1
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Deviers J, Cailliez F, de la Lande A, Kattnig DR. Avian cryptochrome 4 binds superoxide. Comput Struct Biotechnol J 2024; 26:11-21. [PMID: 38204818 PMCID: PMC10776438 DOI: 10.1016/j.csbj.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Flavin-binding cryptochromes are blue-light sensitive photoreceptors that have been implicated with magnetoreception in some species. The photocycle involves an intra-protein photo-reduction of the flavin cofactor, generating a magnetosensitive radical pair, and its subsequent re-oxidation. Superoxide (O2 • - ) is generated in the re-oxidation with molecular oxygen. The resulting O2 • - -containing radical pairs have also been hypothesised to underpin various magnetosensitive traits, but due to fast spin relaxation when tumbling in solution would require immobilisation. We here describe our insights in the binding of superoxide to cryptochrome 4 from C. livia based on extensive all-atom molecular dynamics studies and density-functional theory calculations. The positively charged "crypt" region that leads to the flavin binding pocket transiently binds O2 • - at 5 flexible binding sites centred on arginine residues. Typical binding times amounted to tens of nanoseconds, but exceptional binding events extended to several hundreds of nanoseconds and slowed the rotational diffusion, thereby realising rotational correlation times as large as 1 ns. The binding sites are particularly efficient in scavenging superoxide escaping from a putative generation site close to the flavin-cofactor, possibly implying a functional relevance. We discuss our findings in view of a potential magnetosensitivity of biological flavin semiquinone/superoxide radical pairs.
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Affiliation(s)
- Jean Deviers
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, United Kingdom
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France
| | - Fabien Cailliez
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France
| | - Daniel R. Kattnig
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, United Kingdom
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2
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Tandiana R, Omar KA, Luppi E, Cailliez F, Van-Oanh NT, Clavaguéra C, de la Lande A. Use of Gaussian-Type Functions for Describing Fast Ion-Matter Irradiation with Time-Dependent Density Functional Theory. J Chem Theory Comput 2023; 19:7740-7752. [PMID: 37874960 DOI: 10.1021/acs.jctc.3c00656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The electronic stopping power is an observable property that quantifies the ability of swift ions to penetrate matter to transfer energy to the electron cloud. The recent literature has proven the value of Real-Time Time-Dependent Density Functional Theory to accurately evaluate this property from first-principles, but questions remain regarding the capability of computer codes relying on atom-centered basis functions to capture the physics at play. In this Perspective, we draw attention to the fact that irradiation by swift ions triggers electron emission into the continuum, especially at the Bragg peak. We investigate the ability of Gaussian atomic orbitals (AOC), which were fitted to mimic continuum wave functions, to improve electronic stopping power predictions. AOC are added to standard correlation-consistent basis sets or STO minimal basis sets. Our benchmarks for water irradiation by fast protons clearly advocate for the use of AOC, especially near the Bragg peak. We show that AOC only need to be placed on the molecules struck by the ion. The number of AOC that are added to the usual basis set is relatively small compared to the total number of atomic orbitals, making the use of such a basis set an excellent choice from a computational cost point of view. The optimum basis set combination is applied for the calculation of the stopping power of a proton in water with encouraging agreement with experimental data.
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Affiliation(s)
- Rika Tandiana
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, F-91405 Orsay, France
| | - Karwan Ali Omar
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, F-91405 Orsay, France
- Department of Chemistry, College of Education, University of Sulaimani, 41005 Kurdistan, Iraq
| | - Eleonora Luppi
- Laboratoire de Chimie Théorique, Sorbonne Université and CNRS, F-75005 Paris, France
| | - Fabien Cailliez
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, F-91405 Orsay, France
| | - Nguyen-Thi Van-Oanh
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, F-91405 Orsay, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, F-91405 Orsay, France
| | - Aurélien de la Lande
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, F-91405 Orsay, France
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3
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Řezáč J, de la Lande A. On the Role of Charge Transfer in Many-Body Non-Covalent Interactions. Chemphyschem 2023; 24:e202300329. [PMID: 37405855 DOI: 10.1002/cphc.202300329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 07/06/2023]
Abstract
Charge transfer is one of the mechanisms involved in non-covalent interactions. In molecular dimers, its contribution to pairwise interaction energies has been studied extensively using a variety of interaction energy decomposition schemes. In polar interactions such as hydrogen bonds, it can contribute ten or several tens of percent of the interaction energy. Less is known about its importance in higher-order interactions in many-body systems, mainly because of the lack of methods applicable to this problem. In this work, we extend our method for the quantification of the charge-transfer energy based on constrained DFT to many-body cases and apply it to model trimers extracted from molecular crystals. Our calculations show that charge transfer can account for a large fraction of the total three-body interaction energy. This also has implications for DFT calculations of many-body interactions in general as it is known that many DFT functionals struggle to describe charge-transfer effects correctly.
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Affiliation(s)
- Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10, Prague, Czech Republic
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS, Université Paris Saclay, 91405, Orsay, France
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4
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Tolu D, Guillaumont D, de la Lande A. Irradiation of Plutonium Tributyl Phosphate Complexes by Ionizing Alpha Particles: A Computational Study. J Phys Chem A 2023; 127:7045-7057. [PMID: 37606197 DOI: 10.1021/acs.jpca.3c02117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The PUREX solvent extraction process, widely used for recovering uranium and plutonium from spent nuclear fuel, utilizes an organic solvent composed of tributyl phosphate (TBP). The emission of ionizing particles such as alpha particles, resulting from the decay of plutonium, makes the organic solvent vulnerable to degradation. Here, we study the ultrashort time alpha irradiation of tributylphosphate (TBP) and Pu(NO3)4(TBP)2 complex formed in the PUREX process. Electron dynamics is propagated by Real-Time-Dependent Auxiliary Density Functional Theory (RT-TD-ADFT). We investigate the use of previously proposed absorption boundary conditions (ABC) in the molecular orbital space to treat secondary electron emission. Basis set and exchange correlation functional effects with ABC are reported as well as a detailed analysis of the ABC parametrization. Preliminary results on the water molecule and then on TBP show that the phenomenological nature of the ABC parameters necessitates selecting appropriate values for each system under study. Irradiation of free and complexed TBP shows an influence of the ligands on the variation of atomic charges on the femtosecond time scale. An accumulation of atomic charges in the alkyl chains of TBP is observed in the case where the nitrate groups are predominantly irradiated. In addition, we find that the Pu atom regains its electric charge very rapidly after being hit by the projectile, with the coordination sphere serving as an electron reservoir to preserve its formal redox state. This study paves the road toward a full understanding of the degradation of organic extracants employed in the nuclear industry.
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Affiliation(s)
- Damien Tolu
- CEA, DES, ISEC, DMRC, Université Montpellier, Marcoule, 30207 Bagnols sur Cèze, France
- Institut de Chimie Physique, CNRS, Université Paris Saclay, 15 Avenue Jean Perrin, Paris, 91405, France
| | - Dominique Guillaumont
- CEA, DES, ISEC, DMRC, Université Montpellier, Marcoule, 30207 Bagnols sur Cèze, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS, Université Paris Saclay, 15 Avenue Jean Perrin, Paris, 91405, France
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5
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Parise A, Ciardullo G, Prejanò M, Lande ADL, Marino T. On the Recognition of Natural Substrate CTP and Endogenous Inhibitor ddhCTP of SARS-CoV-2 RNA-Dependent RNA Polymerase: A Molecular Dynamics Study. J Chem Inf Model 2022; 62:4916-4927. [PMID: 36219674 DOI: 10.1021/acs.jcim.2c01002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The novel coronavirus SARS-CoV-2 is the causative agent of the COVID-19 outbreak that is affecting the entire planet. As the pandemic is still spreading worldwide, with multiple mutations of the virus, it is of interest and of help to employ computational methods for identifying potential inhibitors of the enzymes responsible for viral replication. Attractive antiviral nucleotide analogue RNA-dependent RNA polymerase (RdRp) chain terminator inhibitors are investigated with this purpose. This study, based on molecular dynamics (MD) simulations, addresses the important aspects of the incorporation of an endogenously synthesized nucleoside triphosphate, ddhCTP, in comparison with the natural nucleobase cytidine triphosphate (CTP) in RdRp. The ddhCTP species is the product of the viperin antiviral protein as part of the innate immune response. The absence of the ribose 3'-OH in ddhCTP could have important implications in its inhibitory mechanism of RdRp. We built an in silico model of the RNA strand embedded in RdRp using experimental methods, starting from the cryo-electron microscopy structure and exploiting the information obtained by spectrometry on the RNA sequence. We determined that the model was stable during the MD simulation time. The obtained results provide deeper insights into the incorporation of nucleoside triphosphates, whose molecular mechanism by the RdRp active site still remains elusive.
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Affiliation(s)
- Angela Parise
- Dipartimento di Chimica e Tecnologie Chimiche, Università Della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy.,Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
| | - Giada Ciardullo
- Dipartimento di Chimica e Tecnologie Chimiche, Università Della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy
| | - Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università Della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy
| | - Aurélien de la Lande
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università Della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy
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6
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Deviers J, Cailliez F, Gutiérrez BZ, Kattnig DR, de la Lande A. Ab initio derivation of flavin hyperfine interactions for the protein magnetosensor cryptochrome. Phys Chem Chem Phys 2022; 24:16784-16798. [PMID: 35775941 DOI: 10.1039/d1cp05804e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The radicals derived from flavin adenine dinucleotide (FAD) are a corner stone of recent hypotheses about magnetoreception, including the compass of migratory songbirds. These models attribute a magnetic sense to coherent spin dynamics in radical pairs within the flavo-protein cryptochrome. The primary determinant of sensitivity and directionality of this process are the hyperfine interactions of the involved radicals. Here, we present a comprehensive computational study of the hyperfine couplings in the protonated and unprotonated FAD radicals in cryptochrome 4 from C. livia. We combine long (800 ns) molecular dynamics trajectories to accurate quantum chemistry calculations. Hyperfine parameters are derived using auxiliary density functional theory applied to cluster and hybrid QM/MM (Quantum Mechanics/Molecular Mechanics) models comprising the FAD and its significant surrounding environment, as determined by a detailed sensitivity analysis. Thanks to this protocol we elucidate the sensitivity of the hyperfine interaction parameters to structural fluctuations and the polarisation effect of the protein environment. We find that the ensemble-averaged hyperfine interactions are predominantly governed by thermally induced geometric distortions of the flavin. We discuss our results in view of the expected performance of these radicals as part of a magnetoreceptor. Our data could be used to parametrize spin Hamiltonians including not only average values but also standard deviations.
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Affiliation(s)
- Jean Deviers
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, UK.,Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
| | - Fabien Cailliez
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
| | - Bernardo Zúñiga Gutiérrez
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, C. P. 44430, Guadalajara Jal, Mexico
| | - Daniel R Kattnig
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, UK
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
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7
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Korsaye FA, de la Lande A, Ciofini I. Following the density evolution using real time density functional theory and density based indexes: Application to model push-pull molecules. J Comput Chem 2022; 43:1464-1473. [PMID: 35766295 DOI: 10.1002/jcc.26932] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 02/01/2023]
Abstract
Considering as test case a family of organic rod like push-pull molecules, we derived and applied density based index enabling the description and diagnostic of the electronic density evolution in real time-time dependent density functional theory (RT-TDDFT) simulations. In particular, both the charge transfer (CT) distance and a diagnostic index, the DCT and MAC RT respectively, were computed on the fly from the density distribution obtained at a given time and the reference ground state density and their mean values were compared with what obtained at Linear Response-TDDFT level. Besides giving a way of analyzing the density redistribution occurring in time, these tools allowed to show how RT-TDDFT, which is definitely a powerful method to model the evolution of the density in CT or charge separation processes, can be affected by the same artifacts known for LR-TDDFT approaches and, particularly, to those related to the use of approximate exchange correlation functionals. The analysis here performed allowed to identify and discard on fly the electronic configurations corresponding to spurious situations.
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Affiliation(s)
- Feven Alemu Korsaye
- PSL University, CNRS, Chimie ParisTech-PSL, Institute of Chemistry for Life and Health Sciences (i-CLeHS), Theoretical Chemistry and Modelling Group (CTM), Paris, France.,Institut de Chimie Physique, Université Paris Saclay, CNRS, UMR 8000, Orsay, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, Université Paris Saclay, CNRS, UMR 8000, Orsay, France
| | - Ilaria Ciofini
- PSL University, CNRS, Chimie ParisTech-PSL, Institute of Chemistry for Life and Health Sciences (i-CLeHS), Theoretical Chemistry and Modelling Group (CTM), Paris, France
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8
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Deviers J, Cailliez F, de la Lande A, Kattnig DR. Anisotropic magnetic field effects in the re-oxidation of cryptochrome in the presence of scavenger radicals. J Chem Phys 2022; 156:025101. [PMID: 35032990 DOI: 10.1063/5.0078115] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The avian compass and many other of nature's magnetoreceptive traits are widely ascribed to the protein cryptochrome. There, magnetosensitivity is thought to emerge as the spin dynamics of radicals in the applied magnetic field enters in competition with their recombination. The first and dominant model makes use of a radical pair. However, recent studies have suggested that magnetosensitivity could be markedly enhanced for a radical triad, the primary radical pair of which undergoes a spin-selective recombination reaction with a third radical. Here, we test the practicality of this supposition for the reoxidation reaction of the reduced FAD cofactor in cryptochrome, which has been implicated with light-independent magnetoreception but appears irreconcilable with the classical radical pair mechanism (RPM). Based on the available realistic cryptochrome structures, we predict the magnetosensitivity of radical triad systems comprising the flavin semiquinone, the superoxide, and a tyrosine or ascorbyl scavenger radical. We consider many hyperfine-coupled nuclear spins, the relative orientation and placement of the radicals, their coupling by the electron-electron dipolar interaction, and spin relaxation in the superoxide radical in the limit of instantaneous decoherence, which have not been comprehensively considered before. We demonstrate that these systems can provide superior magnetosensitivity under realistic conditions, with implications for dark-state cryptochrome magnetoreception and other biological magneto- and isotope-sensitive radical recombination reactions.
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Affiliation(s)
- Jean Deviers
- Department of Physics and Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD Exeter, United Kingdom
| | - Fabien Cailliez
- Institut de Chimie Physique, Université Paris Saclay, CNRS (UMR 8000), 15 avenue Jean Perrin, 91405 Orsay, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, Université Paris Saclay, CNRS (UMR 8000), 15 avenue Jean Perrin, 91405 Orsay, France
| | - Daniel R Kattnig
- Department of Physics and Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD Exeter, United Kingdom
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9
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de la Lande A, Denisov S, Mostafavi M. The mystery of sub-picosecond charge transfer following irradiation of hydrated uridine monophosphate. Phys Chem Chem Phys 2021; 23:21148-21162. [PMID: 34528029 DOI: 10.1039/d0cp06482c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The early mechanisms by which ionizing rays damage biological structures by so-called direct effects are largely elusive. In a recent picosecond pulse radiolysis study of concentrated uridine monophosphate solutions [J. Ma, S. A. Denisov, J.-L. Marignier, P. Pernot, A. Adhikary, S. Seki and M. Mostafavi, J. Phys. Chem. Lett., 2018, 9, 5105], unexpected results were found regarding the oxidation of the nucleobase. The signature of the oxidized nucleobase could not be detected 5 ps after the electron pulse, but only the oxidized phosphate, raising intriguing questions about the identity of charge-transfer mechanisms that could explain the absence of U+. We address here this question by means of advanced first-principles atomistic simulations of solvated uridine monophosphate, combining Density Functional Theory (DFT) with polarizable embedding schemes. We contrast three very distinct mechanisms of charge transfer covering the atto-, femto- and pico-second timescales. We first investigate the ionization mechanism and subsequent hole/charge migrations on a timescale of attoseconds to a few femtoseconds under the frozen nuclei approximation. We then consider a nuclear-driven phosphate-to-oxidized-nucleobase electron transfer, showing that it is an uncompetitive reaction channel on the sub-picosecond timescale, despite its high exothermicity and significant electronic coupling. Finally, we show that non-adiabatic charge transfer is enabled by femtosecond nuclear relaxation after ionization. We show that electronic decoherence and the electronic coupling strength are the key parameters that determine the hopping probabilities. Our results provide important insight into the interplay between electronics and nuclear motions in the early stages of the multiscale responses of biological matter subjected to ionizing radiation.
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Affiliation(s)
- Aurélien de la Lande
- Institut de Chimie Physique, CNRS, Université Paris Saclay (UMR 8000), 15 Avenue Jean Perrin, 91405, France.
| | - Sergey Denisov
- Institut de Chimie Physique, CNRS, Université Paris Saclay (UMR 8000), 15 Avenue Jean Perrin, 91405, France.
| | - Mehran Mostafavi
- Institut de Chimie Physique, CNRS, Université Paris Saclay (UMR 8000), 15 Avenue Jean Perrin, 91405, France.
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10
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Shafizadeh N, Crestoni ME, de la Lande A, Soep B. Heme ligation in the gas phase. INT REV PHYS CHEM 2021. [DOI: 10.1080/0144235x.2021.1952006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Roma, Italy
| | | | - Benoît Soep
- ISMO-CNRS, Université Paris Saclay, Orsay Cedex, France
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11
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Wu X, Hénin J, Baciou L, Baaden M, Cailliez F, de la Lande A. Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations. Front Chem 2021; 9:650651. [PMID: 34017816 PMCID: PMC8129163 DOI: 10.3389/fchem.2021.650651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
NOX5 is a member of the NADPH oxidase family which is dedicated to the production of reactive oxygen species. The molecular mechanisms governing transmembrane electron transfer (ET) that permits to shuttle electrons over the biological membrane have remained elusive for a long time. Using computer simulations, we report conformational dynamics of NOX5 embedded within a realistic membrane environment. We assess the stability of the protein within the membrane and monitor the existence of cavities that could accommodate dioxygen molecules. We investigate the heme-to-heme electron transfer. We find a reaction free energy of a few tenths of eV (ca. −0.3 eV) and a reorganization free energy of around 1.1 eV (0.8 eV after including electrostatic induction corrections). The former indicates thermodynamically favorable ET, while the latter falls in the expected values for transmembrane inter-heme ET. We estimate the electronic coupling to fall in the range of the μeV. We identify electron tunneling pathways showing that not only the W378 residue is playing a central role, but also F348. Finally, we reveal the existence of two connected O2−binding pockets near the outer heme with fast exchange between the two sites on the nanosecond timescale. We show that when the terminal heme is reduced, O2 binds closer to it, affording a more efficient tunneling pathway than when the terminal heme is oxidized, thereby providing an efficient mechanism to catalyze superoxide production in the final step. Overall, our study reveals some key molecular mechanisms permitting reactive oxygen species production by NOX5 and paves the road for further investigation of ET processes in the wide family of NADPH oxidases by computer simulations.
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Affiliation(s)
- Xiaojing Wu
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, Paris, France
| | - Jérôme Hénin
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, Paris, France
| | - Laura Baciou
- Institut de Chimie Physique, Université Paris Saclay, CNRS (UMR 8000), Orsay, France
| | - Marc Baaden
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, Paris, France
| | - Fabien Cailliez
- Institut de Chimie Physique, Université Paris Saclay, CNRS (UMR 8000), Orsay, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, Université Paris Saclay, CNRS (UMR 8000), Orsay, France
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12
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Abstract
Ionizing rays cause damage to genomes, proteins, and signaling pathways that normally regulate cell activity, with harmful consequences such as accelerated aging, tumors, and cancers but also with beneficial effects in the context of radiotherapies. While the great pace of research in the twentieth century led to the identification of the molecular mechanisms for chemical lesions on the building blocks of biomacromolecules, the last two decades have brought renewed questions, for example, regarding the formation of clustered damage or the rich chemistry involving the secondary electrons produced by radiolysis. Radiation chemistry is now meeting attosecond science, providing extraordinary opportunities to unravel the very first stages of biological matter radiolysis. This review provides an overview of the recent progress made in this direction, focusing mainly on the atto- to femto- to picosecond timescales. We review promising applications of time-dependent density functional theory in this context.
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Affiliation(s)
- Karwan Ali Omar
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France; .,Department of Chemistry, College of Education, University of Sulaimani, 41005 Kurdistan, Iraq
| | - Karim Hasnaoui
- High Performance Computing User Support Team, Institut du Développement et des Ressources en Informatique Scientifique (IDRIS), 91403 Orsay, France.,Maison de la Simulation, CNRS, Commissariat à l'Energie Atomique et aux Énergies Alternatives (CEA), Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France;
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13
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Pei Z, Ou Q, Mao Y, Yang J, Lande ADL, Plasser F, Liang W, Shuai Z, Shao Y. Elucidating the Electronic Structure of a Delayed Fluorescence Emitter via Orbital Interactions, Excitation Energy Components, Charge-Transfer Numbers, and Vibrational Reorganization Energies. J Phys Chem Lett 2021; 12:2712-2720. [PMID: 33705139 PMCID: PMC8272082 DOI: 10.1021/acs.jpclett.1c00094] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recently, Wang and co-workers carried out frontier molecule orbital engineering in the design of m-Cz-BNCz, a thermally activated delayed fluorescence (TADF) molecule that emits pure green light at an external quantum efficiency of 27%. To further understand the underlying molecular design principles, we employed four advanced electronic structure analysis tools. First, an absolutely localized molecular orbitals (ALMO-) based analysis indicates an antibonding combination between the highest occupied molecular orbitals (HOMOs) of the donor 3,6-di-tert-butylcarbazole fragment and the acceptor BNCz fragment, which raises the HOMO energy and red-shifts the fluorescence emission wavelength. Second, excitation energy component analysis reveals that the S1-T1 gap is dominated by two-electron components of the excitation energies. Third, charge transfer number analysis, which is extended to use fragment-based Hirshfeld weights, indicates that the S1 and T1 excited states of m-Cz-BNCz (within time-dependent density functional theory) have notable charge transfer characters (27% for S1 and 12% for T1). This provides a balance between a small single-triplet gap and a substantial fluorescence intensity. Last, a vibrational reorganization energy analysis pinpoints the torsional motion between the BNCz and Cz moieties of m-Cz-BNCz as the source for its wider emission peak than that of p-Cz-BNCz. These four types of analyses are expected to be very valuable in the study and design of other TADF and functional dye molecules.
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Affiliation(s)
- Zheng Pei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Qi Ou
- MOE Key Laboratory of Organic OptoElectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Junjie Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS, Université Paris Saclay, 15 avenue Jean Perrin, F91405 Orsay, France
| | - Felix Plasser
- Department of Chemistry, Loughborough University, Loughborough, LE11 3TU, U.K
| | - Wanzhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zhigang Shuai
- MOE Key Laboratory of Organic OptoElectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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14
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Alvarez-Ibarra A, Parise A, Hasnaoui K, de la Lande A. The physical stage of radiolysis of solvated DNA by high-energy-transfer particles: insights from new first principles simulations. Phys Chem Chem Phys 2020; 22:7747-7758. [DOI: 10.1039/d0cp00165a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electron dynamics simulations based on density functional theory are carried out on nanometric molecular systems to decipher the primary processes following irradiation of bio-macromolecules by high energy transfer charged particles.
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Affiliation(s)
| | - Angela Parise
- Université Paris-Saclay
- CNRS
- Institut de Chimie Physique UMR8000
- Orsay
- France
| | - Karim Hasnaoui
- Institut du Développement et des Ressources en Informatique Scientifique
- Rue John von Neumann
- Orsay
- France
- Maison de la Simulation
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15
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Aarabi M, Soorkia S, Grégoire G, Broquier M, de la Lande A, Soep B, Omidyan R, Shafizadeh N. Water binding to Fe III hemes studied in a cooled ion trap: characterization of a strong 'weak' ligand. Phys Chem Chem Phys 2019; 21:21329-21340. [PMID: 31531442 DOI: 10.1039/c9cp03608c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of a water molecule with ferric heme-iron protoporphyrin ([PP FeIII]+) has been investigated in the gas phase in an ion trap and studied theoretically by density functional theory. It is found that the interaction of water with ferric heme leads to a stable [PP-FeIII-H2O]+ complex in the intermediate spin state (S = 3/2), in the same state as its unligated [PP-FeIII]+ homologue, without spin crossing during water attachment. Using the Van't Hoff equation, the reaction enthalpy for the formation of a Fe-OH2 bond has been determined for [PP-FeIII-H2O]+ and [PP-FeIII-(H2O)2]+. The corrected binding energy for a single Fe-H2O bond is -12.2 ± 0.6 kcal mol-1, while DFT calculations at the OPBE level yield -11.7 kcal mol-1. The binding energy of the second ligation yielding a six coordinated FeIII atom is decreased with a bond energy of -9 ± 0.9 kcal mol-1, well reproduced by calculations as -7.1 kcal mol-1. However, calculations reveal features of a weaker bond type, such as a rather long Fe-O bond with 2.28 Å for the [PP-FeIII-H2O]+ complex and the absence of a spin change by complexation. Thus despite a strong bond with H2O, the FeIII atom does not show, through theoretical modelling, a strong acceptor character in its half filled 3dz2 orbital. It is also observed that the binding properties of H2O to hemes seem strikingly specific to ferric heme and we have shown, experimentally and theoretically, that the affinity of H2O for protonated heme [H PP-Fe]+, an intermediate between FeIII and FeII, is strongly reduced compared to that for ferric heme.
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Affiliation(s)
- Mohammad Aarabi
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Satchin Soorkia
- ISMO, Université Paris-Sud, CNRS UMR 8214, bat 520, Université Paris-Sud 91405, Orsay Cedex, France.
| | - Gilles Grégoire
- ISMO, Université Paris-Sud, CNRS UMR 8214, bat 520, Université Paris-Sud 91405, Orsay Cedex, France.
| | - Michel Broquier
- ISMO, Université Paris-Sud, CNRS UMR 8214, bat 520, Université Paris-Sud 91405, Orsay Cedex, France. and Centre Laser de l'Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France
| | - Aurélien de la Lande
- Laboratoire de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000, 15, rue Jean Perrin, 91405 Orsay Cedex, France
| | - Benoît Soep
- LIDYL, CEA, CNRS, Université Paris-Saclay, UMR 9222 CEA Saclay, F-91191 Gif-sur-Yvette, France
| | - Reza Omidyan
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Niloufar Shafizadeh
- ISMO, Université Paris-Sud, CNRS UMR 8214, bat 520, Université Paris-Sud 91405, Orsay Cedex, France.
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16
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Affiliation(s)
- Daniel Mejía-Rodríguez
- Laboratoire de Chimie Physique, Université Paris Sud/CNRS, Université Paris Saclay, 15 Avenue Jean Perrin, 91405 Orsay, France
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique, Université Paris Sud/CNRS, Université Paris Saclay, 15 Avenue Jean Perrin, 91405 Orsay, France
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17
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de la Lande A, Alvarez-Ibarra A, Hasnaoui K, Cailliez F, Wu X, Mineva T, Cuny J, Calaminici P, López-Sosa L, Geudtner G, Navizet I, Garcia Iriepa C, Salahub DR, Köster AM. Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review. Molecules 2019; 24:molecules24091653. [PMID: 31035516 PMCID: PMC6539060 DOI: 10.3390/molecules24091653] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/18/2022] Open
Abstract
deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born-Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.
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Affiliation(s)
- Aurélien de la Lande
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Aurelio Alvarez-Ibarra
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Karim Hasnaoui
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Fabien Cailliez
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Xiaojing Wu
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, 75005 Paris, France.
| | - Tzonka Mineva
- Matériaux Avancés pour la Catalyse et la Santé, UMR 5253 CNRS/UM/ENSCM, Institut Charles Gerhardt de Montpellier (ICGM) Montpellier CEDEX 5, 34090 Montpellier, France.
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse CEDEX 4, France.
| | - Patrizia Calaminici
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, Mexico.
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
| | - Luis López-Sosa
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
| | - Gerald Geudtner
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
| | - Isabelle Navizet
- Laboratoire Modélisation et Simulation Multi Échelle, Université Paris-Est, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, France.
| | - Cristina Garcia Iriepa
- Laboratoire Modélisation et Simulation Multi Échelle, Université Paris-Est, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, France.
| | - Dennis R Salahub
- Department of Chemistry, Centre for Molecular Simulation, Institute for Quantum Science and Technology and Quantum Alberta, University of Calgary, 2500 University Drive N.W., Calgary, AB T2N 1N4, Canada.
- College of Chemistry and Chemical Engineering, Henan University of Technology, No. 100, Lian Hua Street, High-Tech Development Zone, Zhengzhou 450001, China.
| | - Andreas M Köster
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, Mexico.
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
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18
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Aarabi M, Omidyan R, Soorkia S, Grégoire G, Broquier M, Crestoni ME, de la Lande A, Soep B, Shafizadeh N. The dramatic effect of N-methylimidazole on trans axial ligand binding to ferric heme: experiment and theory. Phys Chem Chem Phys 2019; 21:1750-1760. [PMID: 30623949 DOI: 10.1039/c8cp06210b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The binding energy of CO, O2 and NO to isolated ferric heme, [FeIIIP]+, was studied in the presence and absence of a σ donor (N-methylimidazole and histidine) as the trans axial ligand. This study combines the experimental determination of binding enthalpies by equilibrium measurements in a low temperature ion trap using the van't Hoff equation and high level DFT calculations. It was found that the presence of N-methylimidazole as the axial ligand on the [FeIIIP]+ porphyrin dramatically weakens the [FeIIIP-ligand]+ bond with an up to sevenfold decrease in binding energy owing to the σ donation by N-methylimidazole to the FeIII(3d) orbitals. This trans σ donor effect is characteristic of ligation to iron in hemes in both ferrous and ferric redox forms; however, to date, this has not been observed for ferric heme.
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Affiliation(s)
- Mohammad Aarabi
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran.
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19
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Le Poul N, Colasson B, Thiabaud G, Dit Fouque DJ, Iacobucci C, Memboeuf A, Douziech B, Řezáč J, Prangé T, de la Lande A, Reinaud O, Le Mest Y. Gating the electron transfer at a monocopper centre through the supramolecular coordination of water molecules within a protein chamber mimic. Chem Sci 2018; 9:8282-8290. [PMID: 30542577 PMCID: PMC6240898 DOI: 10.1039/c8sc03124j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 08/29/2018] [Indexed: 11/21/2022] Open
Abstract
Functionality of enzymes is strongly related to water dynamic processes.
Functionality of enzymes is strongly related to water dynamic processes. The control of the redox potential for metallo-enzymes is intimately linked to the mediation of water molecules in the first and second coordination spheres. Here, we report a unique example of supramolecular control of the redox properties of a biomimetic monocopper complex by water molecules. It is shown that the copper complex based on a calix[6]arene covalently capped with a tetradentate [tris(2-methylpyridyl)amine] (tmpa) core, embedding the metal ion in a hydrophobic cavity, can exist in three different states. The first system displays a totally irreversible redox behaviour. It corresponds to the reduction of the 5-coordinate mono-aqua-CuII complex, which is the thermodynamic species in the +II state. The second system is detected at a high redox potential. It is ascribed to an “empty cavity” or “water-free” state, where the CuI ion sits in a 4-coordinate trigonal environment provided by the tmpa cap. This complex is the thermodynamic species in the +I state under “dry conditions”. Surprisingly, a third redox system appears as the water concentration is increased. Under water-saturation conditions, it displays a pseudo-reversible behaviour at a low scan rate at the mid-point from the water-free and aqua species. This third system is not observed with the Cu-tmpa complex deprived of a cavity. In the calix[6]cavity environment, it is ascribed to a species where a pair of water molecules is hosted by the calixarene cavity. A molecular mechanism for the CuII/CuI redox process with an interplay of (H2O)x (x = 0, 1, 2) hosting is proposed on the basis of computational studies. Such an unusual behaviour is ascribed to the unexpected stabilization of the CuI state by inclusion of the pair of water molecules. This phenomenon strongly evidences the drastic influence of the interaction between water molecules and a hydrophobic cavity on controlling the thermodynamics and kinetics of the CuII/CuI electron transfer process.
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Affiliation(s)
- Nicolas Le Poul
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Benoit Colasson
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , UMR CNRS 8601 , Université Paris Descartes , 75006 Paris , France . ;
| | - Grégory Thiabaud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , UMR CNRS 8601 , Université Paris Descartes , 75006 Paris , France . ;
| | - Dany Jeanne Dit Fouque
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Claudio Iacobucci
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Antony Memboeuf
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Bénédicte Douziech
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Flemingovonám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Thierry Prangé
- Laboratoire de Cristallographie et de Résonance Magnétique Nucléaire , Biologiques (CNRS UMR 8015) , Université Paris Descartes , 4, Avenue de l'Observatoire , 75006 Paris , France .
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique , UMR CNRS 8000 , Université Paris Sud , 91405 Orsay , France .
| | - Olivia Reinaud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , UMR CNRS 8601 , Université Paris Descartes , 75006 Paris , France . ;
| | - Yves Le Mest
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
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20
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Shafizadeh N, Boyé-Péronne S, Soorkia S, Cunha de Miranda BK, Garcia GA, Nahon L, Chen S, de la Lande A, Poisson L, Soep B. The surprisingly high ligation energy of CO to ruthenium porphyrins. Phys Chem Chem Phys 2018; 20:11730-11739. [PMID: 29687125 DOI: 10.1039/c8cp01190g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined theoretical and experimental approach has been used to investigate the binding energy of a ruthenium metalloporphyrin ligated with CO, ruthenium tetraphenylporphyrin [RuII TPP], in the RuII oxidation degree. Measurements performed with VUV ionization using the DESIRS beamline at Synchrotron SOLEIL led to adiabatic ionization energies of [RuII TPP] and its complex with CO, [RuII TPP-CO], of 6.48 ± 0.03 eV and 6.60 ± 0.03 eV, respectively, while the ion dissociation threshold of [RuII TPP-CO]+ is measured to be 8.36 ± 0.03 eV using the ground-state neutral complex. These experimental data are used to derive the binding energies of the CO ligand in neutral and cationic complexes (1.88 ± 0.06 eV and 1.76 ± 0.06 eV, respectively) using a Born-Haber cycle. Density functional theory calculations, in very satisfactory agreement with the experimental results, help to get insights into the metal-ligand bond. Notably, the high ligation energies can be rationalized in terms of the ruthenium orbital structure, which is singular compared to that of the iron atom. Thus, beyond indications of a strengthening of the Ru-CO bond due to the decrease in the CO vibrational frequency in the complex as compared to the Fe-CO bond, high-level calculations are essential to accurately describe the metal ligand (CO) bond and show that the Ru-CO bond energy is strongly affected by the splitting of triplet and singlet spin states in uncomplexed [Ru TPP].
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Affiliation(s)
- Niloufar Shafizadeh
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, Université Paris-Sud, Orsay F-91405, France.
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21
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Wu X, Clavaguera C, Lagardère L, Piquemal JP, de la Lande A. AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms. J Chem Theory Comput 2018; 14:2705-2720. [PMID: 29630819 DOI: 10.1021/acs.jctc.7b01128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Møller-Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H2O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulations of cytochromes in two redox states with AMOEBA testing both the 2003 and 2014 AMOEBA water models. These simulations have been carried out with the TINKER-HP (High Performance) program. In conclusion, owing to their ubiquity in biology, we think the present work opens a wide array of applications of the polarizable AMOEBA force field on hemeproteins.
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Affiliation(s)
- Xiaojing Wu
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Carine Clavaguera
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Louis Lagardère
- Sorbonne Université, CNRS , Institut Parisien de Chimie Physique et Théorique (IP2CT) , 4 Place Jussieu , F-75005 , Paris , France.,Sorbonne Université , Institut des Sciences du Calcul et des Données (ISCD) , 4 place Jussieu , F-75005 , Paris , France
| | - Jean-Philip Piquemal
- Sorbonne Université, CNRS , Laboratoire de Chimie Théorique (LCT) , 4 Place Jussieu , F-75005 , Paris , France.,Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States.,Institut Universitaire de France , 75005 , Paris , France
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
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22
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Parise A, Alvarez-Ibarra A, Wu X, Zhao X, Pilmé J, Lande ADL. Quantum Chemical Topology of the Electron Localization Function in the Field of Attosecond Electron Dynamics. J Phys Chem Lett 2018; 9:844-850. [PMID: 29384381 DOI: 10.1021/acs.jpclett.7b03379] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report original analyses of attosecond electron dynamics of molecules subject to collisions by high energy charged particles based on Real-Time Time-Dependent-Density-Functional-Theory simulations coupled to Topological Analyses of the Electron Localization Function (TA-TD-ELF). We investigate irradiation of water and guanine. TA-TD-ELF enables qualitative and quantitative characterizations of bond breaking and formation, of charge migration within topological basins, or of electron attachment to the colliding particle. Whereas the Lewis-VSEPR structure of gas phase water is blown out within a few attoseconds after collision, that of guanine is far more robust and reconstitutes rapidly after impact even though the molecule remains electronically excited. This difference is accounted by the presence of the electron bath surrounding the impact point which enables energy relaxation within the molecule. Our approach should stimulate future studies to unravel the early steps following irradiation of various types of systems (isolated molecules, biomolecules, nanoclusters, solids, etc.) and is also readily applicable to irradiation by photons of various energies.
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Affiliation(s)
- Angela Parise
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS , Université Paris Saclay. 15 avenue Jean Perrin, F91405 Orsay, France
| | - Aurelio Alvarez-Ibarra
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS , Université Paris Saclay. 15 avenue Jean Perrin, F91405 Orsay, France
| | - Xiaojing Wu
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS , Université Paris Saclay. 15 avenue Jean Perrin, F91405 Orsay, France
| | - Xiaodong Zhao
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS , Université Paris Saclay. 15 avenue Jean Perrin, F91405 Orsay, France
| | - Julien Pilmé
- Laboratoire de Chimie Théorique, Sorbonne Universités, Université Pierre et Marie Curie, CNRS , F75005 Paris, France
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS , Université Paris Saclay. 15 avenue Jean Perrin, F91405 Orsay, France
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Wu X, Teuler JM, Cailliez F, Clavaguéra C, Salahub DR, de la Lande A. Simulating Electron Dynamics in Polarizable Environments. J Chem Theory Comput 2017; 13:3985-4002. [DOI: 10.1021/acs.jctc.7b00251] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaojing Wu
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Jean-Marie Teuler
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Fabien Cailliez
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Carine Clavaguéra
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Dennis R. Salahub
- Department
of Chemistry, Centre for Molecular Simulation, Institute for Quantum
Science and Technology and Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
- College
of Chemistry and Chemical Engineering, Henan University of Technology, No. 100, Lian Hua Street, High-Tech Development Zone, Zhengzhou 450001, P. R. China
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
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25
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Gillet N, Lévy B, Moliner V, Demachy I, de la Lande A. Theoretical estimation of redox potential of biological quinone cofactors. J Comput Chem 2017; 38:1612-1621. [PMID: 28470751 DOI: 10.1002/jcc.24802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 11/10/2022]
Abstract
Redox potentials are essential to understand biological cofactor reactivity and to predict their behavior in biological media. Experimental determination of redox potential in biological system is often difficult due to complexity of biological media but computational approaches can be used to estimate them. Nevertheless, the quality of the computational methodology remains a key issue to validate the results. Instead of looking to the best absolute results, we present here the calibration of theoretical redox potential for quinone derivatives in water coupling QM + MM or QM/MM scheme. Our approach allows using low computational cost theoretical level, ideal for long simulations in biological systems, and determination of the uncertainties linked to the calculations. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Natacha Gillet
- Laboratoire de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000. 15, rue Jean Perrin, 91405 Orsay, CEDEX, France.,Departament de Química Física i Analítica, Universitat Jaume I, Castellón, 12071, Spain
| | - Bernard Lévy
- Laboratoire de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000. 15, rue Jean Perrin, 91405 Orsay, CEDEX, France
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, Castellón, 12071, Spain.,Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Isabelle Demachy
- Laboratoire de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000. 15, rue Jean Perrin, 91405 Orsay, CEDEX, France
| | - Aurélien de la Lande
- Laboratoire de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000. 15, rue Jean Perrin, 91405 Orsay, CEDEX, France
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26
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Abstract
We have quantified the energetic contribution of charge transfer to halogen bonding to be about 10% of the interaction energy.
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Affiliation(s)
- Jan Řezáč
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- 166 10 Prague
- Czech Republic
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27
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Martin R, Lacombat F, Espagne A, Dozova N, Plaza P, Yamamoto J, Müller P, Brettel K, de la Lande A. Ultrafast flavin photoreduction in an oxidized animal (6-4) photolyase through an unconventional tryptophan tetrad. Phys Chem Chem Phys 2017; 19:24493-24504. [DOI: 10.1039/c7cp04555g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast photoreduction of animal (6-4) photolyase: delocalized oxidation hole reaches fourth tryptophan in less than 40 ps.
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Affiliation(s)
- Ryan Martin
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Fabien Lacombat
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Agathe Espagne
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Nadia Dozova
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Pascal Plaza
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Junpei Yamamoto
- Division of Chemistry
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | - Pavel Müller
- Institute for Integrative Biology of the Cell (I2BC)
- Joliot
- CEA
- CNRS
- Univ. Paris-Sud
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC)
- Joliot
- CEA
- CNRS
- Univ. Paris-Sud
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
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28
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Gillet N, Berstis L, Wu X, Gajdos F, Heck A, de la Lande A, Blumberger J, Elstner M. Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level. J Chem Theory Comput 2016; 12:4793-4805. [DOI: 10.1021/acs.jctc.6b00564] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Natacha Gillet
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Laura Berstis
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Xiaojing Wu
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, Université Paris Saclay, Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Fruzsina Gajdos
- Department
of Physics and Astronomy, University College London, Gower Street, London WCIE 6BT, United Kingdom
| | - Alexander Heck
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Aurélien de la Lande
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, Université Paris Saclay, Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Jochen Blumberger
- Department
of Physics and Astronomy, University College London, Gower Street, London WCIE 6BT, United Kingdom
| | - Marcus Elstner
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
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29
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Balcerzyk A, Schmidhammer U, Wang F, de la Lande A, Mostafavi M. Ultrafast Scavenging of the Precursor of H(•) Atom, (e(-), H3O(+)), in Aqueous Solutions. J Phys Chem B 2016; 120:9060-6. [PMID: 27472160 DOI: 10.1021/acs.jpcb.6b04944] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Picosecond pulse radiolysis measurements have been performed in several highly concentrated HClO4 and H3PO4 aqueous solutions containing silver ions at different concentrations. Silver ion reduction is used to unravel the ultrafast reduction reactions observed at the end of a 7 ps electron pulse. Solvated electrons and silver atoms are observed by the pulse (electron beam)-probe (supercontinuum light) method. In highly acidic solutions, ultrafast reduction of silver ions is observed, a finding that is not compatible with a reaction between the H(•) atom and silver ions, which is known to be thermally activated. In addition, silver ion reduction is found to be even more efficient in phosphoric acid solution than that in neutral solution. In the acidic solutions investigated here, the species responsible for the reduction of silver atoms is considered to be the precursor of the H(•) atom. This precursor, denoted (e(-), H3O(+)), is a pair constituting an electron (not fully solvated) and H3O(+). Its structure differs from that of the pair of a solvated electron and a hydronium ion (es(-), H3O(+)), which absorbs in the visible region. The (e(-), H3O(+)) pair , called the pre-H(•) atom here, undergoes ultrafast electron transfer and can, like the presolvated electron, reduce silver ions much faster than the H(•) atom. Moreover, it is found that with the same concentration of H3O(+) the reduction reaction is favored in the phosphoric acid solution compared to that in the perchloric acid solution because of the less-efficient electron solvation process. The kinetics show that among the three reducing species, (e(-), H3O(+)), (es(-), H3O(+)), and H(•) atom, the first one is the most efficient.
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Affiliation(s)
- Anna Balcerzyk
- Laboratoire de Chimie Physique, CNRS/Université Paris-Sud , Bâtiment 349, 91405 Orsay, France
| | - Uli Schmidhammer
- Laboratoire de Chimie Physique, CNRS/Université Paris-Sud , Bâtiment 349, 91405 Orsay, France
| | - Furong Wang
- Laboratoire de Chimie Physique, CNRS/Université Paris-Sud , Bâtiment 349, 91405 Orsay, France
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique, CNRS/Université Paris-Sud , Bâtiment 349, 91405 Orsay, France
| | - Mehran Mostafavi
- Laboratoire de Chimie Physique, CNRS/Université Paris-Sud , Bâtiment 349, 91405 Orsay, France
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30
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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31
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de la Lande A, Ha-Thi MH, Chen S, Soep B, Shafizadeh N. Structure of cobalt protoporphyrin chloride and its dimer, observation and DFT modeling. Phys Chem Chem Phys 2016; 18:16700-8. [DOI: 10.1039/c6cp02304e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this article we present a joint study by using time-of-flight mass spectroscopy and density functional theory of cobalt protoporphyrin dimer complexes.
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Affiliation(s)
- Aurélien de la Lande
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Minh-Huong Ha-Thi
- ISMO
- Univ Paris-Sud
- CNRS UMR 8214
- bat 210 Université Paris-Sud
- Université Paris Saclay
| | - Shufeng Chen
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Benoît Soep
- Laboratoire Francis Perrin CEA/DSM/IRAMIS/LIDyL – CNRS URA 2453
- CEA Saclay
- 91191 Gif-sur-Yvette Cedex
- France
| | - Niloufar Shafizadeh
- ISMO
- Univ Paris-Sud
- CNRS UMR 8214
- bat 210 Université Paris-Sud
- Université Paris Saclay
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32
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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33
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Balcerzyk A, Schmidhammer U, Horne G, Wang F, Ma J, Pimblott SM, de la Lande A, Mostafavi M. Unexpected Ultrafast Silver Ion Reduction: Dynamics Driven by the Solvent Structure. J Phys Chem B 2015; 119:10096-101. [DOI: 10.1021/acs.jpcb.5b04907] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anna Balcerzyk
- Laboratoire
de Chimie Physique, CNRS/Université Paris-Sud, Bâtiment
349, 91405 Orsay, France
| | - Uli Schmidhammer
- Laboratoire
de Chimie Physique, CNRS/Université Paris-Sud, Bâtiment
349, 91405 Orsay, France
| | - Gregory Horne
- Laboratoire
de Chimie Physique, CNRS/Université Paris-Sud, Bâtiment
349, 91405 Orsay, France
- Dalton
Cumbrian Facility, The University of Manchester, Westlakes Science and Technology
Park, Moor Row, Cumbria, CA24 3HA, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Furong Wang
- Laboratoire
de Chimie Physique, CNRS/Université Paris-Sud, Bâtiment
349, 91405 Orsay, France
| | - Jun Ma
- Laboratoire
de Chimie Physique, CNRS/Université Paris-Sud, Bâtiment
349, 91405 Orsay, France
| | - Simon M. Pimblott
- Dalton
Cumbrian Facility, The University of Manchester, Westlakes Science and Technology
Park, Moor Row, Cumbria, CA24 3HA, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique, CNRS/Université Paris-Sud, Bâtiment
349, 91405 Orsay, France
| | - Mehran Mostafavi
- Laboratoire
de Chimie Physique, CNRS/Université Paris-Sud, Bâtiment
349, 91405 Orsay, France
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34
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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35
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Narth C, Gillet N, Cailliez F, Lévy B, de la Lande A. Electron transfer, decoherence, and protein dynamics: insights from atomistic simulations. Acc Chem Res 2015; 48:1090-7. [PMID: 25730126 DOI: 10.1021/ar5002796] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electron transfer in biological systems drives the processes of life. From cellular respiration to photosynthesis and enzymatic catalysis, electron transfers (ET) are chemical processes on which essential biological functions rely. Over the last 40 years, scientists have sought understanding of how these essential processes function in biology. One important breakthrough was the discovery that Marcus theory (MT) of electron transfer is applicable to biological systems. Chemists have experimentally collected both the reorganization energies (λ) and the driving forces (ΔG°), two parameters of Marcus theory, for a large variety of ET processes in proteins. At the same time, theoretical chemists have developed computational approaches that rely on molecular dynamics and quantum chemistry calculations to access numerical estimates of λ and ΔG°. Yet another crucial piece in determining the rate of an electron transfer is the electronic coupling between the initial and final electronic wave functions. This is an important prefactor in the nonadiabatic rate expression, since it reflects the probability that an electron tunnels from the electron donor to the acceptor through the intervening medium. The fact that a protein matrix supports electron tunneling much more efficiently than vacuum is now well documented, both experimentally and theoretically. Meanwhile, many chemists have provided examples of the rich physical chemistry that can be induced by protein dynamics. This Account describes our studies of the dynamical effects on electron tunneling. We present our analysis of two examples of natural biological systems through MD simulations and tunneling pathway analyses. Through these examples, we show that protein dynamics sustain efficient tunneling. Second, we introduce two time scales: τcoh and τFC. The former characterizes how fast the electronic coupling varies with nuclear vibrations (which cause dephasing). The latter reflects the time taken by the system to leave the crossing region. In the framework of open quantum systems, τFC is a short time approximation of the characteristic decoherence time of the electronic subsystem in interaction with its nuclear environment. The comparison of the respective values of τcoh and τFC allows us to probe the occurrence of non-Condon effects. We use ab initio MD simulations to analyze how decoherence appears in several biological cofactors. We conclude that we cannot account for its order of magnitude by considering only the atoms or bonds directly concerned with the transfer. Decoherence results from contributions from all atoms of the system appearing with a time delay that increases with the distance from the primarily concerned atoms or bonds. The delay and magnitude of the contributions depend on the chemical nature of the system. Finally, we present recent developments based on constrained DFT for efficient and accurate evaluations of the electronic coupling in ab initio MD simulations. These are promising methods to study the subtle fluctuations of the electronic coupling and the mechanisms of electronic decoherence in biological systems.
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Affiliation(s)
- Christophe Narth
- Laboratoire
de Chimie Théorique, CNRS UMR 7616, Université Pierre et Marie Curie, case courrier 137. 4, Place Jussieu, 75252 Cedex 05 Paris, France
| | - Natacha Gillet
- Laboratoire
de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment
349 - Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Fabien Cailliez
- Laboratoire
de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment
349 - Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Bernard Lévy
- Laboratoire
de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment
349 - Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Aurélien de la Lande
- Laboratoire
de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment
349 - Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
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36
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Řezáč J, de la Lande A. Robust, Basis-Set Independent Method for the Evaluation of Charge-Transfer Energy in Noncovalent Complexes. J Chem Theory Comput 2015; 11:528-37. [DOI: 10.1021/ct501115m] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Řezáč
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique CNRS UMR 8000, Université Paris-Sud. Bât. 349, 15, rue Jean Perrin, 91405 Orsay Cedex, France
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37
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de la Lande A, Moliner V, Salahub D. Measurement and prediction of quantum coherence effects in biological processes. Phys Chem Chem Phys 2015; 17:30772-4. [DOI: 10.1039/c5cp90134k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This themed issue presents a collection of articles on the measurement and prediction of quantum coherence effects in biological processes.
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Affiliation(s)
| | - Vicent Moliner
- Departament de Química Física i Analítica
- Universitat Jaume 1
- 12071 Castelló
- Spain
| | - Dennis Salahub
- Department of Chemistry
- Centre for Molecular Simulation and Institute for Quantum Science and Technology
- University of Calgary
- Alberta
- Canada T2N 1N4
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Gillet N, Lévy B, Moliner V, Demachy I, de la Lande A. Electron and Hydrogen Atom Transfers in the Hydride Carrier Protein EmoB. J Chem Theory Comput 2014; 10:5036-46. [DOI: 10.1021/ct500173y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Natacha Gillet
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000, 15 rue Jean Perrin, 91405 Orsay CEDEX, France
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Bernard Lévy
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000, 15 rue Jean Perrin, 91405 Orsay CEDEX, France
| | - Vicent Moliner
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Isabelle Demachy
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000, 15 rue Jean Perrin, 91405 Orsay CEDEX, France
| | - Aurélien de la Lande
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000, 15 rue Jean Perrin, 91405 Orsay CEDEX, France
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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40
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Pilmé J, Luppi E, Bergès J, Houée-Lévin C, de la Lande A. Topological analyses of time-dependent electronic structures: application to electron-transfers in methionine enkephalin. J Mol Model 2014; 20:2368. [PMID: 25060148 DOI: 10.1007/s00894-014-2368-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/22/2014] [Indexed: 10/25/2022]
Abstract
We have studied electron transfers (ET) between electron donors and acceptors, taking as illustrative example the case of ET in methionine enkephalin. Recent pulse and gamma radiolysis experiments suggested that an ultrafast ET takes place from the C-terminal tyrosine residue to the N-terminal, oxidized, methionine residue. According to standard theoretical frameworks like the Marcus theory, ET can be decomposed into two successive steps: i) the achievement through thermal fluctuations, of a set of nuclear coordinates associated with degeneracy of the two electronic states, ii) the electron tunneling from the donor molecular orbital to the acceptor molecular orbital. Here, we focus on the analysis of the time-dependent electronic dynamics during the tunneling event. This is done by extending the approaches based on the topological analyses of stationary electronic density and of the electron localization function (ELF) to the time-dependent domain. Furthermore, we analyzed isosurfaces of the divergence of the current density, showing the paths that are followed by the tunneling electron from the donor to the acceptor. We show how these functions can be calculated with constrained density functional theory. Beyond this work, the topological tools used here can open up new opportunities for the electronic description in the time-dependent domain.
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Affiliation(s)
- Julien Pilmé
- Laboratoire de Chimie Théorique, UPMC Université Paris 06, UMR 7616, F-75005, Paris, France,
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Brugnara A, Topić F, Rissanen K, Lande ADL, Colasson B, Reinaud O. Selective recognition of fluoride anion in water by a copper(ii) center embedded in a hydrophobic cavity. Chem Sci 2014. [DOI: 10.1039/c4sc01457j] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
CuII coordination combined with hydrophobic pocket hosting allows for strong and selective fluoride binding in water at near neutral pH.
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Affiliation(s)
- Andrea Brugnara
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques
- CNRS UMR 8601
- Université Paris Descartes
- 75006 Paris, France
| | - Filip Topić
- Department of Chemistry
- Nanoscience Center
- University of Jyväskylä
- 40014 Jyväskylä, Finland
| | - Kari Rissanen
- Department of Chemistry
- Nanoscience Center
- University of Jyväskylä
- 40014 Jyväskylä, Finland
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique
- CNRS UMR 8000
- Université Paris-Sud 11
- 91400 Orsay, France
| | - Benoit Colasson
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques
- CNRS UMR 8601
- Université Paris Descartes
- 75006 Paris, France
| | - Olivia Reinaud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques
- CNRS UMR 8601
- Université Paris Descartes
- 75006 Paris, France
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Narth C, Gillet N, Lévy B, Demachy I, de la Lande A. Investigation of the molecular mechanisms of electronic decoherence within a quinone cofactor. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0529] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The notion of decoherence is particularly adapted to discuss the quantum-to-classical transition in the context of chemical reactions. Decoherence can be modeled by computing the time evolution of nuclear wave packets evolving on distinct potential energy surfaces, here using density functional theory (DFT) and Born–Oppenheimer molecular dynamics simulations. We investigate a redox cofactor of biological interest (tryptophan tryptophylquinone, TTQ) found in the enzyme methylamine dehydrogenase. We also report the first systematic comparison of semi-empirical DFT (tight-binding DFT) and classical force field approaches for estimating decoherence in molecular systems. In the TTQ cofactor, we find that decoherence combines structural and dynamical aspects: it is initiated by the divergent motions of few atoms and then propagates dynamically to the remaining atoms. It is the mass effect of all the atoms that leads to decoherence within a few femtosecond.
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Affiliation(s)
- Christophe Narth
- Laboratoire de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment 349 - Campus d’Orsay, 15, avenue Jean Perrin, 91 405 Orsay Cedex, France
- Laboratoire de Chimie Théorique, CNRS UMR 7616, Université Pierre et Marie Curie, case courrier 137, 4, Place Jussieu, 75 252 Paris Cedex 05, France
| | - Natacha Gillet
- Laboratoire de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment 349 - Campus d’Orsay, 15, avenue Jean Perrin, 91 405 Orsay Cedex, France
| | - Bernard Lévy
- Laboratoire de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment 349 - Campus d’Orsay, 15, avenue Jean Perrin, 91 405 Orsay Cedex, France
| | - Isabelle Demachy
- Laboratoire de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment 349 - Campus d’Orsay, 15, avenue Jean Perrin, 91 405 Orsay Cedex, France
| | - Aurélien de la Lande
- Laboratoire de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment 349 - Campus d’Orsay, 15, avenue Jean Perrin, 91 405 Orsay Cedex, France
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El Hammi E, Houée-Lévin C, Řezáč J, Lévy B, Demachy I, Baciou L, de la Lande A. New insights into the mechanism of electron transfer within flavohemoglobins: tunnelling pathways, packing density, thermodynamic and kinetic analyses. Phys Chem Chem Phys 2012; 14:13872-80. [PMID: 22948361 DOI: 10.1039/c2cp41261f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Flavohemoglobins (FlavoHb) are metalloenzymes catalyzing the reaction of nitric oxide dioxygenation. The iron cation of the heme group needs to be preliminarily reduced to the ferrous state to be catalytically competent. This reduction is triggered by a flavin adenine dinucleotide (FAD) prosthetic group which is localized in a distinct domain of the protein. In this paper we obtain new insights into the internal long range electron transfer (over ca. 12 Å) using a combination of experimental and computational approaches. Employing a time-resolved pulse radiolysis technique we report the first direct measurement of the FADH˙→ HemeFe(III) electron transfer rate. A rate constant of (6.8 ± 0.5) × 10(3) s(-1) is found. A large panel of computational approaches are used to provide the first estimation of the thermodynamic characteristics of the internal electron transfer step within flavoHb: both the driving force and the reorganization energy are estimated as a function of the protonated state of the flavin semi-quinone. We also report an analysis of the electron pathways involved in the tunnelling of the electron through the aqueous interface between the globin and the flavin domains.
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Affiliation(s)
- Emna El Hammi
- Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud. Bât. 349-350, Campus d'Orsay. 15, avenue Jean Perrin, 91405 Orsay Cedex, France
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Řezáč J, Lévy B, Demachy I, de la Lande A. Robust and Efficient Constrained DFT Molecular Dynamics Approach for Biochemical Modeling. J Chem Theory Comput 2012; 8:418-27. [DOI: 10.1021/ct200570u] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Bernard Lévy
- Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris-Sud. Bât. 349, Campus d’Orsay, 15 rue Jean Perrin, 91405 Orsay Cedex, France
| | - Isabelle Demachy
- Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris-Sud. Bât. 349, Campus d’Orsay, 15 rue Jean Perrin, 91405 Orsay Cedex, France
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris-Sud. Bât. 349, Campus d’Orsay, 15 rue Jean Perrin, 91405 Orsay Cedex, France
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Lande ADL, Babcock NS, Řezáč J, Lévy B, Sanders BC, Salahub DR. Quantum effects in biological electron transfer. Phys Chem Chem Phys 2012; 14:5902-18. [DOI: 10.1039/c2cp21823b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bonniard L, de la Lande A, Ulmer S, Piquemal JP, Parisel O, Gérard H. Competitive ligand/chelate binding in [Cu(TMPA)]+ and [Cu(tren)]+ based complexes. Catal Today 2011. [DOI: 10.1016/j.cattod.2011.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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de la Lande A, Řezáč J, Lévy B, Sanders BC, Salahub DR. Transmission coefficients for chemical reactions with multiple states: role of quantum decoherence. J Am Chem Soc 2011; 133:3883-94. [PMID: 21344903 DOI: 10.1021/ja107950m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transition-state theory (TST) is a widely accepted paradigm for rationalizing the kinetics of chemical reactions involving one potential energy surface (PES). Multiple PES reaction rate constants can also be estimated within semiclassical approaches provided the hopping probability between the quantum states is taken into account when determining the transmission coefficient. In the Marcus theory of electron transfer, this hopping probability was historically calculated with models such as Landau-Zener theory. Although the hopping probability is intimately related to the question of the transition from the fully quantum to the semiclassical description, this issue is not adequately handled in physicochemical models commonly in use. In particular, quantum nuclear effects such as decoherence or dephasing are not present in the rate constant expressions. Retaining the convenient semiclassical picture, we include these effects through the introduction of a phenomenological quantum decoherence function. A simple modification to the usual TST rate constant expression is proposed: in addition to the electronic coupling, a characteristic decoherence time τ(dec) now also appears as a key parameter of the rate constant. This new parameter captures the idea that molecular systems, although intrinsically obeying quantum mechanical laws, behave semiclassically after a finite but nonzero amount of time (τ(dec)). This new degree of freedom allows a fresh look at the underlying physics of chemical reactions involving more than one quantum state. The ability of the proposed formula to describe the main physical lines of the phenomenon is confirmed by comparison with results obtained from density functional theory molecular dynamics simulations for a triplet to singlet transition within a copper dioxygen adduct relevant to the question of dioxygen activation by copper monooxygenases.
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Affiliation(s)
- Aurélien de la Lande
- Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud 11, Bât. 349, Campus d'Orsay, 15 rue Jean Perrin, 91 405 Orsay Cedex, France.
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Abstract
We present a new QM/MM interface for fast and efficient simulations of organic and biological molecules. The CHARMM/deMon interface has been developed and tested to perform minimization and atomistic simulations for multi-particle systems. The current features of this QM/MM interface include readability for molecular dynamics, tested compatibility with Free Energy Perturbation simulations (FEP) using the dual topology/single coordinate method. The current coupling scheme uses link atoms, but further extensions of the code to incorporate other available schemes are planned. We report the performance of different levels of theory for the treatment of the QM region, while the MM region was represented by a classical force-field (CHARMM27) or a polarizable force-field based on a simple Drude model. The current QM/MM implementation can be coupled to the dual-thermostat method and the VV2 integrator to run molecular dynamics simulations.
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Affiliation(s)
- Bogdan Lev
- Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
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de la Lande A, Salahub DR. Derivation of interpretative models for long range electron transfer from constrained density functional theory. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.11.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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de la Lande A, Salahub D, Moliner V, Gérard H, Piquemal JP, Parisel O. Dioxygen Activation by Mononuclear Copper Enzymes: Insights from a Tripodal Ligand Mimicking Their CuM Coordination Sphere. Inorg Chem 2009; 48:7003-5. [DOI: 10.1021/ic900567z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Aurélien de la Lande
- UPMC Université Paris 6 and CNRS, UMR 7616, Laboratoire de Chimie Théorique, 4 place Jussieu, 75252 Paris Cedex 05, France
- Department of Chemistry and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Dennis Salahub
- Department of Chemistry and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, Box 224, SP-12080 Castelló, Spain
| | - Hélène Gérard
- UPMC Université Paris 6 and CNRS, UMR 7616, Laboratoire de Chimie Théorique, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - Jean-Philip Piquemal
- UPMC Université Paris 6 and CNRS, UMR 7616, Laboratoire de Chimie Théorique, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - Olivier Parisel
- UPMC Université Paris 6 and CNRS, UMR 7616, Laboratoire de Chimie Théorique, 4 place Jussieu, 75252 Paris Cedex 05, France
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