1
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Sokolov M, Hoffmann DS, Dohmen PM, Krämer M, Höfener S, Kleinekathöfer U, Elstner M. Non-adiabatic molecular dynamics simulations provide new insights into the exciton transfer in the Fenna-Matthews-Olson complex. Phys Chem Chem Phys 2024; 26:19469-19496. [PMID: 38979564 DOI: 10.1039/d4cp02116a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
A trajectory surface hopping approach, which uses machine learning to speed up the most time-consuming steps, has been adopted to investigate the exciton transfer in light-harvesting systems. The present neural networks achieve high accuracy in predicting both Coulomb couplings and excitation energies. The latter are predicted taking into account the environment of the pigments. Direct simulation of exciton dynamics through light-harvesting complexes on significant time scales is usually challenging due to the coupled motion of nuclear and electronic degrees of freedom in these rather large systems containing several relatively large pigments. In the present approach, however, we are able to evaluate a statistically significant number of non-adiabatic molecular dynamics trajectories with respect to exciton delocalization and exciton paths. The formalism is applied to the Fenna-Matthews-Olson complex of green sulfur bacteria, which transfers energy from the light-harvesting chlorosome to the reaction center with astonishing efficiency. The system has been studied experimentally and theoretically for decades. In total, we were able to simulate non-adiabatically more than 30 ns, sampling also the relevant space of parameters within their uncertainty. Our simulations show that the driving force supplied by the energy landscape resulting from electrostatic tuning is sufficient to funnel the energy towards site 3, from where it can be transferred to the reaction center. However, the high efficiency of transfer within a picosecond timescale can be attributed to the rather unusual properties of the BChl a molecules, resulting in very low inner and outer-sphere reorganization energies, not matched by any other organic molecule, e.g., used in organic electronics. A comparison with electron and exciton transfer in organic materials is particularly illuminating, suggesting a mechanism to explain the comparably high transfer efficiency.
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Affiliation(s)
- Monja Sokolov
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | - David S Hoffmann
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | - Philipp M Dohmen
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Mila Krämer
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | - Sebastian Höfener
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | | | - Marcus Elstner
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
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2
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Cellini A, Shankar MK, Nimmrich A, Hunt LA, Monrroy L, Mutisya J, Furrer A, Beale EV, Carrillo M, Malla TN, Maj P, Vrhovac L, Dworkowski F, Cirelli C, Johnson PJM, Ozerov D, Stojković EA, Hammarström L, Bacellar C, Standfuss J, Maj M, Schmidt M, Weinert T, Ihalainen JA, Wahlgren WY, Westenhoff S. Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography. Nat Chem 2024; 16:624-632. [PMID: 38225270 PMCID: PMC10997514 DOI: 10.1038/s41557-023-01413-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 11/28/2023] [Indexed: 01/17/2024]
Abstract
Charge-transfer reactions in proteins are important for life, such as in photolyases which repair DNA, but the role of structural dynamics remains unclear. Here, using femtosecond X-ray crystallography, we report the structural changes that take place while electrons transfer along a chain of four conserved tryptophans in the Drosophila melanogaster (6-4) photolyase. At femto- and picosecond delays, photoreduction of the flavin by the first tryptophan causes directed structural responses at a key asparagine, at a conserved salt bridge, and by rearrangements of nearby water molecules. We detect charge-induced structural changes close to the second tryptophan from 1 ps to 20 ps, identifying a nearby methionine as an active participant in the redox chain, and from 20 ps around the fourth tryptophan. The photolyase undergoes highly directed and carefully timed adaptations of its structure. This questions the validity of the linear solvent response approximation in Marcus theory and indicates that evolution has optimized fast protein fluctuations for optimal charge transfer.
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Madan Kumar Shankar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Leigh Anna Hunt
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Leonardo Monrroy
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Jennifer Mutisya
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | - Tek Narsingh Malla
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Piotr Maj
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Lidija Vrhovac
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | | | - Emina A Stojković
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Leif Hammarström
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | - Michał Maj
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | | | - Janne A Ihalainen
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
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3
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Melčák M, Šebesta F, Heyda J, Gray HB, Záliš S, Vlček A. Tryptophan to Tryptophan Hole Hopping in an Azurin Construct. J Phys Chem B 2024; 128:96-108. [PMID: 38145895 PMCID: PMC10788906 DOI: 10.1021/acs.jpcb.3c06568] [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: 10/02/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 12/27/2023]
Abstract
Electron transfer (ET) between neutral and cationic tryptophan residues in the azurin construct [ReI(H126)(CO)3(dmp)](W124)(W122)CuI (dmp = 4,7-Me2-1,10-phenanthroline) was investigated by Born-Oppenheimer quantum-mechanics/molecular mechanics/molecular dynamics (QM/MM/MD) simulations. We focused on W124•+ ← W122 ET, which is the middle step of the photochemical hole-hopping process *ReII(CO)3(dmp•-) ← W124 ← W122 ← CuI, where sequential hopping amounts to nearly 10,000-fold acceleration over single-step tunneling (ACS Cent. Sci. 2019, 5, 192-200). In accordance with experiments, UKS-DFT QM/MM/MD simulations identified forward and reverse steps of W124•+ ↔ W122 ET equilibrium, as well as back ET ReI(CO)3(dmp•-) → W124•+ that restores *ReII(CO)3(dmp•-). Strong electronic coupling between the two indoles (≥40 meV in the crossing region) makes the productive W124•+ ← W122 ET adiabatic. Energies of the two redox states are driven to degeneracy by fluctuations of the electrostatic potential at the two indoles, mainly caused by water solvation, with contributions from the protein dynamics in the W122 vicinity. ET probability depends on the orientation of Re(CO)3(dmp) relative to W124 and its rotation diminishes the hopping yield. Comparison with hole hopping in natural systems reveals structural and dynamics factors that are important for designing efficient hole-hopping processes.
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Affiliation(s)
- Martin Melčák
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- Department
of Physical Chemistry, University of Chemistry
and Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic
| | - Filip Šebesta
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- Department
of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, CZ-121 16 Prague, Czech Republic
| | - Jan Heyda
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- Department
of Physical Chemistry, University of Chemistry
and Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic
| | - Harry B. Gray
- Beckman
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Stanislav Záliš
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ-182 23 Prague, Czech Republic
| | - Antonín Vlček
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- Department
of Chemistry, Queen Mary University of London, London E1 4NS, U.K.
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4
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Raghavan B, Paulikat M, Ahmad K, Callea L, Rizzi A, Ippoliti E, Mandelli D, Bonati L, De Vivo M, Carloni P. Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations. J Chem Inf Model 2023. [PMID: 37319347 DOI: 10.1021/acs.jcim.3c00557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The initial phases of drug discovery - in silico drug design - could benefit from first principle Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics (MD) simulations in explicit solvent, yet many applications are currently limited by the short time scales that this approach can cover. Developing scalable first principle QM/MM MD interfaces fully exploiting current exascale machines - so far an unmet and crucial goal - will help overcome this problem, opening the way to the study of the thermodynamics and kinetics of ligand binding to protein with first principle accuracy. Here, taking two relevant case studies involving the interactions of ligands with rather large enzymes, we showcase the use of our recently developed massively scalable Multiscale Modeling in Computational Chemistry (MiMiC) QM/MM framework (currently using DFT to describe the QM region) to investigate reactions and ligand binding in enzymes of pharmacological relevance. We also demonstrate for the first time strong scaling of MiMiC-QM/MM MD simulations with parallel efficiency of ∼70% up to >80,000 cores. Thus, among many others, the MiMiC interface represents a promising candidate toward exascale applications by combining machine learning with statistical mechanics based algorithms tailored for exascale supercomputers.
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Affiliation(s)
- Bharath Raghavan
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
- Department of Physics, RWTH Aachen University, Aachen 52074, Germany
| | - Mirko Paulikat
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
| | - Katya Ahmad
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
| | - Lara Callea
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Andrea Rizzi
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
- Atomistic Simulations, Italian Institute of Technology, Genova 16163, Italy
| | - Emiliano Ippoliti
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
| | - Davide Mandelli
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Marco De Vivo
- Molecular Modelling and Drug Discovery, Italian Institute of Technology, Genova 16163, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
- Department of Physics and Universitätsklinikum, RWTH Aachen University, Aachen 52074, Germany
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5
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Kubař T, Elstner M, Cui Q. Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines. Annu Rev Biophys 2023; 52:525-551. [PMID: 36791746 PMCID: PMC10810093 DOI: 10.1146/annurev-biophys-111622-091140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become indispensable tools for the study of biomolecules. In this article, we briefly review the basic methodological details of QM/MM approaches and discuss their applications to various energy transduction problems in biomolecular machines, such as long-range proton transports, fast electron transfers, and mechanochemical coupling. We highlight the particular importance for these applications of balancing computational efficiency and accuracy. Using several recent examples, we illustrate the value and limitations of QM/MM methodologies for both ground and excited states, as well as strategies for calibrating them in specific applications. We conclude with brief comments on several areas that can benefit from further efforts to make QM/MM analyses more quantitative and applicable to increasingly complex biological problems.
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Affiliation(s)
- T Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - M Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - Q Cui
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
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6
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Tracy DA, Fernandez-Alberti S, Tretiak S, Roitberg AE. Adiabatic Excited-State Molecular Dynamics with an Explicit Solvent: NEXMD-SANDER Implementation. J Chem Theory Comput 2022; 18:5213-5220. [PMID: 36044726 DOI: 10.1021/acs.jctc.2c00561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a method to link the Nonadiabatic EXcited-state Molecular Dynamics (NEXMD) package to the SANDER package supplied by AMBERTOOLS to provide excited-state adiabatic quantum mechanics/molecular mechanics (QM/MM) simulations. NEXMD is a computational package particularly developed to perform simulations of the photoexcitation and subsequent nonadiabatic electronic and vibrational energy relaxation in large multichromophoric conjugated molecules involving several coupled electronic excited states. The NEXMD-SANDER exchange has been optimized in order to achieve excited-state adiabatic dynamics simulations of large conjugated materials in a QM/MM environment, such as an explicit solvent. Dynamics of a substituted polyphenylene vinylene oligomer (PPV3-NO2) in vacuum and different explicit solvents has been used as a test case by performing comparative analysis of changes in its optical spectrum, state-dependent conformational changes, and quantum bond orderings. The method has been tested and compared with respect to previous implicit solvent implementations. Also, the impact on the expansion of the QM region by including a variable number of solvent molecules has been analyzed. Altogether, these results encourage future implementations of NEXMD simulations using the same combination of methods.
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Affiliation(s)
- Dustin A Tracy
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | | | - Sergei Tretiak
- Theoretical Division, Center for Nonlinear Studies (CNLS) and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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7
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Aggarwal A, Naskar S, Maiti PK. Molecular Rectifiers with a Very High Rectification Ratio Enabled by Oxidative Damage in Double-Stranded DNA. J Phys Chem B 2022; 126:4636-4646. [PMID: 35729785 DOI: 10.1021/acs.jpcb.2c01371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we report a novel strategy to construct highly efficient molecular diodes using oxidatively damaged DNA molecules. Being exposed to several endogenous and exogenous events, DNA suffers from constant oxidative damage, leading to the oxidation of guanine to 8-oxoguanine (8oxoG). Here, we study the charge migration properties of native and oxidatively damaged DNA using a multiscale multiconfigurational methodology comprising molecular dynamics, density functional theory, and kinetic Monte Carlo simulations. We perform a comprehensive study to understand the effect of different concentrations and locations of 8oxoG in a dsDNA sequence on its charge-transport properties and find tunable rectifier properties having potential applications in molecular electronics such as molecular switches and molecular rectifiers. We also discover the negative differential resistance properties of the fully oxidized Drew-Dickerson sequence. The presence of 8oxoG guanine leads to the trapping of charge, thus operating as a charge sink, which reveals how oxidized guanine saves the rest of the genome from further oxidative damage.
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Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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8
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Understanding flavin electronic structure and spectra. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1541] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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9
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Uratani H, Nakai H. Scalable Ehrenfest Molecular Dynamics Exploiting the Locality of Density-Functional Tight-Binding Hamiltonian. J Chem Theory Comput 2021; 17:7384-7396. [PMID: 34860019 DOI: 10.1021/acs.jctc.1c00950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
To explore the science behind excited-state dynamics in high-complexity chemical systems, a scalable nonadiabatic molecular dynamics (MD) technique is indispensable. In this study, by treating the electronic degrees of freedom at the density-functional tight-binding level, we developed and implemented a reduced scaling and multinode-parallelizable Ehrenfest MD method. To achieve this goal, we introduced a concept called patchwork approximation (PA), where the effective Hamiltonian for real-time propagation of the electronic density matrix is partitioned into a set of local parts. Numerical results for giant icosahedral fullerenes, which comprise up to 6000 atoms, suggest that the scaling of the present PA-based method is less than quadratic, which yields a significant advantage over the conventional cubic scaling method in terms of computational time. The acceleration by the parallelization on multiple nodes was also assessed. Furthermore, the electronic and structural dynamics resulting from the perturbation by the external electric field were accurately reproduced with the PA, even when the electronic excitation was spatially delocalized.
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Affiliation(s)
- Hiroki Uratani
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8245, Japan
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10
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Abstract
Hole hopping through tryptophan/tyrosine chains enables rapid unidirectional charge transport over long distances. We have elucidated structural and dynamical factors controlling hopping speed and efficiency in two modified azurin constructs that include a rhenium(I) sensitizer, Re(His)(CO)3(dmp)+, and one or two tryptophans (W1, W2). Experimental kinetics investigations showed that the two closely spaced (3 to 4 Å) intervening tryptophans dramatically accelerated long-range electron transfer (ET) from CuI to the photoexcited sensitizer. In our theoretical work, we found that time-dependent density-functional theory (TDDFT) quantum mechanics/molecular mechanics/molecular dynamics (QM/MM/MD) trajectories of low-lying triplet excited states of ReI(His)(CO)3(dmp)+-W1(-W2) exhibited crossings between sensitizer-localized (*Re) and charge-separated [ReI(His)(CO)3(dmp•-)/(W1 •+ or W2 •+)] (CS1 or CS2) states. Our analysis revealed that the distances, angles, and mutual orientations of ET-active cofactors fluctuate in a relatively narrow range in which the cofactors are strongly coupled, enabling adiabatic ET. Water-dominated electrostatic field fluctuations bring *Re and CS1 states to a crossing where *Re(CO)3(dmp)+←W1 ET occurs, and CS1 becomes the lowest triplet state. ET is promoted by solvation dynamics around *Re(CO)3(dmp)+(W1); and CS1 is stabilized by Re(dmp•-)/W1 •+ electron/hole interaction and enhanced W1 •+ solvation. The second hop, W1 •+←W2, is facilitated by water fluctuations near the W1/W2 unit, taking place when the electrostatic potential at W2 drops well below that at W1 •+ Insufficient solvation and reorganization around W2 make W1 •+←W2 ET endergonic, shifting the equilibrium toward W1 •+ and decreasing the charge-separation yield. We suggest that multiscale TDDFT/MM/MD is a suitable technique to model the simultaneous evolution of photogenerated excited-state manifolds.
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11
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Osswald M, Fingerhut BP. Electron Transfer-Induced Active Site Structural Relaxation in 64-Photolyase of Drosophila melanogaster. J Phys Chem B 2021; 125:8690-8702. [PMID: 34323497 DOI: 10.1021/acs.jpcb.1c02951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While catalytic electron flow and photoreactivation of CPD-photolyases are increasingly understood, the microscopic details of the 64-photolyase repair mechanism are perpetually debated. Here, we investigate in long-time (μs) molecular dynamics simulations combined with extensive quantum mechanical/molecular mechanical (QM/MM) simulations the primary electron transfer (ET) reactions in 64-photolyase of Drosophila melanogaster (D. melanogaster). The characterization of the relative energetics of locally excited and charge separated states in the (6-4) photoproduct enzyme repair complex reveals a charge-separated state involving the adenine moiety of the FADH- cofactor that facilitates reduction of the photoproduct. Microscopic details of the collective reaction coordinate of ET reactions are identified that involve the reorganization of the hydrogen bond network and structural relaxation of the active site. The simulations reveal complex active site relaxation dynamics involving distinguished amino acids (Lys246, His365, and His369), conformational reorganization of the hydroxyl group of the (6-4) photoproduct, and a strengthening of hydrogen bonds with immobilized water molecules. In particular, rotation of the Lys246 side chain is found to impose a double-well character along the reaction coordinate of the ET reaction. Our findings suggest that the primary ET reactions in the (6-4) photoproduct enzyme repair complex of D. melanogaster are governed by a complex multi-minima active site relaxation dynamics and potentially precede the equilibration of the protein. ET pathways mediated by the adenine moiety and the 5' side of the photoproduct are proposed to be relevant for triggering the catalytic (6-4) photoproduct reactivation.
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Affiliation(s)
- Mara Osswald
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
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12
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Yang ZH. Speed-dependent adaptive partitioning in QM/MM MD simulations of displacement damage in solid-state systems. Phys Chem Chem Phys 2021; 23:3417-3428. [PMID: 33506833 DOI: 10.1039/d0cp05149g] [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
Solids undergo displacement damage (DD) when interacting with energetic particles, which may happen during the fabrication of semiconductor devices, in harsh environments and in certain analysis techniques. Simulations of DD generation are usually carried out using classical molecular dynamics (MD), but classical MD does not account for all the effects in DD, as demonstrated by ab initio calculations of model systems in the literature. A complete ab initio simulation of DD generation is impractical due to the large number of atoms involved. In my previous paper [Yang, Phys. Chem. Chem. Phys., 2020, 22, 19307], I developed an adaptive-center (AC) method for the adaptive-partitioning (AP) of quantum mechanics/molecular mechanics (QM/MM) simulations, allowing the active region centers and the QM/MM partition to be determined on-the-fly for energy-conserving AP-QM/MM methods. I demonstrated that the AC-AP-QM/MM is applicable to the simulation of DD generation, so that the active regions can be treated using an ab initio method. The AC method could not be used to identify the fast-moving recoil ions in DD generation as active region centers, however, and the accuracy is negatively affected by the rapid change in the QM/MM partition of the system. In this paper, I extend the AC method and develop a speed-dependent adaptive-center (SDAC) method for accurate AP-QM/MM simulations of DD. The SDAC method is applicable to general problems with speed-dependent active regions, and is compatible with all existing energy-conserving partitioning-by-distance AP-QM/MM methods. The artifact due to the speed-dependent potential energy surface can be made small by choosing suitable criteria. I demonstrate the SDAC method by simulations of DD generation in bulk silicon.
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Affiliation(s)
- Zeng-Hui Yang
- Microsystem and Terahertz Research Center, China Academy of Engineering Physics, Chengdu, 610200, China.
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13
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Holub D, Lamparter T, Elstner M, Gillet N. Biological relevance of charge transfer branching pathways in photolyases. Phys Chem Chem Phys 2019; 21:17072-17081. [PMID: 31313765 DOI: 10.1039/c9cp01609k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The repair of sun-induced DNA lesions by photolyases is driven by a photoinduced electron transfer from a fully reduced FAD to the damaged DNA. A chain of several aromatic residues connecting FAD to solvent ensures the prior photoreduction of the FAD cofactor. In PhrA, a class III CPD photolyase, two branching tryptophan charge transfer pathways have been characterized. According to previous experiments, both pathways play a role in the FAD photoreduction. To provide a molecular insight to the charge transfer abilities of both pathways, we perform multiscales simulations where the protein motion and the positive charge are simultaneously propagated. Our computational approach reveals that one pathway drives a very fast charge transfer whereas the other pathway provides a very good thermodynamic stabilization of the positive charge. During the simulations, the positive charge firstly moves on the fast triad, while a reorganization of the close FAD˙- environment occurs. Then, backward transfers can lead to the propagation of the positive charge on the second pathway. After one nanosecond, we observe a nearly equal probability to find the charge at ending tryptophan of either pathway; eventually the charge distribution will likely evolve towards a charge stabilization on the last tryptophan of the slowest pathway. Our results highlight the role the protein environment, which manages the association of a kinetic and a thermodynamic pathways to trigger a fast and efficient FAD photoreduction.
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Affiliation(s)
- Daniel Holub
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute for Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany.
| | - Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology, Fritz Haber Weg 4, 76131, Karlsruhe, Germany
| | - Marcus Elstner
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute for Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany. and Institute of Biological Interfaces (IBG2), Karlsruhe Institute for Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
| | - Natacha Gillet
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute for Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany.
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14
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Holub D, Kubař T, Mast T, Elstner M, Gillet N. What accounts for the different functions in photolyases and cryptochromes: a computational study of proton transfers to FAD. Phys Chem Chem Phys 2019; 21:11956-11966. [PMID: 31134233 DOI: 10.1039/c9cp00694j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photolyases (PL) and cryptochromes (CRY) are light-sensitive flavoproteins, respectively, involved in DNA repair and signal transduction. Their activation is triggered by an electron transfer process, which partially or fully reduces the photo-activated FAD cofactor. The full reduction additionally requires a proton transfer to the isoalloxazine ring. In plant CRY, an efficient proton transfer takes place within several μs, enabled by a conserved aspartate working as a proton donor, whereas in E. coli PL a proton transfer occurs in the 4 s timescale without any obvious proton donor, indicating the presence of a long-range proton transfer pathway. Unexpectedly, the insertion of an aspartate as a proton donor in a suitable position for proton transfer in E. coli PL does not initiate a transfer process similar to plant CRY, but even prevents the formation of a protonated FAD. In the present work, thanks to a combination of classical molecular dynamics and state-of-the-art DFTB3/MM simulations, we identify a proton transfer pathway from bulk to FAD in E. coli PL associated with a free energy profile in agreement with the experimental kinetics data. The free energy profiles of the proton transfer between aspartate and FAD show an inversion of the driving force between plant CRY and E. coli PL mutants. In the latter, the proton transfer from the aspartate is faster than in plant CRY but also thermodynamically disfavoured, in agreement with the experimental data. Our results further illustrate the fine tuning of the electrostatic FAD environment and the adaptability of the FAD pocket to ensure the divergent functions of the members of the PL-CRY family.
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Affiliation(s)
- Daniel Holub
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute for Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany.
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15
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Sjulstok E, Lüdemann G, Kubař T, Elstner M, Solov'yov IA. Molecular Insights into Variable Electron Transfer in Amphibian Cryptochrome. Biophys J 2019; 114:2563-2572. [PMID: 29874607 DOI: 10.1016/j.bpj.2018.04.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 01/23/2023] Open
Abstract
Cryptochrome proteins are activated by the absorption of blue light, leading to the formation of radical pairs through electron transfer in the active site. Recent experimental studies have shown that once some of the amino acid residues in the active site of Xenopus laevis cryptochrome DASH are mutated, radical-pair formation is still observed. In this study, we computationally investigate electron-transfer pathways in the X. laevis cryptochrome DASH by extensively equilibrating a previously established homology model using molecular dynamics simulations and then mutating key amino acids involved in the electron transfer. The electron-transfer pathways are then probed by using tight-binding density-functional theory. We report the alternative electron-transfer pathways resolved at the molecular level and, through comparison of amino acid sequences for cryptochromes from different species, we demonstrate that one of these alternative electron-transfer pathways could be general for all cryptochrome DASH proteins.
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Affiliation(s)
- Emil Sjulstok
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Gesa Lüdemann
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ilia A Solov'yov
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark.
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16
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Abstract
The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free of mechanistic bombshells? I suggest that this difference originates in the distinct electronic energy landscapes for the two classes of reactions. In proteins, the donor/acceptor-to-bridge energy gap is typically several-fold larger than in NAs. NA ET can access tunneling, hopping, and resonant transport among the bases, and fluctuations can enable switching among mechanisms; protein ET is restricted to tunneling among redox active cofactors and, under strongly oxidizing conditions, a few privileged amino acid side chains. This review aims to provide conceptual unity to DNA and protein ET reaction mechanisms. The establishment of a unified mechanistic framework enabled the successful design of NA experiments that switch electronic coherence effects on and off for ET processes on a length scale of multiple nanometers and promises to provide inroads to directing and detecting charge flow in soft-wet matter.
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Affiliation(s)
- David N Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708, USA; .,Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
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17
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Applications of molecular modeling to flavoproteins: Insights and challenges. Methods Enzymol 2019; 620:277-314. [DOI: 10.1016/bs.mie.2019.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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18
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López-Estrada O, Laguna HG, Barrueta-Flores C, Amador-Bedolla C. Reassessment of the Four-Point Approach to the Electron-Transfer Marcus-Hush Theory. ACS OMEGA 2018; 3:2130-2140. [PMID: 31458519 PMCID: PMC6641260 DOI: 10.1021/acsomega.7b01425] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/08/2018] [Indexed: 05/25/2023]
Abstract
The Marcus-Hush theory has been successfully applied to describe and predict the activation barriers and hence the electron-transfer (ET) rates in several physicochemical and biological systems. This theory assumes that in the ET reaction, the geometry of the free Gibbs energy landscape is parabolic, with equal curvature near the local minimum for both reactants and products. In spite of its achievements, more realistic models have included the assumption of the two parabolas having not the same curvature. This situation is analyzed by the Nelsen's four-point method. As a benchmark to compare the Marcus-Hush approximation to a precise calculation of the excitation energy, we studied the non-ET process of the electronic excitation of the aluminum dimer that has two local minima (3∑g - and 3∏u electronic states) and allows to obtain analytically the Marcus-Hush nonsymmetric parameters. We appraise the ability of the Marcus-Hush formula to approximate the analytical results by using several averages of the two reorganization energies associated with the forward and backward transitions and analyze the error. It is observed that the geometric average minimizes the relative error and that the analytical case is recovered. The main results of this paper are obtained by the application of the Nelsen's four-point method to compute the reorganization energies of a large set of potential π-conjugated molecules proposed for organic photovoltaic devices using the above-mentioned averages for the Marcus-Hush formula. The activation energies obtained with the geometric average are significantly larger for some donor-acceptor pairs in comparison with the previously employed arithmetic average, their differences being suitable for experimental testing.
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19
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Mendive-Tapia D, Mangaud E, Firmino T, de la Lande A, Desouter-Lecomte M, Meyer HD, Gatti F. Multidimensional Quantum Mechanical Modeling of Electron Transfer and Electronic Coherence in Plant Cryptochromes: The Role of Initial Bath Conditions. J Phys Chem B 2017; 122:126-136. [DOI: 10.1021/acs.jpcb.7b10412] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David Mendive-Tapia
- Institut
Charles Gerhardt Montpellier, UMR 5253, CNRS-UM-ENSCM, CTMM, Université Montpellier, CC 15001, Place Eugène Bataillon, 34095 Montpellier, France
- Theoretische
Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, INF 229, D-69120 Heidelberg, Germany
| | - Etienne Mangaud
- Laboratoire
Collisions Agrégats Réactivité, UMR 5589, IRSAMC, Université Toulouse III Paul Sabatier, F-31062 Toulouse, France
| | - Thiago Firmino
- Laboratoire
de Chimie Physique, CNRS, Université Paris-Sud, Université Paris Saclay, Orsay F-91405, France
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique, CNRS, Université Paris-Sud, Université Paris Saclay, Orsay F-91405, France
| | - Michèle Desouter-Lecomte
- Laboratoire
de Chimie Physique, CNRS, Université Paris-Sud, Université Paris Saclay, Orsay F-91405, France
| | - Hans-Dieter Meyer
- Theoretische
Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, INF 229, D-69120 Heidelberg, Germany
| | - Fabien Gatti
- Institut
des Sciences Moléculaires d’Orsay, UMR-CNRS 8214, Université Paris-Sud, Université Paris Saclay, Orsay F-91405, France
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20
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Holub D, Ma H, Krauß N, Lamparter T, Elstner M, Gillet N. Functional role of an unusual tyrosine residue in the electron transfer chain of a prokaryotic (6-4) photolyase. Chem Sci 2017; 9:1259-1272. [PMID: 29675172 PMCID: PMC5887102 DOI: 10.1039/c7sc03386a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/09/2017] [Indexed: 11/21/2022] Open
Abstract
Cryptochromes and photolyases form a flavoprotein family in which the FAD chromophore undergoes light induced changes of its redox state. During this process, termed photoreduction, electrons flow from the surface via conserved amino acid residues to FAD. The bacterial (6-4) photolyase PhrB belongs to a phylogenetically ancient group. Photoreduction of PhrB differs from the typical pattern because the amino acid of the electron cascade next to FAD is a tyrosine (Tyr391), whereas photolyases and cryptochromes of other groups have a tryptophan as direct electron donor of FAD. Mutagenesis studies have identified Trp342 and Trp390 as essential for charge transfer. Trp342 is located at the periphery of PhrB while Trp390 connects Trp342 and Tyr391. The role of Tyr391, which lies between Trp390 and FAD, is however unclear as its replacement by phenylalanine did not block photoreduction. Experiments reported here, which replace Tyr391 by Ala, show that photoreduction is blocked, underlining the relevance of Tyr/Phe at position 391 and indicating that charge transfer occurs via the triad 391-390-342. This raises the question, why PhrB positions a tyrosine at this location, having a less favourable ionisation potential than tryptophan, which occurs at this position in many proteins of the photolyase/cryptochrome family. Tunnelling matrix calculations show that tyrosine or phenylalanine can be involved in a productive bridged electron transfer between FAD and Trp390, in line with experimental findings. Since replacement of Tyr391 by Trp resulted in loss of FAD and DMRL chromophores, electron transfer cannot be studied experimentally in this mutant, but calculations on a mutant model suggest that Trp might participate in the electron transfer cascade. Charge transfer simulations reveal an unusual stabilization of the positive charge on site 391 compared to other photolyases or cryptochromes. Water molecules near Tyr391 offer a polar environment which stabilizes the positive charge on this site, thereby lowering the energetic barrier intrinsic to tyrosine. This opens a second charge transfer channel in addition to tunnelling through the tyrosine barrier, based on hopping and therefore transient oxidation of Tyr391, which enables a fast charge transfer similar to proteins utilizing a tryptophan-triad. Our results suggest that evolution of the first site of the redox chain has just been possible by tuning the protein structure and environment to manage a downhill hole transfer process from FAD to solvent.
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Affiliation(s)
- Daniel Holub
- Department for Theoretical Chemical Biology , Institute for Physical Chemistry , Karlsruhe Institute for Technology , Kaiserstr. 12 , 76131 , Karlsruhe , Germany .
| | - Hongju Ma
- Botanical Institute , Karlsruhe Institute for Technology , Fritz Haber Weg 4 , 76131 , Karlsruhe , Germany
| | - Norbert Krauß
- Botanical Institute , Karlsruhe Institute for Technology , Fritz Haber Weg 4 , 76131 , Karlsruhe , Germany
| | - Tilman Lamparter
- Botanical Institute , Karlsruhe Institute for Technology , Fritz Haber Weg 4 , 76131 , Karlsruhe , Germany
| | - Marcus Elstner
- Department for Theoretical Chemical Biology , Institute for Physical Chemistry , Karlsruhe Institute for Technology , Kaiserstr. 12 , 76131 , Karlsruhe , Germany . .,Institute of Biological Interfaces (IGB2) , Karlsruhe Institute for Technology , Kaiserstr. 12 , 76131 , Karlsruhe , Germany
| | - Natacha Gillet
- Department for Theoretical Chemical Biology , Institute for Physical Chemistry , Karlsruhe Institute for Technology , Kaiserstr. 12 , 76131 , Karlsruhe , Germany .
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21
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Oberhofer H, Reuter K, Blumberger J. Charge Transport in Molecular Materials: An Assessment of Computational Methods. Chem Rev 2017. [PMID: 28644623 DOI: 10.1021/acs.chemrev.7b00086] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The booming field of molecular electronics has fostered a surge of computational research on electronic properties of organic molecular solids. In particular, with respect to a microscopic understanding of transport and loss mechanisms, theoretical studies assume an ever-increasing role. Owing to the tremendous diversity of organic molecular materials, a great number of computational methods have been put forward to suit every possible charge transport regime, material, and need for accuracy. With this review article we aim at providing a compendium of the available methods, their theoretical foundations, and their ranges of validity. We illustrate these through applications found in the literature. The focus is on methods available for organic molecular crystals, but mention is made wherever techniques are suitable for use in other related materials such as disordered or polymeric systems.
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Affiliation(s)
- Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom.,Institute for Advanced Study, Technische Universität München , Lichtenbergstrasse 2 a, D-85748 Garching, Germany
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22
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Wolter M, Elstner M, Kleinekathöfer U, Kubař T. Microsecond Simulation of Electron Transfer in DNA: Bottom-Up Parametrization of an Efficient Electron Transfer Model Based on Atomistic Details. J Phys Chem B 2017; 121:529-549. [PMID: 28045546 DOI: 10.1021/acs.jpcb.6b11384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The transfer of electrons over long distances in complex molecular systems is a phenomenon of significance in both biochemistry and technology. In recent years, we have been developing efficient models to study ET in complex systems, including DNA as a prominent example. Ab initio and model approaches have been combined in an "on-the-fly" calculation of ET parameters, which can be used to propagate nuclear and electronic degrees of freedom simultaneously. These previous efforts have aimed at deriving an efficient nonadiabatic quantum mechanical-molecular mechanical (QM/MM) simulation scheme for ET, making nanosecond simulations of ET in realistic systems possible. This, however, is still insufficient for the treatment of large donor-bridge-acceptor systems, like the ET in DNA, overcoming long adenine bridges. Therefore, we have constructed a theoretical model in a bottom-up manner. All quantum-chemical as well as force-field calculations are substituted by theoretical models of the involved phenomena on a molecular level, including polarization and relaxation of the molecular environment, which are often omitted in other recently developed theoretical models of ET. A nonadiabatic simulation scheme is employed, and no assumptions regarding the ET mechanism are needed. Thus, the predictive power of the simulations is preserved, while pushing the limits of the accessible time scales beyond microseconds. This model-based simulation scheme is applied to ET in various DNA species. Good agreement with the "full" atomistic nonadiabatic QM/MM scheme is observed for the archetypal DNA ET systems, the polyA sequence, as well as the sequences GTnGGG, containing adenines as bridge sites. Furthermore, ET in larger, more complex DNA sequences is simulated, and the results are discussed.
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Affiliation(s)
| | | | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen , 28759 Bremen, Germany
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23
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Faraji S, Dreuw A. Insights into Light-driven DNA Repair by Photolyases: Challenges and Opportunities for Electronic Structure Theory. Photochem Photobiol 2017; 93:37-50. [PMID: 27925218 DOI: 10.1111/php.12679] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/18/2016] [Indexed: 01/25/2023]
Abstract
Ultraviolet radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6-4 photoproducts. (6-4) Photolyases are light-activated enzymes that selectively bind to DNA and trigger repair of mutagenic 6-4 photoproducts via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH- ) to the lesion triggering repair. This review provides an overview of the sequential steps of the repair process, that is light absorption and resonance energy transfer, photoinduced electron transfer and electron-induced splitting mechanisms, with an emphasis on the role of theory and computation. In addition, theoretical calculations and physical properties that can be used to classify specific mechanism are discussed in an effort to trace the fundamental aspects of each individual step and assist the interpretation of experimental data. The current challenges and suggested future directions are outlined for each step, concluding with a view on the future.
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Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Heidelberg, Germany
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24
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Dohn AO, Kjær KS, Harlang TB, Canton SE, Nielsen MM, Møller KB. Electron Transfer and Solvent-Mediated Electronic Localization in Molecular Photocatalysis. Inorg Chem 2016; 55:10637-10644. [DOI: 10.1021/acs.inorgchem.6b01840] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Asmus O. Dohn
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kgs Lyngby, Denmark
| | - Kasper S. Kjær
- Department of Physics, Technical University of Denmark, Building 307 2800 Kgs. Lyngby, Denmark
| | - Tobias B. Harlang
- Department of Physics, Technical University of Denmark, Building 307 2800 Kgs. Lyngby, Denmark
| | - Sophie E. Canton
- Center for
Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Martin M. Nielsen
- Department of Physics, Technical University of Denmark, Building 307 2800 Kgs. Lyngby, Denmark
| | - Klaus B. Møller
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kgs Lyngby, Denmark
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25
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Vaissier V, Van Voorhis T. Adiabatic Approximation in Explicit Solvent Models of RedOx Chemistry. J Chem Theory Comput 2016; 12:5111-5116. [DOI: 10.1021/acs.jctc.6b00746] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Valérie Vaissier
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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26
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Electron flow through biological molecules: does hole hopping protect proteins from oxidative damage? Q Rev Biophys 2016; 48:411-20. [PMID: 26537399 DOI: 10.1017/s0033583515000062] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Biological electron transfers often occur between metal-containing cofactors that are separated by very large molecular distances. Employing photosensitizer-modified iron and copper proteins, we have shown that single-step electron tunneling can occur on nanosecond to microsecond timescales at distances between 15 and 20 Å. We also have shown that charge transport can occur over even longer distances by hole hopping (multistep tunneling) through intervening tyrosines and tryptophans. In this perspective, we advance the hypothesis that such hole hopping through Tyr/Trp chains could protect oxygenase, dioxygenase, and peroxidase enzymes from oxidative damage. In support of this view, by examining the structures of P450 (CYP102A) and 2OG-Fe (TauD) enzymes, we have identified candidate Tyr/Trp chains that could transfer holes from uncoupled high-potential intermediates to reductants in contact with protein surface sites.
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27
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Dinpajooh M, Martin DR, Matyushov DV. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer. Sci Rep 2016; 6:28152. [PMID: 27306204 PMCID: PMC4910110 DOI: 10.1038/srep28152] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/27/2016] [Indexed: 11/12/2022] Open
Abstract
Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work.
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Affiliation(s)
- Mohammadhasan Dinpajooh
- Department of Physics and School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA
| | - Daniel R Martin
- Department of Physics and School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA
| | - Dmitry V Matyushov
- Department of Physics and School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA
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28
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Heck A, Kranz JJ, Elstner M. Simulation of Temperature-Dependent Charge Transport in Organic Semiconductors with Various Degrees of Disorder. J Chem Theory Comput 2016; 12:3087-96. [DOI: 10.1021/acs.jctc.6b00215] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Heck
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
- HEiKA - Heidelberg Karlsruhe Research Partnership, Heidelberg University, Karlsruhe Institute of Technology (KIT), Germany
| | - Julian J. Kranz
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
- HEiKA - Heidelberg Karlsruhe Research Partnership, Heidelberg University, Karlsruhe Institute of Technology (KIT), Germany
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29
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Cailliez F, Müller P, Firmino T, Pernot P, de la Lande A. Energetics of Photoinduced Charge Migration within the Tryptophan Tetrad of an Animal (6–4) Photolyase. J Am Chem Soc 2016; 138:1904-15. [DOI: 10.1021/jacs.5b10938] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Fabien Cailliez
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Pavel Müller
- Institute
for Integrative Biology of the Cell (I2BC), CEA, CNRS, University
Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette
cedex, France
| | - Thiago Firmino
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Pascal Pernot
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
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30
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Firmino T, Mangaud E, Cailliez F, Devolder A, Mendive-Tapia D, Gatti F, Meier C, Desouter-Lecomte M, de la Lande A. Quantum effects in ultrafast electron transfers within cryptochromes. Phys Chem Chem Phys 2016; 18:21442-57. [DOI: 10.1039/c6cp02809h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cryptochromes and photolyases are flavoproteins that may undergo ultrafast charge separation upon electronic excitation of their flavin cofactors.
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Affiliation(s)
- Thiago Firmino
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Etienne Mangaud
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Fabien Cailliez
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Adrien Devolder
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | | | - Fabien Gatti
- CTMM
- Institut Charles Gerhardt UMR 5253
- CNRS/Université de Montpellier
- France
| | - Christoph Meier
- Laboratoire Collisions Agrégats Réactivité
- UMR 5589
- IRSAMC
- Université Toulouse III Paul Sabatier
- Toulouse
| | | | - Aurélien de la Lande
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
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31
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Sjulstok E, Olsen JMH, Solov'yov IA. Quantifying electron transfer reactions in biological systems: what interactions play the major role? Sci Rep 2015; 5:18446. [PMID: 26689792 PMCID: PMC4686879 DOI: 10.1038/srep18446] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/18/2015] [Indexed: 12/20/2022] Open
Abstract
Various biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve light absorption, excited electronic states formation, excitation energy transfer, electrons and protons tunnelling which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between quantum physics and biology. In this paper we consider electron transfer in biological processes, from a theoretical view-point; namely in terms of quantum mechanical and semi-classical models. We systematically characterize the interactions between the moving electron and its biological environment to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe specifically the electron transfer reactions in Arabidopsis thaliana cryptochrome-a signaling photoreceptor protein that became attractive recently due to its possible function as a biological magnetoreceptor.
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Affiliation(s)
- Emil Sjulstok
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.,Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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32
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Blumberger J. Recent Advances in the Theory and Molecular Simulation of Biological Electron Transfer Reactions. Chem Rev 2015; 115:11191-238. [DOI: 10.1021/acs.chemrev.5b00298] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jochen Blumberger
- Department of Physics and
Astronomy, University College London, Gower Street, London WC1E 6BT, U.K
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33
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Heck A, Kranz JJ, Kubař T, Elstner M. Multi-Scale Approach to Non-Adiabatic Charge Transport in High-Mobility Organic Semiconductors. J Chem Theory Comput 2015; 11:5068-82. [DOI: 10.1021/acs.jctc.5b00719] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander Heck
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131 Karlsruhe, Germany
- Heidelberg
Karlsruhe Research Partnership (HEiKA), Heidelberg University, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Julian J. Kranz
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131 Karlsruhe, Germany
- Heidelberg
Karlsruhe Research Partnership (HEiKA), Heidelberg University, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
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34
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Pershin A, Szalay PG. Development of highly accurate approximate scheme for computing the charge transfer integral. J Chem Phys 2015; 143:074109. [DOI: 10.1063/1.4928053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anton Pershin
- Laboratory for Theoretical Chemistry, Institute of Chemistry, Eötvös Loránd University, P.O. Box 32, H-1518 Budapest, Hungary
| | - Péter G. Szalay
- Laboratory for Theoretical Chemistry, Institute of Chemistry, Eötvös Loránd University, P.O. Box 32, H-1518 Budapest, Hungary
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35
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Kubas A, Gajdos F, Heck A, Oberhofer H, Elstner M, Blumberger J. Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT and FODFTB against high-level ab initio calculations. II. Phys Chem Chem Phys 2015; 17:14342-54. [PMID: 25573447 DOI: 10.1039/c4cp04749d] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A new database (HAB7-) of electronic coupling matrix elements (Hab) for electron transfer in seven medium-sized negatively charged π-conjugated organic dimers is introduced. Reference data are obtained with spin-component scaled approximate coupled cluster method (SCS-CC2) and large basis sets. Assessed DFT-based approaches include constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), self-consistent charge density functional tight-binding (FODFTB) and the recently described analytic overlap method (AOM). This complements the previously reported HAB11 database where only cationic dimers were considered. The CDFT method in combination with a functional based on PBE and including 50% of exact exchange (HFX) was found to provide best estimates, with a mean relative unsigned error (MRUE) of 8.2%. CDFT couplings systematically increase with decreasing fraction of HFX as a consequence of increasing delocalisation of the SOMO orbital. The FODFT method is found to be very robust underestimating electronic couplings by 28%. The FODFTB and AOM methods, although orders of magnitude more efficient in terms of computational effort than the DFT approaches, perform well with reasonably small errors of 54% and 29%, respectively, translating in errors in the non-adiabatic electron transfer rate of a factor of 2.4 and 1.7, respectively. We discuss carefully various sources of errors and the scope and limitations of all assessed methods taking into account the results obtained for both HAB7- and HAB11 databases.
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Affiliation(s)
- Adam Kubas
- University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, UK.
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36
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de la Lande A, Gillet N, Chen S, Salahub DR. Progress and challenges in simulating and understanding electron transfer in proteins. Arch Biochem Biophys 2015; 582:28-41. [PMID: 26116376 DOI: 10.1016/j.abb.2015.06.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 06/15/2015] [Accepted: 06/22/2015] [Indexed: 11/19/2022]
Abstract
This Review presents an overview of the most common numerical simulation approaches for the investigation of electron transfer (ET) in proteins. We try to highlight the merits of the different approaches but also the current limitations and challenges. The article is organized into three sections. Section 2 deals with direct simulation algorithms of charge migration in proteins. Section 3 summarizes the methods for testing the applicability of the Marcus theory for ET in proteins and for evaluating key thermodynamic quantities entering the reaction rates (reorganization energies and driving force). Recent studies interrogating the validity of the theory due to the presence of non-ergodic effects or of non-linear responses are also described. Section 4 focuses on the tunneling aspects of electron transfer. How can the electronic coupling between charge transfer states be evaluated by quantum chemistry approaches and rationalized? What interesting physics regarding the impact of protein dynamics on tunneling can be addressed? We will illustrate the different sections with examples taken from the literature to show what types of system are currently manageable with current methodologies. We also take care to recall what has been learned on the biophysics of ET within proteins thanks to the advent of atomistic simulations.
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Affiliation(s)
- Aurélien de la Lande
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris Sud. 15, av. Jean Perrin, 91405 Orsay, France.
| | - Natacha Gillet
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris Sud. 15, av. Jean Perrin, 91405 Orsay, France
| | - Shufeng Chen
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris Sud. 15, av. Jean Perrin, 91405 Orsay, France
| | - Dennis R Salahub
- Department of Chemistry, CMS - Centre for Molecular Simulation and IQST - Institute for Quantum Science and Technology, University of Calgary, 2500 University Drive N.W., Calgary, Alberta T2N 1N4, Canada.
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37
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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38
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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39
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Winkler JR, Gray HB. Could tyrosine and tryptophan serve multiple roles in biological redox processes? PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2015; 373:rsta.2014.0178. [PMID: 25666062 PMCID: PMC4342971 DOI: 10.1098/rsta.2014.0178] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Single-step electron tunnelling reactions can transport charges over distances of 15-20 Åin proteins. Longer-range transfer requires multi-step tunnelling processes along redox chains, often referred to as hopping. Long-range hopping via oxidized radicals of tryptophan and tyrosine, which has been identified in several natural enzymes, has been demonstrated in artificial constructs of the blue copper protein azurin. Tryptophan and tyrosine serve as hopping way stations in high-potential charge transport processes. It may be no coincidence that these two residues occur with greater-than-average frequency in O(2)- and H(2)O(2)-reactive enzymes. We suggest that appropriately placed tyrosine and/or tryptophan residues prevent damage from high-potential reactive intermediates by reduction followed by transfer of the oxidizing equivalent to less harmful sites or out of the protein altogether.
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Affiliation(s)
- Jay R Winkler
- Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Harry B Gray
- Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
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40
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Hong G, Pachter R. Photoactivation of cryptochromes from Drosophila melanogaster and Sylvia borin: insight into the chemical compass mechanism by computational investigation. J Phys Chem B 2015; 119:3883-92. [PMID: 25710635 DOI: 10.1021/jp508871h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Although behavioral studies demonstrated light-induced magnetoreception in the insect Drosophila melanogaster, gaining insight into the possibility that a radical-pair mechanism accounts for the magnetic response of the cryptochrome (DmCry1) is complicated by a number of factors. In addition, the mechanism of magnetoreception for the cryptochrome from the garden warbler bird Sylvia borin (gwCry1a), which demonstrated a long-lived radical pair by transient optical absorption measurements, has also not been rationalized. To assess potential feasibility of a radical-pair mechanism in DmCry1 and gwCry1a, formed by excitation and electron transfer between a Trp-triad and flavin adenine dinucleotide (FAD), further separated by electron transfer within the triad, we applied a combination of theoretical methods, including homology modeling and molecular dynamics (MD) for structure refinement, high-level ab initio theory, and MD simulations using a polarizable force-field for prediction of pKa and the electron transfer rate. Calculated excitation energies, followed by electron transfer in model compounds of DmCry1 that assume proton transfer in conjunction with electron transfer from Trp (W420) to FAD and the predicted pKa for the proximate residue to FAD (Cys416), support a radical-pair mechanism. Furthermore, free-energy and reorganization energies for the Trp-triad in DmCry1 demonstrate facile electron transfer, explained by the local protein environment and exposure to solvent, which in turn enables a large enough distance separation for the radical-pair partners. Results for gwCry1a demonstrated the importance of accounting for relaxed excited-state geometries in validating the first stage of a radical-pair mechanism. This work provides insight into the so-called chemical compass mechanism to explain magnetic-field sensing in DmCry1 and gwCry1a, expanding on previous work on the cyrptochrome from the plant Arabidopsis thaliana (Solov'yov et al. J. Am. Chem. Soc. 2012, 134, 18046-18052. Solov'yov et al., Sci. Rep. 2014, 4, 1-8.).
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Affiliation(s)
- Gongyi Hong
- Air Force Research Laboratory, Wright-Patterson Air Force Base , AFRL/RX, 3005 Hobson Way, Dayton, Ohio 45433, United States
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41
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Lüdemann G, Solov’yov IA, Kubař T, Elstner M. Solvent Driving Force Ensures Fast Formation of a Persistent and Well-Separated Radical Pair in Plant Cryptochrome. J Am Chem Soc 2015; 137:1147-56. [DOI: 10.1021/ja510550g] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gesa Lüdemann
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Ilia A. Solov’yov
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Tomáš Kubař
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
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42
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Kubas A, Hoffmann F, Heck A, Oberhofer H, Elstner M, Blumberger J. Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations. J Chem Phys 2014; 140:104105. [PMID: 24628150 DOI: 10.1063/1.4867077] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We introduce a database (HAB11) of electronic coupling matrix elements (H(ab)) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level of theory, n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate coupled cluster model (SCS)-CC2 are reported for this database to assess the performance of three DFT methods of decreasing computational cost, including constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), and self-consistent charge density functional tight-binding (FODFTB). We find that the CDFT approach in combination with a modified PBE functional containing 50% Hartree-Fock exchange gives best results for absolute H(ab) values (mean relative unsigned error = 5.3%) and exponential distance decay constants β (4.3%). CDFT in combination with pure PBE overestimates couplings by 38.7% due to a too diffuse excess charge distribution, whereas the economic FODFT and highly cost-effective FODFTB methods underestimate couplings by 37.6% and 42.4%, respectively, due to neglect of interaction between donor and acceptor. The errors are systematic, however, and can be significantly reduced by applying a uniform scaling factor for each method. Applications to dimers outside the database, specifically rotated thiophene dimers and larger acenes up to pentacene, suggests that the same scaling procedure significantly improves the FODFT and FODFTB results for larger π-conjugated systems relevant to organic semiconductors and DNA.
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Affiliation(s)
- Adam Kubas
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Felix Hoffmann
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Alexander Heck
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Harald Oberhofer
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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43
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Cailliez F, Müller P, Gallois M, de la Lande A. ATP binding and aspartate protonation enhance photoinduced electron transfer in plant cryptochrome. J Am Chem Soc 2014; 136:12974-86. [PMID: 25157750 DOI: 10.1021/ja506084f] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cryptochromes are flavoproteins encountered in most vegetal and animal species. They play a role of blue-light receptors in plants and in invertebrates. The putative resting state of the FAD cofactor in these proteins is its fully oxidized form, FADox. Upon blue-light excitation, the isoalloxazine ring (ISO) may undergo an ultrafast reduction by a nearby tryptophan residue W400. This primary reduction triggers a cascade of electron and proton transfers, ultimately leading to the formation of the FADH° radical. A recent experimental study has shown that the yield of FADH° formation in Arabidopsis cryptochrome can be strongly modulated by ATP binding and by pH, affecting the protonation state of D396 (proton donor to FAD°(-)). Here we provide a detailed molecular analysis of these effects by means of combined classical molecular dynamics simulations and time-dependent density functional theory calculations. When ATP is present and D396 protonated, FAD remains in close contact with W400, thereby enhancing electron transfer (ET) from W400 to ISO*. In contrast, deprotonation of D396 and absence of ATP introduce flexibility to the photoactive site prior to FAD excitation, with the consequence of increased ISO-W400 distance and diminished tunneling rate by almost two orders of magnitude. We show that under these conditions, ET from the adenine moiety of FAD becomes a competitive relaxation pathway. Overall, our data suggest that the observed effects of ATP and pH on the FAD photoreduction find their roots in the earliest stage of the photoreduction process; i.e., ATP binding and the protonation state of D396 determine the preferred pathway of ISO* relaxation.
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Affiliation(s)
- Fabien Cailliez
- Laboratoire de Chimie Physique, UMR 8000, Université Paris-Sud and CNRS , Orsay F-91405, France
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44
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Gajdos F, Valner S, Hoffmann F, Spencer J, Breuer M, Kubas A, Dupuis M, Blumberger J. Ultrafast Estimation of Electronic Couplings for Electron Transfer between π-Conjugated Organic Molecules. J Chem Theory Comput 2014; 10:4653-60. [DOI: 10.1021/ct500527v] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Fruzsina Gajdos
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
| | - Siim Valner
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
| | - Felix Hoffmann
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität Bochum, Universitätsstrasse
150, 44801 Bochum, Germany
| | - Jacob Spencer
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
| | - Marian Breuer
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
| | - Adam Kubas
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
| | - Michel Dupuis
- Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Jochen Blumberger
- Department
of Physics and Astronomy, University College London, London WC1E 6BT, U.K
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45
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Cui Q, Elstner M. Density functional tight binding: values of semi-empirical methods in an ab initio era. Phys Chem Chem Phys 2014; 16:14368-77. [PMID: 24850383 PMCID: PMC4836871 DOI: 10.1039/c4cp00908h] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Semi-empirical (SE) methods are derived from Hartree-Fock (HF) or Density Functional Theory (DFT) by neglect and approximation of electronic integrals. Thereby, parameters are introduced which have to be determined from reference calculations and/or by fitting to available experimental data. This leads to computational methods that are about 2-3 orders of magnitude faster than the standard HF/DFT methods using medium sized basis sets while being about 3 orders of magnitude slower than empirical force field methods (Molecular Mechanics: MM). Therefore, SE methods are most appropriate for a specific range of applications. These include the study of systems that contain a large number of atoms and therefore being too large for ab initio or DFT methods and also problems where dynamic or entropic effects are particularly important. In the latter case, the errors made by considering a very limited number of molecular structures or neglecting entropic contributions can be much larger than the accuracy lost due to the use of SE methods. Another area where SE methods are attractive concerns the analysis of systems for which reliable MM models are not readily available. Therefore, even in an era when rapid progress is being made in ab initio methods, there is considerable interest in further developing SE methods. We illustrate this point by focusing on the discussion of recent development and application of the Density Functional Tight Binding method.
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46
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Barbatti M. Computational reference data for the photochemistry of cyclobutane pyrimidine dimers. Chemphyschem 2014; 15:3342-54. [PMID: 25044616 DOI: 10.1002/cphc.201402302] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Indexed: 01/19/2023]
Abstract
The cis-syn cyclobutane pyrimidine dimer is one of the major classes of carcinogenic UV-induced DNA photoproducts. In this work, diverse high-level quantum-chemical methods were used to determine the spectroscopic properties of neutral (singlet and triplet) and charged (cation and anion) species of thymine dimers. Maps of potential energy, charge distribution, electron affinity, and ionization potential of the thymidine dimers were computed along the two dimerization coordinates for neutral and charged species, as well as for the singlet excited state. This set of data aims at providing consistent results computed with the same methods as for photodamage and repair. Based on these results, several different photo-, heat-, and charge-induced mechanisms of dimerization and repair are characterized and discussed. Additionally, a new stable dimer with methylmethylidene-hexahydropyrimidine structure was found in the S0 state.
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany).
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47
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Affiliation(s)
- Jay R. Winkler
- Beckman Institute, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125
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48
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Schöppach A, Gnandt D, Koslowski T. Charge transfer in strongly correlated systems: an exact diagonalization approach to model Hamiltonians. J Chem Phys 2014; 140:134101. [PMID: 24712774 DOI: 10.1063/1.4869520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We study charge transfer in bridged di- and triruthenium complexes from a theoretical and computational point of view. Ab initio computations are interpreted from the perspective of a simple empirical Hamiltonian, a chemically specific Mott-Hubbard model of the complexes' π electron systems. This Hamiltonian is coupled to classical harmonic oscillators mimicking a polarizable dielectric environment. The model can be solved without further approximations in a valence bond picture using the method of exact diagonalization and permits the computation of charge transfer reaction rates in the framework of Marcus' theory. In comparison to the exact solution, the Hartree-Fock mean field theory overestimates both the activation barrier and the magnitude of charge-transfer excitations significantly. For triruthenium complexes, we are able to directly access the interruthenium antiferromagnetic coupling strengths.
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Affiliation(s)
- Andreas Schöppach
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, D-79104 Freiburg im Breisgau, Germany
| | - David Gnandt
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, D-79104 Freiburg im Breisgau, Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, D-79104 Freiburg im Breisgau, Germany
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49
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Faraji S, Dreuw A. Physicochemical Mechanism of Light-Driven DNA Repair by (6-4) Photolyases. Annu Rev Phys Chem 2014; 65:275-92. [DOI: 10.1146/annurev-physchem-040513-103626] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, 69120 Heidelberg, Germany; ,
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, 69120 Heidelberg, Germany; ,
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Liu Z, Tan C, Guo X, Li J, Wang L, Zhong D. Dynamic Determination of Active-Site Reactivity in Semiquinone Photolyase by the Cofactor Photoreduction. J Phys Chem Lett 2014; 5:820-825. [PMID: 24803991 PMCID: PMC3985926 DOI: 10.1021/jz500077s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 02/11/2014] [Indexed: 05/07/2023]
Abstract
Photolyase contains a flavin cofactor in a fully reduced form as its functional state to repair ultraviolet-damaged DNA upon blue light absorption. However, after purification, the cofactor exists in its oxidized or neutral semiquinone state. Such oxidization eliminates the repair function, but it can be reverted by photoreduction, a photoinduced process with a series of electron-transfer (ET) reactions. With femtosecond absorption spectroscopy and site-directed mutagenesis, we completely recharacterized such photoreduction dynamics in the semiquinone state. Comparing with all previous studies, we identified a new intramolecular ET pathway, determined stretched ET behaviors, refined all ET time scales, and finally evaluated the driving forces and reorganization energies for eight elementary ET reactions. Combined with the oxidized-state photoreduction dynamics, we elucidated the different active-site properties of the reduction ability and structural flexibility in the oxidized and semiquinone states, leading to the dramatically different ET dynamics and photoreduction efficiency in the two states.
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