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Weng G, Pang A, Vlček V. Spatial Decay and Limits of Quantum Solute-Solvent Interactions. J Phys Chem Lett 2023; 14:2473-2480. [PMID: 36867592 DOI: 10.1021/acs.jpclett.3c00208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Molecular excitations in the liquid-phase environment are renormalized by the surrounding solvent molecules. Herein, we employ the GW approximation to investigate the solvation effects on the ionization energy of phenol in various solvent environments. The electronic effects differ by up to 0.4 eV among the five investigated solvents. This difference depends on both the macroscopic solvent polarizability and the spatial decay of the solvation effects. The latter is probed by separating the electronic subspace and the GW correlation self-energy into fragments. The fragment correlation energy decays with increasing intermolecular distance and vanishes at ∼9 Å, and this pattern is independent of the type of solvent environment. The 9 Å cutoff defines an effective interacting volume within which the ionization energy shift per solvent molecule is proportional to the macroscopic solvent polarizability. Finally, we propose a simple model for computing the ionization energies of molecules in an arbitrary solvent environment.
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Affiliation(s)
- Guorong Weng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Amanda Pang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Vojtěch Vlček
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
- Materials Department, University of California, Santa Barbara, California 93106-5050, United States
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2
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Theoretical Prediction of pH-dependent Electronic Spectra in Aqueous Solution: A Combinational Application of QM/MM Calculations and Constant-pH Simulations with Configuration-Selection Scheme. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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3
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Gonçalves A, Raiol A, da Cunha AR, Manzoni V, Andrade-Filho T, Gester R. Insights on the crossing of the two lowest n-π∗ and π-π∗ absorption lines of thieno[3,4-b]pyrazine in an aqueous environment. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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4
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Theoretical analysis of the influence of C–H$$\cdots $$O bonds on the NMR constants of uracil in DMSO. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02670-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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5
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Solvent effects on low-lying absorptions and vibrational spectra of thieno[3,4-b]pyrazines: the role of unconventional C–H···N bonds. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00703-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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6
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Dimić D. The importance of specific solvent–solute interactions for studying UV–vis spectra of light-responsive molecular switches. CR CHIM 2018. [DOI: 10.1016/j.crci.2018.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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7
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Bistafa C, Kitamura Y, Nagaoka M, Canuto S. Microscopic Origin of Different Hydration Patterns of para-Nitrophenol and Its Anion: A Study Combining Multiconfigurational Calculations and the Free-Energy Gradient Method. J Phys Chem B 2018; 122:9202-9209. [PMID: 30160963 DOI: 10.1021/acs.jpcb.8b06439] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A theoretical study of the solvatochromic shifts of para-nitrophenol ( pNP) and para-nitrophenolate anion ( pNP-) in aqueous solution is presented using a QM/MM methodology with molecular dynamics simulation. The optimized structures in aqueous solution are obtained using both the polarizable continuum and the free-energy gradient methods. For pNP, the calculated redshifts at the CASPT2 (12,10) level are, respectively, 0.71 and 0.94 eV, in good agreement with the experimental ones (0.80-0.83 eV), whereas for pNP-, they are small. The difference between the solvatochromic shifts of pNP and pNP- is calculated as 0.71 eV in good agreement with the experimental one (0.79-0.81 eV). Finally, these shifts are understood in terms of the solvent effect on the solute structure, accurately calculated by the present theoretical treatment.
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Affiliation(s)
- Carlos Bistafa
- Institute of Physics , University of São Paulo , Rua do Matão, 1371 , Cidade Universitária, São Paulo-SP 05508-090 , Brazil.,Graduate School of Informatics , Nagoya University , Furo-cho, Chikusa-ku, Nagoya , Aichi 464-8601 , Japan.,Core Research for Evolutional Science and Technology (CREST) , Japan Science and Technology Agency (JST) , Honmachi, Kawaguchi 332-0012 , Japan
| | - Yukichi Kitamura
- Graduate School of Informatics , Nagoya University , Furo-cho, Chikusa-ku, Nagoya , Aichi 464-8601 , Japan.,Core Research for Evolutional Science and Technology (CREST) , Japan Science and Technology Agency (JST) , Honmachi, Kawaguchi 332-0012 , Japan
| | - Masataka Nagaoka
- Graduate School of Informatics , Nagoya University , Furo-cho, Chikusa-ku, Nagoya , Aichi 464-8601 , Japan.,Core Research for Evolutional Science and Technology (CREST) , Japan Science and Technology Agency (JST) , Honmachi, Kawaguchi 332-0012 , Japan
| | - Sylvio Canuto
- Institute of Physics , University of São Paulo , Rua do Matão, 1371 , Cidade Universitária, São Paulo-SP 05508-090 , Brazil
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8
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Valverde D, Vasconcelos Sanches de Araujo A, Carlos Borin A, Canuto S. Electronic structure and absorption spectra of fluorescent nucleoside analogues. Phys Chem Chem Phys 2017; 19:29354-29363. [PMID: 29075734 DOI: 10.1039/c7cp04885h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This work presents a systematic investigation of the electronic and conformational properties of five new fluorescent nucleobases belonging to the alphabet based on the isothiazole[4,3-d]pyrimidine molecule, very recently synthesized. This is of particular importance in the characterization of the main electronic aspects of these fluorescent nucleosides. The solvent effects of 1,4-dioxane and water were included combining the Sequential Monte Carlo/CASPT2 and the Free Energy Gradient (FEG) methods. For comparison, the Polarizable Continuum method was also used. The geometries of all compounds were optimized in solvent with the largest effects observed in water using the average solvent electrostatic configuration (ASEC) and the FEG approaches. Statistical analysis of the solute-solvent hydrogen bonds is performed and their effect on the absorption spectra analyzed. The dipole moments were calculated and the value obtained from the ASEC-FEG method in water follows the same trend as the natural canonical bases (adenine → uracil → guanine → cytosine). The theoretical results for the absorption spectra obtained from CASPT2(18,13) calculations using the geometries obtained with the ASEC-FEG procedure are in very good agreement with the experimental data. A detailed elucidation of the main aspects of the absorption spectra of the five new fluorescent nucleoside analogues is successfully attempted.
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Affiliation(s)
- Danillo Valverde
- Universidade de São Paulo, Instituto de Física, Rua do Matão 1371, São Paulo, SP CEP 05508-090, Brazil.
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9
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Chen Y, Li Y. QSAR Model-assisted Prediction of Largest Ultraviolet Absorption Wavelength of PCBs Based on Solvent Effects. CHEM LETT 2016. [DOI: 10.1246/cl.160650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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10
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Martínez-Fernández L, Pepino AJ, Segarra-Martí J, Banyasz A, Garavelli M, Improta R. Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models. J Chem Theory Comput 2016; 12:4430-9. [DOI: 10.1021/acs.jctc.6b00518] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- L. Martínez-Fernández
- Istituto di Biostrutture
e Bioimmagini, CNR, Via Mezzocannone
16, I-80134 Napoli, Italy
| | - A. J. Pepino
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, Bologna, Italy
| | - J. Segarra-Martí
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, Bologna, Italy
- École
Normale Supérieure de Lyon, CNRS, UMR 5182, Université de Lyon, 46 Allée d’Italie, F-69364 Lyon Cedex 07, France
| | - A. Banyasz
- LIDYL,
CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - M. Garavelli
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, Bologna, Italy
- École
Normale Supérieure de Lyon, CNRS, UMR 5182, Université de Lyon, 46 Allée d’Italie, F-69364 Lyon Cedex 07, France
| | - R. Improta
- Istituto di Biostrutture
e Bioimmagini, CNR, Via Mezzocannone
16, I-80134 Napoli, Italy
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11
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A complete basis set study of the lowest n–π* and π–π* electronic transitions of acrolein in explicit water environment. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1891-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Oviedo MB, Wong BM. Real-Time Quantum Dynamics Reveals Complex, Many-Body Interactions in Solvated Nanodroplets. J Chem Theory Comput 2016; 12:1862-71. [PMID: 26918732 DOI: 10.1021/acs.jctc.5b01019] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electronic excitations in the liquid phase are surprisingly rich and considerably more complex than either gas-phase or solid-state systems. While the majority of physical and biological processes take place in solvent, our understanding of nonequilibrium excited-state processes in these condensed phase environments remains far from complete. A central and long-standing issue in these solvated environments is the assessment of many-body interactions, particularly when the entire system is out of equilibrium and many quantum states participate in the overall process. Here we present a microscopic picture of solute-solvent electron dynamics and solvatochromic effects, which we uncover using a new real-time quantum dynamics approach for extremely large solvated nanodroplets. In particular, we find that a complex interplay of quantum interactions underlies our observations of solute-solvent effects, and simple macroscopic solvatochromic shifts can even be qualitatively different at the microscopic molecular level in these systems. By treating both the solvent and the solute on the same footing at a quantum-mechanical level, we demonstrate that the electron dynamics in these systems are surprisingly complex, and the emergence of many-body interactions underlies the dynamics in these solvated systems.
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Affiliation(s)
- M Belén Oviedo
- Department of Chemical & Environmental Engineering and Materials Science & Engineering Program, University of California, Riverside , Riverside, California 92521, United States
| | - Bryan M Wong
- Department of Chemical & Environmental Engineering and Materials Science & Engineering Program, University of California, Riverside , Riverside, California 92521, United States
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13
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Ravi Kumar V, Verma C, Umapathy S. Molecular dynamics and simulations study on the vibrational and electronic solvatochromism of benzophenone. J Chem Phys 2016; 144:064302. [DOI: 10.1063/1.4941058] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Modesto-Costa L, Uhl E, Borges I. Water solvent effects using continuum and discrete models: The nitromethane molecule, CH3NO2. J Comput Chem 2015; 36:2260-9. [DOI: 10.1002/jcc.24208] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 08/04/2015] [Accepted: 08/30/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Lucas Modesto-Costa
- Departamento De Química; Instituto Militar De Engenharia; Praça General Tibúrcio, 80 22290-270 Rio De Janeiro Brazil
| | - Elmar Uhl
- Programa De Pós-Graduação Em Engenharia De Defesa, Divisão de Ensino e Pesquisa; Instituto Militar De Engenharia; Praça General Tibúrcio, 80 Rio De Janeiro 22290-270 Brazil
| | - Itamar Borges
- Departamento De Química; Instituto Militar De Engenharia; Praça General Tibúrcio, 80 22290-270 Rio De Janeiro Brazil
- Programa De Pós-Graduação Em Engenharia De Defesa, Divisão de Ensino e Pesquisa; Instituto Militar De Engenharia; Praça General Tibúrcio, 80 Rio De Janeiro 22290-270 Brazil
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15
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Li C, Fu Z, Zhang X, Liu Y, Wang Y. Theoretical study of iron acyl complexes modeling the active site of [Fe]-hydrogenase: Solvation effects play a significant role. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Tuncelli G, Ay AN, Zümreoglu-Karan B. 5-Fluorouracil intercalated iron oxide@layered double hydroxide core-shell nano-composites with isotropic and anisotropic architectures for shape-selective drug delivery applications. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2015; 55:562-8. [PMID: 26117790 DOI: 10.1016/j.msec.2015.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 02/21/2015] [Accepted: 06/02/2015] [Indexed: 11/29/2022]
Abstract
We report the synthesis, characterization and in vitro release behavior of anti-cancer drug carrying iron oxide@layered double hydroxide core-shell nanocomposites with sizes ranging from 40 to 300 nm, good drug loading capacities and soft ferromagnetic properties. HRTEM analyses verified that nearly spherical isotropic carriers were obtained by coating spherical magnetite particles while anisotropic carriers were obtained by coating spindle-shaped hematite particles. They both displayed a fluctuating in vitro release profile with a higher release percentage for the anisotropic carrier.
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Affiliation(s)
- Gülsevde Tuncelli
- Hacettepe University, Chemistry Department, Beytepe Campus, 06800 Ankara, Turkey
| | - Ahmet Nedim Ay
- Hacettepe University, Chemistry Department, Beytepe Campus, 06800 Ankara, Turkey.
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17
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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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18
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Orestes E, Bistafa C, Rivelino R, Canuto S. Including Thermal Disorder of Hydrogen Bonding to Describe the Vibrational Circular Dichroism Spectrum of Zwitterionic l-Alanine in Water. J Phys Chem A 2014; 119:5099-106. [DOI: 10.1021/jp508205k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Ednilsom Orestes
- Instituto
de Química, Universidade Federal Fluminense Campus do Valonguinho, CEP 24020-141, Niterói, RJ, Brazil
| | - Carlos Bistafa
- Instituto
de Física, Universidade de São Paulo, CP 66318, 05914-370 São Paulo, SP, Brazil
| | - Roberto Rivelino
- Instituto
de Física, Universidade de São Paulo, CP 66318, 05914-370 São Paulo, SP, Brazil
- Instituto
de Física, Universidade Federal da Bahia, 40210-340 Salvador, BA, Brazil
| | - Sylvio Canuto
- Instituto
de Física, Universidade de São Paulo, CP 66318, 05914-370 São Paulo, SP, Brazil
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19
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Bistafa C, Georg HC, Canuto S. Combining ab initio multiconfigurational and Free Energy Gradient methods to study the π–π* excited state structure and properties of uracil in water. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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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]
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21
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ZHAO YUAN, CAO ZEXING. ABSORPTION SPECTRA OF NUCLEIC ACID BASES IN WATER ENVIRONMENT: INSIGHTS INTO FROM COMBINED QM/MM AND CLUSTER-CONTINUUM MODEL CALCULATIONS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613410137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Electronic spectra of uracil, thymine, adenine, guanine, and cytosine in the gas phase and aqueous solution have been studied by extensive time-dependent density functional calculations. Calculations show that the Quantum mechanics/molecular mechanics (QM/MM) geometry optimization based on the molecular dynamics (MD) equilibrated configuration can locate an optimal solvated cluster for the base solvation, and the combined QM/MM and cluster-continuum computational protocol is capable of handling the solvent effect on the excited states of nucleic acid bases and providing realistic absorption spectra in water environment with relatively low computational costs. Generally, the vertical excitation energies in aqueous solution by PCM/TD-X3LYP calculations show excellent agreement with the experimental observations and the maximum deviation is less than 0.2 eV. The present results reveal that the hydrogen bond network around the excited-state base and its dipole moment change may remarkably modify the absorption spectra of nucleic acid bases in aqueous solution.
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Affiliation(s)
- YUAN ZHAO
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - ZEXING CAO
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
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22
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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]
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23
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Theoretically describing the 17O magnetic shielding constant of biomolecular systems: uracil and 5-fluorouracil in water environment. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1424-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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