Natural bond orbital analysis in the ONETEP code: Applications to large protein systems

Journal of Computational Chemistry

Volumn 34, Issue 6, 2013, Pages 429-444

  Lee, Louis P ^a   Cole, Daniel J ^a   Payne, Mike C ^a   Skylaris, Chris Kriton ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

biomolecule; hyperconjugation; linear scaling DFT; NBO; ONETEP

Indexed keywords

ATOMIC ORBITAL; BINDING POCKETS; CARBONYL GROUPS; CHEMICAL INFORMATION; CHEMICAL PICTURE; ELECTRONIC DELOCALIZATION; ELECTRONIC EFFECTS; ENTIRE SYSTEM; EXPLICIT SOLVENTS; FIRST PRINCIPLES ELECTRONIC STRUCTURE; HEME GROUP; HYPERCONJUGATION; HYPERCONJUGATIVE INTERACTIONS; LARGE-SCALE CALCULATION; LINEAR-SCALING DFT; LONE PAIR; NATURAL BOND ORBITAL ANALYSIS; NBO; NBO ANALYSIS; NON-ORTHOGONAL; ONETEP; ORBITALS; POST PROCESSING; PROTEIN BACKBONE; PROTEIN SYSTEM; SYSTEM SIZE; WANNIER FUNCTIONS;

BIOMOLECULES; CHARGE TRANSFER; DENSITY FUNCTIONAL THEORY; ELECTRONIC STRUCTURE; HYDROGEN BONDS; MOLECULAR ORBITALS; NANOSYSTEMS; ORTHOGONAL FUNCTIONS; PORPHYRINS; PROTEINS;

CHEMICAL ANALYSIS;

FORMAMIDE; FORMAMIDE DERIVATIVE; METHYLAMINE; PROTEIN; WATER;

ARTICLE; CHEMISTRY; PROTEIN CONFORMATION; QUANTUM THEORY;

FORMAMIDES; METHYLAMINES; PROTEIN CONFORMATION; PROTEINS; QUANTUM THEORY; WATER;

EID: 84873450915     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.23150     Document Type: Article

References (62)

1. A. D. MacKerell, Jr., B. Brooks, C. L. Brooks, III, L. Nilsson, B. Roux, Y. Won, M. Karplus, In Encyclopedia of Computational Chemistry, Vol. 3;, P. v. R. Schleyer, N. A. Allinger, P. A. Kollman, T. Clark, H. F. Schaefer III, J. Gasteiger, Eds.; Wiley: Chichester, 1998; Chapter "Natural Bond Orbital Methods," pp. 1792-1811.
2. A. E. Reed, L. A. Curtiss, F. Weinhold, Chem. Rev. 1988, 88, 899.
3. E. D. Glendening, J. K. Badenhoop, A. E. Reed, J. E. Carpenter, J. A. Bohmann, C. M. Morales, F. Weinhold, NBO 5.9 (http://www.chem.wisc.edu/ ∼nbo5) & the NBO 5.9 Manual, Theoretical Chemistry Institute, University of Wisconsin: Madison, WI. 2011.
4. A. E. Reed, R. B. Weinstock, F. Weinhold, J. Chem. Phys. 1985, 83, 735.
5. B. F. King, F. Weinhold, J. Chem. Phys. 1995, 103, 333.
6. C. Adamo, F. Lelj, J. Chem. Phys. 1995, 103, 10605.
7. F. Weinhold, Nature 2001, 411, 539.
8. V. Pophristic, L. Goodman, Nature 2001, 411, 565.
9. H. Roohi, A. Ebrahimi, F. Alirezapoor, M. Hajealirezahi, Chem. Phys. Lett. 2005, 409, 212.
10. J.-W. Song, H.-J. Lee, Y.-S. Choi, C.-J. Yoon, J. Phys. Chem. A 2006, 110, 2065.
11. F. Claeyssens, K. E. Ranaghan, N. Lawan, S. J. Macrae, F. R. Manby, J. N. Harvey, A. J. Mulholland, Org. Biomol. Chem. 2011, 9, 1578.
12. G. J. Bartlett, A. Choudhary, R. T. Raines, D. N. Woolfson, Nature Chem. Biol. 2010, 6, 615.
13. C. E. Jakobsche, A. Choudhary, S. J. Miller, R. T. Raines, J. Am. Chem. Soc. 2010, 132, 6651.
14. M. L. DeRider, S. J. Wilkens, M. J. Waddell, L. E. Bretscher, F. Weinhold, R. T. Raines, J. L. Markley, J. Am. Chem. Soc. 2002, 124, 2497.
15. A. Mohajeri, F. F. Nobandegani, J. Phys. Chem. A 2008, 112, 281.
16. R. Ludwig, J. Mol. Liq. 2000, 84, 65.
17. C.-K. Skylaris, P. D. Haynes, A. A. Mostofi, M. C. Payne, J. Chem. Phys. 2005, 122, 084119.
18. N. D. M. Hine, P. D. Haynes, A. A. Mostofi, C.-K. Skylaris, M. C. Payne, Comput. Phys. Comm. 2009, 180, 1041.
19. D. J. Cole, C.-K. Skylaris, E. Rajendra, A. R. Venkitaraman, M. C. Payne, Europhys. Lett. 2010, 91, 37004.
20. D. J. Cole, E. Rajendra, M. Roberts-Thomson, B. Hardwick, G. J. McKenzie, M. C. Payne, A. R. Venkitaraman, C.-K. Skylaris, PLoS Comp. Bio. 2011, 7, e1002096.
21. M. W. Schmidt, K. K. Baldridge, J. A. Boatz, S. T. Elbert, M. S. Gordon, J. H. Jensen, S. Koseki, N. Matsunaga, K. A. Nguyen, S. Su, T. L. Windus, M. Dupuis, J. A. Montgomery, J. Comput. Chem. 1993, 14, 1347.
22. C.-K. Skylaris, A. A. Mostofi, P. D. Haynes, O. Dieguez, M. C. Payne, Phys. Rev. B 2002, 66, 035119.
23. E. Prodan, W. Kohn, Science 2005, 102, 11635.
24. A. A. Mostofi, P. D. Haynes, C.-K. Skylaris, M. C. Payne, J. Chem. Phys. 2003, 119, 8842.
25. A. Ruiz-Serrano, N. D. M. Hine, C.-K. Skylaris, J. Chem. Phys. 2012, 136, 234101.
26. D. Sánchez-Portal, E. Artacho, J. M. Soler, J. Phys.: Condens. Matter 1996, 8, 3859.
27. J. P. Foster, F. Weinhold, J. Am. Chem. Soc. 1980, 102, 7211.
28. B. D. Dunnington, J. R. Schmidt, J. Chem. Theory Comput. 2012, 8, 1902.
29. C. Landis, F. Weinhold, In Valency and Bonding; CUP: Cambridge, 2005.
30. I. Solt, P. Kulhánek, I. Simon, S. Winfield, M. C. Payne, G. Csányi, M. Fuxreiter, J. Phys. Chem. B 2009, 113, 5728.
31. J. P. Perdew, K. Burke, M. Ernzerhof, Phys. Rev. Lett. 1996, 77, 3865.
32. N. D. M. Hine, J. Dziedzic, P. D. Haynes, C.-K. Skylaris, J. Chem. Phys. 2011, 135, 204103.
33. D. J. Cole, M. C. Payne, L. C. Ciacchi, Surf. Sci. 2007, 601, 4888.
34. S. J. Clark, M. D. Segall, C. J. Pickard, P. J. Hasnip, M. I. J. Probert, K. Refson, M. C. Payne, Z. Kristallogr. 2005, 220, 567.
35. M. D. Segall, Mol. Phys. 1996, 89, 571.
36. M. D. Segall, R. Shah, C. J. Pickard, M. C. Payne, Phys. Rev. B 1996, 54, 16317.
37. W. Zou, nbo2molden, http://people.smu.edu/wzou/program/n2m.zip (accessed January 9, 2011).
38. G. Schaftenaar, J. Noordik, J. Comput. Aided Mol. Des. 2000, 14, 123.
39. S. Boys, F. Bernardi, Mol. Phys. 1970, 19, 553.
40. P. D. Haynes, C.-K. Skylaris, A. A. Mostofi, M. C. Payne, Chem. Phys. Lett. 2006, 422, 345.
41. E. D. Glendening, J. Phys. Chem. A 2005, 109, 11936.
42. E. D. Glendening, A. Streitwieser, J. Chem. Phys. 1994, 100, 2900.
43. T. J. Dolinsky, J. E. Nielsen, J. A. McCammon, N. A. Baker, Nucl. Acids Res. 2004, 32, W665.
44. T. J. Dolinsky, P. Czodrowski, H. Li, J. E. Nielsen, J. H. Jensen, G. Klebe, N. A. Baker, Nucl. Acids Res. 2007, 35, W522.
45. D. A. Case, T. A. Darden, T. E. Cheatham, III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, M. Crowley, R. C. Walker, W. Zhang, K. M. Merz, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossváry, K. F. Wong, F. Paesani, J. Vanicek, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D. H. Mathews, M. G. Seetin, C. Sagui, V. Babin, P. A. Kollman,; AMBER 10; University of California: San Francisco. 2008
46. V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, C. Simmerling, Proteins 2006, 65, 712.
47. J. S. Olson, G. N. Phillips, Jr., J. Biol. Inorg. Chem. 1997, 2, 544.
48. D. J. Cole, D. D. O'Regan, M. C. Payne, J. Phys. Chem. Lett. 2012, 3, 1448.
49. H. Chen, M. Ikeda-Saito, S. Shaik, J. Am. Chem. Soc. 2008, 130, 14778.
50. I. S. Ufimtsev, N. Luehr, T. J. Martinez, J. Phys. Chem. Lett. 2011, 2, 1789.
51. A. Savchenko, M. Proudfoot, T. Skarina, A. Singer, O. Litvinova, R. Sanishvili, G. Brown, N. Chirgadze, A. F. Yakunin, J. Mol. Biol. 2007, 374, 1091.
52. R. F. W. Bader, Chem. Rev. 1991, 91, 893.
53. F. L. Hirshfeld, Theor. Chim. Acta 1977, 44, 129.
54. N. M. Green, Biochem. J. 1963, 89, 585.
55. J. DeChancie, K. N. Houk, J. Am. Chem. Soc. 2007, 129, 5419.
56. Y. Tong, Y. Mei, Y. L. Li, C. G. Ji, J. Z. H. Zhang, J. Am. Chem. Soc. 2010, 132, 5137.
57. L. Pugliese, A. Coda, M. Malcovati, M. Bolognesi, J. Mol. Biol. 1993, 231, 698.
58. W. L. Jorgensen, Acc. Chem. Res. 2009, 42, 724.
59. L. Pellegrini, D. S. Yu, T. Lo, S. Anand, M. Lee, T. L. Blundell, A. R. Venkitaraman, Nature 2002, 420, 287.
60. S. C. West, Nat. Rev. Mol. Cell Biol. 2003, 4, 435.
61. A. R. Venkitaraman, Annu. Rev. Pathol. 2009, 4, 461.
62. E. Rajendra, A. R. Venkitaraman, Nucl. Acids Res. 2010, 38, 82.