1
|
Palafox MA, Pedraza Velasco MLD, Marín JI, Posada-Moreno P. How proton transfer affects the helical parameters in DNA:DNA microhelices. J Biomol Struct Dyn 2022; 40:13759-13777. [PMID: 34806548 DOI: 10.1080/07391102.2021.1994880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Proton transfer reactions are a widespread phenomenon in many areas of the life sciences and it is one of the origins of the spontaneous point mutations during DNA replication. Because of its importance, many studies have been reported on these reactions. However, the present work is the first one focused on the structural geometrical changes by double proton transfer (DPT). Thus, different Watson-Crick (WC) pairs were optimized first in a simple model with one nucleoside base pair, and in a microhelix form with three nucleoside base pairs. The canonical and few tautomeric forms were considered in DNA:DNA microhelices with A-type and B-type helical forms. The stability of these structures and how the DPT process affects the main geometrical parameters was analyzed, in particular the deformation of the helical parameters. The M06-2X DFT method was used for this purpose. The purine/pyrimidine ring in the keto form appears easier to be deformed than when it is in the enol form. The weaker WC base pair formed with mixed microhelices than with nucleobases alone and the significant deformation of the helical and backbone parameters with the DPT appears to complicate this process in microhelices.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mauricio Alcolea Palafox
- Departamento de Química-Fisica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid. Ciudad Universitaria s/n, Madrid, Spain
| | | | - Josefa Isasi Marín
- Departamento de Química Inorgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Paloma Posada-Moreno
- Departamento de Enfermería, Facultad de Enfermería, Fisioterapia y Podología, Universidad Complutense de Madrid, Madrid, Spain.,Departamento de Enfermería, UCM, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| |
Collapse
|
2
|
Density Functional Method Study on the Cooperativity of Intermolecular H-bonding and π-π + Stacking Interactions in Thymine-[C nmim]Br ( n = 2, 4, 6, 8, 10) Microhydrates. Molecules 2022; 27:molecules27196242. [PMID: 36234781 PMCID: PMC9572290 DOI: 10.3390/molecules27196242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
The exploration of the ionic liquids’ mechanism of action on nucleobase’s structure and properties is still limited. In this work, the binding model of the 1-alkyl-3-methylimidazolium bromide ([Cnmim]Br, n = 2, 4, 6, 8, 10) ionic liquids to the thymine (T) was studied in a water environment (PCM) and a microhydrated surroundings (PCM + wH2O). Geometries of the mono-, di-, tri-, and tetra-ionic thymine (T-wH2O-y[Cnmim]+-xBr−, w = 5~1 and x + y = 0~4) complexes were optimized at the M06-2X/6-311++G(2d, p) level. The IR and UV-Vis spectra, QTAIM, and NBO analysis for the most stable T-4H2O-Br−-1, T-3H2O-[Cnmim]+-Br−-1, T-2H2O-[Cnmim]+-2Br−-1, and T-1H2O-2[Cnmim]+-2Br−-1 hydrates were presented in great detail. The results show that the order of the arrangement stability of thymine with the cations (T-[Cnmim]+) by PCM is stacking > perpendicular > coplanar, and with the anion (T-Br−) is front > top. The stability order for the different microhydrates is following T-5H2O-1 < T-4H2O-Br−-1 < T-3H2O-[Cnmim]+-Br−-1 < T-2H2O-[Cnmim]+-2Br−-1 < T-1H2O-2[Cnmim]+-2Br−-1. A good linear relationship between binding EB values and the increasing number (x + y) of ions has been found, which indicates that the cooperativity of interactions for the H-bonding and π-π+ stacking is varying incrementally in the growing ionic clusters. The stacking model between thymine and [Cnmim]+ cations is accompanied by weaker hydrogen bonds which are always much less favorable than those in T-xBr− complexes; the same trend holds when the clusters in size grow and the length of alkyl chains in the imidazolium cations increase. QTAIM and NBO analytical methods support the existence of mutually reinforcing hydrogen bonds and π-π cooperativity in the systems.
Collapse
|
3
|
Jin L, Shi S, Zhao Y, Luo L, Zhao C, Lu J, Jiang M. Effects of C5-substituent group on the hydrogen peroxide-mediated tautomerisation of protonated cytosine: a theoretical perspective. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1406159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Lingxia Jin
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Shengnan Shi
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Yang Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Liyang Luo
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Caibin Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Jiufu Lu
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Min Jiang
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| |
Collapse
|
4
|
Molchanov S, Gryff-Keller A. Solvation of Amides in DMSO and CDCl3: An Attempt at Quantitative DFT-Based Interpretation of 1H and 13C NMR Chemical Shifts. J Phys Chem A 2017; 121:9645-9653. [DOI: 10.1021/acs.jpca.7b10110] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sergey Molchanov
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Adam Gryff-Keller
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| |
Collapse
|
5
|
Kubica D, Molchanov S, Gryff-Keller A. Solvation of Uracil and Its Derivatives by DMSO: A DFT-Supported 1H NMR and 13C NMR Study. J Phys Chem A 2017; 121:1841-1848. [PMID: 28195476 DOI: 10.1021/acs.jpca.7b00144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
1H NMR and 13C NMR spectra of uracil, thymine, 5-hydroxymethyluracil, 5,6-dihydrouracil, and 5,6-dihydrothymine in DMSO-d6 solutions have been measured. Additionally, molecular structures as well as NMR parameters of these compounds and their various solvates have been calculated using DFT B3LYP/6-311++G(2d,p) PCM(DMSO) method. The analysis of the chemical shift data for these compounds has shown that, indeed, in DMSO solutions they occur as equilibrium mixtures of free molecules and solvates in which solute and solvent molecules are joined by NH···O or OH···O hydrogen bonds. The populations of particular species present in the solutions have been estimated. Moreover, it has been found that 5,6-dihydrothymine exists in DMSO solution preferentially in conformation with the methyl group occupying the pseudoequatorial position. This finding is based on the molecular energy calculations and remains in full agreement with the interpretation of NMR data and theoretical calculations of NMR parameters.
Collapse
Affiliation(s)
- Dominika Kubica
- COBRO - Packaging Research Institute , Konstancińska 11, 02-942 Warsaw, Poland
| | - Sergey Molchanov
- Faculty of Chemistry, Warsaw University of Technology , Noakowskiego 3, 00-664 Warsaw, Poland
| | - Adam Gryff-Keller
- Faculty of Chemistry, Warsaw University of Technology , Noakowskiego 3, 00-664 Warsaw, Poland
| |
Collapse
|
6
|
Martinez-Fernandez L, Fahleson T, Norman P, Santoro F, Coriani S, Improta R. Optical absorption and magnetic circular dichroism spectra of thiouracils: a quantum mechanical study in solution. Photochem Photobiol Sci 2017; 16:1415-1423. [DOI: 10.1039/c7pp00105c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The excited electronic states of thiouracils, the analogues of uracil where the carbonyl oxygens are substituted by sulphur atoms, have been investigated by computing the magnetic circular dichroism (MCD) and one-photon absorption (OPA) spectra at the TD-DFT level of theory.
Collapse
Affiliation(s)
| | - T. Fahleson
- KTH Royal Institute of Technology
- SE-10044 Stockholm
- Sweden
| | - P. Norman
- KTH Royal Institute of Technology
- SE-10044 Stockholm
- Sweden
| | - F. Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR)
- Area della Ricerca del CNR
- I-56124 Pisa
- Italy
| | - S. Coriani
- Department of Chemistry
- Technical University of Denmark
- Denmark
| | - R. Improta
- Istituto di Biostrutture e Bioimmagini-CNR
- I-80134 Napoli
- Italy
- LIDYL
- CEA
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Excited States Behavior of Nucleobases in Solution: Insights from Computational Studies. Top Curr Chem (Cham) 2014; 355:329-57. [DOI: 10.1007/128_2013_524] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
9
|
Muñoz Freán S, Alcolea Palafox M, Rastogi V. Effect of the microhydration on the tautomerism in the anticarcinogenic drug 5-fluorouracil and relationships with other 5-haloderivatives. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
10
|
Relative stability of keto-enol tautomers in 5,6-substituted uracils: Ab initio, DFT and PCM study. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.09.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
11
|
Dybiec K, Molchanov S, Gryff-Keller A. Structure of Neutral Molecules and Monoanions of Selected Oxopurines in Aqueous Solutions As Studied by NMR Spectroscopy and Theoretical Calculations. J Phys Chem A 2011; 115:2057-64. [DOI: 10.1021/jp110888m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Katarzyna Dybiec
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw
| | - Sergey Molchanov
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw
| | - Adam Gryff-Keller
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw
| |
Collapse
|
12
|
Dautova IF, Ivanov SP, Khursan SL. Hydration effect on the stability of the keto-enol tautomers of 5-hydroxy-6-methyluracil. J STRUCT CHEM+ 2010. [DOI: 10.1007/s10947-009-0162-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
13
|
Alcolea Palafox M, Iza N. Tautomerism of the natural thymidine nucleoside and the antiviral analogue D4T. Structure and influence of an aqueous environment using MP2 and DFT methods. Phys Chem Chem Phys 2010; 12:881-93. [DOI: 10.1039/b915566j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
14
|
Rastogi V, Alcolea Palafox M, Guerrero-Martínez A, Tardajos G, Vats J, Kostova I, Schlucker S, Kiefer W. FT-IR and FT-Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometry, atomic charges and some molecular properties of the biomolecule 5-iodouracil. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.10.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
15
|
Bal D, Kraska-Dziadecka A, Gryff-Keller A. Solution Structure of Succinylacetone, An Unsymmetrical β-Diketone, As Studied by 13C NMR and GIAO−DFT Calculations. J Org Chem 2009; 74:8604-9. [DOI: 10.1021/jo901673j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dominika Bal
- Warsaw University of Technology, Faculty of Chemistry, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Anna Kraska-Dziadecka
- Warsaw University of Technology, Faculty of Chemistry, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Adam Gryff-Keller
- Warsaw University of Technology, Faculty of Chemistry, Noakowskiego 3, 00-664 Warsaw, Poland
| |
Collapse
|
16
|
Improta R, Barone V, Lami A, Santoro F. Quantum Dynamics of the Ultrafast ππ*/nπ* Population Transfer in Uracil and 5-Fluoro-Uracil in Water and Acetonitrile. J Phys Chem B 2009; 113:14491-503. [DOI: 10.1021/jp906524p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roberto Improta
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Vincenzo Barone
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Alessandro Lami
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Fabrizio Santoro
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| |
Collapse
|
17
|
|
18
|
Santoro F, Improta R, Barone V. Three-dimensional diabatic models for the ππ* → nπ* excited-state decay of uracil derivatives in solution. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0527-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
19
|
Bagno A, Rastrelli F, Saielli G. Predicting the NMR spectra of nucleotides by DFT calculations: cyclic uridine monophosphate. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:518-524. [PMID: 18327890 DOI: 10.1002/mrc.2204] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We present an experimental and quantum chemical NMR study of the mononucleotide cyclic uridine monophosphate in water. Spectral parameters ((1)H and (13)C chemical shifts and (1)H--(1)H, (13)C--(1)H, (31)P--(13)C and (31)P--(1)H spin-spin coupling constants) have been carefully obtained experimentally and calculated using DFT methods including the solvent effect and the conformational flexibility of the solute. This study confirms that the (1)H and (13)C spectra of polar, flexible molecules in aqueous solution can be predicted with a high level of accuracy, comparable to that obtained for less complex systems.
Collapse
Affiliation(s)
- Alessandro Bagno
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo, 1-35131 Padova, Italy.
| | | | | |
Collapse
|
20
|
Judeinstein P, Iojoiu C, Sanchez JY, Ancian B. Proton Conducting Ionic Liquid Organization as Probed by NMR: Self-Diffusion Coefficients and Heteronuclear Correlations. J Phys Chem B 2008; 112:3680-3. [DOI: 10.1021/jp711298g] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick Judeinstein
- R.M.N. en Milieu Orienté, ICMMO, UMR CNRS 8182, Bâtiment 410, Université Paris-Sud, 91405 Orsay Cedex, France, LEPMI, UMR CNRS 5631-INPG, Université Joseph Fourier, BP.75. 38402 Saint-Martin-d'Hères Cedex, France, and UFR Chimie, Tour 44-54, Université Paris-Diderot, 75251 Paris Cedex, France
| | - Cristina Iojoiu
- R.M.N. en Milieu Orienté, ICMMO, UMR CNRS 8182, Bâtiment 410, Université Paris-Sud, 91405 Orsay Cedex, France, LEPMI, UMR CNRS 5631-INPG, Université Joseph Fourier, BP.75. 38402 Saint-Martin-d'Hères Cedex, France, and UFR Chimie, Tour 44-54, Université Paris-Diderot, 75251 Paris Cedex, France
| | - Jean-Yves Sanchez
- R.M.N. en Milieu Orienté, ICMMO, UMR CNRS 8182, Bâtiment 410, Université Paris-Sud, 91405 Orsay Cedex, France, LEPMI, UMR CNRS 5631-INPG, Université Joseph Fourier, BP.75. 38402 Saint-Martin-d'Hères Cedex, France, and UFR Chimie, Tour 44-54, Université Paris-Diderot, 75251 Paris Cedex, France
| | - Bernard Ancian
- R.M.N. en Milieu Orienté, ICMMO, UMR CNRS 8182, Bâtiment 410, Université Paris-Sud, 91405 Orsay Cedex, France, LEPMI, UMR CNRS 5631-INPG, Université Joseph Fourier, BP.75. 38402 Saint-Martin-d'Hères Cedex, France, and UFR Chimie, Tour 44-54, Université Paris-Diderot, 75251 Paris Cedex, France
| |
Collapse
|
21
|
Alcolea Palafox M, Tardajos G, Guerrero-Martínez A, Rastogi V, Mishra D, Ojha S, Kiefer W. FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular geometry of biomolecule 5-aminouracil. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.07.032] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
22
|
Zhang L, Li H, Hu X, Jalbout AF. Theoretical study of the influence of ribose on the proton transfer phenomenon of nucleic acid bases. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.06.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
23
|
Hu X, Li H, Zhang L, Han S. Tautomerism of Uracil and 5-Bromouracil in a Microcosmic Environment with Water and Metal Ions. What Roles Do Metal Ions Play? J Phys Chem B 2007; 111:9347-54. [PMID: 17625822 DOI: 10.1021/jp0709454] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The base tautomerization processes of uracil/5-bromouracil were investigated in a microcosmic environment with both H2O and Na+ (W-M environment). It was found that uracil was more stable in the W-M environment than in the microcosmic environment with only water, which suggested that the metal ions and water work cooperated to maintain the classical nucleic acid bases. However, 5-bromouracil, a chemical mutagen, was found to be less stable than uracil in the W-M environment. Why the 5-bromouracil is easier to tautomerize and therefore induce gene mutation was explained to some extent. Further research revealed that the water molecule would assist the tautomerization in the W-M environment. However, the metal ions in different regions play absolutely opposite roles: in one region, the metal ions can prevent the base from tautomerizing, whereas in another region, the metal ion can assist the tautomerization process. Furthermore, from the viewpoint of ionization of the base, it seems BrU has a stronger tendency to lose the proton at N3, which is an intrinsic consequence of the bromine atom and is not affected by the metal cation.
Collapse
Affiliation(s)
- Xingbang Hu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
| | | | | | | |
Collapse
|
24
|
Bao X, Liang G, Wong NB, Gu J. Microsolvation Pattern of the Hydrated Radical Anion of Uracil: U-(H2O)n (n = 3−5). J Phys Chem A 2007; 111:666-72. [PMID: 17249757 DOI: 10.1021/jp064761l] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The microsolvation patterns of the uracil radical anion in water clusters U-(H2O)n with n ranging from 3 to 5 were investigated by the density functional theory approach. The electron detachment energies (VDE) of the stable anionic complexes with different numbers of hydration water are predicted. The linear dependence of the VDE value of the most stable anionic complexes with respect to the hydration number suggests the importance of the clustered waters in the microsolvation of the radical anion of the nucleobases. The formation of the water clusters is found to be necessary in the most stable conformers of the tri-, tetra-, and pentahydrated radical anion of uracil. The microsolvation pattern with three or more well-separated hydration water molecules in the first hydration layer is less stable than the arrangement with the waters in tight clusters. The charge transfer between the anionic uracil and the hydration water is high. Good agreement between the experimental and the theoretical vertical detachment energy yield in this study further demonstrates the practicability of the B3LYP/DZP++ approach in the study of radical anions of the DNA subunits.
Collapse
Affiliation(s)
- Xiaoguang Bao
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203, China
| | | | | | | |
Collapse
|
25
|
Seba HB, Thureau P, Ancian B, Thévand A. Combined use of Overhauser spectroscopy and NMR diffusion experiments for mapping the hydration structure of nucleosides: structure and dynamics of uridine in water. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44:1109-17. [PMID: 17016868 DOI: 10.1002/mrc.1909] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Complementary results from 13C intermolecular nuclear Overhauser effects (NOE), 1H-13C heteronuclear Overhauser spectroscopy (HOSEY) and 1H-NMR diffusion measurements were used for probing the structure of the first solvation shell of uridine in water. It is demonstrated that a cyclic dihydrate is formed. The two water molecules produce two hydrogen bonds with the two oxygen atoms from the pyrimidine ring and accept only one hydrogen bond from the amide proton. The dihydrate has only a short lifetime as compared with the rotational correlation time of the free nucleoside. The chemical exchange constant of the amide proton with water is then estimated by diffusion experiments. The results are consistent with previous data obtained for uracil in water and provide interesting information about water accessibility in nucleic acid bases.
Collapse
Affiliation(s)
- Hadj B Seba
- Jeune Equipe 2421 TRACES, Université de Provence, case 512, Centre St Jérôme, 13397 Marseille Cedex 20, France
| | | | | | | |
Collapse
|
26
|
Santoro F, Barone V, Gustavsson T, Improta R. Solvent Effect on the Singlet Excited-State Lifetimes of Nucleic Acid Bases: A Computational Study of 5-Fluorouracil and Uracil in Acetonitrile and Water. J Am Chem Soc 2006; 128:16312-22. [PMID: 17165786 DOI: 10.1021/ja0657861] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first comprehensive quantum mechanical study of solvent effects on the behavior of the two lowest energy excited states of uracil derivatives is presented. The absorption and emission spectra of uracil and 5-fluorouracil in acetonitrile and aqueous solution have been computed at the time-dependent density-functional theory level, using the polarizable continuum model (PCM) to take into account bulk solvent effects. The computed spectra and the solvent shifts provided by our method are close to their experimental counterpart. The S0/S1 conical intersection, located in the presence of hydrogen-bonded solvent molecules by CASSCF (8/8) calculations, indicates that the mechanism of ground-state recovery, involving out-of-plane motion of the 5 substituent, does not depend on the nature of the solvent. Extensive explorations of the excited-state surfaces in the Franck-Condon (FC) region show that solvent can modulate the accessibility of an additional decay channel, involving a dark n/pi* excited state. This finding provides the first unifying explanation for the experimental trend of 5-fluorouracil excited-state lifetime in different solvents. The microscopic mechanisms underlying solvent effects on the excited-state behavior of nucleobases are discussed.
Collapse
Affiliation(s)
- Fabrizio Santoro
- Istituto per i Processi Chimico-Fisici del CNR, Area della Ricerca del CNR di Pisa, via Moruzzi 1, I-56124 Pisa, Italy
| | | | | | | |
Collapse
|
27
|
Shukla M, Leszczynski J. A theoretical study of hydration of 4-thiouracil in the electronic singlet excited state. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2006.03.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
28
|
Nordstierna L, Yushmanov PV, Furó I. Solute-solvent contact by intermolecular cross relaxation. I. The nature of the water-hydrophobic interface. J Chem Phys 2006; 125:074704. [PMID: 16942361 DOI: 10.1063/1.2336199] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Intermolecular cross-relaxation rates between solute and solvent were measured by {1H} 19F nuclear magnetic resonance experiments in aqueous molecular solutions of ammonium perfluoro-octanoate and sodium trifluoroacetate. The experiments performed at three different magnetic fields provide frequency-dependent cross-relaxation rates which demonstrate clearly the lack of extreme narrowing for nuclear spin relaxation by diffusionally modulated intermolecular interactions. Supplemented by suitable intramolecular cross-relaxation, longitudinal relaxation, and self-diffusion data, the obtained cross-relaxation rates are evaluated within the framework of recent relaxation models and provide information about the hydrophobic hydration. In particular, water dynamics around the trifluoromethyl group in ammonium perfluoro-octanoate are more retarded than that in the smaller trifluoroacetate.
Collapse
Affiliation(s)
- Lars Nordstierna
- Division of Physical Chemistry and Industrial NMR Center, Department of Chemistry, Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | | | | |
Collapse
|
29
|
Thureau P, Ancian B, Viel S, Thévand A. Determining chemical exchange rates of the uracil labile protons by NMR diffusion experiments. Chem Commun (Camb) 2006:200-2. [PMID: 16372105 DOI: 10.1039/b513580j] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The exchange rates of the amido-protons of uracil with water were determined by NMR diffusion experiments and the results showed a factor 2 difference in lability between them, which was confirmed by more classical 2D-NMR exchange experiments.
Collapse
Affiliation(s)
- Pierre Thureau
- Jeune Equipe 2421 TRACES, Université de Provence et Paul Cézanne, Centre de St Jérome, 13397 Marseille cedex 20, France
| | | | | | | |
Collapse
|
30
|
Gustavsson T, Bányász A, Lazzarotto E, Markovitsi D, Scalmani G, Frisch MJ, Barone V, Improta R. Singlet Excited-State Behavior of Uracil and Thymine in Aqueous Solution: A Combined Experimental and Computational Study of 11 Uracil Derivatives. J Am Chem Soc 2006; 128:607-19. [PMID: 16402849 DOI: 10.1021/ja056181s] [Citation(s) in RCA: 306] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The excited-state properties of uracil, thymine, and nine other derivatives of uracil have been studied by steady-state and time-resolved spectroscopy. The excited-state lifetimes were measured using femtosecond fluorescence upconversion in the UV. The absorption and emission spectra of five representative compounds have been computed at the TD-DFT level, using the PBE0 exchange-correlation functional for ground- and excited-state geometry optimization and the Polarizable Continuum Model (PCM) to simulate the aqueous solution. The calculated spectra are in good agreement with the experimental ones. Experiments show that the excited-state lifetimes of all the compounds examined are dominated by an ultrafast (<100 fs) component. Only 5-substituted compounds show more complex behavior than uracil, exhibiting longer excited-state lifetimes and biexponential fluorescence decays. The S(0)/S(1) conical intersection, located at CASSCF (8/8) level, is indeed characterized by pyramidalization and out of plane motion of the substituents on the C5 atom. A thorough analysis of the excited-state Potential Energy Surfaces, performed at the PCM/TD-DFT(PBE0) level in aqueous solution, shows that the energy barrier separating the local S(1) minimum from the conical intersection increases going from uracil through thymine to 5-fluorouracil, in agreement with the ordering of the experimental excited-state lifetime.
Collapse
Affiliation(s)
- Thomas Gustavsson
- Laboratoire Francis Perrin, CEA/DSM/DRECAM/SPAM - CNRS URA 2453, CEA Saclay, Gif-sur-Yvette, France.
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Thureau P, Ancian B, Viel S, Thévand A. NMR diffusion and nuclear Overhauser investigation of the hydration properties of thymine: influence of the methyl group. Chem Commun (Camb) 2006:1884-6. [PMID: 16622517 DOI: 10.1039/b601289b] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The absence of preferential hydration in thymine and its lowest water accessibility with respect to uracil were evidenced by NMR diffusion and HOESY experiments; the hydration differences observed between these pyrimidine bases were attributed to the electronic rather than steric properties of the methyl group.
Collapse
Affiliation(s)
- Pierre Thureau
- Jeune Equipe 2421 TRACES, Université de Provence et Paul Cézanne, case 512, Centre de St Jérôme, 13397 Marseille cedex 20, France.
| | | | | | | |
Collapse
|
32
|
Close DM, Crespo-Hernández CE, Gorb L, Leszczynski J. The Influence of Microhydration on the Ionization Energy Thresholds of Uracil and Thymine. J Phys Chem A 2005; 109:9279-83. [PMID: 16833269 DOI: 10.1021/jp053235b] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the present study the ionization energy thresholds (IET's) of uracil and thymine have been calculated (with the B3LYP, PMP2, and P3 levels of theory using the standard 6-31++G(d,p) basis set) with one to three water molecules placed in the first hydration shell. Then (B3LYP) polarizable continuum model (PCM) calculations were performed with one to three waters of the hydration shell included. Calculations show there is a distinct effect of microhydration on uracil and thymine. For uracil, one added water results in a decrease in the IET of about 0.15 eV. The second and third water molecules cause a further decrease by about 0.07 eV each. For thymine, the first water molecule is seen to decrease the IET by about 0.1 eV, while the second and third water molecules cause a further decrease of less than 0.1 eV each. The changes in IET calculated here for thymine with one to three waters of hydration are smaller than the experimental values determined by Kim et al. (Kim, S. K.; Lee, W.; Herschbach, D. R. J. Phys. Chem. 1996, 100, 7933). Preliminary results presented here indicate that the experimental results may involve keto-enol tautomers of thymine. The results of placing the microhydrated structures of uracil and thymine in a PCM cavity was seen to make very little difference in the IET when compared to the IET of ordinary uracil or thymine in a PCM cavity. The implications are that accurate calculations of the IET's of uracil and thymine can be obtained by simply considering long-range solvation effects.
Collapse
Affiliation(s)
- David M Close
- Department of Physics, Box 70652, East Tennessee State University, Johnson City, TN 37614, USA.
| | | | | | | |
Collapse
|
33
|
Shukla MK, Leszczynski J. Effect of Hydration on the Lowest Singlet ππ* Excited-State Geometry of Guanine: A Theoretical Study. J Phys Chem B 2005; 109:17333-9. [PMID: 16853213 DOI: 10.1021/jp0520751] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An ab-initio computational study was performed to investigate the effect of explicit hydration on the ground and lowest singlet PiPi* excited-state geometry and on the selected stretching vibrational frequencies corresponding to the different NH sites of the guanine acting as hydrogen-bond donors. The studied systems consisted of guanine interacting with one, three, five, six, and seven water molecules. Ground-state geometries were optimized at the HF level, while excited-state geometries were optimized at the CIS level. The 6-311G(d,p) basis set was used in all calculations. The nature of potential energy surfaces was ascertained via the harmonic vibrational frequency analysis; all structures were found minima at the respective potential energy surfaces. The changes in the geometry and the stretching vibrational frequencies of hydrogen-bond-donating sites of the guanine in the ground and excited state consequent to the hydration are discussed. It was found that the first solvation shell of the guanine can accommodate up to six water molecules. The addition of the another water molecule distorts the hydrogen-bonding network by displacing other neighboring water molecules away from the guanine plane.
Collapse
Affiliation(s)
- M K Shukla
- Computational Centre for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS 39217, USA
| | | |
Collapse
|
34
|
Improta R, Barone V. Absorption and Fluorescence Spectra of Uracil in the Gas Phase and in Aqueous Solution: A TD-DFT Quantum Mechanical Study. J Am Chem Soc 2004; 126:14320-1. [PMID: 15521728 DOI: 10.1021/ja0460561] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we present the first computations of fluorescence spectra in aqueous solution at an accurate quantum mechanical level. From a methodological point of view, our study shows that by only taking into account both bulk effects and explicit solvent molecules it is possible to reproduce solvent effects on the energy and the intensities of the electronic spectra, especially for what concerns pi/pi* transition. The computed absorption and fluorescence spectra are in a good agreement with the available experimental results. The energy ordering between the lowest energy n-pi* and the pi/pi* transitions in uracil strongly depends on the nature of the embedding medium. The geometry of the first solvation shell is remarkably sensitive to the specific electronic state, suggesting that solvent degrees of freedom can act as S1/S2 coupling modes.
Collapse
Affiliation(s)
- Roberto Improta
- Dipartimento di Chimica, Università Federico II, Complesso Universitario Monte S. Angelo, Via Cintia, I-80126 Napoli, Italy.
| | | |
Collapse
|
35
|
Hu X, Li H, Liang W, Han S. Theoretical Study of the Proton Transfer of Uracil and (Water)n(n= 0−4): Water Stabilization and Mutagenicity for Uracil. J Phys Chem B 2004. [DOI: 10.1021/jp048146y] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
36
|
Gaigeot MP, Sprik M. Ab Initio Molecular Dynamics Study of Uracil in Aqueous Solution. J Phys Chem B 2004. [DOI: 10.1021/jp049940m] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marie-Pierre Gaigeot
- Laboratoire de Modelisation des Systemes Moleculaires Complexes, Université d'Evry val d'Essonne, Rue Pere A Jarland, F-91025, France
| | - Michiel Sprik
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, United Kingdom
| |
Collapse
|
37
|
Shukla MK, Leszczynski J. Interaction of Water Molecules with Cytosine Tautomers: An Excited-State Quantum Chemical Investigation. J Phys Chem A 2002. [DOI: 10.1021/jp021317j] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. K. Shukla
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217
| | - Jerzy Leszczynski
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217
| |
Collapse
|
38
|
Shukla MK, Leszczynski J. Phototautomerism in Uracil: A Quantum Chemical Investigation. J Phys Chem A 2002. [DOI: 10.1021/jp0209650] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. K. Shukla
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217
| | - Jerzy Leszczynski
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217
| |
Collapse
|
39
|
Strickler MA, Gerig JT. Intermolecular Overhauser effects in fluoroalcohol solutions of cyclo-alanylglycine. Biopolymers 2002; 64:227-35. [PMID: 12115130 DOI: 10.1002/bip.10176] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Interactions between the diketopiperazine cyclo-alanylglycine and four fluorinated alcohols in water-fluoroalcohol mixtures were examined by (1)H[(19)F] intermolecular nuclear Overhauser effects (NOE) experiments. The alcohols studied were trifluoroethanol, hexafluoroacetone trihydrate, 1,1,1,3,3,3-hexafluoroisopropanol and perfluoro-t-butanol. The experimental methods used permit detection of solvent-solute NOEs of 0.1% or less. Solute and solvent diffusion coefficients were determined and apparent molecular radii of the fluoroalcohols estimated. Using these data, it was shown that observed (1)H[(19)F] intermolecular NOEs are consistent with expectations based on theory. A method for extending conventional theory to take into account the shape of a solute and the exposure of its hydrogens to solvent is described. This approach gives reasonable agreement with experimental results, particularly if it is assumed that solute-solvent interactions take place in such a way that the fluorines of a fluoroalcohol are preferentially oriented toward the solute during solute-solvent encounters. The results support the suggestion that intermolecular (1)H[(19)F] NOEs may become a useful tool for studies of peptide and protein conformations in fluoroalcohol-water solvent mixtures.
Collapse
Affiliation(s)
- M A Strickler
- Department of Chemistry and Biochemistry, University of California, Santa Barbara 93106, USA
| | | |
Collapse
|
40
|
Bagno A. Probing the solvation shell of organic molecules by intermolecular1H NOESY. J PHYS ORG CHEM 2002. [DOI: 10.1002/poc.543] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
41
|
Ancian B, Canet D, Mutzenhardt P. Measurement of weak heteronuclear (13C–1H) Overhauser effects involving carbons not directly bonded to protons. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)00138-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
42
|
Gadre SR, Babu K, Rendell AP. Electrostatics for Exploring Hydration Patterns of Molecules. 3. Uracil. J Phys Chem A 2000. [DOI: 10.1021/jp001146n] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - K. Babu
- Department of Chemistry, University of Pune, Pune-411 007, India
| | - Alistair P. Rendell
- Supercomputer Facility, Australian National University, Canberra, ACT 0200, Australia
| |
Collapse
|
43
|
Shukla M, Leszczynski J. A DFT investigation on effects of hydration on the tautomeric equilibria of hypoxanthine. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0166-1280(00)00536-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
44
|
Shukla MK, Leszczynski J. Theoretical Study of Proton Transfer in Hypoxanthine Tautomers: Effects of Hydration. J Phys Chem A 2000. [DOI: 10.1021/jp9940912] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. K. Shukla
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J.R. Lynch Street, Jackson, Mississippi 39217 and Department of Physics, Banaras Hindu University, Varanasi-221005, India
| | - Jerzy Leszczynski
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J.R. Lynch Street, Jackson, Mississippi 39217 and Department of Physics, Banaras Hindu University, Varanasi-221005, India
| |
Collapse
|
45
|
|
46
|
Dickinson JA, Hockridge MR, Robertson EG, Simons JP. Molecular and Supramolecular Structures of N-Phenyl Formamide and its Hydrated Clusters. J Phys Chem A 1999. [DOI: 10.1021/jp991254d] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John A. Dickinson
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, U.K
| | - Matthew R. Hockridge
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, U.K
| | - Evan G. Robertson
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, U.K
| | - John P. Simons
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, U.K
| |
Collapse
|
47
|
Current Trends in Modeling Interactions of DNA Fragments with Polar Solvents. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1380-7323(99)80080-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
|