Condensed phase molecular dynamics using interpolated potential energy surfaces with application to the resolvation process of coumarin 153

Journal of Chemical Physics

Volumn 135, Issue 1, 2011, Pages

  Park, Jae Woo ^a   Kim, Hyun Woo ^a   Song, Chang Ik ^a   Rhee, Young Min ^a  

^a Pohang University of Science and Technology (POSTECH)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CONDENSED PHASE; COUMARIN 153; DECOHERENCE; FORCE FIELDS; INTERMOLECULAR INTERACTIONS; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR REACTIONS; POLAR SOLVENTS; RESOLVATION; STABILITY ISSUES; STOKES SHIFT; TIME SIMULATIONS; VIBRATIONAL EFFECTS;

MOLECULAR DYNAMICS; POTENTIAL ENERGY; POTENTIAL ENERGY SURFACES; QUANTUM CHEMISTRY; REACTION KINETICS;

DYNAMICS;

COUMARIN 153; COUMARIN DERIVATIVE; SOLVENT;

ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; THERMODYNAMICS;

COUMARINS; MOLECULAR DYNAMICS SIMULATION; SOLVENTS; THERMODYNAMICS;

EID: 79960215153     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3605302     Document Type: Article

References (87)

1. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University Press, Oxford, 1987).
2. A. R. Leach, Molecular Modelling: Principles and Applications (Pearson Education Limited, Harlow, 2001).
3. D. Frenkel and B. Smit, Understanding Molecular Simulation (Academic, London, 2002).
4. M. Nagaoka, An Easy Guide to Molecular Simulations (Kodansha Scientific, Tokyo, 2008).
5. W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, J. Am. Chem. Soc. 118, 1 1225 (1996). 10.1021/ja9621760 (Pubitemid 26399746)
6. J. N. Onuchic, Z. Luthey-Shulten, and P. G. Wolynes, Annu. Rev. Phys. Chem. 48, 545 (1997). 10.1146/annurev.physchem.48.1.545
7. J. M. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, and D. A. Case, J. Comput Chem. 25, 1157 (2004). 10.1002/jcc.20035
8. V. Daggett, Chem. Rev. 106, 1898 (2006). 10.1021/cr0404242 (Pubitemid 43792785)
9. H. A. Scheraga, M. Khalili, and A. Liwo, Annu. Rev. Phys. Chem. 58, 57 (2007). 10.1146/annurev.physchem.58.032806.104614 (Pubitemid 46877585)
10. B. L. Bhargava, S. Balasubramanian, and M. L. Klein, Chem. Commun. 2008, 3339. 10.1039/B805384G
11. O. Borodin, J. Phys. Chem. B 113, 11463 (2009). 10.1021/jp905220k
12. P. L. Freddolino, C. B. Harrison, Y. Liu, and K. Shulten, Nat. Phys. 6, 751 (2010). 10.1038/nphys1713
13. F. Ingrosso, B. M. Ladanyi, B. Mennucci, M. D. Elola, and J. Tomasi, J. Phys. Chem. B 109, 3553 (2005). 10.1021/jp0456032 (Pubitemid 40352326)
14. K. E. Furse and S. A. Corcelli, J. Am. Chem. Soc. 130, 13103 (2008). 10.1021/ja803728g
15. K. E. Furse, B. A. Lindquis, and S. A. Corcelli, J. Phys. Chem. B 112, 3231 (2008). 10.1021/jp711100f
16. K. E. Furse and S. A. Corcelli, J. Chem. Theory Comput. 5, 1959 (2009). 10.1021/ct9001416
17. J. W. Ponder, C. Wu, P. Ren, V. S. Pande, J. D. Chodera, M. J. Schnieders, I. Haque, D. L. Mobley, D. S. Lambrecht, R. A. Distasio, Jr., M. Head-Gordon, G. N. I. Clark, M. E. Johnson, and T. Head-Gordon, J. Phys. Chem. B 114, 2549 (2010). 10.1021/jp910674d
18. J. Ischtwan and M. A. Collins, J. Chem. Phys. 100, 8080 (1994). 10.1063/1.466801
19. M. J. T. Jordan, K. C. Thompson, and M. A. Collins, J. Chem. Phys. 102, 5647 (1995). 10.1063/1.469296
20. K. C. Thompson, M. J. T. Jordan, and M. A. Collins, J. Chem. Phys. 108, 8302 (1998). 10.1063/1.476259
21. R. P. A. Bettens and M. A. Collins, J. Chem. Phys. 111, 816 (1999). 10.1063/1.479368
22. K. A. Nguyen, I. Rossi, and D. G. Truhlar, J. Chem. Phys. 103, 5522 (1995). 10.1063/1.470536
23. M. J. T. Jordan, K. C. Thompson, and M. A. Collins, J. Chem. Phys. 103, 9669 (1995). 10.1063/1.469982
24. M. J. T. Jordan and M. A. Collins, J. Chem. Phys. 104, 4600 (1996). 10.1063/1.471207
25. T.-S. Ho, T. Hollebeek, H. Rabitz, L. B. Harding, and G. C. Schatz, J. Chem. Phys. 105, 10472 (1996). 10.1063/1.472977
26. Y. M. Rhee, T. G. Lee, S. C. Park, and M. S. Kim, J. Chem. Phys. 106, 1003 (1997). 10.1063/1.473184
27. K. C. Thompson, M. J. T. Jordan, and M. A. Collins, J. Chem. Phys. 108, 564 (1998). 10.1063/1.475419
28. R. P. A. Bettens and M. A. Collins, J. Chem. Phys. 109, 9728 (1998). 10.1063/1.477643 (Pubitemid 128678402)
29. A. H. Duncan and M. A. Collins, J. Chem. Phys. 111, 1346 (1999). 10.1063/1.479393
30. R. P. A. Bettens, T. A. Hansen, and M. A. Collins, J. Chem. Phys. 111, 6322 (1999). 10.1063/1.479937
31. M. A. Collins and D. H. Zhang, J. Chem. Phys. 111, 9924 (1999). 10.1063/1.480344
32. Y. M. Rhee, J. Chem. Phys. 113, 6021 (2000). 10.1063/1.1315348
33. R. O. Fuller, R. P. A. Bettens, and M. A. Collins, J. Chem. Phys. 114, 10711 (2001). 10.1063/1.1354179 (Pubitemid 32419627)
34. K. Song and M. A. Collins, Chem. Phys. Lett. 335, 481 (2001). 10.1016/S0009-2614(01)00020-3 (Pubitemid 33628075)
35. T. Ishida and G. C. Schatz, J. Comput. Chem. 24, 1077 (2003). 10.1002/jcc.10252
36. G. E. Moyano and M. A. Collins, J. Chem. Phys. 119, 5510 (2003). 10.1063/1.1599339
37. G. E. Moyano and M. A. Collins, J. Chem. Phys. 121, 9769 (2004). 10.1063/1.1809579 (Pubitemid 40001632)
38. C. R. Everhuis and M. A. Collins, J. Chem. Phys. 121, 2515 (2004). 10.1063/1.1770756
39. G. E. Moyano, D. Pearson, and M. A. Collins, J. Chem. Phys. 121, 1 2396 (2004). 10.1063/1.1810479 (Pubitemid 41041597)
40. C. R. Everhuis, X. Lin, D. H. Zhang, D. Yarkony, and M. A. Collins, J. Chem. Phys. 123, 134110 (2005). 10.1063/1.2047569 (Pubitemid 41434698)
41. G. E. Moyano and M. A. Collins, Theor. Chem. Acc. 113, 225 (2005). 10.1007/s00214-004-0626-8 (Pubitemid 40675017)
42. E. Martinez-Nunez, S. A. Vazquez, F. J. Aoiz, and J. F. Castillo, J. Phys. Chem. A 110, 1225 (2006). 10.1021/jp052325d (Pubitemid 43235692)
43. G. E. Moyano, S. A. Jones, and M. A. Collins, J. Chem. Phys. 124, 124318 (2006). 10.1063/1.2181571
44. P. N. Abufager, C. Crespos, and H. F. Busnengo, Phys. Chem. Chem. Phys. 9, 2258 (2007). 10.1039/b617209a
45. M. A. Collins, J. Chem. Phys. 127, 024104 (2007). 10.1063/1.2746025 (Pubitemid 47114634)
46. O. Tishchenko and D. G. Truhlar, J. Chem. Phys. 132, 084109 (2010). 10.1063/1.3310296
47. M. Maroncelli and G. R. Fleming, J. Chem. Phys. 89, 5044 (1988). 10.1063/1.455649
48. P. V. Kumar and M. Maroncelli, J. Chem. Phys. 103, 3038 (1995). 10.1063/1.470493
49. M. L. Horng, J. A. Gardecki, A. Papazyan, and M. Maroncelli, J. Phys. Chem. 99, 17311 (1995). 10.1021/j100048a004
50. R. M. Stratt and M. Maroncelli, J. Phys. Chem. 100, 1 2981 (1996). 10.1021/jp9608483
51. J. Ruthmann, S. A. Kovalenko, N. P. Ernsting, and D. Ouw, J. Chem. Phys. 109, 5466 (1998). 10.1063/1.477164 (Pubitemid 128678720)
52. L. R. Martins and M. S. Skaf, Chem. Phys. Lett. 370, 683 (2002). 10.1016/S0009-2614(03)00159-3
53. I. Eom and T. Joo, J. Chem. Phys. 131, 244507 (2009). 10.1063/1.3276680
54. D. Casanova, Y. M. Rhee, and M. Head-Gordon, J. Chem. Phys. 128, 164106 (2008). 10.1063/1.2907724 (Pubitemid 351620497)
55. Y. M. Rhee, D. Casanova, and M. Head-Gordon, J. Chem. Theory Comput. 5, 1224 (2009). 10.1021/ct800509z
56. Y. M. Rhee, D. Casanova, and M. Head-Gordon, J. Phys. Chem. A 113, 10564 (2009). 10.1021/jp903659u
57. C.-I. Song and Y. M. Rhee, Development of force field parameters for oxyluciferin on its electronic ground and excited states., Int. J. Quantum Chem. (in press).
58. C. I. Bayly, P. Cieplak, W. D. Cornell, and P. A. Kollman, J. Phys. Chem. 97, 10269 (1993). 10.1021/j100142a004
59. Y. Jung, R. C. Lochan, A. D. Dutoi, and M. Head-Gordon, J. Chem. Phys. 121, 9793 (2004). 10.1063/1.1809602 (Pubitemid 40001633)
60. Y. M. Rhee and M. Head-Gordon, J. Phys. Chem. A 111, 5314 (2007). 10.1021/jp068409j (Pubitemid 47152464)
61. Y. Shao, L. Fusti-Molnar, Y. Jung, J. Kussmann, C. Ochsenfeld, S. T. Brown, A. T. B. Gilbert, L. V. Slipchenko, S. V. Levchenko, P. ONeill, R. A. D., Jr., R. C. Lochan, T. Wang, G. J. O. Beran, N. A. Besley, J. M. Herbert, C. Y. Lin, T. Van Voorhis, S. H. Chien, A. Sodt, R. P. Steele, V. A. Rassolov, P. E. Maslen, P. P. Korambath, R. D. Adamson, B. Austin, J. Baker, E. F. C. Byrd, H. Dachsel, R. J. Doerksen, A. Dreuw, B. D. Dunietz, A. D. Dutoi, T. R. Furlani, S. R. Gwaltney, A. Heyden, S. Hirata, C.-P. Hsu, G. Kedziora, R. Z. Khalliulin, P. Klunzinger, A. M. Lee, M. S. Lee, W. Liang, I. Lotan, N. Nair, B. Peters, E. I. Proynov, P. A. Pieniazek, Y. M. Rhee, J. Ritchie, E. Rosta, C. D. Sherrill, A. C. Simmonett, J. E. Subotnik, H. L. Woodcock III, W. Zhang, A. T. Bell, K. Chakraborty, D. M. Chipman, F. J. Keil, A. Warshel, W. J. Hehre, H. F. Schaefer III, J. Kong, A. I. Krylov, P. M. W. Gill, and M. Head-Gordon, Phys. Chem. Chem. Phys. 8, 3172 (2006). 10.1039/b517914a
62. R. Fletcher, Practical Methods of Optimization (Wiley, New York, 1987).
63. K. Fukui, J. Phys. Chem. 74, 4161 (1970). 10.1021/j100717a029
64. K. Ishida, K. Morokuma, and A. Komorniki, J. Chem. Phys. 66, 2153 (1977). 10.1063/1.434152
65. C. Gonzalez and H. B. Schlegel, J. Chem. Phys. 90, 2154 (1988). 10.1063/1.456010
66. C. Gonzalez and H. B. Schlegel, J. Phys. Chem. 94, 5523 (1990). 10.1021/j100377a021
67. C. Gonzalez and H. B. Schlegel, J. Chem. Phys. 95, 5853 (1991). 10.1063/1.461606
68. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, J. Chem. Theory Comput. 4, 435 (2008). 10.1021/ct700301q
69. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984). 10.1063/1.448118
70. S. Nosé, J. Chem. Phys. 81, 511 (1984). 10.1063/1.447334
71. M. Parrinello and A. Rahman, J. Appl. Phys. 52, 7182 (1981). 10.1063/1.328693 (Pubitemid 12456820)
72. D. Chandler, Introduction To Modern Statistical Mechanics (Oxford University Press, Oxford, 1987).
73. D. Chandler and P. L. Geissler, J. Chem. Phys. 113, 9759 (2000). 10.1063/1.1290136 (Pubitemid 32085157)
74. R. W. Hockney, in Methods in Computational Physics, edited by, B. Alder, S. Fernbach, and, M. Rotenberg, (Academic Press, New York, 1970), Vol. 9, pp. 135-211.
75. B. Hess, H. Bekker, H. J. C. Berendsen and J. G. E. M. Fraajie, J. Comput. Chem. 18, 1463 (1997). 10.1002/(SICI)1096-987X(199709)18:121463::AID- JCC43.0.CO;2-H
76. C. H. Kim and T. Joo, Opt. Express 16, 20742 (2008). 10.1364/OE.16.020742
77. See supplementary material at http://dx.doi.org/10.1063/1.3605302 E-JCPSA6-135-047125 for fitted RESP charges, and fitted parameters of C153, SRFs plotted, visualized vibrational modes, and figures in logarithmic scales.
78. I. V. Rubtsov and K. Yoshihara, J. Phys. Chem. A 103, 10202 (1999). 10.1021/jp991998r
79. B. O. Roos, P. R. Taylor, and P. E. M. Siegbahn, Chem. Phys. 48, 157 (1980). 10.1016/0301-0104(80)80045-0
80. H.-J. Werner and P. J. Knowles, J. Chem. Phys. 82, 5053 (1985). 10.1063/1.448627
81. P. J. Knowles and H.-J. Werner, Chem. Phys. Lett. 115, 259 (1985). 10.1016/0009-2614(85)80025-7
82. H. Barkhuijsen, R. de Beer, W. M. M. J. Bovée, and D. van Ormondt, J. Magn. Reson. 61, 465 (1985). 10.1016/0022-2364(85)90187-8
83. Avogadro: an open-source molecular builder, and visualization tool. 1.0.1 (2009), see http://avogadro.openmolecules.net.
84. A. Mhlpfordt, R. Schanz, N. P. Ernsting, V. Farztdinov, and S. Grimme, Phys. Chem. Chem. Phys. 1, 3209 (1999). 10.1039/A902491C
85. B. A. Pryor, P. M. Palmer, Y. Chen, and M. R. Topp, Chem. Phys. Lett. 299, 536 (1999). 10.1016/S0009-2614(98)01310-4
86. P. E. M. Lopes, B. Roux, and A. D. MacKerell, Jr., Theor. Chem. Acc. 124, 11 (2009). 10.1007/s00214-009-0617-x
87. P. Cieplak, F.-Y. Dupradeau, Y. Duan, and J. Wang, J. Phys.: Condens. Matter 21, 333102 (2009). 10.1088/0953-8984/21/33/333102