Computational protocols for prediction of solute NMR relative chemical shifts. A case study of L -tryptophan in aqueous solution

Journal of Computational Chemistry

Volumn 32, Issue 13, 2011, Pages 2853-2864

  Eriksen, Janus J ^a   Olsen, Jógvan Magnus H ^b   Aidas, Kȩstutis ^c   Ågren, Hans ^c   Mikkelsen, Kurt V ^a   Kongsted, Jacob ^b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^c ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

NMR; PCM; QM MM; Solvation

Indexed keywords

CLASSICAL MOLECULAR DYNAMICS; COMPUTATIONAL PROTOCOLS; CONFORMATIONAL SEARCH; GEOMETRICAL PARAMETERS; L-TRYPTOPHAN; MD SIMULATION; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATIONS; QM/MM; STABLE CONFORMERS;

AMINO ACIDS; CHEMICAL SHIFT; COMPUTATIONAL CHEMISTRY; COMPUTATIONAL GEOMETRY; CONFORMATIONS; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; SOLUTIONS;

SOLVENT EXTRACTION;

TRYPTOPHAN; WATER;

ARTICLE; CHEMISTRY; METHODOLOGY; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; SOLUTION AND SOLUBILITY;

MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR DYNAMICS SIMULATION; SOLUTIONS; TRYPTOPHAN; WATER;

EID: 79960619447     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21867     Document Type: Article

References (85)

1. Jameson, C. J., Chem Rev 1991, 91, 1375.
2. Helgaker, T.; Jaszuński, M.; Ruud, K., Chem Rev 1999, 99, 293.
3. Friebolin, H., Basic One- and Two-Dimensional NMR Spectroscopy, 4th ed.; Wiley-VCH: Weinheim, Germany, 2005.
4. Bühl, M.; Schleyer, P. V. R., J Am Chem Soc 1992, 114, 477.
5. Cremer, D.; Reichel, F.; Kraka, E., J Am Chem Soc 1991, 113, 9459.
6. Abraham, R. J.; Reid, M., J Chem Soc Perkin Trans 2002, 2, 1081.
7. Auer, A. A.; Gauss, J.; Stanton, J. F., J Chem Phys 2003, 118, 10407.
8. Goedecker, S., Rev Mod Phys 1999, 71, 1085.
9. Watson, M. A.; Salek, P.; Macak, P.; Helgaker, T., J Chem Phys 2004, 121, 2915.
10. Allen, M. J.; Keal, T. F.; Tozer, D., J Chem Phys Lett 2003, 380, 70.
11. Keal, T. W.; Tozer, D. J.; Helgaker, T., Chem Phys Lett 2004, 391, 374.
12. Keal, T. W.; Tozer, D. J., J Chem Phys 2004, 121, 5654.
13. Perdew, J. P.; Burke, K.; Ernzerhof, M., Phys Rev Lett 1996, 77, 3865.
14. Becke, A. D., J Chem Phys 1993, 98, 5648.
15. Ernzerhof, M.; Scuseria, G. E., J Chem Phys 1999, 110, 5029.
16. Adamo, C.; Barone, V., J Chem Phys 1999, 110, 6158.
17. Dirac, P. A. M., Proc Cambridge Philos Soc 1930, 26, 376.
18. Vosko, S. J.; Wilk, L.; Nusair, M., Can J Phys 1980, 58, 1200.
19. Hohenberg, P.; Kohn, W., Phys Rev 1964, 136, B864.
20. Gross, E. K. U.; Dreizler, R. M. Z., Phys A 1981, 302, 103.
21. Herman, F.; Dyke, J. P. v.; Ortenburger, I. B., Phys Rev Lett 1969, 22, 807.
22. Lee, C.; Yang, W.; Parr, R. G., Phys Rev B 1988, 37, 785.
23. Handy, N. C.; Cohen, A., J Mol Phys 2001, 99, 403.
24. Ligabue, A.; Sauer, S. P. A.; Lazzeretti, P., J Chem Phys 2007, 126, 154111.
25. Olsson, L.; Cremer, D., J Chem Phys 1996, 105, 8995.
26. Malkin, V. G.; Malkina, O. L.; Casida, M. E.; Salahub, D. R., J Am Chem Soc 1994, 116, 5898.
27. Kongsted, J.; Aidas, K.; Mikkelsen, K. V.; Sauer, S. P. A., J Chem Theory Comput 2008, 4, 267.
28. Dalton, a molecular electronic structure program, Release 2.0; 2005. Available at.
29. Pavone, M.; Brancato, G.; Morelli, G.; Barone, V., Chem Phys Chem 2006, 7, 148.
30. Aidas, K.; Møgelhøj, A.; Kjær, H.; Nielsen, C. B.; Mikkelsen, K. V.; Ruud, K.; Christiansen, O.; Kongsted, J., J Phys Chem A 2007, 111, 4199.
31. Nielsen, C. B.; Christiansen, O.; Mikkelsen, K. V.; Kongsted, J., J Chem Phys 2007, 126, 154112.
32. Olsen, J. M.; Aidas, K.; Mikkelsen, K. V.; Kongsted, J., J Chem Theory Comput 2010, 6, 249.
33. Tomasi, J.; Mennucci, B.; Cammi, R., Chem Rev 2005, 105, 2999.
34. Avogadro, an open-source molecular builder and visualization tool, Version 1.0.1; 2010. Available at.
35. Hariharan, P. C.; Pople, J. A., Theor Chim Acta 1973, 28, 213.
36. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. A., Jr. ; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, N. J.; Klene, M.; Knox, J. E.; 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.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, a.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J., Gaussian09, Revision A.1; Gaussian, Inc.: Wallingford, CT, 2009.
37. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A., J Comp Chem 2004, 25, 1157.
38. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A., J Am Chem Soc 1995, 117, 5179.
39. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A., J Phys Chem 1993, 97, 10269.
40. Case, D. A.; Darden, T. A.; Cheatham, I., T. E.; L., S. C.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A., Amber10; 2008.
41. Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A., J Mol Graph Model 2006, 25, 247.
42. Weiner, P. K.; Kollman, P. A., J Comput Chem 1981, 2, 287.
43. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, J., S.; Weiner, P. K., J Am Chem Soc 1984, 106, 765.
44. Jørgensen, W. L., J Am Chem Soc 1981, 103, 335.
45. Lifson, S.; Hagler, A. T.; Dauber, P., J Am Chem Soc 1979, 101, 5111.
46. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C., J Comput Phys 1977, 23, 327.
47. Macromodel, version 9.7; Schrödinger, LLC: New York, NY, USA, 2009.
48. (a), Allinger, N. L.; Yuh, Y. H.; Lii, J.-H., J Am Chem Soc 1989, 111, 8551
49. (b), Lii, J.-H.; Allinger, N. L., J Am Chem Soc 1989, 111, 8566
50. (c), Lii, J.-H.; Allinger, N. L., J Am Chem Soc 1989, 111, 8576
51. (d), Lii, J.-H.; Allinger, N. L., J. Comput. Chem. 1991, 12, 186.
52. Lennard-Jones, J. E., Proc R Soc Lond A 1924, 103, 463.
53. Lennard-Jones, J. E., Proc Phys Soc 1931, 43, 461.
54. Buckingham, R. A., Proc R Soc Lond A 1938, 168, 264.
55. Sprague, J. T.; Tai, J. C.; Yuh, Y. H.; Allinger, N. L., J Comput Chem 1987, 8, 581.
56. Kaupp, M.; Bühl, M.; Malkin, V. G., Calculation of NMR and EPR Parameters: Theory and Applications, 1st ed.; Wiley-VCH: Weinheim, Germany, 2004.
57. Ando, I.; Webb, G. A., Theory of NMR Parameters, 1st ed.; Academic Press: London, England, 1983.
58. Sauer, S. P. A., Molecular Electromagnetism: A Computational Chemistry Approach, 1st ed.; Oxford University Press: New York, 2011.
59. Ahlström, P.; Wallqvist, A.; Engström, S.; Jönsson, B., Mol Phys 1989, 68, 563.
60. Kongsted, J.; Osted, A.; Mikkelsen, K. V.; Christiansen, O., J Phys Chem 2003, 107, 2578.
61. Poulsen, T.; Kongsted, J.; Osted, A.; Ogilby, P.; Mikkelsen, K. V., J Chem Phys 2001, 115, 2393.
62. Kongsted, J.; Osted, A.; Mikkelsen, K. V.; Christiansen, O., Mol Phys 2002, 100, 1813.
63. Olsen, J. M.; Aidas, K.; Kongsted, J., J Chem Theory Comput 2010, 6, 3721.
64. Kongsted, J., Nielsen, C. B.; Mikkelsen, K. V.; Christiansen, O.; Ruud, K., J Chem Phys 2007, 126, 34510.
65. Stone, A. J., The Theory of Intermolecular Forces, 1st ed.; Oxford University Press: New York, 1997.
66. Olsen, J.; Jørgensen, P., J Chem Phys 1985, 82, 3235.
67. Salek, P.; Vahtras, O.; Helgaker, T.; Ågren, H., J Phys Chem 2002, 117, 9630.
68. Aidas, K., Whirlpool, a set of tools for quantum chemistry geared towards QM/MM modeling; 2010.
69. Schäfer, A.; Horn, H.; Ahlrichs, R., J Chem Phys 1992, 97, 2571.
70. Schäfer, A.; Huber, C.; Ahlrichs, R., J Chem Phys 1994, 100, 5829.
71. Aidas, K.; Mikkelsen, K. V.; Kongsted, J Phys Chem Chem Phys 2010, 12, 761.
72. Jensen, F., Theor Chem Acc 2000, 104, 484.
73. Christensen, K. A.; Jensen, F., Chem Phys Lett 2000, 317, 400.
74. Amlöf, J.; Helgaker, T.; Taylor, P. R., J Phys Chem 1988, 92, 3029.
75. Dunning, T. H., J Chem Phys 1989, 90, 1007.
76. Guillaume, M.; Ruud, K.; Rizzo, A.; Monti, S.; Lin, Z.; Xu, X., J Phys Chem 2010, 114, 6500.
77. Bagno, A.; Rastrelli, F.; Saielli, G., J. Org. Chem. 2007, 72, 7373.
78. Biagini, S.; Lai, A.; Monduzzi, M.; Saba, G., J Chem Soc, Faraday Trans 2 1983, 79, 491.
79. Levenberg, K., Quart Appl Math 1944, 2, 164.
80. Marquardt, D., SIAM J Appl Math 1963, 11, 431.
81. Press, W. H.; Flannery, B. P.; Teukolsky, S. A.; Vetterling, W. T., Numerical Recipes in C-The Art of Scientific Computing, 2nd ed.; Cambridge University Press: New York, 1992.
82. Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P., Science 1983, 220, 671.
83. Sugita, Y.; Okamoto, Y., Chem Phys Lett 1999, 314, 141.
84. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E., J Chem Phys 1953, 21, 1087.
85. Torrie, G. M.; Valleau, J. P., J Comput Phys 1977, 23, 187.