Modeling of the hydration shell of uracil and thymine

International Journal of Molecular Sciences

Volumn 1, Issue 2, 2000, Pages 17-27

  Shishkin, Oleg V ^a,b   Gorb, Leonid ^b   Leszczynski, Jerzy ^b  

^a INSTITUTE FOR SINGLE CRYSTALS   (Ukraine)

^b JACKSON STATE UNIVERSITY   (United States)

Author keywords

Density functional theory; Hydration; Hydrogen bonds; Molecular structure; Thymine; Uracil

Indexed keywords

AMPHOLYTE; METHYL GROUP; NUCLEIC ACID BASE; THYMINE; URACIL; WATER;

ARTICLE; CALCULATION; DENSITY FUNCTIONAL THEORY; GEOMETRY; HYDRATION; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR BIOLOGY; MOLECULAR MODEL; MOLECULE; STANDARDIZATION; STATISTICAL SIGNIFICANCE;

EID: 0002708969     PISSN: 14220067     EISSN: None     Source Type: Journal    
DOI: 10.3390/ijms1020017     Document Type: Article

References (41)

1. Franklin, R. E.; Gosling, R. G. Nature 1953, 171, 740.
2. Wolf, B.; Hanlon, S. Biochemistry 1975, 14, 1661.
3. Brandes, R.; Rupprecht, A.; Kearns, D. R.; J. Biophys. 1989, 56, 683.
4. Kennard, O.; Hunter, W. N. Angew. Chem., Int. Ed. Engl. 1991, 30, 1254.
5. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1988
6. Poltev, V. I.; Teplukhin, A. V.; Malenkov, G. G. Int. J. Quantum. Chem. 1992, 42, 1499.
7. Sagarik, K.; Corongiu, G.; Clementi, E. J. Mol. Struct. (Theochem) 1991, 235, 355.
8. (a) Miskiewicz, K.; Osman, R.; Weinstein, H. J. Am. Chem. Soc. 1993, 115, 1527;
9. (b) Cramer, C. J.; Truhlar, D. G. Chem. Rev. 1999, 99, 2161.
10. Orozco, M.; Cubero, E.; Barril, X.; Colominas, C.; Luque, F. J. In Computational Molecular Biology; Leszczynski, J., Ed.; Elsevier: Amsterdam, 1999, p 119.
11. Gorb, L.; Leszczynski, J. In Computational Molecular Biology; Leszczynski, J., Ed.; Elsevier: Amsterdam, 1999, p.167.
12. Cramer, C. J.; Truhlar, D. G. Chem. Rev. 1999, 99, 2161.
13. Florian, J.; Sponer, J.; Warshel, A. J. Phys. Chem. 1999, 103, 884.
14. Arora, N.; Jayaram, B. J. Phys. Chem. B 1998, 102, 6139.
15. Broo, A.; Holmen, A. J. Phys. Chem. A 1997, 101, 3589.
16. van Mourik, T.; Price, S. L.; Clary, D. C. J. Phys. Chem. A 1999, 103, 1611.
17. Aleman, C. Chem. Phys. Lett. 1999, 302, 461.
18. Gorb, L.; Leszczynski, J. Int. J. Quantum. Chem. 1998, 70, 855.
19. Gorb, L.; Leszczynski, J. J. Am. Chem. Soc. 1998, 112, 5024.
20. Gorb, L.; Leszczynski, J. Int. J. Quantum. Chem. 1997, 68, 759.
21. Gu, J.; Leszczynski, J. J. Phys. Chem. A 1999, 103, 2744.
22. Shishkin, O. V.; Gorb, L.; Leszczynski, J. Submitted for publication.
23. Chahinian, M.; Seba, H. B.; Ancian, B.; Chem. Phys. Lett. 1998, 285, 337.
24. Aamouche, A.; Berthier, G.; Cadioli, B.; Gallinella, E.; Ghomi, M. J. Mol. Struct. 1998, 426, 307.
25. Pullman, A. In Quantum Theory of Chemical Reactions; Daudel, R., Ed.; Amsterdam, 1980; Vol. 11.
26. Becke, A. D. J. Chem. Phys. 1993, 98, 5648.
27. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785.
28. Miehlich, B.; Savin, A.; Stoll, H.; Preuss, H. Chem. Phys. Lett. 1989, 157, 200.
29. Pudzianowski, A. T. J. Phys. Chem. 1996, 100, 4781.
30. Topol, I. A.; Burt, S. K.; Rasin, A. A. Chem. Phys. Lett. 1995, 47, 112.
31. Gorb, L.; Korkin, A.; Leszczynski, J. J. Mol. Struct. (Theochem) 1998, 454, 217.
32. Reed, A. E.; Curtiss, L. A.; Weinhold, F. Chem. Rev. 1988, 88, 899.
33. Bader, R. W. F. Atoms in Molecules: A Quantum Theory; Oxford University Press: Oxford, 1990.
34. Frisch, M. J.; Trucks, G. W.; Head-Gordon, M.; Gill, P. M. W.; Wong, M. W.; Foresman, J. B.; Johnson, B. G.; Schlegel, H. B.; Rob, M. A.; Replogle, E. S.; Comperts, R.; Andres, J. L.; Raghavachari, K.; Binkley, J. S.; Gonzales, C.; Martin, R. L.; Fox, D. J.; Defrecs, D. J.; Baker, J.; Stewart, J. J. P.; Pople, J. A. GAUSSIAN 94; Gaussian Inc.: Pittsburgh, 1994.
35. Cleland, W. W.; Kreevoy, M. M. Science 1994, 264.
36. Addalsteinsson, H.; Maulitz, A. H.; Bruice, T. C. J. Am. Chem. Soc. 1996, 118, 7689.
37. Desiraju, G. R. Acc. Chem. Res. 1991, 24, 290.
38. Wahl, M. C.; Sundaralingham, M. Trends Biochem. Sci. 1997, 97, 22.
39. Auffinger, P.; Louise-May, S.; Westhof, E. Faraday Discuss. 1996, 103, 151.
40. Shishkin, O. V. J. Mol. Struct. 1998, 447, 1.
41. Shishkin, O. V.; Gorb, L.; Hobza, P.; Leszczynski, J. Submitted for publication.