Graph theoretical generation and analysis of hydrogen-bonded structures with applications to the neutral and protonated water cube and dodecahedral clusters

Journal of Physical Chemistry A

Volumn 102, Issue 17, 1998, Pages 2824-2832

  McDonald, Shannon ^a   Ojamäe, Lars ^b   Singer, Sherwin J ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0013421210     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp9803539     Document Type: Article

References (91)

1. Stillinger, F. H.; David, C. W. J. Chem. Phys. 1978, 69, 1473. David, C. W. J. Chem. Phys. 1980, 73, 3384. Stillinger, F. H.; Weber, T. A. Chem. Phys. Lett. 1981, 79, 259. Weber, T. A.; Stillinger, F. H. J. Phys. Chem. 1982, 86, 1314. Weber, T. A.; Stillinger, F. H. J. Chem. Phys. 1982, 76, 4028. Weber, T. A.; Stillinger, F. H. J. Chem. Phys. 1982, 77, 4150.
2. Stillinger, F. H.; David, C. W. J. Chem. Phys. 1978, 69, 1473. David, C. W. J. Chem. Phys. 1980, 73, 3384. Stillinger, F. H.; Weber, T. A. Chem. Phys. Lett. 1981, 79, 259. Weber, T. A.; Stillinger, F. H. J. Phys. Chem. 1982, 86, 1314. Weber, T. A.; Stillinger, F. H. J. Chem. Phys. 1982, 76, 4028. Weber, T. A.; Stillinger, F. H. J. Chem. Phys. 1982, 77, 4150.
3. Stillinger, F. H.; David, C. W. J. Chem. Phys. 1978, 69, 1473. David, C. W. J. Chem. Phys. 1980, 73, 3384. Stillinger, F. H.; Weber, T. A. Chem. Phys. Lett. 1981, 79, 259. Weber, T. A.; Stillinger, F. H. J. Phys. Chem. 1982, 86, 1314. Weber, T. A.; Stillinger, F. H. J. Chem. Phys. 1982, 76, 4028. Weber, T. A.; Stillinger, F. H. J. Chem. Phys. 1982, 77, 4150.
4. Stillinger, F. H.; David, C. W. J. Chem. Phys. 1978, 69, 1473. David, C. W. J. Chem. Phys. 1980, 73, 3384. Stillinger, F. H.; Weber, T. A. Chem. Phys. Lett. 1981, 79, 259. Weber, T. A.; Stillinger, F. H. J. Phys. Chem. 1982, 86, 1314. Weber, T. A.; Stillinger, F. H. J. Chem. Phys. 1982, 76, 4028. Weber, T. A.; Stillinger, F. H. J. Chem. Phys. 1982, 77, 4150.
5. Stillinger, F. H.; David, C. W. J. Chem. Phys. 1978, 69, 1473. David, C. W. J. Chem. Phys. 1980, 73, 3384. Stillinger, F. H.; Weber, T. A. Chem. Phys. Lett. 1981, 79, 259. Weber, T. A.; Stillinger, F. H. J. Phys. Chem. 1982, 86, 1314. Weber, T. A.; Stillinger, F. H. J. Chem. Phys. 1982, 76, 4028. Weber, T. A.; Stillinger, F. H. J. Chem. Phys. 1982, 77, 4150.
6. Stillinger, F. H.; David, C. W. J. Chem. Phys. 1978, 69, 1473. David, C. W. J. Chem. Phys. 1980, 73, 3384. Stillinger, F. H.; Weber, T. A. Chem. Phys. Lett. 1981, 79, 259. Weber, T. A.; Stillinger, F. H. J. Phys. Chem. 1982, 86, 1314. Weber, T. A.; Stillinger, F. H. J. Chem. Phys. 1982, 76, 4028. Weber, T. A.; Stillinger, F. H. J. Chem. Phys. 1982, 77, 4150.
7. Matsuoka, O.; Clementi, E.; Yoshimine, M. J. Chem. Phys. 1976, 64 (4), 1351.
8. Holland, P. M.; Castleman, A. W., Jr. J. Chem Phys. 1980, 72 (11), 5984.
9. Frisch, M. J.; Del Bene, J. E.; Binkley, J. S.; Schaefer, H. F., III. J. Chem. Phys. 1986, 84 (4), 2279.
10. Coker, D. F.; Miller, R. E.; Watts, R. O. J. Chem. Phys. 1980, 82 (8), 3554.
11. Belford, D. E.; Campbell, E. S. J. Chem. Phys. 1992, 86 (12), 7013.
12. Szalewicz, K.; Cole, S. J.; Kolos, W.; Bartlett, R. J. J. Chem. Phys. 1988, 89 (6), 3662.
13. Dykstra, C. E. J. Chem. Phys. 1989, 91 (10), 6472.
14. Smith, B. J.; Swanton, D. J.; Pople, J. A.; Schaefer, H. F., III. J. Chem. Phys. 1990, 92 (2), 1240.
15. Lee, E. F.; Dyke, J. M. Mol. Phys. 1991, 73, 375.
16. Wei, S.; Shi, Z.; Castleman, A. W., Jr. J. Chem. Phys. 1991, 94 (4), 3268.
17. Knochenmuss, R.; Leutwyler, S. J. Chem Phys. 1992, 96 (7), 5233.
18. Feller, D. J. Chem. Phys. 1992, 96 (8), 6104.
19. Kim, K. S.; Mhin, B. J.; Choi, U. S.; Lee, K. J. Chem. Phys. 1992, 97 (9), 6649.
20. Mhin, B. J.; Kim, J.; Lee, S.; Lee. J. Y.; Kim, K. S. J. Chem. Phys. 1994, 100, 4484.
21. Mó, O.; Yañez, M.; Elguero, J. J. Chem. Phys. 1992, 97 (9), 6628.
22. Wawak, R. J.; Wimmer, M. M.; Scheraga, H. A. J. Phys. Chem. 1992, 96 (12), 5138.
23. Schütz, M.; Bürgi, T.; Leutwyler, S.; Bürgi, H. B. J. Chem. Phys. 1993, 99 (7), 5228; 1994, 100 (2) 1780.
24. Schütz, M.; Bürgi, T.; Leutwyler, S.; Bürgi, H. B. J. Chem. Phys. 1993, 99 (7), 5228; 1994, 100 (2) 1780.
25. Schütz, M.; Klopper, W.; Luthi, H. P.; Leutwyler, S. J. Chem. Phys. 1995, 103 (14), 6114. .
26. Vegiri, A.; Farantos, S. C. J. Chem. Phys. 1993, 98 (5), 4059.
27. Kozack, R. E.; Jordan, P. C. J. Chem. Phys. 1993, 99 (4), 2978.
28. Smith, D. E.; Dang, L. X. J. Chem. Phys. 1994, 101 (9), 7873.
29. Tsai, C. J.; Jordan, K. D. J. Chem. Phys. 1995, 95, 3850.
30. Laasonen, K.; Csajka, F.; Parrinello, M. Chem. Phys. Lett. 1992, 194, 172.
31. Wales, D.; Ohmine, I. J. Chem. Phys. 1993, 98 (9), 7245.
32. Wales, D.; Ohmine, I. J. Chem. Phys. 1993, 98 (9), 7256.
33. Tsai, C. J.; Jordan, K. D. J. Phys Chem. 1993, 97, 5208.
34. Tsai, C. J.; Jordan, K. D. J. Phys. Chem. 1993, 97, 11227.
35. Tsai, C. J.; Jordan, K. D. J. Chem. Phys. 1993, 99 (9), 6957.
36. Tsai, C. J.; Jordan, K. D. Chem. Phys. Lett. 1993, 213 (1,2), 181.
37. Pedulla, J. M.; Vila, F.; Jordan, K. D. J. Chem. Phys. 1996, 105 (24), 11091.
38. Schenter, G.; Glendening, E. J. Phys. Chem. 1996, 100, 17152.
39. Sremaniak, L. S.; Perera, L.; Berkowitz, M. L. J. Chem Phys. 1996, 105 (9), 3715.
40. Ojamäe, L.; Hermansson, K. J. Phys Chem. 1994, 98, 4271.
41. Ojamäe, L.; Shavitt, I.; Singer, S. J. Int. J. Quantum Chem. 1995, 29, 657.
42. Khan, A. J. Phys. Chem. 1995, 99, 12450.
43. Khan, A. Chem. Phys. Lett. 1996, 253, 299.
44. Khan, A. Chem. Phys. Lett. 1996, 258, 574.
45. Khan, A. J. Chem. Phys. 1997, 106 (13), 5537.
46. Tuckerman, M. E.; Marx, D.; Klein, M. L.; Parrinello, M. Science 1997, 275, 817.
47. Vernon, M. F.; Drajnovich, D. J.; Kwok, H. S.; Lisy, J. M.; Shen, Y. R.; Lee, Y. T. J. Chem. Phys. 1982, 77 (1), 47.
48. Pugliano, N.; Saykally, R. J. J. Chem. Phys. 1992, 96 (3), 1832.
49. Pugliano, N.; Cruzan, J. D.; Loeser, J. G.; Saykally, R. J. J. Chem. Phys. 1993, 98 (9), 6600.
50. Liu, Cruzan, and Liu, Cruzan, Saykally, R. Science 1996, 271, 929.
51. Liu, K.; Brown, M. G.; Saykally, R. J.; Gregory, J. K.; Clary, D. C. Nature 1996, 381, 501.
52. Bürgi, T.; Graf, S.; Leutwyler, S.; Klopper, W. J. Chem. Phys. 1995, 103, 1077.
53. Klopper, W.; Schutz, M.; Luthi, H. P.; Leutwyler, S. J. Chem. Phys. 1995 103 (3), 1077.
54. Gregory, J. K.; Clary, D. C. J. Chem. Phys. 1995, 102 (20), 7817.
55. Gregory, J. K.; Clary, D. C.; Liu, K.; Brown, M. G.; Saykally, R. J. Science 1997, 275, 814.
56. Dang, L. X.; Chang, T.-M. J. Chem. Phys. 1997, 106 (19), 8149.
57. Gruenloh, C. J.; Carney, J. R.; Arrington, C. A.; Zwier, T. S.; Fredericks, S. Y.; Jordan, K. D. Science 1997, 276 (5319), 1678.
58. Berry, R. S. In Few-Body Systems and Multiparticle Dynamics; Proceedings of the Symposia of the Topical Group on Few-Body Systems and Multiparticle Dynamics, AIP Conf. No. 162, Micha, D. A., Ed.; AIP: New York, 1987; p 261.
59. Beck, T. L.; Jellinek, J.; Berry, R. S. J. Chem. Phys. 1987, 87, 545.
60. Landman, U.; Barnett, R. N.; Cleveland, C. L.; Luo, J.; Scharf, D.; Jortner, J. In Few-Body Systems and Multiparticle Diynamics; AIP Conference Proceedings, No. 162, Micha, D. A., Ed.; AIP: New York, 1987; p 200.
61. Coe, J. V.; Saykally, R. J. In Ion and Cluster Ion Spectroscopy and Structure: Maier, J. P., Ed.; Elsevier; Amsterdam, 1989.
62. Stillinger, F. H.; Rahman, A. J. Chem. Phys. 1974, 60, 1545.
63. Belch, A. C.; Rice, S. A. J. Chem. Phys. 1987, 86 (10), 5676.
64. Corongiu, C.; Clementi, E. J. Chem. Phys. 1993, 98 (3), 2241.
65. Fletcher, N. H. The Chemical Physics of Ice; Cambridge: New York 1970.
66. Hobbs, P. V. Ice Physics: Oxford: New York, 1974.
67. Xie, Y.; Remington, R. B.; Schaefer, H. F., III. J. Chem. Phys. 1994, 101 (6), 4878.
68. Radhakrishnan, T. P.; Herndon, W. C. J. Phys. Chem. 1991, 95, 10609.
69. Ojamäe, L.; Shavitt, I.; Singer, S. J. Manuscript in preparation.
70. Stewart, J. J. P. J. Comput. Chem. 1989, 10, 209; 1989, 10, 221.
71. Stewart, J. J. P. J. Comput. Chem. 1989, 10, 209; 1989, 10, 221.
72. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Johnson, B. G.; Robb, M. A.; Cheeseman, J. R.; Keith, T.; Petersson, G. A.; Montgomery, J. A.; Raghavachari, K.; Al-Laham, M. A.; Zakrzewski, V. G.; Ortiz, J. V.; Foresman, J. B.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J. L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Binkley, J. S.; Defrees, D. J.; Baker, J.; Stewart, J. P.; Head-Gordon, M.; Gonzalez, C.; Pople, J. A. Gaussian94 (Revision B.3); Gaussian, Inc.: Pittsburgh, PA, 1995.
73. Smith, D. E. Personal communication.
74. Harary, F. Michigan Math. J. 1957, 4, 221.
75. Harary, F., Palmer, E. Bull. Acad. Polon. Sci. Sér. Sci. Math. Astronom. Phys. 1966, 14, 125.
76. Harary, F.; Palmer, E. Can. J. Math 1966, 18, 853.
77. Harary, F. Graph theory; Addison-Wesley: Reading, MA, 1969.
78. Harary, F.; Palmer, E. M. Graphical enumeration; Academic, New York, 1973.
79. Behzad, M.; Chartrand, G.; Lesniak-Foster, L. Graphs and Digraphs; Prindle, Weber and Schmidt: Boston, 1979.
80. Wolfram, S. Mathematica; Wolfram Research: Champaign. IL, 1991.
81. The initial guesses were rather crude. In this case, hydrogens participating in hydrogen bonds were placed 35% of the way along the oxygen-oxygen bond from the donor to the acceptor. The initial H-O-H angle was 90° for double donors and 125.3° for single donors.
82. Kassner, J. L.; Hagen, D. E. J. Chem. Phys. 1976, 64 (4), 1861.
83. Shinohara, H.; Nagashima, U.; Tanaka, H.; Nishi, N. J. Chem. Phys. 1985, 83 (8), 4183.
84. Nagashima, U.; Shinohara, H.; Nishi, N.; Tanaka, H. J. Chem. Phys. 1986, 84 (1), 209.
85. Plummer, P. L. M.; Chen, T. S. J. Phys. Chem. 1983, 87 (21), 4190.
86. Kozack, R. E.; Jordan, P. C. J. Chem. Phys. 1993, 96 (4), 3131.
87. Khan, A. Chem. Phys. Lett. 1994, 217 (4), 443.
88. Laasonen, K.; Klein, M. L. J. Phys. Chem. 1994, 98 (40), 10079.
89. Magnera, T. F.; David, D. E.; Michl, J. Chem. Phys. Lett. 1991, 182, 363.
90. Shi, Z.; Ford, J. V.; Wei, S.; Castleman, A. W., Jr. J. Chem. Phys. 1993, 99 (3), 8009.
91. Using the OSS2 model, we noted that it was possible to obtain additional structures, differing primarily in the OH bond lengths of certain water molecules. This deficiency of the potential was also noted in ref 63. However, in all such cases the energetic difference between such structures was exceedingly small, as was the energy barrier between the structures.