condens. Matter JCOMEL 0953-8984 97, 8050 (1993).
39. T. Wesolowski and A. Warshel, J. Phys.: Condens. Matter JCOMEL 0953-8984 98, 5183 (1994).
40. D. Barker and M. Sprik, Mol. Phys. MOPHAM 0026-8976 10.1080/ 0026897031000114792 101, 1183 (2003).
41. P. Huang and E. A. Carter, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2336428 125, 084102 (2006).
42. D. R. Hamann, M. Schlüter, and C. Chiang, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.43.1494 43, 1494 (1979).
43. G. P. Kerker, J. Phys. C JPSOAW 0022-3719 10.1088/0022-3719/13/9/004 13, L189 (1980).
44. A. Zunger and M. L. Cohen, Phys. Rev. B PLRBAQ 0556-2805 10.1103/PhysRevB.18.5449 18, 5449 (1978).
45. L. Kleinman and D. M. Bylander, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.48.1425 48, 1425 (1982).
46. D. Vanderbilt, Phys. Rev. B PRBMDO 0163-1829 10.1103/PhysRevB.41.7892 41, 7892 (1990).
47. T. Starkloff and J. D. Joannopoulos, Phys. Rev. B PLRBAQ 0556-2805 10.1103/PhysRevB.16.5212 16, 5212 (1977).
48. S. C. Watson, B. J. Jesson, E. A. Carter, and P. A. Madden, Europhys. Lett. EULEEJ 0295-5075 10.1209/epl/i1998-00112-5 41, 37 (1998).
49. V. Shah, D. Nehete, and D. G. Kanhere, Z. Phys. ZEPYAA 0044-3328 10.1007/BF01351576 48, 73 (1928).
50. D. Nehete, V. Shah, and D. G. Kanhere, Phys. Rev. B PRBMDO 0163-1829 10.1103/PhysRevB.53.2126 53, 2126 (1996).
51. A. Dhavale, V. Shah, and D. G. Kanhere, Phys. Rev. A PLRAAN 1050-2947 10.1103/PhysRevA.57.4522 57, 4522 (1998).
52. E. L. Briggs, D. J. Sullivan, and J. Bernholc, Phys. Rev. B PRBMDO 0163-1829 52, 5471 (1995).
53. E. L. Briggs, D. J. Sullivan, and J. Bernholc, Phys. Rev. B PRBMDO 0163-1829 10.1103/PhysRevB.54.14362 54, 14362 (1996).
54. M. Hodak, S. Wang, W. Lu, and J. Bernholc, Phys. Rev. B PRBMDO 0163-1829 10.1103/PhysRevB.76.085108 76, 085108 (2007).
55. J. Ryckaert, G. Ciccotti, and H. Berendsen, J. Comp. Phys. 23, 327 (1977).
56. P. L. Silvestrelli and M. Parrinello, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.479638 111, 3572 (1999).
57. A. Shepard, G. Beers, G. Klein, and L. Rothmann, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1680328 59, 2254 (1973).
58. C. Coulson and D. Eisenbero, Proc. R. Soc. London, Ser. A PRLAAZ 1364-5021 291, 445 (1966).
59. E. Batista, S. Xantheas, and H. Jonsson, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.477058 109, 4546 (1998).
60. M. Heggie, C. L. Latham, and S. Maynard, and R. Jones, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/0009-2614(95)01427-6 249, 485 (1996).
61. Y. Badyal, M. Saboungi, D. Price, S. Shastri, D. Haeffner, and A. Soper, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.481541 112, 9206 (2000).
62. P. L. Silvestrelli and M. Parrinello, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.82.3308 82, 3308 (1999).
63. A. K. Soper, Chem. Phys. CMPHC2 0301-0104 10.1016/S0301-0104(00)00179-8 258, 121 (2000).
64. J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.77.3865 77, 3865 (1996).
65. J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. PRLTAO 0031-9007 78, 1396 (1997).
66. J. Grossman, E. Schwegler, E. Draeger, F. Gygi, and G. Galli, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1630560 120, 300 (2004).
67. E. Schwegler, J. Grossman, F. Gygi, and G. Galli, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1782074 121, 5400 (2004).
68. M. Sprik, J. Hutter, and M. Parrinello, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.471957 105, 1142 (1996).
69. T. Wesolowski, R. Muller, and A. Warshel, J. Phys.: Condens. Matter JCOMEL 0953-8984 100, 15444 (1996).
70. T. Wesolowski and J. Weber, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/0009-2614(95)01281-8 248, 71 (1996).
71. S. Prusiner, Science SCIEAS 0036-8075 10.1126/science.278.5336.245 278, 245 (1997).
72. N. Vassallo and J. Herms, J. Neurochem. JONRA9 0022-3042 86, 538 (2003).
73. N. Inestrosa, W. Cerpa, and L. Varela-Nallar, IUBMB Life IULIF8 1521-6543 57, 645 (2005).
74. D. Brown, K. Qin, J. Herms, A. Madlung, J. Manson, R. Strome, P. Fraser, T. Kruck, A. von Bohlen, W. Schulz-Schaeffer, A. Giese, D. Westaway, and H. Kretzschmar, Nature (London) NATUAS 0028-0836 10.1038/37733 390, 684 (1997).
75. G. Millhauser, Acc. Chem. Res. ACHRE4 0001-4842 10.1021/ar0301678 37, 79 (2004).
76. R. Whittal, H. Ball, F. Cohen, A. Prusiner, and M. Baldwin, Protein Sci. PRCIEI 0961-8368 9, 332 (2000).
77. P. Pauly and D. Harris, J. Biol. Chem. JBCHA3 0021-9258 10.1074/jbc.273.50.33107 273, 33107 (1998).
78. M. Pushie and A. Rauk, JBIC, J. Biol. Inorg. Chem. JJBCFA 0949-8257 10.1007/s00775-002-0386-7 8, 53 (2003).
79. H.-F. Ji and H.-Y. Zhang, Chem. Res. Toxicol. CRTOEC 0893-228X 10.1021/tx034232y 17, 471 (2004).
80. B. Delley, D. E. Ellis, A. J. Freeman, E. J. Baerends, and D. Post, Phys. Rev. B PRBMDO 0163-1829 10.1103/PhysRevB.27.2132 27, 2132 (1983).