Molecular dynamics with restrictions derived from optical spectra

Journal of Computational Chemistry

Volumn 30, Issue 6, 2009, Pages 983-991

  Kaminský, Jakub ^a   Šebek, Jiří ^a   Bouř, Petr ^a  

^a INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

Author keywords

Ab initio; Molecular dynamics; Raman optical activity; Vibrational spectroscopy

Indexed keywords

AB INITIO; ALTERNATIVE ALGORITHMS; BAND-BROADENING; BOLTZMANN; COMPUTATIONAL PROCEDURES; FOURIER TRANSFORMATIONS; GRADIENT TERMS; ITERATIVE UPDATE; MODEL SYSTEM; MOLECULAR DYNAMIC SIMULATIONS; MOLECULAR ENERGIES; OPTICAL SPECTRA; RAMAN OPTICAL ACTIVITY; SPECTRAL MODELING; SPECTRAL OVERLAP;

CONFORMATIONS; FOURIER ANALYSIS; MOLECULAR DYNAMICS; OPTICAL MATERIALS; PROBABILITY DISTRIBUTIONS; VIBRATIONAL SPECTROSCOPY;

DYNAMICS;

EID: 65949104101     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21123     Document Type: Article

References (35)

1. Cantor, C. R.; Timasheff, S. N. In The Proteins; Academic Press: New York, 1982; p 145.
2. Drenth, J. Principles of Protein X-ray Crystallography; Springer-Verlag: Berlin, 1994.
3. Greenfield, N.; Davidson, B.; Fasman, G. D. Biochemistry 1967, 6, 1630.
4. Keiderling, T. A. In Circular Dichroism: Principles and Applications; Berova, N.; Nakanishi, K.; Woody, R. W., Eds.; Wiley: New York, 2000; p 621.
5. Keiderling, T. A.; Kubelka, J.; Hilario, J. In Vibratonal Spectrroscopy of Polymers and Biological Systems; Braiman, M.; Gregoriou, V., Eds.; CRC Press: Boca Raton 2006; pp 253-324.
6. Barron, L. D.; Hecht, L.; McColl, I. H.; Blanch, E. W. Mol Phys 2004, 102, 731.
7. Haesler, J.; Schindelholz, I.; Riguet, E.; Bochet, C. G.; Hug, W. Nature 2007, 446, 526.
8. Andrushchenko, V.; Bouř, P. J Phys Chem A 2007, 111, 9714.
9. Silva, R. A.; Kubelka, J.; Decatur, S. M.; Bouř, P.; Keiderling, T. A. Proc Natl Acad Sci USA 2000, 97, 8318.
10. Chung, H. S.; Ganim, Z.; Jones, K. C.; Tokmakoff, A. Proc Natl Acad Sci USA 2007, 104, 14237.
11. Bouř, P.; Keiderling, T. A. J Phys Chem B 2005, 109, 23687.
12. Kapitán, J.; Baumruk, V.; Kopecký, V., Jr.; Bouř, P. J Am Chem Soc 2006, 128, 2438.
13. Kapitán, J.; Baumruk, V.; Kopecký, V., Jr.; Pohl, R.; Bouř, P. J Am Chem Soc 2006, 128, 13451.
14. Kapitán, J.; Baumruk, V.; Kopecký, V., Jr.; Bouř, P. J Phys Chem A 2006, 110, 4689.
15. Bouř, P.; Kapitán, J.; Baumruk, V. J Phys Chem A 2001, 105, 6362.
16. Buděšínský, M.; Šebestík, J.; Bednárová, L.; Baumruk, V.; Šafařík, M.; Bouř, P. J Org Chem 2008, 73, 1481.
17. Laub, P. B.; Khorasanizadeh, S.; Roder, H. Protein Sci 1995, 4, 973.
18. Yang, S.; Cho, M. J Chem Phys 2005, 123, 134503.
19. Bouř, P. Chem Phys Lett 2002, 365, 82.
20. Šebek, J.; Bouř, P. J Phys Chem A 2008, 112, 2920.
21. Verlet, L. Phys Rev 1967, 159, 201.
22. Ponder, J.; Tinker 4.2; W. Washington University School of Medicine: Saint Louis, 2000.
23. Bouř, P.; Sopková, J.; Bednárová, L.; Maloň, P.; Keiderling, T. A. J Comput Chem 1997, 18, 646.
24. 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.; Bar-one, 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, Rev. A. 1; Gaussian, Inc.; Wallingford, CT, 2004.
25. Barron, L. D. Molecular Light Scattering and Optical Activity; Cambridge University Press: Cambridge, 2004.
26. Kamiya, N.; Watanabe, Y. S.; Ono, S.; Higo, J. Chem Phys Lett 2005, 401, 312.
27. Polavarapu, P. L. Vibrational Spectra: Principles and Applications with Emphasis on Optical Activity; Elsevier: Amsterdam, 1998.
28. Daněček, P.; Bouř, P. J Chem Phys 2007, 126, 224513.
29. Bouř, P. Collect Czech Chem Commun 2005, 70, 1315.
30. Barron, L. D.; Zhu, F.; Hecht, L. Vib Spectrosc 2006, 42, 15.
31. Kaprálová, P.; Hanák, F.; Lazebníček, J. J Chem Phys 2008, 128, 154316.
32. Glättli, A.; Daura, X.; Seebach, D.; van Gunsteren, W. F. J Am Chem Soc 2002, 124, 12972.
33. Šebek, J.; Kejík, Z.; Bouř, P. J Phys Chem A 2006, 110, 4702.
34. Ruud, K.; Helgaker, T.; Bouř, P. J Phys Chem A 2002, 106, 7448.
35. Kim, J.; Huang, R.; Kubelka, J.; Bouř, P.; Keiderling, T. A. J Phys Chem B 2006, 110, 23590.