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Photo-Induced Tautomerism of Isocytosine in Aqueous Solution when Irradiated with UVC Light

Yıl 2024, Cilt: 11 Sayı: 1, 321 - 330, 04.02.2024
https://doi.org/10.18596/jotcsa.1325480

Öz

It was found that the irradiation of aqueous solution of isocytosine with UVC light provokes an oxo-hydroxy phototautomerism of the compound with a rate constant of 5.29× 10-3 min-1. It was observed a backward reaction, after removing the UV light source, with a rate constant of 0.12×10-3 min-1. Two mechanisms of the phototautomerism were investigated at the B3LYP/aug-cc-pVDZ theoretical level in water surroundings (PCM). The first one showed a consecutive dissociation and association of a proton through conical intersections S0/S1 whose structures were located at the same theoretical level in the gas phase. It occurs along the 1πσ* excited-state reaction pathway. The more probable mechanism includes an excited-state H-transfer supported by a water molecule as a catalyst. It occurs along the 1ππ* excited-state reaction pathway which we found over the IRC ground-state energy curve. The water molecule drastically reduces the energy barrier in the ground state as well in the excited state.

Destekleyen Kurum

Bulgarian National Science Fund

Proje Numarası

КP-06-N59/7

Kaynakça

  • 1. Callis PR. Electronic States and Luminescence of Nucleic Acid Systems. Annual Review of Physical Chemistry. 1983 Oct;34:329-28. Available from: <URL>..
  • 2. Daniels MH, Hauswirth WW. Fluorescence of the purine and pyrimidine bases of the nucleic acids in neutral aqueous solution at 300 degrees K. Science 1971 Feb;171:675-2. Available from: <URL>.
  • 3. Crespo-Hernandez CE, Cohen B, Hare PM, Kohler B. Ultrafast Excited-State Dynamics in Nucleic Acids. Chemical Reviews. 2004 Apr;104:1977-42. Available from: <URL>..
  • 4. Cohen B., Crespo-Hernandez CE, Kohler B. Strickler–Berg analysis of excited singlet state dynamics in DNA and RNA nucleosides. Faraday Discussions. 2004 May;127:137-10. Available from: <URL>. .
  • 5. Shukla M., Leszczynski J. (Eds.). Radiation Induced Molecular Phenomena in Nucleic Acids, Springer,2008. ISBN: 978-1-4020-8183-5.
  • 6. Rios AC, Tor Y. On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution. Israel Journal of Chemistry. 2013 May;53:469-14. Available from: <URL>. .
  • 7. Hünig I, Plützer C, Seefeld KA, Löwenich D, Nispel M, Kleinermanns K. Photostability of Isolated and Paired Nucleobases: N-H Dissociation of Adenine and Hydrogen Transfer in its Base Pairs Examined by Laser Spectroscopy. ChemPhysChem 2004 Sep;5:1427-4. Available from: <URL>.
  • 8. Egel R, Lankenau A, Mulkidjanian AY (Eds.). Origins of Life: The Primal Self-Organization, Berlin, Springer-Verlag, 2011. ISBN: 978-3-642-21624-4.
  • 9. Dimitrov BH, Bakalska RI, Delchev VB. Phototautomerism of isocytosine in water medium: theoretical and experimental study. Journal of Structural Chemistry (Zhurnal Strukturnoi Khimii). 2019 Jan;60: 937-10. Available from: <URL>.
  • 10. Bakalska RI, Delchev VB. Comparative study of the relaxation mechanisms of the excited states of cytosine and isocytosine. Journal of Molecular Modeling. 2012 Jul;18:5133-13. Available from: <URL>.
  • 11. Merchan M, Gonzalez-Luque R, Climent T, Serrano-Andres L, Rodriguez E, Reguero M, Pelaez D. Unified Model for the Ultrafast Decay of Pyrimidine Nucleobases. The Journal of Physical Chemistry B 2006 Dec; 110:26471-5. Available from: <URL>..
  • 12. Switzer C, Moroney SE, Benner SA. Enzymatic incorporation of a new base pair into DNA and RNA. Journal of the American Chemical Society. 1989 Oct;111:8322-1. Available from: <URL>.
  • 13. Roberts C, Bandaru R, Switzer C. Theoretical and Experimental Study of Isoguanine and Isocytosine:  Base Pairing in an Expanded Genetic System. Journal of the American Chemical Society. 1997 May; 119:4640-9. Available from: <URL>..
  • 14. Edwards PD, Albert JS, Sylvester M, Aharony D, Andisik D, Callaghan O et al.. Application of Fragment-Based Lead Generation to the Discovery of Novel, Cyclic Amidine β-Secretase Inhibitors with Nanomolar Potency, Cellular Activity, and High Ligand Efficiency. Journal of Medicinal Chemistry. 2007 Nov;50:5912-13. Available from: <URL>.
  • 15. Congreve M, Chessari G, Tisi D, Woodhead AJ. Recent developments in fragment-based drug discovery. Journal of Medicinal Chemistry. 2008 May;51:3661-19. Available from: <URL>.
  • 16. Jeffrey GA, Kinoshita Y. The crystal structure of cytosine monohydrate. Acta Crystallografica. 1963; 16:20-8. Available from: https://doi.org/10.1107/S0365110X63000049.
  • 17. McConnell JF, Sharma BD, Marsh RE. Co-crystallization of Two Tautomers: Crystal Structure of Isocytosine. Nature 1964 Jul;203:399-1. Available from: <URL>.
  • 18. Morita H, Nagakura S. The electronic absorption spectra and the electronic structures of cytosine, isocytosine, and their anions and cations. Theoretica Chimica Acta 1968 Jan;11:279-16. Available from: <URL>. .
  • 19. Dračínský M, Jansa P, Ahonen K, Buděšínský M. Tautomerism and the Protonation/Deprotonation of Isocytosine in Liquid- and Solid-States Studied by NMR Spectroscopy and Theoretical Calculations. European Journal of Organic Chemistry. 2011 Jan; 2011:1544-7. Available from: <URL>.
  • 20. Raczyńska ED. On Analogies in Proton-Transfers for Pyrimidine Bases in the Gas Phase (Apolar Environment)—Cytosine Versus Isocytosine. Symmetry 2023 Jan;15:342. Available from: <URL>.
  • 21. Brown DJ, Lyall JM. The Fine Structure of Cytosine. Australian Journal of Chemistry. 1962;15:851-6. Available from: <URL>.
  • 22. Vranken H, Smets J, Maes G. Infrared spectra and tautomerism of isocytosine; an ab initio and matrix isolation study. Spectrochimica Acta A 1994 May;50:875-14. Available from: <URL>.
  • 23. Nowak MJ, Lapinski L, Fulara J. Matrix isolation studies of cytosine: The separation of the infrared spectra of cytosine tautomers. Spectrochim Acta A 1989;45:229-13. Available from: <URL>.
  • 24. Chmura B, Rode M, Sobolewski AL, Lapinski L, Nowak M. A Computational Study on the Mechanism of Intramolecular Oxo−Hydroxy Phototautomerism Driven by Repulsive πσ* State. The Journal of Physical Chemistry A 2008 Dec;112:13655-6. Available from: <URL>.
  • 25. Sobolewski AL, Domcke W. The chemical physics of the photostability of life. Europhysics News 2006 Oct;37:20-3. Available from: <URL>.
  • 26. Perun S, Sobolewski A, Domcke W. Conical intersections in thymine. The Journal of Physical Chemistry A 2006 Nov;110:13238-6. Available from: <URL>.
  • 27. Delchev VB, Sobolewski AL, Domcke W. Comparison of the non-radiative decay mechanisms of 4-pyrimidinone and uracil: an ab initio study. Physical Chemistry Chemical Physics. 2010 Apr;12:5007–8. Available from: <URL>.
  • 28. Delchev VB, Ivanova IP. Theoretical study of the excited-state reaction paths of the OH- and NH-dissociation processes in barbituric acid. Monatsh Chem. 2012 May;143:1141-9. Available from: <URL>.
  • 29. Becke AD. Density-functional thermochemistry. III. The role of exact exchange. Journal of Chemical Physics. 1993 April; 98:5648-4. Available from: <URL>.
  • 30. Lee C, Yang W, Parr RG. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review B. 1988 Jan ;37:785-4. Available from: <URL>.
  • 31. Hättig C, Weigend F. CC2 excitation energy calculations on large molecules using the resolution of the identity approximation. The Journal of Chemical Physics. 2000 Oct;113:5154-7. Available from: <URL>.
  • 32. Bauernschmitt R, Ahlrichs R. Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory. Chem Phys Lett. 1996 July; 256:454-10. Available from: <URL>.
  • 33. Stratmann RE, Scuseria GE, Frisch MJ. An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules. J Chem Phys. 1998 Nov; 109:8218-6. Available from: <URL>.
  • 34. Miertuš S, Scrocco E, Tomasi J. Electrostatic Interaction of a Solute with a Continuum. A Direct Utilization of ab initio Molecular Potentials for the Prevision of Solvent Effects. Chem Phys. 1981 Feb; 55:117-12. Available from: <URL>.
  • 35. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, et al. Gaussian˜16 Revision C.01. Wallingford, CT: Gaussian, Inc.; 2016.
  • 36. Barca GMJ, Bertoni C, Carrington L, Datta D, De Silva N, Deustua JE, Fedorov DG et al. Recent developments in the general atomic and molecular electronic structure system. The Journal of Chemical Physics. Sep 2020; 152: 154102. Available from: <URL>.
Yıl 2024, Cilt: 11 Sayı: 1, 321 - 330, 04.02.2024
https://doi.org/10.18596/jotcsa.1325480

Öz

Proje Numarası

КP-06-N59/7

Kaynakça

  • 1. Callis PR. Electronic States and Luminescence of Nucleic Acid Systems. Annual Review of Physical Chemistry. 1983 Oct;34:329-28. Available from: <URL>..
  • 2. Daniels MH, Hauswirth WW. Fluorescence of the purine and pyrimidine bases of the nucleic acids in neutral aqueous solution at 300 degrees K. Science 1971 Feb;171:675-2. Available from: <URL>.
  • 3. Crespo-Hernandez CE, Cohen B, Hare PM, Kohler B. Ultrafast Excited-State Dynamics in Nucleic Acids. Chemical Reviews. 2004 Apr;104:1977-42. Available from: <URL>..
  • 4. Cohen B., Crespo-Hernandez CE, Kohler B. Strickler–Berg analysis of excited singlet state dynamics in DNA and RNA nucleosides. Faraday Discussions. 2004 May;127:137-10. Available from: <URL>. .
  • 5. Shukla M., Leszczynski J. (Eds.). Radiation Induced Molecular Phenomena in Nucleic Acids, Springer,2008. ISBN: 978-1-4020-8183-5.
  • 6. Rios AC, Tor Y. On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution. Israel Journal of Chemistry. 2013 May;53:469-14. Available from: <URL>. .
  • 7. Hünig I, Plützer C, Seefeld KA, Löwenich D, Nispel M, Kleinermanns K. Photostability of Isolated and Paired Nucleobases: N-H Dissociation of Adenine and Hydrogen Transfer in its Base Pairs Examined by Laser Spectroscopy. ChemPhysChem 2004 Sep;5:1427-4. Available from: <URL>.
  • 8. Egel R, Lankenau A, Mulkidjanian AY (Eds.). Origins of Life: The Primal Self-Organization, Berlin, Springer-Verlag, 2011. ISBN: 978-3-642-21624-4.
  • 9. Dimitrov BH, Bakalska RI, Delchev VB. Phototautomerism of isocytosine in water medium: theoretical and experimental study. Journal of Structural Chemistry (Zhurnal Strukturnoi Khimii). 2019 Jan;60: 937-10. Available from: <URL>.
  • 10. Bakalska RI, Delchev VB. Comparative study of the relaxation mechanisms of the excited states of cytosine and isocytosine. Journal of Molecular Modeling. 2012 Jul;18:5133-13. Available from: <URL>.
  • 11. Merchan M, Gonzalez-Luque R, Climent T, Serrano-Andres L, Rodriguez E, Reguero M, Pelaez D. Unified Model for the Ultrafast Decay of Pyrimidine Nucleobases. The Journal of Physical Chemistry B 2006 Dec; 110:26471-5. Available from: <URL>..
  • 12. Switzer C, Moroney SE, Benner SA. Enzymatic incorporation of a new base pair into DNA and RNA. Journal of the American Chemical Society. 1989 Oct;111:8322-1. Available from: <URL>.
  • 13. Roberts C, Bandaru R, Switzer C. Theoretical and Experimental Study of Isoguanine and Isocytosine:  Base Pairing in an Expanded Genetic System. Journal of the American Chemical Society. 1997 May; 119:4640-9. Available from: <URL>..
  • 14. Edwards PD, Albert JS, Sylvester M, Aharony D, Andisik D, Callaghan O et al.. Application of Fragment-Based Lead Generation to the Discovery of Novel, Cyclic Amidine β-Secretase Inhibitors with Nanomolar Potency, Cellular Activity, and High Ligand Efficiency. Journal of Medicinal Chemistry. 2007 Nov;50:5912-13. Available from: <URL>.
  • 15. Congreve M, Chessari G, Tisi D, Woodhead AJ. Recent developments in fragment-based drug discovery. Journal of Medicinal Chemistry. 2008 May;51:3661-19. Available from: <URL>.
  • 16. Jeffrey GA, Kinoshita Y. The crystal structure of cytosine monohydrate. Acta Crystallografica. 1963; 16:20-8. Available from: https://doi.org/10.1107/S0365110X63000049.
  • 17. McConnell JF, Sharma BD, Marsh RE. Co-crystallization of Two Tautomers: Crystal Structure of Isocytosine. Nature 1964 Jul;203:399-1. Available from: <URL>.
  • 18. Morita H, Nagakura S. The electronic absorption spectra and the electronic structures of cytosine, isocytosine, and their anions and cations. Theoretica Chimica Acta 1968 Jan;11:279-16. Available from: <URL>. .
  • 19. Dračínský M, Jansa P, Ahonen K, Buděšínský M. Tautomerism and the Protonation/Deprotonation of Isocytosine in Liquid- and Solid-States Studied by NMR Spectroscopy and Theoretical Calculations. European Journal of Organic Chemistry. 2011 Jan; 2011:1544-7. Available from: <URL>.
  • 20. Raczyńska ED. On Analogies in Proton-Transfers for Pyrimidine Bases in the Gas Phase (Apolar Environment)—Cytosine Versus Isocytosine. Symmetry 2023 Jan;15:342. Available from: <URL>.
  • 21. Brown DJ, Lyall JM. The Fine Structure of Cytosine. Australian Journal of Chemistry. 1962;15:851-6. Available from: <URL>.
  • 22. Vranken H, Smets J, Maes G. Infrared spectra and tautomerism of isocytosine; an ab initio and matrix isolation study. Spectrochimica Acta A 1994 May;50:875-14. Available from: <URL>.
  • 23. Nowak MJ, Lapinski L, Fulara J. Matrix isolation studies of cytosine: The separation of the infrared spectra of cytosine tautomers. Spectrochim Acta A 1989;45:229-13. Available from: <URL>.
  • 24. Chmura B, Rode M, Sobolewski AL, Lapinski L, Nowak M. A Computational Study on the Mechanism of Intramolecular Oxo−Hydroxy Phototautomerism Driven by Repulsive πσ* State. The Journal of Physical Chemistry A 2008 Dec;112:13655-6. Available from: <URL>.
  • 25. Sobolewski AL, Domcke W. The chemical physics of the photostability of life. Europhysics News 2006 Oct;37:20-3. Available from: <URL>.
  • 26. Perun S, Sobolewski A, Domcke W. Conical intersections in thymine. The Journal of Physical Chemistry A 2006 Nov;110:13238-6. Available from: <URL>.
  • 27. Delchev VB, Sobolewski AL, Domcke W. Comparison of the non-radiative decay mechanisms of 4-pyrimidinone and uracil: an ab initio study. Physical Chemistry Chemical Physics. 2010 Apr;12:5007–8. Available from: <URL>.
  • 28. Delchev VB, Ivanova IP. Theoretical study of the excited-state reaction paths of the OH- and NH-dissociation processes in barbituric acid. Monatsh Chem. 2012 May;143:1141-9. Available from: <URL>.
  • 29. Becke AD. Density-functional thermochemistry. III. The role of exact exchange. Journal of Chemical Physics. 1993 April; 98:5648-4. Available from: <URL>.
  • 30. Lee C, Yang W, Parr RG. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review B. 1988 Jan ;37:785-4. Available from: <URL>.
  • 31. Hättig C, Weigend F. CC2 excitation energy calculations on large molecules using the resolution of the identity approximation. The Journal of Chemical Physics. 2000 Oct;113:5154-7. Available from: <URL>.
  • 32. Bauernschmitt R, Ahlrichs R. Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory. Chem Phys Lett. 1996 July; 256:454-10. Available from: <URL>.
  • 33. Stratmann RE, Scuseria GE, Frisch MJ. An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules. J Chem Phys. 1998 Nov; 109:8218-6. Available from: <URL>.
  • 34. Miertuš S, Scrocco E, Tomasi J. Electrostatic Interaction of a Solute with a Continuum. A Direct Utilization of ab initio Molecular Potentials for the Prevision of Solvent Effects. Chem Phys. 1981 Feb; 55:117-12. Available from: <URL>.
  • 35. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, et al. Gaussian˜16 Revision C.01. Wallingford, CT: Gaussian, Inc.; 2016.
  • 36. Barca GMJ, Bertoni C, Carrington L, Datta D, De Silva N, Deustua JE, Fedorov DG et al. Recent developments in the general atomic and molecular electronic structure system. The Journal of Chemical Physics. Sep 2020; 152: 154102. Available from: <URL>.
Toplam 36 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Fiziksel Kimya (Diğer)
Bölüm ARAŞTIRMA MAKALELERİ
Yazarlar

Tsvetina Cherneva Bu kişi benim 0000-0003-2500-0667

Mina Todorova Bu kişi benim 0000-0002-0850-0902

Rumyana Bakalska Bu kişi benim 0000-0001-8638-8111

Vassil Delchev 0000-0002-8305-413X

Proje Numarası КP-06-N59/7
Yayımlanma Tarihi 4 Şubat 2024
Gönderilme Tarihi 11 Temmuz 2023
Kabul Tarihi 11 Aralık 2023
Yayımlandığı Sayı Yıl 2024 Cilt: 11 Sayı: 1

Kaynak Göster

Vancouver Cherneva T, Todorova M, Bakalska R, Delchev V. Photo-Induced Tautomerism of Isocytosine in Aqueous Solution when Irradiated with UVC Light. JOTCSA. 2024;11(1):321-30.