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Gerhards L, Werr M, Hübner O, Solov'yov IA, Himmel HJ. Peculiar Differences between Two Copper Complexes Containing Similar Redox-Active Ligands: Density Functional and Multiconfigurational Calculations. Inorg Chem 2024; 63:961-975. [PMID: 38157840 DOI: 10.1021/acs.inorgchem.3c02949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Transition metal complexes featuring redox-active ligands often exhibit multiple redox states, influenced by the interplay between the metal center and the ligand. This study delves into the electronic structures of two mononuclear complexes of copper with two similar redox-active urea azine ligands. The ligands differ by the replacement of an NCH3 moiety by an S atom in the ligand backbone. Experimental analysis yields pronounced electronic structural disparities between these complexes, observable in both the solution and solid phases. Conventional quantum chemical methods, such as density functional theory using different functionals (B3LYP, TPSSh, and CAM-B3LYP), remain inadequate to rationalize the observed spectroscopic anomalies. However, a multiconfigurational approach elucidates the disparate behaviors of these complexes. Multireference perturbation theory, based on complete active space self-consistent field computations, identifies Cu(I) in the case of the complex with the NCH3 containing ligands and a state with substantial Cu(II) contributions in the case of the complex with the S atom containing ligands. In contrast, DFT indicates Cu(I) in both scenarios.
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Affiliation(s)
- Luca Gerhards
- Institute of Physics, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Street 9-11, Oldenburg 26129, Germany
| | - Marco Werr
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
| | - Olaf Hübner
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Street 9-11, Oldenburg 26129, Germany
- Research Center for Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Oldenburg 26111, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von OssietzkyUniversität Oldenburg, Institut Für Physik, Ammerländer Heerstreet 114-118, Oldenburg 26129, Germany
| | - Hans-Jörg Himmel
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
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2
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Qin X, Hansen HA, Honkala K, Melander MM. Cation-induced changes in the inner- and outer-sphere mechanisms of electrocatalytic CO 2 reduction. Nat Commun 2023; 14:7607. [PMID: 37993426 PMCID: PMC10665450 DOI: 10.1038/s41467-023-43300-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023] Open
Abstract
The underlying mechanism of cation effects on CO2RR remains debated. Herein, we study cation effects by simulating both outer-sphere electron transfer (OS-ET) and inner-sphere electron transfer (IS-ET) pathways during CO2RR via constrained density functional theory molecular dynamics (cDFT-MD) and slow-growth DFT-MD (SG-DFT-MD), respectively. Our results show without any cations, only OS-ET is feasible with a barrier of 1.21 eV. In the presence of K+ (Li+), OS-ET shows a very high barrier of 2.93 eV (4.15 eV) thus being prohibited. However, cations promote CO2 activation through IS-ET with the barrier of only 0.61 eV (K+) and 0.91 eV (Li+), generating the key intermediate (adsorbed CO[Formula: see text]). Without cations, CO2-to-CO[Formula: see text](ads) conversion cannot proceed. Our findings reveal cation effects arise from short-range Coulomb interactions with reaction intermediates. These results disclose that cations modulate the inner- and outer-sphere pathways of CO2RR, offering substantial insights on the cation specificity in the initial CO2RR steps.
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Affiliation(s)
- Xueping Qin
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs. Lyngby, 2800, Denmark.
| | - Heine A Hansen
- Department of Energy Conversion and Storage, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs. Lyngby, 2800, Denmark
| | - Karoliina Honkala
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
| | - Marko M Melander
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland.
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3
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Salerno KM, Domenico J, Le NQ, Balakrishnan K, McQuillen RJ, Stiles CD, Solov'yov IA, Martino CF. Long-Time Oxygen and Superoxide Localization in Arabidopsis thaliana Cryptochrome. J Chem Inf Model 2023; 63:6756-6767. [PMID: 37874902 DOI: 10.1021/acs.jcim.3c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Cryptochromes are proteins that are highly conserved across species and in many instances bind the flavin adenine dinucleotide (FAD) cofactor within their photolyase-homology region (PHR) domain. The FAD cofactor has multiple redox states that help catalyze reactions, and absorbs photons at about 450 nm, a feature linked to the light-related functions of cryptochrome proteins. Reactive oxygen species (ROS) are produced from redox reactions involving molecular oxygen and are involved in a myriad of biological processes. Superoxide O2•- is an exemplary ROS that may be formed through electron transfer from FAD to O2, generating an electron radical pair. Although the formation of a superoxide-FAD radical pair has been speculated, it is still unclear if the required process steps could be realized in cryptochrome. Here, we present results from molecular dynamics (MD) simulations of oxygen interacting with the PHR domain of Arabidopsis thaliana cryptochrome 1 (AtCRY1). Using MD simulation trajectories, oxygen binding locations are characterized through both the O2-FAD intermolecular distance and the local protein environment. Oxygen unbinding times are characterized through replica simulations of the bound oxygen. Simulations reveal that oxygen molecules can localize at certain sites within the cryptochrome protein for tens of nanoseconds, and superoxide molecules can localize for significantly longer. This relatively long-duration molecule binding suggests the possibility of an electron-transfer reaction leading to superoxide formation. Estimates of electron-transfer rates using the Marcus theory are performed for the identified potential binding sites. Molecular oxygen binding results are compared with recent results demonstrating long-time oxygen binding within the electron-transfer flavoprotein (ETF), another FAD binding protein.
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Affiliation(s)
- K Michael Salerno
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Janna Domenico
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Nam Q Le
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Krithika Balakrishnan
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Ryan J McQuillen
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Christopher D Stiles
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
- Centre for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
- Centre for Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
| | - Carlos F Martino
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
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4
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Krishnan S, Aksimentiev A, Lindsay S, Matyushov D. Long-Range Conductivity in Proteins Mediated by Aromatic Residues. ACS PHYSICAL CHEMISTRY AU 2023; 3:444-455. [PMID: 37780537 PMCID: PMC10540285 DOI: 10.1021/acsphyschemau.3c00017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 09/30/2023]
Abstract
Single-molecule measurements show that many proteins, lacking any redox cofactors, nonetheless exhibit electrical conductance on the order of a nanosiemen over 10 nm distances, implying that electrons can transit an entire protein in less than a nanosecond when subject to a potential difference of less than 1 V. This is puzzling because, for fast transport (i.e., a free energy barrier of zero), the hopping rate is determined by the reorganization energy of approximately 0.8 eV, and this sets the time scale of a single hop to at least 1 μs. Furthermore, the Fermi energies of typical metal electrodes are far removed from the energies required for sequential oxidation and reduction of the aromatic residues of the protein, which should further reduce the hopping current. Here, we combine all-atom molecular dynamics (MD) simulations of non-redox-active proteins (consensus tetratricopeptide repeats) with an electron transfer theory to demonstrate a molecular mechanism that can account for the unexpectedly fast electron transport. According to our MD simulations, the reorganization energy produced by the energy shift on charging (the Stokes shift) is close to the conventional value of 0.8 eV. However, the non-ergodic sampling of molecular configurations by the protein results in reaction-reorganization energies, extracted directly from the distribution of the electrostatic energy fluctuations, that are only ∼0.2 eV, which is small enough to enable long-range conductivity, without invoking quantum coherent transport. Using the MD values of the reorganization energies, we calculate a current decay with distance that is in agreement with experiment.
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Affiliation(s)
- Siddharth Krishnan
- Department
of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department
of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stuart Lindsay
- Department
of Physics, Arizona State University, Tempe, Arizona 85281, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Dmitry Matyushov
- Department
of Physics, Arizona State University, Tempe, Arizona 85281, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
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Salerno KM, Domenico J, Le NQ, Stiles CD, Solov’yov IA, Martino CF. Long-Time Oxygen Localization in Electron Transfer Flavoprotein. J Chem Inf Model 2022; 62:4191-4199. [PMID: 35998902 PMCID: PMC9472800 DOI: 10.1021/acs.jcim.2c00430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Indexed: 11/30/2022]
Abstract
Reactive oxygen species (ROS) exert a wide range of biological effects from beneficial regulatory function to deleterious oxidative stress. The electron transfer flavoprotein (ETF) is ubiquitous to life and is associated with aerobic metabolism and ROS production due to its location in the mitochondria. Quantifying oxygen localization within the ETF complex is critical for understanding the potential for electron transfer and radical pair formation between flavin adenine dinucleotide (FAD) cofactor and superoxide during ROS formation. Our study employed all-atom molecular dynamics simulations and identified several novel, long-lived oxygen binding sites within the ETF complex that appear near the FAD cofactor. Site locations, the local electrostatic environment, and characteristic oxygen binding times for each site were evaluated to establish factors that may lead to possible charge transfer reactions and superoxide formation within the ETF complex. The study revealed that some oxygen binding sites are naturally linked to protein domain features, suggesting opportunities to engineer and control ROS production and subsequent dynamics.
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Affiliation(s)
- K. Michael Salerno
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
| | - Janna Domenico
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
| | - Nam Q. Le
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
| | - Christopher D. Stiles
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University
Oldenburg, Carl von Ossietzky
Straße 9-11, 26129 Oldenburg, Germany
- Centre
for Neurosensory Science, Carl von Ossietzky
University Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
| | - Carlos F. Martino
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
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