Linear Response Properties Required to Simulate Vibrational Spectra of Biomolecules in Various Media: (R)-Phenyloxirane (A Comparative Theoretical and Spectroscopic Vibrational Study)

Advances in Quantum Chemistry

Volumn 50, Issue , 2005, Pages 91-124

  Jalkanen, K J ^a   Wurtz Jurgensen V ^a   Degtyarenko, I M ^b  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b AALTO UNIVERSITY   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33645502213     PISSN: 00653276     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-3276(05)50006-6     Document Type: Review

References (161)

1. Amos R.D. Chem. Phys. Lett. 87 (1982) 23
2. Amos R.D. Chem. Phys. Lett. 108 (1984) 185
3. Amos R.D. Chem. Phys. Lett. 124 (1986) 376
4. Amos R.D., Handy N.C., Jalkanen K.J., and Stephens P.J. Chem. Phys. Lett. 133 (1987) 21
5. Amos R.D., Jalkanen K.J., and Stephens P.J. J. Phys. Chem. 92 (1988) 5571
6. Amos R.D., and Rice J.E. Cambridge Analytical Derivatives Package (CADPAC). 5.2 edition (1994), Cambridge Univ. Press, Cambridge, UK
7. Andersson Y., Hult E., Apell P., Langreth D.C., and Lundqvist B.I. Solid State Comm. 106 (1998) 235
8. Andersson Y., Langreth D.C., and Lundqvist B.I. Phys. Rev. Lett. 76 (1996) 102
9. Ashvar C.S., Devlin F.J., Bak K.L., Taylor P.R., and Stephens P.J. J. Phys. Chem. 100 (1996) 9262
10. Ashvar C.S., Devlin F.J., and Stephens P.J. J. Am. Chem. Soc. 121 (1999) 2836
11. Ashvar C.S., Devlin F.J., Stephens P.J., Bak K.L., Eggimann T., and Wieser H. J. Phys. Chem. A 102 (1998) 6842
12. Ashvar C.S., Stephens P.J., Eggimann T., and Wieser H. Tetrahedron: Asymmetry 9 (1998) 1107
13. Autschbach J., Patchkovskii S., Ziegler T., van Gisbergen S.J.A., and Baerends E.J. J. Chem. Phys. 117 (2002) 581
14. Bak K.L., Devlin F.J., Ashvar C.S., Taylor P.R., Frisch M.J., and Stephens P.J. J. Phys. Chem. 99 (1995) 14918
15. Bak K.L., Jørgensen P., Helgaker T., Ruud K., and Jensen H.J.Aa. J. Chem. Phys. 98 (1993) 8873
16. Bak K.L., Jørgensen P., Helgaker T., Ruud K., and Jensen H.J.Aa. J. Chem. Phys. 100 (1994) 6621
17. Banerjee A., and Karbola M.K. J. Chem. Phys. 117 (2002) 7845
18. Barron L.D., Bogaard M.P., and Buckingham A.D. J. Am. Chem. Soc. 95 (1973) 603
19. Barron L.D., and Buckingham A.D. Mol. Phys. 20 (1971) 1111
20. Barron L.D., and Buckingham A.D. Annu. Rev. Phys. Chem. 26 (1975) 381
21. Barron L.D., Gargaro A.R., Hecht L., and Polavarapu P.L. Spectrochim Acta A 47 (1991) 1001
22. Barron L.D., Hecht L., Blanch E.W., and Bell A.F. Progr. Biophys. Molecular Biol. 117 (2000) 1
23. Becke A.D. Phys. Rev. A 38 (1988) 3098
24. Becke A.D. J. Chem. Phys. 104 (1996) 1040
25. Becke A.D. J. Chem. Phys. 119 (2003) 2972
26. Berman H., Henrick K., and Nakamura H. Nature Structural Biol. 10 (2003) 980
27. Bohr H.G., Jalkanen K.J., Frimand K., Elstner M., and Suhai S. Chem. Phys. 246 (1999) 13
28. Buckingham A.D., Fowler P.W., and Galwas P.A. Chem. Phys. 112 (1987) 1
29. Cheeseman J.R., Frisch M.J., Devlin F.J., and Stephens P.J. J. Phys. Chem. A 104 (2000) 1039
30. Cheeseman J.R., Frisch M.J., Devlin F.J., and Stephens P.J. Chem. Phys. Lett. 252 (1996) 211
31. Choy T.C. Phys. Rev. A 62 (2000) 012506
32. Chu X., and Dalgarno A. J. Chem. Phys. 121 (2004) 4083
33. Clark T., Chandrasekhar J., Spitznagel G.W., and Schleyer P.v.R. J. Comp. Chem. 4 (1983) 294
34. Colwell S.M., Handy N.C., and Lee A.M. Phys. Rev. A 53 (1996) 1316
35. Craig D.P., and Thirunamachandran T. Mol. Phys. 35 (1978) 825
36. de Lara-Castells M.P., Krems R.V., Buchachenko A.A., Delgado-Barrio G., and Villarreal P. J. Chem. Phys. 115 (2001) 10438
37. I.M. Degtyarenko, PhD thesis, Helsinki University of Technology, 2006 expected
38. Deng Z., Polavarapu P.L., Ford S.J., Hecht L., Barron L.D., Ewig C.S., and Jalkanen K.J. J. Phys. Chem. 100 (1996) 2025
39. Dion M., Rydberg H., Schroeder E., Langreth D.C., and Lundqvist B.I. Phys. Rev. L 92 (2004) 246401
40. Dobson J.F., and Wang J. Phys. Rev. Lett. 82 (1999) 2123
41. Dobson J.F., and Wang J. Phys. Rev. B 62 (2000) 10038
42. Dobson J.F., Wang J., and Gould T. Phys. Rev. B 66 (2002) 081108
43. Dunning Jr. T.H. J. Chem. Phys. 90 (1989) 1007
44. M. Elstner, Weiterentwichlung quantenmechanischer Rechenverfahren fuer organische Molekuele und Polymere, Ph.D. thesis, Universitaet-Gesamthochschule Paderborn, Paderborn, Deutschland, April 1998
45. Elstner M., Hobza P., Suhai S., and Kaxiras E. J. Chem. Phys. 114 (2001) 5149
46. Elstner M., Jalkanen K.J., Knapp-Mohammady M., Frauenheim Th., and Suhai S. Chem. Phys. 263 (2001) 203
47. Elstner M., Jalkanen K.J., Knapp-Mohammady M., Frauenheim Th., and Suhai S. Chem. Phys. 256 (2000) 15
48. Elstner M., Porezag D., Jungnickel G., Elsner J., Haugk M., Frauenheim Th., Suhai S., and Seifert G. Phys. Rev. B 58 (1998) 7260
49. Engel E., Höck A., and Dreizler R.M. Phys. Rev. A 61 (2000) 032502
50. Fernandex-Serra M.V., Junquera J., Jelsch C., and Artacho E. Solid State Comm. 16 (2000) 395
51. Frimand K., and Jalkanen K.J. Chem. Phys. 279 (2002) 161
52. Frimand K., Jalkanen K.J., Bohr H.G., and Suhai S. Chem. Phys. 255 (2000) 165
53. Frisch M.J., Pople J.A., and Binkley J.S. J. Chem. Phys. 80 (1984) 3265
54. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., and Pople J.A. Gaussian 03, Revision C.02 (2003), Gaussian Inc., Pittsburg, PA 15106
55. Fuchs M., and Gonze X. Phys. Rev. B 65 (2002) 235109
56. Goerling A., Heinze H.H., and Levy M. J. Mol. Struct. (Theochem) 501-502 (2000) 271
57. Gribov L.A., and Orville-Thomas W.J. Theory of intensities in the Raman spectra of polyatomic molecules. Theory and Methods of Calculation of Molecular Spectra (1988), John Wiley and Sons, New York 563-595
58. Grimme S. J. Comput. Chem. 25 (2004) 1463
59. Grimme S., Furche F., and Ahlrichs R. Chem. Phys. Lett. 361 (2002) 321
60. Han W.-G., Jalkanen K.J., Elstner M., and Suhai S. J. Phys. Chem. B 102 (1998) 2587
61. Han W.-G., Elstner M., Jalkanen K.J., Frauenheim Th., and Suhai S. Int. J. Quantum Chem. 78 (2000) 459
62. Hansen A.E., Stephens P.J., and Bouman T.D. J. Phys. Chem. 95 (1991) 4255
63. Hecht L., Barron L.D., and Raman J. Spectrosc. 25 (1994) 443
64. Hecht L., and Barron L.D. J. Mol. Struct. 347 (1995) 449
65. Hecht L., Phillips A.L., and Barron L.D. J. Raman Spectrosc. 26 (1995) 727
66. Hehre W.J., Ditchfield R., and Pople J.A. J. Chem. Phys. 56 (1972) 2257
67. Helgaker T., Ruud K., Bak K.L., Jørgensen P., and Olsen J. Faraday Discuss. 99 (1994) 165
68. Holzwarth G., Hsu E.C., Mosher H.S., Faulkner T.R., and Moscowitz A. J. Am. Chem. Soc. 96 (1974) 251
69. Hsu E.C., and Holzwarth G. J. Chem. Phys. 59 (1973) 4678
70. Hult E., Hyldgaard P., Rossmeisl J., and Lundqvist B.I. Phys. Rev. B 64 (2001) 195414
71. Hult E., Rydberg H., and Lundqvist B.I. Phys. Rev. B 59 (1999) 4708
72. K.J. Jalkanen, Vibrational absorption, vibrational circular dichroism and magnetic susceptibilities, Ph.D. thesis, University of Southern California, Los Angeles, CA, USA, 1989
73. Jalkanen K.J., Elstner M., and Suhai S. J. Mol. Struct. (Theochem) 675 (2004) 61
74. Jalkanen K.J., Nieminen R.M., Frimand K., Bohr J., Bohr H.G., Wade R.C., Tajkhorshid E., and Suhai S. Chem. Phys. 265 (2001) 125
75. Jalkanen K.J., Nieminen R.M., Knapp-Mohammady M., and Suhai S. Int. J. Quantum Chem. 92 (2003) 239
76. Jalkanen K.J., and Stephens P.J. J. Phys. Chem. 95 (1991) 5446
77. Jalkanen K.J., Stephens P.J., Amos R.D., and Handy N.C. Chem. Phys. Lett. 142 (1987) 153
78. Jalkanen K.J., Stephens P.J., Amos R.D., and Handy N.C. J. Phys. Chem. 92 (1988) 1781
79. Jalkanen K.J., Stephens P.J., Lazzeretti P., and Zanasi R. J. Chem. Phys. 90 (1988) 3204
80. Jalkanen K.J., and Suhai S. Chem. Phys. 208 (1996) 81
81. Johnson B.G., and Florian J. Chem. Phys. Lett. 247 (1995) 120
82. Kamiya M., Tsuneda T., and Hirao K. J. Chem. Phys. 117 (2002) 6010
83. Kawiecki R.W., Devlin F.J., Stephens P.J., and Amos R.D. J. Phys. Chem. 95 (1991) 9817
84. Keiderling T.A. Protein structural studies using vibrational circular dichroism spectroscopy. Spectroscopic Methods For Determining Protein Structure in Solution (1996), VCH Publishers Inc., 69451 Weinheim, Germany 163-189
85. Keiderling T.A. Curr. Opin. Chem. Biol. 6 (2002) 682
86. Kendall R.A., Dunning Jr. T.H., and Harrison R.J. J. Chem. Phys. 96 (1992) 6796
87. Knapp-Mohammady M., Jalkanen K.J., Nardi F., Wade R.C., and Suhai S. Chem. Phys. 240 (1999) 63
88. Kohn W., Meir Y., and Makarov D.E. Phys. Rev. Lett. 80 (1998) 4153
89. Komornicki A., and McIver J.W. J. Chem. Phys. 70 (1979) 2014
90. Kurita N., Inoue H., and Sekino H. Chem. Phys. Lett. 370 (2003) 161
91. Kurita N., and Sekino H. Int. J. Quantum Chem. 91 (2003) 355
92. Lee A.M., Colwell S.M., and Handy N.C. Chem. Phys. Lett. 229 (1994) 225
93. Lee A.M., and Handy N.C. Phys. Rev. A 59 (1999) 209
94. Lee A.M., Handy N.C., and Colwell S.M. J. Chem. Phys. 103 (1995) 10095
95. Lee C., Yang W., and Parr R.G. Phys. Rev. B 37 (1988) 785
96. Lein M., Dobson J.F., and Gross E.K.U. J. Comp. Chem. 20 (1999) 12
97. Long D.A. Raman Spectroscopy (1977), McGraw-Hill, New York
98. Lord R.C. Appl. Spectrosc. 31 (1977) 187
99. Lund O., Frimand K., Gorodkin J., Bohr H.G., Bohr J., Hansen J., and Brunak S. Protein Eng. 10 (1997) 1241
100. Lundqvist B.I., Hult E., Rydberg H., Bogicevic A., Strömquist J., and Langreth D.C. Progr. Surf. Sci. 59 (1998) 149
101. Magyar R.J., Fleszar A., and Gross E.K.U. Phys. Rev. B 69 (2004) 045111
102. Mele F., Mineva T., Russo N., and Toscano M. Theor. Chim Acta 91 (1995) 169
103. Mennucci R., Tomasi J., Cammi R., Cheeseman J.R., Frisch M.J., Devlin F.J., Gabriel S., and Stephens P.J. J. Phys. Chem. A 106 (2002) 6102
104. Mulkerrin M.G. Protein structure analysis using circular dichroism. Spectroscopic Methods for Proteins in Solution (1996), VCH Publishers Inc., 69451 Weinheim, Germany 5-27
105. Ordejon P., Artacho E., and Soler J.M. Phys. Rev. B (Rapid Comm.) 53 (1996) R10441
106. Ordejon P., Artacho E., and Soler J.M. The SIESTA method for linear scaling ab initio simulations. PHI-K Newsletter 53 (1996) 134
107. Patey M.D., and Dessent C.E.H. J. Phys. Chem. A 106 (2002) 4623
108. Perdew J.P. Electronic Structure Theory of Solids (1991), Akademie Verlag, Berlin p. 11
109. Perdew J.P., Burke K., and Ernyerhoh M. Phys. Rev. Lett. 77 (1996) 3865
110. Perdew J.P., Burke K., and Ernyerhoh M. Phys. Rev. Lett. 78 (1997) 1396
111. Perdew J.P., Chevary J.A., Vosko S.H., Jackson K.A., Pederson M.R., Singh D.J., and Fiolhais C. Phys. Rev. B 46 (1992) 6671
112. Perdew J.P., Chevary J.A., Vosko S.H., Jackson K.A., Pederson M.R., Singh D.J., and Fiolhais C. Phys. Rev. B 48 (1993) 4978
113. Perez-Jorda J.M., San-Fabian E., and Perez-Jimenez A.J. J. Chem. Phys. 110 (1999) 1916
114. Person W., and Zerbi G. Vibrational Intensities in Infrared and Raman Spectroscopy (1982), Elsevier, Amsterdam
115. Peterson K.A., Woon D.W., and Dunning Jr. T.H. J. Chem. Phys. 100 (1994) 7410
116. Polavarapu P.L. J. Phys. Chem. 94 (1990) 8106
117. Pu J., Gao J., and Truhlar D.G. J. Phys. Chem. A 108 (2004) 5454
118. Runge E., and Gross E.K.U. Phys. Rev. Lett. 52 (1984) 997
119. Ruud K., Helgaker T., and Bour P. J. Phys. Chem. A 106 (2002) 7448
120. Rydberg H., Dion M., Jacobson N., Schroeder E., Hyldgaard P., Simak S.I., Langreth D.C., and Lundqvist B.I. Phys. Rev. Lett. 91 (2003) 126402
121. Salek P., Vahtras O., Helgaker T., and Ågren H. J. Chem. Phys. 117 (2002) 9630
122. Sanchez-Portal D., Ordejon P., Artacho E., and Soler J.M. Int. J. Quantum Chem. 65 (1997) 453
123. Sankey O.F., and Niklewski D.J. Phys. Rev. B 40 (1989) 3979
124. Sankey O.F., Niklewski D.J., Drabold D.A., and Dow J.D. Phys. Rev. B 41 (1990) 12750
125. Schlosser D.W., Devlin F.J., Jalkanen K.J., and Stephens P.J. Chem. Phys. Lett. 88 (1982) 286
126. Slater J.C. Phys. Rev. 81 (1951) 385
127. Soler J.M., Artacho E., Gale J.D., Garcia A., Junquera J., Ordejon P., and Sanchez-Portal D. J. Phys.: Condens. Matter 14 (2002) 2745
128. Sottile F., Olevano V., and Reining L. Phys. Rev. Lett. 91 (2003) 056402
129. Staroverov V.N., Scuseria G.E., Tao J., and Perdew J.P. J. Chem. Phys. 1190 (2003) 12129
130. Stephens P.J. J. Phys. Chem. 89 (1985) 748
131. Stephens P.J. J. Phys. Chem. 91 (1987) 1712
132. Stephens P.J., Chabalowski C., Devlin F.J., and Jalkanen K.J. Chem. Phys. Lett. 225 (1994) 247
133. Stephens P.J., Jalkanen K.J., Amos R.D., Lazzeretti P., and Zanasi R. J. Phys. Chem. 94 (1990) 1811
134. Stephens P.J., and Lowe M.A. Annu. Rev. Phys. Chem. 36 (1985) 213
135. Subramanian V., Sivanesan D., Padmanabhan J., Lakshiminarayanan N., and Ramasami T. Proc. Indian Acad. Sci. (Chem. Sci.) 111 (1999) 369
136. Surewicz W.K., and Mantsch H.M. Infrared absorption methods for examining protein structure. Spectroscopic Methods for Proteins in Solution (1996), VCH Publishers Inc., 69451 Weinheim, Germany 135-162
137. Tajkhorshid E., Jalkanen K.J., and Suhai S. J. Phys. Chem. B 102 (1998) 5899
138. Tensyeyer L.G., and Kauffman III E.W. Protein structure as revealed by nonresonance Raman spectroscopy. Spectroscopic Methods for Proteins in Solution (1996), VCH Publishers Inc., 69451 Weinheim, Germany 69-95
139. Troullier N., and Martins J.L. Phys. Rev. B 43 (1991) 1993
140. Tsuzuki S., and Lüthi H.P. J. Chem. Phys. 114 (2001) 3949
141. van Mourik T., and Gdanitz R.J. J. Chem. Phys. 116 (2002) 9620
142. van Mourik T., Wilson A.K., and Dunning Jr. T.H. Mol. Phys. 96 (1999) 529
143. van Remoortere P., Mertz J.E., Scriven L.E., and Davis H.T. J. Chem. Phys. 110 (1999) 2621
144. Vasiliev I., and Martin R.M. Phys. Rev. A 69 (2004) 052508
145. Vignale G., Rasolt M., and Geldart D.J.W. Adv. Quantum Chem. 21 (1990) 235
146. Vosko S.H., Wilk L., and Nusair M. Cand. J. Phys. 58 (1980) 1200
147. Wesolowski T.A., Ellinger Y., and Weber J. J. Chem. Phys. 108 (1998) 6078
148. Wilson A.K., van Mourik T., and Dunning Jr. T.H. J. Mol. Struct. (Theochem) 288 (1996) 339
149. Witek H.A., Irle S., and Morokuma K. J. Chem. Phys. 121 (2004) 5163
150. Witek H.A., and Morokuma K. J. Comp. Chem. 25 (2004) 1858
151. Woon D.E., and Dunning Jr. T.H. J. Chem. Phys. 100 (1994) 2975
152. Wu Q., Ayers P.W., and Yang W. J. Chem. Phys. 119 (2003) 2978
153. Wu Q., and Yang W. J. Chem. Phys. 116 (2002) 515
154. Wu X., Vargas M.C., Nayak S., Lotrich V., and Scoles G. J. Chem. Phys. 115 (2001) 8748
155. Xu X., and Goddard III W.A. J. Phys. Chem. A 108 (2004) 2305
156. Xu X., and Goddard III W.A. Proc. Natl. Acad. Sci. 101 (2004) 2673
157. Yanai T., Tew D.P., and Handy N.C. Chem. Phys. Lett. 393 (2004) 51
158. T. Yanai, D.P. Tew, N.C. Handy, A new hydrid exchange-functional using the Coulomb-Attenuating Method (CAM-B3LYP). Response theory and molecular properties, Sønderborg, Denmark, May 2004
159. Yu G.-S., Freedman T.B., Nafie L.A., Deng T., and Polavarapu P.L. J. Phys. Chem. 99 (1995) 835
160. Zhao Y., and Truhlar D.G. J. Phys. Chem. A 108 (2004) 6908
161. Zilles B.A., and Person W.B. J. Chem. Phys. 79 (1983) 65