1
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Barrios Herrera L, Lourenço MP, Hostaš J, Calaminici P, Köster AM, Tchagang A, Salahub DR. Active-learning for global optimization of Ni-Ceria nanoparticles: The case of Ce 4-xNi xO 8- x (x = 1, 2, 3). J Comput Chem 2024; 45:1643-1656. [PMID: 38551129 DOI: 10.1002/jcc.27346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/15/2024] [Accepted: 03/05/2024] [Indexed: 06/04/2024]
Abstract
Ni-CeO2 nanoparticles (NPs) are promising nanocatalysts for water splitting and water gas shift reactions due to the ability of ceria to temporarily donate oxygen to the catalytic reaction and accept oxygen after the reaction is completed. Therefore, elucidating how different properties of the Ni-Ceria NPs relate to the activity and selectivity of the catalytic reaction, is of crucial importance for the development of novel catalysts. In this work the active learning (AL) method based on machine learning regression and its uncertainty is used for the global optimization of Ce(4-x)NixO(8-x) (x = 1, 2, 3) nanoparticles, employing density functional theory calculations. Additionally, further investigation of the NPs by mass-scaled parallel-tempering Born-Oppenheimer molecular dynamics resulted in the same putative global minimum structures found by AL, demonstrating the robustness of our AL search to learn from small datasets and assist in the global optimization of complex electronic structure systems.
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Affiliation(s)
- Lizandra Barrios Herrera
- Department of Chemistry, Department of Physics and Astronomy, CMS Centre for Molecular Simulation, IQST Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Canada
| | - Maicon Pierre Lourenço
- Departamento de Química e Física, Centro de Ciências Exatas, Naturais e da Saúde (CCENS), Universidade Federal do Espírito Santo, Espírito Santo, Brasil
| | - Jiří Hostaš
- Department of Chemistry, Department of Physics and Astronomy, CMS Centre for Molecular Simulation, IQST Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Canada
- Digital Technologies Research Centre, National Research Council of Canada, Ottawa, Canada
| | | | | | - Alain Tchagang
- Digital Technologies Research Centre, National Research Council of Canada, Ottawa, Canada
| | - Dennis R Salahub
- Department of Chemistry, Department of Physics and Astronomy, CMS Centre for Molecular Simulation, IQST Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Canada
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2
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Jiang H, Ryde U. Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand. Dalton Trans 2024; 53:11500-11513. [PMID: 38916132 DOI: 10.1039/d4dt00937a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
We have studied whether dissociation of the S2B sulfide ligand from one of its two coordinating Fe ions may affect the later parts of the reaction mechanism of nitrogenase. Such dissociation has been shown to be favourable for the E2-E4 states in the reaction mechanism, but previous studies have assumed that S2B either remains bridging or has fully dissociated from the active-site FeMo cluster. We employ combined quantum mechanical and molecular mechanical (QM/MM) calculations with two density-functional theory methods, r2SCAN and TPSSh. To make dissociation of S2B possible, we have added a proton to this group throughout the reaction. We study the reaction starting from the E4 state with N2H2 bound to the cluster. Our results indicate that half-dissociation of S2B is unfavourable in most steps of the reaction mechanism. We observe favourable half-dissociation of S2B only when NH or NH2 is bound to the cluster, bridging Fe2 and Fe6. However, the former state is most likely not involved in the reaction mechanism and the latter state is only an intermittent intermediate of the E7 state. Therefore, half-dissociation of S2B seems to play only a minor role in the later parts of the reaction mechanism of nitrogenase. Our suggested mechanism with a protonated S2B is alternating (the two N atoms of the substrate is protonated in an alternating manner) and the substrate prefers to bind to Fe2, in contrast to the preferred binding to Fe6 observed when S2B is unprotonated and bridging Fe2 and Fe6.
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Affiliation(s)
- Hao Jiang
- Department of Computational Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
| | - Ulf Ryde
- Department of Computational Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
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3
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Leyser da Costa Gouveia T, Maganas D, Neese F. Restricted Open-Shell Hartree-Fock Method for a General Configuration State Function Featuring Arbitrarily Complex Spin-Couplings. J Phys Chem A 2024; 128:5041-5053. [PMID: 38886177 PMCID: PMC11215774 DOI: 10.1021/acs.jpca.4c00688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024]
Abstract
In this work, we present a general spin restricted open-shell Hartree-Fock (ROHF) implementation that is able to generate self-consistent field (SCF) wave functions for an arbitrary configuration state function (CSF). These CSFs can contain an arbitrary number of unpaired electrons in arbitrary spin-couplings. The resulting method is named CSF-ROHF. We demonstrate that starting from the ROHF energy expression, for example, the one given by Edwards and Zerner, it is possible to obtain the values of the ROHF vector-coupling coefficients by setting up an open-shell for each group of consecutive parallel-coupled spins dictated by the unique spin-coupling pattern of any given CSF. To achieve this important and nontrivial goal, we employ the machinery of the iterative configuration expansion configuration interaction (ICE-CI) method, which is able to tackle general CI problems on the basis of spin-adapted CSFs. This development allows for the efficient generation of SCF spin-eigenfunctions for systems with complex spin-coupling patterns, such as polymetallic chains and metal clusters, while maintaining SCF scaling with system size (quadratic or less, depending on the specific algorithm and approximations chosen).
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Affiliation(s)
| | - Dimitrios Maganas
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Frank Neese
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
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4
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Ansari M, Bhattacharjee S, Pantazis DA. Correlating Structure with Spectroscopy in Ascorbate Peroxidase Compound II. J Am Chem Soc 2024; 146:9640-9656. [PMID: 38530124 PMCID: PMC11009960 DOI: 10.1021/jacs.3c13169] [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: 11/23/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/27/2024]
Abstract
Structural and spectroscopic investigations of compound II in ascorbate peroxidase (APX) have yielded conflicting conclusions regarding the protonation state of the crucial Fe(IV) intermediate. Neutron diffraction and crystallographic data support an iron(IV)-hydroxo formulation, whereas Mössbauer, X-ray absorption (XAS), and nuclear resonance vibrational spectroscopy (NRVS) studies appear consistent with an iron(IV)-oxo species. Here we examine APX with spectroscopy-oriented QM/MM calculations and extensive exploration of the conformational space for both possible formulations of compound II. We establish that irrespective of variations in the orientation of a vicinal arginine residue and potential reorganization of proximal water molecules and hydrogen bonding, the Fe-O distances for the oxo and hydroxo forms consistently fall within distinct, narrow, and nonoverlapping ranges. The accuracy of geometric parameters is validated by coupled-cluster calculations with the domain-based local pair natural orbital approach, DLPNO-CCSD(T). QM/MM calculations of spectroscopic properties are conducted for all structural variants, encompassing Mössbauer, optical, X-ray absorption, and X-ray emission spectroscopies and NRVS. All spectroscopic observations can be assigned uniquely to an Fe(IV)═O form. A terminal hydroxy group cannot be reconciled with the spectroscopic data. Under no conditions can the Fe(IV)═O distance be sufficiently elongated to approach the crystallographically reported Fe-O distance. The latter is consistent only with a hydroxo species, either Fe(IV) or Fe(III). Our findings strongly support the Fe(IV)═O formulation of APX-II and highlight unresolved discrepancies in the nature of samples used across different experimental studies.
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Affiliation(s)
- Mursaleem Ansari
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
| | - Sinjini Bhattacharjee
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
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5
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Levin G, Yasmin M, Pieńko T, Yehishalom N, Hanna R, Kleifeld O, Glaser F, Schuster G. The protein phosphorylation landscape in photosystem I of the desert algae Chlorella sp. THE NEW PHYTOLOGIST 2024; 242:544-557. [PMID: 38379464 DOI: 10.1111/nph.19603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/28/2024] [Indexed: 02/22/2024]
Abstract
The phosphorylation of photosystem II (PSII) and its antenna (LHCII) proteins has been studied, and its involvement in state transitions and PSII repair is known. Yet, little is known about the phosphorylation of photosystem I (PSI) and its antenna (LHCI) proteins. Here, we applied proteomics analysis to generate a map of the phosphorylation sites of the PSI-LHCI proteins in Chlorella ohadii cells that were grown under low or extreme high-light intensities (LL and HL). Furthermore, we analyzed the content of oxidized tryptophans and PSI-LHCI protein degradation products in these cells, to estimate the light-induced damage to PSI-LHCI. Our work revealed the phosphorylation of 17 of 22 PSI-LHCI subunits. The analyses detected the extensive phosphorylation of the LHCI subunits Lhca6 and Lhca7, which is modulated by growth light intensity. Other PSI-LHCI subunits were phosphorylated to a lesser extent, including PsaE, where molecular dynamic simulation proposed that a phosphoserine stabilizes ferredoxin binding. Additionally, we show that HL-grown cells accumulate less oxidative damage and degradation products of PSI-LHCI proteins, compared with LL-grown cells. The significant phosphorylation of Lhca6 and Lhca7 at the interface with other LHCI subunits suggests a physiological role during photosynthesis, possibly by altering light-harvesting characteristics and binding of other subunits.
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Affiliation(s)
- Guy Levin
- Faculty of Biology, Technion, Haifa, 32000, Israel
| | | | - Tomasz Pieńko
- Schulich Faculty of Chemistry, Technion, Haifa, 32000, Israel
| | | | - Rawad Hanna
- Faculty of Biology, Technion, Haifa, 32000, Israel
| | | | - Fabian Glaser
- The Lorry I. Lokey Center for Life Sciences and Engineering, Technion, Haifa, 32000, Israel
| | - Gadi Schuster
- Faculty of Biology, Technion, Haifa, 32000, Israel
- Grand Technion Energy Program, Technion, Haifa, 32000, Israel
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6
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Vysotskiy VP, Filippi C, Ryde U. Scalar Relativistic All-Electron and Pseudopotential Ab Initio Study of a Minimal Nitrogenase [Fe(SH) 4H] - Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods. J Phys Chem A 2024; 128:1358-1374. [PMID: 38324717 PMCID: PMC10895656 DOI: 10.1021/acs.jpca.3c05808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/09/2024]
Abstract
Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to organisms. The detailed mechanism of this enzyme is currently not known, and computational studies are complicated by the fact that different density functional theory (DFT) methods give very different energetic results for calculations involving nitrogenase models. Recently, we designed a [Fe(SH)4H]- model with the fifth proton binding either to Fe or S to mimic different possible protonation states of the nitrogenase active site. We showed that the energy difference between these two isomers (ΔE) is hard to estimate with quantum-mechanical methods. Based on nonrelativistic single-reference coupled-cluster (CC) calculations, we estimated that the ΔE is 101 kJ/mol. In this study, we demonstrate that scalar relativistic effects play an important role and significantly affect ΔE. Our best revised single-reference CC estimates for ΔE are 85-91 kJ/mol, including energy corrections to account for contributions beyond triples, core-valence correlation, and basis-set incompleteness error. Among coupled-cluster approaches with approximate triples, the canonical CCSD(T) exhibits the largest error for this problem. Complementary to CC, we also used phaseless auxiliary-field quantum Monte Carlo calculations (ph-AFQMC). We show that with a Hartree-Fock (HF) trial wave function, ph-AFQMC reproduces the CC results within 5 ± 1 kJ/mol. With multi-Slater-determinant (MSD) trials, the results are 82-84 ± 2 kJ/mol, indicating that multireference effects may be rather modest. Among the DFT methods tested, τ-HCTH, r2SCAN with 10-13% HF exchange with and without dispersion, and O3LYP/O3LYP-D4, and B3LYP*/B3LYP*-D4 generally perform the best. The r2SCAN12 (with 12% HF exchange) functional mimics both the best reference MSD ph-AFQMC and CC ΔE results within 2 kJ/mol.
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Affiliation(s)
- Victor P. Vysotskiy
- Department
of Computational Chemistry, Lund University,
Chemical Centre, SE-221 00 Lund, Sweden
| | - Claudia Filippi
- MESA+
Institute for Nanotechnology, University
of Twente, P.O. Box 217, Enschede 7500 AE, Netherlands
| | - Ulf Ryde
- Department
of Computational Chemistry, Lund University,
Chemical Centre, SE-221 00 Lund, Sweden
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7
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Jiang H, Ryde U. H 2 formation from the E 2-E 4 states of nitrogenase. Phys Chem Chem Phys 2024; 26:1364-1375. [PMID: 38108422 DOI: 10.1039/d3cp05181a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Nitrogenase is the only enzyme that can cleave the strong triple bond in N2, making nitrogen available for biological lifeforms. The active site is a MoFe7S9C cluster (the FeMo cluster) that binds eight electrons and protons during one catalytic cycle, giving rise to eight intermediate states E0-E7. It is experimentally known that N2 binds to the E4 state and that H2 is a compulsory byproduct of the reaction. However, formation of H2 is also an unproductive side reaction that should be avoided, especially in the early steps of the reaction mechanism (E2 and E3). Here, we study the formation of H2 for various structural interpretations of the E2-E4 states using combined quantum mechanical and molecular mechanical (QM/MM) calculations and four different density-functional theory methods. We find large differences in the predictions of the different methods. B3LYP strongly favours protonation of the central carbide ion and H2 cannot form from such structures. On the other hand, with TPSS, r2SCAN and TPSSh, H2 formation is strongly exothermic for all structures and En and therefore need strict kinetic control to be avoided. For the E2 state, the kinetic barriers for the low-energy structures are high enough to avoid H2 formation. However, for both the E3 and E4 states, all three methods predict that the best structure has two hydride ions bridging the same pair of Fe ions (Fe2 and Fe6) and these two ions can combine to form H2 with an activation barrier of only 29-57 kJ mol-1, corresponding to rates of 7 × 102 to 5 × 107 s-1, i.e. much faster than the turnover rate of the enzyme (1-5 s-1). We have also studied H-atom movements within the FeMo cluster, showing that the various protonation states can quite freely be interconverted (activation barriers of 12-69 kJ mol-1).
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Affiliation(s)
- Hao Jiang
- Department of Computational Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
| | - Ulf Ryde
- Department of Computational Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
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8
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Jiang H, Lundgren KJM, Ryde U. Protonation of Homocitrate and the E 1 State of Fe-Nitrogenase Studied by QM/MM Calculations. Inorg Chem 2023; 62:19433-19445. [PMID: 37987624 DOI: 10.1021/acs.inorgchem.3c02329] [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: 11/22/2023]
Abstract
Nitrogenase is the only enzyme that can cleave the strong triple bond in N2, making nitrogen available for biological life. There are three isozymes of nitrogenase, differing in the composition of the active site, viz., Mo, V, and Fe-nitrogenase. Recently, the first crystal structure of Fe-nitrogenase was presented. We have performed the first combined quantum mechanical and molecular mechanical (QM/MM) study of Fe-nitrogenase. We show with QM/MM and quantum-refinement calculations that the homocitrate ligand is most likely protonated on the alcohol oxygen in the resting E0 state. The most stable broken-symmetry (BS) states are the same as for Mo-nitrogenase, i.e., the three Noodleman BS7-type states (with a surplus of β spin on the eighth Fe ion), which maximize the number of nearby antiferromagnetically coupled Fe-Fe pairs. For the E1 state, we find that protonation of the S2B μ2 belt sulfide ion is most favorable, 14-117 kJ/mol more stable than structures with a Fe-bound hydride ion (the best has a hydride ion on the Fe2 ion) calculated with four different density-functional theory methods. This is similar to what was found for Mo-nitrogenase, but it does not explain the recent EPR observation that the E1 state of Fe-nitrogenase should contain a photolyzable hydride ion. For the E1 state, many BS states are close in energy, and the preferred BS state differs depending on the position of the extra proton and which density functional is used.
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Affiliation(s)
- Hao Jiang
- Department of Computational Chemistry, Lund University, Chemical Centre, P.O. Box 124, Lund SE-221 00, Sweden
| | - Kristoffer J M Lundgren
- Department of Computational Chemistry, Lund University, Chemical Centre, P.O. Box 124, Lund SE-221 00, Sweden
| | - Ulf Ryde
- Department of Computational Chemistry, Lund University, Chemical Centre, P.O. Box 124, Lund SE-221 00, Sweden
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9
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Zhai H, Lee S, Cui ZH, Cao L, Ryde U, Chan GKL. Multireference Protonation Energetics of a Dimeric Model of Nitrogenase Iron-Sulfur Clusters. J Phys Chem A 2023; 127:9974-9984. [PMID: 37967028 PMCID: PMC10694817 DOI: 10.1021/acs.jpca.3c06142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023]
Abstract
Characterizing the electronic structure of the iron-sulfur clusters in nitrogenase is necessary to understand their role in the nitrogen fixation process. One challenging task is to determine the protonation state of the intermediates in the nitrogen fixing cycle. Here, we use a dimeric iron-sulfur model to study relative energies of protonation at C, S, or Fe. Using a composite method based on coupled cluster and density matrix renormalization group energetics, we converge the relative energies of four protonated configurations with respect to basis set and correlation level. We find that accurate relative energies require large basis sets as well as a proper treatment of multireference and relativistic effects. We have also tested ten density functional approximations for these systems. Most of them give large errors in their relative energies. The best performing functional in this system is B3LYP, which gives mean absolute and maximum deviations of only 10 and 13 kJ/mol with respect to our correlated wave function estimates, respectively, comparable to the uncertainty in our correlated estimates. Our work provides benchmark results for the calibration of new approximate electronic structure methods and density functionals for these problems.
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Affiliation(s)
- Huanchen Zhai
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Seunghoon Lee
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Zhi-Hao Cui
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Lili Cao
- Department
of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department
of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Garnet Kin-Lic Chan
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
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10
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Wappett D, Goerigk L. Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set. J Chem Theory Comput 2023; 19:8365-8383. [PMID: 37943578 PMCID: PMC10688432 DOI: 10.1021/acs.jctc.3c00558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023]
Abstract
We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO-CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob's ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.
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Affiliation(s)
- Dominique
A. Wappett
- School of Chemistry, The University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University
of Melbourne, Melbourne, Victoria 3010, Australia
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11
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Lu Y, Sen K, Yong C, Gunn DSD, Purton JA, Guan J, Desmoutier A, Abdul Nasir J, Zhang X, Zhu L, Hou Q, Jackson-Masters J, Watts S, Hanson R, Thomas HN, Jayawardena O, Logsdail AJ, Woodley SM, Senn HM, Sherwood P, Catlow CRA, Sokol AA, Keal TW. Multiscale QM/MM modelling of catalytic systems with ChemShell. Phys Chem Chem Phys 2023; 25:21816-21835. [PMID: 37097706 DOI: 10.1039/d3cp00648d] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.
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Affiliation(s)
- You Lu
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Kakali Sen
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Chin Yong
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - David S D Gunn
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - John A Purton
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Jingcheng Guan
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Alec Desmoutier
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Jamal Abdul Nasir
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Xingfan Zhang
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Lei Zhu
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Qing Hou
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Joe Jackson-Masters
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Sam Watts
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Rowan Hanson
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Harry N Thomas
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Omal Jayawardena
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Andrew J Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Scott M Woodley
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Hans M Senn
- School of Chemistry, University of Glasgow, Joseph Black Building, Glasgow G12 8QQ, UK
| | - Paul Sherwood
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - C Richard A Catlow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Alexey A Sokol
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Thomas W Keal
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
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12
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Pang Y, Bjornsson R. The E3 state of FeMoco: one hydride, two hydrides or dihydrogen? Phys Chem Chem Phys 2023; 25:21020-21036. [PMID: 37522223 DOI: 10.1039/d3cp01106b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Hydrides are present in the reduced states of the iron-molybdenum cofactor (FeMoco) of Mo nitrogenase and are believed to play a key mechanistic role in the dinitrogen reduction reaction catalyzed by the enzyme. Two hydrides are present in the E4 state according to 1H ENDOR and there is likely a single hydride in the E2 redox state. The 2-hydride E4 state has been experimentally observed to bind N2 and it has been speculated that E3 may bind N2 as well. However, the E3 state has not been directly observed and very little is known about its molecular and electronic structure or reactivity. In recent computational studies, we have explored the energy surfaces of the E2 and E4 by QM/MM modelling, and found that the most stable hydride isomers contain bridging or partially bridging hydrides with an open protonated belt sulfide-bridge. In this work we systematically explore the energy surface of the E3 redox state, comparing single hydride and two-hydride isomers with varying coordination and bridging vs. terminal sulfhydryl groups. We also include a model featuring a triply protonated carbide. The results are only mildly dependent on the QM-region size. The three most stable E3 isomers at the r2SCAN level of theory have in common: an open belt sulfide-bridge (terminal sulfhydryl group on Fe6) and either 2 bridging hydrides (between Fe2 and Fe6), 1 bridging-1-terminal hydride (around Fe2 and Fe6) or a dihydrogen ligand bound at the Fe2 site. Analyzing the functional dependency of the results, we find that functionals previously found to predict accurate structures of spin-coupled Fe/Mo dimers and FeMoco (TPSSh, B97-D3, r2SCAN, and B3LYP*) are in generally good agreement about the stability of these 3 E3 isomers. However, B3LYP*, similar to its parent B3LYP method, predicts a triply protonated carbide isomer as the most stable isomer, an unlikely scenario in view of the lack of experimental evidence for carbide protonation occurring in reduced FeMoco states. Distinguishing further between the 3 hydride isomers is difficult and this flexible coordination nature of hydrides suggests that multiple hydride isomers could be present during experimental conditions. N2 binding was explored and resulted in geometries with 2 bridging hydrides and N2 bound to either Fe2 or Fe6 with a local low-spin state on the Fe. N2 binding is predicted to be mildly endothermic, similar to the E2 state, and it seems unlikely that the E3 state is capable of binding N2.
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Affiliation(s)
- Yunjie Pang
- College of Chemistry, Beijing Normal University, 100875, Beijing, China
- Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 17 Rue des Martyrs, F-38054 Grenoble, Cedex, France.
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Ziółkowska A, Witwicki M. Understanding the Exchange Interaction between Paramagnetic Metal Ions and Radical Ligands: DFT and Ab Initio Study on Semiquinonato Cu(II) Complexes. Int J Mol Sci 2023; 24:ijms24044001. [PMID: 36835412 PMCID: PMC9959031 DOI: 10.3390/ijms24044001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
The exchange coupling, represented by the J parameter, is of tremendous importance in understanding the reactivity and magnetic behavior of open-shell molecular systems. In the past, it was the subject of theoretical investigations, but these studies are mostly limited to the interaction between metallic centers. The exchange coupling between paramagnetic metal ions and radical ligands has hitherto received scant attention in theoretical studies, and thus the understanding of the factors governing this interaction is lacking. In this paper, we use DFT, CASSCF, CASSCF/NEVPT2, and DDCI3 methods to provide insight into exchange interaction in semiquinonato copper(II) complexes. Our primary objective is to identify structural features that affect this magnetic interaction. We demonstrate that the magnetic character of Cu(II)-semiquinone complexes are mainly determined by the relative position of the semiquinone ligand to the Cu(II) ion. The results can support the experimental interpretation of magnetic data for similar systems and can be used for the in-silico design of magnetic complexes with radical ligands.
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Affiliation(s)
- Aleksandra Ziółkowska
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Maciej Witwicki
- Faculty of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-283 Wroclaw, Poland
- Correspondence:
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Dance I. The binding of reducible N 2 in the reaction domain of nitrogenase. Dalton Trans 2023; 52:2013-2026. [PMID: 36691966 DOI: 10.1039/d2dt03599e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The binding of N2 to FeMo-co, the catalytic site of the enzyme nitrogenase, is central to the conversion to NH3, but also has a separate role in promoting the N2-dependent HD reaction (D2 + 2H+ + 2e- → 2HD). The protein surrounding FeMo-co contains a clear channel for ingress of N2, directly towards the exo-coordination position of Fe2, a position which is outside the catalytic reaction domain. This led to the hypothesis [I. Dance, Dalton Trans., 2022, 51, 12717] of 'promotional' N2 bound at exo-Fe2, and a second 'reducible' N2 bound in the reaction domain, specifically the endo-coordination position of Fe2 or Fe6. The range of possibilities for the binding of reducible N2 in the presence of bound promotional N2 is described here, using density functional simulations with a 486 atom model of the active site and surrounding protein. The pathway for ingress of the second N2 through protein, past the first N2 at exo-Fe2, and tumbling into the binding domain between Fe2 and Fe6, is described. The calculations explore 24 structures involving 6 different forms of hydrogenated FeMo-co, including structures with S2BH unhooked from Fe2 but tethered to Fe6. The calculations use the most probable electronic states. End-on (η1) binding of N2 at the endo position of either Fe2 or Fe6 is almost invariably exothermic, with binding potential energies ranging up to -18 kcal mol-1. Many structures have binding energies in the range -6 to -14 kcal mol-1. The relevant entropic penalty for N2 binding from a diffusible position within the protein is estimated to be 4 kcal mol-1, and so the binding free energies for reducible N2 are suitably negative. N2 binding at endo-Fe2 is stronger than at endo-Fe6 in three of the six structure categories. In many cases the reaction domain containing reducible N2 is expanded. These results inform computational simulation of the subsequent steps in which surrounding H atoms transfer to reducible N2.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, Australia.
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Zhang X, Wang Z, Li Z, Shaik S, Wang B. [4Fe–4S]-Mediated Proton-Coupled Electron Transfer Enables the Efficient Degradation of Chloroalkenes by Reductive Dehalogenases. ACS Catal 2023. [DOI: 10.1021/acscatal.2c06306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xuan Zhang
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zikuan Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Zhen Li
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Binju Wang
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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Jiang H, Svensson OKG, Ryde U. QM/MM Study of Partial Dissociation of S2B for the E 2 Intermediate of Nitrogenase. Inorg Chem 2022; 61:18067-18076. [DOI: 10.1021/acs.inorgchem.2c02488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hao Jiang
- Department of Theoretical Chemistry, Lund University, Chemical Centre, SE-221 00Lund, Sweden
| | - Oskar K. G. Svensson
- Department of Theoretical Chemistry, Lund University, Chemical Centre, SE-221 00Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, SE-221 00Lund, Sweden
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Atanasov M, Spiller N, Neese F. Magnetic exchange and valence delocalization in a mixed valence [Fe 2+Fe 3+Te 2] + complex: insights from theory and interpretations of magnetic and spectroscopic data. Phys Chem Chem Phys 2022; 24:20760-20775. [PMID: 36043991 DOI: 10.1039/d2cp02975h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mixed valence binuclear Fe2.5+-Fe2.5+ (Robin-Day Class III) transition metal complex, [Fe2.5+μTe2Fe2.5+]1-, composed of two FeN2Te2 pseudo-tetrahedral units with μ-bridging Te2- ligands was reported to exist in an unprecedented S = 3/2 ground state (Nature Chemistry, https://doi.org/10.1038/s41557-021-00853-5). For this and the homologous complexes containing Se2- and S2-, the Anderson-Hasegawa double exchange spin-Hamiltonian was broadly used to interpret the corresponding structural, spectroscopic and magnetic data. First principles multireference ab initio calculations are used here to simulate magnetic and spectroscopic EPR data; analysis of the results affords a rationale for the stabilization of the S = 3/2 ground state of the Fe2 pair. Complete Active Space Self-Consistent Field (CASSCF) calculations and dynamical correlation accounted for by means of N-Electron Valence Perturbation Theory to Second Order (NEVPT2) reproduce well the g-factors determined from simulations of X-band EPR spectra. A crucial technical tool to achieve these results is: (i) use of a localized orbital formulation of the many-particle problem at the scalar-relativistic CASSCF step; (ii) choice of state averaging over states of a given spin (at the CASCI/NEVPT2 step); and (iii) accounting for spin-orbit coupling within the non-relativistic Born-Oppenheimer (BO) many-particle basis using Quasi-Degenerate Perturbation Theory (QDPT). The inclusion of the S = 5/2 spin manifold reproduced the observed increase in the magnetic susceptibility (χT) in the high temperature range (T > 100 K), which is explained by thermal population of the S = 5/2 excited state at energy 160 cm-1 above the S = 3/2 ground state. Theoretical values of χT from experimentally reported data points in the temperature range from 3 to 30 K were further computed and analyzed using a model which takes spin-phonon coupling into account. The model considerations and the computational protocols of this study are generally applicable to any Class I/II mixed valence dimer. The work can potentially stimulate further experimental and theoretical work on bi- and oligonuclear transition metal complexes of importance to bioinorganic chemistry and life sciences.
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Affiliation(s)
- M Atanasov
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany. .,Institute of General and Inorganic Chemistry, Bulgarian Academy of Science, Akad-Georgi Bontchev Str. Bl.11, 1113-Sofia, Bulgaria
| | - N Spiller
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany.
| | - F Neese
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany.
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