Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives
We report on the density functional theory (DFT) modelling of structural, energetic and NMR parameters of uracil and its derivatives (5-halogenouracil (5XU), X = F, Cl, Br and I) in vacuum and in water using the polarizable continuum model (PCM) and the solvent model density (SMD) approach. On the b...
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MDPI AG
2020-08-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/25/17/3931 |
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| author | Kacper Rzepiela Aneta Buczek Teobald Kupka Małgorzata A. Broda |
| author_facet | Kacper Rzepiela Aneta Buczek Teobald Kupka Małgorzata A. Broda |
| author_sort | Kacper Rzepiela |
| collection | DOAJ |
| description | We report on the density functional theory (DFT) modelling of structural, energetic and NMR parameters of uracil and its derivatives (5-halogenouracil (5XU), X = F, Cl, Br and I) in vacuum and in water using the polarizable continuum model (PCM) and the solvent model density (SMD) approach. On the basis of the obtained results, we conclude that the intramolecular electrostatic interactions are the main factors governing the stability of the six tautomeric forms of uracil and 5XU. Two indices of aromaticity, the harmonic oscillator model of aromaticity (HOMA), satisfying the geometric criterion, and the nuclear independent chemical shift (NICS), were applied to evaluate the aromaticity of uracil and its derivatives in the gas phase and water. The values of these parameters showed that the most stable tautomer is the least aromatic. A good performance of newly designed xOPBE density functional in combination with both large aug-cc-pVQZ and small STO(1M)−3G basis sets for predicting chemical shifts of uracil and 5-fluorouracil in vacuum and water was observed. As a practical alternative for calculating the chemical shifts of challenging heterocyclic compounds, we also propose B3LYP calculations with small STO(1M)−3G basis set. The indirect spin–spin coupling constants predicted by B3LYP/aug-cc-pVQZ(mixed) method reproduce the experimental data for uracil and 5-fluorouracil well. |
| first_indexed | 2024-03-10T16:44:32Z |
| format | Article |
| id | doaj.art-0e8ceb8ca4014bad84a2ad6d3973e196 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T16:44:32Z |
| publishDate | 2020-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-0e8ceb8ca4014bad84a2ad6d3973e1962023-11-20T11:40:05ZengMDPI AGMolecules1420-30492020-08-012517393110.3390/molecules25173931Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen DerivativesKacper Rzepiela0Aneta Buczek1Teobald Kupka2Małgorzata A. Broda3Department of Physical Chemistry and Molecular Modeling, Faculty of Chemistry, University of Opole, 48 Oleska Street, 45−052 Opole, PolandDepartment of Physical Chemistry and Molecular Modeling, Faculty of Chemistry, University of Opole, 48 Oleska Street, 45−052 Opole, PolandDepartment of Physical Chemistry and Molecular Modeling, Faculty of Chemistry, University of Opole, 48 Oleska Street, 45−052 Opole, PolandDepartment of Physical Chemistry and Molecular Modeling, Faculty of Chemistry, University of Opole, 48 Oleska Street, 45−052 Opole, PolandWe report on the density functional theory (DFT) modelling of structural, energetic and NMR parameters of uracil and its derivatives (5-halogenouracil (5XU), X = F, Cl, Br and I) in vacuum and in water using the polarizable continuum model (PCM) and the solvent model density (SMD) approach. On the basis of the obtained results, we conclude that the intramolecular electrostatic interactions are the main factors governing the stability of the six tautomeric forms of uracil and 5XU. Two indices of aromaticity, the harmonic oscillator model of aromaticity (HOMA), satisfying the geometric criterion, and the nuclear independent chemical shift (NICS), were applied to evaluate the aromaticity of uracil and its derivatives in the gas phase and water. The values of these parameters showed that the most stable tautomer is the least aromatic. A good performance of newly designed xOPBE density functional in combination with both large aug-cc-pVQZ and small STO(1M)−3G basis sets for predicting chemical shifts of uracil and 5-fluorouracil in vacuum and water was observed. As a practical alternative for calculating the chemical shifts of challenging heterocyclic compounds, we also propose B3LYP calculations with small STO(1M)−3G basis set. The indirect spin–spin coupling constants predicted by B3LYP/aug-cc-pVQZ(mixed) method reproduce the experimental data for uracil and 5-fluorouracil well.https://www.mdpi.com/1420-3049/25/17/39315-halogenouracil (5XU)tautomersDFTaromaticityNICSHOMA |
| spellingShingle | Kacper Rzepiela Aneta Buczek Teobald Kupka Małgorzata A. Broda Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives Molecules 5-halogenouracil (5XU) tautomers DFT aromaticity NICS HOMA |
| title | Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives |
| title_full | Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives |
| title_fullStr | Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives |
| title_full_unstemmed | Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives |
| title_short | Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives |
| title_sort | factors governing the chemical stability and nmr parameters of uracil tautomers and its 5 halogen derivatives |
| topic | 5-halogenouracil (5XU) tautomers DFT aromaticity NICS HOMA |
| url | https://www.mdpi.com/1420-3049/25/17/3931 |
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