A Convergence study of QM/MM isomerization energies with the selected size of the QM Region for peptidic systems

Journal of Physical Chemistry A

Volumn 113, Issue 43, 2009, Pages 11734-11741

  Sumowski, Chris Vanessa ^a   Ochsenfeld, Christian ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE CENTER; BASIS SETS; CONVERGENCE BEHAVIORS; FASTER CONVERGENCE; MODEL PEPTIDES; MP2/6-31G; REGION SIZE; SIMPLE MODEL; SYSTEM SIZE; SYSTEMATIC STUDY;

AMINES; METHOD OF MOMENTS; MOLECULAR MECHANICS; PROTON TRANSFER;

ATOMS;

PEPTIDE; TRIOSEPHOSPHATE ISOMERASE;

AMINO ACID SEQUENCE; ARTICLE; BIOCATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; ISOMERISM; METABOLISM; MOLECULAR GENETICS; PROTEIN CONFORMATION; QUANTUM THEORY; THERMODYNAMICS;

AMINO ACID SEQUENCE; BIOCATALYSIS; ISOMERISM; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN CONFORMATION; QUANTUM THEORY; THERMODYNAMICS; TRIOSE-PHOSPHATE ISOMERASE;

EID: 70350402094     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp902876n     Document Type: Article

References (72)

1. Ochsenfeld, C.; Kussmann, J.; Lambrecht, D. S. Linear-Scaling Methods in Quantum Chemistry. In Reviews in Computational Chemistry; Lipkowitz, K. B., Cundari, T. R., Eds.; VCH Publishers: New York, 2007; Vol.23.
2. Knowles, P.; Schütz, M.; Werner, H.-J. Ab Initio Methods for Electron Correlation in Molecules. In Modern Methods and Algorithms of Quantum Chemistry; Grotendorst, J., Ed.; John von Neumann Institute for Computing: Jülich, 2000; Vol.3.
3. Scuseria, G. E. J. Phys. Chem. A 1999, 103, 4782.
4. Head-Gordon, M. J. Phys. Chem. 1996, 100, 13213.
5. Ochsenfeld, C.; Kussmann, J.; Koziol, F. Angew. Chem. Int. Ed. 2004, 43, 4485.
6. Lambrecht, D. S.; Ochsenfeld, C. J. Chem. Phys. 2005, 123,184101.
7. Sałek, P.; Høst, S.; Thøgersen, L.; Jørgen.sen, P.; Manninen, P.; Olsen, J.; Jansík, B.; Reine, S.; Pawlowski, F.; Tellgren, E.; Helgaker, T.; Coriani, S. J. Chem. Phys. 2007, 126, 114110.
8. Rudberg, E.; Rubensson, E. H.; Salek, P. J. Chem, Phys. 2008, 128, 184106.
9. Doser, B.; Lambrecht, D. S.; Kussmann, J.; Ochsenfeld, C. J. Chem. Phys. 2009, 130, 064107.
10. Sherwood, P. Hybrid Quantum. Mechanics/Molecular Mechanics Approaches. In Modern Methods and Algorithms of Quantum Chemistry; Grotendorst, J., Ed.; John von Neumann Institute for Computing: Jülich, 2000; Vol.3.
11. Gao, J.; Truhlar, D. G. Annu. Rev. Phys. Chem. 2002, 53, 467.
12. Senn, H. M.; Thiel, W. Top. Curr. Chem. 2007, 268, 173.
13. Senn, H. M.; Thiel, W. Angew Chem., Int. Ed. 2009, 48, 1198.
14. Senn, H. M.; Thiel, W. Curr. Opin. Chem. Biol. 2007, 11, 182.
15. Mulholland, A. J. Drug Discovery Today 2005, 10, 1393.
16. Garcia-Viloca, M.; Gao, J.; Karplus, M.; Truhlar, D. G. Science 2004, 303, 186.
17. Warshel, A. Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 425.
18. Martí, S.; Roca, M.; Andrés, J.; Moliner, V.; Silla, E.; Tuñón, I.; Bertrán, J. Chem. Soc Rev. 2004, 33, 98.
19. Friesner, R. A.; Guallar, V. Annu. Rev. Phys. Chem. 2005, 56, 389.
20. Sherwood, P.; et al. J. Mol. Struct. (THEOCHEM) 2003, 632, 1.
21. Klähn, M.; Braun-Sand, S.; Rosta, E.; Warshel, A. J. Phys. Chem. B 2005 109, 15645.
22. Eurenius, K. P.; Chatfield, D. C.; Brooks, B. R.; Hodoscek, M. Int. J. Quantum Chem. 1996, 60, 1189.
23. Riccardi, D.; Schaefer, P.; Yang, Y.; Yu, H.; Ghosh, N.; Prat-Resina, X.; König, P.; Li, G.; Xu, D.; Guo, H.; Elstner, M.; Cui, Q. J. Phys. Chem. B 2006, 110, 6458.
24. Sharma, R.; Thorley, M.; McNamara, J. P.; Watt. C I. F.; Burton, N. A. Phys. Chem. Chem. Phys. 2008, 10, 2475.
25. Greatbanks, S. P.; Gready, J. E.; Limaye, A. C.; Rendell, A. P. J. Comput. Chem. 2000, 21, 788.
26. Ferré, N.; Assfeld, X.; Rivail, J.-L. J. Comput. Chem. 2002, 23, 610.
27. Riccardi, D.; Li, G.; Cui, Q. J. Phys. Chem. B 2004, 108, 6467.
28. Claeyssens, F.; Harvey, J. N.; Manby, F. R.; Mata, R. A.; Mulholland, A. J.; Ranaghan, K. E.; Schütz, M.; Thiel, S.; Thiel, W.; Werner, H.-J. Angew. Chem. 2006, 118, 7010.
29. Lennartz, C.; Schäfer, A.; Terstegen, F.; Thiel, W. J. phys. Chem. B 2002, 106, 1758.
30. Mata, R. A.; Werner, H.-J.; Thiel, S.; Thiel, W. J. Chem. Phys. 2008, 128, 025104.
31. Altun, A.; Thiel, W. J. Phys. Chem. B 2005, 109, 1268.
32. König, P. H.; Hoffmann, M.; Frauenheim, T.; Cui, Q. J. Phys. Chem. B 2005, 109, 9082.
33. Hall, R. J.; Hindle, S. A.; Burton, N. A.; Hillier, I. H. J. Comput. Chem. 2000, 21, 1433.
34. Reuter, N.; Dejaegere, A.; Maigret, B.; Karplus, M. J. Phys. Chem. A 2000, 104, 1720.
35. Amara, P.; Field, M. J. Theor. Chem. Acc. 2003, 109, 43.
36. Antes, I.; Thiel, W. J. Phys. Chem. A 1999, 103, 9290.
37. Bakowies, D.; Thiel, W. J. Phys. Chem. 1996, 100, 10580.
38. Crespo, A.; Scherlis, D. A.; Marti, M. A.; Ordejón, P.; Roitberg, A. E.; Estrin, D. A. J. phys. Chem. B 2003, 107, 13728.
39. Altun, A.; Shaik, S.; Thiel, W. J. Comput. Chem. 2006, 27, 1324.
40. Ochsenfeld, C.; White, C. A.; Head-Gordon, M. J. Chem. Phys. 1998, 109, 1663.
41. Ochsenfeld, C. Chem. Phys. Lett. 2000, 327, 216.
42. White, C. A.; Johnson, B. G.; Gill, P. M. W.; Head-Gordon, M. Chem. Phys. Lett. 1994, 230, 8.
43. White, C. A.; Head-Gordon, M. J. Chem. Phys. 1994, 101, 6593.
44. Lambrecht, D. S.; Doser, B.; Ochsenfeld, C. J. Chem. Phys. 2005, 123, 184102.
45. Doser, B.; Lambrecht, D. S.; Ochsenfeld, C. Phys. Chem. Chem. Phys. 2008, 10, 3335.
46. The LSN and GLUP patches in the CHARMM22 force field were used as provided in the CHARMM package version c34b2.
47. Hartree, D. R. Proc. Cambridge Philos. Soc. 1928, 24, 89.
48. Fock, V. Z. Phys. 1930, 61, 126.
49. Roothaan, C. C. J. Rev. Mod. Phys. 1951, 23, 69.
50. Møller, C.; Plesset, M. S. Phys. Rev. 1934, 46, 618.
51. Jung, Y.; Lochan, R. C.; Dutoi, A. D.; Head-Gordon, M. J. Chem. Phys 2004, 121, 9793.
52. Development version of the program package Q-Chem. http:// www.q-chem.com.
53. Binkley, J. S.; Pople, J. A.; Hehre, W. J. J. Am. Chem. Soc. 1980, 102, 939.
54. Hehre, W.; Ditchfield, R.; Pople, J. J. Chem. Phys. 1972, 56, 2257.
55. Hariharan, P. C.; Pople, J. A. Theor. Chem. Acc. 1973, 28, 213.
56. Clark, T.; Chandrasekhar, J.; Spitznagel, G.; v, R. Schleyer, P. J. Comput. Chem. 1983, 4, 294.
57. Schäfer, A.; Horn, H.; Ahlrichs, R. J. Chem. Phys. 1992, 97, 2571.
58. Antes, I.; Thiel, W. Hybrid Quantum. Mechanical and Molecular Mechanical Methods. In ACS Symposium Series; Gao, J., Ed.; American Chemical Society: Washington, DC, 1998; Vol.712.
59. de Vries, A. H.; Sherwood, P.; Collins, S. J.; Rigby, A. M.; Rigutto, M..; Kramer, G. J. Phys. Chem. B 1999, 103, 6133.
60. MacKerell Jr., A. D.; et al. J. Phys. Chem. B 1998, 102, 3586.
61. Brooks, B. R.; Bruccoleri, R. E.; Olafson, D. J.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
62. MacKerell Jr., A. D.; Brooks III, C. L.; Nilsson, L.; Roux, B.; Won, Y.; Karplus, M. CHARMM: The Energy Function and Its Parameterization, with an Overview of the Program. In The Encyclopedia of Computational Chemistry; v. R. Schleyer, P., Eds.; John Wiley & Sons: Chichester, 1998; Vol.1.
63. Smith, W.; Forester, T. J. Mol. Graph. 1996, 14, 136.
64. Schrödinger Inc., Portland OR, Maestro 7.5, 2005.
65. Asada, T.; Takahashi, T.; Koseki, S. Theor. Chem. Ace. 2008, 120, 263.
66. Melo, A.; Ramos, M.; Floriano, W. B.; Gomes, J.; Leão, J.; Magalhães, A.; Maigret, B.; Nascimento, M. C.; Reuter, N. J Mol. Struct. (THEOCHEM) 1999, 463, 81.
67. Davenport, R. C.; Bash, P. A.; Seaton, B. A.; Karplus, M.; Petsko, G. A.; Ringe, D. Biochemistry 1991, 30, 5821.
68. Bash, P. A.; Field, M. J.; Davenport, R. C.; Petsko, G. A.; Ringe, D.; Karplus, M. Biochemistry 1991, 30, 5826.
69. Zhang, Z.; Sugio, S.; Komives, E. A.; Liu, K. D.; Knowles, J. R.; Petsko, G. A.; Ringe, D. Biochemistry 1994, 33, 2830.
70. Neria, E.; Karplus, M. Chem. Phys. Lett. 1997, 267, 23.
71. Cui, Q.; Karplus, M. J. Phys. Chem. B 2002, 106, 1768.
72. 20