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EPR Spectroscopy of Cu(II) Complexes: Prediction of g-Tensors Using Double-Hybrid Density Functional Theory. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8040036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Computational electron paramagnetic resonance (EPR) spectroscopy is an important field of applied quantum chemistry that contributes greatly to connecting spectroscopic observations with the fundamental description of electronic structure for open-shell molecules. However, not all EPR parameters can be predicted accurately and reliably for all chemical systems. Among transition metal ions, Cu(II) centers in inorganic chemistry and biology, and their associated EPR properties such as hyperfine coupling and g-tensors, pose exceptional difficulties for all levels of quantum chemistry. In the present work, we approach the problem of Cu(II) g-tensor calculations using double-hybrid density functional theory (DHDFT). Using a reference set of 18 structurally and spectroscopically characterized Cu(II) complexes, we evaluate a wide range of modern double-hybrid density functionals (DHDFs) that have not been applied previously to this problem. Our results suggest that the current generation of DHDFs consistently and systematically outperform other computational approaches. The B2GP-PLYP and PBE0-DH functionals are singled out as the best DHDFs on average for the prediction of Cu(II) g-tensors. The performance of the different functionals is discussed and suggestions are made for practical applications and future methodological developments.
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Intermediate Detection in the Casiopeina-Cysteine Interaction Ending in the Disulfide Bond Formation and Copper Reduction. Molecules 2021; 26:molecules26195729. [PMID: 34641275 PMCID: PMC8510402 DOI: 10.3390/molecules26195729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/25/2022] Open
Abstract
A strategy to improve the cancer therapies involves agents that cause the depletion of the endogenous antioxidant glutathione (GSH), increasing its efflux out of cells and inducing apoptosis in tumoral cells due to the presence of reactive oxygen species. It has been shown that Casiopeina copper complexes caused a dramatic intracellular GSH drop, forming disulfide bonds and reducing CuII to CuI. Herein, through the determination of the [CuII]-SH bond before reduction, we present evidence of the adduct between cysteine and one Casiopeina as an intermediate in the cystine formation and as a model to understand the anticancer activity of copper complexes. Evidence of such an intermediate has never been presented before.
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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: 3.0] [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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Das D, Dutta S, Dowerah D, Deka RC. Unveiling the Role of Hydrogen Bonding and g-Tensor in the Interaction of Ru-Bis-DMSO with Amino Acid Residue and Human Serum Albumin. J Phys Chem B 2020; 124:6459-6474. [PMID: 32628490 DOI: 10.1021/acs.jpcb.0c02186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Density functional theory calculations have been carried out to observe the role of hydrogen bonding in hydrolysis and the coordination mechanism of three amino acid residues (histidine, cysteine, and alanine) with Ru-bis-DMSO complex via which the complex tends to interact with the HSA protein receptor. The interaction mechanism shows that ruthenium complexes prefer to bind protein receptor through cysteine and histidine residues rather than through alanine, which has been confirmed by DFT evaluated H-bonding and g-tensor analysis. The number of H-bonds plays a major role in stabilizing the intermediates and transition states involved in the Ru-bis-DMSO and amino acid residue interactions. Our theoretical g-tensor values are in good agreement with the available experimental results. Further QM/MM calculation on the Ru-bis-DMSO-HSA adducts reveals that the adduct is more stable when Ru gets coordinated with histidine imidazole rather than cysteine. These investigations helped us in understanding the type of amino acid residue responsible for binding the metal complex Ru-bis-DMSO with the carrier protein HSA.
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Affiliation(s)
- Dharitri Das
- Department of Chemical Sciences, Tezpur University, Tezpur, 784028, Assam, India
| | - Snigdha Dutta
- Department of Chemical Sciences, Tezpur University, Tezpur, 784028, Assam, India
| | - Dikshita Dowerah
- Department of Chemical Sciences, Tezpur University, Tezpur, 784028, Assam, India
| | - Ramesh Chandra Deka
- Department of Chemical Sciences, Tezpur University, Tezpur, 784028, Assam, India
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Shin J, Gwon S, Kim S, Lee J, Park K. Correlation between the C-C Cross-Coupling Activity and C-to-Ni Charge Transfer Transition of High-Valent Ni Complexes. J Am Chem Soc 2020; 142:4173-4183. [PMID: 32057242 DOI: 10.1021/jacs.9b10405] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
High-valent Ni complexes have proven to be good platforms for diverse cross-coupling reactions that are otherwise difficult to be achieved with conventional low-valent catalysts. However, their reductive elimination (RE) activities are still significantly variable by up to 5 orders of magnitude, depending on the supporting ligand and oxidation state of the Ni center. To elucidate frontier molecular orbitals (FMOs) that determine the RE activity of the Ni center, the electronic structures of cycloneophyl (CH2C(CH3)2-o-C6H4) NiIII and NiIV complexes have been characterized by utilizing various transition metal-based spectroscopic techniques such as electronic absorption, magnetic circular dichroism, electron paramagnetic resonance, resonance Raman, and X-ray absorption spectroscopies. In combination with density functional theory computations, the spectroscopic analyses have shown that the energies of the C-to-Ni charge-transfer (CT) electronic transitions are strongly correlated to the rates of C-C bond-forming RE reaction. This correlation suggests that the kinetic barrier of the RE reaction is determined by energy cost for internal CT (ICT) from the coordinated carbon moiety to the Ni center, and that FMOs involved in the RE reaction and the C-to-Ni CT electronic transitions are essentially identical. This FMO determination has led us to discover that photoexcitation to the C-to-Ni CT excited states accelerates the C-C cross-coupling reaction by up to 105 times, as the CT electronic transition can substitute for the rate-determining ICT step of the RE reaction at the ground electronic state.
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Affiliation(s)
- Jeongcheol Shin
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Suyeon Gwon
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Samhwan Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jiseon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kiyoung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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DFT Protocol for EPR Prediction of Paramagnetic Cu(II) Complexes and Application to Protein Binding Sites. MAGNETOCHEMISTRY 2018. [DOI: 10.3390/magnetochemistry4040055] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
With the aim to provide a general protocol to interpret electron paramagnetic resonance (EPR) spectra of paramagnetic copper(II) coordination compounds, density functional theory (DFT) calculations of spin Hamiltonian parameters g and A for fourteen Cu(II) complexes with different charges, donor sets, and geometry were carried out using ORCA software. The performance of eleven functionals was tested, and on the basis of the mean absolute percent deviation (MAPD) and standard deviation (SD), the ranking of the functionals for Az is: B3LYP > B3PW91 ~ B3P86 > PBE0 > CAM-B3LYP > TPSSh > BH and HLYP > B2PLYP > MPW1PW91 > ω-B97x-D >> M06; and for gz is: PBE0 > BH and HLYP > B2PLYP > ω-B97x-D > B3PW91~B3LYP~B3P86 > CAM-B3LYP > TPSSh~MPW1PW91 >> M06. With B3LYP the MAPD with respect to A z exp t l is 8.6% with a SD of 4.2%, while with PBE0 the MAPD with respect to g z exp t l is 2.9% with a SD of 1.1%. The results of the validation confirm the fundamental role of the second order spin-orbit contribution to Az. The computational procedure was applied to predict the values of gz and Az of the adducts formed by Cu(II) with albumin and two fragments of prion protein, 106–126 and 180–193.
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Ding CC, Wu SY, Xu YQ, Wu LN, Zhang LJ. DFT studies for three Cu(II) coordination polymers: Geometrical and electronic structures, g factors and UV–visible spectra. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Comba P, Dovalil N, Hanson GR, Harmer JR, Noble CJ, Riley MJ, Seibold B. Insights into the Electronic Structure of CuII Bound to an Imidazole Analogue of Westiellamide. Inorg Chem 2014; 53:12323-36. [DOI: 10.1021/ic5014413] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter Comba
- Anorganisch-Chemisches
Institut, Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Nina Dovalil
- Anorganisch-Chemisches
Institut, Universität Heidelberg, D-69120 Heidelberg, Germany
| | | | | | | | | | - Bjoern Seibold
- Anorganisch-Chemisches
Institut, Universität Heidelberg, D-69120 Heidelberg, Germany
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Hernández-Guzmán J, Sun L, Mehta AK, Dong J, Lynn DG, Warncke K. Copper(II)-bis-histidine coordination structure in a fibrillar amyloid β-peptide fragment and model complexes revealed by electron spin echo envelope modulation spectroscopy. Chembiochem 2013; 14:1762-71. [PMID: 24014287 PMCID: PMC3864031 DOI: 10.1002/cbic.201300236] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Indexed: 11/09/2022]
Abstract
Truncated and mutated amyloid-β (Aβ) peptides are models for systematic study-in homogeneous preparations-of the molecular origins of metal ion effects on Aβ aggregation rates, types of aggregate structures formed, and cytotoxicity. The 3D geometry of bis-histidine imidazole coordination of Cu(II) in fibrils of the nonapetide acetyl-Aβ(13-21)H14A has been determined by powder (14) N electron spin echo envelope modulation (ESEEM) spectroscopy. The method of simulation of the anisotropic combination modulation is described and benchmarked for a Cu(II) -bis-cis-imidazole complex of known structure. The revealed bis-cis coordination mode, and the mutual orientation of the imidazole rings, for Cu(II) in Ac-Aβ(13-21)H14A fibrils are consistent with the proposed β-sheet structural model and pairwise peptide interaction with Cu(II) , with an alternating [-metal-vacancy-]n pattern, along the N-terminal edge. Metal coordination does not significantly distort the intra-β-strand peptide interactions, which provides a possible explanation for the acceleration of Ac-Aβ(13-21)H14A fibrillization by Cu(II) , through stabilization of the associated state and low-reorganization integration of β-strand peptide pair precursors.
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Affiliation(s)
- Jessica Hernández-Guzmán
- Dr. J. Hernández-Guzmán, Dr. L. Sun, Prof. K. Warncke Department of Physics Emory University Atlanta, Georgia 30322-2430
| | - Li Sun
- Dr. J. Hernández-Guzmán, Dr. L. Sun, Prof. K. Warncke Department of Physics Emory University Atlanta, Georgia 30322-2430
| | - Anil K. Mehta
- Dr. A. K. Mehta, Dr. J. Dong, Prof. D. G. Lynn Department of Chemistry Emory University Atlanta, Georgia 30322-2430
| | - Jijun Dong
- Dr. A. K. Mehta, Dr. J. Dong, Prof. D. G. Lynn Department of Chemistry Emory University Atlanta, Georgia 30322-2430
| | - David G. Lynn
- Dr. A. K. Mehta, Dr. J. Dong, Prof. D. G. Lynn Department of Chemistry Emory University Atlanta, Georgia 30322-2430
| | - Kurt Warncke
- Dr. J. Hernández-Guzmán, Dr. L. Sun, Prof. K. Warncke Department of Physics Emory University Atlanta, Georgia 30322-2430
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Eaton SS, Eaton GR. The world as viewed by and with unpaired electrons. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 223:151-63. [PMID: 22975244 PMCID: PMC3496796 DOI: 10.1016/j.jmr.2012.07.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 07/26/2012] [Accepted: 07/27/2012] [Indexed: 06/01/2023]
Abstract
Recent advances in electron paramagnetic resonance (EPR) include capabilities for applications to areas as diverse as archeology, beer shelf life, biological structure, dosimetry, in vivo imaging, molecular magnets, and quantum computing. Enabling technologies include multifrequency continuous wave, pulsed, and rapid scan EPR. Interpretation is enhanced by increasingly powerful computational models.
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Affiliation(s)
- Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208, USA
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Sanna D, Pecoraro VL, Micera G, Garribba E. Application of DFT methods to the study of the coordination environment of the VO2+ ion in V proteins. J Biol Inorg Chem 2012; 17:773-90. [PMID: 22526563 DOI: 10.1007/s00775-012-0895-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 03/18/2012] [Indexed: 11/24/2022]
Abstract
Density functional theory (DFT) methods were used to simulate the environment of vanadium in several V proteins, such as vanadyl-substituted carboxypeptidase (sites A and B), vanadyl-substituted chloroplast F(1)-ATPase (CF(1); site 3), the reduced inactive form of vanadium bromoperoxidase (VBrPO; low- and high-pH sites), and vanadyl-substituted imidazole glycerol phosphate dehydratase (IGPD; sites α, β, and γ). Structural, electron paramagnetic resonance, and electron spin echo envelope modulation parameters were calculated and compared with the experimental values. All the simulations were performed in water within the framework of the polarizable continuum model. The angular dependence of [Formula: see text] and [Formula: see text] on the dihedral angle θ between the V=O and N-C bonds and on the angle φ between the V=O and V-N bonds, where N is the coordinated aromatic nitrogen atom, was also found. From the results it emerges that it is possible to model the active site of a vanadium protein through DFT methods and determine its structure through the comparison between the calculated and experimental spectroscopic parameters. The calculations confirm that the donor sets of sites B and A of vanadyl-substituted carboxypeptidase are [[Formula: see text], H(2)O, H(2)O, H(2)O] and [N(His)(||), N(His)(⊥), [Formula: see text], H(2)O], and that the donor set of site 3 of CF(1)-ATPase is [[Formula: see text], OH(Thr), H(2)O, H(2)O, [Formula: see text]]. For VBrPO, the coordination modes [N(His)(||), N(His)(∠), OH(Ser), H(2)O, H(2)O(ax)] for the low-pH site and [N(His)(||), N(His)(∠), OH(Ser), OH(-), H(2)O(ax)] or [N(His)(||), N(His)(∠), [Formula: see text], H(2)O] for the high-pH site, with an imidazole ring of histidine strongly displaced from the equatorial plane, can be proposed. Finally, for sites α, β, and γ of IGPD, the subsequent deprotonation of one, two, and three imidazole rings of histidine and the participation of a carboxylate group of a glutamate residue ([N(His)(||), [Formula: see text], H(2)O, H(2)O], [N(His)(||), N(His)(||), [Formula: see text], H(2)O], and [N(His)(||), N(His)(||), [Formula: see text], OH(-), [Formula: see text]], respectively) seems to be the most plausible hypothesis.
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Affiliation(s)
- Daniele Sanna
- Istituto CNR di Chimica Biomolecolare, Trav. La Crucca 3, 07040, Sassari, Italy
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Micera G, Garribba E. The Effect of Trigonal Bipyramidal Distortion of Pentacoordinate VIVO2+ Species on their Structural, Electronic and Spectroscopic Parameters. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201100422] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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de Almeida KJ, Ramalho. TC, Rinkevicius Z, Vahtras O, Ågren H, Cesar A. Theoretical Study of Specific Solvent Effects on the Optical and Magnetic Properties of Copper(II) Acetylacetonate. J Phys Chem A 2011; 115:1331-9. [DOI: 10.1021/jp109826p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. J. de Almeida
- Departamento de Química, Universidade Federal de Lavras, CP 3037, Lavras, MG, Brasil
| | - T. C. Ramalho.
- Departamento de Química, Universidade Federal de Lavras, CP 3037, Lavras, MG, Brasil
| | - Z. Rinkevicius
- Department of Theoretical Chemistry, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - O. Vahtras
- Department of Theoretical Chemistry, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - H. Ågren
- Department of Theoretical Chemistry, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - A. Cesar
- Departamento de Química, Universidade Federal de Minas Gerais, Avenida Antonio Carlos, 6627, CEP-31270-901, Belo Horizonte, Minas Gerais, Brasil
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Micera G, Garribba E. Application of DFT Methods in the Study of VIVO2+-Peptide Interactions. Eur J Inorg Chem 2010. [DOI: 10.1002/ejic.201000382] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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