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INVESTIGATION OF TAUTOMERIC STRUCTURES OF 6-AZA-2-THIOURACIL-5-CARBOXYLIC ACID USING VIBRATIONAL SPECTROSCOPY ALONG WITH DFT THEORETICAL METHOD

Year 2021, Volume: 22 Issue: 1, 23 - 35, 26.03.2021
https://doi.org/10.18038/estubtda.765162

Abstract

Molecular structure, tautomeric forms, vibrational modes, optic and electronic properties of 6-Aza-2-thiouracil-5-carboxylic acid (6A2T5CA) molecule were characterized by FT-IR, Raman, UV-VIS spectral methods and DFT method. The experimental results Show that FT-IR and Raman spectroscopic methods could be used to determine the different tautomeric forms of 6A2T5CA molecule clearly. Although title molecule has different tautomeric forms such as oxo and hydroxy because of inter molecular interactions, it has other tautomeric forms, as well due to intra molecular interaction of functional groups within the molecule. In particular, such structures change between each other depending on the solvent. Differences in some vibrational bands were observed in IR and Raman spectra of the molecule which were dissolved in ethanol and water and the solid form. These differences were observed especially in N-H and O-H functional groups. In addition, vibrational modes, optimized structures, energy values, electronic transitions and HOMO-LUMO energy values of tautomeric forms were calculated using B32LYP/6-311G(2d,2p) level of theory. Experimentally obtained results were compared with theoretically obtained results and it was indicated that there was a good agreement between each other. It was also observed that the molecule has a different tautomeric form when it was dissolved in ethanol, however the molecule has another tautomeric form when it was dissolved in water.

Supporting Institution

Eskisehir Osmangazi University

Project Number

201846014

References

  • [1] Saenger, W. Principles of Nucleic Acid Structure. Springer-Verlag, New York Berlin Heidelberg, Tokyo, 1984.
  • [2] Beck, CF, Howlett, G. The nature of the miscoding caused by growth in the presence of 2-thiouracil. J Mol Biol 1977; 111: 1-17.
  • [3] Nei, YW, Akinyemi, TE, Kaczan, CM, Steill, JD, Berden, G, Oomens, J, Rodgers, MT. Infrared multiple photon dissociation action spectroscopy of sodiated uracil and thiouracils: Effects of thioketo-substitution on gas-phase conformation. Int J Mass Spectrom 2011; 308(2–3): 191-202.
  • [4] Gottschalk, E, Kopp, E, Lezius, AG. A synthetic DNA with unusual base-pairing. Eur J Biochem 1971; 24: 168-182.
  • [5]Bretner, M, Kulikowski, T, Dzik, JM, Rode, W, Shugar, D. 2-Thio derivatives of dUrd and 5-fluoro-dUrd and their 5'-monophosphates: synthesis, interaction with tumor thymidylate synthase, and in vitro antitumor activity. J Med Chem 1993; 36: 3611-3617.
  • [6]Beck, CF, Howlett, GJ. The nature of the miscoding caused by growth in the presence of 2-thiouracil. J Mol Biol 1977; 111: 1-17.
  • [7] Kryachko, ES, Nguyen, MT, Zeeger-Huyskens, T. Thiouracils:  Acidity, Basicity, and Interaction with Water. J Phys Chem A 2001; 105: 3379-3387.
  • [8] Moustafa, H, El-Taher, S, Shıbl, MF, Hilal R. Equilibrium Geometry and Gas-Phase Proton Affinity of 2-Thiouracil Derivatives. Int J Quantum Chem 2002; 87: 378–388.
  • [9]Li, YS, Jalilian, MR, Durig, JR. Microwave spectrum of indene. J Mol Struct; 51: 171-174.
  • [10] Yan, J, Jin, S, Wang, B. A novel redox-sensitive protecting group for boronic acids, MPMP-diol. Tetrahedron Lett 2005; 46: 8503-8505.
  • [11] Rauhut, G, Pulay, P. Transferable Scaling Factors for Density Functional Derived Vibrational Force Fields. J Phys Chem 1995; 99: 3093-3100.
  • [12] Lee, SY. Molecular Structure and Vibrational Spectra of Biphenyl in the Ground and the Lowest Triplet States. Density Functional Theory Study. B Korean Chem Soc 1998; 19(1): 93-98.
  • [13] Frisch, MJ, et al. Gaussian 09, Revision A. 1, Gaussian, Inc, Wallingford, CT. 2009.
  • [14] Rauhut, G, Pulay, P. Transferable scaling factors for density functional derived vibrational force fields. J Phys Chem 1995; 99: 3093-3100.
  • [15] Baker, J, Jarzecki, AA, Pulay, P. Direct scaling of primitive valence force Constants:  an alternative approach to scaled quantum mechanical force fields. J Phys Chem A 1998; 102: 1412-1414.
  • [16] Tiekink, ERT. Crystal structure of 2-thiouracil. Z Kristallogr 1989; 187: 79-84.
  • [17] Stuart, B. Infrared Spectroscopy: Fundamentals and Applications. Wiley India Ed. 2010.
  • [18] Dikmen, G. 4-Methyl-1H-Indazole-5-Boronic acid: Crystal structure, vibrational spectra and DFT simulations. J Mol Struct 2017; 1150: 299-306.
  • [19] Oomens, J, Meijer, G, Helden, GV. An infrared spectroscopic study of protonated and cationic indazole. Int J Mass Spectrom 2006; 249–250: 199-205
  • [20] Dikmen, G, Alver, Ö. NMR, FT-IR, Raman and UV–Vis spectroscopic investigation and DFT study of 6-Bromo-3-Pyridinyl Boronic Acid. J Mol Struct 2015; 1099: 625-632.
  • [21] Li, Y, Liu, Y, Wang, H, Xiong, X, Wei, P, Li, F. Synthesis, Crystal Structure, Vibration Spectral, and DFT Studies of 4-Aminoantipyrine and Its Derivatives. Molecules 2013; 18: 877-893.
  • [22] Seshadri, S, Gunasekaran, S, Muthu, S. Vibrational spectroscopy investigation using density functional theory on 7‐chloro‐3‐methyl‐2H‐1,2,4‐ benzothiadiazine 1,1‐dioxide. J Raman Spectrosc 2009; 40: 639-644.
  • [23] Solaichamya, R, Karpagama, J. Structural and Vibrational studies (FT-IR, FT-Raman) of Voglibose using DFT calculation. ILCPA 2016; 64: 45-62.
  • [24] Puviarasan, N, Arjunan, V, Mohan, S. FT-IR and FT-Raman Studies on 3-Aminophthalhydrazide and N-Aminophthalimide. Turk J Chem 2002; 26: 323-333.
  • [25]Rajesh, SP, Gunasekaran, T, Gnanasambandan, SS. Molecular structure and vibrational analysis of Trifluoperazine by FT-IR, FT-Raman and UV–Vis spectroscopies combined with DFT calculations. Spectrochim Acta A: 2015; 137: 1184-1193.
  • [26] Kosov, DS, Popelier, PLA. Atomic Partitioning of Molecular Electrostatic Potentials. J Phys Chem A 2000; 104: 7339-7345.
  • [27] Suvitha, A, Periandy, S, Gayathri, P. NBO, HOMO–LUMO, UV, NLO, NMR and vibrational analysis of veratrole using FT-IR, FT-Raman, FT-NMR spectra and HF–DFT computational methods. Spectrochim Acta A: 2015; 138: 357-369.

INVESTIGATION OF TAUTOMERIC STRUCTURES OF 6-AZA-2-THIOURACIL-5-CARBOXYLIC ACID USING VIBRATIONAL SPECTROSCOPY ALONG WITH DFT THEORETICAL METHOD

Year 2021, Volume: 22 Issue: 1, 23 - 35, 26.03.2021
https://doi.org/10.18038/estubtda.765162

Abstract

Molecular structure, tautomeric forms, vibrational modes, optic and electronic properties of 6-Aza-2-thiouracil-5-carboxylic acid (6A2T5CA) molecule were characterized by FT-IR, Raman, UV-VIS spectral methods and DFT method. The experimental results Show that FT-IR and Raman spectroscopic methods could be used to determine the different tautomeric forms of 6A2T5CA molecule clearly. Although title molecule has different tautomeric forms such as oxo and hydroxy because of inter molecular interactions, it has other tautomeric forms, as well due to intra molecular interaction of functional groups within the molecule. In particular, such structures change between each other depending on the solvent. Differences in some vibrational bands were observed in IR and Raman spectra of the molecule which were dissolved in ethanol and water and the solid form. These differences were observed especially in N-H and O-H functional groups. In addition, vibrational modes, optimized structures, energy values, electronic transitions and HOMO-LUMO energy values of tautomeric forms were calculated using B32LYP/6-311G(2d,2p) level of theory. Experimentally obtained results were compared with theoretically obtained results and it was indicated that there was a good agreement between each other. It was also observed that the molecule has a different tautomeric form when it was dissolved in ethanol, however the molecule has another tautomeric form when it was dissolved in water.

Project Number

201846014

References

  • [1] Saenger, W. Principles of Nucleic Acid Structure. Springer-Verlag, New York Berlin Heidelberg, Tokyo, 1984.
  • [2] Beck, CF, Howlett, G. The nature of the miscoding caused by growth in the presence of 2-thiouracil. J Mol Biol 1977; 111: 1-17.
  • [3] Nei, YW, Akinyemi, TE, Kaczan, CM, Steill, JD, Berden, G, Oomens, J, Rodgers, MT. Infrared multiple photon dissociation action spectroscopy of sodiated uracil and thiouracils: Effects of thioketo-substitution on gas-phase conformation. Int J Mass Spectrom 2011; 308(2–3): 191-202.
  • [4] Gottschalk, E, Kopp, E, Lezius, AG. A synthetic DNA with unusual base-pairing. Eur J Biochem 1971; 24: 168-182.
  • [5]Bretner, M, Kulikowski, T, Dzik, JM, Rode, W, Shugar, D. 2-Thio derivatives of dUrd and 5-fluoro-dUrd and their 5'-monophosphates: synthesis, interaction with tumor thymidylate synthase, and in vitro antitumor activity. J Med Chem 1993; 36: 3611-3617.
  • [6]Beck, CF, Howlett, GJ. The nature of the miscoding caused by growth in the presence of 2-thiouracil. J Mol Biol 1977; 111: 1-17.
  • [7] Kryachko, ES, Nguyen, MT, Zeeger-Huyskens, T. Thiouracils:  Acidity, Basicity, and Interaction with Water. J Phys Chem A 2001; 105: 3379-3387.
  • [8] Moustafa, H, El-Taher, S, Shıbl, MF, Hilal R. Equilibrium Geometry and Gas-Phase Proton Affinity of 2-Thiouracil Derivatives. Int J Quantum Chem 2002; 87: 378–388.
  • [9]Li, YS, Jalilian, MR, Durig, JR. Microwave spectrum of indene. J Mol Struct; 51: 171-174.
  • [10] Yan, J, Jin, S, Wang, B. A novel redox-sensitive protecting group for boronic acids, MPMP-diol. Tetrahedron Lett 2005; 46: 8503-8505.
  • [11] Rauhut, G, Pulay, P. Transferable Scaling Factors for Density Functional Derived Vibrational Force Fields. J Phys Chem 1995; 99: 3093-3100.
  • [12] Lee, SY. Molecular Structure and Vibrational Spectra of Biphenyl in the Ground and the Lowest Triplet States. Density Functional Theory Study. B Korean Chem Soc 1998; 19(1): 93-98.
  • [13] Frisch, MJ, et al. Gaussian 09, Revision A. 1, Gaussian, Inc, Wallingford, CT. 2009.
  • [14] Rauhut, G, Pulay, P. Transferable scaling factors for density functional derived vibrational force fields. J Phys Chem 1995; 99: 3093-3100.
  • [15] Baker, J, Jarzecki, AA, Pulay, P. Direct scaling of primitive valence force Constants:  an alternative approach to scaled quantum mechanical force fields. J Phys Chem A 1998; 102: 1412-1414.
  • [16] Tiekink, ERT. Crystal structure of 2-thiouracil. Z Kristallogr 1989; 187: 79-84.
  • [17] Stuart, B. Infrared Spectroscopy: Fundamentals and Applications. Wiley India Ed. 2010.
  • [18] Dikmen, G. 4-Methyl-1H-Indazole-5-Boronic acid: Crystal structure, vibrational spectra and DFT simulations. J Mol Struct 2017; 1150: 299-306.
  • [19] Oomens, J, Meijer, G, Helden, GV. An infrared spectroscopic study of protonated and cationic indazole. Int J Mass Spectrom 2006; 249–250: 199-205
  • [20] Dikmen, G, Alver, Ö. NMR, FT-IR, Raman and UV–Vis spectroscopic investigation and DFT study of 6-Bromo-3-Pyridinyl Boronic Acid. J Mol Struct 2015; 1099: 625-632.
  • [21] Li, Y, Liu, Y, Wang, H, Xiong, X, Wei, P, Li, F. Synthesis, Crystal Structure, Vibration Spectral, and DFT Studies of 4-Aminoantipyrine and Its Derivatives. Molecules 2013; 18: 877-893.
  • [22] Seshadri, S, Gunasekaran, S, Muthu, S. Vibrational spectroscopy investigation using density functional theory on 7‐chloro‐3‐methyl‐2H‐1,2,4‐ benzothiadiazine 1,1‐dioxide. J Raman Spectrosc 2009; 40: 639-644.
  • [23] Solaichamya, R, Karpagama, J. Structural and Vibrational studies (FT-IR, FT-Raman) of Voglibose using DFT calculation. ILCPA 2016; 64: 45-62.
  • [24] Puviarasan, N, Arjunan, V, Mohan, S. FT-IR and FT-Raman Studies on 3-Aminophthalhydrazide and N-Aminophthalimide. Turk J Chem 2002; 26: 323-333.
  • [25]Rajesh, SP, Gunasekaran, T, Gnanasambandan, SS. Molecular structure and vibrational analysis of Trifluoperazine by FT-IR, FT-Raman and UV–Vis spectroscopies combined with DFT calculations. Spectrochim Acta A: 2015; 137: 1184-1193.
  • [26] Kosov, DS, Popelier, PLA. Atomic Partitioning of Molecular Electrostatic Potentials. J Phys Chem A 2000; 104: 7339-7345.
  • [27] Suvitha, A, Periandy, S, Gayathri, P. NBO, HOMO–LUMO, UV, NLO, NMR and vibrational analysis of veratrole using FT-IR, FT-Raman, FT-NMR spectra and HF–DFT computational methods. Spectrochim Acta A: 2015; 138: 357-369.
There are 27 citations in total.

Details

Primary Language English
Journal Section Articles
Authors

Gökhan Dikmen 0000-0003-0304-3527

Project Number 201846014
Publication Date March 26, 2021
Published in Issue Year 2021 Volume: 22 Issue: 1

Cite

AMA Dikmen G. INVESTIGATION OF TAUTOMERIC STRUCTURES OF 6-AZA-2-THIOURACIL-5-CARBOXYLIC ACID USING VIBRATIONAL SPECTROSCOPY ALONG WITH DFT THEORETICAL METHOD. Estuscience - Se. March 2021;22(1):23-35. doi:10.18038/estubtda.765162