Hydrogen bond dynamics of histamine monocation in aqueous solution: Car-parrinello molecular dynamics and vibrational spectroscopy study

Journal of Physical Chemistry B

Volumn 115, Issue 19, 2011, Pages 5999-6010

  Stare, Jernej ^a   Mavri, Janez ^a,b   Grdadolnik, Jože ^a,b   Zidar, Jernej ^a,b   Maksić, Zvonimir B ^c   Vianello, Robert ^a,c  

^a NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^b EN FIST CENTRE OF EXCELLENCE   (Slovenia)

^c RUDER BO KOVI INSTITUTE   (Croatia)

Author keywords

[No Author keywords available]

Indexed keywords

DEUTERIUM; FOURIER ANALYSIS; FOURIER TRANSFORMS; HYDROGEN; INFRARED SPECTROSCOPY; MOLECULAR DYNAMICS; MOLECULES; PH; PROTONS; QUANTUM ELECTRONICS; REGRESSION ANALYSIS; SPECTRUM ANALYSIS; STRETCHING; VIBRATIONAL SPECTROSCOPY;

AMINO GROUP; AMINOETHYL GROUPS; AQUEOUS SOLUTIONS; AUTOCORRELATION FUNCTIONS; BOND DISTANCE; CAR-PARRINELLO MOLECULAR DYNAMICS; CAR-PARRINELLO MOLECULAR DYNAMICS SIMULATIONS; CHEMICAL BONDINGS; COMPUTATIONAL ANALYSIS; COMPUTATIONAL STUDIES; DEGREES OF FREEDOM; DEUTERATIONS; DINGER EQUATION; ENZYME REACTIVE; EXPERIMENTAL SPECTRA; FOURIER TRANSFORMATIONS; FUTURE APPLICATIONS; HIGHER FREQUENCIES; HYDROGEN BONDINGS; MONOCATIONS; PHYSIOLOGICAL PH; POSTERIORI; PROTON POTENTIALS; PROTONATED; QUANTUM EFFECTS; RECEPTOR ACTIVATION; RED-SHIFTED; SNAPSHOT ANALYSIS; SOLVENT MOLECULES; STRETCHING VIBRATIONS; STRONGLY CORRELATED SYSTEMS; WATER MOLECULE;

HYDROGEN BONDS;

EID: 79956139168     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp111175e     Document Type: Article

References (109)

1. Buckingham, A. D.; Del Bene, J. E.; McDowell, S. A. C. Chem. Phys. Lett. 2008, 463, 1
2. Hydrogen Transfer Reactions; Hynes, J. T.; Klinman, J. P.; Limbach, H.-H.; Schowen, R. L., Eds.; Wiley-VCH: Weinheim, Germany, 2006.
3. Maréchal, Y. The Hydrogen Bond and the Water Molecule; Elsevier: Amsterdam, 2007.
4. Proton Transfer in Hydrogen-Bonded System; Bountis, D., Ed.; Plenum: New York, 1992.
5. Busca, G. Chem. Rev. 2007, 107, 5366
6. Busca, G. Chem. Rev. 2010, 110, 2217
7. Electron and Proton Transfer in Chemistry and Biology; Müller, A.; Ratajczak, H.; Junge, W.; Diemann, E., Eds.; Elsevier: Amsterdam, 1992.
8. Dror, R. O.; Arlow, D. H.; Borhani, D. W.; Jensen, M. Á.; Piana, S.; Shaw, D. E. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 4689
9. Dobson, P. D.; Kell, D. B. Nature 2008, 7, 205
10. Bucher, D.; Rothlisberger, U. J. Gen. Physiol. 2010, 135, 549
11. Dror, R. O.; Jensen, M. Á.; Borhani, D. W.; Shaw, D. E. J. Gen. Physiol. 2010, 135, 555
12. Silva, J. R.; Rudy, Y. J. Gen. Physiol. 2010, 135, 575
13. Barger, G.; Dale, H. H. J. Physiol. (London) 1910, 41, 19
14. Pegg, A. E. Cancer Res. 1988, 759, 48
15. Hill, S. J.; Ganellin, C. R.; Timmerman, H.; Schwartz, J. C.; Shankley, N. P.; Young, J. M.; Schunack, W.; Levi, R.; Haas, H. L. Pharmacol. Rev. 1997, 49, 253
16. Schneider, E.; Rolli-Derkinderen, M.; Arock, M.; Dy, M. Trends Immunol. 2002, 23, 255
17. Passani, M. B.; Giannoni, P.; Bucherelli, C.; Baldi, E.; Blandina, P. Biochem. Pharmacol. 2007, 73, 1113
18. Tashiro, M.; Yanai, K. Brain Nerve 2007, 59, 221
19. Sheppard, N. In Hydrogen Bonding; Hadži, D.; Thomson, H., Eds.; Pergamon Press: London, 1959.
20. Bratos, S.; Leicknam, J.-Cl.; Gallot, G.; Ratajczak, H. In Ultrafast Hydrogen Bonding and Proton Transfer Processes in the Condensed Phase; Elsaesser, T.; Bakker, H. J., Eds.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 2002, (and references therein).
21. Cho, M. Chem. Rev. 2008, 108, 1331
22. Kim, Y. S.; Hochstrasser, R. M. J. Phys. Chem. B 2009, 113, 8231
23. Tew, D. P.; Klopper, W.; Heckert, M.; Gauss, J. J. Phys. Chem. A 2007, 111, 11242
24. Martin, J. M.; Lee, T. J.; Taylor, P. R.; Francois, J.-P. J. Chem. Phys. 1995, 103, 2589
25. Burcl, R.; Handy, N. C.; Carter, S. Spectrochim. Acta, Part A 2003, 59, 1881
26. Boese, A. D.; Martin, J. J. Phys. Chem. A 2004, 108, 3085
27. Barone, V. J. Chem. Phys. 2005, 122, 014108
28. Puzzarini, C.; Barone, V. Phys. Chem. Chem. Phys. 2008, 10, 6991
29. Bowman, J. M. Acc. Chem. Res. 1986, 19, 202
30. Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471
31. Pirc, G.; Stare, J.; Mavri, J. J. Chem. Phys. 2010, 132, 224506
32. Wong, K. F.; Sonnenberg, J. L.; Paesani, F.; Yamamoto, T.; Vaníček, J.; Zhang, W.; Schlegel, H. B.; Case, D. A.; Cheatham, T. E., III; Miller, W. H.; Voth, G. A. J. Chem. Theory Comput. 2010, 6, 2566
33. Swalina, C.; Wang, Q.; Chakraborty, A.; Hammes-Schiffer, S. J. Phys. Chem. A 2007, 111, 2206
34. Webb, S. P.; Iordanov, T.; Hammes-Schiffer, S. J. Chem. Phys. 2002, 117, 4106
35. Demšar, K.; Stare, J.; Mavri, J. J. Mol. Struct. 2007, 844-845, 215
36. Stare, J.; Mavri, J. Comput. Phys. Commun. 2002, 143, 222-240
37. Stare, J.; Balint-Kurti, G. G. J. Phys. Chem. A 2003, 107, 7204
38. Mavri, J.; Grdadolnik, J. J. Phys. Chem. A 2001, 105, 2039
39. Došlić, N.; Kühn, O. Z. Phys. Chem. 2003, 217, 1507
40. Matanović, I.; Došlić, N. J. Phys. Chem. A 2005, 109, 4185
41. Bowman, J. M. Acc. Chem. Res. 1986, 19, 202
42. Rauhut, G.; Knizia, G.; Werner, H. J. J. Chem. Phys. 2009, 130, 054105
43. Relph, R. A.; Guasco, T. L.; Elliott, B. M.; Kamrath, M. Z.; McCoy, A. B.; Steele, R. P.; Schofield, D. P.; Jordan, K. D.; Viggiano, A. A.; Ferguson, E. E.; Johnson, M. A. Science 2010, 327, 308
44. Wójcik, M. J.; Kwiendacz, J.; Boczar, M.; Boda, Ö.; Ozaki, Y. Chem. Phys. 2010, 372, 72
45. Paiva, T. B.; Tominaga, M.; Paiva, A. C. M. J. Med. Chem. 1970, 1, 689
46. Perdan-Pirkmajer, K.; Mavri, J.; Kržan, M. J. Mol. Model. 2010, 16, 1151
47. Ramírez, F. J.; Tuñón, I.; Collado, J. A.; Silla, E. J. Am. Chem. Soc. 2003, 125, 2328
48. Weisntein, H.; Chou, E.; Johnson, C. L.; Kang, S.; Green, J. P. Mol. Pharmacol. 1976, 12, 738
49. Collado, J. A.; Tuñón, I.; Silla, E.; Ramírez, F. J. J. Phys. Chem. A 2000, 104, 2120
50. Bellocq, A. M.; Garrigou-Lagrange, C. J. Chim. Phys. Physicochim. Biol. 1970, 64, 1544
51. Collado, J. A.; Ramírez, F. J. J. Raman Spectrosc. 1999, 30, 391
52. Collado, J. A.; Ramírez, F. J. J. Raman Spectrosc. 2000, 31, 925
53. Drozdzewski, P.; Kordon, E. Spectrochim. Acta 2000, 56, 1299
54. Drozdzewski, P.; Kordon, E. Spectrochim. Acta 2000, 56, 2459
55. Drozdzewski, P.; Kordon, E. Vib. Spectrosc. 2000, 24, 243-248
56. Ganellin, C. R. J. Pharm. Pharmacol. 1973, 25, 787
57. Worth, G. A.; Richards, W. G. J. Am. Chem. Soc. 1994, 116, 139
58. Arteca, G. A.; Hernández-Laguna, A.; Rández, J. J.; Smeyers, Y. G.; Mezey, P. J. Comput. Chem. 1991, 12, 705
59. Xerri, B.; Flament, J.-P.; Petitjean, H.; Berthomieu, C.; Berthomieu, D. J. Phys. Chem. B 2009, 113, 15119
60. Bertie, J. E.; Lan, Z. J. Chem. Phys. 1996, 105, 8502
61. Grdadolnik, J.; Maréchal, Y. J. Mol. Struct. 2002, 615, 177
62. Grobelnik, B.; Grdadolnik, J. Acta Chim. Sloven 2008, 55, 978
63. CPMD V3.13, Copyright IBM Corp 1990-2008, Copyright MPI fuer Festkoerperforschung Stuttgart 1997-2001.
64. Becke, A. Phys. Rev. A 1988, 38, 3098
65. Lee, C.; Yang, W.; Parr, R. Phys. Rev. B 1988, 37, 785
66. Troullier, N.; Martins, J. L. Phys. Rev. B 1991, 43, 1993
67. Nosé, S. J. Chem. Phys. 1984, 81, 511
68. Nosé, S. Mol. Phys. 1984, 52, 255
69. Hoover, W. G. Phys. Rev. A 1985, 31, 1695
70. VandeVondele, J.; Krack, M.; Mohamed, F.; Parrinello, M.; Chassaing, T.; Hutter, J. Comput. Phys. Commun. 2005, 167, 103
71. Ojamae, L.; Hermansson, K.; Probst, M. Chem. Phys. Lett. 1992, 191, 500
72. Ojamae, L.; Tegenfeldt, J.; Lindgren, J.; Hermansson, K. Chem. Phys. Lett. 1992, 195, 97
73. Rey, R.; Moller, K. B.; Hynes, J. T. J. Phys. Chem. A 2002, 106, 11993
74. Moller, K. B.; Rey, R.; Hynes, J. T. J. Phys. Chem. A 2004, 108, 1275
75. Corcelli, S. A.; Lawrence, C. P.; Skinner, J. L. J. Chem. Phys. 2004, 120, 8107
76. Balint-Kurti, G. G.; Dixon, R. N.; Marston, C. C. Int. Rev. Phys. Chem. 1992, 11, 317
77. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586
78. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187
79. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577
80. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33
81. 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, Jr., J. A.; 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, Ö.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian 09, revision A.1; Gaussian, Inc.: Wallingford, CT, 2009.
82. Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999
83. Silvestrelli, P. L.; Bernasconi, M.; Parrinello, M. Chem. Phys. Lett. 1997, 277, 478
84. Bernasconi, M.; Silvestrelli, P. L.; Parinello, M. Phys. Rev. Lett. 1998, 81, 1235
85. Putrino, A.; Parrinello, M. Phys. Rev. Lett. 2002, 88, 176401
86. Wannier, G. H. Phys. Rev. 1937, 52, 191
87. Gaigeot, M.-P.; Sprik, M. J. Phys. Chem. A 2003, 107, 10344
88. Gaigeot, M.-P. J. Phys. Chem. A 2008, 112, 13507
89. Johnson, R. D., III; Irikura, K. K.; Kacker, R. N.; Kessel, R. J. Chem. Theory Comput. 2010, 6, 2822
90. Alecu, I. M.; Zheng, J.; Zhao, Y.; Truhlar, D. G. J. Chem. Theory Comput. 2010, 6, 2872
91. Isotope Effects in Chemistry and Biology; Kohen, A.; Limbach, H.-H., Eds.; CRC Press: New York, 2005.
92. Salanne, M.; Simon, C.; Madden, P. A. Phys. Chem. Chem. Phys. 2011, 13, 6305
93. Marx, D.; Hutter, J. Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods; Cambridge University Press: Cambridge, U.K., 2009.
94. Perrin, C. A. Acc. Chem. Res. 2010, 43, 1550
95. Pejov, L.; Spangberg, D.; Hermansson, L. J. Phys. Chem. A 2005, 109, 5144
96. Ojamäe, L.; Tegenfeldt, J.; Lindgren, J.; Hermansson, K. Chem. Phys. Lett. 1992, 195, 97
97. Li, S.; Schmidt, J. R.; Piryatinski, A.; Lawrence, C. P.; Skinner, J. L. J. Phys. Chem. B 2006, 110, 18933
98. Bakker, H. J.; Skinner, J. L. Chem. Rev. 2010, 110, 1498
99. Yan, Y.; Kuhn, O. Phys. Chem. Chem. Phys. 2010, 12, 15695
100. Yan, Y.; Petković, M.; Krishnan, G. M.; Kuhn, O. J. Mol. Struct. 2010, 972, 68
101. Cyrański, M. K.; Jezierska, A.; Klimentowska, P.; Panek, J. J.; Zukowska, G. Z.; Sporzyński, A. J. Chem. Phys. 2008, 128, 124512
102. Stare, J.; Panek, J.; Eckert, J.; Grdadolnik, J.; Mavri, J.; Hadži, D. J. Phys. Chem. A 2008, 112, 1576
103. Jezierska, A.; Panek, J.; Borštnik, U.; Mavri, J.; Janežič, D. J. Phys. Chem. B 2007, 111, 5243
104. Quantum Tunneling in Enzyme-Catalysed Reactions; Alleman, R. K.; Scrutton, N. S., Eds.; RSC Publishing: Cambridge, 2009.
105. Ubbelohde, A. R.; Gallagher, K. J. Acta Crystallogr. 1955, 8, 71
106. Rosta, E.; Klähn, M.; Warshel, A. J. Phys. Chem. B 2006, 110, 2934
107. Carloni, P.; Rothlisberger, U.; Parrinello, M. Acc. Chem. Res. 2002, 35, 455
108. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions; John Wiley & Sons: New York, 1997.
109. Nygaard, R.; Frimurer, T. M.; Holst, B.; Rosenkilde, M. M.; Schwartz, T. W. Trends Pharmacol. Sci. 2009, 30, 249