Skip to main content

Combined Matrix-Isolation FT-IR and AB Initio 6-31 + + G** Studies on the Tautomerism and H-bonding Properties of Nucleic Acid Bases and Simpler Model Molecules

  • Chapter

Part of the book series: NATO ASI Series ((ASIC,volume 483))

Abstract

A step-by-step experimental and ab initio 6–31 + + G** research approach has been developed for interpretation of FT-IR spectra of H-bonded complexes of different tautomers of nucleic acid bases. The first step of this procedure involves a detailed study of a large number of relatively simple compounds, each modeling one or more H-bonding sites of cytosine, adenine and guanine. The application of this method is illustrated with the results obtained for the tautomerism of 1-CH3-adenine and 1-CH3-cytosine, and for some H-bonded complexes of imidazole and 4-NH2-pyridine with water. Comparison between the experimental and ab initio calculated parameters for the H-bonded complexes allows some correlations to be established. Apart from practical application of the correlation curves, e.g. interpretation of the complicated FT-IR spectra of H-bonded nucleic acid bases, more fundamental information can also be obtained from die correlations.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer-Verlag, New York

    Google Scholar 

  2. Jeffrey, G. A. and Saenger, W. (1991) Hydrogen Bonding in Biological Structure, Springer-Verlag, Berlin

    Google Scholar 

  3. LÖdwdin, P.O. (1965) Quantum genetics and the aperiodic solid. Some aspects on the biological problems of heredity, mutations, aging, and tumors in view of the quantum theory of the DNA molecule, Adv. Quantum Chem. 2, 213–360

    Article  Google Scholar 

  4. Crick, F.H.C. (1966), Codon - anticodong pairing: the wobble hypothesis, J.Mol.Biol. 19, 548–555

    Article  Google Scholar 

  5. Morgan, A.R. (1993) Base mismatches and mutagenesis: how important is tautomerism ? Trends Biochem. Science 18, 160–163

    Article  CAS  Google Scholar 

  6. Fazakerley, G.V., Gdaniec, Z. and Sowers, L.C. (1993) Base-pair induced shifts in the tautomeric equilibrium of a modified DNA base, J.Mol.Biol. 230, 6–10

    Article  CAS  Google Scholar 

  7. Maes, G. (1991) in P.L. Huyskens, W.A.P. Luck and Th. Zeegers-Huyskens (eds.) Intermolecular Forces. An Introduction to Modern Methods and Results, Springer-Verlag, Berlin, pp. 195–216

    Google Scholar 

  8. Graindourze, M., Grootaers, T., Smets, J., Zeegers-Huyskens, Th. and Maes, G. (1991) FT-IR spectroscopic study of uracil derivatives and their hydrogen-bonded complexes with proton donors. III. Hydrogen bonding of uracils with H20 in Ar matrices, J.Mol.Struct. 243, 37–60

    Article  CAS  Google Scholar 

  9. Maes, G., Graindourze, M. and Smets, J. (1991) IV. Self-association of uracils in Ar matrices: differentiation between open and closed dimers, J.Mol.Struct. 248, 89–110

    Article  Google Scholar 

  10. Smets, J., Graindourze, M., Zeegers-Huyskens, Th. and Maes, G. (1994) V.Complexes of uracils with hydrogen chloride in Ar matrices, J.Mol.Struct. 318, 37–53

    Article  Google Scholar 

  11. Szczesniak, M., Szczepaniak, K., Kwiatkowski, J.S., KuBUlat, K. and Person, W.B. (1988)Matrix-isolation infrared studies of nucleic acid constituents. 5. Experimental matrix-isolation and theoretical ab initio SCF MO study of the infrared spectra of cytosine monomers, J.Am.Chem.Soc. 110, 8319–8330

    Article  CAS  Google Scholar 

  12. Nowak, M.J., Rostkowska, H., Lapinski, L., Kwiatkowski, J.S. and Leszczynski, J. (1994)Tautomerism N(9)H⇔N(7)H of purine, adenine, and 2-chloro-adenine: combined experimental IR matrix isolation and ab initio quantum mechanical studies, J.Phys.Chem. 98, 2813–2816

    Article  CAS  Google Scholar 

  13. Szczepaniak, K. and Szczesniak, M. (1987) Matrix isolation IR studies of nucleic acid constituents. Part 4*. Guanine and 9-methylguanine monomers and their keto-enol tautomerism, J.Mol.Struct. 156, 29–42

    Article  CAS  Google Scholar 

  14. Les, A. and Adamowicz, L. (1990) Theoretical ab initio study of the protomeric tautomerism of 2-hydroxypyrimidine, 4-hydroxypyrimidine, and their derivatives, J.Phys.Chem. 94, 7021–7032

    Article  CAS  Google Scholar 

  15. Nowak, M.J., Rostkowska, H., Lapinski, L., Kwiatkowski, J.S. and Leszczynski, J. (1994) Experimental matrix isolation and theoretical ab initio HF/6–31G(d,p) studies of infrared spectra of purine, adenine and 2-chloroadenine, Spectrochim.Acta A 50, 1081–1094

    Article  Google Scholar 

  16. Gould, I.R., Vincent, M.A. and Hillier, I.H. (1993) A theoretical study of the infrared spectra of guanine tautomers, Spectrochim.Acta A. 49, 1727–1734

    Article  Google Scholar 

  17. Maes, G. (1981) An infrared study of pyridine-pyridine and pyridine-H2O interactions by the matrix isolation method, Bull.Soc.Chim. Beig. 90, 1093–1107

    Article  CAS  Google Scholar 

  18. Destexhe, A., Smets, J., Adamowicz, L. and Maes, G. (1994) Matrix-isolation FT-IR studies and ab initio calculations of hydrogen-bonded complexes of molecules modeling cytosine or isocytosine tautomers. 1. Pyridine and pyrimidine complexes with H20 in Ar matrices, J.Phys.Chem. 98, 1506–1514

    Article  CAS  Google Scholar 

  19. Latajka, Z., Ratajczak, H. and Person, W.B. (1989) On the reliability of SCF ab initio calculations of vibrational frequencies and intensities of hydrogen-bonded systems, J.Mol.Struct. 194, 89–105

    Article  CAS  Google Scholar 

  20. Kwiatkowski J.S., Zielinski, T.J. and Rein R. (1986) Quantum mechanical prediction of tautomeric equilibria, Adv. Quantum Chem. 18, 85–130

    Article  CAS  Google Scholar 

  21. GAUSSIAN 92 (1992); Frisch, C.PM.J., Trucks, G.W., Head-Gordon, M., Gill, P.M.W., Wong, M.W., Foresman, J.B., Johnson, B.G., Schlegel, H.B., Robb, M.A., Replogie, E.S., Gomperts, R., Andres, J.L. Raghavachari, K., Binkley, J.S., Gonzales, C., Martin, R.L., Fox, D.J., Defrees, D.J., Baker, J., Stewart, J.J.P. and Pople, J.A., Revision C, Gaussian Inc., Pittsburgh PA

    Google Scholar 

  22. Smets, J., Adamowicz, L. and Maes, G. (1995) Matrix-isolation FT-IR studies and ab initio calculations of H-bonded complexes of molecules modeling cytosine or isocytosine tautomers. 5. l-CH3-Cytosine complexes with water in Ar matrices, J.Phys.Chem. (in press)

    Google Scholar 

  23. van Duijneveldt, F.B., van Duijneveldt-van de Rijdt, J.G.C.M. and van Lenthe, J.H. (1994) State of the art in counterpoise theory, Chem.Rev. 94, 1873–1885

    Article  Google Scholar 

  24. Pullman, B., Berthod, H. and Dreyfus, M. (1969) Amine-imine tautomerism in adenines, Theoret.chim. Acta (Berlin) 15, 265–268

    Article  CAS  Google Scholar 

  25. Kanaskova, Y.D., Sukhorukov, B.I., Pentin, Y.A. and Komarovskaya, G.V. (1970) Infrared spectrum of solid 1-methyladenine, Bull.Acad.Sci.USSR Div.Chem.Sci., 1637-1641

    Google Scholar 

  26. Dreyfus, M., Dodin, G., Bensaude, O. and Dubois, J.E. (1977) Tautomerism of purines. 2.Amino-imino tautomerism in 1-alkyladenines, J.Am.Chem.Soc. 99. 7027–7037

    Article  CAS  Google Scholar 

  27. Pivovarov, V.B., Stepanian, S.G., Reva. ID., Sheina. G.G. and Blagoi, Yu.P. (1995) Infrared spectra and the structure of 1 -methyladenine in an argon matrix and solutions, Spectrochim.Acta A 51, 843–853

    Article  Google Scholar 

  28. Smets, J., Adamowicz, L. and Maes, G. (1995) Matrix-isolation FT-IR studies and ab initio calculations of molecules modeling cytosine or isocytosine tautomers. 2. 4-aminopyridine and 4-aminopyrimidine complexes with HzO in Ar matrices, J. Phys. Chem. 99, 6387–6400

    Article  CAS  Google Scholar 

  29. Shugar, D. and Szczepaniak, K. (1981) Tautomerism of pyrimidines and purines in the gas phase and in low-temperature matrices, and some biological implications. Int.J.Quantum Chem. XX, 573–585

    Article  CAS  Google Scholar 

  30. Schoone, K.(1995) Matrix-isolation FT-IR and ab initio 6–31 + + G** research of the tautomeric and H-bonding properties of adenines and some simpler model molecules, M.Sc. Thesis, Univ. of Leuven

    Google Scholar 

  31. Field, M.J. and Hillier, I.H. (1987) Non-dissociative proton transfer in 2-pyridone-2-hydroxypyridine. An ah initio molecular orbital study, J. Chem. Soc. Perkin Trans. II 2, 617–622

    Article  Google Scholar 

  32. Moreno, M. and Miller, W.H. (1990) On the tautomerization reaction 2-pyridone*±2-hydroxypyridine: an ab initio study, Chem.Phys.Lett. 171, 475–479

    Article  CAS  Google Scholar 

  33. Fabian, W.M.F. (1990) AMI calculations on the tautomerism of free and hydrated hydroxypyridines: barriers to proton transfer in 2-hydroxypyridine-pyrid-2(lH)-one and effect of solvation and self-association, J. Phys. Org. Chem. 3, 332–338

    Article  CAS  Google Scholar 

  34. Les, A., Adamowicz, L., Nowak, M.J. and Lapinski, L. (1994) Concerted biprotonic tautomerism of 2-hydroxypyridine, J.Mol.Struct. (Theochem.) 312, 157–166

    Article  Google Scholar 

  35. Kwiatkowski, J.S. and Leszczynski, J. Temperature-dependent thermodynamic contributions to the relative tautomeric stabilities of nucleic acid bases. Chem.Phys.Lett. 204, 430–434

    Google Scholar 

  36. Smets, J. (1993) Combined matrix-isolation FT-IR and ab initio 6–31 + + G** study of the tautomeric and H-bonding properties of molecules modeling cytosines and isocytosines, Ph.D.Thesis, Univ. of Leuven

    Google Scholar 

  37. Katritzky, R.K. and Karelson, M. (1991) AMI calculations of reaction field effects on tautomeric equilibria of NA pyrimidine and purine bases and their 1-methyl analogues, J.Am.Chem.Soc. 113, 1561–1566

    Article  CAS  Google Scholar 

  38. Szczesniak, M., Leszczynski, J. and Person, W.B. (1992) Identification of the imino-oxo form of 1- methylcytosine, J.Am.Chem.Soc. 114, 2731–2733

    Article  CAS  Google Scholar 

  39. Les, A. and Kukawska-Tarnawska, B. (1986) Tautomerism of biologically important pyrimidines and purines. Part I. Theoretical predictions, J.Mol.Struct. (Theochem.) 148, 45–60

    Article  Google Scholar 

  40. Person, W.B., Szczepaniak, K., Szczesniak, M., Kwiatkowski, J.S., Hernandez, L. and Czerminski, R. (1989) Tautomerism of nucleic acid bases and the effect of molecular interactions on tautomeric equilibria, J.Mol.Struct. 194, 239–258

    Article  CAS  Google Scholar 

  41. Szczesniak, M., Nowak, M.J. and Szczepaniak, K. (1984) Infrared matrix isolation studies on tautomerism of cytosine and isocytosine methyl-derivatives, J.Mol.Struct. 115, 221–224

    Article  CAS  Google Scholar 

  42. Radchenko, Ye.D., Plokhotnichenko, A.M., Sheina, G.G. and Blagoi, Yu.P. (1983) Infrared spectra of cytosine and its derivatives in an argon matrix at low temperature, Biophysics 28, 592–598

    Google Scholar 

  43. Nagy, P.I., Durant, G.J. and Smith, D.A. (1993) Theoretical studies on hydration of pyrrole, imidazole and protonated imidazole in the gas phase and aqueous solution, J.Am. Chem. Soc. 115, 2912–2922

    Article  CAS  Google Scholar 

  44. Van Bael, M.K., Schoone, K., Houben, L., Smets, J., Mc Carthy, W., Adamowicz, L., Nowak, M.J. and Maes, G., Matrix-isolation FT-IR studies and ab initio calculations of hydrogen-bonded complexes of molecules modeling adenine and guanine tautomers. 1. H-bonding of imidazoles with H2O in Ar matrices, J.Phys. Chem. (submitted)

    Google Scholar 

  45. Engdahl, A. and Nelander, B. (1989) Water in krypton matrices, J.Mol.Struct. 193, 101–109

    Article  CAS  Google Scholar 

  46. Lias, S.G., Liebman, J.F. and Levin, R.D. Evaluated gas phase basicities and proton affinities of molecules; heats of formation of protonated molecules, J.Phys. Chem. Ref. Data 13, 695–808

    Google Scholar 

  47. Zeegers-Huyskens, Th. (1986) Enthalpies of hydrogen bonds and proton affinities, J.Mol.Struct. (Theochem.) 135, 93–103

    Article  Google Scholar 

  48. Schidberg, D. and Luck, W.A.P. (1979) IR studies of water in complexes, Faraday Trans. I 1, 762–773

    Article  Google Scholar 

  49. Smets, J., McCarthy, W., Maes, G. and Adamowicz, L., Correlations between ab initio and experimental data for isolated 1:1 H-bonded complexes of pyridine and imidazole derivatives with water, J.Am. Chem. Soc. (submitted)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1996 Kluwer Academic Publishers

About this chapter

Cite this chapter

Maes, G.H., Smets, J., Adamowicz, L. (1996). Combined Matrix-Isolation FT-IR and AB Initio 6-31 + + G** Studies on the Tautomerism and H-bonding Properties of Nucleic Acid Bases and Simpler Model Molecules. In: Fausto, R. (eds) Low Temperature Molecular Spectroscopy. NATO ASI Series, vol 483. Springer, Dordrecht. https://doi.org/10.1007/978-94-009-0281-7_5

Download citation

  • DOI: https://doi.org/10.1007/978-94-009-0281-7_5

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-010-6611-2

  • Online ISBN: 978-94-009-0281-7

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics