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Mechanism of the highly effective peptide bond hydrolysis by MOF-808 catalyst under biologically relevant conditions. Phys Chem Chem Phys 2020; 22:25136-25145. [PMID: 33118561 DOI: 10.1039/d0cp04775a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Efficient and selective hydrolysis of inert peptide bonds is of paramount importance. MOF-808, a metal-organic framework based on Zr6 nodes, can hydrolyze peptide bonds efficiently under biologically relevant conditions. However, the details of the catalyst structure and of the underlying catalytic reaction mechanism are challenging to establish. By means of DFT calculations we first investigate the speciation of the Zr6 nodes and identify the nature of ligands that bind to the Zr6O8H4-x core in aqueous conditions. The core is predicted to strongly prefer a Zr6O8H4 protonation state and to be predominantly decorated by bridging formate ligands, giving Zr6(μ3-O)4(μ3-OH)4(BTC)2(HCOO)6 and Zr6(μ3-O)4(μ3-OH)4(BTC)2(HCOO)5(OH)(H2O) as the most favorable structures at physiological pH. The GlyGly peptide can bind MOF in several different ways, with the preferred structure involving coordination through the terminal carboxylate analogously to the binding mode of formate ligand. The pre-reactive binding mode in which the amide carbonyl oxygen coordinates the metal core lies 7 kcal higher in free energy. The preferred reaction pathway is predicted to have two close-lying transition states, either of which could be the rate-determining step: nucleophilic attack on the amide carbon atom and C-N bond breaking, with calculated relative free energies of 31 and 32 kcal mol-1, respectively. Replacement of formate by water and hydroxide at the Zr6 node is predicted to be possible, but does not appear to play a role in the hydrolysis mechanism.
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2
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Electronic Structure of Neutral and Anionic Iron–Nitrosyl Corrole. A Multiconfigurational and Density Matrix Renormalization Group Investigation. Inorg Chem 2020; 59:11493-11502. [DOI: 10.1021/acs.inorgchem.0c01312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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3
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Abstract
MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
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Advances in the synthesis, characterisation, and mechanistic understanding of active sites in Fe-zeolites for redox catalysts. Dalton Trans 2020; 49:14749-14757. [PMID: 33140781 DOI: 10.1039/d0dt01857k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The recent research developments on the active sites in Fe-zeolites for redox catalysis are discussed. Building on the characterisation of the α-Fe/α-O active sites in the beta and chabazite zeolites, we demonstrate a bottom-up approach to successfully understand and develop Fe-zeolite catalysts. We use the room temperature benzene to phenol reaction as a relevant example. We then suggest how the spectroscopic identification of other monomeric and dimeric iron sites could be tackled. The challenges in the characterisation of active sites and intermediates in NOX selective catalytic reduction catalysts and further development of catalysts for mild partial methane oxidation are briefly discussed.
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Chemical Mimics of Aspartate‐Directed Proteases: Predictive and Strictly Specific Hydrolysis of a Globular Protein at Asp−X Sequence Promoted by Polyoxometalate Complexes Rationalized by a Combined Experimental and Theoretical Approach. Chemistry 2019; 25:14370-14381. [DOI: 10.1002/chem.201902675] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/13/2019] [Indexed: 11/10/2022]
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6
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Glycolaldehyde as a Bio-Based C2 Platform Chemical: Catalytic Reductive Amination of Vicinal Hydroxyl Aldehydes. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02437] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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8
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Electronic Structure of N-Bridged High-Valent Diiron-Oxo. Chemistry 2019; 25:12491-12496. [PMID: 31313861 DOI: 10.1002/chem.201902766] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/14/2019] [Indexed: 11/09/2022]
Abstract
Density functional theory (DFT) and an advanced ab initio technique based on density matrix renormalization group (DMRG-CASPT2) were employed to investigate a reactive N-bridged high-valent diiron-oxo species involved in H-abstraction reactions. We studied in detail two important doublet states, the ground state with two iron(IV) centers and a mixed valence FeV -FeIV excited state. We found that the latter state is low-lying. Furthermore, its electronic structure and spin density imply that it has significantly higher H-abstraction reactivity than the ground state. This low-lying excited state might be the reason behind the high oxidation reactivity of this diiron-oxo species towards methane.
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Low-Lying Electromeric States in Chloro-Ligated Iron(IV)-Oxo Porphyrin as a Model for Compound I, Studied with Second-Order Perturbation Theory Based on Density Matrix Renormalization Group. J Chem Theory Comput 2019; 15:3033-3043. [PMID: 30995039 DOI: 10.1021/acs.jctc.9b00166] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Employing second-order perturbation theory based on the density matrix renormalization group (DMRG-CASPT2), this work aims at providing a quantitative description of the spin state energetics of a chloro-ligated iron(IV)-oxo porphyrin as a model for the cytochromes P450 active species, also known as compound I (Cpd I). We explored DMRG-CASPT2 to its full extent with an extensive active space (up to 31 active orbitals) as well as a large number of renormalized states m (up to 10000). Different flavors of DMRG-CASPT2, using either the costly exact 4-particle reduced density matrix (4-RDM) or the cheaper cumulant approximated 4-RDM (cu(4)), were analyzed. All flavors essentially converge to similar relative energies between different spin states. Including a correction for the protein environment, we found a quartet FeIVO ground state and, more importantly, a thermally accessible doublet FeVO excited state that might directly contribute to the reactivity of this iron-oxo species. Our results also showed that cheaper approaches, such as CASPT2 based on a smaller active space or the cumulant approximation DMRG-cu(4)-CASPT2, are capable of accurately describing the spin state energetics of this species.
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10
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Abstract
In a large variety of studies, the coupled-cluster method with singles, doubles, and perturbative triples (CCSD(T)) is used as a reference for benchmarking the performance of density functional theory (DFT) functionals. In the case of open-shell species, this theory can be applied in different forms depending on the restricted or unrestricted treatment of spin. In this study, we show that these different approaches can produce results which deviate by ∼5 kcal/mol for different species on the potential energy surfaces. This was demonstrated for a simple model of the C-H activation carried out by non-heme iron enzymes. Assessing the limits of CCSD(T) prior to its use as a general benchmark tool is warranted. This was done using higher-order coupled-cluster calculations as well as multiconfigurational second-order perturbation theory (CASPT2), since iron-oxo species present some multireference character. Furthermore, we tested two different implementations of the local coupled-cluster method and compared them to the CCSD(T) results, showing that even though these novel approaches are promising, without further developments they appear not to be suitable for describing two-state reactivity of the system investigated in the current study. Additionally, we implemented and assessed the performance of the hotspot approach for the local unrestricted CCSD(T) scheme which aims at reducing the pair error for systems containing transition metals.
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11
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Abstract
[NiFe] hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons. This seemingly simple reaction has attracted much attention because of the prospective use of H2 as a clean fuel. In this paper, we have studied the full reaction mechanism of this enzyme with various computational methods. Geometries were obtained with combined quantum mechanical and molecular mechanics (QM/MM) calculations. To get more accurate energies and obtain a detailed account of the surroundings, we performed big-QM calculations with 819 atoms in the QM region. Moreover, QM/MM thermodynamic cycle perturbation calculations were performed to obtain free energies. Finally, density matrix renormalisation group complete active space self-consistent field calculations were carried out to study the electronic structures of the various states in the reaction mechanism. Our calculations indicate that the Ni-L state is not involved in the reaction mechanism. Instead, the Ni-C state is reduced by one electron and then the bridging hydride ion is transferred to the sulfur atom of Cys546 as a proton and the two electrons transfer to the Ni ion. This step turned out to be rate-determining with an energy barrier of 58 kJ/mol, which is consistent with the experimental rate of 750 ± 90 s-1 (corresponding to ∼52 kJ/mol). The cleavage of the H-H bond is facile with an energy barrier of 33 kJ/mol, according to our calculations. We also find that the reaction energies are sensitive to the size of the QM system, the basis set, and the density functional theory method, in agreement with previous studies.
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12
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Fingerprinting Electronic Structure of Heme Iron by Ab Initio Modeling of Metal L-Edge X-ray Absorption Spectra. J Chem Theory Comput 2018; 15:477-489. [DOI: 10.1021/acs.jctc.8b00658] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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13
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Switching the Spin-Crossover Phenomenon by Ligand Design on Imidazole–Diazineiron(II) Complexes. Inorg Chem 2018; 57:14603-14616. [DOI: 10.1021/acs.inorgchem.8b02278] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Spectroscopic Identification of the α-Fe/α-O Active Site in Fe-CHA Zeolite for the Low-Temperature Activation of the Methane C-H Bond. J Am Chem Soc 2018; 140:12021-12032. [PMID: 30169036 DOI: 10.1021/jacs.8b05877] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The formation of single-site α-Fe in the CHA zeolite topology is demonstrated. The site is shown to be active in oxygen atom abstraction from N2O to form a highly reactive α-O, capable of methane activation at room temperature to form methanol. The methanol product can subsequently be desorbed by online steaming at 200 °C. For the intermediate steps of the reaction cycle, the evolution of the Fe active site is monitored by UV-vis-NIR and Mössbauer spectroscopy. A B3LYP-DFT model of the α-Fe site in CHA is constructed, and the ligand field transitions are calculated by CASPT2. The model is experimentally substantiated by the preferential formation of α-Fe over other Fe species, the requirement of paired framework aluminum and a MeOH/Fe ratio indicating a mononuclear active site. The simple CHA topology is shown to mitigate the heterogeneity of iron speciation found on other Fe-zeolites, with Fe2O3 being the only identifiable phase other than α-Fe formed in Fe-CHA. The α-Fe site is formed in the d6r composite building unit, which occurs frequently across synthetic and natural zeolites. Finally, through a comparison between α-Fe in Fe-CHA and Fe-*BEA, the topology's 6MR geometry is found to influence the structure, the ligand field, and consequently the spectroscopy of the α-Fe site in a predictable manner. Variations in zeolite topology can thus be used to rationally tune the active site properties.
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Cover Feature: Protein‐Assisted Formation and Stabilization of Catalytically Active Polyoxometalate Species (Chem. Eur. J. 40/2018). Chemistry 2018. [DOI: 10.1002/chem.201802890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Protein-Assisted Formation and Stabilization of Catalytically Active Polyoxometalate Species. Chemistry 2018; 24:10099-10108. [PMID: 29797738 DOI: 10.1002/chem.201802052] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/17/2018] [Indexed: 01/24/2023]
Abstract
The effect of the protein environment on the formation and stabilization of an elusive catalytically active polyoxometalate (POM) species, K6 [Hf(α2 -P2 W17 O61 )] (1), is reported. In the co-crystal of hen egg-white lysozyme (HEWL) with 1, the catalytically active monomeric species is observed, originating from the dimeric 1:2 POM form, while it is intrinsically unstable under physiological pH conditions. The protein-assisted dissociation of the dimeric POM was rationalized by means of DFT calculations. The dissociation process is unfavorable in bulk water, but becomes favorable in the protein-POM complex due to the low dielectric response at the protein surface. The crystal structure shows that the monomeric form is stabilized by electrostatic and water-mediated hydrogen bonding interactions with the protein. It interacts at three distinct sites, close to the aspartate-containing hydrolysis sites, demonstrating high selectivity towards peptide bonds containing this residue.
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Toward Highly Accurate Spin State Energetics in First-Row Transition Metal Complexes: A Combined CASPT2/CC Approach. J Chem Theory Comput 2018; 14:2446-2455. [PMID: 29614218 DOI: 10.1021/acs.jctc.8b00057] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In previous work on the performance of multiconfigurational second-order perturbation theory (CASPT2) in describing spin state energetics in first-row transition metal systems [ Pierloot et al. J. Chem. Theory Comput. 2017 , 13 , 537 - 553 ], we showed that standard CASPT2 works well for valence correlation but does not describe the metal semicore (3s3p) correlation effects accurately. This failure is partially responsible for the well-known bias toward high-spin states of CASPT2. In this paper, we expand our previous work and show that this bias could be partly removed with a combined CASPT2/CC approach: using high-quality CASPT2 with extensive correlation-consistent basis sets for valence correlation and low-cost CCSD(T) calculations with minimal basis sets for the metal semicore (3s3p) correlation effects. We demonstrate that this approach is efficient by studying the spin state energetics of a series of iron complexes modeling important intermediates in oxidative catalytic processes in chemistry and biochemistry. On the basis of a comparison with bare CCSD(T) results from this and previous work, the average error of the CASPT2/CC approach is estimated at around 2 kcal mol-1 in favor of high spin states.
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19
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The dioxygen adducts of iron and manganese porphyrins: electronic structure and binding energy. Phys Chem Chem Phys 2018; 20:17009-17019. [DOI: 10.1039/c8cp03078b] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The electronic structures of adducts of O2 and metal porphyrins were thoroughly investigated by highly accurate DMRG-CASPT2.
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20
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Dinuclear Iron(II) Spin-Crossover Compounds: A Theoretical Study. Chemistry 2017; 24:5183-5190. [DOI: 10.1002/chem.201704441] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Indexed: 11/06/2022]
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21
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Identification of α-Fe in High-Silica Zeolites on the Basis of ab Initio Electronic Structure Calculations. Inorg Chem 2017; 56:10681-10690. [DOI: 10.1021/acs.inorgchem.7b01653] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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22
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Spin State Energetics in First-Row Transition Metal Complexes: Contribution of (3s3p) Correlation and Its Description by Second-Order Perturbation Theory. J Chem Theory Comput 2017; 13:537-553. [DOI: 10.1021/acs.jctc.6b01005] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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H2binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods. Phys Chem Chem Phys 2017; 19:10590-10601. [DOI: 10.1039/c7cp01331k] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CCSD(T) and DMRG-CASPT2 calculations show that H2prefers to bind to Ni rather than to Fe in [NiFe] hydrogenase.
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Phosphate Ester Bond Hydrolysis Promoted by Lanthanide-Substituted Keggin-type Polyoxometalates Studied by a Combined Experimental and Density Functional Theory Approach. Inorg Chem 2016; 55:9898-9911. [PMID: 27657461 DOI: 10.1021/acs.inorgchem.6b01802] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Hydrolytic cleavage of 4-nitrophenyl phosphate (NPP), a commonly used DNA model substrate, was examined in the presence of series of lanthanide-substituted Keggin-type polyoxometalates (POMs) [Me2NH2]11[CeIII(PW11O39)2], [Me2NH2]10[CeIV(PW11O39)2] (abbreviated as (CeIV(PW11)2), and K4[EuPW11O39] by means of NMR and luminescence spectroscopies and density functional theory (DFT) calculations. Among the examined complexes, the Ce(IV)-substituted Keggin POM (CeIV(PW11)2) showed the highest reactivity, and its aqueous speciation was fully determined under different conditions of pD, temperature, concentration, and ionic strength by means of 31P and 31P diffusion-ordered NMR spectroscopy. The cleavage of the phosphoester bond of NPP in the presence of (CeIV(PW11)2) proceeded with an observed rate constant kobs = (5.31 ± 0.06) × 10-6 s-1 at pD 6.4 and 50 °C. The pD dependence of NPP hydrolysis exhibits a bell-shaped profile, with the fastest rate observed at pD 6.4. The formation constant (Kf = 127 M-1) and catalytic rate constant (kc = 19.41 × 10-5 s-1) for the NPP-Ce(IV)-Keggin POM complex were calculated, and binding between CeIV(PW11)2 and the phosphate group of NPP was also evidenced by the change of the chemical shift of the 31P nucleus in NPP upon addition of the POM complex. DFT calculations revealed that binding of NPP to the parent catalyst CeIV(PW11)2 is thermodynamically unlikely. On the contrary, formation of complexes with the monomeric 1:1 species, CeIVPW11, is considered to be more favorable, and the most stable complex, [CeIVPW11(H2O)2(NPP-κO)2]7-, was found to involve two NPP ligands coordinated to the CeIVcenter of CeIVPW11 in the monodentate fashion. The formation of such species is considered to be responsible for the hydrolytic activity of CeIV(PW11)2 toward phosphomonoesters. On the basis of these findings a principle mechanism for the hydrolysis of NPP by the POM is proposed.
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25
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The active site of low-temperature methane hydroxylation in iron-containing zeolites. Nature 2016; 536:317-21. [PMID: 27535535 DOI: 10.1038/nature19059] [Citation(s) in RCA: 228] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/13/2016] [Indexed: 12/21/2022]
Abstract
An efficient catalytic process for converting methane into methanol could have far-reaching economic implications. Iron-containing zeolites (microporous aluminosilicate minerals) are noteworthy in this regard, having an outstanding ability to hydroxylate methane rapidly at room temperature to form methanol. Reactivity occurs at an extra-lattice active site called α-Fe(ii), which is activated by nitrous oxide to form the reactive intermediate α-O; however, despite nearly three decades of research, the nature of the active site and the factors determining its exceptional reactivity are unclear. The main difficulty is that the reactive species-α-Fe(ii) and α-O-are challenging to probe spectroscopically: data from bulk techniques such as X-ray absorption spectroscopy and magnetic susceptibility are complicated by contributions from inactive 'spectator' iron. Here we show that a site-selective spectroscopic method regularly used in bioinorganic chemistry can overcome this problem. Magnetic circular dichroism reveals α-Fe(ii) to be a mononuclear, high-spin, square planar Fe(ii) site, while the reactive intermediate, α-O, is a mononuclear, high-spin Fe(iv)=O species, whose exceptional reactivity derives from a constrained coordination geometry enforced by the zeolite lattice. These findings illustrate the value of our approach to exploring active sites in heterogeneous systems. The results also suggest that using matrix constraints to activate metal sites for function-producing what is known in the context of metalloenzymes as an 'entatic' state-might be a useful way to tune the activity of heterogeneous catalysts.
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Cumulant Approximated Second-Order Perturbation Theory Based on the Density Matrix Renormalization Group for Transition Metal Complexes: A Benchmark Study. J Chem Theory Comput 2016; 12:4352-61. [DOI: 10.1021/acs.jctc.6b00714] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Molecular Insight from DFT Computations and Kinetic Measurements into the Steric Factors Influencing Peptide Bond Hydrolysis Catalyzed by a Dimeric Zr(IV)-Substituted Keggin Type Polyoxometalate. Inorg Chem 2016; 55:9316-28. [DOI: 10.1021/acs.inorgchem.6b01461] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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28
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Role of the Imide Axial Ligand in the Spin and Oxidation State of Manganese Corrole and Corrolazine Complexes. Inorg Chem 2016; 55:5274-80. [DOI: 10.1021/acs.inorgchem.6b00194] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Spin State Energetics and Oxyl Character of Mn-Oxo Porphyrins by Multiconfigurational ab Initio Calculations: Implications on Reactivity. Inorg Chem 2016; 55:5168-79. [DOI: 10.1021/acs.inorgchem.5b02920] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Theoretical Study of the Dissociation Energy of First-Row Metallocenium Ions. J Chem Theory Comput 2015; 10:3681-8. [PMID: 26588513 DOI: 10.1021/ct500376c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The bond dissociation energy of a series of metallocenium ions, i.e., the energy difference of the reaction MCp2(+) → MCp(+) + Cp· (with M = Ti, V, Cr, Mn, Fe, Co, and Ni), was studied by means of multiconfigurational perturbation theory (CASPT2, RASPT2, NEVPT2) and restricted coupled cluster theory (CCSD(T)). From a comparison between the results obtained from these different methods, and a detailed analysis of their treatment of electron correlation effects, a set of MCp(+)-Cp binding energies are proposed with an accuracy of 5 kcal/mol. The computed results are in good agreement with the experimental data measured by threshold photoelectron photoion coincidence (TPEPICO) spectroscopy but disagree with the more recent threshold collision-induced dissociation (TCID) experiments.
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Reactivity of Dimeric Tetrazirconium(IV) Wells-Dawson Polyoxometalate toward Dipeptide Hydrolysis Studied by a Combined Experimental and Density Functional Theory Approach. Inorg Chem 2015; 54:11477-92. [PMID: 26599585 DOI: 10.1021/acs.inorgchem.5b02122] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Detailed kinetic studies on the hydrolysis of glycylglycine (Gly-Gly) in the presence of the dimeric tetrazirconium(IV)-substituted Wells-Dawson-type polyoxometalate Na14[Zr4(P2W16O59)2(μ3-O)2(OH)2(H2O)4] · 57H2O (1) were performed by a combination of (1)H, (13)C, and (31)P NMR spectroscopies. The catalyst was shown to be stable under a broad range of reaction conditions. The effect of pD on the hydrolysis of Gly-Gly showed a bell-shaped profile with the fastest hydrolysis observed at pD 7.4. The observed rate constant for the hydrolysis of Gly-Gly at pD 7.4 and 60 °C was 4.67 × 10(-7) s(-1), representing a significant acceleration as compared to the uncatalyzed reaction. (13)C NMR data were indicative for coordination of Gly-Gly to 1 via its amide oxygen and amine nitrogen atoms, resulting in a hydrolytically active complex. Importantly, the effective hydrolysis of a series of Gly-X dipeptides with different X side chain amino acids in the presence of 1 was achieved, and the observed rate constant was shown to be dependent on the volume, chemical nature, and charge of the X amino acid side chain. To give a mechanistic explanation of the observed catalytic hydrolysis of Gly-Gly, a detailed quantum-chemical study was performed. The theoretical results confirmed the nature of the experimentally suggested binding mode in the hydrolytically active complex formed between Gly-Gly and 1. To elucidate the role of 1 in the hydrolytic process, both the uncatalyzed and the polyoxometalate-catalyzed reactions were examined. In the rate-determining step of the uncatalyzed Gly-Gly hydrolysis, a carboxylic oxygen atom abstracts a proton from a solvent water molecule and the nascent OH nucleophile attacks the peptide carbon atom. Analogous general-base activity of the free carboxylic group was found to take place also in the case of polyoxometalate-catalyzed hydrolysis as the main catalytic effect originates from the -C═O···Zr(IV) binding.
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Multinuclear diffusion NMR spectroscopy and DFT modeling: a powerful combination for unraveling the mechanism of phosphoester bond hydrolysis catalyzed by metal-substituted polyoxometalates. Chemistry 2015; 21:4428-39. [PMID: 25652658 DOI: 10.1002/chem.201405810] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Indexed: 02/04/2023]
Abstract
A detailed reaction mechanism is proposed for the hydrolysis of the phosphoester bonds in the DNA model substrate bis(4-nitrophenyl) phosphate (BNPP) in the presence of the Zr(IV)-substituted Keggin type polyoxometalate (Et2NH2)8[{α-PW11O39Zr(μ-OH)(H2O)}2]⋅7 H2O (ZrK 2:2) at pD 6.4. Low-temperature (31)P DOSY spectra at pD 6.4 gave the first experimental evidence for the presence of ZrK 1:1 in fast equilibrium with ZrK 2:2 in purely aqueous solution. Moreover, theoretical calculations identified the ZrK 1:1 form as the potentially active species in solution. The reaction intermediates involved in the hydrolysis were identified by means of (1)H/(31)P NMR studies, including EXSY and DOSY NMR spectroscopy, which were supported by DFT calculations. This experimental/theoretical approach enabled the determination of the structures of four intermediate species in which the starting compound BNPP, nitrophenyl phosphate (NPP), or the end product phosphate (P) is coordinated to ZrK 1:1. In the proposed reaction mechanism, BNPP initially coordinates to ZrK 1:1 in a monodentate fashion, which results in hydrolysis of the first phosphoester bond in BNPP and formation of NPP. EXSY NMR studies showed that the bidentate complex between NPP and ZrK 1:1 is in equilibrium with monobound and free NPP. Subsequently, hydrolysis of NPP results in P, which is in equilibrium with its monobound form.
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A computational study of the glycylserine hydrolysis at physiological pH: a zwitterionic versus anionic mechanism. Org Biomol Chem 2014; 12:1395-404. [PMID: 24430931 DOI: 10.1039/c3ob42372g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The hydrolysis of GlySer at physiological pH was investigated by modeling the most feasible reaction mechanisms in aqueous phase at the MP2/6-311+(2df,2p)//SMD-M06/6-311+(2df,2p) level of the theory. To refine the energies of the most relevant transition states along the reaction paths the cluster-continuum concept was adopted. The hydrolytic process could proceed through two competitive mechanisms involving either the zwitterionic or the anionic form of GlySer. The calculations suggest that at physiological pH the actual mechanism is most probably mixed, anionic-zwitterionic. In this reaction scheme the first stage of N→O acyl transfer involves the anionic form whereas the second stage, during which the resultant ester is hydrolyzed, most likely involves the zwitterionic ester form of GlySer. The energy requirement for the first reaction stage is estimated to be slightly lower than for the second one. The calculated activation parameters (e.g. ΔG(#) = 27.8 kcal mol(-1)) for the nucleophilic addition of a water molecule to the ester carbonyl group of the zwitterionic ester are in good agreement with the experimentally determined values at pD 7.4 (ΔG(#) = 28.7 kcal mol(-1)).
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Accurate calculations of geometries and singlet–triplet energy differences for active-site models of [NiFe] hydrogenase. Phys Chem Chem Phys 2014; 16:7927-38. [DOI: 10.1039/c4cp00253a] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The relative stability of singlet and triplet state models of [NiFe] hydrogenase have been studied by advanced quantum-mechanical methods.
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A Mechanistic Study of the Spontaneous Hydrolysis of Glycylserine as the Simplest Model for Protein Self-Cleavage. Chemistry 2013; 20:456-66. [DOI: 10.1002/chem.201303564] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Indexed: 11/05/2022]
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36
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Theoretical modelling of photoswitching of hyperpolarisabilities in ruthenium complexes. Chemistry 2013; 19:15955-63. [PMID: 24123546 PMCID: PMC4068215 DOI: 10.1002/chem.201301380] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Indexed: 11/17/2022]
Abstract
Static excited-state polarisabilities and hyperpolarisabilities of three RuII ammine complexes are computed at the density functional theory (DFT) and several correlated ab initio levels. Most accurate modelling of the low energy electronic absorption spectrum is obtained with the hybrid functionals B3LYP, B3P86 or M06 for the complex [RuII(NH3)5(MeQ+)]3+ (MeQ+=N-methyl-4,4′-bipyridinium, 3) in acetonitrile. The match with experimental data is less good for [RuII(NH3)5L]3+ (L=N-methylpyrazinium, 2; N-methyl-4-{E,E-4-(4-pyridyl)buta-1,3-dienyl}pyridinium, 4). These calculations confirm that the first dipole- allowed excited state (FDAES) has metal-to-ligand charge-transfer (MLCT) character. Both the solution and gas-phase results obtained for 3 by using B3LYP, B3P86 or M06 are very similar to those from restricted active-space SCF second-order perturbation theory (RASPT2) with a very large basis set and large active space. However, the time-dependent DFT λmax predictions from the long-range corrected functionals CAM-B3LYP, LC-ωPBE and wB97XB and also the fully ab initio resolution of identity approximate coupled-cluster method (gas-phase only) are less accurate for all three complexes. The ground state (GS) two-state approximation first hyperpolarisability β2SA for 3 from RASPT2 is very close to that derived experimentally via hyper-Rayleigh scattering, whereas the corresponding DFT-based values are considerably larger. The β responses calculated by using B3LYP, B3P86 or M06 increase markedly as the π-conjugation extends on moving along the series 2→4, for both the GS and FDAES species. All three functionals predict substantial FDAES β enhancements for each complex, increasing with the π-conjugation, up to about sevenfold for 4. Also, the computed second hyperpolarisabilities γ generally increase in the FDAES, but the results vary between the different functionals.
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Electronic Spectra of N-Heterocyclic Pentacyanoferrate(II) Complexes in Different Solvents, Studied by Multiconfigurational Perturbation Theory. Inorg Chem 2013; 52:10653-63. [DOI: 10.1021/ic401704r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Mn@Si14+: a singlet fullerene-like endohedrally doped silicon cluster. Phys Chem Chem Phys 2013; 15:5493-8. [DOI: 10.1039/c3cp43390k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Unraveling the Mechanisms of Carboxyl Ester Bond Hydrolysis Catalyzed by a Vanadate Anion. Inorg Chem 2012; 51:9619-28. [DOI: 10.1021/ic300620b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Hydrolytic Activity of Vanadate toward Serine-Containing Peptides Studied by Kinetic Experiments and DFT Theory. Inorg Chem 2012; 51:8848-59. [DOI: 10.1021/ic300761g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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Fourteen-electron ring model and the anomalous magnetic circular dichroism of meso-triarylsubporphyrins. J Phys Chem A 2012; 116:3960-7. [PMID: 22435833 DOI: 10.1021/jp302623q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The MCD spectra of meso-triarylsubporphyrins show a sign anomaly which is correlated with the acceptor properties of the aryl substituent. From the spectra, magnetic moments of the excited states are determined. In the context of a simplified orbital model, the sign change is attributed to the quenching of the magnetic moment of the LUMO by acceptor orbitals of the substituent. The actual calculation of this moment presents a major challenge to computational methods. It is shown that wave function techniques based on CASSCF underestimate the covalency effects that are responsible for the quenching. In contrast, a CI method based on DFT orbitals yields excellent results, which fully support the orbital model.
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Low-Energy States of Manganese–Oxo Corrole and Corrolazine: Multiconfiguration Reference ab Initio Calculations. Inorg Chem 2012; 51:4002-6. [DOI: 10.1021/ic201972f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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43
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A Multiconfigurational Perturbation Theory and Density Functional Theory Study on the Heterolytic Dissociation Enthalpy of First-Row Metallocenes. J Chem Theory Comput 2012; 8:883-92. [DOI: 10.1021/ct200875m] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Multiconfigurational Second-Order Perturbation Theory Restricted Active Space (RASPT2) Studies on Mononuclear First-Row Transition-Metal Systems. J Chem Theory Comput 2011; 7:3961-77. [DOI: 10.1021/ct200597h] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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46
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Correction to “Binding of CO, NO, and O2 to Heme by Density Functional and Multireference ab Initio Calculations”. J Phys Chem A 2011. [DOI: 10.1021/jp2018633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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DFT and Ab Initio Study of Iron-Oxo Porphyrins: May They Have a Low-Lying Iron(V)-Oxo Electromer? J Chem Theory Comput 2011; 7:898-908. [DOI: 10.1021/ct1006168] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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48
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Multiconfigurational Second-Order Perturbation Theory Restricted Active Space (RASPT2) Method for Electronic Excited States: A Benchmark Study. J Chem Theory Comput 2010; 7:153-68. [PMID: 26606229 DOI: 10.1021/ct100478d] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The recently developed second-order perturbation theory restricted active space (RASPT2) method has been benchmarked versus the well-established complete active space (CASPT2) approach. Vertical excitation energies for valence and Rydberg excited states of different groups of organic (polyenes, acenes, heterocycles, azabenzenes, nucleobases, and free base porphin) and inorganic (nickel atom and copper tetrachloride dianion) molecules have been computed at the RASPT2 and multistate (MS) RASPT2 levels using different reference spaces and compared with CASPT2, CCSD, and experimental data in order to set the accuracy of the approach, which extends the applicability of multiconfigurational perturbation theory to much larger and complex systems than previously. Relevant aspects in multiconfigurational excited state quantum chemistry such as the valence-Rydberg mixing problem in organic molecules or the double d-shell effect for first-row transition metals have also been addressed.
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Multireference ab initio calculations of g tensors for trinuclear copper clusters in multicopper oxidases. J Phys Chem B 2010; 114:7692-702. [PMID: 20469875 DOI: 10.1021/jp103098r] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
EPR spectroscopy has proven to be an indispensable tool in elucidating the structure of metal sites in proteins. In recent years, experimental EPR data have been complemented by theoretical calculations, which have become a standard tool of many quantum chemical packages. However, there have only been a few attempts to calculate EPR g tensors for exchange-coupled systems with more than two spins. In this work, we present a quantum chemical study of structural, electronic, and magnetic properties of intermediates in the reaction cycle of multicopper oxidases and of their inorganic models. All these systems contain three copper(II) ions bridged by hydroxide or O(2-) anions and their ground states are antiferromagnetically coupled doublets. We demonstrate that only multireference methods, such as CASSCF/CASPT2 or MRCI can yield qualitatively correct results (compared to the experimental values) and consider the accuracy of the calculated EPR g tensors as the current benchmark of quantum chemical methods. By decomposing the calculated g tensors into terms arising from interactions of the ground state with the various excited states, the origin of the zero-field splitting is explained. The results of the study demonstrate that a truly quantitative prediction of the g tensors of exchange-coupled systems is a great challenge to contemporary theory. The predictions strongly depend on small energy differences that are difficult to predict with sufficient accuracy by any quantum chemical method that is applicable to systems of the size of our target systems.
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