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Gabas F, Di Liberto G, Ceotto M. Vibrational investigation of nucleobases by means of divide and conquer semiclassical dynamics. J Chem Phys 2019; 150:224107. [PMID: 31202241 DOI: 10.1063/1.5100503] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we report a computational study of the vibrational features of four different nucleobases employing the divide-and-conquer semiclassical initial value representation molecular dynamics method. Calculations are performed on uracil, cytosine, thymine, and adenine. Results show that the overall accuracy with respect to experiments is within 20 wavenumbers, regardless of the dimensionality of the nucleobase. Vibrational estimates are accurate even in the complex case of cytosine, where two relevant conformers are taken into account. These results are promising in the perspective of future studies on more complex systems, such as nucleotides or nucleobase pairs.
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Affiliation(s)
- Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Giovanni Di Liberto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
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2
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Buchholz M, Grossmann F, Ceotto M. Simplified approach to the mixed time-averaging semiclassical initial value representation for the calculation of dense vibrational spectra. J Chem Phys 2018; 148:114107. [DOI: 10.1063/1.5020144] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Max Buchholz
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy
| | - Frank Grossmann
- Institut für Theoretische Physik, Technische Universität Dresden, 01062 Dresden, Germany
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy
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3
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Kovac PA, Cina JA. Mixed quantum/semiclassical wave-packet dynamical method for condensed-phase molecular spectroscopy signals. J Chem Phys 2017; 147:224112. [DOI: 10.1063/1.5003386] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Philip A. Kovac
- Department of Chemistry and Biochemistry, and Oregon Center for Optical, Molecular, and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
| | - Jeffrey A. Cina
- Department of Chemistry and Biochemistry, and Oregon Center for Optical, Molecular, and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
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4
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Lu L, Zhu S, Zhang H, Li F, Zhang S. Theoretical study of complexation of resveratrol with cyclodextrins and cucurbiturils: structure and antioxidative activity. RSC Adv 2015. [DOI: 10.1039/c4ra14737e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The inclusion complexation of resveratrol with cyclodextrins and cucurbiturils and the influence of complexation on the antioxidative activity of resveratrol have been theoretically studied.
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Affiliation(s)
- Lilin Lu
- The State Key Laboratory of Refractories and Metallurgy
- Wuhan University of Science and Technology
- Wuhan 430081
- China
- Hubei Province Key Laboratory of Coal Conversion and New Carbon Materials
| | - Shufang Zhu
- School of Resource and Environmental Engineering
- Wuhan University of Science and Technology
- Wuhan 430081
- China
| | - Haijun Zhang
- The State Key Laboratory of Refractories and Metallurgy
- Wuhan University of Science and Technology
- Wuhan 430081
- China
| | - Faliang Li
- The State Key Laboratory of Refractories and Metallurgy
- Wuhan University of Science and Technology
- Wuhan 430081
- China
| | - Shaowei Zhang
- The State Key Laboratory of Refractories and Metallurgy
- Wuhan University of Science and Technology
- Wuhan 430081
- China
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5
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Cheng X, Cina JA. Variational mixed quantum/semiclassical simulation of dihalogen guest and rare-gas solid host dynamics. J Chem Phys 2014; 141:034113. [DOI: 10.1063/1.4887457] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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6
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On the Transferability of Three Water Models Developed by Adaptive Force Matching. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-63378-1.00002-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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7
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Huo P, Coker DF. Consistent schemes for non-adiabatic dynamics derived from partial linearized density matrix propagation. J Chem Phys 2012; 137:22A535. [DOI: 10.1063/1.4748316] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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8
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Buchholz M, Goletz CM, Grossmann F, Schmidt B, Heyda J, Jungwirth P. Semiclassical Hybrid Approach to Condensed Phase Molecular Dynamics: Application to the I2Kr17 Cluster. J Phys Chem A 2012; 116:11199-210. [DOI: 10.1021/jp305084f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Max Buchholz
- Institut für Theoretische
Physik, Technische Universität Dresden, 01062 Dresden, Germany
| | | | - Frank Grossmann
- Institut für Theoretische
Physik, Technische Universität Dresden, 01062 Dresden, Germany
| | - Burkhard Schmidt
- Institut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Jan Heyda
- Institute for Soft Matter and Functional
Materials, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, 14109 Berlin,
Germany
| | - Pavel Jungwirth
- Institute of Organic
Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech
Republic
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9
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Huo P, Coker DF. Semi-classical path integral non-adiabatic dynamics: a partial linearized classical mapping Hamiltonian approach. Mol Phys 2012. [DOI: 10.1080/00268976.2012.684896] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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10
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Huo P, Coker DF. Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems. J Chem Phys 2012; 136:115102. [DOI: 10.1063/1.3693019] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Huo P, Coker DF. Communication: Partial linearized density matrix dynamics for dissipative, non-adiabatic quantum evolution. J Chem Phys 2011; 135:201101. [DOI: 10.1063/1.3664763] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Pengfei Huo
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
| | - David F. Coker
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
- Complex Adaptive Systems Laboratory, Department of Physics, University College Dublin, Dublin 4, Ireland
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Segale D, Apkarian VA. Dissipative quantum coherent dynamics probed in phase-space: Electronically resonant 5-color 4-wave mixing on I2(B) in solid Kr. J Chem Phys 2011; 135:024203. [DOI: 10.1063/1.3598959] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D. Segale
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
| | - V. A. Apkarian
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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13
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Huo P, Coker DF. Iterative linearized density matrix propagation for modeling coherent excitation energy transfer in photosynthetic light harvesting. J Chem Phys 2010; 133:184108. [DOI: 10.1063/1.3498901] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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14
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Linearized approximations for condensed phase non-adiabatic dynamics: Multi-layered baths and Brownian dynamics implementation. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.02.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Liu J, Miller WH. A simple model for the treatment of imaginary frequencies in chemical reaction rates and molecular liquids. J Chem Phys 2009; 131:074113. [DOI: 10.1063/1.3202438] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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16
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Dunkel ER, Bonella S, Coker DF. Iterative linearized approach to nonadiabatic dynamics. J Chem Phys 2008; 129:114106. [DOI: 10.1063/1.2976441] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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