IR spectra of phosphate ions in aqueous solution: Predictions of a DFT/MM approach compared with observations

Journal of Physical Chemistry A

Volumn 108, Issue 29, 2004, Pages 6186-6194

  Klähn, Marco ^a   Mathias, Gerald ^b   Kötting, Carsten ^a   Nonella, Marco ^b   Schlitter, Jürgen ^a   Gerwert, Klaus ^a   Tavan, Paul ^b  

^a RUHR UNIVERSITY BOCHUM   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; HYDRATION; INFRARED SPECTROSCOPY; PROBABILITY DENSITY FUNCTION; SOLUTIONS;

INSTANTANEOUS NORMAL-MODE ANALYSIS (INMA); MOLECULAR MECHANICS (MM);

MOLECULAR DYNAMICS;

EID: 3342946959     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp048617g     Document Type: Article

References (41)

1. Hohenberg, P.; Kohn, W. Phys. Rev. B 1964, 136, 864-870.
2. Kohn, W.; Sham, L. J. Phys. Rev. A 1965, 140, 1133-1138.
3. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, revision A.5; Gaussian, Inc.: Pittsburgh, PA, 1999.
4. Hutter, J.; Alavi, A.; Deutsch, T.; Bernasconi, M.; Goedecker, S.; Marx, D.; Tuckermann, T.; Parrinello, M. CPMD, Version 3.4.0; MPI für Festkörperforschung and IBM Zurich Research Laboratory.
5. Nonella, M.; Tavan, P. Chem. Phys. 1995, 199, 19-32.
6. Zhou, X.; Mole, S. J.; Liu, R. Vib. Spectrosc. 1996, 12, 73-79.
7. Neugebauer, J.; Hess, B. A. J. Chem. Phys. 2003, 118, 7215-7225.
8. Eichinger, M.; Tavan, P.; Hutter, J.; Parrinello, M. J. Chem. Phys. 1999, 110, 10452-10467.
9. Eichinger, M. Thesis, Ludwig-Maximilians Universität München, Germany, 1999.
10. Cui, Q.; Karplus, M. J. Chem. Phys. 2000, 112, 1133-1149.
11. Nonella, M.; Mathias, G.; Tavan, P. J. Phys. Chem. A 2003, 107, 8638-8647.
12. Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227-249.
13. MacKerell, A. D.; et al. J. Phys. Chem. 1998, 102, 3586-3616.
14. Guillot, B. J. Mol Liquids 2002, 101, 219-260.
15. Ponder, J. W.; Case, D. A. Adv. Protein Chem. 2003, 66, 27-85.
16. Tavan, P.; Carstens, H.; Mathias, G. Molecular dynamics simulations of proteins and peptides: Problems, achievements, and perspectives. In Handbook of Protein Folding; Buchner, J., Kiefhaber, T., Eds.; Wiley-VCH: Weinheim, Germany, 2004, in press.
17. Mathias, G.; Eichinger, M.; Carstens, H.; Stork, M.; Weiss, A.; Heller, H.; Grubmüller, H.; Egwolf, B.; Niedermeier, C.; Tavan, P. EGOMMII users guide; Lehrstuhl für BioMolekulare Optik, Ludwig Maximilian Universität München, Oettingenstrasse 67, D-80538 München, unpublished.
18. Nonella, M.; Mathias, G.; Eichinger, M.; Tavan, P. J. Phys. Chem. B 2003, 107, 316-322.
19. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: Oxford, UK, 1996.
20. 10
21. Gerwert, K. Molecular Reaction Mechanism of Proteins Monitored by Time-resolved FT-IR Difference Spectroscopy. In Handbook of Vibrational Spectroscopy; Chalmers, J. M., Griffiths, P. R., Eds.; John Wiley: Chichester, UK, 2001; Vol. 5.
22. Cepus, V.; Goody, R. S.; Scheidig, A. J.; Gerwert, K. Biochemistry 1998, 37, 10263-10271.
23. Allin, C.; Gerwert, K. Biochemistry 2001, 40, 3037-3046.
24. Allin, C.; Ahmadian, M. R.; Wittinghofer, A.; Gerwert, K. Proc. Natl. Acad. Sci. 2001, 98, 7754-7759.
25. Baril, J.; Max, J.-J.; Chapados, C. Can. J. Chem. 2000, 78, 490-507.
26. Becke, A. D. Phys. Rev. A 1988, 38, 3098-3100.
27. Perdew, J. P. Phys. Rev. B 1986, 33, 8822-8824.
28. Boesch, S. E.; Wheeler, R. A. J. Phys. Chem. 1995, 99, 8125-8134.
29. Hertwig, R. H.; Koch, W. J. Comput. Chem. 1995, 16, 576-585.
30. Becke, A. D. J. Chem. Phys. 1993, 98, 1372-1377, 5648-5652.
31. Lee, C.; Yang, W.; Parr, R. C. Phys. Rev. B 1988, 37, 785-789.
32. Hartwigsen, C.; Goedecker, S.; Hutter, J. Phys. Rev. B 1998, 58, 3641-3662.
33. Jorgensen, W. L.; et al. J. Chem. Phys. 1983, 79, 926-935.
34. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
35. Neria, E.; Fischer, S.; Karplus, M. J. Chem. Phys. 1996, 105, 1902-1921.
36. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
37. Mathias, G.; Egwolf, B.; Nonella, M.; Tavan, P. J. Chem. Phys. 2003, 118, 10847-10860.
38. Niedermeier, C.; Tavan, P. J. Chem. Phys. 1994, 101, 734-748.
39. Niedermeier, C.; Tavan, P. Mol. Simul. 1996, 17, 57-66.
40. Herres, W.; Gronholz, J. Comput. Appl. Lab. 1984, 2, 216-220.
41. Laasonen, K.; Sprik, M.; Parrinello, M.; Car, R. J. Chem. Phys. 1993, 99, 9080-9089.