51
|
Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| |
Collapse
|
52
|
Kananenka AA, Hsieh CY, Cao J, Geva E. Nonadiabatic Dynamics via the Symmetrical Quasi-Classical Method in the Presence of Anharmonicity. J Phys Chem Lett 2018; 9:319-326. [PMID: 29239614 DOI: 10.1021/acs.jpclett.7b03002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The symmetrical quasi-classical (SQC) method recently proposed by Miller and Cotton allows one to simulate nonadiabatic dynamics based on an algorithm with classical-like scaling with respect to system size. This is made possible by casting the electronic degrees of freedom in terms of mapping variables that can be propagated in a classical-like manner. While SQC was shown to be rather accurate when applied to benchmark models with harmonic electronic potential energy surfaces, it was also found to become inaccurate and to suffer numerical instabilities when applied to anharmonic systems. In this paper, we propose an extended SQC (E-SQC) methodology for overcoming those discrepancies by describing the anharmonic nuclear modes, which are coupled to the electronic degrees of freedom, in terms of classical-like mapping variables. The accuracy of E-SQC relative to standard SQC is demonstrated on benchmark models with quartic and Morse potential energy surfaces.
Collapse
Affiliation(s)
- Alexei A Kananenka
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Chang-Yu Hsieh
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02319, United States
- Singapore-MIT Alliance for Research and Technology (SMART) Center , Singapore 487373
| | - Jianshu Cao
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02319, United States
- Singapore-MIT Alliance for Research and Technology (SMART) Center , Singapore 487373
| | | |
Collapse
|
53
|
Loco D, Jurinovich S, Cupellini L, Menger MFSJ, Mennucci B. The modeling of the absorption lineshape for embedded molecules through a polarizable QM/MM approach. Photochem Photobiol Sci 2018; 17:552-560. [DOI: 10.1039/c8pp00033f] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present a polarizable QM/MM strategy to simulate the absorption line shape of chromophores embedded in complex matrices, including both homogeneous and inhomogeneous broadening.
Collapse
Affiliation(s)
- Daniele Loco
- Department of Chemistry
- University of Pisa
- Pisa
- Italy
| | | | | | | | | |
Collapse
|
54
|
Claridge K, Padula D, Troisi A. How fine-tuned for energy transfer is the environmental noise produced by proteins around biological chromophores? Phys Chem Chem Phys 2018; 20:17279-17288. [DOI: 10.1039/c8cp02613k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Analysis of intermolecular motions of pigment–protein complexes shows no significant difference in influence of local environment despite different biological functions.
Collapse
Affiliation(s)
- Kirsten Claridge
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | - Daniele Padula
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | | |
Collapse
|
55
|
Valleau S, Studer RA, Häse F, Kreisbeck C, Saer RG, Blankenship RE, Shakhnovich EI, Aspuru-Guzik A. Absence of Selection for Quantum Coherence in the Fenna-Matthews-Olson Complex: A Combined Evolutionary and Excitonic Study. ACS CENTRAL SCIENCE 2017; 3:1086-1095. [PMID: 29104925 PMCID: PMC5658757 DOI: 10.1021/acscentsci.7b00269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Indexed: 06/07/2023]
Abstract
We present a study on the evolution of the Fenna-Matthews-Olson bacterial photosynthetic pigment-protein complex. This protein complex functions as an antenna. It transports absorbed photons-excitons-to a reaction center where photosynthetic reactions initiate. The efficiency of exciton transport is therefore fundamental for the photosynthetic bacterium's survival. We have reconstructed an ancestor of the complex to establish whether coherence in the exciton transport was selected for or optimized over time. We have also investigated the role of optimizing free energy variation upon folding in evolution. We studied whether mutations which connect the ancestor to current day species were stabilizing or destabilizing from a thermodynamic viewpoint. From this study, we established that most of these mutations were thermodynamically neutral. Furthermore, we did not see a large change in exciton transport efficiency or coherence, and thus our results predict that exciton coherence was not specifically selected for.
Collapse
Affiliation(s)
- Stéphanie Valleau
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
| | - Romain A. Studer
- European
Bioinformatics Institute (EMBL-EBI),
Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, U.K.
| | - Florian Häse
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
| | - Christoph Kreisbeck
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
| | - Rafael G. Saer
- Departments
of Biology and Chemistry, Washington University
in Saint Louis, One Brookings
Drive, St. Louis, Missouri 63130, United States
| | - Robert E. Blankenship
- Departments
of Biology and Chemistry, Washington University
in Saint Louis, One Brookings
Drive, St. Louis, Missouri 63130, United States
| | - Eugene I. Shakhnovich
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
| | - Alán Aspuru-Guzik
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
- Bio-inspired
Solar Energy Program, Canadian Institute
for Advanced Research, Toronto, Ontario M5G 1Z8, Canada
| |
Collapse
|
56
|
Padula D, Lee MH, Claridge K, Troisi A. Chromophore-Dependent Intramolecular Exciton–Vibrational Coupling in the FMO Complex: Quantification and Importance for Exciton Dynamics. J Phys Chem B 2017; 121:10026-10035. [DOI: 10.1021/acs.jpcb.7b08020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Daniele Padula
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Myeong H. Lee
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Kirsten Claridge
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Alessandro Troisi
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
- Department
of Chemistry and Materials Innovation Factory, University of Liverpool, Liverpool L69 7ZD, U.K
| |
Collapse
|
57
|
Andreussi O, Prandi IG, Campetella M, Prampolini G, Mennucci B. Classical Force Fields Tailored for QM Applications: Is It Really a Feasible Strategy? J Chem Theory Comput 2017; 13:4636-4648. [DOI: 10.1021/acs.jctc.7b00777] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Oliviero Andreussi
- Institute
of Computational Science, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6904 Lugano, Switzerland
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne, Switzerland
| | - Ingrid G. Prandi
- Department
of Chemistry, University of Pisa, Via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Marco Campetella
- Department
of Chemistry, University of Pisa, Via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Giacomo Prampolini
- CNR,
UOS Pisa, Istituto di Chimica dei Composti OrganoMetallici ICCOM CNR, Area della Ricerca, Via Giuseppe Moruzzi 1, I-56124 Pisa, Italy
| | - Benedetta Mennucci
- Department
of Chemistry, University of Pisa, Via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| |
Collapse
|
58
|
Mallus MI, Schallwig M, Kleinekathöfer U. Relation between Vibrational Dephasing Time and Energy Gap Fluctuations. J Phys Chem B 2017. [PMID: 28625060 DOI: 10.1021/acs.jpcb.7b02693] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dephasing processes are present in basically all applications in which quantum mechanics plays a role. These applications certainly include excitation energy and charge transfer in biological systems. In a previous study, we have analyzed the vibrational dephasing time as a function of energy gap fluctuation for a large set of molecular simulations. In that investigation, individual molecular subunits were the focus of the calculations. The set of studied molecules included bacteriochlorophylls in Fenna-Matthews-Olson and light-harvesting system 2 complexes as well as bilins in PE545 aggregates. The present work extends this study to entire complexes, including the respective intermolecular couplings. Again, it can be concluded that a universal and inverse proportionality exists between dephasing time and variance of the excitonic energy gap fluctuations, whereas the respective proportionality constants can be rationalized using the energy gap autocorrelation functions. Furthermore, these findings can be extended to the gaps between higher-lying neighboring excitonic states.
Collapse
Affiliation(s)
- Maria Ilaria Mallus
- Department of Physics and Earth Sciences, Jacobs University Bremen , Campus Ring 1, 28759 Bremen, Germany
| | - Maximilian Schallwig
- Department of Physics and Earth Sciences, Jacobs University Bremen , Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen , Campus Ring 1, 28759 Bremen, Germany
| |
Collapse
|
59
|
Lee MK, Bravaya KB, Coker DF. First-Principles Models for Biological Light-Harvesting: Phycobiliprotein Complexes from Cryptophyte Algae. J Am Chem Soc 2017; 139:7803-7814. [DOI: 10.1021/jacs.7b01780] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mi Kyung Lee
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Ksenia B. Bravaya
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - David F. Coker
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| |
Collapse
|
60
|
Teh HH, Cheng YC. On the accuracy of the LSC-IVR approach for excitation energy transfer in molecular aggregates. J Chem Phys 2017; 146:144105. [DOI: 10.1063/1.4979894] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Hung-Hsuan Teh
- Department of Chemistry and Center for Quantum Science and Engineering, National Taiwan University, Taipei City 106, Taiwan
| | - Yuan-Chung Cheng
- Department of Chemistry and Center for Quantum Science and Engineering, National Taiwan University, Taipei City 106, Taiwan
| |
Collapse
|
61
|
Aghtar M, Kleinekathöfer U, Curutchet C, Mennucci B. Impact of Electronic Fluctuations and Their Description on the Exciton Dynamics in the Light-Harvesting Complex PE545. J Phys Chem B 2017; 121:1330-1339. [DOI: 10.1021/acs.jpcb.6b10772] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mortaza Aghtar
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carles Curutchet
- Departament
de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica
and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi
13, I-56124 Pisa, Italy
| |
Collapse
|
62
|
Provorse MR, Peev T, Xiong C, Isborn CM. Convergence of Excitation Energies in Mixed Quantum and Classical Solvent: Comparison of Continuum and Point Charge Models. J Phys Chem B 2016; 120:12148-12159. [DOI: 10.1021/acs.jpcb.6b09176] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Makenzie R. Provorse
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Thomas Peev
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Chou Xiong
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| |
Collapse
|
63
|
Lewis NHC, Gruenke NL, Oliver TAA, Ballottari M, Bassi R, Fleming GR. Observation of Electronic Excitation Transfer Through Light Harvesting Complex II Using Two-Dimensional Electronic-Vibrational Spectroscopy. J Phys Chem Lett 2016; 7:4197-4206. [PMID: 27704843 PMCID: PMC6314458 DOI: 10.1021/acs.jpclett.6b02280] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Light-harvesting complex II (LHCII) serves a central role in light harvesting for oxygenic photosynthesis and is arguably the most important photosynthetic antenna complex. In this work, we present two-dimensional electronic-vibrational (2DEV) spectra of LHCII isolated from spinach, demonstrating the possibility of using this technique to track the transfer of electronic excitation energy between specific pigments within the complex. We assign the spectral bands via comparison with the 2DEV spectra of the isolated chromophores, chlorophyll a and b, and present evidence that excitation energy between the pigments of the complex are observed in these spectra. Finally, we analyze the essential components of the 2DEV spectra using singular value decomposition, which makes it possible to reveal the relaxation pathways within this complex.
Collapse
Affiliation(s)
- Nicholas H C Lewis
- Department of Chemistry, University of California , Berkeley, California 94 720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, California 94720, United States
| | - Natalie L Gruenke
- Department of Chemistry, University of California , Berkeley, California 94 720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, California 94720, United States
| | - Thomas A A Oliver
- Department of Chemistry, University of California , Berkeley, California 94 720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, California 94720, United States
| | - Matteo Ballottari
- Dipartimento di Biotecnologie, Facoltà di Scienze, Universitá di Verona , Strada Le Grazie, I-37134 Verona, Italia
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Facoltà di Scienze, Universitá di Verona , Strada Le Grazie, I-37134 Verona, Italia
| | - Graham R Fleming
- Department of Chemistry, University of California , Berkeley, California 94 720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, California 94720, United States
| |
Collapse
|
64
|
Chandrasekaran S, Pothula KR, Kleinekathöfer U. Protein Arrangement Effects on the Exciton Dynamics in the PE555 Complex. J Phys Chem B 2016; 121:3228-3236. [DOI: 10.1021/acs.jpcb.6b05803] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | - Karunakar Reddy Pothula
- Department of Physics and
Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and
Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| |
Collapse
|
65
|
Zheng F, Jin M, Mančal T, Zhao Y. Study of Electronic Structures and Pigment–Protein Interactions in the Reaction Center of Thermochromatium tepidum with a Dynamic Environment. J Phys Chem B 2016; 120:10046-10058. [DOI: 10.1021/acs.jpcb.6b06628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fulu Zheng
- Division
of Materials Science, Nanyang Technological University, Singapore 639798, Singapore
| | - Mengting Jin
- Division
of Materials Science, Nanyang Technological University, Singapore 639798, Singapore
| | - Tomáš Mančal
- Faculty
of Mathematics and Physics, Charles University in Prague, Ke Karlovu
5, 121 16 Prague
2, Czech Republic
| | - Yang Zhao
- Division
of Materials Science, Nanyang Technological University, Singapore 639798, Singapore
| |
Collapse
|
66
|
Lee MK, Coker DF. Modeling Electronic-Nuclear Interactions for Excitation Energy Transfer Processes in Light-Harvesting Complexes. J Phys Chem Lett 2016; 7:3171-3178. [PMID: 27472379 DOI: 10.1021/acs.jpclett.6b01440] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
An accurate approach for computing intermolecular and intrachromophore contributions to spectral densities to describe the electronic-nuclear interactions relevant for modeling excitation energy transfer processes in light harvesting systems is presented. The approach is based on molecular dynamics (MD) calculations of classical correlation functions of long-range contributions to excitation energy fluctuations and a separate harmonic analysis and single-point gradient quantum calculations for electron-intrachromophore vibrational couplings. A simple model is also presented that enables detailed analysis of the shortcomings of standard MD-based excitation energy fluctuation correlation function approaches. The method introduced here avoids these problems, and its reliability is demonstrated in accurate predictions for bacteriochlorophyll molecules in the Fenna-Matthews-Olson pigment-protein complex, where excellent agreement with experimental spectral densities is found. This efficient approach can provide instantaneous spectral densities for treating the influence of fluctuations in environmental dissipation on fast electronic relaxation.
Collapse
Affiliation(s)
- Mi Kyung Lee
- Department of Chemistry, Boston University , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - David F Coker
- Department of Chemistry, Boston University , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| |
Collapse
|
67
|
Kell A, Blankenship RE, Jankowiak R. Effect of Spectral Density Shapes on the Excitonic Structure and Dynamics of the Fenna–Matthews–Olson Trimer from Chlorobaculum tepidum. J Phys Chem A 2016; 120:6146-54. [DOI: 10.1021/acs.jpca.6b03107] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Robert E. Blankenship
- Departments
of Chemistry and Biology, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | | |
Collapse
|
68
|
Häse F, Valleau S, Pyzer-Knapp E, Aspuru-Guzik A. Machine learning exciton dynamics. Chem Sci 2016; 7:5139-5147. [PMID: 30155164 PMCID: PMC6020119 DOI: 10.1039/c5sc04786b] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/01/2016] [Indexed: 12/19/2022] Open
Abstract
Obtaining the exciton dynamics of large photosynthetic complexes by using mixed quantum mechanics/molecular mechanics (QM/MM) is computationally demanding. We propose a machine learning technique, multi-layer perceptrons, as a tool to reduce the time required to compute excited state energies. With this approach we predict time-dependent density functional theory (TDDFT) excited state energies of bacteriochlorophylls in the Fenna-Matthews-Olson (FMO) complex. Additionally we compute spectral densities and exciton populations from the predictions. Different methods to determine multi-layer perceptron training sets are introduced, leading to several initial data selections. In addition, we compute spectral densities and exciton populations. Once multi-layer perceptrons are trained, predicting excited state energies was found to be significantly faster than the corresponding QM/MM calculations. We showed that multi-layer perceptrons can successfully reproduce the energies of QM/MM calculations to a high degree of accuracy with prediction errors contained within 0.01 eV (0.5%). Spectral densities and exciton dynamics are also in agreement with the TDDFT results. The acceleration and accurate prediction of dynamics strongly encourage the combination of machine learning techniques with ab initio methods.
Collapse
Affiliation(s)
- Florian Häse
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , 02138 , USA . ; Tel: +1-617-384-8188
- Physik-Department T38 , Technische Universität München , Garching , 85748 , Germany
| | - Stéphanie Valleau
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , 02138 , USA . ; Tel: +1-617-384-8188
| | - Edward Pyzer-Knapp
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , 02138 , USA . ; Tel: +1-617-384-8188
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , 02138 , USA . ; Tel: +1-617-384-8188
| |
Collapse
|
69
|
Higashi M, Saito S. Quantitative Evaluation of Site Energies and Their Fluctuations of Pigments in the Fenna–Matthews–Olson Complex with an Efficient Method for Generating a Potential Energy Surface. J Chem Theory Comput 2016; 12:4128-37. [DOI: 10.1021/acs.jctc.6b00516] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Masahiro Higashi
- Department
of Chemistry, Biology and Marine Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Shinji Saito
- Department
of Theoretical and Computational Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| |
Collapse
|
70
|
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.
Collapse
|
71
|
Reinot T, Chen J, Kell A, Jassas M, Robben KC, Zazubovich V, Jankowiak R. On the Conflicting Estimations of Pigment Site Energies in Photosynthetic Complexes: A Case Study of the CP47 Complex. ANALYTICAL CHEMISTRY INSIGHTS 2016; 11:35-48. [PMID: 27279733 PMCID: PMC4892206 DOI: 10.4137/aci.s32151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/10/2016] [Accepted: 04/26/2016] [Indexed: 01/14/2023]
Abstract
We focus on problems with elucidation of site energies
(E0n) for photosynthetic complexes (PSCs) in order to raise some genuine concern regarding the conflicting estimations propagating in the literature. As an example, we provide a stern assessment of the site energies extracted from fits to optical spectra of the widely studied CP47 antenna complex of photosystem II from spinach, though many general comments apply to other PSCs as well. Correct values of
E0n for chlorophyll (Chl) a in CP47 are essential for understanding its excitonic structure, population dynamics, and excitation energy pathway(s). To demonstrate this, we present a case study where simultaneous fits of multiple spectra (absorption, emission, circular dichroism, and nonresonant hole-burned spectra) show that several sets of parameters can fit the spectra very well. Importantly, we show that variable emission maxima (690–695 nm) and sample-dependent bleaching in nonresonant hole-burning spectra reported in literature could be explained, assuming that many previously studied CP47 samples were a mixture of intact and destabilized proteins. It appears that the destabilized subpopulation of CP47 complexes could feature a weakened hydrogen bond between the 131-keto group of Chl29 and the PsbH protein subunit, though other possibilities cannot be entirely excluded, as discussed in this work. Possible implications of our findings are briefly discussed.
Collapse
Affiliation(s)
- Tonu Reinot
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Jinhai Chen
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Adam Kell
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Mahboobe Jassas
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Kevin C Robben
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | | | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, KS, USA.; Department of Physics, Kansas State University, Manhattan, KS, USA
| |
Collapse
|
72
|
Lee MK, Huo P, Coker DF. Semiclassical Path Integral Dynamics: Photosynthetic Energy Transfer with Realistic Environment Interactions. Annu Rev Phys Chem 2016; 67:639-68. [DOI: 10.1146/annurev-physchem-040215-112252] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mi Kyung Lee
- Department of Chemistry, Boston University, Boston, Massachusetts 02215;
| | - Pengfei Huo
- Department of Chemistry, University of Rochester, Rochester, New York 14627;
| | - David F. Coker
- Department of Chemistry, Boston University, Boston, Massachusetts 02215;
| |
Collapse
|
73
|
Mallus MI, Aghtar M, Chandrasekaran S, Lüdemann G, Elstner M, Kleinekathöfer U. Relation between Dephasing Time and Energy Gap Fluctuations in Biomolecular Systems. J Phys Chem Lett 2016; 7:1102-1108. [PMID: 26950038 DOI: 10.1021/acs.jpclett.6b00134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Excitation energy and charge transfer are fundamental processes in biological systems. Because of their quantum nature, the effect of dephasing on these processes is of interest especially when trying to understand their efficiency. Moreover, recent experiments have shown quantum coherences in such systems. As a first step toward a better understanding, we studied the relationship between dephasing time and energy gap fluctuations of the individual molecular subunits. A larger set of molecular simulations has been investigated to shed light on this dependence. This set includes bacterio-chlorophylls in Fenna-Matthews-Olson complexes, the PE545 aggregate, the LH2 complexes, DNA, photolyase, and cryptochromes. For the individual molecular subunits of these aggregates it has been confirmed quantitatively that an inverse proportionality exists between dephasing time and average gap energy fluctuation. However, for entire complexes including the respective intermolecular couplings, such a relation still needs to be verified.
Collapse
Affiliation(s)
- Maria Ilaria Mallus
- Department of Physics and Earth Sciences, Jacobs University Bremen , Campus Ring 1, 28759 Bremen, Germany
| | - Mortaza Aghtar
- Department of Physics and Earth Sciences, Jacobs University Bremen , Campus Ring 1, 28759 Bremen, Germany
| | | | - Gesa Lüdemann
- Institute of Physical Chemistry, Karlsruhe Institute of Technology , 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology , 76131 Karlsruhe, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen , Campus Ring 1, 28759 Bremen, Germany
| |
Collapse
|
74
|
Abstract
The design of optimal light-harvesting (supra)molecular systems and materials is one of the most challenging frontiers of science. Theoretical methods and computational models play a fundamental role in this difficult task, as they allow the establishment of structural blueprints inspired by natural photosynthetic organisms that can be applied to the design of novel artificial light-harvesting devices. Among theoretical strategies, the application of quantum chemical tools represents an important reality that has already reached an evident degree of maturity, although it still has to show its real potentials. This Review presents an overview of the state of the art of this strategy, showing the actual fields of applicability but also indicating its current limitations, which need to be solved in future developments.
Collapse
Affiliation(s)
- Carles Curutchet
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , via G. Moruzzi 13, 56124 Pisa, Italy
| |
Collapse
|
75
|
Megow J, Kulesza A, May V. A mixed quantum-classical description of pheophorbide a linear absorption spectra: Quantum-corrections of the Qy- and Qx-absorption vibrational satellites. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2015.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
76
|
Kenny EP, Kassal I. Benchmarking Calculations of Excitonic Couplings between Bacteriochlorophylls. J Phys Chem B 2015; 120:25-32. [DOI: 10.1021/acs.jpcb.5b08817] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elise P. Kenny
- Centre
for Engineered Quantum
Systems, Centre for Quantum Computation and Communication Technology,
and School of Mathematics and Physics, The University of Queensland, Brisbane QLD 4072, Australia
| | - Ivan Kassal
- Centre
for Engineered Quantum
Systems, Centre for Quantum Computation and Communication Technology,
and School of Mathematics and Physics, The University of Queensland, Brisbane QLD 4072, Australia
| |
Collapse
|
77
|
Pfalzgraff WC, Kelly A, Markland TE. Nonadiabatic Dynamics in Atomistic Environments: Harnessing Quantum-Classical Theory with Generalized Quantum Master Equations. J Phys Chem Lett 2015; 6:4743-4748. [PMID: 26563917 DOI: 10.1021/acs.jpclett.5b02131] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The development of methods that can efficiently and accurately treat nonadiabatic dynamics in quantum systems coupled to arbitrary atomistic environments remains a significant challenge in problems ranging from exciton transport in photovoltaic materials to electron and proton transfer in catalysis. Here we show that our recently introduced MF-GQME approach, which combines Ehrenfest mean field theory with the generalized quantum master equation framework, is able to yield quantitative accuracy over a wide range of charge-transfer regimes in fully atomistic environments. This is accompanied by computational speed-ups of up to 3 orders of magnitude over a direct application of Ehrenfest theory. This development offers the opportunity to efficiently investigate the atomistic details of nonadiabatic quantum relaxation processes in regimes where obtaining accurate results has previously been elusive.
Collapse
Affiliation(s)
- William C Pfalzgraff
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Aaron Kelly
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| |
Collapse
|
78
|
Jia X, Mei Y, Zhang JZH, Mo Y. Hybrid QM/MM study of FMO complex with polarized protein-specific charge. Sci Rep 2015; 5:17096. [PMID: 26611739 PMCID: PMC4661465 DOI: 10.1038/srep17096] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/26/2015] [Indexed: 12/20/2022] Open
Abstract
The Fenna-Matthews-Olson (FMO) light-harvesting complex is now one of the primary model systems for the study of excitation energy transfer (EET). However, the mechanism of the EET in this system is still controversial. In this work, molecular dynamics simulations and the electrostatic-embedding quantum-mechanics/molecular-mechanics single-point calculations have been employed to predict the energy transfer pathways utilizing the polarized protein-specific charge (PPC), which provides a more realistic description of Coulomb interaction potential in the protein than conventional mean-field charge scheme. The recently discovered eighth pigment has also been included in this study. Comparing with the conventional mean-field charges, more stable structures of FMO complex were found under PPC scheme during molecular dynamic simulation. Based on the electronic structure calculations, an exciton model was constructed to consider the couplings during excitation. The results show that pigments 3 and 4 dominate the lowest exciton levels whereas the highest exciton level are mainly constituted of pigments 1 and 6. This observation agrees well with the assumption based on the spatial distribution of the pigments. Moreover, the obtained spectral density in this study gives a reliable description of the diverse local environment embedding each pigment.
Collapse
Affiliation(s)
- Xiangyu Jia
- State Key Laboratory of Precision Spectroscopy and Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy and Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - John Z H Zhang
- State Key Laboratory of Precision Spectroscopy and Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Department of Chemistry, New York University, New York, NY 10003
| | - Yan Mo
- State Key Laboratory of Precision Spectroscopy and Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| |
Collapse
|
79
|
Megow J. How Van der Waals Interactions Influence the Absorption Spectra of PheophorbideaComplexes: A Mixed Quantum-Classical Study. Chemphyschem 2015; 16:3101-7. [DOI: 10.1002/cphc.201500326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Indexed: 11/08/2022]
|
80
|
Wang X, Ritschel G, Wüster S, Eisfeld A. Open quantum system parameters for light harvesting complexes from molecular dynamics. Phys Chem Chem Phys 2015; 17:25629-41. [DOI: 10.1039/c5cp03891j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We elucidate the difference between various parameter extraction methods and demonstrate sensitivity to molecular dynamics equilibration.
Collapse
Affiliation(s)
- Xiaoqing Wang
- Max-Planck-Institut für Physik komplexer Systeme
- D-01187 Dresden
- Germany
| | - Gerhard Ritschel
- Max-Planck-Institut für Physik komplexer Systeme
- D-01187 Dresden
- Germany
| | - Sebastian Wüster
- Max-Planck-Institut für Physik komplexer Systeme
- D-01187 Dresden
- Germany
| | - Alexander Eisfeld
- Max-Planck-Institut für Physik komplexer Systeme
- D-01187 Dresden
- Germany
| |
Collapse
|