5. Computational chemistry applied to vibrational spectroscopy: A tool for characterization of nucleic acid bases and some of their 5-substituted derivatives
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M. Alcolea Palafox
Abstract
Computational chemistry can be applied to vibrational spectroscopy in different ways, such as for a better characterization and assignment of all the bands of the experimental spectra, as a tool in the identification of the tautomers present in the gas phase and in the solid state through their spectra and for the simulation of the solid and liquid phase of a compound and the consequent simulation and interpretation of their spectra. In the present study, as an example of the applicability of computational chemistry, the structure and spectra of cytosine and uracil nucleic acid bases and two cytosine derivatives are shown. The FTIR and Raman spectra were analysed with the support of ab initio (Hartree-Fock (HF), MP2) and density functional theory (DFT) (B3LYP, PBE, B-P, etc.) calculations using several basis sets and several scaling equations. The calculations predict an easier tautomerization of cytosine than uracil molecule, but the tautomerization is hindered in the 5-bromocytosine molecule. Thus, in the solid state, this molecule only exists in the amino-oxo tautomeric form.
Abstract
Computational chemistry can be applied to vibrational spectroscopy in different ways, such as for a better characterization and assignment of all the bands of the experimental spectra, as a tool in the identification of the tautomers present in the gas phase and in the solid state through their spectra and for the simulation of the solid and liquid phase of a compound and the consequent simulation and interpretation of their spectra. In the present study, as an example of the applicability of computational chemistry, the structure and spectra of cytosine and uracil nucleic acid bases and two cytosine derivatives are shown. The FTIR and Raman spectra were analysed with the support of ab initio (Hartree-Fock (HF), MP2) and density functional theory (DFT) (B3LYP, PBE, B-P, etc.) calculations using several basis sets and several scaling equations. The calculations predict an easier tautomerization of cytosine than uracil molecule, but the tautomerization is hindered in the 5-bromocytosine molecule. Thus, in the solid state, this molecule only exists in the amino-oxo tautomeric form.
Chapters in this book
- Frontmatter i
- Preface of the Book of Proceedings of the Virtual Conference on Computational Science (VCCS-2016) v
- Contents vii
- List of contributing authors xi
- 1. Addressing the challenges of standalone multi-core simulations in molecular dynamics 1
- 2. Optical and magnetic properties of free-standing silicene, germanene and T-graphene system 23
- 3. Theoretical study of the electronic states of newly detected dications. Case of MgS2+ AND SiN2+ 71
- 4. Analytical Solution of Pantograph Equation with Incommensurate Delay 93
- 5. Computational chemistry applied to vibrational spectroscopy: A tool for characterization of nucleic acid bases and some of their 5-substituted derivatives 117
- 6. Mechanism of nucleophilic substitution reactions of 4-(4’-nitro)phenylnitrobenzofurazan ether with aniline in acetonitrile 153
- 7. Computational methods in preformulation study for pharmaceutical solid dosage forms of therapeutic proteins 163
- 8. Computational Investigation of Cationic, Anionic and Neutral Ag2AuN (N = 1–7) Nanoalloy Clusters 173
- 9. Evacuation simulation using Hybrid Space Discretisation and Application to Large Underground Rail Tunnel Station 191
- 10. DFT study of anthocyanidin and anthocyanin pigments for Dye-Sensitized Solar Cells: Electron injecting from the excited states and adsorption onto TiO2 (anatase) surface 205
- 11. Elemental Two-Dimensional Materials Beyond Graphene 219
- Index 229
Chapters in this book
- Frontmatter i
- Preface of the Book of Proceedings of the Virtual Conference on Computational Science (VCCS-2016) v
- Contents vii
- List of contributing authors xi
- 1. Addressing the challenges of standalone multi-core simulations in molecular dynamics 1
- 2. Optical and magnetic properties of free-standing silicene, germanene and T-graphene system 23
- 3. Theoretical study of the electronic states of newly detected dications. Case of MgS2+ AND SiN2+ 71
- 4. Analytical Solution of Pantograph Equation with Incommensurate Delay 93
- 5. Computational chemistry applied to vibrational spectroscopy: A tool for characterization of nucleic acid bases and some of their 5-substituted derivatives 117
- 6. Mechanism of nucleophilic substitution reactions of 4-(4’-nitro)phenylnitrobenzofurazan ether with aniline in acetonitrile 153
- 7. Computational methods in preformulation study for pharmaceutical solid dosage forms of therapeutic proteins 163
- 8. Computational Investigation of Cationic, Anionic and Neutral Ag2AuN (N = 1–7) Nanoalloy Clusters 173
- 9. Evacuation simulation using Hybrid Space Discretisation and Application to Large Underground Rail Tunnel Station 191
- 10. DFT study of anthocyanidin and anthocyanin pigments for Dye-Sensitized Solar Cells: Electron injecting from the excited states and adsorption onto TiO2 (anatase) surface 205
- 11. Elemental Two-Dimensional Materials Beyond Graphene 219
- Index 229
