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Zinc oxide nanosheet as a promising route for carrier 5-fluorouracil anticancer drug in the presence metal impurities: Insights from DFT calculations. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2020.113079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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On the aromaticity of uracil and its 5-halogeno derivatives as revealed by theoretically derived geometric and magnetic indexes. Struct Chem 2020. [DOI: 10.1007/s11224-020-01682-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractThe problem of aromaticity in heterocyclic rings of uracil and its 5-halogenoderivatives (5XU) was analyzed theoretically by calculating modified harmonic oscillator model of aromaticity (HOMA) for Heterocycle Electron Delocalization (HOMHED), nucleus-independent chemical shift parameters (NICS) and the so-called scan experiments, using helium-3 atom as a magnetic probe. The impact of halogen electronegativity on C5 atom’s NBO charges was also investigated. Water, as a polar environment, has a negligible impact on 5XU aromaticity. The most stable diketo tautomer shows a very low aromaticity while the “rare” dihydroxy form (tautomer No 6) is aromatic and resembles benzene. This is in agreement with traditional drawing of chemical formula of uracil’s six-membered ring, directly showing three alternating single and double bonds in its tautomer No 6. No good correlation between magnetic and geometric indexes of aromaticity for the studied 5XU tautomers was found. Linear correlation between the magnitude of NICS minimum, as well as the distance of the minimum above uracil ring plane center from 3He NMR chemical shift scan plot with respect to halogen electronegativity were observed. A strong linear dependence of magnetic index of aromaticity and the electronegativity of 5X substituent was observed.
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Rzepiela K, Buczek A, Kupka T, Broda MA. Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives. Molecules 2020; 25:E3931. [PMID: 32872098 PMCID: PMC7504704 DOI: 10.3390/molecules25173931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 01/10/2023] Open
Abstract
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.
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Affiliation(s)
| | | | - Teobald Kupka
- Department of Physical Chemistry and Molecular Modeling, Faculty of Chemistry, University of Opole, 48 Oleska Street, 45−052 Opole, Poland; (K.R.); (A.B.)
| | - Małgorzata A. Broda
- Department of Physical Chemistry and Molecular Modeling, Faculty of Chemistry, University of Opole, 48 Oleska Street, 45−052 Opole, Poland; (K.R.); (A.B.)
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Palafox MA, Chalanchi SM, Isasi J, Premkumar R, Franklin Benial AM, Rastogi VK. Effect of bromine atom on the different tautomeric forms of microhydrated 5-bromouracil, in the DNA:RNA microhelix and in the interaction with human proteins. J Biomol Struct Dyn 2020; 38:5443-5463. [DOI: 10.1080/07391102.2019.1704878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- M. Alcolea Palafox
- Facultad de Ciencias Químicas, Departamento de Química-Fisica, Universidad Complutense de Madrid, Madrid, Spain
| | - S. M. Chalanchi
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
| | - J. Isasi
- Facultad de Ciencias Químicas, Departamento de Química Inorgánica, Universidad Complutense de Madrid, Madrid, Spain
| | - R. Premkumar
- PG and Research Department of Physics, N.M.S.S.V.N. College, Madurai, Tamil Nadu, India
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Alcolea Palafox M, Franklin Benial AM, K Rastogi V. Biomolecules of 2-Thiouracil, 4-Thiouracil and 2,4-Dithiouracil: A DFT Study of the Hydration, Molecular Docking and Effect in DNA:RNAMicrohelixes. Int J Mol Sci 2019; 20:E3477. [PMID: 31311161 PMCID: PMC6678171 DOI: 10.3390/ijms20143477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022] Open
Abstract
The molecular structure of 2-thiouracil, 4-thiouracil and 2,4-dithiouracil was analyzed under the effect of the first and second hydration shell by using the B3LYP density functional (DFT) method, and the results were compared to those obtained for the uracil molecule. A slight difference in the water distribution appears in these molecules. On the hydration of these molecules several trends in bond lengths and atomic charges were established. The ring in uracil molecule appears easier to be deformed and adapted to different environments as compared to that when it is thio-substituted. Molecular docking calculations of 2-thiouracil against three different pathogens: Bacillus subtilis, Escherichia coli and Candida albicans were carried out. Docking calculations of 2,4-dithiouracil ligand with various targeted proteins were also performed. Different DNA: RNA hybrid microhelixes with uridine, 2-thiouridine, 4-thiouridine and 2,4-dithiouridine nucleosides were optimized in a simple model with three nucleotide base pairs. Two main types of microhelixes were analyzed in detail depending on the intramolecular H-bond of the 2'-OH group. The weaker Watson-Crick (WC) base pair formed with thio-substituted uracil than with unsubstituted ones slightly deforms the helical and backbone parameters, especially with 2,4-dithiouridine. However, the thio-substitution significantly increases the dipole moment of the A-type microhelixes, as well as the rise and propeller twist parameters.
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Affiliation(s)
- M Alcolea Palafox
- Departamento de Química-Física, Facultad de CienciasQuímicas, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | | | - V K Rastogi
- Indian Spectroscopy Society, KC 68/1, Old Kavinagar, Ghaziabad 201002, India
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Alcolea Palafox M, Rastogi V, Singh S. Effect of the sulphur atom on geometry and spectra of the biomolecule 2-thiouracil and in the WC base pair 2-thiouridine-adenosine. Influence of water in the first hydration shell. J Biomol Struct Dyn 2017; 36:1225-1254. [DOI: 10.1080/07391102.2017.1318304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- M. Alcolea Palafox
- Facultad de Ciencias Químicas, Departamento de Química-Fisica1, Universidad Complutense, Madrid 28040, Spain
| | - V.K. Rastogi
- R.D. Foundation Group of Institutions, NH-58, Kadrabad, Modinagar, Ghaziabad, India
- Indian Spectroscopy Society, KC 68/1, Old Kavinagar, Ghaziabad 201 002, India
| | - S.P. Singh
- Department of Physics, Dr B R Ambedkar Govt Degree College, Mainpuri, India
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DFT Calculations and Molecular Dynamics Simulation Study on the Adsorption of 5-Fluorouracil Anticancer Drug on Graphene Oxide Nanosheet as a Drug Delivery Vehicle. J Inorg Organomet Polym Mater 2017. [DOI: 10.1007/s10904-017-0525-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Langmaier J, Pižl M, Samec Z, Záliš S. Extreme Basicity of Biguanide Drugs in Aqueous Solutions: Ion Transfer Voltammetry and DFT Calculations. J Phys Chem A 2016; 120:7344-50. [DOI: 10.1021/acs.jpca.6b04786] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jan Langmaier
- J.
Heyrovský Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Martin Pižl
- J.
Heyrovský Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
- Department
of Inorganic Chemistry, University of Chemistry and Technology, Prague 6, Technická 5, 166 28, Czech Republic
| | - Zdeněk Samec
- J.
Heyrovský Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Stanislav Záliš
- J.
Heyrovský Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
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Simulation of the solid state and the first and second hydration shell of the xanthine oxidase inhibitor allopurinol: Structures obtained using DFT and MP2 methods. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.01.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Palafox MA. Structure and conformational analysis of the anti-HIV reverse transcriptase inhibitor AZT using MP2 and DFT methods. Differences with the natural nucleoside thymidine. Simulation of the 1st phosphorylation step with ATP. Phys Chem Chem Phys 2015; 16:24763-83. [PMID: 25317835 DOI: 10.1039/c4cp03695f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A comprehensive quantum-chemical investigation of the conformational landscape of the HIV-1 reverse transcriptase inhibitor AZT (3'-azido-3'-deoxythymidine) nucleoside analogue was carried out. The whole conformational parameters (χ, γ, β, δ, ϕ, P, νmax) were analysed as well as the NBO charges. The search located at least 55 stable structures, 9 of which were by MP2 within a 1 kcal mol(-1) electronic energy range of the global minimum. Most conformers were anti or high-anti around the glycoside bond and with North sugar ring puckering angles. The distribution of all the conformers according to the ranges of stability of the characteristic torsional angles was established. The results obtained were in accordance with those found in related anti-HIV nucleoside analogues. The best conformer in the anti form corresponded to the calculated values by MP2 of χ = -126.9°, β = 176.4° and γ = 49.1°. An analysis of the lowest vibrations in conformer C1 was carried out. The first hydration shell was simulated and the structural differences with the natural nucleoside deoxythymidine (dT) were determined. The first phosphorylation step was simulated by interacting ATP with the best hydrated clusters of AZT and dT. The Na cations act as a bridge between the phosphate moieties of ATP making it easy for -P3O3 to receive the H5' proton from AZT or dT. A proton-transfer mechanism is proposed through the water molecules. When the number of the water molecules surrounding AZT is lower than 8, the first phosphorylation step of AZT can be carried out. However, the appropriate orientation of the O5'-H in dT avoids this limitation and it can be performed with large numbers of water molecules.
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Affiliation(s)
- M Alcolea Palafox
- Chemical Physics Department, Chemistry Faculty, Complutense University, Ciudad Universitaria, Madrid-28040, Spain.
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Cuellar A, Alcolea Palafox M, Rastogi VK, Kiefer W, Schlücker S, Rathor SK. FT-IR and FT-Raman spectra of 5-fluoroorotic acid with solid state simulation by DFT methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 132:430-445. [PMID: 24887505 DOI: 10.1016/j.saa.2014.04.107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/11/2014] [Accepted: 04/22/2014] [Indexed: 06/03/2023]
Abstract
FT-Raman and FT-IR studies of the biomolecule 5-fluoroorotic acid in the solid state were carried out. The unit cell found in the crystal was simulated as a tetramer form by density functional calculations. They were performed to clarify wavenumber assignments of the experimental observed bands in the spectra. Correlations with the molecule of uracil were made, and specific scale equations were employed to scale the wavenumbers of 5-fluoroorotic acid. Good reproduction of the experimental wavenumbers is obtained and the % error is very small in the majority of the bands. This fact confirms our simplified solid state model. The molecular structure was fully optimized using DFT and MP2 methods. The relative stability of both the syn and anti conformations was investigated, and the anti-form was found to be slightly more stable, by 7.49 kJ/mol at the MP2 level. The structures of all possible tautomeric forms were determined. The keto-form appeared as the most stable one. The NBO atomic charges and several thermodynamic parameters were also calculated.
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Affiliation(s)
- A Cuellar
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Madrid 28040, Spain
| | - M Alcolea Palafox
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Madrid 28040, Spain.
| | - V K Rastogi
- R D Foundation Group of Institutions, NH-58, Kadrabad, Modinagar, Ghaziabad, India; Indian Spectroscopy Society, KC 68/1, Old Kavinagar, Ghaziabad 201 002, India.
| | - W Kiefer
- University of Würzburg, Institute for Physical and Theoretical Chemistry, Am Hubland, D-97074 Würzburg, Germany
| | - S Schlücker
- University of Duisburg-Essen, Faculty of Chemistry, Universitätsstr. 5, D-45141 Essen, Germany
| | - S K Rathor
- Indian Spectroscopy Society, KC 68/1, Old Kavinagar, Ghaziabad 201 002, India
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Brovarets’ OO, Yurenko YP, Hovorun DM. The significant role of the intermolecular CH⋯O/N hydrogen bonds in governing the biologically important pairs of the DNA and RNA modified bases: a comprehensive theoretical investigation. J Biomol Struct Dyn 2014; 33:1624-52. [DOI: 10.1080/07391102.2014.968623] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Ortiz S, Alvarez-Ros MC, Palafox MA, Rastogi VK, Balachandran V, Rathor SK. FT-IR and FT-Raman spectra of 6-chlorouracil: molecular structure, tautomerism and solid state simulation. A comparison between 5-chlorouracil and 6-chlorouracil. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 130:653-668. [PMID: 24856263 DOI: 10.1016/j.saa.2014.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/27/2014] [Accepted: 04/01/2014] [Indexed: 06/03/2023]
Abstract
A Raman and IR study of the biomolecule 6-chlorouracil was carried out in the solid state. The unit cell found in the crystal was simulated as a tetramer form by density functional calculations. Specific scale factors and scaling equations deduced from uracil molecule were employed in the predicted wavenumbers of 6-chlorouracil. The scaled wavenumbers were used in the reassignment of the IR and Raman experimental bands. Good reproduction of the experimental wavenumbers is obtained and the % error is very small in the majority of cases. A comparison between the molecular structure and charge distribution of 6-chlorouracil and 5-chlorouracil molecules was presented. The effect of the hydration with the PCM model in the molecular structure and charges was discussed. The optimum tautomers of 6-chlorouracil were optimized and analyzed. Six of them were related to those of uracil molecule. The effect of the halogen substitution in the sixth position of the pyrimidine ring in the stability of the different tautomers was evaluated. HOMO and LUMO orbital energy analysis were carried out.
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Affiliation(s)
- S Ortiz
- Departamento de Química-Física-I, Facultad de Ciencias Químicas, UCM, Madrid 28040, Spain
| | - M C Alvarez-Ros
- Departamento de Química-Física-I, Facultad de Ciencias Químicas, UCM, Madrid 28040, Spain
| | - M Alcolea Palafox
- Departamento de Química-Física-I, Facultad de Ciencias Químicas, UCM, Madrid 28040, Spain.
| | - V K Rastogi
- R.D. Foundation Group of Institutions, NH-58, Kadrabad, Modinagar, Ghaziabad, India; Indian Spectroscopy Society, KC-68/1, Old Kavinagar, Ghaziabad 201 002, India.
| | - V Balachandran
- Department of Physics, Arignar Anna Government Arts College, Musiri, Tiruchirappalli 621211, India
| | - S K Rathor
- Indian Spectroscopy Society, KC-68/1, Old Kavinagar, Ghaziabad 201 002, India
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