Circular hydrogen bond networks on the surface of β-ribofuranose in aqueous solution

Journal of Physical Chemistry B

Volumn 109, Issue 25, 2005, Pages 12603-12611

  Suzuki, Teppei ^a   Sota, Takayuki ^a  

^a WASEDA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AXIAL LATTICE; DIPOLE MOMENTS; ROTAMERS; STRUCTURAL COMPATIBILITY;

COMPUTATIONAL METHODS; COMPUTER SIMULATION; CRYSTAL STRUCTURE; HYDRATION; HYDROGEN BONDS; PARAMETER ESTIMATION; SOLUTIONS; X RAY DIFFRACTION;

SUGARS;

DRUG DERIVATIVE; OXYGEN; RIBOSE; WATER;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ELECTRON; HYDROGEN BOND; SOLUTION AND SOLUBILITY;

ELECTRONS; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR CONFORMATION; OXYGEN; RIBOSE; SOLUTIONS; WATER;

EID: 22744435440     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp050100x     Document Type: Article

References (113)

1. Kabayama, M.; Patterson, D. Can. J. Chem. 1958, 36, 563-575.
2. Schmidt, R. K.; Karplus. M.; Brady, J. W. J. Am. Chem. Soc. 1996, 118, 541-546.
3. Liu, Q.; Brady, J. W. J. Am. Chem. Soc. 1996, 118, 12276-12286.
4. Leroux, B.; Bizot, H.; Brady, J. W.; Tran, V. Chem. Phys. 1997, 216, 349-363.
5. Molteni, C.; Parrinello, M. J. Am. Chem. Soc. 1998, 120, 2168-2171.
6. Franks, F. Pure Appl. Chem. 1987, 59, 1189-1202 and references therein.
7. Uedaira, H.; Ikura, M.; Uedaira, H. Bull. Chem. Soc. Jpn. 1989, 62, 1-4 and references therein.
8. Cheetham, N. W. H.; Lam, K. Aust. J. Chem. 1996, 49, 365-369.
9. Warner, D. T. Nature 1962, 196, 1055-1058.
10. (a) Galema, S. A.; Blandamer, M. J.; Engberts, J. B. F. N. J. Am. Chem. Soc. 1990, 112, 9665-9666.
11. (b) Galema, S. A.; Høiland, H. J. Phys. Chem. 1991, 95, 5321-5326.
12. (c) Galema, S. A.; Engberts. J. B. F. N.; Høiland, H.; Førland, G. M. J. Phys. Chem. 1993, 97, 6885-6889.
13. (d) Galema, S. A.; Howard, E.; Engberts, J. B. F. N.; Grigera, J. R. Carbohydr. Res. 1994, 126, 215-225.
14. Saenger, W. Nature 1979, 279, 343-344.
15. Steiner, T. Angew. Chem., Int. Ed. 2002, 41, 48-76.
16. Saenger, W.; Steiner, T. Acta Crystallogr., Sect. A 1998, 54,798805.
17. (a) Brady, J. W. J. Am. Chem. Soc. 1986, 108, 8153-8160.
18. (b) Brady, J. W. Carbohydr. Res. 1987, 165, 306-312.
19. Ha, S. N.; Giammona, A.; Field, M.; Brady, J. W. Carbohydr. Res. 1988, 180, 207-221.
20. Polavarapu, P. L.; Ewig, C. S. J. Comput. Chem. 1992, 13, 1255-1261.
21. Salzner, U.; von Rague Schleyer, P. J. Org. Chem. 1994, 59, 2138-2155.
22. Barrows, S. E.; Dulles, F. J.; Cramer, C. J.; French, A. D.; Truhlar, D. G. Carbohydr. Res. 1995, 276, 219-251.
23. Dowd, M. K.; French, A. D.; Reilly, P. J. Carbohydr. Res. 1994, 264, 1-19.
24. Csonka, G. I.; Éliás, K.; Csizmadia, I. G. Chem. Phys. Lett. 1996, 257, 49-60.
25. Jebber, K. A.; Zhang, K.; Cassady, C. J.; Chung-Philips, A. J. Am. Chem. Soc. 1996, 118, 10515-10524.
26. Brown, J. A.; Wladkowski, B. D. J. Am. Chem. Soc. 1996, 118, 1190-1193.
27. Csonka, G. I.; Kolossváry, I.; Császár, P.; Éliás, K.; Csizmadia, I. G. THEOCHEM 1997, 395-396, 29-40.
28. Damm, W.; Frontera, A.; Tirado-Rives, J.; Jorgensen, W. L. J. Comput. Chem. 1997, 18, 1955-1970.
29. Simmerling, C.; Fox, T.; Kollman, P. A. J. Am. Chem. Soc. 1998, 120, 5771-5782.
30. Barrows, S. E.; Storer, J. W.; Cramer, C. J.; French, A. D.; Truhlar, D. G. J. Comput. Chem. 1998, 19, 1111-1129.
31. Wladkowski, B. D.; Chenoweth, S. A.; Jones, K. E.; Brown, J. W. J. Phys. Chem. A 1998, 102, 5086-5092.
32. Csonka, G. I. THEOCHEM 2002, 584, 1-4.
33. Lii, J.-H.; Chen, K.-H.; Aligner, N. L. J. Comput. Chem. 2003, 24, 1504-1513 and references therein.
34. Appell, M.; Strati, G.; Willett, J. L.; Momany, F. A. Carbohydr. Res. 2004, 339, 537-551.
35. Kouwijzer, M. L. C. E.; van Eijck, B. P.; Kroes, S. J.; Kroon, J. J. Comput. Chem. 1993, 14, 1281-1289.
36. Kouwijzer, M. L. C. E.; van Eijck, B. P.; Koojiman, H.; Kroon, J. Acta Crystallogr., Sect. B 1995, 51, 209-220.
37. Molteni, C.; Parrinello, M. Chem. Phys. Lett. 1997, 275, 409-413.
38. Cramer, C. J.; Truhlar, D. G. J. Am. Chem. Soc. 1993, 115, 5745-5753.
39. Zuccarello, F.; Buemi, G. Carbohydr. Res. 1995, 273, 129-145.
40. Cramer, C. J.; Truhlar, D. G.; French, A. D. Carbohydr. Res. 1997, 298, 1-14.
41. Ma, B.; Schaefer, H. F., III; Allinger, N. L. J. Am. Chem. Soc. 1998, 120, 3411-3422.
42. Hoffmann, M.; Rychlewski, J. J. Am. Chem. Soc. 2001, 123, 2308-2316.
43. Momany, F. A.; Appell, M.; Strati, G.; Willett, J. L. Carbohydr. Res. 2004, 339, 553-567.
44. Klein, R. A. J. Am. Chem. Soc. 2002, 124, 13931-13937.
45. Suzuki, T.; Sota, T. J. Chem. Phys. 2003, 119, 10133-10137.
46. Brady, J. W. J. Am. Chem. Soc. 1989, 111, 5155-5165.
47. Van Eijck, B. P.; Kroon-Batenburg, L. M. J.; Kroon, J. J. Mol. Struct. 1990, 237, 315-325.
48. Ha, S.; Gao, J.; Tidor, B.; Brady, J. W.; Karplus, M. J. Am. Chem. Soc. 1991, 113, 1553-1557.
49. Van Eijck, B. P.; Hooft, R. W. W.; Kroon, J. J. Phys. Chem. 1993, 97, 12093-12099.
50. Glennon, T M.; Zheng, Y.-J.; Le Grand, S. M.; Schutzberg, B. A.; Merz, K. M., Jr. J. Comput. Chem. 1994, 15, 1019-1040.
51. Corchado, J. C.; Sánchez, M. L.; Aguilar, M. A. J. Am. Chem. Soc. 2004, 126, 7311-7319.
52. Kirschner, K. N.; Woods, R. J. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10541-10545.
53. Serianni. A. S.; Chipman, D. M. J. Am. Chem. Soc. 1987, 109, 5297-5303.
54. Kline, P. C.; Serianni, A. S. J. Am. Chem. Soc. 1990, 112, 7373-7381.
55. Podlasek, C. A.; Stripe, W. A.; Carmichael, I.; Shang, M.; Basu, B.; Serianni, A. S. J. Am. Chem. Soc. 1996, 118, 1413-1425.
56. Church, T. J.; Carmichael, I.; Serianni, A. S. J. Am. Chem. Soc. 1997, 119, 8946-8964.
57. Kennedy, J.; Wu, J.; Drew, K.; Carmichael, I.; Serianni, A. S. J. Am. Chem. Soc. 1997, 119, 8933-8945.
58. Brameld, K. A.; Goddard, W. A., III. J. Am. Chem. Soc. 1999, 121, 985-993.
59. Gordon, M. T.; Lowary, T. L.; Hadad, C. M. J. Am. Chem. Soc. 1999, 121, 9682-9692.
60. Coloran, F.; Zhu, Y.; Osborn, J.; Carmichael, I.; Serianni, A. S. J. Am. Chem. Soc. 2000, 122, 6435-6448.
61. Cloran, F.; Carmichael, I.; Serianni, A. S. J. Am. Chem. Soc. 2001, 123, 4781-4791 and references therein.
62. Harvey, S. C.; Prabhakaran, M. J. Phys. Chem. 1987, 91, 4799-4801.
63. Van Eijck, B. P.; Kroon, J. J. Mol. Struct. 1989, 195, 133-146.
64. Plavec, J.; Tong, W.; Chattopadhyaya, J. J. Am. Chem. Soc. 1993, 115, 9734-9746.
65. Tomimoto, M.; Go, N. J. Phys. Chem. 1995, 99, 563-577.
66. Gabb, H. A.; Lavery, R.; Prévost, C. J. Comput. Chem. 1995, 16, 667-680.
67. Grůza, J.; Koča, J.; Pérez, S.; Imberty, A. THEOCHEM 1998, 424, 269-280.
68. Dejaegere, A. P.; Case, D. A. J. Phys. Chem. A 1998, 102, 5280-5289.
69. Houseknecht, J. B.; McCarren, P. R.; Lowary, T. L.; Hadad, C. M. J. Am. Chem. Soc. 2001, 123, 8811-8824.
70. Guler, L. P.; Yu, Y.-Q.; Kenttämaa, H. I. J. Phys. Chem. A 2002, 106, 6754-6764.
71. Houseknecht, J. B.; Altona, C.; Hadad, C. M.; Lowary, T. L. J. Org. Chem. 2002, 67, 4647-4651.
72. Boero, M.; Terakura, K.; Tateno, M. J. Am. Chem. Soc. 2002, 124, 8949-8957.
73. To our knowledge, only the trajectory-averaged hydration structure around β-ribofuranose was reported in ref 59.
74. (a) Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471-2474.
75. (b) Parrinello, M. Solid State Commun. 1997, 102, 107-120.
76. (c) Marx, D.; Hutter, J. In Modern Methods and Algorithms of Quantum Chemistry; Grotendorst, J., Ed.; NIC, FZ: Jülich, Germany, 2000; pp 301-449; see also http://www.theochem.ruhr-uni-bochum.de/research/marx/cprev.en.html.
77. (a) Altonoa, C.; Sundaralingam, M. J. Am. Chem. Soc. 1972, 94, 8205-8212.
78. (b) Rao, S. T.; Westhof, E.; Sundaralingam, M. Acta Crystallogr., Sect. A 1981, 37, 421-425.
79. (a) Hohenberg, P.; Kohn, W. Phys. Rev. 1964, 136, B864-B871.
80. (b) Kohn, W.; Sham, L. J. Phys. Rev. 1965, 140, A1133-A1138.
81. (c) Parr, R. G.; Yang, W. In Density-Functional Theory of Atoms and Molecules; Breslow, R., Goodenough, J. B., Halpern, J., Rowlingson, J. S., Eds. ; The International Series of Monographs on Chemistry 16; Oxford University Press: New York, 1989.
82. (a) Becke, A. D. Phys. Rev. A 1988, 38, 3098-3100.
83. (b) Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789.
84. (a) Sprik, M.; Hutter, J.; Parrinello, M. J. Chem. Phys. 1996, 105, 1142-1152.
85. (b) Silvestrelli, P. L.; Bernasconi, M.; Parrinello, M. Chem. Phys. Lett. 1997, 277, 478-482.
86. (c) Marx, D.; Tuckerman, M. E.; Hutter, J.; Parrinello, M. Nature 1999, 397, 601-604.
87. (d) Geissler, P. L.; Dellago, C.; Chandler, D.; Hutter, J.; Parrinello, M. Science 2001, 291, 2121-2124.
88. (e) Tuckerman, M. E., Marx, D.; Parrinello, M. Nature 2002, 417, 925-929.
89. (f) Chen, B.; Ivanov, I.; Klein, M. L.; Parrinello, M. Phys. Rev. Lett. 2003, 91, 215503. See also references cited in c-f.
90. (a) Silvestrelli, P. L.; Parrinello, M. Phys. Rev. Lett. 1999, 82, 3308-3311.
91. (b) Silvestrelli, P. L.; Parrinello, M. J. Chem. Phys. 1999, 111, 3572-3580.
92. (a) Gaigeot, M.-P.; Sprik, M. J. Phys. Chem. B 2003, 107, 10344-10358.
93. (b) Gaigeot, M.-P.; Sprik, M. J. Phys. Chem. B 2004, 108, 7458-7467.
94. Goedecker, S.; Teter, M.; Hutter, J. Phys. Rev. B 1996, 54, 1703-1710.
95. We used CPMD, version 3.7 (IBM Corp, 1990-2003, and Max-Plank-Institut für Festkörperforshung Stuttgart, 1997-2001), developed by J. Hutter et al.
96. Tuckerman, M. E.; Parrinello, M. J. Chem. Phys. 1994, 101, 1302-1315.
97. Grossman, J. C.; Schwegler, E.; Draeger, E. W.; Gygi, F.; Galli, G. J. Chem. Phys. 2004, 120, 300-311.
98. Kuo, I.-F. W.; Mundy, C. J.; McGrath, M. J.; Siepmann, J. I.; VandeVondele, J.; Sprik, M.; Hutter, J.; Chen, B.; Klein, M. L.; Mohamed, F.; Krack, M.; Parrinello, M. J. Phys. Chem. B 2004, 108, 12990-12998.
99. Martyna, G. J.; Klein, M. L.; Tuckerman, M. E. J. Chem. Phys. 1992, 97, 2635-2643.
100. Pagliai, M.; Raugei, S.; Cardini, G.; Schettino, V. THEOCHEM 2003, 630, 141-149.
101. (a) Marzari, N.; Vanderbilt, D. Phys. Rev. B 1997, 56, 12847-12865.
102. (b) Silvestrelli, P. L.; Marzari, N.; Vanderbilt, D.; Parrinello, M. Solid State Commun. 1998, 107, 7-11.
103. Marzari, N.; Souza, I.; Vanderbilt, D. Psi-K Newsletter 2003, 57, 129-168; see http://psi-k.dl.ac.uk.
104. Wales, D. J.; Walsh, T. R. J. Chem. Phys. 1996, 105, 6957-6971.
105. Graf, S.; Mohr, W.; Leutwyler, S. J. Chem. Phys. 1999, 110, 7893-7908.
106. Liu, K.; Brown, M. G.; Cruzan, J. D.; Saykally, R. J. Science 1996, 277, 62-64.
107. (b) Liu, K.; Brown, M. G.; Cruzan, J. D.; Saykally, R. J. J. Phys. Chem. A 1997, 101, 9011-9021.
108. Keutsch, F. N.; Saykally, R. J. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10533-10540.
109. Lightstone, F. C.; Schwegler, E.; Hood, R. Q.; Gygi, F.; Galli, G. Chem. Phys. Lett. 2001, 343, 549-555.
110. Bakó, I.; Hutter, J.; Pálinkás, G. J. Chem. Phys. 2002, 117, 9838-9843.
111. (a) Laaksonen, L. J. Mol. Graphics 1992, 10, 33-34.
112. (b) Bergman, D. L.; Laaksonen, L.; Laaksonen, A. J. Mol. Graphics Modell. 1997, 15, 301-306; see also http://www.csc.fi/gopenmol.
113. VondeVonde, J.; Mohamed, F.; Krack, M.; Hutter, J.; Sprik, M.; Parrinello, M. J. Chem. Phys. 2005, 122, 014515.