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Boto RA, Cebreiro-Gallardo A, Menchón RE, Casanova D. Electron-Spin Relaxation in Boron-Doped Graphene Nanoribbons. J Chem Theory Comput 2024; 20:9906-9916. [PMID: 39547821 DOI: 10.1021/acs.jctc.4c00933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2024]
Abstract
Boron-doped graphene nanoribbons are promising platforms for developing organic materials with magnetic properties. Boron dopants can be used to create localized magnetic states in nanoribbons with tunable interactions. Controlling the coherence times of these magnetic states is the very first step in designing materials for quantum computation or information storage. In this work, we address the connection between the relaxation time and the position of the dopants for a series of boron-doped graphene nanofragments. We combine Redfield theory and ab initio calculations of magnetic properties to unveil the mechanism that governs spin relaxation in solution. We demonstrate that relaxation times can be in the order of 1 ms for the selected graphene nanofragments. A detailed analysis of the relaxation mechanism reveals that the spin decoherence is fundamentally driven by fluctuations of the spin-orbit coupling, and the hyperfine interaction facilitated by the thermal motion of the graphene nanofragments. The close connection between relaxation time, hyperfine interaction and the spin-orbit coupling offers the perspective of designing attractive materials with long-lived spin states.
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Affiliation(s)
- Roberto A Boto
- Donostia International Physics Center DIPC, Paseo Manuel Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Antonio Cebreiro-Gallardo
- Donostia International Physics Center DIPC, Paseo Manuel Lardizabal 4, 20018 Donostia-San Sebastián, Spain
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), PK 1072, 20080 Donostia, Euskadi, Spain
| | - Rodrigo E Menchón
- Donostia International Physics Center DIPC, Paseo Manuel Lardizabal 4, 20018 Donostia-San Sebastián, Spain
- Facultad de Ciencias Exactas, Ingeniería y Agrimensura (FCEIA), Universidad Nacional de Rosario (UNR), Rosario 2000, Argentina
- Instituto de Física Rosario (IFIR), Rosario 2000, Argentina
| | - David Casanova
- Donostia International Physics Center DIPC, Paseo Manuel Lardizabal 4, 20018 Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
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2
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Neese F. A perspective on the future of quantum chemical software: the example of the ORCA program package. Faraday Discuss 2024; 254:295-314. [PMID: 39051881 DOI: 10.1039/d4fd00056k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
The field of computational chemistry has made an impressive impact on contemporary chemical research. In order to carry out computational studies on actual systems, sophisticated software is required in form of large-scale quantum chemical program packages. Given the enormous diversity and complexity of the methods that need to be implementation in such packages, it is evident that these software pieces are very large (millions of code lines) and extremely complex. Most of the packages in widespread use by the computational chemistry community have had a development history of decades. Given the rapid progress in the hardware and a lack of resources (time, workforce, money), it is not possible to keep redesigning these program packages from scratch in order to keep up with the ever more quickly shifting hardware landscape. In this perspective, some aspects of the multitude of challenges that the developer community faces are discussed. While the task at hand - to ensure that quantum chemical program packages can keep evolving and make best use of the available hardware - is daunting, there are also new evolving opportunities. The problems and potential cures are discussed with the example of the ORCA package that has been developed in our research group.
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Affiliation(s)
- Frank Neese
- Department of Molecular Theory and Spectroscopy, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany.
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3
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Thasitha S, Tsuppayakorn-Aek P, Udomkijmongkol A, Khammuang S, Kaewmaraya T, Hussain T, Bovornratanaraks T, Kotmool K. First-principles study on structural stabilities, mechanical properties, and biaxial strain-induced superconductivity in Janus MoWC monolayer. Phys Chem Chem Phys 2024; 26:19696-19704. [PMID: 38835236 DOI: 10.1039/d4cp01215a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
The unique attributes of hydrophilicity, expansive surface groups, remarkable flexibility, and superior conductivity converge in MXene, a pioneering 2D material. Owing to MXene's exceptional properties, diverse strategies have been explored to enhance its characteristics. Janus MXene and stress-strain response considerations represent the primary avenues of interest today. In this study, we investigated the Janus MXene structure under biaxial stress using first-principles calculations. The most stable configuration of Janus MoWC MXene identified in our analysis exhibits an atomic arrangement known as the hexagonal (2H) phase. Subsequently, we examined the mechanical and electronic properties of 2H-MoWC when subjected to biaxial strain. Our findings indicate that the 2H phase of Janus MoWC MXene demonstrates superior strength compared to the tetragonal (1T) phase. Analysis of the ELF of the 2H-MoWC structure unveiled that the robust C-C bond within the material is the underlying factor enabling the 2H phase to withstand a maximum of 9% tensile strain. Furthermore, we demonstrate that 2H-MoWC is a superconductor with the superconducting temperature (Tc) of 1.6 K, and the superconductivity of 2H phase can be enhanced by biaxial strain with the Tc reaching 7 K. This study offers comprehensive insights into the properties of Janus MoWC monolayer under biaxial stress, positioning it as a promising candidate for 2D straintronic applications.
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Affiliation(s)
- Sirinee Thasitha
- College of Advanced Manufacturing Innovation, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand.
| | - Prutthipong Tsuppayakorn-Aek
- Extreme Conditions Physics Research Laboratory and Center of Excellence in Physics of Energy Materials (CE:PEM), Department of Physics, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Anan Udomkijmongkol
- College of Advanced Manufacturing Innovation, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand.
| | - Satchakorn Khammuang
- College of Advanced Manufacturing Innovation, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand.
| | - Thanayut Kaewmaraya
- Integrated Nanotechnology Research Center, Department of Physics, Khon Kaen University, Khon Kaen, Thailand
- Institute of Nanomaterials Research and Innovation for Energy (IN-RIE), NANOTEC-KKU RNN on Nanomaterials Research and Innovation for Energy, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Tanveer Hussain
- School of Science and Technology, University of New England, Armidale, New South Wales 2351, Australia
| | - Thiti Bovornratanaraks
- Extreme Conditions Physics Research Laboratory and Center of Excellence in Physics of Energy Materials (CE:PEM), Department of Physics, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Thailand Center of Excellence in Physics, Ministry of Higher Education, Science, Research and Innovation, 328 Si Ayutthaya Road, Bangkok, 10400, Thailand
| | - Komsilp Kotmool
- College of Advanced Manufacturing Innovation, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand.
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4
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Allen JP, Szczuka C, Smith HE, Jónsson E, Eichel RA, Granwehr J, Grey CP. Coordination of dissolved transition metals in pristine battery electrolyte solutions determined by NMR and EPR spectroscopy. Phys Chem Chem Phys 2024; 26:19505-19520. [PMID: 38979604 PMCID: PMC11253248 DOI: 10.1039/d4cp01663g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/30/2024] [Indexed: 07/10/2024]
Abstract
The solvation of dissolved transition metal ions in lithium-ion battery electrolytes is not well-characterised experimentally, although it is important for battery degradation mechanisms governed by metal dissolution, deposition, and reactivity in solution. This work identifies the coordinating species in the Mn2+ and Ni2+ solvation spheres in LiPF6/LiTFSI-carbonate electrolyte solutions by examining the electron-nuclear spin interactions, which are probed by pulsed EPR and paramagnetic NMR spectroscopy. These techniques investigate solvation in frozen electrolytes and in the liquid state at ambient temperature, respectively, also probing the bound states and dynamics of the complexes involving the ions. Mn2+ and Ni2+ are shown to primarily coordinate to ethylene carbonate (EC) in the first coordination sphere, while PF6- is found primarily in the second coordination sphere, although a degree of contact ion pairing does appear to occur, particularly in electrolytes with low EC concentrations. NMR results suggest that Mn2+ coordinates more strongly to PF6- than to TFSI-, while the opposite is true for Ni2+. This work provides a framework to experimentally determine the coordination spheres of paramagnetic metals in battery electrolyte solutions.
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Affiliation(s)
- Jennifer P Allen
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, Cambridge, UK.
- The Faraday Institution, Quad One, Harwell Science and Innovation Campus, Didcot OX11 0RA, UK
| | - Conrad Szczuka
- Institute of Energy and Climate Research (IEK-9), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, 52056 Aachen, Germany
| | - Holly E Smith
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, Cambridge, UK.
| | - Erlendur Jónsson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, Cambridge, UK.
| | - Rüdiger-A Eichel
- Institute of Energy and Climate Research (IEK-9), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, 52056 Aachen, Germany
| | - Josef Granwehr
- Institute of Energy and Climate Research (IEK-9), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52056 Aachen, Germany
| | - Clare P Grey
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, Cambridge, UK.
- The Faraday Institution, Quad One, Harwell Science and Innovation Campus, Didcot OX11 0RA, UK
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Islam MA, Pell AJ. Delving into theoretical and computational considerations for accurate calculation of chemical shifts in paramagnetic transition metal systems using quantum chemical methods. Phys Chem Chem Phys 2024; 26:12786-12798. [PMID: 38619872 DOI: 10.1039/d4cp00683f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The chemical shielding tensor for a paramagnetic system has been derived from the macroscopically observed magnetization using the perturbation theory. An approach to calculate the paramagnetic chemical shifts in transition metal systems based on the spin-only magnetic susceptibility directly evaluated from the ab initio Hilbert space of the electronic Zeeman Hamiltonian has been discussed. Computationally, several advantages are associated with this approach: (a) it includes the state-specific paramagnetic Curie (first-order) and Van Vleck (second-order) contributions of the paramagnetic ion to the paramagnetic chemical shifts; (b) thus it avoids the system-specific modeling and evaluating effectively in terms of the electron paramagnetic resonance (EPR) spin Hamiltonian parameters of the magnetic moment of the paramagnetic ion formulated previously; (c) it can be utilized both in the point-dipole (PD) approximation (in the long-range) and with the quantum chemical (QC) method based the hyperfine tensors (in the short-range). Additionally, we have examined the predictive performance of various density functional theory (DFT) functionals of different families and commonly used core-augmented basis sets for nuclear magnetic resonance (NMR) chemical shifts. A selection of transition metal ion complexes with and without first-order orbital contributions, namely the [M(AcPyOx)3(BPh)]+ complexes of M = Mn2+, Ni2+ and Co2+ ions and CoTp2 complex and their reported NMR chemical shifts are studied from QC methods for illustration.
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Affiliation(s)
- Md Ashraful Islam
- Centre de RMN à Très Hauts Champs de Lyon, UMR-5082, CNRS/UCB Lyon 1/ENS de Lyon, 69100 Villeurbanne, France.
| | - Andrew J Pell
- Centre de RMN à Très Hauts Champs de Lyon, UMR-5082, CNRS/UCB Lyon 1/ENS de Lyon, 69100 Villeurbanne, France.
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6
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Rosenboom J, Taube F, Teichmeier L, Villinger A, Reinhard M, Demeshko S, Bennati M, Bresien J, Corzilius B, Schulz A. Rational Design of a Phosphorus-Centered Disbiradical. Angew Chem Int Ed Engl 2024; 63:e202318210. [PMID: 38117661 DOI: 10.1002/anie.202318210] [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: 11/29/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/22/2023]
Abstract
Phosphorus-centered disbiradicals, in which the radical sites exist as individual spin doublets with weak spin-spin interaction have not been known so far. Starting from monoradicals of the type [⋅P(μ-NTer)2 P-R], we have now succeeded in linking two such monoradical phosphorus centers by appropriate choice of a linker. To this end, biradical [⋅P(μ-NTer)2 P⋅] (1) was treated with 1,6-dibromohexane, affording the brominated species {Br[P(μ-NTer)]2 }2 C6 H12 (3). Subsequent reduction with KC8 led to the formation of the disbiradical {⋅[P(μ-NTer)]2 }2 C6 H12 (4) featuring a large distance between the radical phosphorus sites in the solid state and formally the highest biradical character observed in a P-centered biradical so far, approaching 100 %. EPR spectroscopy revealed a three-line signal in solution with a considerably larger exchange interaction than would be expected from the molecular structure of the single crystal. Quantum chemical calculations revealed a highly dynamic conformational space; thus, the two radical sites can approach each other with a much smaller distance in solution. Further reduction of 4 resulted in the formation of a potassium salt featuring the first structurally characterized P-centered distonic radical anion (5- ). Moreover, 4 could be used in small molecule activation.
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Affiliation(s)
- Jan Rosenboom
- Institut für Chemie, Universität Rostock, Albert-Einstein-Straße 3a, 18059, Rostock, Germany
| | - Florian Taube
- Institut für Chemie, Universität Rostock, Albert-Einstein-Straße 3a, 18059, Rostock, Germany
| | - Leon Teichmeier
- Institut für Chemie, Universität Rostock, Albert-Einstein-Straße 3a, 18059, Rostock, Germany
| | - Alexander Villinger
- Institut für Chemie, Universität Rostock, Albert-Einstein-Straße 3a, 18059, Rostock, Germany
| | - Maik Reinhard
- Georg-August-Universität Göttingen, Tammannstr. 4/6, 37077, Göttingen, Germany
- MPINAT, Research Group ESR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Serhiy Demeshko
- Georg-August-Universität Göttingen, Tammannstr. 4/6, 37077, Göttingen, Germany
| | - Marina Bennati
- Georg-August-Universität Göttingen, Tammannstr. 4/6, 37077, Göttingen, Germany
- MPINAT, Research Group ESR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Jonas Bresien
- Institut für Chemie, Universität Rostock, Albert-Einstein-Straße 3a, 18059, Rostock, Germany
| | - Björn Corzilius
- Institut für Chemie, Universität Rostock, Albert-Einstein-Straße 3a, 18059, Rostock, Germany
- Leibniz-Institut für Katalyse e.V., Albert-Einstein-Straße 29a, 18059, Rostock, Germany
- Department Life, Light & Matter, Universität Rostock, Albert-Einstein-Straße 25, 18059, Rostock, Germany
| | - Axel Schulz
- Institut für Chemie, Universität Rostock, Albert-Einstein-Straße 3a, 18059, Rostock, Germany
- Leibniz-Institut für Katalyse e.V., Albert-Einstein-Straße 29a, 18059, Rostock, Germany
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7
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Kumar P, Devkota L, Casey MC, Fischer AA, Lindeman SV, Fiedler AT. Reversible Dioxygen Binding to Co(II) Complexes with Noninnocent Ligands. Inorg Chem 2022; 61:16664-16677. [PMID: 36206536 PMCID: PMC11218047 DOI: 10.1021/acs.inorgchem.2c02246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of mononuclear Co(II) complexes with noninnocent (redox-active) ligands are prepared that exhibit metal-ligand cooperativity during the reversible binding of O2. The complexes have the general formula, [CoII(LS,N)(TpR2)] (R = Me, Ph), where LS,N is a bidentate o-aminothiophenolate and TpR2 is a hydrotris(pyrazol-1-yl)borate scorpionate with R-substituents at the 3- and 5-positions. Exposure to O2 at room temperature results in one-electron oxidation and deprotonation of LS,N. The oxidized derivatives possess substantial "singlet diradical" character arising from antiferromagnetic coupling between an iminothiosemiquinonate (ITSQ•-) ligand radical and a low-spin Co(II) ion. The [CoII(TpMe2)(X2ITSQ)] complexes, where X = H or tBu, coordinate O2 reversibly at reduced temperatures to provide Co/O2 adducts. The O2 binding reactions closely resemble those previously reported by our group (Kumar et al., J. Am. Chem. Soc. 2019,141, 10984-10987) for the related complexes [CoII(TpMe2)(tBu2SQ)] and [CoII(TpMe2)(tBu2ISQ)], where tBu2(I)SQ represents 4,6-di-tert-butyl-(2-imino)semiquinonate radicals. In each case, the oxygenation reaction proceeds via the addition of O2 to both the cobalt ion and the ligand radical, generating metallocyclic cobalt(III)-alkylperoxo structures. Thermodynamic measurements elucidate the relationship between O2 affinity and redox potentials of the (imino)(thio)semiquinonate radicals, as well as energetic differences between these reactions and conventional metal-based oxygenations. The results highlight the utility and versatility of noninnocent ligands in the design of O2-absorbing compounds.
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Affiliation(s)
- Praveen Kumar
- Department of Chemistry, Marquette University, 1414 W. Clybourn Street, Milwaukee, Wisconsin53233, United States
| | - Laxmi Devkota
- Department of Chemistry, Marquette University, 1414 W. Clybourn Street, Milwaukee, Wisconsin53233, United States
| | - Maximilian C Casey
- Department of Chemistry, Marquette University, 1414 W. Clybourn Street, Milwaukee, Wisconsin53233, United States
| | - Anne A Fischer
- Department of Chemistry, Marquette University, 1414 W. Clybourn Street, Milwaukee, Wisconsin53233, United States
| | - Sergey V Lindeman
- Department of Chemistry, Marquette University, 1414 W. Clybourn Street, Milwaukee, Wisconsin53233, United States
| | - Adam T Fiedler
- Department of Chemistry, Marquette University, 1414 W. Clybourn Street, Milwaukee, Wisconsin53233, United States
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Jana RD, Chakraborty B, Paria S, Ohta T, Singh R, Mandal S, Paul S, Itoh S, Paine TK. Dioxygen Activation and Mandelate Decarboxylation by Iron(II) Complexes of N4 Ligands: Evidence for Dioxygen-Derived Intermediates from Cobalt Analogues. Inorg Chem 2022; 61:10461-10476. [PMID: 35759790 DOI: 10.1021/acs.inorgchem.2c01308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The isolation, characterization, and dioxygen reactivity of monomeric [(TPA)MII(mandelate)]+ (M = Fe, 1; Co, 3) and dimeric [(BPMEN)2MII2(μ-mandelate)2]2+ (M = Fe, 2; Co, 4) (TPA = tris(2-pyridylmethyl)amine and BPMEN = N1,N2-dimethyl-N1,N2-bis(pyridin-2-yl-methyl)ethane-1,2-diamine) complexes are reported. The iron(II)- and cobalt(II)-mandelate complexes react with dioxygen to afford benzaldehyde and benzoic acid in a 1:1 ratio. In the reactions, one oxygen atom from dioxygen is incorporated into benzoic acid, but benzaldehyde does not derive any oxygen atom from dioxygen. While no O2-derived intermediate is observed with the iron(II)-mandelate complexes, the analogous cobalt(II) complexes react with dioxygen at a low temperature (-80 °C) to generate the corresponding cobalt(III)-superoxo species (S), a key intermediate implicated in the initiation of mandelate decarboxylation. At -20 °C, the cobalt(II)-mandelate complexes bind dioxygen reversibly leading to the formation of μ-1,2-peroxo-dicobalt(III)-mandelate species (P). The geometric and electronic structures of the O2-derived intermediates (S and P) have been established by computational studies. The intermediates S and P upon treatment with a protic acid undergo decarboxylation to afford benzaldehyde (50%) with a concomitant formation of the corresponding μ-1,2-peroxo-μ-mandelate-dicobalt(III) (P1) species. The crystal structure of a peroxide species isolated from the cobalt(II)-carboxylate complex [(TPA)CoII(MPA)]+ (5) (MPA = 2-methoxyphenylacetate) supports the composition of P1. The observations of the dioxygen-derived intermediates from cobalt complexes and their electronic structure analyses not only provide information about the nature of active species involved in the decarboxylation of mandelate but also shed light on the mechanistic pathway of two-electron versus four-electron reduction of dioxygen.
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Affiliation(s)
- Rahul Dev Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Biswarup Chakraborty
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Sayantan Paria
- Department of Molecular Chemistry, Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takehiro Ohta
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH LP Center, Koto 1-1-1, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Reena Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Sourav Mandal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Satadal Paul
- Department of Chemistry, Bangabasi Morning College, 19, Rajkumar Chakraborty Sarani, Kolkata 700009, India
| | - Shinobu Itoh
- Department of Molecular Chemistry, Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tapan Kanti Paine
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
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9
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Jaworski A, Hedin N. Electron correlation and vibrational effects in predictions of paramagnetic NMR shifts. Phys Chem Chem Phys 2022; 24:15230-15244. [PMID: 35703010 DOI: 10.1039/d2cp01206e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic structure calculations are fundamentally important for the interpretation of nuclear magnetic resonance (NMR) spectra from paramagnetic systems that include organometallic and inorganic compounds, catalysts, or metal-binding sites in proteins. Prediction of induced paramagnetic NMR shifts requires knowledge of electron paramagnetic resonance (EPR) parameters: the electronic g tensor, zero-field splitting D tensor, and hyperfine A tensor. The isotropic part of A, called the hyperfine coupling constant (HFCC), is one of the most troublesome properties for quantum chemistry calculations. Yet, even relatively small errors in calculations of HFCC tend to propagate into large errors in the predicted NMR shifts. The poor quality of A tensors that are currently calculated using density functional theory (DFT) constitutes a bottleneck in improving the reliability of interpretation of the NMR spectra from paramagnetic systems. In this work, electron correlation effects in calculations of HFCCs with a hierarchy of ab initio methods were assessed, and the applicability of different levels of DFT approximations and the coupled cluster singles and doubles (CCSD) method was tested. These assessments were performed for the set of selected test systems comprising an organic radical, and complexes with transition metal and rare-earth ions, for which experimental data are available. Severe deficiencies of DFT were revealed but the CCSD method was able to deliver good agreement with experimental data for all systems considered, however, at substantial computational costs. We proposed a more computationally tractable alternative, where the A was computed with the coupled cluster theory exploiting locality of electron correlation. This alternative is based on the domain-based local pair natural orbital coupled cluster singles and doubles (DLPNO-CCSD) method. In this way the robustness and reliability of the coupled cluster theory were incorporated into the modern formalism for the prediction of induced paramagnetic NMR shifts, and became applicable to systems of chemical interest. This approach was verified for the bis(cyclopentadienyl)vanadium(II) complex (Cp2V; vanadocene), and the metal-binding site of the Zn2+ → Co2+ substituted superoxide dismutase (SOD) metalloprotein. Excellent agreement with experimental NMR shifts was achieved, which represented a substantial improvement over previous theoretical attempts. The effects of vibrational corrections to orbital shielding and hyperfine tensor were evaluated and discussed within the second-order vibrational perturbation theory (VPT2) framework.
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Affiliation(s)
- Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Niklas Hedin
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
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10
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Rosenboom J, Chojetzki L, Suhrbier T, Rabeah J, Villinger A, Wustrack R, Bresien J, Schulz A. Radical Reactivity of the Biradical [⋅P(μ-NTer) 2 P⋅] and Isolation of a Persistent Phosphorus-Cantered Monoradical [⋅P(μ-NTer) 2 P-Et]. Chemistry 2022; 28:e202200624. [PMID: 35445770 PMCID: PMC9322606 DOI: 10.1002/chem.202200624] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Indexed: 11/06/2022]
Abstract
The activation of C-Br bonds in various bromoalkanes by the biradical [⋅P(μ-NTer)2 P⋅] (1) (Ter=2,6-bis-(2,4,6-trimethylphenyl)-phenyl) is reported, yielding trans-addition products of the type [Br-P(μ-NTer)2 P-R] (2), so-called 1,3-substituted cyclo-1,3-diphospha-2,4-diazanes. This addition reaction, which represents a new easy approach to asymmetrically substituted cyclo-1,3-diphospha-2,4-diazanes, was investigated mechanistically by different spectroscopic methods (NMR, EPR, IR, Raman); the results suggested a stepwise radical reaction mechanism, as evidenced by the in-situ detection of the phosphorus-centered monoradical [⋅P(μ-NTer)2 P-R].< To provide further evidence for the radical mechanism, [⋅P(μ-NTer)2 P-Et] (3Et⋅) was synthesized directly by reduction of the bromoethane addition product [Br-P(μ-NTer)2 P-Et] (2 a) with magnesium, resulting in the formation of the persistent phosphorus-centered monoradical [⋅P(μ-NTer)2 P-Et], which could be isolated and fully characterized, including single-crystal X-ray diffraction. Comparison of the EPR spectrum of the radical intermediate in the addition reaction with that of the synthesized new [⋅P(μ-NTer)2 P-Et] radical clearly proves the existence of radicals over the course of the reaction of biradical [⋅P(μ-NTer)2 P⋅] (1) with bromoethane. Extensive DFT and coupled cluster calculations corroborate the experimental data for a radical mechanism in the reaction of biradical [⋅P(μ-NTer)2 P⋅] with EtBr. In the field of hetero-cyclobutane-1,3-diyls, the demonstration of a stepwise radical reaction represents a new aspect and closes the gap between P-centered biradicals and P-centered monoradicals in terms of radical reactivity.
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Affiliation(s)
- Jan Rosenboom
- Institut für Chemie, UniversitätAlbert-Einstein-Straße 3a18059RostockGermany
| | - Lukas Chojetzki
- Institut für Chemie, UniversitätAlbert-Einstein-Straße 3a18059RostockGermany
| | - Tim Suhrbier
- Institut für Chemie, UniversitätAlbert-Einstein-Straße 3a18059RostockGermany
| | - Jabor Rabeah
- Leibniz-Institut für Katalyse e.V.Albert-Einstein-Straße 29a18059RostockGermany
| | - Alexander Villinger
- Institut für Chemie, UniversitätAlbert-Einstein-Straße 3a18059RostockGermany
| | - Ronald Wustrack
- Institut für Chemie, UniversitätAlbert-Einstein-Straße 3a18059RostockGermany
| | - Jonas Bresien
- Institut für Chemie, UniversitätAlbert-Einstein-Straße 3a18059RostockGermany
| | - Axel Schulz
- Institut für Chemie, UniversitätAlbert-Einstein-Straße 3a18059RostockGermany
- Leibniz-Institut für Katalyse e.V.Albert-Einstein-Straße 29a18059RostockGermany
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11
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Shafei R, Maganas D, Strobel PJ, Schmidt PJ, Schnick W, Neese F. Electronic and Optical Properties of Eu 2+-Activated Narrow-Band Phosphors for Phosphor-Converted Light-Emitting Diode Applications: Insights from a Theoretical Spectroscopy Perspective. J Am Chem Soc 2022; 144:8038-8053. [PMID: 35471974 PMCID: PMC9100680 DOI: 10.1021/jacs.2c00218] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In this work, we
present a computational protocol that is able
to predict the experimental absorption and emission spectral shapes
of Eu2+-doped phosphors. The protocol is based on time-dependent
density functional theory and operates in conjunction with an excited-state
dynamics approach. It is demonstrated that across the study set consisting
of representative examples of nitride, oxo-nitride, and oxide Eu2+-doped phosphors, the energy distribution and the band shape
of the emission spectrum are related to the nature of the 4f–5d
transitions that are probed in the absorption process. Since the 4f
orbitals are very nearly nonbonding, the decisive quantity is the
covalency of the 5d acceptor orbitals that become populated in the electronically excited state that leads
to emission. The stronger the (anti) bonding interaction between the
lanthanide and the ligands is in the excited state, the larger will
be the excited state distortion. Consequently, the corresponding emission
will get broader due to the vibronic progression that is induced by
the structural distortion. In addition, the energy separation of the
absorption bands that are dominated by states with valence 4f–5d
and a metal to ligand charge transfer character defines a measure
for the thermal quenching of the studied Eu2+-doped phosphors.
Based on this analysis, simple descriptors are identified that show
a strong correlation with the energy position and bandwidth of the
experimental emission bands without the need for elaborate calculations.
Overall, we believe that this study serves as an important reference
for designing new Eu2+-doped phosphors with desired photoluminescence
properties.
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Affiliation(s)
- Rami Shafei
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany.,Department of Chemistry, Faculty of Science, Beni-Suef University, Salah Salem Str, Beni-Suef 62511, Egypt
| | - Dimitrios Maganas
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Philipp Jean Strobel
- Lumileds Phosphor Center Aachen, Lumileds (Germany) GmbH, Philipsstraße 8, Aachen 52068 , Germany
| | - Peter J Schmidt
- Lumileds Phosphor Center Aachen, Lumileds (Germany) GmbH, Philipsstraße 8, Aachen 52068 , Germany
| | - Wolfgang Schnick
- Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, München 81377, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
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12
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Lang L, Ravera E, Parigi G, Luchinat C, Neese F. Theoretical analysis of the long-distance limit of NMR chemical shieldings. J Chem Phys 2022; 156:154115. [PMID: 35459319 DOI: 10.1063/5.0088162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
After some years of controversy, it was recently demonstrated how to obtain the correct long-distance limit [point-dipole approximation (PDA)] of pseudo-contact nuclear magnetic resonance chemical shifts from rigorous first-principles quantum mechanics [Lang et al., J. Phys. Chem. Lett. 11, 8735 (2020)]. This result confirmed the classical Kurland-McGarvey theory. In the present contribution, we elaborate on these results. In particular, we provide a detailed derivation of the PDA both from the Van den Heuvel-Soncini equation for the chemical shielding tensor and from a spin Hamiltonian approximation. Furthermore, we discuss in detail the PDA within the approximate density functional theory and Hartree-Fock theories. In our previous work, we assumed a relatively crude effective nuclear charge approximation for the spin-orbit coupling operator. Here, we overcome this assumption by demonstrating that the derivation is also possible within the fully relativistic Dirac equation and even without the assumption of a specific form for the Hamiltonian. Crucial ingredients for the general derivation are a Hamiltonian that respects gauge invariance, the multipolar gauge, and functional derivatives of the Hamiltonian, where it is possible to identify the first functional derivative with the electron number current density operator. The present work forms an important foundation for future extensions of the Kurland-McGarvey theory beyond the PDA, including induced magnetic quadrupole and higher moments to describe the magnetic hyperfine field.
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Affiliation(s)
- Lucas Lang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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13
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Lagostina V, Romeo E, Maria Ferrari A, Maurino V, Chiesa M. Monomeric (VO2+) and dimeric mixed valence (V2O33+) vanadium species at the surface of shape controlled TiO2 anatase nano crystals. J Catal 2022. [DOI: 10.1016/j.jcat.2021.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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14
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Diószegi R, Bonczidai-Kelemen D, Bényei AC, May NV, Fábián I, Lihi N. Copper(II) Complexes of Pyridine-2,6-dicarboxamide Ligands with High SOD Activity. Inorg Chem 2022; 61:2319-2332. [PMID: 35029102 DOI: 10.1021/acs.inorgchem.1c03728] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Copper(II) complexes of pyridine-based ligands functionalized with alanine (PydiAla) and tyrosine (PydiTyr) moieties have been synthesized as novel superoxide dismutase mimics. The complexes were characterized by pH-potentiometric, spectroscopic (UV-vis, circular dichroism, mass spectrometry, electron paramagnetic resonance spectroscopy), computational (DFT), and X-ray diffraction methods. Both ligands form high stability copper(II) complexes via the (Npy,N-,N-) donor set supported by the binding of the carboxylate pendant arms. Although the coordination mode is the same for the two systems, the tyrosine containing counterpart exhibits increased copper(II) binding affinity, which is most likely due to the presence of the aromatic moiety of the side chains. Both copper(II) complexes are capable of binding N-methylimidazole, and the formation of the corresponding ternary species was observed at physiological pH. The binary and ternary copper(II) complexes exhibit high SOD activity. The PydiTyr complex exhibits about 1 order of magnitude higher activity than the PydiAla complex. This is probably due to the presence of the phenolic OH group in the former species, which promotes the binding of the superoxide anion radical to the metal center. The results serve as a basis for designing highly efficient copper(II) mimics for medical and practical applications.
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Affiliation(s)
- Róbert Diószegi
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
- Doctoral School of Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | - Dóra Bonczidai-Kelemen
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
- Doctoral School of Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | - Attila Cs Bényei
- Department of Physical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | - Nóra V May
- Centre for Structural Science, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - István Fábián
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
- MTA-DE Redox and Homogeneous Reaction Mechanisms Research Group, University of Debrecen, H-4032 Debrecen, Hungary
| | - Norbert Lihi
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
- MTA-DE Redox and Homogeneous Reaction Mechanisms Research Group, University of Debrecen, H-4032 Debrecen, Hungary
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15
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From the Physicochemical Characteristic of Novel Hesperetin Hydrazone to Its In Vitro Antimicrobial Aspects. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030845. [PMID: 35164110 PMCID: PMC8839478 DOI: 10.3390/molecules27030845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022]
Abstract
Microorganisms are able to give rise to biofilm formation on food matrixes and along food industry infrastructures or medical equipment. This growth may be reduced by the application of molecules preventing bacterial adhesion on these surfaces. A new Schiff base ligand, derivative of hesperetin, HABH (2-amino-N'-(2,3-dihydro-5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)chromen-4-ylidene)benzohydrazide), and its copper complex, CuHABH [CuLH2(OAc)], were designed, synthesized and analyzed in terms of their structure and physicochemical properties, and tested as antibacterial agents. Their structures both in a solid state and in solution were established using several methods: FT-IR, 1H NMR, 13C NMR, UV-Vis, FAB MS, EPR, ESI-MS and potentiometry. Coordination binding of the copper(II) complex dominating at the physiological pH region in the solution was found to be the same as that detected in the solid state. Furthermore, the interaction between the HABH and CuHABH with calf-thymus DNA (CT-DNA) were investigated. These interactions were tracked by UV-Vis, CD (circular dichroism) and spectrofluorimetry. The results indicate a stronger interaction of the CuHABH with the CT-DNA than the HABH. It can be assumed that the nature of the interactions is of the intercalating type, but in the high concentration range, the complex can bind to the DNA externally to phosphate residues or to a minor/major groove. The prepared compounds possess antibacterial and antibiofilm activities against Gram-positive and Gram-negative bacteria. Their antagonistic activity depends on the factor-strain test system. The glass was selected as a model surface for the experiments on antibiofilm activity. The adhesion of bacterial cells to the glass surface in the presence of the compounds was traced by luminometry and the best antiadhesive action against both bacterial strains was detected for the CuHABH complex. This molecule may play a crucial role in disrupting exopolymers (DNA/proteins) in biofilm formation and can be used to prevent bacterial adhesion especially on glass equipment.
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16
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Szych LS, Pilopp Y, Bresien J, Villinger A, Rabeah J, Schulz A. Ein persistentes phosphanyl‐substituiertes Thioketylradikalanion. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lilian Sophie Szych
- Institut für Chemie Universität Rostock Albert-Einstein-Straße 3a 18059 Rostock Deutschland
| | - Yannic Pilopp
- Institut für Chemie Universität Rostock Albert-Einstein-Straße 3a 18059 Rostock Deutschland
| | - Jonas Bresien
- Institut für Chemie Universität Rostock Albert-Einstein-Straße 3a 18059 Rostock Deutschland
| | - Alexander Villinger
- Institut für Chemie Universität Rostock Albert-Einstein-Straße 3a 18059 Rostock Deutschland
| | - Jabor Rabeah
- Leibniz-Institut für Katalyse e.V. an der Universität Rostock Albert-Einstein-Straße 29a 18059 Rostock Deutschland
| | - Axel Schulz
- Institut für Chemie Universität Rostock Albert-Einstein-Straße 3a 18059 Rostock Deutschland
- Leibniz-Institut für Katalyse e.V. an der Universität Rostock Albert-Einstein-Straße 29a 18059 Rostock Deutschland
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17
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Pavlov AA, Novikov VV, Nikovskiy IA, Melnikova EK, Nelyubina YV, Aleshin DY. Analysis of reduced paramagnetic shifts as an effective tool in NMR spectroscopy. Phys Chem Chem Phys 2022; 24:1167-1173. [PMID: 34931208 DOI: 10.1039/d1cp04648a] [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 recently introduced concept of reduced paramagnetic shifts (RPS) in NMR spectroscopy is applied here to a series of paramagnetic complexes with different metal ions, such as iron(II), iron(III) and cobalt(II), in different coordination environments of N-donor ligands, including a unique trigonal-prismatic geometry that is behind some record single-molecule magnet behaviours. A simple, almost visual analysis of the chemical shifts as a function of temperature, which is at the core of this approach, allows for a correct signal assignment and evaluation of the anisotropy of the magnetic susceptibility, the key indicator of a good single molecule magnet, that often cannot be done using traditional techniques rooted in quantum chemistry and NMR spectroscopy. The proposed approach thus emerged as a powerful alternative in deciphering the NMR spectra of paramagnetic compounds for applications in data processing and storage, magnetic resonance imaging and structural biology.
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Affiliation(s)
- Alexander A Pavlov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991, Moscow, Russia. .,Moscow Institute of Physics and Technology, Institutskiy per., 9, Dolgoprudny, Moscow Region, 141701, Russia
| | - Valentin V Novikov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991, Moscow, Russia. .,National Research University Higher School of Economics, Miasnitskaya Str. 20, Moscow 101000, Russia
| | - Igor A Nikovskiy
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991, Moscow, Russia.
| | - Elizaveta K Melnikova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991, Moscow, Russia. .,Lomonosov Moscow State University, Leninskie Gory, Moscow, 119991, Russia
| | - Yulia V Nelyubina
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991, Moscow, Russia. .,Moscow Institute of Physics and Technology, Institutskiy per., 9, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitry Y Aleshin
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991, Moscow, Russia.
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18
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Valigura D, Rajnák C, Titis J, Moncol J, Bieńko A, Boca R. Unusual Slow Magnetic Relaxation in a Mononuclear Copper(II) Complex. Dalton Trans 2022; 51:5612-5616. [DOI: 10.1039/d2dt00023g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A hexacoordinate Cu(II) complex with the {CuO4O’N} donor set shows an intermolecular π-πstacking owing to which a 1D-chain structure is formed. The DC magnetic data at low temperature is consistent...
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19
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Yu XY, Wu SY, Shen GQ, Yan L, Wei ZT, Li XY. Density functional theory calculations of copper-doped rutile crystals: Local structural, electronic, optical, and electron paramagnetic resonance properties. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:104-112. [PMID: 34212405 DOI: 10.1002/mrc.5190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
The local structural, electronic, optical, and electron paramagnetic resonance (EPR) properties are uniformly studied for Cu2+ -doped rutile (TiO2 ) crystals by using the density functional theory (DFT) calculations. The local cation-oxygen bond lengths and planar bond angle, band gap, Mulliken charge and overlapping population, density of state (DOS), and UV-Vis absorption spectra are calculated for pure and copper-doped rutile. The smaller overlapping population of Cu-O bonds in the doped system than Ti-O bonds in pure rutile reflects weaker orbital admixtures or covalency of the former. Compared with pure rutile, Cu2+ doping leads to significant redshift of the UV-Vis absorption band and the narrow impurity band in visible and near-infrared regions arising from the Cu2+ d-d transitions and narrowing of the band gap by about 0.636 eV, possibly suggesting enhancement of visible light activity. The Cu dopant induces a spin magnetic moment of 0.74 μB for the doped rutile. The calculated UV-Vis absorption spectra and spin Hamiltonian parameters for copper-doped rutile show reasonable agreement with the experimental data and some improvement related to the previous perturbation formula calculations. Present systematic studies would be helpful to understand the mechanisms of the enhancement in the optical and magnetic properties of this material with transition-metal (especially Cu2+ ) dopants.
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Affiliation(s)
- Xing-Yuan Yu
- Department of Applied Physics, School of Physics, University of Electronic Science and Technology of China, Chengdu, China
| | - Shao-Yi Wu
- Department of Applied Physics, School of Physics, University of Electronic Science and Technology of China, Chengdu, China
| | - Gao-Qiang Shen
- Department of Applied Physics, School of Physics, University of Electronic Science and Technology of China, Chengdu, China
| | - Li Yan
- Department of Applied Physics, School of Physics, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhang-Ting Wei
- Department of Applied Physics, School of Physics, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiao-Yu Li
- Department of Applied Physics, School of Physics, University of Electronic Science and Technology of China, Chengdu, China
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20
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Bonczidai-Kelemen D, Sciortino G, May NV, Garribba E, Fábián I, Lihi N. Introducing the penicillamine moiety into a metallopeptide mimicking the NiSOD enzyme: electronic and kinetic effects. Inorg Chem Front 2022. [DOI: 10.1039/d1qi01025e] [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
The novel NiSOD related metallopeptide incorporates penicillamine moiety in the active center which alters both the electronic and kinetic features.
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Affiliation(s)
- Dóra Bonczidai-Kelemen
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032, Debrecen, Hungary
| | - Giuseppe Sciortino
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Technology, 43007 Tarragona, Spain
| | - Nóra V. May
- Centre for Structural Science, Research Centre for Natural Sciences, H-1117, Budapest, Hungary
| | - Eugenio Garribba
- Dipartimento di Scienze Mediche, Chirurgiche e Sperimentali, Università di Sassari, I-07100 Sassari, Italy
| | - István Fábián
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032, Debrecen, Hungary
- MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group, University of Debrecen, H-4032, Debrecen, Hungary
| | - Norbert Lihi
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032, Debrecen, Hungary
- MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group, University of Debrecen, H-4032, Debrecen, Hungary
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21
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York NJ, Lockart MM, Pierce BS. Low-Spin Cyanide Complexes of 3-Mercaptopropionic Acid Dioxygenase (MDO) Reveal the Impact of Outer-Sphere SHY-Motif Residues. Inorg Chem 2021; 60:18639-18651. [PMID: 34883020 PMCID: PMC10078988 DOI: 10.1021/acs.inorgchem.1c01519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
3-Mercaptopropionic acid (3MPA) dioxygenase (MDO) is a non-heme Fe(II)/O2-dependent oxygenase that catalyzes the oxidation of thiol-substrates to yield the corresponding sulfinic acid. Hydrogen-bonding interactions between the Fe-site and a conserved set of three outer-sphere residues (Ser-His-Tyr) play an important catalytic role in the mechanism of this enzyme. Collectively referred to as the SHY-motif, the functional role of these residues remains poorly understood. Here, catalytically inactive Fe(III)-MDO precomplexed with 3MPA was titrated with cyanide to yield a low-spin (S = 1/2) (3MPA/CN)-bound ternary complex (referred to as 1C). UV-visible and electron paramagnetic resonance (EPR) spectroscopy were used to monitor the binding of 3MPA and cyanide. Comparisons of results obtained from SHY-motif variants (H157N and Y159F) were performed to investigate specific H-bonding interactions. For the wild-type enzyme, the binding of 3MPA- and cyanide to the enzymatic Fe-site is selective and results in a homogeneous ternary complex. However, this selectivity is lost for the Y159F variant, suggesting that H-bonding interactions contributed from Tyr159 gate ligand coordination at the Fe-site. Significantly, the g-values for the low-spin ferric site are diagnostic of the directionality of Tyr159 H-bond donation. Computational models coupled with CASSCF/NEVPT2-calculated g-values were used to verify that a major shift in the central g-value (g2) displayed between wild-type and SHY variants could be attributed to the loss of Tyr159 H-bond donation to the Fe-bound cyanide. Applied to native cosubstrate, this H-bond donation provides a means to stabilize Fe-bound dioxygen and potentially explains the attenuated (∼15-fold) rate of catalytic turnover previously reported for MDO SHY-motif variants.
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Affiliation(s)
- Nicholas J York
- Department of Chemistry & Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, Alabama 35487, United States
| | - Molly M Lockart
- Department of Chemistry & Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, Alabama 35487, United States
| | - Brad S Pierce
- Department of Chemistry & Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, Alabama 35487, United States
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22
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Pessoa JC, Santos MF, Correia I, Sanna D, Sciortino G, Garribba E. Binding of vanadium ions and complexes to proteins and enzymes in aqueous solution. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214192] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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23
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Schulz A, Szych LS, Pilopp Y, Bresien J, Villinger A, Rabeah J. A Persistent Phosphanyl-Substituted Thioketyl Radical Anion. Angew Chem Int Ed Engl 2021; 61:e202114792. [PMID: 34843637 PMCID: PMC9303638 DOI: 10.1002/anie.202114792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 12/05/2022]
Abstract
Alkali metal salts, M+[Ter(iPr)P−C(=S)−P(iPr)2S].− (M=Na, K; 2_M; Ter=2,6‐bis‐(2,4,6‐trimethylphenyl)phenyl) containing a room‐temperature‐stable thioketyl radical anion were obtained by reduction of the thioketone precursor, Ter(iPr)P−C(=S)−P(iPr)2S (1), with alkali metals (Na, K). Single‐crystal X‐ray studies as well as EPR spectroscopy revealed the unequivocal existence of a thioketyl radical anion in the solid state and in solution, respectively. The computed Mulliken spin density within 2_M is mainly located at the sulfur (49 %) and the carbonyl carbon (33 %) atoms. Upon adding [2.2.2]‐cryptand to the radical species 2_K to minimize the interionic interaction, an activation reaction was observed, yielding a potassium salt with a phosphanyl thioether based anion, [K(crypt)]+[Ter(iPr)P−C(−S‐iPr)−P(iPr)2S]− (3) as the product of an intermolecular shift of an iPr group from a second anion. The products were fully characterized and application of the radical anion as a reducing agent was demonstrated.
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Affiliation(s)
- Axel Schulz
- Universität Rostock, Institut für Chemie, Albert-Einstein-Str. 3a, 18059, Rostock, GERMANY
| | - Lilian Sophie Szych
- Universität Rostock Mathematisch-Naturwissenschaftliche Fakultät: Universitat Rostock Mathematisch-Naturwissenschaftliche Fakultat, Chemie, GERMANY
| | - Yannic Pilopp
- Universität Rostock Mathematisch-Naturwissenschaftliche Fakultät: Universitat Rostock Mathematisch-Naturwissenschaftliche Fakultat, Chemie, GERMANY
| | - Jonas Bresien
- Universität Rostock Mathematisch-Naturwissenschaftliche Fakultät: Universitat Rostock Mathematisch-Naturwissenschaftliche Fakultat, Chemie, GERMANY
| | - Alexander Villinger
- Universität Rostock Mathematisch-Naturwissenschaftliche Fakultät: Universitat Rostock Mathematisch-Naturwissenschaftliche Fakultat, Chemie, GERMANY
| | - Jabor Rabeah
- Leibniz Institute for Catalysis: Leibniz-Institut fur Katalyse eV, Chemie, GERMANY
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24
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Ugone V, Pisanu F, Sanna D, Garribba E. Interaction of the potent antitumoral compounds Casiopeinas® with blood serum and cellular bioligands. J Inorg Biochem 2021; 224:111566. [PMID: 34418714 DOI: 10.1016/j.jinorgbio.2021.111566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 12/16/2022]
Abstract
Casiopeinas® are among the few CuII compounds patented for their antitumor activity, but their mode of action has not been fully elucidated yet. One of them, Cas II-gly, is formed by 4,7-dimethyl-1,10-phenanthroline (Me2phen) and glycinato (Gly). In blood and cells, Cas II-gly can keep its identity or form mixed species with serum or cytosol bioligands (bL or cL) with composition CuII-Me2phen-bL/cL, CuII-Gly-bL/cL, or CuII-bL/cL. In this study, the binding of Cas II-gly with low molecular mass bioligands of blood serum (citric, L-lactic acid, and L-histidine) and cytosol (reduced glutathione (GSH), reduced nicotinamide adenine dinucleotide (NADH), adenosine triphosphate (ATP), and l-ascorbic acid) was examined through the application of instrumental (ElectroSpray Ionization-Mass Spectrometry and Electron Paramagnetic Resonance) and computational (Density Functional Theory) methods. The results indicated that mixed species CuII-Me2phen-bL/cL are formed, with the bioligands replacing glycinato. The formation of these adducts may participate in the copper transport toward the target organs and facilitate the cellular uptake or, in constrast, preclude it. In the systems with GSH, NADH and L-ascorbate, a redox reaction occurs with the partial oxidation of cL to the corresponding oxidized form (GSSG, NAD+ and dehydroascorbate) which interact with CuII. Formed CuI ion does not give complexation reactions with reduced or oxidized form of bioligands for its 'soft' character and low affinity for oxygen and nitrogen donors compared to CuII. However, CuI could promote Fenton-like reactions with production of reactive oxygen species (ROS) related to the antitumor activity of Casiopeinas®.
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Affiliation(s)
- Valeria Ugone
- Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Trav. La Crucca 3, I-07100 Sassari, Italy
| | - Federico Pisanu
- Dipartimento di Chimica e Farmacia, Università di Sassari, Via Vienna 2, I-07100 Sassari, Italy
| | - Daniele Sanna
- Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Trav. La Crucca 3, I-07100 Sassari, Italy.
| | - Eugenio Garribba
- Dipartimento di Chimica e Farmacia, Università di Sassari, Via Vienna 2, I-07100 Sassari, Italy.
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25
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Bruzzese PC, Salvadori E, Jäger S, Hartmann M, Civalleri B, Pöppl A, Chiesa M. 17O-EPR determination of the structure and dynamics of copper single-metal sites in zeolites. Nat Commun 2021; 12:4638. [PMID: 34330914 PMCID: PMC8324863 DOI: 10.1038/s41467-021-24935-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
The bonding of copper ions to lattice oxygens dictates the activity and selectivity of copper exchanged zeolites. By 17O isotopic labelling of the zeolite framework, in conjunction with advanced EPR methodologies and DFT modelling, we determine the local structure of single site CuII species, we quantify the covalency of the metal-framework bond and we assess how this scenario is modified by the presence of solvating H216O or H217O molecules. This enables to follow the migration of CuII species as a function of hydration conditions, providing evidence for a reversible transfer pathway within the zeolite cage as a function of the water pressure. The results presented in this paper establish 17O EPR as a versatile tool for characterizing metal-oxide interactions in open-shell systems.
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Affiliation(s)
- Paolo Cleto Bruzzese
- grid.9647.c0000 0004 7669 9786Felix Bloch Institute for Solid State Physics, Universität Leipzig, Leipzig, Germany ,grid.7605.40000 0001 2336 6580Department of Chemistry and NIS Centre of Excellence, University of Turin, Torino, Italy
| | - Enrico Salvadori
- grid.7605.40000 0001 2336 6580Department of Chemistry and NIS Centre of Excellence, University of Turin, Torino, Italy
| | - Stefan Jäger
- Erlangen Center for Interface Research and Catalysis (ECRC), Erlangen, Germany
| | - Martin Hartmann
- Erlangen Center for Interface Research and Catalysis (ECRC), Erlangen, Germany
| | - Bartolomeo Civalleri
- grid.7605.40000 0001 2336 6580Department of Chemistry and NIS Centre of Excellence, University of Turin, Torino, Italy
| | - Andreas Pöppl
- grid.9647.c0000 0004 7669 9786Felix Bloch Institute for Solid State Physics, Universität Leipzig, Leipzig, Germany
| | - Mario Chiesa
- grid.7605.40000 0001 2336 6580Department of Chemistry and NIS Centre of Excellence, University of Turin, Torino, Italy
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26
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Sproules S. Oxo versus Sulfido Coordination at Tungsten: A Spectroscopic and Correlated Ab Initio Electronic Structure Study. Inorg Chem 2021; 60:9057-9063. [PMID: 34096284 DOI: 10.1021/acs.inorgchem.1c01055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tungsten ion that resides at the active site of a unique class of enzymes only found in esoteric hyperthermophilic archaea bacteria is known to possess at least one terminal chalcogenide ligand. The identity of this as either an oxo or sulfido (or both) is difficult to ascertain from structural studies; therefore, small-molecule analogues are developed to calibrate and substantiate spectroscopic signatures obtained from native proteins. The electronic structures of Tp*WECl2 (E = O, S; Tp* = hydrotris(3,5-dimethylpyrazol-1-yl)borate) have been scrutinized using electronic, electron paramagnetic resonance (EPR), and X-ray absorption spectroscopy to assess the impact of terminal chalcogen on the adjacent cis chloride ligands. Examination at the Cl K-edge provides a direct probe of the bonding and therein lability of these chloride ligands, and in conjunction with density functional theoretical and multireference calculations reveals greater bond covalency in Tp*WOCl2 compared to Tp*WSCl2. The computational model and electronic structure assignment are corroborated by the reproduction of spin-Hamiltonian parameters, whose magnitude is dominated by the sizeable spin-orbit coupling of tungsten.
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Affiliation(s)
- Stephen Sproules
- WestCHEM, School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
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27
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Ravera E, Gigli L, Suturina EA, Calderone V, Fragai M, Parigi G, Luchinat C. A High-Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties. Angew Chem Int Ed Engl 2021; 60:14960-14966. [PMID: 33595173 DOI: 10.1002/anie.202101149] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 12/13/2022]
Abstract
Metalloproteins constitute a significant fraction of the proteome of all organisms and their characterization is critical for both basic sciences and biomedical applications. A large portion of metalloproteins bind paramagnetic metal ions, and paramagnetic NMR spectroscopy has been widely used in their structural characterization. However, the signals of nuclei in the immediate vicinity of the metal center are often broadened beyond detection. In this work, we show that it is possible to determine the coordination environment of the paramagnetic metal in the protein at a resolution inaccessible to other techniques. Taking the structure of a diamagnetic analogue as a starting point, a geometry optimization is carried out by fitting the pseudocontact shifts obtained from first principles quantum chemical calculations to the experimental ones.
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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28
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Ravera E, Gigli L, Suturina EA, Calderone V, Fragai M, Parigi G, Luchinat C. A High‐Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Lucia Gigli
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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29
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Schulz C, van Gastel M, Pantazis DA, Neese F. Converged Structural and Spectroscopic Properties for Refined QM/MM Models of Azurin. Inorg Chem 2021; 60:7399-7412. [PMID: 33939922 PMCID: PMC8154437 DOI: 10.1021/acs.inorgchem.1c00640] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 12/27/2022]
Abstract
Blue copper proteins continue to challenge experiment and theory with their electronic structure and spectroscopic properties that respond sensitively to the coordination environment of the copper ion. In this work, we report state-of-the art electronic structure studies for geometric and spectroscopic properties of the archetypal "Type I" copper protein azurin in its Cu(II) state. A hybrid quantum mechanics/molecular mechanics (QM/MM) approach is used, employing both density functional theory (DFT) and coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) methods for the QM region, the latter method making use of the domain-based local pair natural orbital (DLPNO) approach. Models of increasing QM size are employed to investigate the convergence of critical geometric parameters. It is shown that convergence is slow and that a large QM region is critical for reproducing the short experimental Cu-SCys112 distance. The study of structural convergence is followed by investigation of spectroscopic parameters using both DFT and DLPNO-CC methods and comparing these to the experimental spectrum using simulations. The results allow us to examine for the first time the distribution of spin densities and hyperfine coupling constants at the coupled cluster level, leading us to revisit the experimental assignment of the 33S hyperfine splitting. The wavefunction-based approach to obtain spin-dependent properties of open-shell systems demonstrated here for the case of azurin is transferable and applicable to a large array of bioinorganic systems.
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Affiliation(s)
- Christine
E. Schulz
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Maurice van Gastel
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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30
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Pell AJ. A method to calculate the NMR spectra of paramagnetic species using thermalized electronic relaxation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 326:106939. [PMID: 33744830 DOI: 10.1016/j.jmr.2021.106939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
For paramagnetic species, it has been long understood that the hyperfine interaction between the unpaired electrons and the nucleus results in a nuclear magnetic resonance (NMR) peak that is shifted by a paramagnetic shift, rather than split by the coupling, due to an averaging of the electronic magnetic moment caused by electronic relaxation that is fast in comparison to the hyperfine coupling constant. However, although this feature of paramagnetic NMR has formed the basis of all theories of the paramagnetic shift, the precise theory and mechanism of the electronic relaxation required to predict this result has never been discussed, nor has the assertion been tested. In this paper, we show that the standard semi-classical Redfield theory of relaxation fails to predict a paramagnetic shift, as does any attempt to correct for the semi-classical theory using modifications such as the inhomogeneous master equation or Levitt-di Bari thermalization. In fact, only the recently-introduced Lindbladian theory of relaxation in magnetic resonance [J.Magn.Reson., 310, 106645 (2019)] is able to correctly predict the paramagnetic shift tensor and relaxation-induced linewidth in pNMR. Furthermore, this new formalism is able to predict the NMR spectra of paramagnetic species outside the high-temperature and weak-order limits, and is therefore also applicable to dynamic nuclear polarization. The formalism is tested by simulations of five case studies, which include Fermi-contact and spin-dipolar hyperfine couplings, g-anisotropy, zero-field splitting, high and low temperatures, and fast and slow electronic relaxation.
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Affiliation(s)
- Andrew J Pell
- Department of Materials and Environmental Chemistry, Stockholm University, Svänte Arrhenius väg 16 C, 106 91 Stockholm, Sweden; Centre de RMN Trés Hauts Champs de Lyon (UMR5082 CNRS/ENS-Lyon/Université Claude Bernard Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France.
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31
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Orio M, Bindra JK, van Tol J, Giorgi M, Dalal NS, Bertaina S. Quantum dynamics of Mn 2+ in dimethylammonium magnesium formate. J Chem Phys 2021; 154:154201. [PMID: 33887944 DOI: 10.1063/5.0046984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Dimethylammonium magnesium formate, [(CH3)2NH2][Mg(HCOO)3] or DMAMgF, is a model used to study high temperature hybrid perovskite-like dielectrics. This compound displays an order-disorder phase transition at about 260 K. Using multifrequency electron spin resonance in continuous wave and pulsed modes, we herein present the quantum dynamics of the Mn2+ ion probe in DMAMgF. In the high temperature paraelectric phase, we observe a large distribution of the zero field splitting that is attributed to the high local disorder and further supported by density functional theory computations. In the low temperature ferroelastic phase, a single structure phase is detected and shown to contain two magnetic structures. The complex electron paramagnetic resonance signals were identified by means of the Rabi oscillation method combined with the crystal field kernel density estimation.
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Affiliation(s)
- M Orio
- CNRS, Aix-Marseille Université, Centrale Marseille, iSm2, Institut des Sciences Moléculaires de Marseille, Marseille, France
| | - J K Bindra
- Department of Chemistry, Florida State University, Tallahassee, Florida 32310, USA
| | - J van Tol
- The National High Magnetic Field Laboratory, Tallahassee, Florida 32310, USA
| | - M Giorgi
- Aix Marseille Université, CNRS, Centrale Marseille, FSCM, Spectropole, Marseille, France
| | - N S Dalal
- Department of Chemistry, Florida State University, Tallahassee, Florida 32310, USA
| | - S Bertaina
- CNRS, Aix-Marseille Université, IM2NP (UMR 7334), Institut Matériaux Microélectronique et Nanosciences de Provence, Marseille, France
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32
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Farcaş AA, Bende A. Theoretical modeling of the singlet-triplet spin transition in different Ni(II)-diketo-pyrphyrin-based metal-ligand octahedral complexes. Phys Chem Chem Phys 2021; 23:4784-4795. [PMID: 33599640 DOI: 10.1039/d0cp05366j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structural stability, charge transfer effects and strength of the spin-orbit couplings in different Ni(ii)-ligand complexes have been studied at the DFT (B3LYP and CAM-B3LYP) and coupled cluster (DLPNO-CCSD(T)) levels of theory. Accordingly, two different, porphyrin- and diketo-pyrphyrin-based four-coordination macrocycles as planar ligands as well as pyridine (or pyrrole) and mesylate anion molecular groups as vertical ligands were considered in order to build metal-organic complexes with octahedral coordination configurations. For each molecular system, the identification of equilibrium geometries and the intersystem crossing (the minimum energy crossing) points between the potential energy surfaces of the singlet and triplet spin states is followed by computing the spin-orbit couplings between the two spin states. Structures, based on the diketo-pyrphyrin macrocycle as the planar ligand, show stronger six-coordination metal-organic complexes due to the extra electrostatic interaction between the positively charged central metal cation and the negatively charged vertical ligands. The results also show that the magnitude of the spin-orbit coupling is influenced by the atomic positions of deprotonations of the ligands, and implicitly the direction of the charge transfer between the ligand and the central metal ion.
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Affiliation(s)
- Alex-Adrian Farcaş
- Faculty of Physics, "Babeş-Bolyai" University, Mihail Kogalniceanu Street No. 1, Ro-400084 Cluj-Napoca, Romania
| | - Attila Bende
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Donat Street, No. 67-103, Ro-400293 Cluj-Napoca, Romania.
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33
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Ravera E, Gigli L, Czarniecki B, Lang L, Kümmerle R, Parigi G, Piccioli M, Neese F, Luchinat C. A Quantum Chemistry View on Two Archetypical Paramagnetic Pentacoordinate Nickel(II) Complexes Offers a Fresh Look on Their NMR Spectra. Inorg Chem 2021; 60:2068-2075. [PMID: 33478214 PMCID: PMC7877564 DOI: 10.1021/acs.inorgchem.0c03635] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Quantum chemical methods for calculating paramagnetic NMR observables are becoming
increasingly accessible and are being included in the inorganic chemistry practice.
Here, we test the performance of these methods in the prediction of proton hyperfine
shifts of two archetypical high-spin pentacoordinate nickel(II) complexes (NiSAL-MeDPT
and NiSAL-HDPT), which, for a variety of reasons, turned out to be perfectly suited to
challenge the predictions to the finest level of detail. For NiSAL-MeDPT, new NMR
experiments yield an assignment that perfectly matches the calculations. The slightly
different hyperfine shifts from the two “halves” of the molecules related
by a pseudo-C2 axis, which are experimentally divided into
two well-defined spin systems, are also straightforwardly distinguished by the
calculations. In the case of NiSAL-HDPT, for which no X-ray structure is available, the
quality of the calculations allowed us to refine its structure using as a starting
template the structure of NiSAL-MeDPT. State-of-the-art
quantum chemical methods and paramagnetism-tailored
NMR experiments provide a deep insight on the relation between the
spectra and the electronic structure for two paramagnetic pentacoordinate
nickel(II) complexes.
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Affiliation(s)
- Enrico Ravera
- Department of Chemistry "Ugo Schiff″, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Lucia Gigli
- Department of Chemistry "Ugo Schiff″, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Barbara Czarniecki
- Bruker Biospin Corporation, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Lucas Lang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Rainer Kümmerle
- Bruker Biospin Corporation, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Giacomo Parigi
- Department of Chemistry "Ugo Schiff″, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Mario Piccioli
- Department of Chemistry "Ugo Schiff″, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Claudio Luchinat
- Department of Chemistry "Ugo Schiff″, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
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34
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Kisgeropoulos EC, Manesis AC, Shafaat HS. Ligand Field Inversion as a Mechanism to Gate Bioorganometallic Reactivity: Investigating a Biochemical Model of Acetyl CoA Synthase Using Spectroscopy and Computation. J Am Chem Soc 2021; 143:849-867. [PMID: 33415980 DOI: 10.1021/jacs.0c10135] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biological global carbon cycle is largely regulated through microbial nickel enzymes, including carbon monoxide dehydrogenase (CODH), acetyl coenzyme A synthase (ACS), and methyl coenzyme M reductase (MCR). These systems are suggested to utilize organometallic intermediates during catalysis, though characterization of these species has remained challenging. We have established a mutant of nickel-substituted azurin as a scaffold upon which to develop protein-based models of enzymatic intermediates, including the organometallic states of ACS. In this work, we report the comprehensive investigation of the S = 1/2 Ni-CO and Ni-CH3 states using pulsed EPR spectroscopy and computational techniques. While the Ni-CO state shows conventional metal-ligand interactions and a classical ligand field, the Ni-CH3 hyperfine interactions between the methyl protons and the nickel indicate a closer distance than would be expected for an anionic methyl ligand. Structural analysis instead suggests a near-planar methyl ligand that can be best described as cationic. Consistent with this conclusion, the frontier molecular orbitals of the Ni-CH3 species indicate a ligand-centered LUMO, with a d9 population on the metal center, rather than the d7 population expected for a typical metal-alkyl species generated by oxidative addition. Collectively, these data support the presence of an inverted ligand field configuration for the Ni-CH3 Az species, in which the lowest unoccupied orbital is centered on the ligands rather than the more electropositive metal. These analyses provide the first evidence for an inverted ligand field within a biological system. The functional relevance of the electronic structures of both the Ni-CO and Ni-CH3 species are discussed in the context of native ACS, and an inverted ligand field is proposed as a mechanism by which to gate reactivity both within ACS and in other thiolate-containing metalloenzymes.
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Affiliation(s)
- Effie C Kisgeropoulos
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anastasia C Manesis
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
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35
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Bors I, Purgel M, Fehér PP, Varga T, Speier G, Korecz L, Kaizer J. Unexpected radical mechanism in a [4+1] cycloaddition reaction. NEW J CHEM 2021. [DOI: 10.1039/d1nj00660f] [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
The mechanism of the cheletropic reaction of monoimines with PPh3via unexpected radical intermediates resulting in oxazaphospholes has been discussed based on EPR, UV-vis and DFT calculations.
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Affiliation(s)
- István Bors
- Research Group of Bioorganic and Biocoordination Chemistry
- University of Pannonia
- Veszprém H-8200
- Hungary
| | - Mihály Purgel
- Department of Physical Chemistry
- University of Debrecen
- Debrecen H-4032
- Hungary
| | - Péter Pál Fehér
- Institute of Organic Chemistry
- Research Centre for Natural Sciences
- Budapest H-1117
- Hungary
| | - Tamás Varga
- Department of Process Engineering
- University of Pannonia
- Veszprém H-8200
- Hungary
| | - Gábor Speier
- Research Group of Bioorganic and Biocoordination Chemistry
- University of Pannonia
- Veszprém H-8200
- Hungary
| | - László Korecz
- Institute of Materials and Environmental Chemistry
- Research Centre for Natural Sciences
- Budapest H-1117
- Hungary
| | - József Kaizer
- Research Group of Bioorganic and Biocoordination Chemistry
- University of Pannonia
- Veszprém H-8200
- Hungary
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36
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Sciortino G, Maréchal JD, Garribba E. Integrated experimental/computational approaches to characterize the systems formed by vanadium with proteins and enzymes. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01507e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An integrated instrumental/computational approach to characterize metallodrug–protein adducts at the molecular level is reviewed. A series of applications are described, focusing on potential vanadium drugs with a generalization to other metals.
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Affiliation(s)
- Giuseppe Sciortino
- Departament de Química
- Universitat Autònoma de Barcelona
- Cerdanyola del Vallès
- Barcelona 08193
- Spain
| | - Jean-Didier Maréchal
- Departament de Química
- Universitat Autònoma de Barcelona
- Cerdanyola del Vallès
- Barcelona 08193
- Spain
| | - Eugenio Garribba
- Dipartimento di Chimica e Farmacia
- Università di Sassari
- 07100 Sassari
- Italy
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37
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Theibich YA, Sauer SP, Leggio LL, Hedegård ED. Estimating the accuracy of calculated electron paramagnetic resonance hyperfine couplings for a lytic polysaccharide monooxygenase. Comput Struct Biotechnol J 2020; 19:555-567. [PMID: 33510861 PMCID: PMC7807142 DOI: 10.1016/j.csbj.2020.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 11/07/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are enzymes that bind polysaccharides followed by an (oxidative) disruption of the polysaccharide surface, thereby boosting depolymerization. The binding process between the LPMO catalytic domain and polysaccharide is key to the mechanism and establishing structure-function relationships for this binding is therefore crucial. The hyperfine coupling constants (HFCs) from EPR spectroscopy have proven useful for this purpose. Unfortunately, EPR does not provide direct structural data and therefore the experimental EPR parameters have to be supported with parameters calculated with density functional theory. Yet, calculated HFCs are extremely sensitive to the employed computational setup. Using the LPMO Ls(AA9)A catalytic domain, we here quantify the importance of several choices in the computational setup, ranging from the use of specialized basis, the underlying structures, and the employed exchange-correlation functional. We show that specialized basis sets are an absolute necessity, and also that care has to be taken in the optimization of the underlying structure: only by allowing large parts of the protein around the active site to structurally relax could we obtain results that uniformly reproduced experimental trends. We compare our results to previously published X-ray structures and experimental HFCs for Ls(AA9)A as well as to recent experimental/theoretical results for another (AA10) family of LPMOs.
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Affiliation(s)
- Yusuf A. Theibich
- Department of Chemistry, University of University, Copenhagen, Denmark
| | | | - Leila Lo Leggio
- Department of Chemistry, University of University, Copenhagen, Denmark
| | - Erik D. Hedegård
- Division of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
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38
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Dimethyl sulfoxide as a strongly coordinating solvent: 3′,4′-dihydroxyflavone-Cu(II)-DMSO system case study. ACTA CHIMICA SLOVACA 2020. [DOI: 10.2478/acs-2020-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
Dimethyl sulfoxide (DMSO) is an aprotic organic solvent widely used in laboratory practice due to its ability to dissolve both polar and nonpolar compounds. However, DMSO is also commonly known as a strongly coordinating solvent, especially towards transition metal containing complexes. In this study, estimation of the coordination ability of DMSO towards the Cu(II) ion was attempted, employing a model system composed of 3′,4′-dihydroxyflavone-Cu(II) complex in the presence of explicit DMSO molecules, using the density functional theory (DFT). Nature of the Cu-DMSO chemical interaction (i.e. Cu-O bonding) was studied within the framework of quantum theory of atoms in molecules (QTAIM). Impact of DMSO coordination on the charge and spin distribution at Cu(II) ion was inspected using Mulliken population and QTAIM analysis.
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39
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Gómez-Piñeiro RJ, Pantazis DA, Orio M. Comparison of Density Functional and Correlated Wave Function Methods for the Prediction of Cu(II) Hyperfine Coupling Constants. Chemphyschem 2020; 21:2667-2679. [PMID: 33201578 PMCID: PMC7756273 DOI: 10.1002/cphc.202000649] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/13/2020] [Indexed: 12/19/2022]
Abstract
The reliable prediction of Cu(II) hyperfine coupling constants remains a challenge for quantum chemistry. Until recently only density functional theory (DFT) could target this property for systems of realistic size. However, wave function based methods become increasingly applicable. In the present work, we define a large set of Cu(II) complexes with experimentally known hyperfine coupling constants and use it to investigate the performance of modern quantum chemical methods for the prediction of this challenging spectroscopic parameter. DFT methods are evaluated against orbital‐optimized second‐order Møller‐Plesset (OO‐MP2) theory and coupled cluster calculations including singles and doubles excitations, driven by the domain‐based local pair natural orbital approach (DLPNO‐CCSD). Special attention is paid to the definition of a basis set that converges adequately toward the basis set limit for the given property for all methods considered in this study, and a specifically optimized basis set is proposed for this purpose. The results suggest that wave function based methods can supplant but do not outcompete DFT for the calculation of Cu(II) hyperfine coupling constants. Mainstream hybrid functionals such as B3PW91 remain on average the best choice.
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Affiliation(s)
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Maylis Orio
- Aix-Marseille Université, CNRS, iSm2, Marseille, France
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40
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Lang L, Ravera E, Parigi G, Luchinat C, Neese F. Solution of a Puzzle: High-Level Quantum-Chemical Treatment of Pseudocontact Chemical Shifts Confirms Classic Semiempirical Theory. J Phys Chem Lett 2020; 11:8735-8744. [PMID: 32930598 PMCID: PMC7584370 DOI: 10.1021/acs.jpclett.0c02462] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
A recently popularized approach for the calculation of pseudocontact shifts (PCSs) based on first-principles quantum chemistry (QC) leads to different results than the classic "semiempirical" equation involving the susceptibility tensor. Studies that attempted a comparison of theory and experiment led to conflicting conclusions with respect to the preferred theoretical approach. In this Letter, we show that after inclusion of previously neglected terms in the full Hamiltonian, one can deduce the semiempirical equations from a rigorous QC-based treatment. It also turns out that in the long-distance limit, one can approximate the complete A tensor in terms of the g tensor. By means of Kohn-Sham density functional theory calculations, we numerically confirm the long-distance expression for the A tensor and the theoretically predicted scaling behavior of the different terms. Our derivation suggests a computational strategy in which one calculates the susceptibility tensor and inserts it into the classic equation for the PCS.
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Affiliation(s)
- Lucas Lang
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Enrico Ravera
- Magnetic
Resonance Center (CERM), University of Florence,
and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine
(CIRMMP), via Sacconi
6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Giacomo Parigi
- Magnetic
Resonance Center (CERM), University of Florence,
and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine
(CIRMMP), via Sacconi
6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Claudio Luchinat
- Magnetic
Resonance Center (CERM), University of Florence,
and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine
(CIRMMP), via Sacconi
6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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41
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Ghassemi Tabrizi S, Arbuznikov AV, Jiménez-Hoyos CA, Kaupp M. Hyperfine-Coupling Tensors from Projected Hartree-Fock Theory. J Chem Theory Comput 2020; 16:6222-6235. [PMID: 32841008 DOI: 10.1021/acs.jctc.0c00617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We assess the calculation of hyperfine coupling (HFC) tensors by different variants of Projected Hartree-Fock (PHF) theory. For a set of small main-group S = 1/2 radicals (BO, CO+, CN, AlO, vinyl, methyl, ethynyl), spin-symmetry as well as complex-conjugation and point-group symmetry are first broken in a reference determinant, and then variationally restored, in the frame of the modern formulation of PHF theory. Historically, PHF theory was basically restricted to the restoration of spin symmetry from an unrestricted HF determinant (conserving Sz symmetry). This afforded unsatisfactory HFCs. We obtain far better results for isotropic (and anisotropic) HFCs when the variational energy is further lowered by working with generalized determinants that completely break spin symmetry, and when additional symmetries are used. Specifically, complex-conjugation projection recovers a substantial fraction of the dynamical correlation energy in small molecules, and the detailed equations for combined complex-conjugation, spin- and point-group projection in the density-matrix/diagonalization formulation of PHF theory are here reported for the first time. The compact representation of the PHF wave function allows for a straightforward evaluation of the spin-density matrix and of HFC tensors with little effort. The promising performance of PHF theory may motivate the application of post-PHF methods to the calculation of HFC tensors.
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Affiliation(s)
- Shadan Ghassemi Tabrizi
- Institut für Chemie, Theoretische Chemie, Technische Universität Berlin, Sekr. C7, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Alexei V Arbuznikov
- Institut für Chemie, Theoretische Chemie, Technische Universität Berlin, Sekr. C7, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Carlos A Jiménez-Hoyos
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie, Technische Universität Berlin, Sekr. C7, Strasse des 17. Juni 135, 10623 Berlin, Germany
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42
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Sciortino G, Sanna D, Lubinu G, Maréchal J, Garribba E. Unveiling VIVO2+Binding Modes to Human Serum Albumins by an Integrated Spectroscopic–Computational Approach. Chemistry 2020; 26:11316-11326. [DOI: 10.1002/chem.202001492] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/02/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Giuseppe Sciortino
- Department de QuímicaUniversitat Autònoma de Barcelona 08193 Cerdanyola del Vallés, Barcelona Spain
- Dipartimento di Chimica e FarmaciaUniversità di Sassari Via Vienna 2 07100 Sassari Italy
| | - Daniele Sanna
- Istituto di Chimica BiomolecolareConsiglio Nazionale delle Ricerche Trav. La Crucca 3 07100 Sassari Italy
| | - Giuseppe Lubinu
- Dipartimento di Chimica e FarmaciaUniversità di Sassari Via Vienna 2 07100 Sassari Italy
| | - Jean‐Didier Maréchal
- Department de QuímicaUniversitat Autònoma de Barcelona 08193 Cerdanyola del Vallés, Barcelona Spain
| | - Eugenio Garribba
- Dipartimento di Chimica e FarmaciaUniversità di Sassari Via Vienna 2 07100 Sassari Italy
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43
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Sun Q, Zhang X, Banerjee S, Bao P, Barbry M, Blunt NS, Bogdanov NA, Booth GH, Chen J, Cui ZH, Eriksen JJ, Gao Y, Guo S, Hermann J, Hermes MR, Koh K, Koval P, Lehtola S, Li Z, Liu J, Mardirossian N, McClain JD, Motta M, Mussard B, Pham HQ, Pulkin A, Purwanto W, Robinson PJ, Ronca E, Sayfutyarova ER, Scheurer M, Schurkus HF, Smith JET, Sun C, Sun SN, Upadhyay S, Wagner LK, Wang X, White A, Whitfield JD, Williamson MJ, Wouters S, Yang J, Yu JM, Zhu T, Berkelbach TC, Sharma S, Sokolov AY, Chan GKL. Recent developments in the PySCF program package. J Chem Phys 2020; 153:024109. [DOI: 10.1063/5.0006074] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Qiming Sun
- AxiomQuant Investment Management LLC, Shanghai 200120, China
| | - Xing Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Samragni Banerjee
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Peng Bao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Marc Barbry
- Simbeyond B.V., P.O. Box 513, NL-5600 MB, Eindhoven, The Netherlands
| | - Nick S. Blunt
- Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Nikolay A. Bogdanov
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - George H. Booth
- Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Jia Chen
- Department of Physics, University of Florida, Gainesville, Florida 32611, USA
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Zhi-Hao Cui
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Janus J. Eriksen
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Yang Gao
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, USA
| | - Sheng Guo
- Google Inc., Mountain View, California 94043, USA
| | - Jan Hermann
- FU Berlin, Department of Mathematics and Computer Science, Arnimallee 6, 14195 Berlin, Germany
- TU Berlin, Machine Learning Group, Marchstr. 23, 10587 Berlin, Germany
| | - Matthew R. Hermes
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
| | - Kevin Koh
- Department of Chemistry and Biochemistry, The University of Notre Dame du Lac, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
| | - Peter Koval
- Simune Atomistics S.L., Avenida Tolosa 76, Donostia-San Sebastian, Spain
| | - Susi Lehtola
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A. I. Virtasen aukio 1), FI-00014 Helsinki, Finland
| | - Zhendong Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Junzi Liu
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Narbe Mardirossian
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, California 91320, USA
| | | | - Mario Motta
- IBM Almaden Research Center, San Jose, California 95120, USA
| | - Bastien Mussard
- Department of Chemistry, University of Colorado, Boulder, Colorado 80302, USA
| | - Hung Q. Pham
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
| | - Artem Pulkin
- QuTech and Kavli Institute of Nanoscience, Delft University of Technology, The Netherlands
| | - Wirawan Purwanto
- Information Technology Services, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Paul J. Robinson
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Enrico Ronca
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), Via G. Moruzzi, 1, 56124 Pisa, Italy
| | - Elvira R. Sayfutyarova
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University of Heidelberg, 205 Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Henry F. Schurkus
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - James E. T. Smith
- Department of Chemistry, University of Colorado, Boulder, Colorado 80302, USA
| | - Chong Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Shi-Ning Sun
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, USA
| | - Shiv Upadhyay
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Lucas K. Wagner
- Department of Physics and Institute for Condensed Matter Theory, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - Xiao Wang
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, USA
| | - Alec White
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - James Daniel Whitfield
- Department of Physics and Astronomy, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - Mark J. Williamson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | | - Jun Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jason M. Yu
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Tianyu Zhu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Timothy C. Berkelbach
- Department of Chemistry, Columbia University, New York, New York 10027, USA
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, USA
| | - Sandeep Sharma
- Department of Chemistry, University of Colorado, Boulder, Colorado 80302, USA
| | - Alexander Yu. Sokolov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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44
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Moltved KA, Kepp KP. Using electronegativity and hardness to test density functionals. J Chem Phys 2020; 152:244113. [PMID: 32610960 DOI: 10.1063/5.0006189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Density functional theory (DFT) is used in thousands of papers each year, yet lack of universality reduces DFT's predictive capacity, and functionals may produce energy-density imbalances. The absolute electronegativity (χ) and hardness (η) directly reflect the energy-density relationship via the chemical potential ∂E/∂N and we thus hypothesized that they probe universality. We studied χ and η for atoms Z = 1-36 using 50 diverse functionals covering all major classes. Very few functionals describe both χ and η well. η benefits from error cancellation, whereas χ is marred by error propagation from IP and EA; thus, almost all standard GGA and hybrid functionals display a plateau in the MAE at ∼0.2 eV-0.3 eV for η. In contrast, variable performance for χ indicates problems in describing the chemical potential by DFT. The accuracy and precision of a functional is far from linearly related, yet for a universal functional, we expect linearity. Popular functionals such as B3LYP, PBE, and revPBE perform poorly for both properties. Density sensitivity calculations indicate large density-derived errors as occupation of degenerate p- and d-orbitals causes "non-universality" and large dependency on exact exchange. Thus, we argue that performance for χ for the same systems is a hallmark of an important aspect of universality by probing ∂E/∂N. With this metric, B98, B97-1, PW6B95D3, MN-15, rev-TPSS, HSE06, and APFD are the most "universal" among the tested functionals. B98 and B97-1 are accurate for very diverse metal-ligand bonds, supporting that a balanced description of ∂E/∂N and ∂E2/∂N2, via χ and η, is probably a first simple probe of universality.
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Affiliation(s)
- Klaus A Moltved
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, Denmark
| | - Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, Denmark
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45
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Neese F, Wennmohs F, Becker U, Riplinger C. The ORCA quantum chemistry program package. J Chem Phys 2020; 152:224108. [DOI: 10.1063/5.0004608] [Citation(s) in RCA: 697] [Impact Index Per Article: 139.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Frank Neese
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany
- FAccTs GmbH, Rolandstr. 67, 50677 Köln, Germany
| | - Frank Wennmohs
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Ute Becker
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany
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46
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Lazorski MS, Schapiro I, Gaddie RS, Lehnig AP, Atanasov M, Neese F, Steiner UE, Elliott CM. Spin-chemical effects on intramolecular photoinduced charge transfer reactions in bisphenanthroline copper(i)-viologen dyad assemblies. Chem Sci 2020; 11:5511-5525. [PMID: 32874494 PMCID: PMC7448374 DOI: 10.1039/d0sc00830c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/11/2020] [Indexed: 11/21/2022] Open
Abstract
Two covalently linked donor-acceptor copper phenanthroline complexes (C-A dyads) of interest for solar energy conversion/storage schemes, [Cu(i)(Rphen(OMV)2 4+)2]9+ = RC+A4 8+ with RC+ = [Cu(i)Rphen2]+ involving 2,9-methyl (R = Me) or 2,9-phenyl (R = Ph)-phenanthroline ligands that are 5,6-disubstituted by 4-(n-butoxy) linked methylviologen electron acceptor groups (A2+ = OMV2+), have been synthesized and investigated via quantum chemical calculations and nanosecond laser flash spectroscopy in 1,2-difluorobenzene/methanol (dfb/MeOH) mixtures. Upon photoexcitation, charge transfer (CT) states RC2+A+A3 6+ are formed in less than one ns and decay by charge recombination on a time scale of 6-45 ns. The CT lifetime of RC2+A+A3 6+ has a strong dependence on MeOH solvent fraction when R = Me, but is unaffected if R = Ph. This solvent effect is due to coordination of MeOH solvent in MeC+A4 8+ (i.e. exciplex formation) allowed by conformational flattening of the ligand sphere, which cannot occur in PhC+A4 8+ having bulkier Phphen ligand framework. Interestingly, the decay time of the CT state increases for both species at low magnetic fields with a maximum increase of ca. 30% at ca. 150 mT, then decreases as the field is increased up to 1500 mT, the highest field investigated. This magnetic field effect (MFE) is due to magnetic modulation of the spin dynamics interconverting 3CT and 1CT states. A quantitative modeling according to the radical pair mechanism involving ab initio multireference calculations of the complexes revealed that the spin process is dominated by the effect of Cu hyperfine coupling. The external magnetic field suppresses the hyperfine coupling induced spin state mixing thereby lengthening the CT decay time. This effect is counteracted by the field dependent processes of T0-S mixing through the Δg-mechanism and by a local mode spin-orbit mechanism. Further, the maximum MFE is limited by a finite rate of direct recombination of 3CT states and the spin-rotational mechanism of spin relaxation. This study provides a first comprehensive characterization of Cu(ii)-complex spin chemistry and highlights how spin chemistry can be used to manipulate solar energy harvesting and storage materials.
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Affiliation(s)
- Megan S Lazorski
- Department of Chemistry , Colorado State University , Fort Collins , CO 80523 , USA .
| | - Igor Schapiro
- Max Planck Institute for Chemical Energy Conversion , D-45470 Mülheim an der Ruhr , Germany
| | - Ross S Gaddie
- Department of Chemistry , Colorado State University , Fort Collins , CO 80523 , USA .
| | - Ammon P Lehnig
- Department of Chemistry , Colorado State University , Fort Collins , CO 80523 , USA .
| | - Mihail Atanasov
- Max Planck Institute for Chemical Energy Conversion , D-45470 Mülheim an der Ruhr , Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion , D-45470 Mülheim an der Ruhr , Germany
| | - Ulrich E Steiner
- Department of Chemistry , University of Konstanz , Universitätsstraße 14 , Konstanz , 78457 , Germany
| | - C Michael Elliott
- Department of Chemistry , Colorado State University , Fort Collins , CO 80523 , USA .
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47
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Zhang GJ, Wu SY, Liang CH, Fan YM, Luo YJ, Guo JX, Li XY. DFT calculations of the local structures and the EPR parameters for Rh2+ doped AO (A = Mg, Ca) crystals. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Chen J, Hu C, Stanton JF, Hill S, Cheng HP, Zhang XG. Decoherence in Molecular Electron Spin Qubits: Insights from Quantum Many-Body Simulations. J Phys Chem Lett 2020; 11:2074-2078. [PMID: 32097549 DOI: 10.1021/acs.jpclett.0c00193] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Quantum states are described by wave functions whose phases cannot be directly measured but which play a vital role in quantum effects such as interference and entanglement. The loss of the relative phase information, termed decoherence, arises from the interactions between a quantum system and its environment. Decoherence is perhaps the biggest obstacle on the path to reliable quantum computing. Here we show that decoherence occurs even in an isolated molecule, although not all phase information is lost, via a theoretical study of a central electron spin qubit interacting with nearby nuclear spins in prototypical magnetic molecules. The residual coherence, which is molecule-dependent, provides a microscopic rationalization for the nuclear spin diffusion barrier proposed to explain experiments. The contribution of nearby molecules to the decoherence has a nontrivial dependence on separation, peaking at intermediate distances. Molecules that are far away affect only the long-time behavior. Because the residual coherence is simple to calculate and correlates well with the coherence time, it can be used as a descriptor for coherence in magnetic molecules. This work will help establish design principles for enhancing coherence in molecular spin qubits and serve to motivate further theoretical work.
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Affiliation(s)
- Jia Chen
- Department of Physics, University of Florida, Gainesville, Florida 32611, United States
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
- Center for Molecular Magnetic Quantum Materials, Gainesville, Florida, United States
| | - Cong Hu
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, United States
| | - John F Stanton
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
- Center for Molecular Magnetic Quantum Materials, Gainesville, Florida, United States
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Stephen Hill
- Center for Molecular Magnetic Quantum Materials, Gainesville, Florida, United States
- Department of Physics and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, United States
| | - Hai-Ping Cheng
- Department of Physics, University of Florida, Gainesville, Florida 32611, United States
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
- Center for Molecular Magnetic Quantum Materials, Gainesville, Florida, United States
| | - Xiao-Guang Zhang
- Department of Physics, University of Florida, Gainesville, Florida 32611, United States
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
- Center for Molecular Magnetic Quantum Materials, Gainesville, Florida, United States
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Fischer AA, Miller JR, Jodts RJ, Ekanayake DM, Lindeman SV, Brunold TC, Fiedler AT. Spectroscopic and Computational Comparisons of Thiolate-Ligated Ferric Nonheme Complexes to Cysteine Dioxygenase: Second-Sphere Effects on Substrate (Analogue) Positioning. Inorg Chem 2019; 58:16487-16499. [PMID: 31789510 DOI: 10.1021/acs.inorgchem.9b02432] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Parallel spectroscopic and computational studies of iron(III) cysteine dioxygenase (CDO) and synthetic models are presented. The synthetic complexes utilize the ligand tris(4,5-diphenyl-1-methylimidazol-2-yl)phosphine (Ph2TIP), which mimics the facial three-histidine triad of CDO and other thiol dioxygenases. In addition to the previously reported [FeII(CysOEt)(Ph2TIP)]BPh4 (1; CysOEt is the ethyl ester of anionic l-cysteine), the formation and crystallographic characterization of [FeII(2-MTS)(Ph2TIP)]BPh4 (2) is reported, where the methyl 2-thiosalicylate anion (2-MTS) resembles the substrate of 3-mercaptopropionate dioxygenase (MDO). One-electron chemical oxidation of 1 and 2 yields ferric species that bind cyanide and azide anions, which have been used as spectroscopic probes of O2 binding in prior studies of FeIII-CDO. The six-coordinate FeIII-CN and FeIII-N3 adducts are examined with UV-vis absorption, electron paramagnetic resonance (EPR), and resonance Raman (rRaman) spectroscopies. In addition, UV-vis and rRaman studies of cysteine- and cyanide-bound FeIII-CDO are reported for both the wild-type (WT) enzyme and C93G variant, which lacks the Cys-Tyr cross-link that is present in the second coordination sphere of the WT active site. Density functional theory (DFT) and ab initio calculations are employed to provide geometric and electronic structure descriptions of the synthetic and enzymatic FeIII adducts. In particular, it is shown that the complete active space self-consistent field (CASSCF) method, in tandem with n-electron valence state second-order perturbation theory (NEVPT2), is capable of elucidating the structural basis of subtle shifts in EPR g values for low-spin FeIII species.
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Affiliation(s)
- Anne A Fischer
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53201 , United States
| | - Joshua R Miller
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Richard J Jodts
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Danushka M Ekanayake
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53201 , United States
| | - Sergey V Lindeman
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53201 , United States
| | - Thomas C Brunold
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Adam T Fiedler
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53201 , United States
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First-Principles Calculation of Transition Metal Hyperfine Coupling Constants with the Strongly Constrained and Appropriately Normed (SCAN) Density Functional and its Hybrid Variants. MAGNETOCHEMISTRY 2019. [DOI: 10.3390/magnetochemistry5040069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Density functional theory (DFT) is used extensively for the first-principles calculation of hyperfine coupling constants in both main-group and transition metal systems. As with many other properties, the performance of DFT for hyperfine coupling constants is of variable quality, particularly for transition metal complexes, because it strongly depends on the nature of the chemical system and the type of approximation to the exchange-correlation functional. Recently, a meta-generalized-gradient approximation (mGGA) functional was proposed that obeys all known exact constraints for such a method, known as the Strongly Constrained and Appropriately Normed (SCAN) functional. In view of its theoretically superior formulation a benchmark set of complexes is used to assess the performance of SCAN for the challenging case of transition metal hyperfine coupling constants. In addition, two global hybrid versions of the functional, SCANh and SCAN0, are described and tested. The values computed with the new functionals are compared with experiment and with those of other DFT approximations. Although the original SCAN and the SCAN-based hybrids may offer improved hyperfine coupling constants for specific systems, no uniform improvement is observed. On the contrary, there are specific cases where the new functionals fail badly due to a flawed description of the underlying electronic structure. Therefore, despite these methodological advances, systematically accurate and system-independent prediction of transition metal hyperfine coupling constants with DFT remains an unmet challenge.
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