1
|
Sarngadharan P, Holtkamp Y, Kleinekathöfer U. Protein Effects on the Excitation Energies and Exciton Dynamics of the CP24 Antenna Complex. J Phys Chem B 2024; 128:5201-5217. [PMID: 38756003 PMCID: PMC11145653 DOI: 10.1021/acs.jpcb.4c01637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
In this study, the site energy fluctuations, energy transfer dynamics, and some spectroscopic properties of the minor light-harvesting complex CP24 in a membrane environment were determined. For this purpose, a 3 μs-long classical molecular dynamics simulation was performed for the CP24 complex. Furthermore, using the density functional tight binding/molecular mechanics molecular dynamics (DFTB/MM MD) approach, we performed excited state calculations for the chlorophyll a and chlorophyll b molecules in the complex starting from five different positions of the MD trajectory. During the extended simulations, we observed variations in the site energies of the different sets as a result of the fluctuating protein environment. In particular, a water coordination to Chl-b 608 occurred only after about 1 μs in the simulations, demonstrating dynamic changes in the environment of this pigment. From the classical and the DFTB/MM MD simulations, spectral densities and the (time-dependent) Hamiltonian of the complex were determined. Based on these results, three independent strongly coupled chlorophyll clusters were revealed within the complex. In addition, absorption and fluorescence spectra were determined together with the exciton relaxation dynamics, which reasonably well agrees with experimental time scales.
Collapse
Affiliation(s)
- Pooja Sarngadharan
- School of Science, Constructor
University, Campus Ring
1, 28759 Bremen, Germany
| | - Yannick Holtkamp
- School of Science, Constructor
University, Campus Ring
1, 28759 Bremen, Germany
| | | |
Collapse
|
2
|
Cignoni E, Suman D, Nigam J, Cupellini L, Mennucci B, Ceriotti M. Electronic Excited States from Physically Constrained Machine Learning. ACS CENTRAL SCIENCE 2024; 10:637-648. [PMID: 38559300 PMCID: PMC10979507 DOI: 10.1021/acscentsci.3c01480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 04/04/2024]
Abstract
Data-driven techniques are increasingly used to replace electronic-structure calculations of matter. In this context, a relevant question is whether machine learning (ML) should be applied directly to predict the desired properties or combined explicitly with physically grounded operations. We present an example of an integrated modeling approach in which a symmetry-adapted ML model of an effective Hamiltonian is trained to reproduce electronic excitations from a quantum-mechanical calculation. The resulting model can make predictions for molecules that are much larger and more complex than those on which it is trained and allows for dramatic computational savings by indirectly targeting the outputs of well-converged calculations while using a parametrization corresponding to a minimal atom-centered basis. These results emphasize the merits of intertwining data-driven techniques with physical approximations, improving the transferability and interpretability of ML models without affecting their accuracy and computational efficiency and providing a blueprint for developing ML-augmented electronic-structure methods.
Collapse
Affiliation(s)
- Edoardo Cignoni
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, 56126 Pisa, Italy
| | - Divya Suman
- Laboratory
of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale
de Lausanne, 1015 Lausanne, Switzerland
| | - Jigyasa Nigam
- Laboratory
of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale
de Lausanne, 1015 Lausanne, Switzerland
| | - Lorenzo Cupellini
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, 56126 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, 56126 Pisa, Italy
| | - Michele Ceriotti
- Laboratory
of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale
de Lausanne, 1015 Lausanne, Switzerland
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
3
|
Maity S, Kleinekathöfer U. Recent progress in atomistic modeling of light-harvesting complexes: a mini review. PHOTOSYNTHESIS RESEARCH 2023; 156:147-162. [PMID: 36207489 PMCID: PMC10070314 DOI: 10.1007/s11120-022-00969-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
In this mini review, we focus on recent advances in the atomistic modeling of biological light-harvesting (LH) complexes. Because of their size and sophisticated electronic structures, multiscale methods are required to investigate the dynamical and spectroscopic properties of such complexes. The excitation energies, in this context also known as site energies, excitonic couplings, and spectral densities are key quantities which usually need to be extracted to be able to determine the exciton dynamics and spectroscopic properties. The recently developed multiscale approach based on the numerically efficient density functional tight-binding framework followed by excited state calculations has been shown to be superior to the scheme based on pure classical molecular dynamics simulations. The enhanced approach, which improves the description of the internal vibrational dynamics of the pigment molecules, yields spectral densities in good agreement with the experimental counterparts for various bacterial and plant LH systems. Here, we provide a brief overview of those results and described the theoretical foundation of the multiscale protocol.
Collapse
Affiliation(s)
- Sayan Maity
- 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
|
4
|
Calderón LF, Chuang C, Brumer P. Electronic-Vibrational Resonance Does Not Significantly Alter Steady-State Transport in Natural Light-Harvesting Systems. J Phys Chem Lett 2023; 14:1436-1444. [PMID: 36734680 DOI: 10.1021/acs.jpclett.2c03842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Oscillations in time-dependent two-dimensional electronic spectra appear as evidence of quantum coherence in light-harvesting systems related to electronic-vibrational resonant interactions. Nature, however, takes place in a non-equilibrium steady-state; therefore, the relevance of these arguments to the natural process is unclear. Here, we examine the role of intramolecular vibrations in the non-equilibrium steady-state of photosynthetic dimers in the natural scenario of incoherent light excitation. Specifically, we analyze the PEB dimer in the cryptophyte algae PE545 antenna protein. It is found that vibrations resonant with the energy difference between exciton states only marginally increase the quantum yield and the imaginary part of the intersite coherence that is relevant for transport compared to non-resonant vibrations in the natural non-equilibrium steady-state. That is, the electronic-vibrational resonance interaction does not significantly enhance energy transport under natural incoherent light excitation conditions.
Collapse
Affiliation(s)
- Leonardo F Calderón
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Grupo de Física Computacional en Materia Condensada, Escuela de Física, Facultad de Ciencias, Universidad Industrial de Santander, Carrera 27 Calle 9, Bucaramanga, Santander 680002, Colombia
| | - Chern Chuang
- 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
| |
Collapse
|
5
|
Sarngadharan P, Maity S, Kleinekathöfer U. Spectral densities and absorption spectra of the core antenna complex CP43 from photosystem II. J Chem Phys 2022; 156:215101. [DOI: 10.1063/5.0091005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Besides absorbing light, the core antenna complex CP43 of photosystem II is of great importance in transferring excitation energy from the antenna complexes to the reaction center. Excitation energies, spectral densities, and linear absorption spectra of the complex have been evaluated by a multiscale approach. In this scheme, quantum mechanics/molecular mechanics molecular dynamics simulations are performed employing the parameterized density functional tight binding (DFTB) while the time-dependent long-range-corrected DFTB scheme is applied for the excited state calculations. The obtained average spectral density of the CP43 complex shows a very good agreement with experimental results. Moreover, the excitonic Hamiltonian of the system along with the computed site-dependent spectral densities was used to determine the linear absorption. While a Redfield-like approximation has severe shortcomings in dealing with the CP43 complex due to quasi-degenerate states, the non-Markovian full second-order cumulant expansion formalism is able to overcome the drawbacks. Linear absorption spectra were obtained, which show a good agreement with the experimental counterparts at different temperatures. This study once more emphasizes that by combining diverse techniques from the areas of molecular dynamics simulations, quantum chemistry, and open quantum systems, it is possible to obtain first-principle results for photosynthetic complexes, which are in accord with experimental findings.
Collapse
Affiliation(s)
- Pooja Sarngadharan
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Sayan Maity
- 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
|
6
|
Maity S, Sarngadharan P, Daskalakis V, Kleinekathöfer U. Time-dependent atomistic simulations of the CP29 light-harvesting complex. J Chem Phys 2021; 155:055103. [PMID: 34364345 DOI: 10.1063/5.0053259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Light harvesting as the first step in photosynthesis is of prime importance for life on earth. For a theoretical description of photochemical processes during light harvesting, spectral densities are key quantities. They serve as input functions for modeling the excitation energy transfer dynamics and spectroscopic properties. Herein, a recently developed procedure is applied to determine the spectral densities of the pigments in the minor antenna complex CP29 of photosystem II, which has recently gained attention because of its active role in non-photochemical quenching processes in higher plants. To this end, the density functional-based tight binding (DFTB) method has been employed to enable simulation of the ground state dynamics in a quantum-mechanics/molecular mechanics (QM/MM) scheme for each chlorophyll pigment. Subsequently, the time-dependent extension of the long-range corrected DFTB approach has been used to obtain the excitation energy fluctuations along the ground-state trajectories also in a QM/MM setting. From these results, the spectral densities have been determined and compared for different force fields and to spectral densities from other light-harvesting complexes. In addition, time-dependent and time-independent excitonic Hamiltonians of the system have been constructed and applied to the determination of absorption spectra as well as exciton dynamics.
Collapse
Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Pooja Sarngadharan
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str. 3603, Limassol, Cyprus
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| |
Collapse
|
7
|
Acharyya N, Ovcharenko R, Fingerhut BP. On the role of non-diagonal system-environment interactions in bridge-mediated electron transfer. J Chem Phys 2020; 153:185101. [PMID: 33187441 DOI: 10.1063/5.0027976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bridge-mediated electron transfer (ET) between a donor and an acceptor is prototypical for the description of numerous most important ET scenarios. While multi-step ET and the interplay of sequential and direct superexchange transfer pathways in the donor-bridge-acceptor (D-B-A) model are increasingly understood, the influence of off-diagonal system-bath interactions on the transfer dynamics is less explored. Off-diagonal interactions account for the dependence of the ET coupling elements on nuclear coordinates (non-Condon effects) and are typically neglected. Here, we numerically investigate with quasi-adiabatic propagator path integral simulations the impact of off-diagonal system-environment interactions on the transfer dynamics for a wide range of scenarios in the D-B-A model. We demonstrate that off-diagonal system-environment interactions can have profound impact on the bridge-mediated ET dynamics. In the considered scenarios, the dynamics itself does not allow for a rigorous assignment of the underlying transfer mechanism. Furthermore, we demonstrate how off-diagonal system-environment interaction mediates anomalous localization by preventing long-time depopulation of the bridge B and how coherent transfer dynamics between donor D and acceptor A can be facilitated. The arising non-exponential short-time dynamics and coherent oscillations are interpreted within an equivalent Hamiltonian representation of a primary reaction coordinate model that reveals how the complex vibronic interplay of vibrational and electronic degrees of freedom underlying the non-Condon effects can impose donor-to-acceptor coherence transfer on short timescales.
Collapse
Affiliation(s)
- Nirmalendu Acharyya
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Roman Ovcharenko
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| |
Collapse
|
8
|
Maity S, Bold BM, Prajapati JD, Sokolov M, Kubař T, Elstner M, Kleinekathöfer U. DFTB/MM Molecular Dynamics Simulations of the FMO Light-Harvesting Complex. J Phys Chem Lett 2020; 11:8660-8667. [PMID: 32991176 DOI: 10.1021/acs.jpclett.0c02526] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Because of the size of light-harvesting complexes and the involvement of electronic degrees of freedom, computationally these systems need to be treated with a combined quantum-classical description. To this end, Born-Oppenheimer molecular dynamics simulations have been employed in a quantum mechanics/molecular mechanics (QM/MM) fashion for the ground state followed by excitation energy calculations again in a QM/MM scheme for the Fenna-Matthews-Olson (FMO) complex. The self-consistent-charge density functional tight-binding (DFTB) method electrostatically coupled to a classical description of the environment was applied to perform the ground-state dynamics. Subsequently, long-range-corrected time-dependent DFTB calculations were performed to determine the excitation energy fluctuations of the individual bacteriochlorophyll a molecules. The spectral densities obtained using this approach show an excellent agreement with experimental findings. In addition, the fluctuating site energies and couplings were used to estimate the exciton transfer dynamics.
Collapse
Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Beatrix M Bold
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | | | - Monja Sokolov
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
- Institute of Biological Interfaces, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| |
Collapse
|
9
|
Analysis of Photosynthetic Systems and Their Applications with Mathematical and Computational Models. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10196821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In biological and life science applications, photosynthesis is an important process that involves the absorption and transformation of sunlight into chemical energy. During the photosynthesis process, the light photons are captured by the green chlorophyll pigments in their photosynthetic antennae and further funneled to the reaction center. One of the most important light harvesting complexes that are highly important in the study of photosynthesis is the membrane-attached Fenna–Matthews–Olson (FMO) complex found in the green sulfur bacteria. In this review, we discuss the mathematical formulations and computational modeling of some of the light harvesting complexes including FMO. The most recent research developments in the photosynthetic light harvesting complexes are thoroughly discussed. The theoretical background related to the spectral density, quantum coherence and density functional theory has been elaborated. Furthermore, details about the transfer and excitation of energy in different sites of the FMO complex along with other vital photosynthetic light harvesting complexes have also been provided. Finally, we conclude this review by providing the current and potential applications in environmental science, energy, health and medicine, where such mathematical and computational studies of the photosynthesis and the light harvesting complexes can be readily integrated.
Collapse
|
10
|
Jiang L, Rogers DM, Hirst JD, Do H. Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene. J Chem Theory Comput 2020; 16:5150-5162. [DOI: 10.1021/acs.jctc.0c00399] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ling Jiang
- Department of Chemical and Environmental Engineering, University of Nottingham—Ningbo China, Ningbo 315100, China
| | - David M. Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Hainam Do
- Department of Chemical and Environmental Engineering, University of Nottingham—Ningbo China, Ningbo 315100, China
- New Materials Institute, University of Nottingham—Ningbo China, Ningbo 315042, China
| |
Collapse
|
11
|
Tong Z, Huai Z, Mei Y, Mo Y. Reproducing the low-temperature excitation energy transfer dynamics of phycoerythrin 545 light-harvesting complex with a structure-based model Hamiltonian. J Chem Phys 2020; 152:135101. [DOI: 10.1063/1.5135999] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Zhengqing Tong
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Zhe Huai
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Yan Mo
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| |
Collapse
|
12
|
Kim Y, Morozov D, Stadnytskyi V, Savikhin S, Slipchenko LV. Predictive First-Principles Modeling of a Photosynthetic Antenna Protein: The Fenna-Matthews-Olson Complex. J Phys Chem Lett 2020; 11:1636-1643. [PMID: 32013435 DOI: 10.1021/acs.jpclett.9b03486] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
High efficiency of light harvesting in photosynthetic pigment-protein complexes is governed by evolutionary-perfected protein-assisted tuning of individual pigment properties and interpigment interactions. Due to the large number of spectrally overlapping pigments in a typical photosynthetic complex, experimental methods often fail to unambiguously identify individual chromophore properties. Here, we report a first-principles-based modeling protocol capable of predicting properties of pigments in protein environment to a high precision. The technique was applied to successfully uncover electronic properties of the Fenna-Matthews-Olson (FMO) pigment-protein complex. Each of the three subunits of the FMO complex contains eight strongly coupled bacteriochlorophyll a (BChl a) pigments. The excitonic structure of FMO can be described by an electronic Hamiltonian containing excitation (site) energies of BChl a pigments and electronic couplings between them. Several such Hamiltonians have been developed in the past based on the information from various spectroscopic measurements of FMO; however, fine details of the excitonic structure and energy transfer in FMO, especially assignments of short-lived high-energy sites, remain elusive. Utilizing polarizable embedding quantum mechanics/molecular mechanics with the effective fragment potentials, we computed the electronic Hamiltonian of FMO that is in general agreement with previously reported empirical Hamiltonians and quantitatively reproduces experimental absorption and circular dichroism spectra of the FMO protein. The developed computational protocol is sufficiently simple and can be utilized for predictive modeling of other wild-type and mutated photosynthetic pigment-protein complexes.
Collapse
Affiliation(s)
- Yongbin Kim
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland
| | - Valentyn Stadnytskyi
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
- Laboratory of Chemical Physics, National Institute of Diabetes, Digestion and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland 20892, United States
| | - Sergei Savikhin
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| |
Collapse
|
13
|
|
14
|
Zuehlsdorff TJ, Hong H, Shi L, Isborn CM. Influence of Electronic Polarization on the Spectral Density. J Phys Chem B 2019; 124:531-543. [DOI: 10.1021/acs.jpcb.9b10250] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Tim J. Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Hanbo Hong
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| |
Collapse
|
15
|
Schelter I, Foerster JM, Gardiner AT, Roszak AW, Cogdell RJ, Ullmann GM, de Queiroz TB, Kümmel S. Assessing density functional theory in real-time and real-space as a tool for studying bacteriochlorophylls and the light-harvesting complex 2. J Chem Phys 2019; 151:134114. [DOI: 10.1063/1.5116779] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Ingo Schelter
- Theoretical Physics IV, University of Bayreuth, Bayreuth, Germany
| | - Johannes M. Foerster
- Theoretical Physics IV and Computational Biochemistry, University of Bayreuth, Bayreuth, Germany
| | | | - Aleksander W. Roszak
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Richard J. Cogdell
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Stephan Kümmel
- Theoretical Physics IV, University of Bayreuth, Bayreuth, Germany
| |
Collapse
|
16
|
|
17
|
Tong Z, Huai Z, Mei Y, Mo Y. Influence of the Protein Environment on the Electronic Excitation of Chromophores in the Phycoerythrin 545 Light–Harvesting Complex: A Combined MD-QM/MM Method with Polarized Protein–Specific Charge Scheme. J Phys Chem B 2019; 123:2040-2049. [DOI: 10.1021/acs.jpcb.8b11764] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Zhengqing Tong
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Zhe Huai
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Yan Mo
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| |
Collapse
|
18
|
Mallus MI, Shakya Y, Prajapati JD, Kleinekathöfer U. Environmental effects on the dynamics in the light-harvesting complexes LH2 and LH3 based on molecular simulations. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
19
|
Cupellini L, Corbella M, Mennucci B, Curutchet C. Electronic energy transfer in biomacromolecules. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1392] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale University of Pisa Pisa Italy
| | - Marina Corbella
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Química Teòrica i Computacional (IQTC‐UB), Facultat de Farmàcia i Ciències de l'Alimentació Universitat de Barcelona Barcelona Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale University of Pisa Pisa Italy
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Química Teòrica i Computacional (IQTC‐UB), Facultat de Farmàcia i Ciències de l'Alimentació Universitat de Barcelona Barcelona Spain
| |
Collapse
|
20
|
Blau SM, Bennett DIG, Kreisbeck C, Scholes GD, Aspuru-Guzik A. Local protein solvation drives direct down-conversion in phycobiliprotein PC645 via incoherent vibronic transport. Proc Natl Acad Sci U S A 2018; 115:E3342-E3350. [PMID: 29588417 PMCID: PMC5899487 DOI: 10.1073/pnas.1800370115] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mechanisms controlling excitation energy transport (EET) in light-harvesting complexes remain controversial. Following the observation of long-lived beats in 2D electronic spectroscopy of PC645, vibronic coherence, the delocalization of excited states between pigments supported by a resonant vibration, has been proposed to enable direct excitation transport from the highest-energy to the lowest-energy pigments, bypassing a collection of intermediate states. Here, we instead show that for phycobiliprotein PC645 an incoherent vibronic transport mechanism is at play. We quantify the solvation dynamics of individual pigments using ab initio quantum mechanics/molecular mechanics (QM/MM) nuclear dynamics. Our atomistic spectral densities reproduce experimental observations ranging from absorption and fluorescence spectra to the timescales and selectivity of down-conversion observed in transient absorption measurements. We construct a general model for vibronic dimers and establish the parameter regimes of coherent and incoherent vibronic transport. We demonstrate that direct down-conversion in PC645 proceeds incoherently, enhanced by large reorganization energies and a broad collection of high-frequency vibrations. We suggest that a similar incoherent mechanism is appropriate across phycobiliproteins and represents a potential design principle for nanoscale control of EET.
Collapse
Affiliation(s)
- Samuel M Blau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Doran I G Bennett
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Bio-Inspired Solar Energy Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada
| | - Christoph Kreisbeck
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Gregory D Scholes
- Bio-Inspired Solar Energy Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138;
- Bio-Inspired Solar Energy Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada
| |
Collapse
|
21
|
Sonani RR, Roszak AW, Ortmann de Percin Northumberland C, Madamwar D, Cogdell RJ. An improved crystal structure of C-phycoerythrin from the marine cyanobacterium Phormidium sp. A09DM. PHOTOSYNTHESIS RESEARCH 2018; 135:65-78. [PMID: 28918447 PMCID: PMC5783998 DOI: 10.1007/s11120-017-0443-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 09/08/2017] [Indexed: 06/07/2023]
Abstract
C-Phycoerythrin (PE) from Phormidium sp. A09DM has been crystallized using different conditions and its structure determined to atomic resolution (1.14 Å). In order for the pigment present, phycoerythrobilin (PEB), to function as an efficient light-harvesting molecule it must be held rigidly (Kupka and Scheer in Biochim Biophys Acta 1777:94-103, 2008) and, moreover, the different PEB molecules in PE must be arranged, relative to each other, so as to promote efficient energy transfer between them. This improved structure has allowed us to define in great detail the structure of the PEBs and their binding sites. These precise structural details will facilitate theoretical calculations of each PEB's spectroscopic properties. It was possible, however, to suggest a model for which chromophores contribute to the different regions of absorption spectrum and propose a tentative scheme for energy transfer. We show that some subtle differences in one of these PEB binding sites in two of the 12 subunits are caused by crystal contacts between neighboring hexamers in the crystal lattice. This explains some of the differences seen in previous lower resolution structures determined at two different pH values (Kumar et al. in Photosyn Res 129:17-28, 2016).
Collapse
Affiliation(s)
- Ravi R Sonani
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Vadtal Road, Satellite Campus, Bakrol, Anand, Gujarat, 388315, India
| | - Aleksander W Roszak
- Institute of Molecular Cell an Systems Biology, University of Glasgow, 120 University Place, Glasgow, G12 8TA, UK.
| | | | - Datta Madamwar
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Vadtal Road, Satellite Campus, Bakrol, Anand, Gujarat, 388315, India.
| | - Richard J Cogdell
- Institute of Molecular Cell an Systems Biology, University of Glasgow, 120 University Place, Glasgow, G12 8TA, UK
| |
Collapse
|
22
|
Fornari RP, Rowe P, Padula D, Troisi A. Importance and Nature of Short-Range Excitonic Interactions in Light Harvesting Complexes and Organic Semiconductors. J Chem Theory Comput 2017. [DOI: 10.1021/acs.jctc.7b00328] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rocco P. Fornari
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Patrick Rowe
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Daniele Padula
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alessandro Troisi
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| |
Collapse
|
23
|
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
|
24
|
Pinheiro S, Curutchet C. Can Förster Theory Describe Stereoselective Energy Transfer Dynamics in a Protein-Ligand Complex? J Phys Chem B 2017; 121:2265-2278. [PMID: 28235382 DOI: 10.1021/acs.jpcb.7b00217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Förster resonance energy transfer (FRET) reactions involving ligands and aromatic amino acids can substantially impact the fluorescence properties of a protein-ligand complex, an impact intimately related to the corresponding binding mode. Structural characterization of such binding events in terms of intermolecular distances can be done through the well-known R-6 distance-dependent Förster rate expression. However, such an interpretation suffers from uncertainties underlying Förster theory in the description of the electronic coupling that promotes FRET, mostly related to the dipole-dipole orientation factor, dielectric screening effects, and deviations from the ideal dipole approximation. Here, we investigate how Förster approximations impact the prediction of energy transfer dynamics in the complex between flurbiprofen (FBP) and human serum albumin (HSA), as well as a model FBP-Trp dyad, in which recent observation of enantioselective fluorescence quenching has been ascribed to energy transfer from FBP to Trp. To this end, we combine classical molecular dynamics simulations with polarizable quantum mechanics/molecular mechanics calculations that allow overcoming Förster approximations. On the basis of our results, we discuss the potential of structure-based simulations in the characterization of drug-binding events through fluorescence techniques. Overall, we find an excellent agreement between theory and experiment both in terms of enantioselectivity and FRET times, thus strongly supporting the reliability of the binding modes proposed for the (S) and (R) enantiomers of FBP. In particular, we show that the dynamic quenching arises from a small fraction of drug bound to the secondary site of HSA at the interface between subdomains IIA and IIB, whereas the enantioselectivity arises from the larger flexibility of the (S)-FBP enantiomer in the binding pocket.
Collapse
Affiliation(s)
- Silvana Pinheiro
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona , Av. Joan XXIII s/n, Barcelona 08028, Spain
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona , Av. Joan XXIII s/n, Barcelona 08028, Spain
| |
Collapse
|