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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 DOI: 10.1021/acs.jpcb.4c01637] [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: 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.
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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
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2
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Brütting M, Foerster JM, Kümmel S. Understanding Primary Charge Separation in the Heliobacterial Reaction Center. J Phys Chem Lett 2023; 14:3092-3102. [PMID: 36951395 DOI: 10.1021/acs.jpclett.3c00377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The homodimeric reaction center of heliobacteria retains features of the ancestral reaction center and can thus provide insights into the evolution of photosynthesis. Primary charge separation is expected to proceed in a two-step mechanism along either of the two reaction center branches. We reveal the first charge-separation step from first-principles calculations based on time-dependent density functional theory with an optimally tuned range-separated hybrid and ab initio Born-Oppenheimer molecular dynamics: the electron is most likely localized on the electron transfer cofactor 3 (EC3, OH-chlorophyll a), and the hole on the adjacent EC2. Including substantial parts of the surrounding protein environment into the calculations shows that a distinct structural mechanism is decisive for the relative energetic positioning of the electronic excitations: specific charged amino acids in the vicinity of EC3 lower the energy of charge-transfer excitations and thus facilitate efficient charge separation. These results are discussed considering recent experimental insights.
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3
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Sen S, Visscher L. Towards the description of charge transfer states in solubilised LHCII using subsystem DFT. PHOTOSYNTHESIS RESEARCH 2023; 156:39-57. [PMID: 35988131 PMCID: PMC10070235 DOI: 10.1007/s11120-022-00950-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/04/2022] [Indexed: 05/05/2023]
Abstract
Light harvesting complex II (LHCII) in plants and green algae have been shown to adapt their absorption properties, depending on the concentration of sunlight, switching between a light harvesting and a non-harvesting or quenched state. In a recent work, combining classical molecular dynamics (MD) simulations with quantum chemical calculations (Liguori et al. in Sci Rep 5:15661, 2015) on LHCII, it was shown that the Chl611-Chl612 cluster of the terminal emitter domain can play an important role in modifying the spectral properties of the complex. In that work the importance of charge transfer (CT) effects was highlighted, in re-shaping the absorption intensity of the chlorophyll dimer. Here in this work, we investigate the combined effect of the local excited (LE) and CT states in shaping the energy landscape of the chlorophyll dimer. Using subsystem Density Functional Theory over the classical [Formula: see text]s MD trajectory we look explicitly into the excitation energies of the LE and the CT states of the dimer and their corresponding couplings. Upon doing so, we observe a drop in the excitation energies of the CT states, accompanied by an increase in the couplings between the LE/LE and the LE/CT states facilitated by a shorter interchromophoric distance upon equilibration. Both these changes in conjunction, effectively produces a red-shift of the low-lying mixed exciton/CT states of the supramolecular chromophore pair.
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Affiliation(s)
- Souloke Sen
- Division of Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Lucas Visscher
- Division of Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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4
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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.
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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.
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5
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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.
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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
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6
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Gómez S, Giovannini T, Cappelli C. Multiple Facets of Modeling Electronic Absorption Spectra of Systems in Solution. ACS PHYSICAL CHEMISTRY AU 2022; 3:1-16. [PMID: 36718266 PMCID: PMC9881242 DOI: 10.1021/acsphyschemau.2c00050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022]
Abstract
In this Perspective, we outline the essential physicochemical aspects that need to be considered when building a reliable approach to describe absorption properties of solvated systems. In particular, we focus on how to properly model the complexity of the solvation phenomenon, arising from dynamical aspects and specific, strong solute-solvent interactions. To this end, conformational and configurational sampling techniques, such as Molecular Dynamics, have to be coupled to accurate fully atomistic Quantum Mechanical/Molecular Mechanics (QM/MM) methodologies. By exploiting different illustrative applications, we show that an effective reproduction of experimental spectral signals can be achieved by delicately balancing exhaustive sampling, hydrogen bonding, mutual polarization, and nonelectrostatic effects.
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7
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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.
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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
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8
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Cignoni E, Slama V, Cupellini L, Mennucci B. The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol. J Chem Phys 2022; 156:120901. [DOI: 10.1063/5.0086275] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The function of light-harvesting complexes is determined by a complex network of dynamic interactions among all the different components: the aggregate of pigments, the protein, and the surrounding environment. Complete and reliable predictions on these types of composite systems can be only achieved with an atomistic description. In the last few decades, there have been important advances in the atomistic modeling of light-harvesting complexes. These advances have involved both the completeness of the physical models and the accuracy and effectiveness of the computational protocols. In this Perspective, we present an overview of the main theoretical and computational breakthroughs attained so far in the field, with particular focus on the important role played by the protein and its dynamics. We then discuss the open problems in their accurate modeling that still need to be addressed. To illustrate an effective computational workflow for the modeling of light harvesting complexes, we take as an example the plant antenna complex CP29 and its H111N mutant.
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Affiliation(s)
- Edoardo Cignoni
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Vladislav Slama
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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9
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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.
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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
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10
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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.
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11
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Cupellini L, Bondanza M, Nottoli M, Mennucci B. Successes & challenges in the atomistic modeling of light-harvesting and its photoregulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148049. [PMID: 31386831 DOI: 10.1016/j.bbabio.2019.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022]
Abstract
Light-harvesting is a crucial step of photosynthesis. Its mechanisms and related energetics have been revealed by a combination of experimental investigations and theoretical modeling. The success of theoretical modeling is largely due to the application of atomistic descriptions combining quantum chemistry, classical models and molecular dynamics techniques. Besides the important achievements obtained so far, a complete and quantitative understanding of how the many different light-harvesting complexes exploit their structural specificity is still missing. Moreover, many questions remain unanswered regarding the mechanisms through which light-harvesting is regulated in response to variable light conditions. Here we show that, in both fields, a major role will be played once more by atomistic descriptions, possibly generalized to tackle the numerous time and space scales on which the regulation takes place: going from the ultrafast electronic excitation of the multichromophoric aggregate, through the subsequent conformational changes in the embedding protein, up to the interaction between proteins.
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Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy.
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12
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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]
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13
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Macrocycle ring deformation as the secondary design principle for light-harvesting complexes. Proc Natl Acad Sci U S A 2018; 115:E9051-E9057. [PMID: 30194231 DOI: 10.1073/pnas.1719355115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Natural light-harvesting is performed by pigment-protein complexes, which collect and funnel the solar energy at the start of photosynthesis. The identity and arrangement of pigments largely define the absorption spectrum of the antenna complex, which is further regulated by a palette of structural factors. Small alterations are induced by pigment-protein interactions. In light-harvesting systems 2 and 3 from Rhodoblastus acidophilus, the pigments are arranged identically, yet the former has an absorption peak at 850 nm that is blue-shifted to 820 nm in the latter. While the shift has previously been attributed to the removal of hydrogen bonds, which brings changes in the acetyl moiety of the bacteriochlorophyll, recent work has shown that other mechanisms are also present. Using computational and modeling tools on the corresponding crystal structures, we reach a different conclusion: The most critical factor for the shift is the curvature of the macrocycle ring. The bending of the planar part of the pigment is identified as the second-most important design principle for the function of pigment-protein complexes-a finding that can inspire the design of novel artificial systems.
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Beltrán-Leiva MJ, Páez-Hernández D, Arratia-Pérez R. Theoretical Determination of Energy Transfer Processes and Influence of Symmetry in Lanthanide(III) Complexes: Methodological Considerations. Inorg Chem 2018; 57:5120-5132. [DOI: 10.1021/acs.inorgchem.8b00159] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- María J. Beltrán-Leiva
- Relativistic Molecular Physics (ReMoPh) Group, Ph.D. Program in Molecular Physical Chemistry, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile
| | - Dayán Páez-Hernández
- Relativistic Molecular Physics (ReMoPh) Group, Ph.D. Program in Molecular Physical Chemistry, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile
- Center of Applied Nanosciences (CANS), Facultad de Ciencias Exactas, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile
| | - Ramiro Arratia-Pérez
- Relativistic Molecular Physics (ReMoPh) Group, Ph.D. Program in Molecular Physical Chemistry, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile
- Center of Applied Nanosciences (CANS), Facultad de Ciencias Exactas, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile
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15
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Abramavicius D, Chorošajev V, Valkunas L. Tracing feed-back driven exciton dynamics in molecular aggregates. Phys Chem Chem Phys 2018; 20:21225-21240. [DOI: 10.1039/c8cp00682b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Excitation, exciton transport, dephasing and energy relaxation, and finally detection processes shift molecular systems into a specific superposition of quantum states causing localization, local heating and finally excitonic polaronic effects.
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Affiliation(s)
| | | | - Leonas Valkunas
- Institute of Chemical Physics
- Vilnius University
- Vilnius
- Lithuania
- Center for Physical Sciences and Technology
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16
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Zhang J, Zhu C, Liang W. Benchmarking calculations of spectral densities for the diagonal and nondiagonal exciton-phonon coupling of tetracene crystal. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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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.
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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
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18
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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
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19
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Anda A, De Vico L, Hansen T. Intermolecular Modes between LH2 Bacteriochlorophylls and Protein Residues: The Effect on the Excitation Energies. J Phys Chem B 2017; 121:5499-5508. [PMID: 28485594 DOI: 10.1021/acs.jpcb.7b02071] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light-harvesting system 2 (LH2) executes the primary processes of photosynthesis in purple bacteria; photon absorption, and energy transportation to the reaction center. A detailed mechanistic insight into these operations is obscured by the complexity of the light-harvesting systems, particularly by the chromophore-environment interaction. In this work, we focus on the effects of the protein residues that are ligated to the bacteriochlorophylls (BChls) and construct potential energy surfaces of the ground and first optically excited state for the various BChl-residue systems where we in each case consider two degrees of freedom in the intermolecular region. We find that the excitation energies are only slightly affected by the considered modes. In addition, we see that axial ligands and hydrogen-bonded residues have opposite effects on both excitation energies and oscillator strengths by comparing to the isolated BChls. Our results indicate that only a small part of the chromophore-environment interaction can be associated with the intermolecular region between a BChl and an adjacent residue, but that it may be possible to selectively raise or lower the excitation energy at the axial and planar residue positions, respectively.
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Affiliation(s)
- André Anda
- Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Luca De Vico
- Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen, Denmark.,Department of Biotechnology, Chemistry and Pharmacy, University of Siena , via Aldo Moro 2, 53100 Siena, Italy
| | - Thorsten Hansen
- Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen, Denmark
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20
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Li SB, Geng Y, Duan YA, Sun GY, Zhang M, Qiu YQ, Su ZM. Theoretical study on the charge transfer mechanism at donor/acceptor interface: Why TTF/TCNQ is inadaptable to photovoltaics? J Chem Phys 2016; 145:244705. [DOI: 10.1063/1.4972005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Shuang-Bao Li
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, People’s Republic of China
| | - Yun Geng
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, People’s Republic of China
| | - Yu-Ai Duan
- Department of Chemistry, Capital Normal University, Beijing 100048, People’s Republic of China
| | - Guang-Yan Sun
- Department of Chemistry, Faculty of Science, Yanbian University, Yanji 133002, People’s Republic of China
| | - Min Zhang
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, People’s Republic of China
| | - Yong-Qing Qiu
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, People’s Republic of China
| | - Zhong-Min Su
- Department of Chemistry, Faculty of Science, Yanbian University, Yanji 133002, People’s Republic of China
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21
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Cupellini L, Jurinovich S, Campetella M, Caprasecca S, Guido CA, Kelly SM, Gardiner AT, Cogdell R, Mennucci B. An Ab Initio Description of the Excitonic Properties of LH2 and Their Temperature Dependence. J Phys Chem B 2016; 120:11348-11359. [PMID: 27791372 DOI: 10.1021/acs.jpcb.6b06585] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The spectroscopic properties of light-harvesting (LH) antennae in photosyntehtic organisms represent a fingerprint that is unique for each specific pigment-protein complex. Because of that, spectroscopic observations are generally combined with structural data from X-ray crystallography to obtain an indirect representation of the excitonic properties of the system. Here, an alternative strategy is presented which goes beyond this empirical approach and introduces an ab initio computational description of both structural and electronic properties and their dependence on the temperature. The strategy is applied to the peripheral light-harvesting antenna complex (LH2) present in purple bacteria. By comparing this model with the one based on the crystal structure, a detailed, molecular level explanation of the absorption and circular dichroism (CD) spectra and their temperature dependence is achieved. The agreement obtained with the experiments at both low and room temperature lays the groundwork for an atomistic understanding of the excitation dynamics in the LH2 system.
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Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Marco Campetella
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Stefano Caprasecca
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Ciro A Guido
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Sharon M Kelly
- Life Sciences Biomolecular Sci, Joseph Black Building, University of Glasgow , Glasgow G12 8QQ, Scotland
| | - Alastair T Gardiner
- Glasgow Biomedical Research Centre, Institute of Molecular Cell and Systems Biology, University of Glasgow , 126 University Place, Glasgow G12 8TA, Scotland
| | - Richard Cogdell
- Glasgow Biomedical Research Centre, Institute of Molecular Cell and Systems Biology, University of Glasgow , 126 University Place, Glasgow G12 8TA, Scotland
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
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22
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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
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23
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Loco D, Jurinovich S, Di Bari L, Mennucci B. A fast but accurate excitonic simulation of the electronic circular dichroism of nucleic acids: how can it be achieved? Phys Chem Chem Phys 2016; 18:866-77. [PMID: 26646952 DOI: 10.1039/c5cp06341h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present and discuss a simple and fast computational approach to the calculation of electronic circular dichroism spectra of nucleic acids. It is based on a exciton model in which the couplings are obtained in terms of the full transition-charge distributions, as resulting from TDDFT methods applied on the individual nucleobases. We validated the method on two systems, a DNA G-quadruplex and a RNA β-hairpin whose solution structures have been accurately determined by means of NMR. We have shown that the different characteristics of composition and structure of the two systems can lead to quite important differences in the dependence of the accuracy of the simulation on the excitonic parameters. The accurate reproduction of the CD spectra together with their interpretation in terms of the excitonic composition suggest that this method may lend itself as a general computational tool to both predict the spectra of hypothetic structures and define clear relationships between structural and ECD properties.
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Affiliation(s)
- Daniele Loco
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
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24
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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: 77] [Impact Index Per Article: 9.6] [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.
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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
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25
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Mirkovic T, Ostroumov EE, Anna JM, van Grondelle R, Govindjee, Scholes GD. Light Absorption and Energy Transfer in the Antenna Complexes of Photosynthetic Organisms. Chem Rev 2016; 117:249-293. [PMID: 27428615 DOI: 10.1021/acs.chemrev.6b00002] [Citation(s) in RCA: 569] [Impact Index Per Article: 71.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The process of photosynthesis is initiated by the capture of sunlight by a network of light-absorbing molecules (chromophores), which are also responsible for the subsequent funneling of the excitation energy to the reaction centers. Through evolution, genetic drift, and speciation, photosynthetic organisms have discovered many solutions for light harvesting. In this review, we describe the underlying photophysical principles by which this energy is absorbed, as well as the mechanisms of electronic excitation energy transfer (EET). First, optical properties of the individual pigment chromophores present in light-harvesting antenna complexes are introduced, and then we examine the collective behavior of pigment-pigment and pigment-protein interactions. The description of energy transfer, in particular multichromophoric antenna structures, is shown to vary depending on the spatial and energetic landscape, which dictates the relative coupling strength between constituent pigment molecules. In the latter half of the article, we focus on the light-harvesting complexes of purple bacteria as a model to illustrate the present understanding of the synergetic effects leading to EET optimization of light-harvesting antenna systems while exploring the structure and function of the integral chromophores. We end this review with a brief overview of the energy-transfer dynamics and pathways in the light-harvesting antennas of various photosynthetic organisms.
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Affiliation(s)
- Tihana Mirkovic
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Evgeny E Ostroumov
- Department of Chemistry, Princeton University , Washington Road, Princeton, New Jersey 08544, United States
| | - Jessica M Anna
- Department of Chemistry, University of Pennsylvania , 231 S. 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Rienk van Grondelle
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam , De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Govindjee
- Department of Biochemistry, Center of Biophysics & Quantitative Biology, and Department of Plant Biology, University of Illinois at Urbana-Champaign , 265 Morrill Hall, 505 South Goodwin Avenue, Urbana, Illinois 61801, United States
| | - Gregory D Scholes
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.,Department of Chemistry, Princeton University , Washington Road, Princeton, New Jersey 08544, United States
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26
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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;
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27
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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.
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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
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28
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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.
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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
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29
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Popescu B, Rahman H, Kleinekathöfer U. Chebyshev Expansion Applied to Dissipative Quantum Systems. J Phys Chem A 2016; 120:3270-7. [PMID: 26845380 DOI: 10.1021/acs.jpca.5b12237] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To determine the dynamics of a molecular aggregate under the influence of a strongly time-dependent perturbation within a dissipative environment is still, in general, a challenge. The time-dependent perturbation might be, for example, due to external fields or explicitly treated fluctuations within the environment. Methods to calculate the dynamics in these cases do exist though some of these approaches assume that the corresponding correlation functions can be written as a weighted sum of exponentials. One such theory is the hierarchical equations of motion approach. If the environment, however, is described by a complex spectral density or if its temperature is low, these approaches become very inefficient. Therefore, we propose a scheme based on a Chebyshev decomposition of the bath correlation functions and detail the respective quantum master equations within second-order perturbation theory in the environmental coupling. Similar approaches have recently been proposed for systems coupled to Fermionic reservoirs. The proposed scheme is tested for a simple two-level system and compared to existing results. Furthermore, the advantages and disadvantages of the present Chebyshev approach are discussed.
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Affiliation(s)
- Bogdan Popescu
- Department of Physics and Earth Sciences, Jacobs University Bremen , Campus Ring 1, 28759 Bremen, Germany
| | - Hasan Rahman
- 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
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30
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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
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31
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Rosnik AM, Curutchet C. Theoretical Characterization of the Spectral Density of the Water-Soluble Chlorophyll-Binding Protein from Combined Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulations. J Chem Theory Comput 2015; 11:5826-37. [DOI: 10.1021/acs.jctc.5b00891] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andreana M. Rosnik
- Department
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, Barcelona, Barcelona 08028, Spain
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Carles Curutchet
- Department
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, Barcelona, Barcelona 08028, Spain
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32
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Steinmann C, Kongsted J. Electronic Energy Transfer in Polarizable Heterogeneous Environments: A Systematic Investigation of Different Quantum Chemical Approaches. J Chem Theory Comput 2015; 11:4283-93. [DOI: 10.1021/acs.jctc.5b00470] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Casper Steinmann
- Department of Physics, Chemistry,
and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry,
and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
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33
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Chandrasekaran S, Aghtar M, Valleau S, Aspuru-Guzik A, Kleinekathöfer U. Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins. J Phys Chem B 2015; 119:9995-10004. [DOI: 10.1021/acs.jpcb.5b03654] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - Mortaza Aghtar
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Stéphanie Valleau
- 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
| | - Ulrich Kleinekathöfer
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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34
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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.
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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
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