MOVIPAC: Vibrational spectroscopy with a robust meta-program for massively parallel standard and inverse calculations

Journal of Computational Chemistry

Volumn 33, Issue 27, 2012, Pages 2186-2198

  Weymuth, Thomas ^a   Haag, Moritz P ^a   Kiewisch, Karin ^a,e   Luber, Sandra ^a,f   Schenk, Stephan ^a,g   Jacob, Christoph R ^b   Herrmann, Carmen ^c   Neugebauer, Johannes ^d   Reiher, Markus ^a  

^a ETH ZURICH   (Switzerland)

^b KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^c UNIVERSITY OF HAMBURG   (Germany)

^d TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

^e VU UNIVERSITY AMSTERDAM   (Netherlands)

^f YALE UNIVERSITY   (United States)

^g BASF SE   (Germany)

Author keywords

helical structures; parallel calculations; quantum chemistry; subsystem approaches; vibrational spectroscopy

Indexed keywords

ALANINE RESIDUES; CARTESIAN TENSORS; FULL SPECTRUM; HELICAL STRUCTURES; INVERSE CALCULATION; PARALLEL CALCULATION; PARALLELIZATIONS; RAMAN OPTICAL ACTIVITY; SUBSYSTEM APPROACHES; TRANSFER METHOD;

AMINO ACIDS; QUANTUM CHEMISTRY; VIBRATIONAL SPECTRA;

VIBRATIONAL SPECTROSCOPY;

ADENINE; AMINO ACID; THYMINE;

ALGORITHM; ARTICLE; CHEMISTRY; COMPUTER PROGRAM; INFRARED SPECTROPHOTOMETRY; QUANTUM THEORY; RAMAN SPECTROMETRY;

ADENINE; ALGORITHMS; AMINO ACIDS; QUANTUM THEORY; SOFTWARE; SPECTROPHOTOMETRY, INFRARED; SPECTRUM ANALYSIS, RAMAN; THYMINE;

EID: 84866733104     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.23036     Document Type: Article

References (107)

1. E. B. Wilson, Jr., J. C. Decius, P. C. Cross, Molecular Vibrations: The Theory of Infrared and Raman Vibrational Spectra; Dover Publications: New York, 1980.
2. S. Heislbetz, G. Rauhut, J. Chem. Phys. 2010, 132, 124102.
3. D. M. Benoit, Front. Biosci. 2009, 14, 4229.
4. M. Sparta, M. B. Hansen, E. Matito, D. Toffoli, O. Christiansen, J. Chem. Theory Comput. 2010, 6, 3162.
5. J. M. Bowman, T. Carrington, H.-D. Meyer, Mol. Phys. 2008, 106, 2145.
6. N. Matsunaga, G. M. Chaban, R. B. Gerber, J. Chem. Phys. 2002, 117, 3541.
7. L. Pele, R. B. Gerber, J. Chem. Phys. 2008, 128, 165105.
8. M. Schmitz, P. Tavan, In Modern Methods for Theoretical Physical Chemistry of Biopolymers;, E. B. Starikov, J. P. Lewis, S. Tanaka, Eds.; Elsevier Science: Amsterdam, 2006, p. 159.
9. J. Jeon, S. Yang, J.-H. Choi, M. Cho, Acc. Chem. Res. 2009, 42, 1280.
10. D. Marx, J. Hutter, Ab Initio Molecular Dynamics: Basic Theory And Advanced Methods; Cambridge University Press: New York, 2009.
11. C. Herrmann, M. Reiher, Top. Curr. Chem. 2007, 268, 85.
12. L. D. Barron, Molecular Light Scattering and Optical Activity, 2nd ed.; Cambridge University Press: Cambridge, 2004.
13. W. Schneider, W. Thiel, Chem. Phys. Lett. 1989, 157, 367.
14. J. Neugebauer, B. A. Hess, J. Chem. Phys. 2003, 118, 7215.
15. A. Adel, D. M. Dennison, Phys. Rev. 1933, 43, 716.
16. M. Reiher, G. Brehm, S. Schneider, J. Phys. Chem. A 2004, 108, 734.
17. M. Reiher, B. A. Hess, Adv. Inorg. Chem. 2004, 56, 55.
18. G. Brehm, M. Reiher, S. Schneider, J. Phys. Chem. A 2002, 106, 12024.
19. G. Brehm, M. Reiher, B. L. Guennic, M. Leibold, S. Schindler, F. W. Heinemann, S. Schneider, J. Raman Spectrosc. 2006, 37, 108.
20. G. Rauhut, P. Pulay, J. Phys. Chem. 1995, 99, 3093.
21. G. Rauhut, P. Pulay, J. Phys. Chem. 1995, 99, 14572.
22. L. Yu, C. Greco, M. Bruschi, U. Ryde, L. De Gioia, M. Reiher, Inorg. Chem. 2011, 50, 3888.
23. A. P. Scott, L. Radom, J. Phys. Chem. 1996, 100, 16502.
24. J. W. Tye, M. Y. Darensbourg, M. B. Hall, J. Comput. Chem. 2006, 27, 1454.
25. P. Pulay, G. Fogarasi, G. Pongor, J. E. Boggs, A. Vargha, J. Am. Chem. Soc. 1983, 105, 7037.
26. J. Neugebauer, M. Reiher, C. Kind, B. A. Hess, J. Comput. Chem. 2002, 23, 895.
27. B. A. Hess, N UMFREQ, University of Erlangen-Nürnberg, 2001. (Based on work by S. Grimme, University of Bonn, 1998, with contributions from C. Marian and M. Gastreich.)
28. M. Reiher, J. Neugebauer, J. Chem. Phys. 2003, 118, 1634.
29. C. Herrmann, J. Neugebauer, M. Reiher, New J. Chem. 2007, 31, 818.
30. K. Kiewisch, J. Neugebauer, M. Reiher, J. Chem. Phys. 2008, 129, 204103.
31. S. Luber, J. Neugebauer, M. Reiher, J. Chem. Phys. 2009, 130, 064105.
32. S. Luber, M. Reiher, ChemPhysChem 2009, 10, 2049.
33. K. Kiewisch, S. Luber, J. Neugebauer, M. Reiher, Chimia 2009, 63, 270.
34. J. Neugebauer, B. A. Hess, J. Chem. Phys. 2004, 120, 11564.
35. W. G. Bickley, Math. Gaz. 1941, 25, 19.
36. R. Ahlrichs, M. Bär, M. Häser, H. Horn, C. Kölmel, Chem. Phys. Lett. 1989, 162, 165.
37. A. D. Becke, Phys. Rev. A 1988, 38, 3098.
38. J. P. Perdew, Phys. Rev. B 1986, 33, 8822.
39. F. Weigend, R. Ahlrichs, Phys. Chem. Chem. Phys. 2005, 7, 3297.
40. F. Weigend, Phys. Chem. Chem. Phys. 2006, 8, 1057.
41. D. Rappoport, F. Furche, J. Chem. Phys. 2007, 126, 201104.
42. ISO/IEC JTC1/SC22, International standardization subcommittee for programming languages, their environments and system software interfaces, Available at: http://www.open-std.org/jtc1/sc22/. Accessed on May 30, 2012.
43. GNU autoconf, Available at: www.gnu.org/software/autoconf. Accessed on May 30, 2012.
44. GNU automake, Available at: www.gnu.org/software/automake. Accessed on May 30, 2012.
45. N. A. Besley, K. A. Metcalf, J. Chem. Phys. 2007, 126, 035101.
46. A. Ghysels, D. Van Neck, V. Van Speybroeck, M. Waroquier, J. Chem. Phys. 2007, 126, 224102.
47. A. Ghysels, V. Van Speybroeck, E. Pauwels, D. Van Neck, B. R. Brooks, M. Waroquier, J. Chem. Theory Comput. 2009, 5, 1203.
48. P. Bouř, J. Sopková, L. Bednárová, P. Maloň, T. A. Keiderling, J. Comput. Chem. 1997, 18, 646.
49. E. R. Davidson, J. Comp. Phys. 1975, 17, 87.
50. C. W. Murray, S. C. Racine, E. R. Davidson, J. Comput. Phys. 1992, 103, 382.
51. M. Reiher, J. Neugebauer, Phys. Chem. Chem. Phys. 2004, 6, 4621.
52. J. Neugebauer, Phys. Rep. 2010, 489, 1.
53. B. R. Brooks, M. Karplus, Proc. Natl. Acad. Sci. USA 1985, 82, 4995.
54. B. R. Brooks, D. Janežič, M. Karplus, J. Comput. Chem. 1995, 16, 1522.
55. F. Filippone, M. Parrinello, Chem. Phys. Lett. 2001, 345, 179.
56. F. Filippone, S. Meloni, M. Parrinello, J. Chem. Phys. 2001, 115, 636.
57. J. Neugebauer, M. Reiher, J. Comput. Chem. 2004, 25, 587.
58. J. Neugebauer, M. Reiher, J. Phys. Chem. A 2004, 108, 2053.
59. A. L. Kaledin, J. Chem. Phys. 2005, 122, 184106.
60. M. Reiher, J. Neugebauer, J. Chem. Phys. 2005, 123, 117101.
61. A. L. Kaledin, M. Kaledin, J. M. Bowman, J. Chem. Theory Comput. 2006, 2, 166.
62. T. B. Adler, N. Borho, M. Reiher, M. A. Suhm, Angew. Chem. Int. Ed. Engl. 2006, 45, 3440.
63. C. Herrmann, K. Ruud, M. Reiher, ChemPhysChem 2006, 7, 2189.
64. C. Herrmann, M. Reiher, Surf. Sci. 2006, 9, 1891.
65. C. Herrmann, J. Neugebauer, M. Reiher, J. Comput. Chem. 2008, 29, 2460.
66. A. Schäfer, C. Huber, R. Ahlrichs, J. Chem. Phys. 1994, 100, 5829.
67. J. Boereboom, M. C. van Hemert, J. Neugebauer, ChemPhysChem 2011, 12, 3157.
68. E. J. Heller, R. Sundberg, D. Tannor, J. Phys. Chem. 1982, 86, 1822.
69. A. B. Myers, Chem. Rev. 1996, 96, 911.
70. H. Torii, Y. Ueno, A. Sakamoto, M. Tasumi, J. Phys. Chem. A 1999, 103, 5557.
71. H. Torii, J. Comput. Chem. 2002, 23, 997.
72. N. S. Bieler, M. P. Haag, C. R. Jacob, M. Reiher, J. Chem. Theory Comput. 2011, 7, 1867.
73. S. Yamamoto, P. Bouř, Collect. Czech. Chem. Commun. 2011, 76, 567.
74. C. R. Jacob, M. Reiher, J. Chem. Phys. 2009, 130, 084106.
75. C. R. Jacob, S. Luber, M. Reiher, J. Phys. Chem. B 2009, 113, 6558.
76. V. Liégeois, C. R. Jacob, B. Champagne, M. Reiher, J. Phys. Chem. A 2010, 114, 7198.
77. C. R. Jacob, S. Luber, M. Reiher, Chem. Eur. J. 2009, 15, 13491.
78. T. Weymuth, C. R. Jacob, M. Reiher, J. Phys. Chem. B 2010, 114, 10649.
79. M. Reiher, V. Liégeois, K. Ruud, J. Phys. Chem. A 2005, 109, 7567.
80. S. Luber, C. Herrmann, M. Reiher, J. Phys. Chem. B 2008, 112, 2218.
81. S. Grimme, J. Comput. Chem. 2006, 27, 1787.
82. T. Schwabe, S. Grimme, Phys. Chem. Chem. Phys. 2007, 9, 3397.
83. J. Antony, S. Grimme, Phys. Chem. Chem. Phys. 2006, 8, 5287.
84. J. Antony, B. Brüske, S. Grimme, Phys. Chem. Chem. Phys. 2009, 11, 8440.
85. S. Grimme, J. Antony, S. Ehrlich, H. Krieg, J. Chem. Phys. 2010, 132, 154104.
86. S. Grimme, J. Antony, T. Schwabe, C. Mück-Lichtenfeld, Org. Biomol. Chem. 2007, 5, 741.
87. N. Marom, A. Tkatchenko, M. Scheffler, L. Kronik, J. Chem. Theory Comput. 2010, 6, 81.
88. S. Luber, M. Reiher, Chem. Phys. 2008, 346, 212.
89. S. Grimme, F. Furche, R. Ahlrichs, Chem. Phys. Lett. 2002, 361, 321.
90. K. Eichkorn, O. Treutler, H. Öhm, M. Häser, R. Ahlrichs, Chem. Phys. Lett. 1995, 240, 283.
91. K. Eichkorn, O. Treutler, H. Öhm, M. Häser, R. Ahlrichs, Chem. Phys. Lett. 1995, 242, 652.
92. Available at: ftp://ftp.chemie.uni-karlsruhe.de/pub/jbasen.
93. W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graphics 1996, 14, 33.
94. S. Luber, M. Reiher, ChemPhysChem 2010, 11, 1876.
95. C. Johannessen, L. Hecht, C. Merten, ChemPhysChem 2011, 12, 1419.
96. S. Luber, M. Reiher, J. Phys. Chem. B 2010, 114, 1057.
97. T. Weymuth, C. R. Jacob, M. Reiher, ChemPhysChem 2011, 12, 1165.
98. S. Luber, M. Reiher, J. Phys. Chem. A 2009, 113, 8268.
99. C. Herrmann, K. Ruud, M. Reiher, Chem. Phys. 2008, 343, 200.
100. C. R. Jacob, S. Luber, M. Reiher, ChemPhysChem 2008, 9, 2177.
101. S. Luber, J. Neugebauer, M. Reiher, J. Chem. Phys. 2010, 132, 044113.
102. W. Hug, Chem. Phys. 2001, 264, 53.
103. G. te Velde, F. M. Bickelhaupt, S. J. A. van Gisbergen, C. F. Guerra, E. J. Baerends, J. G. Snijders, T. Ziegler, J. Comput. Chem. 2001, 22, 931.
104. T. Helgaker, H. J. Aa. Jensen, P. Jørgensen, J. Olsen, K. Ruud, H. Ågren, A. A. Auer, K. L. Bak, V. Bakken, O. Christiansen, S. Coriani, P. Dahle, E. K. Dalskov, T. Enevoldsen, B. Fernandez, C. Hättig, K. Hald, A. Halkier, H. Heiberg, H. Hettema, D. Jonsson, S. Kirpekar, R. Kobayashi, H. Koch, K. V. Mikkelsen, P. Norman, M. J. Packer, T. B. Pedersen, T. A. Ruden, A. Sanchez, T. Saue, S. P. A. Sauer, B. Schimmelpfenning, K. O. Sylvester-Hvid, P. R. Taylor, O. Vahtras, Dalton, A Molecular Electronic Structure Program, Release 1.2, 2001.
105. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, Ö. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian 09 Revision A.1; Gaussian Inc.: Wallingford CT, 2009.
106. R. D. Amos, A. Bernhardsson, A. Berning, P. Celani, D. L. Cooper, M. J. O. Deegan, A. J. Dobbyn, F. Eckert, C. Hampel, G. Hetzer, P. J. Knowles, T. Korona, R. Lindh, A. Lloyd, S. J. McNicholas, F. R. Manby, W. Meyer, M. E. Mura, A. Nicklass, P. Palmieri, R. Pitzer, G. Rauhut, M. Schtz, U. Schumann, H. Stoll, A. J. Stone, R. Tarroni, T. Thorsteinsson, H.-J. Werner, Molpro, A Package of Ab Initio Programs, designed by, H.-J. Werner, and, P. J. Knowles, version 2002.1, 2002.
107. F. Aquilante, L. de Vico, N. Ferré, G. Ghigo, P.-A. Malmqvist, P. Neogrády, T. B. Pedersen, M. Pitoňák, M. Reiher, B. O. Roos, L. Serrando-Andrés, M. Urban, V. Veryazov, R. Lindh, J. Comput. Chem. 2009, 31, 224.