1
|
Drosou M, Bhattacharjee S, Pantazis DA. Combined Multireference-Multiscale Approach to the Description of Photosynthetic Reaction Centers. J Chem Theory Comput 2024. [PMID: 39116215 DOI: 10.1021/acs.jctc.4c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
A first-principles description of the primary photochemical processes that drive photosynthesis and sustain life on our planet remains one of the grand challenges of modern science. Recent research established that explicit incorporation of protein electrostatics in excited-state calculations of photosynthetic pigments, achieved for example with quantum-mechanics/molecular-mechanics (QM/MM) approaches, is essential for a meaningful description of the properties and function of pigment-protein complexes. Although time-dependent density functional theory has been used productively so far in QM/MM approaches for the study of such systems, this methodology has limitations. Here we pursue for the first time a QM/MM description of the reaction center in the principal enzyme of oxygenic photosynthesis, Photosystem II, using multireference wave function theory for the high-level QM region. We identify best practices and establish guidelines regarding the rational choice of active space and appropriate state-averaging for the efficient and reliable use of complete active space self-consistent field (CASSCF) and the N-electron valence state perturbation theory (NEVPT2) in the prediction of low-lying excited states of chlorophyll and pheophytin pigments. Given that the Gouterman orbitals are inadequate as a minimal active space, we define specific minimal and extended active spaces for the NEVPT2 description of electronic states that fall within the Q and B bands. Subsequently, we apply our multireference-QM/MM protocol to the description of all pigments in the reaction center of Photosystem II. The calculations reproduce the electrochromic shifts induced by the protein matrix and the ordering of site energies consistent with the identity of the primary donor (ChlD1) and the experimentally known asymmetric and directional electron transfer. The optimized protocol sets the stage for future multireference treatments of multiple pigments, and hence for multireference studies of charge separation, while it is transferable to the study of any photoactive embedded tetrapyrrole system.
Collapse
Affiliation(s)
- Maria Drosou
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Sinjini Bhattacharjee
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
2
|
Pirnia A, Maqdisi R, Mittal S, Sener M, Singharoy A. Perspective on Integrative Simulations of Bioenergetic Domains. J Phys Chem B 2024; 128:3302-3319. [PMID: 38562105 DOI: 10.1021/acs.jpcb.3c07335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.
Collapse
Affiliation(s)
- Adam Pirnia
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
| | - Ranel Maqdisi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
| | - Sumit Mittal
- VIT Bhopal University, Sehore 466114, Madhya Pradesh, India
| | - Melih Sener
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Abhishek Singharoy
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
| |
Collapse
|
3
|
Allan L, Zuehlsdorff TJ. Taming the third order cumulant approximation to linear optical spectroscopy. J Chem Phys 2024; 160:074108. [PMID: 38380749 DOI: 10.1063/5.0182745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
The second order cumulant method offers a promising pathway to predicting optical properties in condensed phase systems. It allows for the computation of linear absorption spectra from excitation energy fluctuations sampled along molecular dynamics (MD) trajectories, fully accounting for vibronic effects, direct solute-solvent interactions, and environmental polarization effects. However, the second order cumulant approximation only guarantees accurate line shapes for energy gap fluctuations obeying Gaussian statistics. A third order correction has recently been derived but often yields unphysical spectra or divergent line shapes for moderately non-Gaussian fluctuations due to the neglect of higher order terms in the cumulant expansion. In this work, we develop a corrected cumulant approach, where the collective effect of neglected higher order contributions is approximately accounted for through a dampening factor applied to the third order cumulant term. We show that this dampening factor can be expressed as a function of the skewness and kurtosis of energy gap fluctuations and can be parameterized from a large set of randomly sampled model Hamiltonians for which exact spectral line shapes are known. This approach is shown to systematically remove unphysical contributions in the form of negative absorbances from cumulant spectra in both model Hamiltonians and condensed phase systems sampled from MD and dramatically improves over the second order cumulant method in describing systems exhibiting Duschinsky mode mixing effects. We successfully apply the approach to the coumarin-153 dye in toluene, obtaining excellent agreement with experiment.
Collapse
Affiliation(s)
- Lucas Allan
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| |
Collapse
|
4
|
Mai M, Zazubovich V, Mansbach RA. Identification of Residues Potentially Involved in Optical Shifts in the Water-Soluble Chlorophyll a-Binding Protein through Molecular Dynamics Simulations. J Phys Chem B 2024; 128:1371-1384. [PMID: 38299975 PMCID: PMC10876061 DOI: 10.1021/acs.jpcb.3c06889] [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: 10/17/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Abstract
Reversible light and thermally induced spectral shifts are universally observed in a wide variety of pigment-protein complexes at temperatures ranging from cryogenic to ambient. In this paper, we employed large-scale molecular dynamics (MD) simulations of a prototypical pigment-protein complex to better understand these shifts at a molecular scale. Although multiple mechanisms have been proposed over the years, no verification of these proposals via MD simulations has thus far been performed; our work represents the first step in this direction. From simulations of the water-soluble chlorophyll-binding protein complex, we determined that rearrangements of long hydrogen bonds were unlikely to be the origin of the multiwell landscape features necessary to explain observed spectral shifts. We also assessed small motions of amino acid residues and identified side chain rotations of some of these residues as likely candidates for the origin of relevant multiwell landscape features. The protein free-energy landscapes associated with side chain rotations feature energy barriers of around 1100-1600 cm-1, in agreement with optical spectroscopy results, with the most promising residue type associated with experimental signatures being serine, which possesses a symmetric triple-well landscape and moment of inertia of a relevant magnitude.
Collapse
Affiliation(s)
- Martina Mai
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
| | - Valter Zazubovich
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
| | - Rachael A. Mansbach
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
| |
Collapse
|
5
|
Dani R, Kundu S, Makri N. Coherence Maps and Flow of Excitation Energy in the Bacterial Light Harvesting Complex 2. J Phys Chem Lett 2023; 14:3835-3843. [PMID: 37067041 DOI: 10.1021/acs.jpclett.3c00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
We present and analyze coherence maps [ J. Phys. Chem. B 2022, 126, 9361-9375] to investigate the quantum coherences that are created, sustained, and damped by vibrational modes during the transfer of excitation energy from the B800 (outer) to the B850 (inner) ring of the light harvesting complex 2 (LH2) of purple bacteria with a variety of initial conditions. The reduced density matrix of the 24-pigment complex, where the ground and excited electronic states of each bacteriochlorophyll are explicitly coupled to 50 intramolecular vibrations at room temperature, is obtained from fully quantum-mechanical small matrix path integral (SMatPI) calculations. The coherence maps show a very rapid localization within the outer ring, accompanied by the formation of inter-ring quantum superpositions that evolve to a partial quantum delocalization at equilibrium, and quantify in state-to-state detail the flow of energy within the complex.
Collapse
Affiliation(s)
- Reshmi Dani
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Sohang Kundu
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Nancy Makri
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois, Urbana, Illinois 61801, United States
- Illinois Quantum Information Science and Technology Center, University of Illinois, Urbana, Illinois 61801, United States
| |
Collapse
|
6
|
Feighan O, Manby FR, Bourne-Worster S. An efficient protocol for excited states of large biochromophores. J Chem Phys 2023; 158:024107. [PMID: 36641400 DOI: 10.1063/5.0132417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Efficient energy transport in photosynthetic antenna is a long-standing source of inspiration for artificial light harvesting materials. However, characterizing the excited states of the constituent chromophores poses a considerable challenge to mainstream quantum chemical and semiempirical excited state methods due to their size and complexity and the accuracy required to describe small but functionally important changes in their properties. In this paper, we explore an alternative approach to calculating the excited states of large biochromophores, exemplified by a specific method for calculating the Qy transition of bacteriochlorophyll a, which we name Chl-xTB. Using a diagonally dominant approximation to the Casida equation and a bespoke parameterization scheme, Chl-xTB can match time-dependent density functional theory's accuracy and semiempirical speed for calculating the potential energy surfaces and absorption spectra of chlorophylls. We demonstrate that Chl-xTB (and other prospective realizations of our protocol) can be integrated into multiscale models, including concurrent excitonic and point-charge embedding frameworks, enabling the analysis of biochromophore networks in a native environment. We exploit this capability to probe the low-frequency spectral densities of excitonic energies and interchromophore interactions in the light harvesting antenna protein LH2 (light harvesting complex 2). The impact of low-frequency protein motion on interchromophore coupling and exciton transport has routinely been ignored due to the prohibitive costs of including it in simulations. Our results provide a more rigorous basis for continued use of this approximation by demonstrating that exciton transition energies are unaffected by low-frequency vibrational coupling to exciton interaction energies.
Collapse
Affiliation(s)
- Oliver Feighan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Susannah Bourne-Worster
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| |
Collapse
|
7
|
Cho KH, Rhee YM. Computational elucidations on the role of vibrations in energy transfer processes of photosynthetic complexes. Phys Chem Chem Phys 2021; 23:26623-26639. [PMID: 34842245 DOI: 10.1039/d1cp04615b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coupling between pigment excitations and nuclear movements in photosynthetic complexes is known to modulate the excitation energy transfer (EET) efficiencies. Toward providing microscopic information, researchers often apply simulation techniques and investigate how vibrations are involved in EET processes. Here, reports on such roles of nuclear movements are discussed from a theory perspective. While vibrations naturally present random thermal fluctuations that can affect energy transferring characteristics, they can also be intertwined with exciton structures and create more specific non-adiabatic energy transfer pathways. For reliable simulations, a bath model that accurately mimics a given molecular system is required. Methods for obtaining such a model in combination with quantum chemical electronic structure calculations and molecular dynamics trajectory simulations are discussed. Various quantum dynamics simulation tools that can handle pigment-to-pigment energy transfers together with their vibrational characters are also touched on. Behaviors of molecular vibrations often deviate from ideality, especially when all-atom details are included, which practically forces us to treat them classically. We conclude this perspective by considering some recent reports that suggest that classical descriptions of bath effects with all-atom details may still produce valuable information for analyzing sophisticated contributions by vibrations to EET processes.
Collapse
Affiliation(s)
- Kwang Hyun Cho
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| |
Collapse
|
8
|
Zuehlsdorff TJ, Shedge SV, Lu SY, Hong H, Aguirre VP, Shi L, Isborn CM. Vibronic and Environmental Effects in Simulations of Optical Spectroscopy. Annu Rev Phys Chem 2021; 72:165-188. [DOI: 10.1146/annurev-physchem-090419-051350] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Including both environmental and vibronic effects is important for accurate simulation of optical spectra, but combining these effects remains computationally challenging. We outline two approaches that consider both the explicit atomistic environment and the vibronic transitions. Both phenomena are responsible for spectral shapes in linear spectroscopy and the electronic evolution measured in nonlinear spectroscopy. The first approach utilizes snapshots of chromophore-environment configurations for which chromophore normal modes are determined. We outline various approximations for this static approach that assumes harmonic potentials and ignores dynamic system-environment coupling. The second approach obtains excitation energies for a series of time-correlated snapshots. This dynamic approach relies on the accurate truncation of the cumulant expansion but treats the dynamics of the chromophore and the environment on equal footing. Both approaches show significant potential for making strides toward more accurate optical spectroscopy simulations of complex condensed phase systems.
Collapse
Affiliation(s)
- Tim J. Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Sapana V. Shedge
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Shao-Yu Lu
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Hanbo Hong
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Vincent P. Aguirre
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Liang Shi
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Christine M. Isborn
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| |
Collapse
|
9
|
Kehrer J, Richter R, Foerster JM, Schelter I, Kümmel S. Self-interaction correction, electrostatic, and structural influences on time-dependent density functional theory excitations of bacteriochlorophylls from the light-harvesting complex 2. J Chem Phys 2020; 153:144114. [PMID: 33086803 DOI: 10.1063/5.0014938] [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
First-principles calculations offer the chance to obtain a microscopic understanding of light-harvesting processes. Time-dependent density functional theory can have the computational efficiency to allow for such calculations. However, the (semi-)local exchange-correlation approximations that are computationally most efficient fail to describe charge-transfer excitations reliably. We here investigate whether the inexpensive average density self-interaction correction (ADSIC) remedies the problem. For the systems that we study, ADSIC is even more prone to the charge-transfer problem than the local density approximation. We further explore the recently reported finding that the electrostatic potential associated with the chromophores' protein environment in the light-harvesting complex 2 beneficially shifts spurious excitations. We find a great sensitivity on the chromophores' atomistic structure in this problem. Geometries obtained from classical molecular dynamics are more strongly affected by the spurious charge-transfer problem than the ones obtained from crystallography or density functional theory. For crystal structure geometries and density-functional theory optimized ones, our calculations confirm that the electrostatic potential shifts the spurious excitations out of the energetic range that is most relevant for electronic coupling.
Collapse
Affiliation(s)
- Juliana Kehrer
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Rian Richter
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
| | | | - Ingo Schelter
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Stephan Kümmel
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
| |
Collapse
|
10
|
Chen MS, Zuehlsdorff TJ, Morawietz T, Isborn CM, Markland TE. Exploiting Machine Learning to Efficiently Predict Multidimensional Optical Spectra in Complex Environments. J Phys Chem Lett 2020; 11:7559-7568. [PMID: 32808797 DOI: 10.1021/acs.jpclett.0c02168] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The excited-state dynamics of chromophores in complex environments determine a range of vital biological and energy capture processes. Time-resolved, multidimensional optical spectroscopies provide a key tool to investigate these processes. Although theory has the potential to decode these spectra in terms of the electronic and atomistic dynamics, the need for large numbers of excited-state electronic structure calculations severely limits first-principles predictions of multidimensional optical spectra for chromophores in the condensed phase. Here, we leverage the locality of chromophore excitations to develop machine learning models to predict the excited-state energy gap of chromophores in complex environments for efficiently constructing linear and multidimensional optical spectra. By analyzing the performance of these models, which span a hierarchy of physical approximations, across a range of chromophore-environment interaction strengths, we provide strategies for the construction of machine learning models that greatly accelerate the calculation of multidimensional optical spectra from first principles.
Collapse
Affiliation(s)
- Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Tobias Morawietz
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
11
|
Zuehlsdorff TJ, Hong H, Shi L, Isborn CM. Nonlinear spectroscopy in the condensed phase: The role of Duschinsky rotations and third order cumulant contributions. J Chem Phys 2020; 153:044127. [PMID: 32752702 DOI: 10.1063/5.0013739] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
First-principles modeling of nonlinear optical spectra in the condensed phase is highly challenging because both environment and vibronic interactions can play a large role in determining spectral shapes and excited state dynamics. Here, we compute two dimensional electronic spectroscopy (2DES) signals based on a cumulant expansion of the energy gap fluctuation operator, with specific focus on analyzing mode mixing effects introduced by the Duschinsky rotation and the role of the third order term in the cumulant expansion for both model and realistic condensed phase systems. We show that for a harmonic model system, the third order cumulant correction captures effects introduced by a mismatch in curvatures of ground and excited state potential energy surfaces, as well as effects of mode mixing. We also demonstrate that 2DES signals can be accurately reconstructed from purely classical correlation functions using quantum correction factors. We then compute nonlinear optical spectra for the Nile red and methylene blue chromophores in solution, assessing the third order cumulant contribution for realistic systems. We show that the third order cumulant correction is strongly dependent on the treatment of the solvent environment, revealing the interplay between environmental polarization and the electronic-vibrational coupling.
Collapse
Affiliation(s)
- Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Hanbo Hong
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Liang Shi
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| |
Collapse
|
12
|
Rao R, Basak N. Development of novel strategies for higher fermentative biohydrogen recovery along with novel metabolites from organic wastes: The present state of the art. Biotechnol Appl Biochem 2020; 68:421-444. [PMID: 32474946 DOI: 10.1002/bab.1964] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 05/30/2020] [Indexed: 01/15/2023]
Abstract
Depletion of fossil fuels and environmental concern has compelled us to search for alternative fuel. Hydrogen is considered as a dream fuel as it has high energy content (142 kJ g-1 ) and is not chemically bound to carbon. At present, fossil fuel-based methods for producing hydrogen require high-energy input, which makes the processes expensive. The major processes for biohydrogen production are biophotolysis, microbial electrolysis, dark fermentation, and photofermentation. Fermentative hydrogen production has the additional advantages of potentially using various waste streams from different industries as feedstock. Novel strategies to enhance the productivity of fermentative hydrogen production include optimization in pretreatment methods, integrated fermentation systems (sequential and combined fermentation), use of nanoparticles as additives, metabolic engineering of microorganisms, improving the light utilization efficiency, developing more efficient photobioreactors, etc. More focus has been given to produce biohydrogen in a biorefinery approach in which, along with hydrogen gas, other metabolites (ethanol, butyric acid, 1,3-propanediol, etc.) are also produced, which have direct/indirect industrial applications. In present review, various emerging technologies that highlight biohydrogen production methods as effective and sustainable methods on a large scale have been critically reviewed. The possible future developments are also outlined.
Collapse
Affiliation(s)
- Raman Rao
- Department of Biotechnology, Dr. B. R Ambedkar National Institute of Technology, Jalandhar, 144 011, India
| | - Nitai Basak
- Department of Biotechnology, Dr. B. R Ambedkar National Institute of Technology, Jalandhar, 144 011, India
| |
Collapse
|
13
|
Liguori N, Croce R, Marrink SJ, Thallmair S. Molecular dynamics simulations in photosynthesis. PHOTOSYNTHESIS RESEARCH 2020; 144:273-295. [PMID: 32297102 PMCID: PMC7203591 DOI: 10.1007/s11120-020-00741-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/24/2020] [Indexed: 05/12/2023]
Abstract
Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.
Collapse
Affiliation(s)
- Nicoletta Liguori
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
| | - Roberta Croce
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| |
Collapse
|
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
|
Cho KH, Chung S, Rhee YM. Efficiently Transplanting Potential Energy Interpolation Database between Two Systems: Bacteriochlorophyll Case with FMO and LH2 Complexes. J Chem Inf Model 2019; 59:4228-4238. [PMID: 31487163 DOI: 10.1021/acs.jcim.9b00472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Generating a reliable potential energy surface (PES) is an important issue for studying the dynamics of any system with computational simulations. Interpolation mechanics/molecular mechanics (IM/MM) based on a PES interpolation scheme is a useful tool in that regard as it provides an accuracy of a quantum chemistry (QC) level while maintaining its computational cost comparable to conventional MM force fields. Despite this benefit, constructing the database for interpolation itself is still challenging and time-consuming. Here, we present a method with which we can construct the IM database of one system based on a preexisting data set for another related system. We adopt the case of constructing bacteriochlorophyll PESs for the light-harvesting 2 (LH2) complex by utilizing already available IM database for the BChls from the Fenna-Matthews-Olson (FMO) complex. In this method, the IM database from FMO is first transplanted to LH2 by considering BChl displacement vectors that take into account the geometry differences induced by the protein scaffolds. From this transplanted primitive database entries, a relatively small number of effective ones are selected by a survival process based on a genetic algorithm such that the IM energies evaluated at geometries in a conveniently collected prediction set can closely match with the reference QC energies. The selection process is expedited by using two different levels of basis sets for the QC calculations. To demonstrate the utility of the PES thus constructed, we carry out 1 ns of IM/MM dynamics simulations with the finally optimized BChl database for LH2. Indeed, the energy profiles of the snapshots are found to be closely matching with the reference QC calculation data, with only ∼0.07 eV of errors in the ground- and excited-state energies and ∼0.008 eV of errors in the transition energies. We also show that properly selecting data points is actually quite important for generating an IM PES toward performing molecular dynamics simulations.
Collapse
Affiliation(s)
- Kwang Hyun Cho
- Department of Chemistry , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Korea
| | - Seyoung Chung
- Department of Chemistry , Pohang University of Science and Technology (POSTECH) , Pohang 37673 , Korea
| | - Young Min Rhee
- Department of Chemistry , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Korea
| |
Collapse
|
17
|
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
|