1
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de Moraes MMF, Tecmer P. Towards reliable and efficient modeling of [Cu 2O 2] 2+-based compound electronic structures with the partially fixed reference space protocols. Phys Chem Chem Phys 2024; 26:19742-19754. [PMID: 38984390 DOI: 10.1039/d4cp01309c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
This work reports a computationally efficient approach for reliable modeling of complex electronic structures based on [Cu2O2]2+ moieties. Specifically, we explore the recently developed partially fixed reference space (PFRS) protocol to minimize the active space size, taking into account the double d-shell effects. We show that the ground-state electronic structure of the core [Cu2O2]2+ model system is dominated by the d9/d10 occupations. The PFRS-crafted active spaces are further used to generate the reference wave functions for the multi-reference coupled cluster, configuration interaction, and multi-reference perturbation theory calculations. Specifically, we demonstrate that the bare [Cu2O2]2+ core can be modeled qualitatively using active spaces as small as CAS(2,2)PFRS. To obtain quantitative agreement with the reference DMRG(32,62)CI calculations, the CAS(4,4) has to be used in conjunction with the MRCCSD correction on top of it. This reliable and computationally efficient protocol is further used to model the electronic structure and properties of ammonia coordinated [Cu2O2]2+ complexes. Finally, based on the large amount of available experimental data regarding the oxo-peroxo equilibrium of [Cu2O2]2+-based systems, it is possible to formulate educated guesses regarding the effect of each experimental variable over each d-occupancy-specific state. With a large sample size of d-occupancy-specific state dependence with ligands and solvents, it should be possible to propose new ligands with specific d-occupancy and, therefore, oxidative properties based on the d-occupancy energy gaps of relatively low-cost calculations.
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Affiliation(s)
- Matheus Morato F de Moraes
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland.
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2
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Chaussy L, Chilkuri VG, Humbel S, Nava P. Spectroscopy of End-On Copper(II) Superoxido Complexes: A Wave Function-Based Analysis. Inorg Chem 2024; 63:8038-8049. [PMID: 38659336 DOI: 10.1021/acs.inorgchem.3c04401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Wave function methods are employed to analyze the ground and low-lying excited states of bipyramid trigonal copper(II) superoxido complexes, up to their characteristic ligand to metal charge transfer band. Several multireference methods have been combined to provide new insights into the interpretation of their experimental absorption spectra. We show that the intraligand transition on the dioxygen leads to a dark state. Among the results, we shall highlight the finding of doubly excited states in the region of the d-d transitions and the subtle interplay between Cu(I) and Cu(II) in the ground and excited states. Some of these findings could be obtained only with multireference methods.
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Affiliation(s)
- Léo Chaussy
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille 13397, France
| | | | - Stéphane Humbel
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille 13397, France
| | - Paola Nava
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille 13397, France
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3
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Drosou M, Pantazis DA. Redox Isomerism in the S 3 State of the Oxygen-Evolving Complex Resolved by Coupled Cluster Theory. Chemistry 2021; 27:12815-12825. [PMID: 34288176 PMCID: PMC8518824 DOI: 10.1002/chem.202101567] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Indexed: 01/19/2023]
Abstract
The electronic and geometric structures of the water-oxidizing complex of photosystem II in the steps of the catalytic cycle that precede dioxygen evolution remain hotly debated. Recent structural and spectroscopic investigations support contradictory redox formulations for the active-site Mn4 CaOx cofactor in the final metastable S3 state. These range from the widely accepted MnIV 4 oxo-hydroxo model, which presumes that O-O bond formation occurs in the ultimate transient intermediate (S4 ) of the catalytic cycle, to a MnIII 2 MnIV 2 peroxo model representative of the contrasting "early-onset" O-O bond formation hypothesis. Density functional theory energetics of suggested S3 redox isomers are inconclusive because of extreme functional dependence. Here, we use the power of the domain-based local pair natural orbital approach to coupled cluster theory, DLPNO-CCSD(T), to present the first correlated wave function theory calculations of relative stabilities for distinct redox-isomeric forms of the S3 state. Our results enabled us to evaluate conflicting models for the S3 state of the oxygen-evolving complex (OEC) and to quantify the accuracy of lower-level theoretical approaches. Our assessment of the relevance of distinct redox-isomeric forms for the mechanism of biological water oxidation strongly disfavors the scenario of early-onset O-O formation advanced by literal interpretations of certain crystallographic models. This work serves as a case study in the application of modern coupled cluster implementations to redox isomerism problems in oligonuclear transition metal systems.
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Affiliation(s)
- Maria Drosou
- Inorganic Chemistry LaboratoryNational and Kapodistrian University of AthensPanepistimiopolisZografou15771Greece
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an derRuhrGermany
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4
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Lan Z, Mallikarjun Sharada S. A framework for constructing linear free energy relationships to design molecular transition metal catalysts. Phys Chem Chem Phys 2021; 23:15543-15556. [PMID: 34254089 DOI: 10.1039/d1cp02278d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A computational framework for ligand-driven design of transition metal complexes is presented in this work. We propose a general procedure for the construction of active site-specific linear free energy relationships (LFERs), which are inspired from Hammett and Taft correlations in organic chemistry and grounded in the activation strain model (ASM). Ligand effects are isolated and quantified in terms of their contribution to interaction and strain energy components of ASM. Scalar descriptors that are easily obtainable are then employed to construct the complete LFER. We successfully demonstrate proof-of-concept by constructing and applying an LFER to CH activation with enzyme-inspired [Cu2O2]2+ complexes. The key benefit of using ASM is a built-in compensation or error cancellation between LFER prediction of interaction and strain terms, resulting in accurate barrier predictions for 37 of the 47 catalysts examined in this study. The LFER is also transferable with respect to level of theory and flexible towards the choice of reference system. The absence of interaction-strain compensation or poor model performance for the remaining systems is a consequence of the approximate nature of the chosen interaction energy descriptor and LFER construction of the strain term, which focuses largely on trends in substrate and not catalyst strain.
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Affiliation(s)
- Zhenzhuo Lan
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, USA.
| | - Shaama Mallikarjun Sharada
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, USA. and Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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5
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Besalú-Sala P, Magallón C, Costas M, Company A, Luis JM. Mechanistic Insights into the ortho-Defluorination-Hydroxylation of 2-Halophenolates Promoted by a Bis(μ-oxo)dicopper(III) Complex. Inorg Chem 2020; 59:17018-17027. [PMID: 33156988 DOI: 10.1021/acs.inorgchem.0c02246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
C-F bonds are one of the most inert functionalities. Nevertheless, some [Cu2O2]2+ species are able to defluorinate-hydroxylate ortho-fluorophenolates in a chemoselective manner over other ortho-halophenolates. Albeit it is known that such reactivity is promoted by an electrophilic attack of a [Cu2O2]2+ core over the arene ring, the crucial details of the mechanism that explain the chemo- and regioselectivity of the reaction remain unknown, and it has not being determined either if CuII2(η2:η2-O2) or CuIII2(μ-O)2 species are responsible for the initial attack on the arene. Herein, we present a combined theoretical and experimental mechanistic study to unravel the origin of the chemoselectivity of the ortho-defluorination-hydroxylation of 2-halophenolates by the [Cu2(O)2(DBED)2]2+ complex (DBED = N,N'-di-tert-butylethylenediamine). Our results show that the equilibria between (side-on)peroxo (P) and bis(μ-oxo) (O) isomers plays a key role in the mechanism, with the latter being the reactive species. Furthermore, on the basis of quantum-mechanical calculations, we were able to rationalize the chemoselective preference of the [Cu2(O)2(DBED)2]2+ catalyst for the C-F activation over C-Cl and C-H activations.
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Affiliation(s)
- Pau Besalú-Sala
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Carla Magallón
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Anna Company
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Josep M Luis
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
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6
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Bahlke MP, Mogos N, Proppe J, Herrmann C. Exchange Spin Coupling from Gaussian Process Regression. J Phys Chem A 2020; 124:8708-8723. [DOI: 10.1021/acs.jpca.0c05983] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Marc Philipp Bahlke
- Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Natnael Mogos
- Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Jonny Proppe
- Institute of Physical Chemistry, Georg-August University, Tammannstr. 6, 37077 Göttingen, Germany
| | - Carmen Herrmann
- Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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7
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Negri C, Selleri T, Borfecchia E, Martini A, Lomachenko KA, Janssens TVW, Cutini M, Bordiga S, Berlier G. Structure and Reactivity of Oxygen-Bridged Diamino Dicopper(II) Complexes in Cu-Ion-Exchanged Chabazite Catalyst for NH 3-Mediated Selective Catalytic Reduction. J Am Chem Soc 2020; 142:15884-15896. [PMID: 32830975 PMCID: PMC8011910 DOI: 10.1021/jacs.0c06270] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Indexed: 01/14/2023]
Abstract
The NH3-mediated selective catalytic reduction (NH3-SCR) of NOx over Cu-ion-exchanged chabazite (Cu-CHA) catalysts is the basis of the technology for abatement of NOx from diesel vehicles. A crucial step in this reaction is the activation of oxygen. Under conditions for low-temperature NH3-SCR, oxygen only reacts with CuI ions, which are present as mobile CuI diamine complexes [CuI(NH3)2]+. To determine the structure and reactivity of the species formed by oxidation of these CuI diamine complexes with oxygen at 200 °C, we have followed this reaction, using a Cu-CHA catalyst with a Si/Al ratio of 15 and 2.6 wt% Cu, by X-ray absorption spectroscopies (XANES and EXAFS) and diffuse reflectance UV-Vis spectroscopy, with the support of DFT calculations and advanced EXAFS wavelet transform analysis. The results provide unprecedented direct evidence for the formation of a [Cu2(NH3)4O2]2+ mobile complex with a side-on μ-η2,η2-peroxo diamino dicopper(II) structure, accounting for 80-90% of the total Cu content. These [Cu2(NH3)4O2]2+ are completely reduced to [CuI(NH3)2]+ at 200 °C in a mixture of NO and NH3. Some N2 is formed as well, which suggests the role of the dimeric complexes in the low-temperature NH3-SCR reaction. The reaction of [Cu2(NH3)4O2]2+ complexes with NH3 leads to a partial reduction of the Cu without any formation of N2. The reaction with NO results in an almost complete reduction to CuI, under the formation of N2. This indicates that the low-temperature NH3-SCR reaction proceeds via a reaction of these complexes with NO.
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Affiliation(s)
- Chiara Negri
- Department
of Chemistry and NIS Centre, University
of Turin, Via Giuria
7, I-10125 Turin, Italy
| | - Tommaso Selleri
- Dipartimento
di Energia, Laboratorio di Catalisi e Processi
Catalitici, Politecnico
di Milano, Via La Masa 34, I-20156 Milano, Italy
| | - Elisa Borfecchia
- Department
of Chemistry and NIS Centre, University
of Turin, Via Giuria
7, I-10125 Turin, Italy
| | - Andrea Martini
- Department
of Chemistry and NIS Centre, University
of Turin, Via Giuria
7, I-10125 Turin, Italy
- Smart
Materials Research Institute, Southern Federal
University, Sladkova
Street 174/28, 344090 Rostov-on-Don, Russia
| | - Kirill A. Lomachenko
- European
Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble Cedex 9, France
| | | | - Michele Cutini
- Department
of Chemistry and NIS Centre, University
of Turin, Via Giuria
7, I-10125 Turin, Italy
| | - Silvia Bordiga
- Department
of Chemistry and NIS Centre, University
of Turin, Via Giuria
7, I-10125 Turin, Italy
| | - Gloria Berlier
- Department
of Chemistry and NIS Centre, University
of Turin, Via Giuria
7, I-10125 Turin, Italy
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8
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Abe T, Shiota Y, Itoh S, Yoshizawa K. Theoretical rationalization for the equilibrium between (μ-η 2:η 2-peroxido)Cu IICu II and bis(μ-oxido)Cu IIICu III complexes: perturbational effects from ligand frameworks. Dalton Trans 2020; 49:6710-6717. [PMID: 32368776 DOI: 10.1039/d0dt01001d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DFT calculations are carried out to investigate the geometric effects of the supporting ligands in the relative energies of the (μ-η2:η2-peroxido)CuIICuII complex 1 and the bis(μ-oxido)CuIIICuIII complex 2. The N3-tridentate ligand bearing acyclic propane diamine framework La preferentially provided 1, whereas the N3-tridentate ligand with cyclic diamine framework such as 1,4-diazacycloheptane Lb gave 2 after the oxygenation of the corresponding CuI complexes as reported previously [S. Itoh, et al., Inorg. Chem., 2014, 53, 8786-8794]. Calculations at the B3LYP*-D3 level of theory can reasonably explain the experimental results in relative energies, structures and harmonic frequencies of 1 and 2. Perturbational effects of the diamine chelates of La and Lb especially on the equilibrium of 1 and 2 are investigated in detail. In the range from 2.30 Å to 3.40 Å of the N-N distance in the diamine moiety, 1 is more stable than 2 by 8.4 kcal mol-1 at the distance of 3.40 Å. Calculated potential energies indicate that the decrease in the N-N distance is associated with a decrease in energy of 2, leading that 2 can be most stabilized at the N-N distance of 2.60 Å. Furthermore, molecular orbitals analyses are performed to explain that the energy gaps between the σ* orbital of the O-O bond and the dx2-y2 orbitals of the CuII ions of 1 get small as the diamine moiety is shrunk, leading to facilitate the O-O bond cleavage from 1 to 2.
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Affiliation(s)
- Tsukasa Abe
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Japan.
| | - Yoshihito Shiota
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Japan.
| | - Shinobu Itoh
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Japan.
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9
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Chen L, Janssens TVW, Grönbeck H. A comparative test of different density functionals for calculations of NH 3-SCR over Cu-Chabazite. Phys Chem Chem Phys 2019; 21:10923-10930. [PMID: 31089628 DOI: 10.1039/c9cp01576k] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A general challenge in density functional theory calculations is to simultaneously account for different types of bonds. One such example is reactions in zeolites where both van der Waals and chemical bonds should be described accurately. Here, we use different exchange-correlation functionals to explore O2 dissociation over pairs of Cu(NH3)2+ complexes in Cu-Chabazite. This is an important part of selective catalytic reduction of NOx using NH3 as a reducing agent. The investigated functionals are PBE, PBE+U, PBE+D, PBE+U+D, PBE-cx, BEEF and HSE06+D. We find that the potential energy landscape for O2 activation and dissociation depends critically on the choice of functional. However, the van der Waals contributions are similarly described by the functionals accounting for this interaction. The discrepancies in the potential energy surface are instead related to different descriptions of the Cu-O chemical bond. By investigating the electronic, structural and energetic properties of reference systems including bulk copper oxides and (Cu2O2)2+ enzymatic crystals, we find that the PBE+U approach together with van der Waals corrections provides a reasonable simultaneous accuracy of the different bonds in the systems.
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Affiliation(s)
- Lin Chen
- Department of Physics and Competence Centre for Catalysis, Chalmers University of Technology, SE-412 96 Göteborg, Sweden.
| | - Ton V W Janssens
- Umicore Denmark ApS, Nøjsomhedsvej 20, DK-2800 Kgs. Lyngby, Denmark
| | - Henrik Grönbeck
- Department of Physics and Competence Centre for Catalysis, Chalmers University of Technology, SE-412 96 Göteborg, Sweden.
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10
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Tsuchimochi T, Ten-No SL. Extending spin-symmetry projected coupled-cluster to large model spaces using an iterative null-space projection technique. J Comput Chem 2018; 40:265-278. [PMID: 30520115 DOI: 10.1002/jcc.25587] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 11/06/2022]
Abstract
Recently, we introduced an orbital-invariant approximate coupled-cluster (CC) method in the spin-projection manifold. The multi-determinantal property of spin-projection means that the parametrization in the spin-extended CC (ECC) ansatz is nonorthogonal and overcomplete. Therefore, the linear dependencies must be removed by an orthogonalization procedure to obtain meaningful solutions. Multi-reference methods often achieve this by diagonalizing a metric of the equation system, but this is not feasible with ECC because of the enormous size of the metric, a consequence of the incomplete active space of the spin-projected Hartree-Fock reference. As a result, the applicability of ECC has been limited to small benchmark systems, for which the ansatz was shown to be superior to the configuration interaction and linearized approximations. In this article, we provide a solution to this problem that completely avoids the metric diagonalization by iteratively projecting out its null-space from the working equations. As the additional computational cost required for this iterative projection is only marginal, it greatly expands the application range of ECC. We demonstrate the potential of approximate ECC by studying the complete basis set limit of F2 and transition metal complexes such as NiO, Mn2 , and [Cu2 O2 ]2+ , which have all been hindered by the prohibitively large metric size. We also identify the potential inadequacy of the molecular orbitals given by spin-projected Hartree-Fock in some cases, and propose possible solutions. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Takashi Tsuchimochi
- Graduate School of Science, Technology, and Innovation, Kobe University, Kobe, Hyogo, 657-0025, Japan
| | - Seiichiro L Ten-No
- Graduate School of Science, Technology, and Innovation, Kobe University, Kobe, Hyogo, 657-0025, Japan
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11
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Lan Z, Sharada SM. Computational strategies to probe CH activation in dioxo-dicopper complexes. Phys Chem Chem Phys 2018; 20:25602-25614. [PMID: 30283932 DOI: 10.1039/c8cp05096a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We employ density functional theory and energy decomposition analysis to probe the mechanism of CH activation in dioxo-dicopper complexes. The electrophilicity of monodentate N-donor ligands coordinated to Cu is systematically varied to examine the response of barriers to the two proposed pathways - one-step oxo-insertion and two-step radical recombination. Electron-withdrawing ligand stabilize the oxo-insertion transition state via charge transfer interactions, and therefore lead to lower barriers. On the other hand, barriers to the CH activation step in the radical recombination mechanism exhibit almost no dependence on N-donor electrophilicity. Based on the similarities between calculated and experimental Hammett relationships, the oxo-insertion pathway appears to be the preferred mechanism of CH activation in dioxo-dicopper catalysts.
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Affiliation(s)
- Zhenzhuo Lan
- Mork Family Department of Chemical Engineering and Materials Science, 3651 Watt Way VHE516, University of Southern California, Los Angeles, CA 90089, USA.
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12
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Witte M, Herres-Pawlis S. Relativistic effects at the Cu 2O 2 core - a density functional theory study. Phys Chem Chem Phys 2017; 19:26880-26889. [PMID: 28952623 DOI: 10.1039/c7cp04686c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work presents for the first time the impact of relativistic effects on the Cu2O2 peroxide dicopper(ii)-bis(μ-oxo) dicopper (iii) equilibrium bonding motif in existing tyrosinase model complexes [Cu2(btmgp)2(μ-O)2]2+ and [Cu2{HC(tBuPz)2Py}2(O2)]2+ [S. Herres et al., Inorg. Chim. Acta, 2005, 358, 1089; S. Herres-Pawlis et al., Eur. J. Inorg. Chem., 2005, 3815; A. Hoffmann et al., Angew. Chem., Int. Ed., 2013, 52, 5398]. We use density functional theory (TPSSh/cc-pVTZ+D3BJ) with various relativistic approaches (ECPs, DKH, ZORA) to tackle the question of impact and find, as already known for small model complexes in the literature, that the O core is more stabilized with respect to the P core by the relativistic influence [D. G. Liakos and F. Neese, J. Chem. Theory Comput., 2011, 7, 1511]. Whereas DKH and ZORA yield similar results, ECPs underestimate the predicted effect. By calculating the functional of the relativistic overlap change, we can exactly identify the relativistic changes at the molecular orbital level and narrow down the affected MOs. Thus, by performing a detailed bond analysis utilizing the overlap population, we are able to rationalize the effects at the chemical level by finding relativistic bond stabilization in both isomers, which is more dominating in the O core. In conclusion, relativistic effects already play an important role in dicopper cores and should be considered.
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Affiliation(s)
- Matthias Witte
- RWTH Aachen University, Institute of Inorganic Chemistry, Chair of Bioinorganic Chemistry, Landoltweg 1, 52074 Aachen, Germany.
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13
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Boguslawski K, Tecmer P. Benchmark of Dynamic Electron Correlation Models for Seniority-Zero Wave Functions and Their Application to Thermochemistry. J Chem Theory Comput 2017; 13:5966-5983. [DOI: 10.1021/acs.jctc.6b01134] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Katharina Boguslawski
- Institute
of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
- Faculty
of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Paweł Tecmer
- Institute
of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
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14
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Gupta P, Diefenbach M, Holthausen MC, Förster M. Copper-Mediated Selective Hydroxylation of a Non-activated C−H Bond in Steroids: A DFT Study of Schönecker's Reaction. Chemistry 2016; 23:1427-1435. [DOI: 10.1002/chem.201604829] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Puneet Gupta
- Institut für Anorganische und Analytische Chemie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany
- Present address: Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
| | - Martin Diefenbach
- Institut für Anorganische und Analytische Chemie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany
| | - Max C. Holthausen
- Institut für Anorganische und Analytische Chemie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany
| | - Moritz Förster
- Institut für Anorganische und Analytische Chemie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Straße 7 60438 Frankfurt am Main Germany
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15
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Roemelt M, Guo S, Chan GKL. A projected approximation to strongly contracted N-electron valence perturbation theory for DMRG wavefunctions. J Chem Phys 2016; 144:204113. [DOI: 10.1063/1.4950757] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michael Roemelt
- Frick Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44789 Bochum, Germany
- Max-Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Sheng Guo
- Frick Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Garnet K.-L. Chan
- Frick Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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16
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Da Silva JCS, Pennifold RCR, Harvey JN, Rocha WR. A radical rebound mechanism for the methane oxidation reaction promoted by the dicopper center of a pMMO enzyme: a computational perspective. Dalton Trans 2016; 45:2492-504. [DOI: 10.1039/c5dt02638e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Hydrogen Atom Transfer (HAT) promoted by a triplet state of the bis-oxoCu2(iii) core generates a new radical rebound mechanism for the hydroxylation of methane catalyzed by the binuclear copper site of a pMMO enzyme.
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Affiliation(s)
- Júlio C. S. Da Silva
- BioMat: Biomaterial Modeling Group
- Departamento de Química Fundamental
- CCEN
- Universidade Federal de Pernambuco
- Cidade Universitária
| | | | | | - Willian R. Rocha
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular
- Departamento de Química
- ICEX
- Universidade Federal de Minas Gerais
- Belo Horizonte
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17
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Hoffmann A, Herres-Pawlis S. Donor-driven conformational flexibility in a real-life catalytic dicopper(ii) peroxo complex. Phys Chem Chem Phys 2016; 18:6430-40. [DOI: 10.1039/c5cp05009j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformers of the real-life tyrosinase model [Cu2O2{HC(3-tBuPz)2(Py)}2]2+which displays catalytic hydroxylation reactivity were investigated by density functional theory (DFT) studies including second-order perturbation theory and charge decomposition analysis (CDA).
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Affiliation(s)
- A. Hoffmann
- Lehrstuhl für Bioanorganische Chemie
- Institut für Anorganische Chemie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - S. Herres-Pawlis
- Lehrstuhl für Bioanorganische Chemie
- Institut für Anorganische Chemie
- RWTH Aachen University
- 52074 Aachen
- Germany
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18
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Rohrmüller M, Hoffmann A, Thierfelder C, Herres-Pawlis S, Schmidt WG. The Cu2O2torture track for a real-life system: [Cu2(btmgp)2O2]2+oxo and peroxo species in density functional calculations†. J Comput Chem 2015; 36:1672-85. [DOI: 10.1002/jcc.23983] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/26/2015] [Accepted: 05/28/2015] [Indexed: 01/23/2023]
Affiliation(s)
- Martin Rohrmüller
- Universität Paderborn, Department Physik, Lehrstuhl für Theoretische Physik; Pohlweg 55 33095 Paderborn Germany
| | - Alexander Hoffmann
- RWTH Aachen University, Fachgruppe Chemie, Lehrstuhl für Bioanorganische Chemie; Landoltweg 1 52074 Aachen Germany
| | - Christian Thierfelder
- Universität Paderborn, Department Physik, Lehrstuhl für Theoretische Physik; Pohlweg 55 33095 Paderborn Germany
| | - Sonja Herres-Pawlis
- RWTH Aachen University, Fachgruppe Chemie, Lehrstuhl für Bioanorganische Chemie; Landoltweg 1 52074 Aachen Germany
| | - Wolf Gero Schmidt
- Universität Paderborn, Department Physik, Lehrstuhl für Theoretische Physik; Pohlweg 55 33095 Paderborn Germany
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19
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Abstract
A method is suggested to build simple multiconfigurational wave functions specified uniquely by an energy cutoff Λ. These are constructed from a model space containing determinants with energy relative to that of the most stable determinant no greater than Λ. The resulting Λ-CI wave function is adaptive, being able to represent both single-reference and multireference electronic states. We also consider a more compact wave function parameterization (Λ+SD-CI), which is based on a small Λ-CI reference and adds a selection of all the singly and doubly excited determinants generated from it. We report two heuristic algorithms to build Λ-CI wave functions. The first is based on an approximate prescreening of the full configuration interaction space, while the second performs a breadth-first search coupled with pruning. The Λ-CI and Λ+SD-CI approaches are used to compute the dissociation curve of N2 and the potential energy curves for the first three singlet states of C2. Special attention is paid to the issue of energy discontinuities caused by changes in the size of the Λ-CI wave function along the potential energy curve. This problem is shown to be solvable by smoothing the matrix elements of the Hamiltonian. Our last example, involving the Cu2O2(2+) core, illustrates an alternative use of the Λ-CI method: as a tool to both estimate the multireference character of a wave function and to create a compact model space to be used in subsequent high-level multireference coupled cluster computations.
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Affiliation(s)
- Francesco A Evangelista
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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20
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Saito T, Thiel W. Quantum mechanics/molecular mechanics study of oxygen binding in hemocyanin. J Phys Chem B 2014; 118:5034-43. [PMID: 24762083 DOI: 10.1021/jp5003885] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report a combined quantum mechanics/molecular mechanics (QM/MM) study on the mechanism of reversible dioxygen binding in the active site of hemocyanin (Hc). The QM region is treated by broken-symmetry density functional theory (DFT) with spin projection corrections. The X-ray structures of deoxygenated (deoxyHc) and oxygenated (oxyHc) hemocyanin are well reproduced by QM/MM geometry optimizations. The computed relative energies strongly depend on the chosen density functional. They are consistent with the available thermodynamic data for oxygen binding in hemocyanin and in synthetic model complexes when the BH&HLYP hybrid functional with 50% Hartree-Fock exchange is used. According to the QM(BH&HLYP)/MM results, the reaction proceeds stepwise with two sequential electron transfer (ET) processes in the triplet state followed by an intersystem crossing to the singlet product. The first ET step leads to a nonbridged superoxo CuB(II)-O2(•-) intermediate via a low-barrier transition state. The second ET step is even more facile and yields a side-on oxyHc complex with the characteristic Cu2O2 butterfly core, accompanied by triplet-singlet intersystem crossing. The computed barriers are very small so that the two ET processes are expected to very rapid and nearly simultaneous.
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Affiliation(s)
- Toru Saito
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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21
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Jover J, Spuhler P, Zhao L, McArdle C, Maseras F. Toward a mechanistic understanding of oxidative homocoupling: the Glaser–Hay reaction. Catal Sci Technol 2014. [DOI: 10.1039/c4cy00322e] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The full reaction mechanism for the copper catalyzed oxidative coupling of two terminal alkynes is computationally characterized with DFT methods
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Affiliation(s)
- Jesús Jover
- Institute of Chemical Research of Catalonia (ICIQ)
- 43007 Tarragona, Spain
| | | | - Ligang Zhao
- Henkel AG & Co. KGaA
- 40589 Düsseldorf, Germany
| | | | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ)
- 43007 Tarragona, Spain
- Departament de Química
- Universitat Autònoma de Barcelona
- Barcelona, Spain
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22
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Chen Y, Sakaki S. Theoretical Study of Mononuclear Nickel(I), Nickel(0), Copper(I), and Cobalt(I) Dioxygen Complexes: New Insight into Differences and Similarities in Geometry and Bonding Nature. Inorg Chem 2013; 52:13146-59. [DOI: 10.1021/ic402059b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yue Chen
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano-Nishihiraki-cho
34-4, Sakyo-ku, Kyoto 606-8103, Japan
| | - Shigeyoshi Sakaki
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano-Nishihiraki-cho
34-4, Sakyo-ku, Kyoto 606-8103, Japan
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23
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Sun Y, Chen H. Performance of Density Functionals for Activation Energies of Zr-Mediated Reactions. J Chem Theory Comput 2013; 9:4735-43. [DOI: 10.1021/ct400432x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yuanyuan Sun
- Beijing National
Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry,
Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Hui Chen
- Beijing National
Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry,
Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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24
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Shiota Y, Juhász G, Yoshizawa K. Role of Tyrosine Residue in Methane Activation at the Dicopper Site of Particulate Methane Monooxygenase: A Density Functional Theory Study. Inorg Chem 2013; 52:7907-17. [DOI: 10.1021/ic400417d] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoshihito Shiota
- Institute for Materials
Chemistry and Engineering and International Research Center for Molecular
System, Kyushu University, Fukuoka 819-0395,
Japan
| | - Gergely Juhász
- Institute for Materials
Chemistry and Engineering and International Research Center for Molecular
System, Kyushu University, Fukuoka 819-0395,
Japan
| | - Kazunari Yoshizawa
- Institute for Materials
Chemistry and Engineering and International Research Center for Molecular
System, Kyushu University, Fukuoka 819-0395,
Japan
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25
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Poater A, Solà M. Complete σ* intramolecular aromatic hydroxylation mechanism through O2 activation by a Schiff base macrocyclic dicopper(I) complex. Beilstein J Org Chem 2013; 9:585-93. [PMID: 23616799 PMCID: PMC3628990 DOI: 10.3762/bjoc.9.63] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 03/01/2013] [Indexed: 02/05/2023] Open
Abstract
In this work we analyze the whole molecular mechanism for intramolecular aromatic hydroxylation through O2 activation by a Schiff hexaazamacrocyclic dicopper(I) complex, [Cu(I) 2(bsH2m)](2+). Assisted by DFT calculations, we unravel the reaction pathway for the overall intramolecular aromatic hydroxylation, i.e., from the initial O2 reaction with the dicopper(I) species to first form a Cu(I)Cu(II)-superoxo species, the subsequent reaction with the second Cu(I) center to form a μ-η(2):η(2)-peroxo-Cu(II) 2 intermediate, the concerted peroxide O-O bond cleavage and C-O bond formation, followed finally by a proton transfer to an alpha aromatic carbon that immediately yields the product [Cu(II) 2(bsH2m-O)(μ-OH)](2+).
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Affiliation(s)
- Albert Poater
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, E-17071 Girona, Spain ; Catalan Institute for Water Research (ICRA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, E-17003 Girona, Spain
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26
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Dancing multiplicity states supported by a carboxylated group in dicopper structures bonded to O2. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1336-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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27
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Samanta K, Jiménez-Hoyos CA, Scuseria GE. Exploring Copper Oxide Cores Using the Projected Hartree–Fock Method. J Chem Theory Comput 2012; 8:4944-9. [DOI: 10.1021/ct300689e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kousik Samanta
- Department of Chemistry, Rice
University, Houston, Texas 77005, United States
| | | | - Gustavo E. Scuseria
- Department of Chemistry, Rice
University, Houston, Texas 77005, United States
- Department of Physics and Astronomy,
Rice University, Houston, Texas 77005, United States
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28
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Comba P, Martin B, Muruganantham A, Straub J. Structure, Bonding, and Catecholase Mechanism of Copper Bispidine Complexes. Inorg Chem 2012; 51:9214-25. [DOI: 10.1021/ic3004917] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Peter Comba
- Universität Heidelberg, Anorganisch-Chemisches
Institut, INF 270, D-69120 Heidelberg, Germany
| | - Bodo Martin
- Universität Heidelberg, Anorganisch-Chemisches
Institut, INF 270, D-69120 Heidelberg, Germany
| | - Amsaveni Muruganantham
- Universität Heidelberg, Anorganisch-Chemisches
Institut, INF 270, D-69120 Heidelberg, Germany
| | - Johannes Straub
- Universität Heidelberg, Anorganisch-Chemisches
Institut, INF 270, D-69120 Heidelberg, Germany
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29
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Kozlowski PM, Kumar M, Piecuch P, Li W, Bauman NP, Hansen JA, Lodowski P, Jaworska M. The Cobalt–Methyl Bond Dissociation in Methylcobalamin: New Benchmark Analysis Based on Density Functional Theory and Completely Renormalized Coupled-Cluster Calculations. J Chem Theory Comput 2012; 8:1870-94. [DOI: 10.1021/ct300170y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pawel M. Kozlowski
- Department of Chemistry, University
of Louisville,
2320 South Brook St., Louisville, Kentucky 40292, United States
| | - Manoj Kumar
- Department of Chemistry, University
of Louisville,
2320 South Brook St., Louisville, Kentucky 40292, United States
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Wei Li
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Nicholas P. Bauman
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Jared A. Hansen
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Piotr Lodowski
- Institute
of Chemistry, University of Silesia, Szkolna
9, PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Institute
of Chemistry, University of Silesia, Szkolna
9, PL-40 006 Katowice, Poland
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30
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Magoon GR, Aguilera-Iparraguirre J, Green WH, Lutz JJ, Piecuch P, Wong HW, Oluwole OO. Detailed chemical kinetic modeling of JP-10 (exo-tetrahydrodicyclopentadiene) high-temperature oxidation: Exploring the role of biradical species in initial decomposition steps. INT J CHEM KINET 2012. [DOI: 10.1002/kin.20702] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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31
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González L, Escudero D, Serrano-Andrés L. Progress and Challenges in the Calculation of Electronic Excited States. Chemphyschem 2011; 13:28-51. [DOI: 10.1002/cphc.201100200] [Citation(s) in RCA: 310] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 08/05/2011] [Indexed: 11/09/2022]
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32
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Tran VT, Hendrickx MFA. Description of the geometric and electronic structures responsible for the photoelectron spectrum of FeO4−. J Chem Phys 2011; 135:094505. [DOI: 10.1063/1.3626559] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Correlated wavefunction methods in bioinorganic chemistry. J Biol Inorg Chem 2011; 16:821-9. [PMID: 21541855 DOI: 10.1007/s00775-011-0787-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 04/20/2011] [Indexed: 10/18/2022]
Abstract
In this commentary the challenges faced in the application of wavefunction-based ab initio methods to (open-shell) transition metal complexes of (bio)inorganic interest are briefly touched on. Both single-reference and multireference methods are covered. It is stressed that the generation and nature of the reference wavefunction is a subject of major importance. How erroneous results can be easily obtained even with coupled-cluster theory is illustrated through the example of the septet-quintet separation in iron(IV)-oxo complexes. Second, the interplay between relativistic and correlation effects is important. This is demonstrated with coupled-cluster calculations on models for dinuclear copper active sites, where relativity has a major influence on the relative stabilities of the bis(μ-oxo) and side-on peroxo species.
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34
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Liakos DG, Neese F. Interplay of Correlation and Relativistic Effects in Correlated Calculations on Transition-Metal Complexes: The (Cu2O2)2+ Core Revisited. J Chem Theory Comput 2011; 7:1511-23. [DOI: 10.1021/ct1006949] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dimitrios G. Liakos
- Lehrstuhl für Theoretische Chemie, Universität Bonn, Wegelerstrasse 12, D-53115 Bonn, Germany
| | - Frank Neese
- Lehrstuhl für Theoretische Chemie, Universität Bonn, Wegelerstrasse 12, D-53115 Bonn, Germany
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35
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Pittner J, Piecuch† P. Method of moments for the continuous transition between the Brillouin–Wigner-type and Rayleigh–Schrödinger-type multireference coupled cluster theories. Mol Phys 2010. [DOI: 10.1080/00268970902824235] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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Viegas LP, Branco A, Varandas AJC. How Well Can Kohn−Sham DFT Describe the HO2 + O3 Reaction? J Chem Theory Comput 2010; 6:2751-61. [DOI: 10.1021/ct100364x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luís P. Viegas
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal
| | - Adriana Branco
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal
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37
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38
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Kowalski K, Valiev M. Extensive regularization of the coupled cluster methods based on the generating functional formalism: application to gas-phase benchmarks and to the SN2 reaction of CHCl3 and OH- in water. J Chem Phys 2010; 131:234107. [PMID: 20025314 DOI: 10.1063/1.3270957] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The recently introduced energy expansion based on the use of generating functional (GF) [K. Kowalski and P. D. Fan, J. Chem. Phys. 130, 084112 (2009)] provides a way of constructing size-consistent noniterative coupled cluster (CC) corrections in terms of moments of the CC equations. To take advantage of this expansion in a strongly interacting regime, the regularization of the cluster amplitudes is required in order to counteract the effect of excessive growth of the norm of the CC wave function. Although proven to be efficient, the previously discussed form of the regularization does not lead to rigorously size-consistent corrections. In this paper we address the issue of size-consistent regularization of the GF expansion by redefining the equations for the cluster amplitudes. The performance and basic features of proposed methodology are illustrated on several gas-phase benchmark systems. Moreover, the regularized GF approaches are combined with quantum mechanical molecular mechanics module and applied to describe the S(N)2 reaction of CHCl(3) and OH(-) in aqueous solution.
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Affiliation(s)
- Karol Kowalski
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, K8-91 Battelle, P.O. Box 999, Richland, Washington 99352, USA.
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39
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Chen H, Song J, Lai W, Wu W, Shaik S. Multiple Low-Lying States for Compound I of P450cam and Chloroperoxidase Revealed from Multireference Ab Initio QM/MM Calculations. J Chem Theory Comput 2010; 6:940-53. [DOI: 10.1021/ct9006234] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hui Chen
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, State Key Laboratory of Physical Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, P. R. China
| | - Jinshuai Song
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, State Key Laboratory of Physical Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, P. R. China
| | - Wenzhen Lai
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, State Key Laboratory of Physical Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, P. R. China
| | - Wei Wu
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, State Key Laboratory of Physical Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, P. R. China
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel, State Key Laboratory of Physical Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, P. R. China
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40
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Viegas LP, Varandas AJC. HO2 + O3 Reaction: Ab Initio Study and Implications in Atmospheric Chemistry. J Chem Theory Comput 2010; 6:412-20. [DOI: 10.1021/ct900370q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luís P. Viegas
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal
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41
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Sadowsky D, McNeill K, Cramer CJ. Electronic structures of [n]-cyclacenes (n = 6–12) and short, hydrogen-capped, carbon nanotubes. Faraday Discuss 2010. [DOI: 10.1039/b906882a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Cramer CJ, Truhlar DG. Density functional theory for transition metals and transition metal chemistry. Phys Chem Chem Phys 2009; 11:10757-816. [PMID: 19924312 DOI: 10.1039/b907148b] [Citation(s) in RCA: 1063] [Impact Index Per Article: 70.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.
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Affiliation(s)
- Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, USA.
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43
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Poater A. Oxidation of Copper(I) Hexaaza Macrocyclic Dinuclear Complexes. J Phys Chem A 2009; 113:9030-40. [DOI: 10.1021/jp9040716] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Albert Poater
- Modeling Lab for Nanostructures and Catalysis (MoLNaC), Dipartimento di Chimica, Università degli Studi di Salerno, via Ponte don Melillo, Fisciano (SA) 84084, Italy
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44
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Kong L, Shamasundar KR, Demel O, Nooijen M. State specific equation of motion coupled cluster method in general active space. J Chem Phys 2009; 130:114101. [DOI: 10.1063/1.3089302] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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45
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Shiota Y, Yoshizawa K. Comparison of the Reactivity of Bis(μ-oxo)CuIICuIII and CuIIICuIII Species to Methane. Inorg Chem 2008; 48:838-45. [DOI: 10.1021/ic8003933] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yoshihito Shiota
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
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46
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Güell M, Luis JM, Solà M, Siegbahn PEM. Theoretical study of the hydroxylation of phenolates by the Cu(2)O (2)(N,N'-dimethylethylenediamine) (2) (2+) complex. J Biol Inorg Chem 2008; 14:229-42. [PMID: 18972140 DOI: 10.1007/s00775-008-0443-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Accepted: 10/08/2008] [Indexed: 12/21/2022]
Abstract
Tyrosinase catalyzes the ortho hydroxylation of monophenols and the subsequent oxidation of the diphenolic products to the resulting quinones. In efforts to create biomimetic copper complexes that can oxidize C-H bonds, Stack and coworkers recently reported a synthetic mu-eta(2):eta(2)-peroxodicopper(II)(DBED)(2) complex (DBED is N,N'-di-tert-butylethylenediamine), which rapidly hydroxylates phenolates. A reactive intermediate consistent with a bis-mu-oxo-dicopper(III)-phenolate complex, with the O-O bond fully cleaved, is observed experimentally. Overall, the evidence for sequential O-O bond cleavage and C-O bond formation in this synthetic complex suggests an alternative mechanism to the concerted or late-stage O-O bond scission generally accepted for the phenol hydroxylation reaction performed by tyrosinase. In this work, the reaction mechanism of this peroxodicopper(II) complex was studied with hybrid density functional methods by replacing DBED in the mu-eta(2):eta(2)-peroxodicopper(II)(DBED)(2) complex by N,N'-dimethylethylenediamine ligands to reduce the computational costs. The reaction mechanism obtained is compared with the existing proposals for the catalytic ortho hydroxylation of monophenol and the subsequent oxidation of the diphenolic product to the resulting quinone with the aim of gaining some understanding about the copper-promoted oxidation processes mediated by 2:1 Cu(I)O(2)-derived species.
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Affiliation(s)
- Mireia Güell
- Departament de Química, Institut de Química Computacional, Universitat de Girona, Campus de Montilivi, 17071, Girona, Spain
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Ge Y, Gordon MS, Piecuch P, Włoch M, Gour JR. Breaking Bonds of Open-Shell Species with the Restricted Open-Shell Size Extensive Left Eigenstate Completely Renormalized Coupled-Cluster Method. J Phys Chem A 2008; 112:11873-84. [DOI: 10.1021/jp806029z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Piotr Piecuch
- Department of Chemistry and Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824
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48
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Demel O, Shamasundar KR, Kong L, Nooijen M. Application of Double Ionization State-Specific Equation of Motion Coupled Cluster Method to Organic Diradicals. J Phys Chem A 2008; 112:11895-902. [PMID: 18956856 DOI: 10.1021/jp800577q] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ondřej Demel
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1 Canada
| | - K. R. Shamasundar
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1 Canada
| | - Liguo Kong
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1 Canada
| | - Marcel Nooijen
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1 Canada
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49
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Malmqvist PA, Pierloot K, Shahi ARM, Cramer CJ, Gagliardi L. The restricted active space followed by second-order perturbation theory method: theory and application to the study of CuO2 and Cu2O2 systems. J Chem Phys 2008; 128:204109. [PMID: 18513012 DOI: 10.1063/1.2920188] [Citation(s) in RCA: 365] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A multireference second-order perturbation theory using a restricted active space self-consistent field wave function as reference (RASPT2/RASSCF) is described. This model is particularly effective for cases where a chemical system requires a balanced orbital active space that is too large to be addressed by the complete active space self-consistent field model with or without second-order perturbation theory (CASPT2 or CASSCF, respectively). Rather than permitting all possible electronic configurations of the electrons in the active space to appear in the reference wave function, certain orbitals are sequestered into two subspaces that permit a maximum number of occupations or holes, respectively, in any given configuration, thereby reducing the total number of possible configurations. Subsequent second-order perturbation theory captures additional dynamical correlation effects. Applications of the theory to the electronic structure of complexes involved in the activation of molecular oxygen by mono- and binuclear copper complexes are presented. In the mononuclear case, RASPT2 and CASPT2 provide very similar results. In the binuclear cases, however, only RASPT2 proves quantitatively useful, owing to the very large size of the necessary active space.
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Affiliation(s)
- Per Ake Malmqvist
- Department of Theoretical Chemistry, University of Lund, P.O. Box 124, S-221 00 Lund, Sweden
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50
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A comparison of single-reference coupled-cluster and multi-reference configuration interaction methods for representative cuts of the potential energy surface. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.02.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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