Analysis of the Cartesian Tensor Transfer Method for calculating vibrational spectra of polypeptides

Journal of Chemical Theory and Computation

Volumn 7, Issue 6, 2011, Pages 1867-1881

  Bieler, Noah S ^a   Haag, Moritz P ^a   Jacob, Christoph R ^b   Reiher, Markus ^a  

^a ETH ZURICH   (Switzerland)

^b KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79959245335     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct2001478     Document Type: Article

References (108)

1. Vass, E.; Hollosi, M.; Besson, F.; Buchet, R. Chem. Rev. 2003, 103, 1917-1954
2. Barth, A. Biochim. Biophys. Acta, Bioenerg. 2007, 1767, 1073-1101
3. Carey, P. R. J. Biol. Chem. 1999, 274, 26625-26628
4. Thomas, G. J., Jr. Biopolymers 2002, 67, 214-225
5. Holzwarth, G.; Hsu, E. C.; Mosher, H. S.; Faulkner, T. R.; Moscowitz, A. J. Am. Chem. Soc. 1974, 96, 251-252
6. Keiderling, T. A. In Circular Dichroism: Principles and Applications, 2 nd ed.; Berova, N.; Nakanishi, K.; Woody, R. W., Eds.; Wiley-VCH: New York, 2000; pp 621-666.
7. Silva, R. A. G. D.; Kubelka, J.; Bou?, P.; Decatur, S. M.; Keiderling, T. A. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 8318-8323
8. Kubelka, J.; Silva, R. A. G. D.; Keiderling, T. A. J. Am. Chem. Soc. 2002, 124, 5325-5332
9. Barron, L. D. Molecular Light Scattering and Optical Activity, 2 nd ed.; Cambridge University Press: Cambridge, U. K., 2004; pp 327-381.
10. Barron, L. D.; Bogaard, M. P.; Buckingham, A. D. J. Am. Chem. Soc. 1973, 95, 603-605
11. Hug, W.; Kint, S.; Bailey, G. F.; Scherer, J. R. J. Am. Chem. Soc. 1975, 97, 5589-5590
12. Barron, L. D.; Hecht, L.; McColl, I. H.; Blanch, E. W. Mol. Phys. 2004, 102, 731-744
13. Zhu, F.; Isaacs, N. W.; Hecht, L.; Tranter, G. E.; Barron, L. D. Chirality 2006, 18, 103-115
14. Barron, L. D.; Buckingham, A. D. Chem. Phys. Lett. 2010, 492, 199-213
15. Schweitzer-Stenner, R. J. Raman Spectrosc. 2001, 32, 711-732
16. Asher, S. A.; Ianoul, A.; Mix, G.; Boyden, M. N.; Karnoup, A.; Diem, M.; Schweitzer-Stenner, R. J. Am. Chem. Soc. 2001, 123, 11775-11781
17. Schweitzer-Stenner, R. J. Raman Spectrosc. 2005, 36, 276-278
18. Huang, C.-Y.; Balakrishnan, G.; Spiro, T. G. J. Raman Spectrosc. 2006, 37, 277-282
19. Hamm, P.; Lim, M.; Hochstrasser, R. M. J. Phys. Chem. B 1998, 102, 6123-6138
20. Ganim, Z.; Chung, H. S.; Smith, A. W.; DeFlores, L. P.; Jones, K. C.; Tokmakoff, A. Acc. Chem. Res. 2008, 41, 432-441
21. Zhuang, W.; Hayashi, T.; Mukamel, S. Angew. Chem., Int. Ed. 2009, 48, 3750-3781
22. Polfer, N. C.; Oomens, J.; Suhai, S.; Paizs, B. J. Am. Chem. Soc. 2007, 129, 5887-5897
23. Lagutschenkov, A.; Langer, J.; Berden, G.; Oomens, J.; Dopfer, O. J. Phys. Chem. A 2010, 114, 13268-13276
24. Rossi, M.; Blum, V.; Kupser, P.; von Helden, G.; Bierau, F.; Pagel, K.; Meijer, G.; Scheffler, M. J. Phys. Chem. Lett. 2010, 1, 3465-3470
25. Rizzo, T. R.; Stearns, J. A.; Boyarkin, O. V. Int. Rev. Phys. Chem. 2009, 28, 481
26. Nagornova, N. S.; Rizzo, T. R.; Boyarkin, O. V. J. Am. Chem. Soc. 2010, 132, 4040-4041
27. Herrmann, C.; Reiher, M. Top. Curr. Chem. 2007, 268, 85-132
28. Hug, W. Chem. Phys. 2001, 264, 53-69
29. Jacob, Ch. R.; Reiher, M. J. Chem. Phys. 2009, 130, 084106
30. Hug, W.; Fedorovsky, M. Theor. Chem. Acc. 2008, 119, 113-131
31. Jacob, Ch. R.; Luber, S.; Reiher, M. Chem.-Eur. J. 2009, 15, 13491-13508
32. Jacob, Ch. R.; Luber, S.; Reiher, M. J. Phys. Chem. B 2009, 113, 6558-6573
33. Liégeois, V.; Jacob, Ch. R.; Champagne, B.; Reiher, M. J. Phys. Chem. A 2010, 114, 7198-7212
34. Weymuth, T.; Jacob, Ch. R.; Reiher, M. J. Phys. Chem. B 2010, 114, 10649-10660
35. Reiher, M.; Neugebauer, J. J. Chem. Phys. 2003, 118, 1634-1641
36. Reiher, M.; Neugebauer, J. Phys. Chem. Chem. Phys. 2004, 6, 4621-4629
37. Herrmann, C.; Neugebauer, J.; Reiher, M. New J. Chem. 2007, 31, 818-831
38. Kiewisch, K.; Neugebauer, J.; Reiher, M. J. Chem. Phys. 2008, 129, 204103
39. Kiewisch, K.; Luber, S.; Neugebauer, J.; Reiher, M. Chimia 2009, 63, 270-274
40. Luber, S.; Neugebauer, J.; Reiher, M. J. Chem. Phys. 2009, 130, 064105
41. Luber, S.; Reiher, M. ChemPhysChem 2009, 10, 2049-2057
42. Ghysels, A.; Van Neck, D.; Van Speybroeck, V.; Verstraelen, T.; Waroquier, M. J. Chem. Phys. 2007, 126, 224102
43. Ghysels, A.; Van Neck, D.; Brooks, B. R.; Van Speybroeck, V.; Waroquier, M. J. Chem. Phys. 2009, 130, 084107
44. Bou?, P.; Sopková, J.; Bednárová, L.; Malo?, P.; Keiderling, T. A. J. Comput. Chem. 1997, 18 (5) 646-659
45. Bou?, P.; Zaruba, K.; Urbanova, M.; Setnicka, V.; Matejka, P.; Fiedler, Z.; Kral, V.; Volka, K. Chirality 2000, 12, 191-198
46. Kubelka, J.; Keiderling, T. J. Am. Chem. Soc. 2001, 123, 6142-6150
47. Mazaleyrat, J.; Wright, K.; Gaucher, A.; Wakselman, M.; Oancea, S.; Formaggio, F.; Toniolo, C.; Setnicka, V.; Kapitan, J.; Keiderling, T. Tetrahedron: Asymmetry 2003, 14, 1879-1893
48. Huang, R.; Setnicka, V.; Etienne, M. A.; Kim, J.; Kubelka, J.; Hammer, R. P.; Keiderling, T. A. J. Am. Chem. Soc. 2007, 129, 13592-13603
49. Grahnen, J. A.; Amunson, K. E.; Kubelka, J. J. Phys. Chem. B 2010, 114, 13011-13020
50. Bou?, P.; Kapitan, J.; Baumruk, V. J. Phys. Chem. A 2001, 105, 6362-6368
51. Bou?, P.; McCann, J.; Wieser, H. J. Phys. Chem. A 1997, 101, 9783-9790
52. Bou?, P.; McCann, J.; Wieser, H. J. Phys. Chem. A 1998, 102, 102-110
53. Bou?, P.; Kubelka, J.; Keiderling, T. Biopolymers 2000, 53, 380-395
54. Kubelka, J.; Keiderling, T. J. Am. Chem. Soc. 2001, 123, 12048-12058
55. Hilario, J.; Kubelka, J.; Syud, F.; Gellman, S.; Keiderling, T. Biopolymers 2002, 67, 233-236
56. Andrushchenko, V.; Wieser, H.; Bou?, P. J. Phys. Chem. B 2002, 106, 12623-12634
57. Hilario, J.; Kubelka, J.; Keiderling, T. J. Am. Chem. Soc. 2003, 125, 7562-7574
58. Huang, R.; Kubelka, J.; Barber-Armstrong, W.; Silva, R.; Decatur, S.; Keiderling, T. J. Am. Chem. Soc. 2004, 126, 2346-2354
59. Andrushchenko, V.; Wieser, H.; Bou?, P. J. Phys. Chem. B 2004, 108, 3899-3911
60. Bou?, P.; Keiderling, T. J. Phys. Chem. B 2005, 109, 5348-5357
61. Setnicka, V.; Huang, R.; Thomas, C.; Etienne, M.; Kubelka, J.; Hammer, R.; Keiderling, T. J. Am. Chem. Soc. 2005, 127, 4992-4993
62. Kubelka, J.; Huang, R.; Keiderling, T. J. Phys. Chem. B 2005, 109, 8231-8243
63. Bou?, P.; Andrushchenko, V.; Kabelac, M.; Maharaj, V.; Maharaj, V. J. Phys. Chem. B 2005, 109, 20579-20587
64. Bou?, P.; Keiderling, T. J. Phys. Chem. B 2005, 109, 23687-23697
65. Kim, J.; Huang, R.; Kubelka, J.; Bou?, P.; Keiderling, T. A. J. Phys. Chem. B 2006, 110, 23590-23602
66. Turner, D. R.; Kubelka, J. J. Phys. Chem. B 2007, 111, 1834-1845
67. Kapitan, J.; Baumruk, V.; Bou?, P. J. Am. Chem. Soc. 2006, 128 (7) 2438-2443
68. Zhu, F.; Kapitan, J.; Tranter, G. E.; Pudney, P. D. A.; Isaacs, N. W.; Hecht, L.; Barron, L. D. Proteins 2008, 70, 823-833
69. Budesinsky, M.; Sebestik, J.; Bednarova, L.; Baumruk, V.; Safarik, M.; Bou?, P. J. Org. Chem. 2008, 73, 1481-1489
70. Kapitan, J.; Zhu, F.; Hecht, L.; Gardiner, J.; Seebach, D.; Barron, L. D. Angew. Chem., Int. Ed. 2008, 47, 6392-6394
71. Budesinsky, M.; Danecek, P.; Bednarova, L.; Kapitan, J.; Baumruk, V.; Bou?, P. J. Phys. Chem. A 2008, 112, 8633-8640
72. Sebek, J.; Kapitan, J.; Sebestik, J.; Baumruk, V.; Bou?, P. J. Phys. Chem. A 2009, 113 (27) 7760-7768
73. Hudecova, J.; Kapitan, J.; Baumruk, V.; Hammer, R. P.; Keiderling, T. A.; Bou?, P. J. Phys. Chem. A 2010, 114, 7642-7651
74. Yamamoto, S.; Straka, M.; Watarai, H.; Bou?, P. Phys. Chem. Chem. Phys. 2010, 12, 11021-11032
75. Herrmann, C.; Ruud, K.; Reiher, M. ChemPhysChem 2006, 7, 2189-2196
76. Jacob, Ch. R.; Luber, S.; Reiher, M. ChemPhysChem 2008, 9, 2177-2180
77. Luber, S.; Reiher, M. J. Phys. Chem. B 2010, 114, 1057-1063
78. Luber, S.; Reiher, M. Chem. Phys. 2008, 346, 212-223
79. Quinet, O.; Champagne, B. J. Chem. Phys. 2001, 115, 6293-6299
80. Rappoport, D.; Furche, F. J. Chem. Phys. 2005, 122, 064105
81. Quinet, O.; Liegeois, V.; Champagne, B. J. Chem. Theory Comput. 2005, 1, 444-452
82. Liegeois, V.; Ruud, K.; Champagne, B. J. Chem. Phys. 2007, 127, 204105
83. Ruud, K.; Thorvaldsen, A. J. Chirality 2009, 21, E54-E67
84. Bast, R.; Ekström, U.; Gao, B.; Helgaker, T.; Ruud, K.; Thorvaldsen, A. J. Phys. Chem. Chem. Phys. 2011, 13, 2627
85. Altmann, S. L. Rotations, Quaternions and Double Groups; Oxford University Press: New York, 1986; pp 201-223.
86. Kearsly, S. K. J. Comput. Chem. 1990, 11 (10) 1187-1192
87. Kneller, G. R. Mol. Simul. 1991, 7, 113-119
88. Neugebauer, J.; Reiher, M.; Kind, C.; Hess, B. A. J. Comput. Chem. 2002, 23, 895-910
89. SNF 4.0.0 program for the quantum chemical calculation of vibrational spectra. Neugebauer, J.; Herrmann, C.; Luber, S.; Reiher, M. www.reiher.ethz.ch/software/snf (accessed Apr 04, 2011).
90. Turbomole. Ahlrichs, R. http://www.turbomole.com (accessed Apr 04, 2011).
91. Perdew, J. P. Phys. Rev. B 1986, 33, 8822-8824
92. Becke, A. D. Phys. Rev. A 1988, 38, 3098-3100
93. Schäfer, A.; Huber, C.; Ahlrichs, R. J. Chem. Phys. 1994, 100, 5829-5835
94. Turbomole basis set library. ftp://ftp.chemie.uni-karlsruhe.de/pub/basen (accessed Apr 04, 2011).
95. Turbomole auxiliary basis sets. ftp://ftp.chemie.uni-karlsruhe.de/pub/ jbasen (accessed Apr 04, 2011).
96. Eichkorn, K.; Treutler, O.; Öhm, H.; Häser, M.; Ahlrichs, R. Chem. Phys. Lett. 1995, 240, 283-289
97. PyVib2, a program for analyzing vibrational motion and vibrational spectra. Fedorovsky, M. http://pyvib2.sourceforge.net (accessed Apr 04, 2011).
98. Oboodi, M. R.; Alva, C.; Diem, M. J. Phys. Chem. 1984, 88, 501-505
99. Diem, M.; Lee, O.; Roberts, G. M. J. Phys. Chem. 1992, 96, 548-554
100. Luber, S.; Herrmann, C.; Reiher, M. J. Phys. Chem. B 2008, 112, 2218-2232
101. Bou?, P.; Keiderling, T. A. J. Chem. Phys. 2002, 117, 4126-4132
102. Senn, H.-M.; Thiel, W. Top. Curr. Chem. 2007, 268, 173-290
103. Senn, H. M.; Thiel, W. Angew. Chem., Int. Ed. 2009, 48, 1198-1229
104. Jacob, Ch. R.; Neugebauer, J.; Jensen, L.; Visscher, L. Phys. Chem. Chem. Phys. 2006, 8, 2349-2359
105. Kiewisch, K.; Eickerling, G.; Reiher, M.; Neugebauer, J. J. Chem. Phys. 2008, 128, 044114
106. Jacob, Ch. R.; Visscher, L. J. Chem. Phys. 2008, 128, 155102
107. Neugebauer, J. J. Chem. Phys. 2009, 131, 084104
108. Neugebauer, J.; Curutchet, C.; Munoz-Losa, A.; Mennucci, B. J. Chem. Theory Comput. 2010, 6, 1843-1851