Modeling of tautomerism of pyridine-2(1H )-thione from vapor to solution †

Abstract

Using the well-characterized pyridine-2(1H )-thione (1)/pyridine-2-thiol (2) system as a model of thiated nucleobases in DNA or RNA, ab initio (HF, MP2 and MP4) and density functional theory (B3LYP) methods using large basis sets were applied to reproduce structures and tautomerization free energies. Hydrogen bonds of the dimerized thione 1 in the solid state were well-reproduced by the B3LYP method. Electronic correlation similarly stabilized both 1 and 2 protomers, and so the gas-phase free energy of the 1/2 equilibrium was equally overestimated by 4 kJ mol^–1 in favour of the 2 by HF, MP2(full) or MP4(SDTQ)/6-311+G(2d,p) ab initio methods. Otherwise, the B3LYP method systematically overestimated the relative stability of 1, but using the 6-311+G(2d,p) basis set, the error was comparable to ab initio methods. Dunning’s D95+(2d,p) and Aug-cc-pVDZ basis sets gave worse protomeric free energies than Pople’s basis sets using the B3LYP method. The nonspecific solvent effect on 1/2 protomerization was accurately predicted (within 2 kJ mol^–1) by the SCIPCM self-consistent reaction field (SCRF ) methodology at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d) level of theory. The Onsager SCRF method or HF theoretical treatment of the solvent effects gave less good results.

References

1. J. B. Hobbs, Comprehensive Medicinal Chemistry, ed. C. Hansch, Pergamon Press, Oxford, 1990, vol. 2, ch. 7.3.
2. C. Alhambra, F. Luque, J. Estelrich and M. Orozco, J. Org. Chem., 1995, 60, 969.
3. M. J. Stewart, J. Leszczynsky, Y. V. Rubin and Y. P. Blagoi, J. Phys. Chem., 1997, 101, 4753.
4. M. J. Nowak, L. Lapinski, J. S. Kwiatkowski and J. Leszczynsky, Computational Chemistry: Reviews of Current Trends, ed. J. Leszczynsky, World ScientiWc Pub. Co. Pte. Ltd., Singapore, 1997, vol. 2, ch. 4, and references cited therein.
5. M. J. Nowak, L. Lapinski, H. Rostkowska, A. Les and L. Adamowcz, J. Phys. Chem., 1990, 94, 7406 and references cited therein.
6. P. Beak, J. B. Covington and J. M. White, J. Org. Chem., 1980, 45, 1347.
7. J. Powling and H. J. Bernstein, J. Am. Chem. Soc., 1951, 73, 4353.
8. U. Ohms, H. Guth, A. Kutoglu and C. Scheringer, Acta Crystallogr., Sect. B, 1982, 38, 831.
9. J. S. Kwiatkowski and J. Leszczynsky, J. Mol. Struct., 1996, 376, 325.
10. V. Martinez-Merino and M. J. Gil, J. Chem. Soc., Perkin Trans. 2, 1999, 33.
11. J. B. Foresman and Æ. Frisch, Exploring Chemistry with Electronic Structure Methods, 2nd edn., Gaussian Inc., Pittsburgh, PA, 1996.
12. G=H–TS=(E+RT)–TS=[(E₀+E_vib+E_rot+E_transl)+ RT]–TS where E₀=E_elec+ ZPE.
13. A. D. Becke, J. Chem. Phys., 1993, 98, 5648.
14. J. P. Perdew, Phys. Rev. B, 1986, 33, 8822.
15. J. P. Perdew and Y. Wang, Phys. Rev. B, 1992, 45, 13244.
16. T. H. Dunning Jr. and P. J. Hay, Modern Theoretical Chemistry, ed. H. F. Schaefer, III, Plenum, New York, 1976, pp. 1–28.
17. D. E. Woon and T. H. Dunning Jr., J. Chem. Phys., 1993, 98, 1358.
18. R. A. Kendall, T. H. Dunning Jr. and R. J. Harrison, J. Chem. Phys., 1992, 96, 6796.
19. (a) C. Møller and M. S. Plesset, Phys. Rev., 1934, 46, 618; (b) M. Head-Gordon, J. A. Pople and M. J. Frisch, Chem. Phys. Lett., 1988, 153, 503; (c) M. J. Frisch, M. Head-Gordon and J. A. Pople, Chem. Phys. Lett., 1990, 166, 275; (d) M. J. Frisch, M. Head-Gordon and J. A. Pople, Chem. Phys. Lett., 1990, 166, 281.
20. A. Les and L. Adamowicz, J. Am. Chem. Soc., 1990, 112, 1504.
21. C. Colominas, F. J. Luque and M. Orozco, J. Am. Chem. Soc., 1996, 118, 6811.
22. J. Rak, P. Skurski, M. Gutowski, L. Jozwiak and J. Blazejowski, J. Phys. Chem., 1997, 101, 283.
23. M. J. Frisch, G. W. Trucks, H. B. Schlegel, P. M. W. Gill, B. G. Johnson, M. A. Robb, J. R. Cheeseman, T. A. Keith, G. A. Petersson, J. A. Montgomery, K. Raghavachari, M. A. Al-Latham, V. G. Zakrzewski, J. V. Ortiz, J. B. Foresman, J. Cioslowski, B. B. Stefanov, A. Nanayakara, M. Challacombe, C. Y. Peng, P. Y. Ayala, W. Chen, M. W. Wong, J. L. Andrés, E. S. Replogle, R. Gomperts, R. L. Martin, D. J. Fox, J. S. Binkley, D. J. Defrees, J. Baker, J. J. P. Stewart, M. Head-Gordon, C. González and J. A. Pople, GAUSSIAN94, Revision C.3, Gaussian, Inc., Pittsburgh, PA, 1995.
24. W. J. Hehre, L. Radom, P. v. R. Schleyer and J. A. Pople, Ab initio Molecular Orbital Theory, Wiley, New York, 1986.
25. (a) M. J. Frisch, J. S. Binkley and J. A. Pople, J. Chem. Phys., 1984, 80, 3265; (b) A. D. McLean and G. S. Chandler, J. Chem. Phys., 1980, 72, 5639; (c) R. Krishnan, J. S. Binkley, R. Seeger and J. A. Pople, J. Chem. Phys., 1980, 72, 650.
26. J. Urban, P. R. Schreiner, G. Vacek, P. v. R. Schleyer, J. Q. Huang and J. Leszczynsky, Chem. Phys. Lett., 1997, 264, 441.
27. (a) R. Krishnan and J. A. Pople, Int. J. Quantum Chem., 1978, 14, 91; (b) R. Krishnan, M. J. Frisch and J. A. Pople, J. Chem. Phys., 1980, 72, 4244.
28. M. W. Wong, M. J. Frisch and K. B. Wiberg, J. Am. Chem. Soc., 1991, 113, 4776.
29. M. W. Wong, K. B. Wiberg and M. J. Frisch, J. Am. Chem. Soc., 1992, 114, 523.
30. M. W. Wong, K. B. Wiberg and M. J. Frisch, J. Am. Chem. Soc., 1992, 114, 1645.
31. (a) S. Miertus, E. Scrocco and J. Tomasi, Chem. Phys., 1981, 55, 117; (b) J. Tomasi, R. Bonaccorsi, R. Cammi and F. O. Valle, J. Mol. Struct., 1991, 234, 401; (c) J. Tomasi and M. Persico, Chem. Rev., 1994, 94, 2027.
32. CRC Handbook of Chemistry and Physics, ed. D. R. Lide and H. P. R. Frederikse, 75th edn., CRC Press, Boca Raton, FL, 1994.