Multilevel and density functional electronic structure calculations of proton affinities and gas-phase basicities involved in biological phosphoryl transfer

Journal of Physical Chemistry A

Volumn 110, Issue 2, 2006, Pages 791-797

  Range, Kevin ^a,c   López, Carlos Silva ^b   Moser, Adam ^a   York, Darrin M ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF VIGO   (Spain)

^c LOCK HAVEN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GAS-PHASE BASICITY; PROTON AFFINITY;

ALKALINITY; ELECTRONIC STRUCTURE; ENTHALPY; ENTROPY; MOLECULAR DYNAMICS; PROTONS;

PROBABILITY DENSITY FUNCTION;

PHOSPHOTRANSFERASE; PROTON;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; ELECTRON; GAS;

ELECTRONS; GASES; MODELS, MOLECULAR; PHOSPHOTRANSFERASES; PROTONS;

EID: 31544481866     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp054360q     Document Type: Article

References (53)

1. Pliego, J. R., Jr.; Riveros, J. M. J. Phys. Chem. A 2002, 106, 7434-7439.
2. da Silva, C. O.; da Silva, E. C.; Nascimento, M. A. C. J. Phys. Chem. A 1999, 103, 11194-11199.
3. Jencks, W. P. Chem. Rev. 1985, 85 (6), 511-527.
4. Perreault, D. M.; Anslyn, E. V. Angew. Chem., Int. Ed. Engl. 1997, 36, 432-450.
5. Goedecker, S. Rev. Mod. Phys. 1999, 71, 1085-1123.
6. Yang, W.; Pérez-Jordá, J. M. In Encyclopedia of Computational Chemistry; von Schleyer, P. R., Ed.; John Wiley and Sons: New York, 1998; pp 1496-1513.
7. Khandogin, J.; Musier-Forsyth, K.; York, D. M. J. Mol. Biol. 2003, 330, 993-1004.
8. Khandogin, J.; York, D. M. Proteins 2004, 56, 724-737.
9. Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227-249.
10. Gao, J.; Truhlar, D. G. Annu. Rev. Phys. Chem. 2002, 53, 467-505.
11. Garcia-Viloca, M.; Gao, J.; Karplus, M.; Truhlar, D. G. Science 2004, 301, 186-195.
12. Head-Gordon, M. J. Phys. Chem. 1996, 100, 13213-13225.
13. Ochterski, J. W.; Petersson, G. A.; Montgomery, J. A., Jr. J. Chem. Phys. 1996, 104 (7), 2598-2619.
14. Montgomery, J. A., Jr.; Frisch, M. J.; Ochterski, J. W.; Petersson, G. A. J. Chem. Phys. 1999, 110 (6), 2822-2827.
15. Montgomery, J. A., Jr.; Frisch, M. J.; Ochterski, J. W.; Petersson, G. A. J. Chem. Phys. 2000, 112, 6532-6542.
16. Petersson, G. A.; Tensfeldt, T. G.; Montgomery, J. A., Jr. J. Chem. Phys. 1991, 94 (9), 6091-6101.
17. Curtiss, L. A.; Jones, C.; Trucks, G. W.; Raghavachari, K.; Pople, J. A. J. Chem. Phys. 1990, 93 (4), 2537-2545.
18. Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Rassolov, V.; Pople, J. A. J. Chem. Phys. 1998, 109, 7764-7776.
19. Curtiss, L. A.; Redfern, P. C.; Rassolov, V.; Kedziora, G.; Pople, J. A. J. Chem. Phys. 2001, 114 (21), 9287-9295.
20. Martin, J. M. L.; de Oliveira, G. J. Chem. Phys. 1999, 111, 1843-1856.
21. Parthiban, S.; Martin, J. M. L. J. Chem. Phys. 2001, 114 (14), 6014-6029.
22. Fast, P. L.; Truhlar, D. G. J. Phys. Chem. A 2000, 104, 6111-6116.
23. Lynch, B. J.; Truhlar, D. G. J. Phys. Chem. A 2003, 107 (19), 3898-3906.
24. Zhao, Y.; Lynch, B. J.; Truhlar, D. G. Phys. Chem. Chem. Phys. 2005, 7, 43-52.
25. Lynch, B. J.; Zhao, Y.; Truhlar, D. G. J. Phys. Chem. A 2005, 109, 1643-1649.
26. Parr, R.; Yang, W. Density-Functional Theory of Atoms and Molecules; Oxford University Press: New York, 1989.
27. Zhao, Y.; González-García, N.; Truhlar, D. G. J. Phys. Chem. A 2005, 109, 2012-2018.
28. Zhao, Y.; Truhlar, D. G. J. Phys. Chem. A 2005, 109, 5656-5667.
29. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; 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 03, revision B.05; Gaussian, Inc.: Wallingford, CT, 2003.
30. Werner, H.-J.; Knowles, P. J.; Lindh, R.; Schütz, M.; Celani, P.; Korona, T.; Manby, F. R.; Rauhut, G.; Amos, R. D.; Bernhardsson, A.; Berning, A.; Cooper, D. L.; Deegan, M. J. O.; Dobbyn, A. J.; Eckert, F.; Hampel, C.; Hetzer, G.; Lloyd, A. W.; McNicholas, S. J.; Meyer, W.; Mura, M. E.; Nicklass, A.; Palmieri, P.; Pitzer, R.; Schumann, U.; Stoll, H.; Stone, A. J.; Tarroni, R.; Thorsteinsson, T. MOLPRO, version 2002.6, a package of ab initio programs. 2003.
31. Rodgers, J. M.; Lynch, B. J.; Fast, P. L.; Zhao, Y.; Pu, J.; Chuang, Y.-Y.; Truhlar, D. G. Multilevel version 3.1/g03. University of Minnesota, Minneapolis, 2002.
32. Baboul, A. G.; Curtiss, L. A.; Redfern, P. C.; Raghavachari, K. J. Chem. Phys. 1999, 110, 7650-7657.
33. Pokon, E. K.; Liptak, M. D.; Feldgus, S.; Shields, G. C. J. Phys. Chem. A 2001, 105, 10483-10487.
34. Becke, A. D. J. Chem. Phys. 1993, 98 (7), 5648-5652.
35. Becke, A. D. Phys. Rev. A 1988, 38, 3098-3100.
36. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789.
37. Adamo, C.; Scuseria, G. E. J. Chem. Phys. 1999, 111, 2889-2899.
38. Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1996, 77, 3865-3868.
39. Becke, A. D. J. Chem. Phys. 1996, 104 (3), 1040-1046.
40. Adamo, C.; Barone, V. J. Chem. Phys. 1998, 108 (2), 664-675.
41. Kurth, S.; Perdew, J. P.; Blaha, P. Int. J. Quantum Chem. 1999, 75, 889-909.
42. Zhao, Y.; Truhlar, D. G. J. Chem. Theory Comput. 2005, 1 (3), 415-432.
43. Zhao, Y.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 6908-6918.
44. McNaught, A. D.; Wilkinson, A. Compendium of Chemical Terminology: IUPAC Recommendations, 2nd ed.; Blackwell Science, Inc.: Oxford, U.K., 1997.
45. nd ed.; John Wiley & Sons: Chichester, England, 2002.
46. McQuarrie, D. A. Statistical Mechanics; University Science Books: Mill Valley, CA, 1973.
47. Range, K.; Riccardi, D.; Cui, Q.; Elstner, M.; York, D. M. Phys. Chem. Chem. Phys. 2005, 7, 3070-3079.
48. Linstrom, P., Mallard, W., Eds. NIST Chemistry WebBook, NIST Standard Reference Database Number 69; National Institute of Standards and Technology: Gaithersburg, MD; 2003.
49. Harris, H. C.; Harris, D. C. Quantitative Chemical Analysis, 6th ed.; W. H. Freeman Co.: New York, 2002.
50. DeTuri, V. F.; Ervin, K. M. J. Phys. Chem. A 1999, 103, 6911-6920.
51. Bartmess, J. E.; Scott, J. A.; Robert T. McIver, J. J. Am. Chem. Soc. 1979, 101, 6056-6063.
52. Hengge, A. C. Acc. Chem. Res. 2002, 35, 105-112.
53. + are 205.7 and 212.9 kcal/mol, respectively (see ref 48). The corresponding GPB/PA errors in kcal/mol are -0.8/-1.0 for CBS-QB3, +0.6/-0.4 for G3B3, 1.1/0.1 for G3MP2B3, 1.0/0.9 for MCG3/3, 0.8/0.7 for MC-QCISD/3, 2.4/1.3 for MPW1KCIS, 2.2/1.1 for PBE1KCIS, 1.8/0.4 for MPW1B95, 1.6/0.5 for PBEO, 1.1/1.0 for B1B95, and 1.9/0.7 for B3LYP.