1
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Lyu N, Soley MB, Batista VS. Tensor-Train Split-Operator KSL (TT-SOKSL) Method for Quantum Dynamics Simulations. J Chem Theory Comput 2022; 18:3327-3346. [PMID: 35649210 DOI: 10.1021/acs.jctc.2c00209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Numerically exact simulations of quantum reaction dynamics, including nonadiabatic effects in excited electronic states, are essential to gain fundamental insights into ultrafast chemical reactivity and rigorous interpretations of molecular spectroscopy. Here, we introduce the tensor-train split-operator KSL (TT-SOKSL) method for quantum simulations in tensor-train (TT)/matrix product state (MPS) representations. TT-SOKSL propagates the quantum state as a tensor train using the Trotter expansion of the time-evolution operator, as in the tensor-train split-operator Fourier transform (TT-SOFT) method. However, the exponential operators of the Trotter expansion are applied using a rank-adaptive TT-KSL scheme instead of using the scaling and squaring approach as in TT-SOFT. We demonstrate the accuracy and efficiency of TT-SOKSL as applied to simulations of the photoisomerization of the retinal chromophore in rhodopsin, including nonadiabatic dynamics at a conical intersection of potential energy surfaces. The quantum evolution is described in full dimensionality by a time-dependent wavepacket evolving according to a two-state 25-dimensional model Hamiltonian. We find that TT-SOKSL converges faster than TT-SOFT with respect to the maximally allowed memory requirement of the tensor-train representation and better preserves the norm of the time-evolving state. When compared to the corresponding simulations based on the TT-KSL method, TT-SOKSL has the advantage of avoiding the need to construct the matrix product state Laplacian by exploiting the linear scaling of multidimensional tensor-train Fourier transforms.
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Affiliation(s)
- Ningyi Lyu
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Micheline B Soley
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States.,Yale Quantum Institute, Yale University, P.O. Box 208334, New Haven, Connecticut 06520-8263, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States.,Yale Quantum Institute, Yale University, P.O. Box 208334, New Haven, Connecticut 06520-8263, United States
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2
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Soley MB, Bergold P, Gorodetsky AA, Batista VS. Functional Tensor-Train Chebyshev Method for Multidimensional Quantum Dynamics Simulations. J Chem Theory Comput 2021; 18:25-36. [PMID: 34898201 DOI: 10.1021/acs.jctc.1c00941] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methods for efficient simulations of multidimensional quantum dynamics are essential for theoretical studies of chemical systems where quantum effects are important, such as those involving rearrangements of protons or electronic configurations. Here, we introduce the functional tensor-train Chebyshev (FTTC) method for rigorous nuclear quantum dynamics simulations. FTTC is essentially the Chebyshev propagation scheme applied to the initial state represented in a continuous analogue tensor-train format. We demonstrate the capabilities of FTTC as applied to simulations of proton quantum dynamics in a 50-dimensional model of hydrogen-bonded DNA base pairs.
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Affiliation(s)
- Micheline B Soley
- Yale Quantum Institute, Yale University, P.O. Box 208334, New Haven, Connecticut 06520-8263, United States.,Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Paul Bergold
- Zentrum Mathematik, Technical University of Munich, Boltzmannstr. 3, 85748 Garching, Germany
| | - Alex A Gorodetsky
- Department of Aerospace Engineering, University of Michigan, 1320 Beal Avenue, Ann Arbor, Michigan 48109-2140, United States
| | - Victor S Batista
- Yale Quantum Institute, Yale University, P.O. Box 208334, New Haven, Connecticut 06520-8263, United States.,Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States.,Energy Sciences Institute, Yale University, P.O. Box 27394, West Haven, Connecticut 06516-7394, United States
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3
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Pieroni C, Marsili E, Lauvergnat D, Agostini F. Relaxation dynamics through a conical intersection: Quantum and quantum-classical studies. J Chem Phys 2021; 154:034104. [PMID: 33499611 DOI: 10.1063/5.0036726] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We study the relaxation process through a conical intersection of a photo-excited retinal chromophore model. The analysis is based on a two-electronic-state two-dimensional Hamiltonian developed by Hahn and Stock [J. Phys. Chem. B 104 1146 (2000)] to reproduce, with a minimal model, the main features of the 11-cis to all-trans isomerization of the retinal of rhodopsin. In particular, we focus on the performance of various trajectory-based schemes to nonadiabatic dynamics, and we compare quantum-classical results to the numerically exact quantum vibronic wavepacket dynamics. The purpose of this work is to investigate, by analyzing electronic and nuclear observables, how the sampling of initial conditions for the trajectories affects the subsequent dynamics.
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Affiliation(s)
- Carlotta Pieroni
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - Emanuele Marsili
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - David Lauvergnat
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
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4
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Dey D, Henriksen NE. On Weak-Field (One-Photon) Coherent Control of Photoisomerization. J Phys Chem Lett 2020; 11:8470-8476. [PMID: 32936656 DOI: 10.1021/acs.jpclett.0c02273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Photochemistry induced by phase-coherent laser light is an intriguing topic. The possibility of weak-field (one-photon) phase-only control of photoisomerization is controversial. Experimental studies on the weak-field coherent control of cis-trans isomerization have led to conflicting results. Here we address this issue by quantum dynamical calculations, focusing on a mechanism where different "phase-shaped" wave packets are quickly stabilized ("dumped") in the trans configuration because of prompt energy dissipation. We systematically investigate different relaxation rates with the system-bath dynamics described within the time-dependent Hartree approximation leading to a friction-type force. We find evidence for phase control of trans-isomer yields (about 5%) in this model with pure energy dissipation given sufficiently strong dampening.
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Affiliation(s)
- Diptesh Dey
- Department of Chemistry, Technical University of Denmark, Building 207, DK-2800 Lyngby, Denmark
| | - Niels E Henriksen
- Department of Chemistry, Technical University of Denmark, Building 207, DK-2800 Lyngby, Denmark
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5
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Marsili E, Olivucci M, Lauvergnat D, Agostini F. Quantum and Quantum-Classical Studies of the Photoisomerization of a Retinal Chromophore Model. J Chem Theory Comput 2020; 16:6032-6048. [PMID: 32931266 DOI: 10.1021/acs.jctc.0c00679] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report an in-depth analysis of the photo-induced isomerization of the 2-cis-penta-2,4-dieniminium cation: a minimal model of the 11-cis retinal protonated Schiff base chromophore of the dim-light photoreceptor rhodopsin. Based on recently developed three-dimensional potentials parametrized on ab initio multi-state multi-configurational second-order perturbation theory data, we perform quantum-dynamical studies. In addition, simulations based on various quantum-classical methods, among which Tully surface hopping and the coupled-trajectory approach derived from the exact factorization, allow us to validate their performance against vibronic wavepacket propagation and, therefore, a purely quantum treatment. Quantum-dynamics results uncover qualitative differences with respect to the two-dimensional Hahn-Stock potentials, widely used as model potentials for the isomerization of the same chromophore, due to the increased dimensionality and three-mode correlation. Quantum-classical simulations show, instead, that three-dimensional model potentials are capable of capturing a number of features revealed by atomistic simulations and experimental observations. In particular, a recently reported vibrational phase relationship between double-bond torsion and hydrogen-out-of-plane modes critical for rhodopsin isomerization efficiency is correctly reproduced.
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Affiliation(s)
- Emanuele Marsili
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France.,Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - David Lauvergnat
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
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6
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Dodin A, Brumer P. Light-induced processes in nature: Coherences in the establishment of the nonequilibrium steady state in model retinal isomerization. J Chem Phys 2019; 150:184304. [DOI: 10.1063/1.5092981] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Amro Dodin
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Paul Brumer
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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7
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Sala M, Egorova D. Quantum dynamics of multi-dimensional rhodopsin photoisomerization models: Approximate versus accurate treatment of the secondary modes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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8
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Videla PE, Markmann A, Batista VS. Floquet Study of Quantum Control of the Cis-Trans Photoisomerization of Rhodopsin. J Chem Theory Comput 2018; 14:1198-1205. [PMID: 29425032 DOI: 10.1021/acs.jctc.7b01217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding how to control reaction dynamics of polyatomic systems by using ultrafast laser technology is a fundamental challenge of great technological interest. Here, we report a Floquet theoretical study of the effect of light-induced potentials on the ultrafast cis-trans photoisomerization dynamics of rhodopsin. The Floquet Hamiltonian involves an empirical 3-state 25-mode model with frequencies and excited-state gradients parametrized to reproduce the rhodopsin electronic vertical excitation energy, the resonance Raman spectrum, and the photoisomerization time and efficiency as probed by ultrafast spectroscopy. We simulate the excited state relaxation dynamics using the time-dependent self-consistent field method, as described by a 3-state 2-mode nuclear wavepacket coupled to a Gaussian ansatz of 23 vibronic modes. We analyze the reaction time and product yield obtained with pulses of various widths and intensity profiles, defining 'dressed states' where the perturbational effect of the pulses is naturally decoupled along the different reaction channels. We find pulses that delay the excited-state photoisomerization for hundreds of femtoseconds, and we gain insights on the underlying control mechanisms. The reported findings provide understanding of quantum control, particularly valuable for the development of ultrafast optical switches based on visual pigments.
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Affiliation(s)
- Pablo E Videla
- Department of Chemistry , Yale University , P.O. Box 208107, New Haven , Connecticut 06520-8107 , United States.,Energy Sciences Institute , Yale University , P.O. Box 27394, West Haven , Connecticut 06516-7394 , United States
| | - Andreas Markmann
- Department of Chemistry , Yale University , P.O. Box 208107, New Haven , Connecticut 06520-8107 , United States.,Energy Sciences Institute , Yale University , P.O. Box 27394, West Haven , Connecticut 06516-7394 , United States
| | - Victor S Batista
- Department of Chemistry , Yale University , P.O. Box 208107, New Haven , Connecticut 06520-8107 , United States.,Energy Sciences Institute , Yale University , P.O. Box 27394, West Haven , Connecticut 06516-7394 , United States
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9
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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10
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Tscherbul TV, Brumer P. Excitation of Biomolecules with Incoherent Light: Quantum Yield for the Photoisomerization of Model Retinal. J Phys Chem A 2014; 118:3100-11. [DOI: 10.1021/jp501700t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- T. V. Tscherbul
- Chemical Physics
Theory Group, Department of Chemistry, and Center for Quantum Information and
Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - P. Brumer
- Chemical Physics
Theory Group, Department of Chemistry, and Center for Quantum Information and
Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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11
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Conyard J, Addison K, Heisler IA, Cnossen A, Browne WR, Feringa BL, Meech SR. Ultrafast dynamics in the power stroke of a molecular rotary motor. Nat Chem 2012; 4:547-51. [PMID: 22717439 DOI: 10.1038/nchem.1343] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 03/26/2012] [Indexed: 11/09/2022]
Abstract
Light-driven molecular motors convert light into mechanical energy through excited-state reactions. Unidirectional rotary molecular motors based on chiral overcrowded alkenes operate through consecutive photochemical and thermal steps. The thermal (helix inverting) step has been optimized successfully through variations in molecular structure, but much less is known about the photochemical step, which provides power to the motor. Ultimately, controlling the efficiency of molecular motors requires a detailed picture of the molecular dynamics on the excited-state potential energy surface. Here, we characterize the primary events that follow photon absorption by a unidirectional molecular motor using ultrafast fluorescence up-conversion measurements with sub 50 fs time resolution. We observe an extraordinarily fast initial relaxation out of the Franck-Condon region that suggests a barrierless reaction coordinate. This fast molecular motion is shown to be accompanied by the excitation of coherent excited-state structural motion. The implications of these observations for manipulating motor efficiency are discussed.
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Affiliation(s)
- Jamie Conyard
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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12
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Affiliation(s)
- David R. Yarkony
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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13
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Spanner M, Arango CA, Brumer P. Communication: Conditions for one-photon coherent phase control in isolated and open quantum systems. J Chem Phys 2010; 133:151101. [DOI: 10.1063/1.3491366] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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14
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Affiliation(s)
- Victor S. Batista
- Department of Chemistry, Yale University, New Haven, CT 06520–8107, USA
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15
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Kim J, Wu Y, Brédas JL, Batista VS. Quantum Dynamics of the Excited-State Intramolecular Proton Transfer in 2-(2′-Hydroxyphenyl)benzothiazole. Isr J Chem 2009. [DOI: 10.1560/ijc.49.2.187] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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16
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Control of retinal isomerization in bacteriorhodopsin in the high-intensity regime. Proc Natl Acad Sci U S A 2009; 106:10896-900. [PMID: 19564608 DOI: 10.1073/pnas.0904589106] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A learning algorithm was used to manipulate optical pulse shapes and optimize retinal isomerization in bacteriorhodopsin, for excitation levels up to 1.8 x 10(16) photons per square centimeter. Below 1/3 the maximum excitation level, the yield was not sensitive to pulse shape. Above this level the learning algorithm found that a Fourier-transform-limited (TL) pulse maximized the 13-cis population. For this optimal pulse the yield increases linearly with intensity well beyond the saturation of the first excited state. To understand these results we performed systematic searches varying the chirp and energy of the pump pulses while monitoring the isomerization yield. The results are interpreted including the influence of 1-photon and multiphoton transitions. The population dynamics in each intermediate conformation and the final branching ratio between the all-trans and 13-cis isomers are modified by changes in the pulse energy and duration.
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17
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Rego LG, Santos LF, Batista VS. Coherent Control of Quantum Dynamics with Sequences of Unitary Phase-Kick Pulses. Annu Rev Phys Chem 2009; 60:293-320. [DOI: 10.1146/annurev.physchem.040808.090409] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coherent-optical-control schemes exploit the coherence of laser pulses to change the phases of interfering dynamical pathways and manipulate dynamical processes. These active control methods are closely related to dynamical decoupling techniques, popularized in the field of quantum information. Inspired by nuclear magnetic resonance spectroscopy, dynamical decoupling methods apply sequences of unitary operations to modify the interference phenomena responsible for the system dynamics thus also belonging to the general class of coherent-control techniques. This article reviews related developments in the fields of coherent optical control and dynamical decoupling, emphasizing the control of tunneling and decoherence in general model systems. Considering recent experimental breakthroughs in the demonstration of active control of a variety of systems, we anticipate that the reviewed coherent-control scenarios and dynamical-decoupling methods should raise significant experimental interest.
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Affiliation(s)
- Luis G.C. Rego
- Departamento de Física, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900 Brazil
| | - Lea F. Santos
- Department of Physics, Yeshiva University, New York, New York 10016
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
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18
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Barbatti M, Belz S, Leibscher M, Lischka H, Manz J. Sensitivity of femtosecond quantum dynamics and control with respect to non-adiabatic couplings: Model simulations for the cis–trans isomerization of the dideuterated methaniminium cation. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.01.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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20
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Chen X, Batista VS. The MP/SOFT methodology for simulations of quantum dynamics: Model study of the photoisomerization of the retinyl chromophore in visual rhodopsin. J Photochem Photobiol A Chem 2007. [DOI: 10.1016/j.jphotochem.2007.05.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Prokhorenko VI, Nagy AM, Waschuk SA, Brown LS, Birge RR, Dwayne Miller RJ. Response to Comment on "Coherent Control of Retinal Isomerization in Bacteriorhodopsin". Science 2007. [DOI: 10.1126/science.1137032] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Valentyn I. Prokhorenko
- Institute for Optical Sciences, Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
- Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | - Andrea M. Nagy
- Institute for Optical Sciences, Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
- Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | - Stephen A. Waschuk
- Institute for Optical Sciences, Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
- Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | - Leonid S. Brown
- Institute for Optical Sciences, Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
- Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | - Robert R. Birge
- Institute for Optical Sciences, Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
- Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | - R. J. Dwayne Miller
- Institute for Optical Sciences, Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
- Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
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22
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Nuernberger P, Vogt G, Brixner T, Gerber G. Femtosecond quantum control of molecular dynamics in the condensed phase. Phys Chem Chem Phys 2007; 9:2470-97. [PMID: 17508081 DOI: 10.1039/b618760a] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review the progress in controlling quantum dynamical processes in the condensed phase with femtosecond laser pulses. Due to its high particle density the condensed phase has both high relevance and appeal for chemical synthesis. Thus, in recent years different methods have been developed to manipulate the dynamics of condensed-phase systems by changing one or multiple laser pulse parameters. Single-parameter control is often achieved by variation of the excitation pulse's wavelength, its linear chirp or its temporal subpulse separation in case of pulse sequences. Multiparameter control schemes are more flexible and provide a much larger parameter space for an optimal solution. This is realized in adaptive femtosecond quantum control, in which the optimal solution is iteratively obtained through the combination of an experimental feedback signal and an automated learning algorithm. Several experiments are presented that illustrate the different control concepts and highlight their broad applicability. These fascinating achievements show the continuous progress on the way towards the control of complex quantum reactions in the condensed phase.
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Affiliation(s)
- Patrick Nuernberger
- Universität Würzburg, Physikalisches Institut, Am Hubland, 97074 Würzburg, Germany
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23
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Prokhorenko VI, Nagy AM, Waschuk SA, Brown LS, Birge RR, Miller RJD. Coherent Control of Retinal Isomerization in Bacteriorhodopsin. Science 2006; 313:1257-61. [PMID: 16946063 DOI: 10.1126/science.1130747] [Citation(s) in RCA: 217] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Optical control of the primary step of photoisomerization of the retinal molecule in bacteriorhodopsin from the all-trans to the 13-cis state was demonstrated under weak field conditions (where only 1 of 300 retinal molecules absorbs a photon during the excitation cycle) that are relevant to understanding biological processes. By modulating the phases and amplitudes of the spectral components in the photoexcitation pulse, we showed that the absolute quantity of 13-cis retinal formed upon excitation can be enhanced or suppressed by +/-20% of the yield observed using a short transform-limited pulse having the same actinic energy. The shaped pulses were shown to be phase-sensitive at intensities too low to access different higher electronic states, and so these pulses apparently steer the isomerization through constructive and destructive interference effects, a mechanism supported by observed signatures of vibrational coherence. These results show that the wave properties of matter can be observed and even manipulated in a system as large and complex as a protein.
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Affiliation(s)
- Valentyn I Prokhorenko
- Institute for Optical Sciences, Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, M5S3H6, Toronto, Ontario, Canada
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24
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Wu Y, Batista VS. Matching-pursuit split-operator Fourier-transform simulations of excited-state intramolecular proton transfer in 2-(2′-hydroxyphenyl)-oxazole. J Chem Phys 2006; 124:224305. [PMID: 16784272 DOI: 10.1063/1.2202847] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The excited-state intramolecular proton-transfer dynamics associated with the keto-enolic tautomerization reaction in 2-(2(')-hydroxyphenyl)-oxazole is simulated according to a numerically exact quantum-dynamics propagation method and a full-dimensional excited-state potential energy surface, based on an ab initio reaction surface Hamiltonian. The reported simulations involve the propagation of 35-dimensional wave packets according to the recently developed matching-pursuit/split-operator-Fourier-transform (MP/SOFT) method by Wu and Batista. The underlying propagation scheme recursively applies the time-evolution operator as defined by the Trotter expansion to second order accuracy in dynamically adaptive coherent-state expansions. Computations of time-dependent survival amplitudes, photoabsorption cross sections, and time-dependent reactant(product) populations are compared to the corresponding calculations based on semiclassical approaches, including the Herman-Kluk semiclassical initial value representation method. The reported results demonstrate the capabilities of the MP/SOFT method as a valuble computational tool to study ultrafast reaction dynamics in polyatomic systems as well as to validate semiclassical simulations of complex (nonintegrable) quantum dynamics in multidimensional model systems.
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Affiliation(s)
- Yinghua Wu
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, USA
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Rego LGC, Abuabara SG, Batista VS. Model study of coherent quantum dynamics of hole states in functionalized semiconductor nanostructures. J Chem Phys 2005; 122:154709. [PMID: 15945658 DOI: 10.1063/1.1873712] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Functionalization of semiconductor nanocrystals can be achieved by anchoring organic ligands to the surface dangling bonds. The resulting surface complexes often introduce electronic states in the semiconductor band gap. These interband states sensitize the host material for photoabsorption at frequencies characteristic of the molecular adsorbates, leading to the well-known process of photoexcitation and subsequent femtosecond interfacial electron transfer. This paper investigates the relaxation dynamics of hole states, energetically localized deep in the semiconductor band gap, after the ultrafast electron-hole pair separation due to interfacial electron transfer. Mixed quantum-classical methods, based on mean-field nuclear dynamics approximated by ab initio density functional theory molecular dynamics simulations, reveal superexchange hole tunneling between adjacent adsorbate molecules in a model study of functionalized TiO2-anatase nanostructures. It is shown that electronic coherences can persist for hundreds of picoseconds under cryogenic and vacuum conditions, despite the partial intrinsic decoherence induced by thermal ionic motion, providing results of broad theoretical and experimental interest.
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Affiliation(s)
- Luis G C Rego
- Department of Physics, Universidade Federal de Santa Catarina, Florianopolis, SC 88040-900, Brazil
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Abstract
An overview of theories related to vibrational energy relaxation (VER) in proteins is presented. VER of a selected mode in cytochrome c is studied by using two theoretical approaches. One approach is the equilibrium simulation approach with quantum correction factors, and the other is the reduced model approach, which describes the protein as an ensemble of normal modes interacting through nonlinear coupling elements. Both methods result in similar estimates of the VER time (subpicoseconds) for a CD stretching mode in the protein at room temperature. The theoretical predictions are in accord with previous experimental data. A perspective on directions for the detailed study of time scales and mechanisms of VER in proteins is presented.
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Affiliation(s)
- Hiroshi Fujisaki
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
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Gascon JA, Batista VS. QM/MM study of energy storage and molecular rearrangements due to the primary event in vision. Biophys J 2004; 87:2931-41. [PMID: 15339806 PMCID: PMC1304767 DOI: 10.1529/biophysj.104.048264] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The energy storage and the molecular rearrangements due to the primary photochemical event in rhodopsin are investigated by using quantum mechanics/molecular mechanics hybrid methods in conjunction with high-resolution structural data of bovine visual rhodopsin. The analysis of the reactant and product molecular structures reveals the energy storage mechanism as determined by the detailed molecular rearrangements of the retinyl chromophore, including rotation of the (C11-C12) dihedral angle from -11 degrees in the 11-cis isomer to -161 degrees in the all-trans product, where the preferential sense of rotation is determined by the steric interactions between Ala-117 and the polyene chain at the C13 position, torsion of the polyene chain due to steric constraints in the binding pocket, and stretching of the salt bridge between the protonated Schiff base and the Glu-113 counterion by reorientation of the polarized bonds that localize the net positive charge at the Schiff-base linkage. The energy storage, computed at the ONIOM electronic-embedding approach (B3LYP/6-31G*:AMBER) level of theory and the S0-->S1 electronic-excitation energies for the dark and product states, obtained at the ONIOM electronic-embedding approach (TD-B3LYP/6-31G*//B3LYP/6-31G*:AMBER) level of theory, are in very good agreement with experimental data. These results are particularly relevant to the development of a first-principles understanding of the structure-function relations in prototypical G-protein-coupled receptors.
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Affiliation(s)
- Jose A Gascon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA
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