201
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Vacher M, Bearpark MJ, Robb MA, Malhado JP. Electron Dynamics upon Ionization of Polyatomic Molecules: Coupling to Quantum Nuclear Motion and Decoherence. PHYSICAL REVIEW LETTERS 2017; 118:083001. [PMID: 28282194 DOI: 10.1103/physrevlett.118.083001] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Indexed: 05/23/2023]
Abstract
Knowledge about the electronic motion in molecules is essential for our understanding of chemical reactions and biological processes. The advent of attosecond techniques opens up the possibility to induce electronic motion, observe it in real time, and potentially steer it. A fundamental question remains the factors influencing electronic decoherence and the role played by nuclear motion in this process. Here, we simulate the dynamics upon ionization of the polyatomic molecules paraxylene and modified bismethylene-adamantane, with a quantum mechanical treatment of both electron and nuclear dynamics using the direct dynamics variational multiconfigurational Gaussian method. Our simulations give new important physical insights about the expected decoherence process. We have shown that the decoherence of electron dynamics happens on the time scale of a few femtoseconds, with the interplay of different mechanisms: the dephasing is responsible for the fast decoherence while the nuclear overlap decay may actually help maintain it and is responsible for small revivals.
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Affiliation(s)
- Morgane Vacher
- Department of Chemistry-Ångström, Uppsala University, Uppsala 75120, Sweden and Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | - Michael J Bearpark
- Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | - Michael A Robb
- Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | - João Pedro Malhado
- Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
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202
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Penfold TJ. Accelerating direct quantum dynamics using graphical processing units. Phys Chem Chem Phys 2017; 19:19601-19608. [DOI: 10.1039/c7cp01473b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The direct dynamics variational multi-configurational Gaussian (DD-vMCG) method is combined with electronic structure calculations accelerated by Graphical Processing Units (GPUs). This is used to identify GPU acceleration will have a significant effect for both ground and excited state simulations.
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Affiliation(s)
- T. J. Penfold
- School of Chemistry
- Newcastle University
- Newcastle upon Tyne
- UK
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203
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Moreno Carrascosa A, Kirrander A. Ab initio calculation of inelastic scattering. Phys Chem Chem Phys 2017; 19:19545-19553. [DOI: 10.1039/c7cp02054f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We calculate nonresonant inelastic electron and X-ray scattering cross sections for bound-to-bound transitions in atoms and molecules from ab initio electronic wavefunctions.
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Affiliation(s)
| | - Adam Kirrander
- EaStCHEM
- School of Chemistry
- University of Edinburgh
- EH9 3FJ Edinburgh
- UK
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204
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Using quantum dynamics simulations to follow the competition between charge migration and charge transfer in polyatomic molecules. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2016.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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205
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Marquetand P, Nogueira JJ, Mai S, Plasser F, González L. Challenges in Simulating Light-Induced Processes in DNA. Molecules 2016. [PMCID: PMC6155660 DOI: 10.3390/molecules22010049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments.
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206
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Borrelli R, Gelin MF. The Generalized Coherent State ansatz: Application to quantum electron-vibrational dynamics. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.05.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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207
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Larsson HR, Hartke B, Tannor DJ. Efficient molecular quantum dynamics in coordinate and phase space using pruned bases. J Chem Phys 2016; 145:204108. [DOI: 10.1063/1.4967432] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- H. R. Larsson
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, 24098 Kiel, Germany
| | - B. Hartke
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, 24098 Kiel, Germany
| | - D. J. Tannor
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
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208
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Alborzpour JP, Tew DP, Habershon S. Efficient and accurate evaluation of potential energy matrix elements for quantum dynamics using Gaussian process regression. J Chem Phys 2016; 145:174112. [DOI: 10.1063/1.4964902] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jonathan P. Alborzpour
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - David P. Tew
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Scott Habershon
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
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209
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Curchod BFE, Agostini F, Gross EKU. An exact factorization perspective on quantum interferences in nonadiabatic dynamics. J Chem Phys 2016; 145:034103. [DOI: 10.1063/1.4958637] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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210
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Coden M, Fresch B, Moro GJ. Quantum Statistical Ensemble Resilient to Thermalization. J Phys Chem A 2016; 120:5071-82. [PMID: 27164180 DOI: 10.1021/acs.jpca.6b00274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sampling of the wave function within a suitable ensemble is an important tool in the statistical analysis of a molecule interacting with its environment. The uniform statistical distribution of quantum pure states in an active space is often the privileged choice. However, such a distribution with constant average populations of eigenstates is not preserved upon the interaction between quantum systems. This appears as a severe methodological shortcoming, as long as a quantum system can be always considered as the result of interactions among previously isolated subsystems. In the present work we formulate an alternative statistical ensemble of pure states that is robust with respect to interaction, and it is thus preserved when subsystems are merged. It is derived from the condition of invariance of the average populations upon interaction between quantum systems in the same thermal state. These average populations allow a simple identification of the thermodynamic properties of the system. We find that such a statistical distribution is robust with respect to interaction of systems at different temperatures reproducing the thermalization of macroscopic bodies, and for this reason we identify it as the Thermalization Resilient Ensemble.
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Affiliation(s)
- Maurizio Coden
- Dipartimento di Scienze Chimiche, Università di Padova , 35131 Padova, Italy
| | - Barbara Fresch
- Dipartimento di Scienze Chimiche, Università di Padova , 35131 Padova, Italy.,Départment de Chimie, Université de Liège , B4000 Liège, Belgium
| | - Giorgio J Moro
- Dipartimento di Scienze Chimiche, Università di Padova , 35131 Padova, Italy
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211
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Vacher M, Bearpark MJ, Robb MA. Direct methods for non-adiabatic dynamics: connecting the single-set variational multi-configuration Gaussian (vMCG) and Ehrenfest perspectives. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1937-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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212
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Challenges facing an understanding of the nature of low-energy excited states in photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1627-1640. [PMID: 27372198 DOI: 10.1016/j.bbabio.2016.06.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 01/09/2023]
Abstract
While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.
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213
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Humeniuk A, Mitrić R. Non-adiabatic dynamics around a conical intersection with surface-hopping coupled coherent states. J Chem Phys 2016; 144:234108. [DOI: 10.1063/1.4954189] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Alexander Humeniuk
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany
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214
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Kong X, Markmann A, Batista VS. Time-Sliced Thawed Gaussian Propagation Method for Simulations of Quantum Dynamics. J Phys Chem A 2016; 120:3260-9. [DOI: 10.1021/acs.jpca.5b12192] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiangmeng Kong
- Department of Chemistry, Yale University, 225 Prospect
Street, New Haven, Connecticut 06520-8107, United States
| | - Andreas Markmann
- Department of Chemistry, Yale University, 225 Prospect
Street, New Haven, Connecticut 06520-8107, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, 225 Prospect
Street, New Haven, Connecticut 06520-8107, United States
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215
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Kirrander A, Saita K, Shalashilin DV. Ultrafast X-ray Scattering from Molecules. J Chem Theory Comput 2016; 12:957-67. [PMID: 26717255 DOI: 10.1021/acs.jctc.5b01042] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Adam Kirrander
- EaStCHEM,
School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Kenichiro Saita
- EaStCHEM,
School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
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216
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Fernandez-Alberti S, Makhov DV, Tretiak S, Shalashilin DV. Non-adiabatic excited state molecular dynamics of phenylene ethynylene dendrimer using a multiconfigurational Ehrenfest approach. Phys Chem Chem Phys 2016; 18:10028-40. [DOI: 10.1039/c5cp07332d] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Photoinduced dynamics of electronic and vibrational unidirectional energy transfer between meta-linked building blocks in a phenylene ethynylene dendrimer is simulated using a multiconfigurational Ehrenfest in time-dependent diabatic basis (MCE-TDDB) method.
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Affiliation(s)
| | | | - Sergei Tretiak
- Center for Nonlinear Studies (CNLS)
- and Center for Integrated Nanotechnologies (CINT)
- Los Alamos National Laboratory
- Los Alamos
- USA
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217
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Richings GW, Worth GA. A Practical Diabatisation Scheme for Use with the Direct-Dynamics Variational Multi-Configuration Gaussian Method. J Phys Chem A 2015; 119:12457-70. [DOI: 10.1021/acs.jpca.5b07921] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gareth W. Richings
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Graham A. Worth
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
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218
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Polyak I, Allan CSM, Worth GA. A complete description of tunnelling using direct quantum dynamics simulation: Salicylaldimine proton transfer. J Chem Phys 2015; 143:084121. [DOI: 10.1063/1.4929478] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Iakov Polyak
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Charlotte S. M. Allan
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Graham A. Worth
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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