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Zhang J, Li X. The effect of water-mediated catalysis on the intramolecular proton-transfer reactions of the isomers of 5-chlorouracil: a theoretical study. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2019; 75:554-561. [PMID: 31062712 DOI: 10.1107/s2053229619004856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/09/2019] [Indexed: 11/10/2022]
Abstract
The geometrical structures and thermal energies (E), enthalpies (H) and Gibbs free energies (G) of 13 isomers of 5-chlorouracil (5ClU) in the gas and water phases were investigated using the density functional theory (DFT) method at the M06-2X/6-311++g(3df,3pd) level. The isomers of 5ClU can be microhydrated at different molecular target sites. The mono- and dihydrated forms are the most stable in both the gas and water phases, and, because of the intermolecular interactions, the hydrations lead to a degree of change in the stability trend. Two types of isomerizations were considered: the internal H-O bond rotations in which the H atom rotates 180° around the C-O bond and the intramolecular proton-transfer reactions in which an H atom is transferred between an O atom and a neighbouring N atom. The forward and backward energy barriers for isomerizations of nonhydrated 5ClU were calculated. In addition, 16 optimized transition-state structures for water-mediated catalysis on isomerizations of 5ClU were investigated. The forward and backward proton-transfer energy barriers of water-mediated catalysis on isomerizations of 5ClU were obtained. The results indicate that the catalytic effect of two H2O molecules is much greater than that of one H2O molecule in isomerizations of 5ClU.
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Affiliation(s)
- Jian Zhang
- School of Chemistry and Material Science, Shanxi Normal University, Linfen 041004, People's Republic of China
| | - Xiu Li
- School of Chemistry and Material Science, Shanxi Normal University, Linfen 041004, People's Republic of China
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Othmani H, Ben Said R, Terzi N, Jaidane NE, Mogren Al Mogren M, Elmarghany A, Hochlaf M. Structural, energetic and spectroscopic characterisation of 5-fluorouracil anticarcinogenic drug isomers, tautomers and ions. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1548715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- H. Othmani
- Laboratoire de Modélisation et Simulation Multi Echelle, Université Paris-Est, MSME UMR 8208 CNRS, Champs-sur-Marne, France
- Faculté des Sciences de Tunis, Laboratoire de Spectroscopie Atomique, Moléculaire et Applications-LSAMA, Université de Tunis El-Manar, Tunis, Tunisia
| | - R. Ben Said
- Department of Chemistry, College of Science & Arts at Al-Rass, Qassim University, Al-Rass, Kingdom of Saudi Arabia
- Unité de recherche Physico-Chimie des Matériaux à l’Etat Condensé, Département de Chimie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - N. Terzi
- Faculté des Sciences de Tunis, Laboratoire de Spectroscopie Atomique, Moléculaire et Applications-LSAMA, Université de Tunis El-Manar, Tunis, Tunisia
| | - N.-E. Jaidane
- Faculté des Sciences de Tunis, Laboratoire de Spectroscopie Atomique, Moléculaire et Applications-LSAMA, Université de Tunis El-Manar, Tunis, Tunisia
| | - M. Mogren Al Mogren
- Chemistry Department, Faculty of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - A. Elmarghany
- Chemistry Department, Faculty of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
- Faculty of Science, Suez University, Suez, Egypt
| | - M. Hochlaf
- Laboratoire de Modélisation et Simulation Multi Echelle, Université Paris-Est, MSME UMR 8208 CNRS, Champs-sur-Marne, France
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Palafox MA. DFT computations on vibrational spectra: Scaling procedures to improve the wavenumbers. PHYSICAL SCIENCES REVIEWS 2018. [DOI: 10.1515/psr-2017-0184] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The performance of ab initio and density functional theory (DFT) methods in calculating the vibrational wavenumbers in the isolated state was analyzed. To correct the calculated values, several scaling procedures were described in detail. The two linear scaling equation (TLSE) procedure leads to the lowest error and it is recommended for scaling. A comprehensive compendium of the main scale factors and scaling equations available to date for a good accurate prediction of the wavenumbers was also shown. Examples of each case were presented, with special attention to the benzene and uracil molecules and to some of their derivatives. Several DFT methods and basis sets were used. After scaling, the X3LYP/DFT method leads to the lowest error in these molecules. The B3LYP method appears closely in accuracy, and it is also recommended to be used. The accuracy of the results in the solid state was shown and several additional corrections are presented.
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Palafox MA, Rastogi V. 6-Aminouracil: Geometries and spectra in the isolated state and in the solid state simulation. A comparison with 5-aminouracil. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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A DFT analysis of the molecular structure, vibrational spectra and other molecular properties of 5-nitrouracil and comparison with uracil. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.096] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sun S, Brown A. Simulation of the Resonance Raman Spectra for 5-Halogenated (F, Cl, and Br) Uracils. J Phys Chem A 2015; 119:3961-71. [DOI: 10.1021/acs.jpca.5b01052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuai Sun
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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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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