Chapter 5 Current trends in modeling interactions of DNA fragments with polar solvents

Theoretical and Computational Chemistry

Volumn 8, Issue C, 1999, Pages 167-209

  Gorb, Leonid ^a   Leszczynski, Jerzy ^a  

^a JACKSON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77956679639     PISSN: 13807323     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1380-7323(99)80080-6     Document Type: Chapter

References (178)

1. Franklin R.E., and Gosling R.G. Nature 171 (1953) 740
2. Wolf B., and Hanlon S. Biochemistry 14 (1975) 1661
3. Cohen G., and Eisenberg H. Biopolymers 6 (1968) 1077
4. Hearst J.E., and Vinograd J. Proc. Nat. Acad. Sci. USA 47 (1961) 825
5. Hearst J.E. Biopolymers 3 (1965) 57
6. Falk M., Hartman K.A., and Lord R.C. J. Am. Chem. Soc. 84 (1962) 3843
7. Falk M., Hartman K.A., and Lord R.C. J. Am. Chem. Soc. 85 (1963) 387
8. Falk M., Hartman K.A., and Lord R.C. J. Am. Chem. Soc. 85 (1963) 391
9. Falk M., Poole A.G., and Goymour C.G. Can. J. Chem. 48 (1970) 1536
10. Brandes R., Rupprecht A., and Kearns D.R. J. Biophys. 56 (1989) 683
11. Diverdi J.A., and Opella S.J. J. Mol. Biol. 149 (1981) 307
12. Shindo H., Hiyama Y., Roy S., Cohen J.S., and Torchia D.A. Bull. Chem. Soc. Jpn. 60 (1980) 1631
13. Saenger W. Principles of Nucleic Acid Structure (1983), Springer-Verlag, New York
14. Texter J. Prog. Biophys. Mol. Biol. 33 (1978) 83
15. Westhof E. Int. J. Biol. Macromol. 9 (1987) 186
16. Westhof E. Ann. Rev. Biophys. Biophys. Chem. 17 (1988) 125
17. Berman H.M. Ann. NY Acad. Sci. 486 (1986) 166
18. (in Russian). Maleev V.Ya. Biofizika 38 (1993) 789
19. Westhof E., and Beveridge D.L. In: Franc F. (Ed). Water Science Reviews vol. 1 (1989), Cambridge University Press, New York
20. Petruska J., Sowers L.C., and Godman M.F. Proc. Nat. Acad. Sci. USA 83 (1986) 1559
21. Tomasi J., and Persico M. Chem. Rev. 94 (1994) 2027
22. Cossi M., Barone V., Cammi R., and Tomasi J. Chem. Phys. Lett. 255 (1996) 327
23. Onsager L. J. Am. Chem. Soc. 58 (1936) 1486
24. Born M. Z. Phys. 1 (1920) 45
25. Pomelli S., and Tomasi J. Theor. Chem. Acc. 96 (1997) 39
26. Rivail J.-L., and Rinaldi D. In: Leszczynski J. (Ed). Compuational Chemistry: Reviews of Current Trends vol. 1 (1996), World Scientific, Singapore
27. Rivail J.-L., and Rinaldi D. Chem. Phys. 18 (1976) 233
28. Rinaldi D., and Rivail J.-L. Theor. Chim. Acta. 32 (1973) 57
29. Rivail J.-L., and Rinaldi D. Chem. Phys. 18 (1976) 233
30. Rinaldi D., and Rivail J.-L. Theor. Chim. Acta. 32 (1973) 57
31. Rivail J.-L., and Rinaldi D. Chem. Phys. 18 (1976) 233
32. Rinaldi D., and Rivail J.-L. Theor. Chim. Acta. 32 (1973) 57
33. Rivail J.-L., and Rinaldi D. Chem. Phys. 18 (1976) 233
34. Rivail J.-L., Rinaldi D., and Ruiz-Lopez M.F. In: Formosinho S.J. (Ed). Theoretical and Computational Models for Organic Chemistry (1991), Kluwer, Dordrecht
35. Rivail J.-L., and Terryn B. J. Chim. Phys. 79 (1982) 1
36. Rinaldi D., Ruiz-Lopez M.F., and Rivail J.-L. J. Chem. Phys. 78 (1983) 834
37. Rinaldi D., Costa-Cabral B.J., and Rivail J.-L. Chem. Phys. Lett. 125 (1986) 495
38. harrison S.W., Nolte N.J., and Beveridge D. J. Phys. Chem. 80 (1976) 2580
39. Rinaldi D. J. Comput. Chem. 6 (1982) 155
40. Richards F.M. Ann. Rev. Biophys. Bioenerg. 6 (1977) 151
41. D. Rinaldi and R.R. Pappalardo, SCRFPAC, QCPE 622.
42. Dillet V., Rinaldi D., and Rivail J.-L. J. Phys. Chem. 98 (1994) 5034
43. Dillet V., Rinaldi D., Ágyán J.G., and Rivail J.-L. Chem. Phys. Lett. 202 (1993) 18
44. Cramer C.J., and Truhlar D.G. In: Tapia O., and Bertran J. (Eds). Solvent Effects and Chemical Reactivity (1996), Kluwer, Dordrecht
45. (in Russian). Gorb L.G., Abronin I.A., Kharchevnikova N.V., and Zhidomirov G.M. Zhurn. Fiz. Khim. 58 (1984) 9
46. London F. Z. Phys. 60 (1930) 245
47. Linder B. J. Chem. Phys. 33 (1960) 668
48. Linder B. J. Chem. Phys. 35 (1961) 371
49. Linder B. J. Chem. Phys. 37 (1962) 963
50. Linder B. Adv. Chem. Phys. 12 (1967) 225
51. Costa Cabral B.J., Rinaldi D., and Rivail J.-L. C. R. Acad. Sci. Paris 298 II (1984) 675
52. Rivail J.-L., and Cartier A. Mol. Phys. 36 (1978) 1085
53. Rivail J.-L., and Cartier A. Chem. Phys. Lett. 61 (1979) 469
54. Bötcher C.J.F. Theory of Electric Polarization (1952), Elsevier, Amsterdam
55. Harned H.S., and Owen B. The Physical Chemistry of Electrolite Solutions (1973), Reinhold, New York
56. Aguilar M.A., and Oliveras del Valle F.J. Chem. Phys. 138 (1989) 327
57. Uglig H.H. J. Phys. Chem. 41 (1937) 1215
58. Sinanoglu O. J. Chem. Phys. 75 (1981) 463
59. Tanaka H.J. J. Chem. Phys. 86 (1987) 1512
60. Pierotti R.A. Chem. Rev. 76 (1976) 717
61. Reiss H. Adv. Chem. Phys. 9 (1965) 1
62. Cramer C.J., and Truhlar D.G. J. Am. Chem. Soc. 113 (1991) 8305
63. Tucker S.C., and Truhlar D. Chem. Phys. Lett. 157 (1989) 164
64. Cramer C.J., and Truhlar D.G. Science 256 (1992) 212
65. Still W.C., Tempczyk A., Hawley R.C., and Hendrickson T. J. Am. Chem. Soc. 112 (1990) 6127
66. Cramer C.J., and Truhlar D.G. J. Comp.-Aid. Mol. Design. 6 (1992) 629
67. Cramer C.J., and Truhlar D.G. In: Politzer P., and Muray J.S. (Eds). Quantitative Treatments of Solute/Solvent Interactions (1994), Elsevier
68. Liotard D.A., Hawkins G.D., Lynch G.C., Cramer C.J., and Truhlar C.J. J. Comput. Chem. 16 (1995) 442
69. Hawkins G.D., Cramer C.J., and Truhlar D.G. Chem. Phys. Lett. 246 (1995) 122
70. Cramer C.J., and Truhlar D.G. J. Comput. Chem. 13 (1992) 1089
71. Dewar M.J.S., Zoebisch E.G., Healy E.E., and Stewart J.J.P. J. Am. Chem. Soc. 107 (1985) 3902
72. Dewar M.J.S., and Zoebisch E.G. J. Mol. Struct. (Theochem) 180 (1988) 1
73. Dewar M.J.S., and Yate-Ching Y. Inorg. Chem. 29 (1990) 3881
74. Stewart J.J.P. J. Comput. Chem. 10 (1989) 221
75. Giesen D.J., Storer J.W., Cramer C.J., and Truhlar D.G. J. Am. Chem. Soc. 117 (1995) 1057
76. Giesen D.J., Cramer C.J., and Truhlar D.G. J. Phys. Chem. 99 (1995) 7137
77. Barrows S., Dulles F.J., Cramer C.J., Truhlar D.G., and French A.D. Carbohydr. Res. 256 (1995) 219
78. Chambers C.C., Hawkins G.D., Cramer C.J., and Truhlar D.G. J. Phys. Chem. 100 (1996) 16385
79. Hawkins G.D., Cramer C.J., and Truhlar D.G. J. Phys. Chem. 100 (1996) 19824
80. Sponer J., Leszczynski J., and Hobza P. J. Biomol. Struct. and Dynamics 14 (1996) 117
81. Car R., and Parrinello M. Phys. Rev. Lett. 55 (1985) 2471
82. Tuckerman M., Laasonen K., Sprik M., and Parrinello M. J. Phys. Chem. 99 (1995) 5749
83. Sprik M., Hutter J., and Parrinello M. J. Chem. Phys. 105 (1996) 1142
84. Laasonen K., Sprik M., and Parrinello M. J. Chem. Phys. 99 (1993) 9080
85. Laasonen K.E., and Klein M.L. J. Phys. Chem. 101 (1997) 98
86. Markham L.K., and Hudson B.S. J. Phys. Chem. 100 (1996) 2731
87. Jasien P.G., and Stevens W.J. J. Chem. Phys. 84 (1986) 3271
88. Nguyen K.A., Gordon M.S., and Truhlar D.G. J. Am. Chem. Soc. 113 (1991) 1596
89. Dixon D.A., Dobbs K.D., and Valentini J.J. J. Phys. Chem. 98 (1994) 13435
90. Demetropoulos I.N., Gerothanansis I.P., Vakka C., and Kakavas C. J. Chem. Soc. Faraday Trans. 92 (1996) 921
91. Zhang Q., Bell R., and Truong T.N. J. Phys. Chem. 99 (1995) 592
92. Pranata J., and Davis G.D. J. Phys. Chem. 99 (1995) 14340
93. Doig A.J., and Williams D.H. J. Am. Chem. Soc. 114 (1992) 338
94. Wong M.W., Wiberg K.B., and Frisch M.J. J. Am. Chem. Soc. 114 (1992) 1645
95. Chen X.G., Schweitzer-Stenner R., Krimm S., Mirkin N.G., and Asher S.A. J. Am. Chem. Soc. 116 (1994) 11141
96. Wang X.C., Nichols J., Feyereisen M., Gutovski M., Boatz J., Haymet A.D.J., and Simons J. J. Phys. Chem. 95 (1991) 10419
97. Craw J.S., Guest J.M., Cooper M.D., Burton N.A., and Hillier I.H. J. Phys. Chem. 100 (1996) 6304
98. Scheiner S., and Wang L. J. Am. Chem. Soc. 115 (1993) 1958
99. Scheiner S., and Duang X. Biophys. J. 60 (1991) 874
100. Nagaoka M., Okuno Y., and Yamabe T. J. Am. Chem. Soc. 113 (1991) 769
101. Nagaoka M., Okuno Y., and Yamabe T. J. Phys. Chem. 98 (1994) 12506
102. Bell R., and Truong T.N. J. Chem. Phys. 101 (1994) 10442
103. Bell R.L., Taveras D.L., Truong T.N., and Simons J. Int. J. Quant. Chem. 63 (1997) 861
104. Krug J.P., Popelier P.L.A., and Bader R.F.W. J. Phys. Chem. 96 (1992) 7604
105. Antonczak S., Ruiz-Lopez M.F., and Rivail J.-L. J. Am. Chem. Soc. 116 (1994) 3912
106. Rinaldi D., Ruiz-Lopez M.F., and Rivail J.-L. J. Chem. Phys. 78 (1983) 834
107. Rinaldi D., Rivail J.-L., and Rguini N. J. Comp. Chem. 13 (1992) 675
108. Kwiatkowski J.S., Zelinski T.J., and Rein R. Advan. Quantum. Chem. 18 (1986) 85
109. Beak P., Covington J.B., and Simth S.G. J. Am. Chem. Soc. 98 (1976) 186
110. Beak P. Acc. Chem. Res. 10 (1977) 186
111. Suradi S., El Saiad N., Pilcher G., and Skinner H.A. J. Chem. Thermodyn. 14 (1982) 45
112. Beak P., Covington J.B., Smith S.G., White J.M., and Zeiger J.M. J. Org. Chem. 45 (1980) 1354
113. Beak P., Fry F.S., Lee J., and Steele F. J. Am. Chem. Soc. 98 (1976) 171
114. Schlegel H.B., Gund P., and Fluder E.M. J. Am. Chem. Soc. 104 (1982) 5347
115. Scanlan M.J., and Hillier I.H. Chem. Phys. Lett 107 (1984) 330
116. Field M.J., and Hillier I.H. J. Chem. Soc. Perkin Trans. II (1987) 617
117. Adamowicz L. Chem. Phys. Lett. 161 (1989) 73
118. Moreno M., and Miller W.H. Chem. Phys. Lett. 171 (1990) 475
119. Slanina Z., Les A., and Adamowicz L. J. Mol. Struct (THEOCHEM) 257 (1992) 491
120. Les A., Adamowicz L., Nowak M.J., and Lapinski L. J. Mol. Struct (THEOCHEM) 277 (1992) 313
121. Parchment O.G., Burton N.A., and Hillier I.H. Chem. Phys. Lett. 203 (1993) 46
122. Mitchel A.G., Trudel Y., and Dion C. Int. J. Quantum. Chem. 46 (1993) 183
123. Del Bene J.E. J. Phys. Chem. 98 (1994) 5902
124. Held A., and Pratt D.W. J. Am. Chem. Soc. 115 (1993) 9708
125. Buyl F., Smets J., Maes G., and Adamowicz L. J. Phys. Chem. 99 (1995) 14967
126. Nowak M.J., Szczepaniak K., Barski A., and Shugar D. Z. Naturforsch 33C (1978) 876
127. Aue D.H., Betowski L.D., Davidson W.R., Bowers M.T., Beak P., and Lee J. J. Am. Chem. Soc. 102 (1980) 1174
128. Nilmos M.R., Kelley D.F., and Bernstein E.R. J. Phys. Chem. 93 (1989) 643
129. Frank J., and Katrizky A.R. J. Chem. Soc. Perkin. Trans. II (1976) 1428
130. Kuzuya M., Noguchi A., and Okuda T. J. Chem. Soc. Perkin. Trans. II (1985) 1423
131. Kwiatkowski J.S., Bartlett R.J., and Person W.B. J. Am. Chem. Soc. 110 (1988) 2353
132. Karelson M.M., Katrizky A.R., Szafran M., and Zerner M.C. J. Org. Chem. 54 (1989) 6030
133. Barone V., and Adamo C. J. Comp. Chem. 15 (1994) 395
134. Les A., and Adamowicz L. J. Phys. Chem. 94 (1990) 7021
135. Buyl F., Smets J., Maes G., and Adamowicz L. J. Phys. Chem. 99 (1995) 14967
136. Destexhe A., Smets J., Adamowicz L., and Maes G. J. Phys. Chem. 98 (1994) 1506
137. Smets J., Adamowicz L., and Maes G. J. Phys. Chem. 99 (1995) 6387
138. Luque F.J., Lopez-Bes J.M., Cemeli J., Aroztegui M., and Orozco M. Theor. Chem. Acc. 96 (1997) 105
139. Orozco M., Cubero E., Barril X., Colominas C., Luque F., and Luque J. In: Leszczynski J. (Ed). Computational Molecular Biology (1999), Elsevier Science
140. Gorb L., and Leszczynski J. J. Am. Chem. Soc. 120 (1998) 5024
141. Broo A., and Holmen A. J. Phys. Chem. 101 (1997) 3589
142. Gorb L., and Leszczynski J. Int. J. Quant. Chem. 65 (1997) 759
143. Gorb L., and Leszczynski J. Int. J. Quant. Chem. 70 (1998) 855
144. L. Gorb, Y. Podolyan and J. Leszczynski, J. Mol. Structure (THEOCHEM) (in press).
145. Stepanian S.G., Sheina G.G., Radchenko E.D., and Blagoi Yu.P. J. Mol. Structure 270 (1992) 459
146. Sponer J., Hobza P., and Leszczynski J. In: Leszczynski J. (Ed). Computational Chemistry: Reviews of Current Trends vol. 1 (1996), World Scientific, Singapore
147. Kwiatkowski J.S., Lesing B., Palmer M.H., and Saenger W. Z. Naturforsch 37c (1982) 937
148. Riggs N.V. Chem. Phys. Lett. 177 (1991) 447
149. Leszczynski J. Int. J. Quantum. Chem. Quantum. Biol. Symp. 19 (1992) 43
150. Govorun D.N., Danchuk V.D., Mishchuk Ya.R., Kondratyuk I.V., Radomsky N.F., and Zheltovsky N.V. J. Mol. Struct. 267 (1992) 99
151. Trollope K.I., Gould I.R., and Hillier I.H. Chem. Phys. Lett. 209 (1993) 113
152. Sponer J., and Hobza P. J. Am. Chem. Soc. 116 (1994) 709
153. Smets J., Smith D.M.A., Elkadi Y., and Adamowicz L. J. Phys. Chem. 101 (1997) 9152
154. Chahinian M., Seba H.B., and Ancian B. Chem. Phys. Lett. 285 (1998) 337
155. O. Shishkin, L. Gorb and J. Leszczynski, (manuscript in preparation).
156. Watson J.D., and Crick F.H. Nature 171 (1953) 737
157. Löwdin P.O. Adv. Quant. Chem. 2 (1965) 213
158. Colominas C., Luque F.J., and Orozco M. J. Am. Chem. Soc. 118 (1996) 6811
159. Cramer C.J., and Truhlar D.G. Chem. Phys. Lett. 198 (1992) 74
160. Gold I.R., Green D.V.S., Young P., and Hiller I.H. J. Org. Chem. 57 (1992) 4434
161. J. Gu and J. Leszczynski, J. Phys. Chem. (in press).
162. Szczepaniak K., Szczepaniak M., Szajda W., Person W.B., and Leszczynski J. J. Can. Chem. 69 (1991) 1718
163. Szczepaniak K., and Szczepaniak M. J. Mol. Struct. 156 (1987) 29
164. (engl.edn.). Radchenko E.D., Plohotnichenko A.M., Sheina G.G., and Blagoi Yu.P. Biophysics 28 (1983) 559
165. Stepanian S.G., Sheina G.G., Radchenko E.D., and Blagoi Yu.P. J. Mol. Struct. 131 (1985) 333
166. Graindourze M., Smets Y., Zeegers-Huyskens Th., and Maes G.J. J. Mol. Struct. 222 (1990) 345
167. LeBreton P.R., Yang X., Urano S., Fetzer S., Min Y., Leonard N.J., and Kumar S. J. Am. Chem. Soc. 119 (1990) 2138
168. Nowak M.J., Lapinski L., Kwiatkowski J.S., and Leszczynski J. In: Leszczynski J. (Ed). Current Trend in Computational Chemistry. Review of Current Trends Vol 2 (1997), World Scientific, Singapore
169. Shugar D., and Psoda A. In: Saender W. (Ed). Landolt-Börnstein-New series: Biophysics of Nucleic Acids Vol. VII/1d (1990), Springer, Berlin
170. L. Gorb and J. Leszczynski, (manuscript in preparation).
171. L. Gorb, J. Sponer and J. Leszczynski, (manuscript in preparation).
172. Zhanpeisov N.U., and Leszczynski J. J. Phys. Chem. B 102 (1998) 6167
173. Zhanpeisov N.U., and Leszczynski J. Int. J. Quant. Chem 69 (1998) 37
174. Zhanpeisov N.U., and Leszczynski J. J. Phys. Chem. B 102 (1998) 9109
175. Ohta Y., Nishimoto K., Tanaka H., Baba Y., and Kagemoto A. J. Chem. Soc. Jpn 62 (1989) 2441
176. Schneider B., and Berman H. Biophys. J. 69 (1995) 2661
177. Schneider B., Cohen D., and Berman H. Biopolymers 32 (1992) 725
178. Zhanpeisov N.U., Sponer J., and Leszczynski J. J. Phys. Chem. A 102 (1998) 10374