Ab initio Raman spectra of β-lactamase inhibitor intermediates bound to E166a SHV β-lactamase

Journal of Chemical Theory and Computation

Volumn 5, Issue 8, 2009, Pages 2158-2172

  Miani, Andrea ^a   Helfand, Marion Skalweit ^b   Raugei, Simone ^a  

^a DEMOCRITOS NATIONAL SIMULATION CENTER   (Italy)

^b LOUIS STOKES CLEVELAND VA MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 73649113158     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct900131q     Document Type: Article

References (48)

1. Helfand, M.S.; Totir, M.A.; Carey, M.P.; A, M, H.; Bonomo, R.A.; Carey, P.R. Biochemistry 2003, 42, 13386-13392.
2. Helfand, M.S.; Taracila, M.A.; Totir, M.A.; Bonomo, R.A.; Buynak, J.D.; van den Akker, F.; Carey, P.R. Biochemistry 2007, 46, 8689-8699.
3. Carey, P.R. Annu. Rev. Phys. Chem. 2006, 57, 527-554.
4. Padayatti, P.S.; Helfand, M.S.; Totir, M.A.; Carey, M.P.; Carey, P.R.; Bonomo, R.A.; van den Akker, F. Biochemistry 2004, 43, 843-848.
5. Kalp, M.; Totir, M.A.; Buynak, J.D.; Carey, P.R.J. Am. Chem. Soc. 2009, 131, 2338-2347.
6. Bonomo, R.A.; Rice, L.B.J. Gerontol A-Biol 1999, 4, B260-B267.
7. Miani, A.; Raugei, S.; Carloni, P.; Helfand, M.J. Phys. Chem. B 2007, 111, 2621-2630.
8. Klähn, M.; Mathias, G.; Kötting, C.; Nonella, M.; Schlitter, J.; Gerwert, K.; Tavan, P.J. Phys. Chem. A 2004, 108, 6186-6194.
9. Nonella, M.; Mathias, G.; Tavan, P.J. Phys. Chem. A 2003, 107, 8638-8647.
10. Cui, Q.; Karplus, M.J. Chem. Phys. 2000, 112, 1133-1149.
11. Case, D.; III, T. C.; Darden, T.; Gohlke, H.; Luo, R.; Jr, K.M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R.J. Com-put. Chem. 2005, 26, 1668-1688.
12. Jorgensen, W.L.; Chandrasekhar, J.; Madura, J.D.; Impey, R.W.; Klein, M.L.J. Chem. Phys. 1983, 70, 926-935.
13. Wang, J.; Wolf, R.M.; Caldwell, J.W.; Kollman, P.A.; Case, D.A.J. Comput. Chem. 2004, 25, 1157-1174.
14. Becke, A.D.J. Chem. Phys. 1993, 98, 5648-5652.
15. Wang, J.; Wang, W.; Kollman, P.A.; Case, D.A.J. Mol. Graphics Modell. 2006, 25, 247-260.
16. 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.; Strat-mann, 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 C.02.
17. Berendsen, H.J.C.; Postma, J.P.M.; DiNola, A.; Haak, J.R.J. Chem. Phys. 1984, 81, 3684-3690.
18. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A.E.; Berendsen, H.J.C. J. Comput. Chem. 2005, 26, 1701-1718.
19. Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471-2474.
20. Marx, D.; Hutter, J. Ab initio molecular dynamics: Theory and Implementation. In Modern Methods and algorithms of quantum chemistry; Grotendorst, J., Ed.; John von Neumann Institute for Computing: Jülich, 2000; NIC series, Vol. 1, pp 301-349.
21. Laio, A.; VandeVondele, J.; Rothlisberger, U.J. Chem. Phys. 2002, 116, 6941-6947.
22. Laio, A.; VandeVondele, J.; Rothlisberger, U.J. Phys. Chem. B 2002, 106, 7300-7307.
23. Becke, A.D. Phys. Rev. A 1988, 38, 3098-3100.
24. Lee, C.; Yang, W.; Parr, R.G. Phys. Rev. B1988, 37, 785-789.
25. Troullier, N.; Martins, J.L. Phys. Rev. B1991, 43, 1993-2006.
26. See, e. g.; Sprik, M.; Hutter, J.; Parrinello, M.J. Chem. Phys. 1996, 105, 1142.
27. Giannozzi, P. In Computational Approaches to NoVel Condensed Matter Systems, Proceed-ings of 3rd Gordon Godfrey Workshop on Condensed Physics; Neilson, D., Das, M.P., Ed.; Plenum: New York, 1995.
28. Hutter, J.; Alavi, A.; Deutch, T.; Bernasconi, M.; Goedecker, S.; Marx, D.; Tuckerman, M.; Parrinello, M. CPMD; Copy-right IBM Corp 1990-2008, Copyright MPI fur Festkorper-forschung Stuttgart 1997-2001. http://www.cpmd.org/ (accessed month day, year).
29. Wang, J.; Cieplak, P.; Kollman, P.A.J. Comput. Chem. 2000, 21, 1049-1074.
30. Marthyna, G.J.; Klein, M.L.; Tukerman, M.E.J. Chem. Phys. 1992, 97, 2635.
31. T, H.; Dunning, J.J. Chem. Phys. 1989, 90, 1007-1023.
32. Hall, G.G.; Smith, C.M. Int. J. Quantum Chem. 1984, 25, 881-890.
33. Smith, C.M.; Hall, G.G. Theor. Chim. Acta 1986, 69, 63-69.
34. Hay, P.J.; Wadt, W.R.J. Chem. Phys. 1985, 82, 270-283.
35. Gordon, R.G.J. Chem. Phys. 1965, 42, 3658-3664.
36. McQuarrie, D.A. Statistical Mechanics; Harper Collins Publisher: New York, 1973.
37. Bader, J.S.; Berne, B.J.J. Chem. Phys. 1994, 100, 8359-8366.
38. Herzberg, G. Molecular Spectra and Molecular Structure; Krieger Publishing Company: 1991, Vol. 2.
39. Porezag, D.; Pederson, M. Phys. Rev. B 1996, 54, 7830-7836.
40. Chaban, G.M.; Gerber, R.B. Theor. Chem. Acc. 2008, 120, 273-279.
41. Martinez, M.; Gaigeot, M.P.; Borgis, D.; Vuilleumier, R.J. Chem. Phys. 2005, 125, 144106.
42. Wheeler, R.A.; Dong, H. ChemPhysChem 2003, 4, 1227-1230.
43. Max, J.-J.; Chapados, C.J. Chem. Phys. 2004, 120, 6625-6641.
44. Zhang, X.K.; Lewars, E.G.; March, R.E.; Parnis, J.M.J. Phys. Chem. 1993, 97, 4320-4325.
45. Dong, J.; Lu, X.; Wei, Y.; Luo, L.; Dunaway-Mariano, D.; Carey, P.R. Biochemistry 2003, 42, 9482-9490.
46. Marzari, N.; Vanderbilt, D. Phys. Rev. B 1997, 56, 12847-12862.
47. Carnevale, V.; Raugei, S.; Micheletti, C.; Carloni, P.J. Chem. Phys. B 2007, 111, 12327-12332.
48. Daněček, P.; Kapitán, J.; Baumruk, V.; Bednárová, L.; Jr., V. K.; Bouř, P.J. Chem. Phys. 2007, 126, 224513.