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Casanova D. Second-order perturbative corrections to the restricted active space configuration interaction with the hole and particle approach. J Chem Phys 2014; 140:144111. [DOI: 10.1063/1.4870638] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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2
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Quantum mechanical calculations suggest that lytic polysaccharide monooxygenases use a copper-oxyl, oxygen-rebound mechanism. Proc Natl Acad Sci U S A 2013; 111:149-54. [PMID: 24344312 DOI: 10.1073/pnas.1316609111] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) exhibit a mononuclear copper-containing active site and use dioxygen and a reducing agent to oxidatively cleave glycosidic linkages in polysaccharides. LPMOs represent a unique paradigm in carbohydrate turnover and exhibit synergy with hydrolytic enzymes in biomass depolymerization. To date, several features of copper binding to LPMOs have been elucidated, but the identity of the reactive oxygen species and the key steps in the oxidative mechanism have not been elucidated. Here, density functional theory calculations are used with an enzyme active site model to identify the reactive oxygen species and compare two hypothesized reaction pathways in LPMOs for hydrogen abstraction and polysaccharide hydroxylation; namely, a mechanism that employs a η(1)-superoxo intermediate, which abstracts a substrate hydrogen and a hydroperoxo species is responsible for substrate hydroxylation, and a mechanism wherein a copper-oxyl radical abstracts a hydrogen and subsequently hydroxylates the substrate via an oxygen-rebound mechanism. The results predict that oxygen binds end-on (η(1)) to copper, and that a copper-oxyl-mediated, oxygen-rebound mechanism is energetically preferred. The N-terminal histidine methylation is also examined, which is thought to modify the structure and reactivity of the enzyme. Density functional theory calculations suggest that this posttranslational modification has only a minor effect on the LPMO active site structure or reactivity for the examined steps. Overall, this study suggests the steps in the LPMO mechanism for oxidative cleavage of glycosidic bonds.
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Bandeira NAG, Guennic BL. Calculation of Magnetic Couplings in Hydrogen-Bonded Cu(II) Complexes Using Density Functional Theory. J Phys Chem A 2012; 116:3465-73. [DOI: 10.1021/jp300618v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nuno A G Bandeira
- Université de Lyon, CNRS, Institut de Chimie de Lyon, Ecole Normale Supérieure de Lyon, France
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4
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Rokob TA, Srnec M, Rulíšek L. Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives. Dalton Trans 2012; 41:5754-68. [DOI: 10.1039/c2dt12423h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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5
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Bonniard L, de la Lande A, Ulmer S, Piquemal JP, Parisel O, Gérard H. Competitive ligand/chelate binding in [Cu(TMPA)]+ and [Cu(tren)]+ based complexes. Catal Today 2011. [DOI: 10.1016/j.cattod.2011.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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6
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Valero R, Illas F, Truhlar DG. Magnetic Coupling in Transition-Metal Binuclear Complexes by Spin-Flip Time-Dependent Density Functional Theory. J Chem Theory Comput 2011; 7:3523-31. [DOI: 10.1021/ct200393s] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rosendo Valero
- Research Unit “Molecular Physical Chemistry”, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Francesc Illas
- Departament de Química Física and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, C/Martí i Franquès 1, E-08028 Barcelona, Spain
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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Yang K, Peverati R, Truhlar DG, Valero R. Density functional study of multiplicity-changing valence and Rydberg excitations of p-block elements: Delta self-consistent field, collinear spin-flip time-dependent density functional theory (DFT), and conventional time-dependent DFT. J Chem Phys 2011; 135:044118. [DOI: 10.1063/1.3607312] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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8
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de la Lande A, Řezáč J, Lévy B, Sanders BC, Salahub DR. Transmission coefficients for chemical reactions with multiple states: role of quantum decoherence. J Am Chem Soc 2011; 133:3883-94. [PMID: 21344903 DOI: 10.1021/ja107950m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transition-state theory (TST) is a widely accepted paradigm for rationalizing the kinetics of chemical reactions involving one potential energy surface (PES). Multiple PES reaction rate constants can also be estimated within semiclassical approaches provided the hopping probability between the quantum states is taken into account when determining the transmission coefficient. In the Marcus theory of electron transfer, this hopping probability was historically calculated with models such as Landau-Zener theory. Although the hopping probability is intimately related to the question of the transition from the fully quantum to the semiclassical description, this issue is not adequately handled in physicochemical models commonly in use. In particular, quantum nuclear effects such as decoherence or dephasing are not present in the rate constant expressions. Retaining the convenient semiclassical picture, we include these effects through the introduction of a phenomenological quantum decoherence function. A simple modification to the usual TST rate constant expression is proposed: in addition to the electronic coupling, a characteristic decoherence time τ(dec) now also appears as a key parameter of the rate constant. This new parameter captures the idea that molecular systems, although intrinsically obeying quantum mechanical laws, behave semiclassically after a finite but nonzero amount of time (τ(dec)). This new degree of freedom allows a fresh look at the underlying physics of chemical reactions involving more than one quantum state. The ability of the proposed formula to describe the main physical lines of the phenomenon is confirmed by comparison with results obtained from density functional theory molecular dynamics simulations for a triplet to singlet transition within a copper dioxygen adduct relevant to the question of dioxygen activation by copper monooxygenases.
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Affiliation(s)
- Aurélien de la Lande
- Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud 11, Bât. 349, Campus d'Orsay, 15 rue Jean Perrin, 91 405 Orsay Cedex, France.
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9
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de la Lande A, Maddaluno J, Parisel O, Darden TA, Piquemal JP. Study of the docking of competitive inhibitors at a model of tyrosinase active site: insights from joint broken-symmetry/Spin-Flip DFT computations and ELF topological analysis. Interdiscip Sci 2010; 2:3-11. [PMID: 20396590 DOI: 10.1007/s12539-010-0096-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Following our previous study (Piquemal et al., New J. Chem., 2003, 27, 909), we present here a DFT study of the inhibition of the Tyrosinase enzyme. Broken-symmetry DFT computations are supplemented with Spin-Flip TD-DFT calculations, which, for the first time, are applied to such a dicopper enzyme. The chosen biomimetic model encompasses a dioxygen molecule, two Cu(II) cations, and six imidazole rings. The docking energy of a natural substrate, namely phenolate, together with those of several inhibitor and non-inhibitor compounds, are reported and show the ability of the model to rank the most potent inhibitors in agreement with experimental data. With respect to broken-symmetry calculations, the Spin-Flip TD-DFT approach reinforces the possibility for theory to point out potent inhibitors: the need for the deprotonation of the substrates, natural or inhibitors, is now clearly established. Moreover, Electron Localization Function (ELF) topological analysis computations are used to deeply track the particular electronic distribution of the Cu-O-Cu three-center bonds involved in the enzymatic Cu(2)O(2) metallic core (Piquemal and Pilmé, J. Mol. Struct.: Theochem, 2006, 77, 764). It is shown that such bonds exhibit very resilient out-of-plane density expansions that play a key role in docking interactions: their 3D-orientation could be the topological electronic signature of oxygen activation within such systems.
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Affiliation(s)
- A de la Lande
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, Paris, France
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10
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Rinkevicius Z, Ågren H. Spin-flip time dependent density functional theory for singlet–triplet splittings in σ,σ-biradicals. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.03.074] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Ashley DC, Brinkley DW, Roth JP. Oxygen Isotope Effects as Structural and Mechanistic Probes in Inorganic Oxidation Chemistry. Inorg Chem 2010; 49:3661-75. [DOI: 10.1021/ic901778g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Daniel C. Ashley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - David W. Brinkley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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12
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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: 1079] [Impact Index Per Article: 71.9] [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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13
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de la Lande A, Salahub D, Moliner V, Gérard H, Piquemal JP, Parisel O. Dioxygen Activation by Mononuclear Copper Enzymes: Insights from a Tripodal Ligand Mimicking Their CuM Coordination Sphere. Inorg Chem 2009; 48:7003-5. [DOI: 10.1021/ic900567z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Aurélien de la Lande
- UPMC Université Paris 6 and CNRS, UMR 7616, Laboratoire de Chimie Théorique, 4 place Jussieu, 75252 Paris Cedex 05, France
- Department of Chemistry and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Dennis Salahub
- Department of Chemistry and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, Box 224, SP-12080 Castelló, Spain
| | - Hélène Gérard
- UPMC Université Paris 6 and CNRS, UMR 7616, Laboratoire de Chimie Théorique, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - Jean-Philip Piquemal
- UPMC Université Paris 6 and CNRS, UMR 7616, Laboratoire de Chimie Théorique, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - Olivier Parisel
- UPMC Université Paris 6 and CNRS, UMR 7616, Laboratoire de Chimie Théorique, 4 place Jussieu, 75252 Paris Cedex 05, France
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14
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Over D, de la Lande A, Zeng X, Parisel O, Reinaud O. Replacement of a Nitrogen by a Phosphorus Donor in Biomimetic Copper Complexes: a Surprising and Informative Case Study with Calix[6]arene-Based Cryptands. Inorg Chem 2009; 48:4317-30. [DOI: 10.1021/ic802253t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Diana Over
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Université Paris Descartes (Paris 5), 45 rue des Saints Pères, 75006 Paris, France, Laboratoire de Chimie Théorique, UMR CNRS 7616, Université Pierre et Marie Curie (Paris 6), 4, place Jussieu, F-75252, Paris Cedex 05, France, Key Laboratory of Display Materials & Photoelectrical Devices (Ministry of Education), School of Materials Science & Engineering, Tianjin University of Technology, Tianjin 300384, China, and
| | - Aurélien de la Lande
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Université Paris Descartes (Paris 5), 45 rue des Saints Pères, 75006 Paris, France, Laboratoire de Chimie Théorique, UMR CNRS 7616, Université Pierre et Marie Curie (Paris 6), 4, place Jussieu, F-75252, Paris Cedex 05, France, Key Laboratory of Display Materials & Photoelectrical Devices (Ministry of Education), School of Materials Science & Engineering, Tianjin University of Technology, Tianjin 300384, China, and
| | - Xianshun Zeng
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Université Paris Descartes (Paris 5), 45 rue des Saints Pères, 75006 Paris, France, Laboratoire de Chimie Théorique, UMR CNRS 7616, Université Pierre et Marie Curie (Paris 6), 4, place Jussieu, F-75252, Paris Cedex 05, France, Key Laboratory of Display Materials & Photoelectrical Devices (Ministry of Education), School of Materials Science & Engineering, Tianjin University of Technology, Tianjin 300384, China, and
| | - Olivier Parisel
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Université Paris Descartes (Paris 5), 45 rue des Saints Pères, 75006 Paris, France, Laboratoire de Chimie Théorique, UMR CNRS 7616, Université Pierre et Marie Curie (Paris 6), 4, place Jussieu, F-75252, Paris Cedex 05, France, Key Laboratory of Display Materials & Photoelectrical Devices (Ministry of Education), School of Materials Science & Engineering, Tianjin University of Technology, Tianjin 300384, China, and
| | - Olivia Reinaud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Université Paris Descartes (Paris 5), 45 rue des Saints Pères, 75006 Paris, France, Laboratoire de Chimie Théorique, UMR CNRS 7616, Université Pierre et Marie Curie (Paris 6), 4, place Jussieu, F-75252, Paris Cedex 05, France, Key Laboratory of Display Materials & Photoelectrical Devices (Ministry of Education), School of Materials Science & Engineering, Tianjin University of Technology, Tianjin 300384, China, and
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15
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Smirnov VV, Lanci MP, Roth JP. Computational Modeling of Oxygen Isotope Effects on Metal-Mediated O2 Activation at Varying Temperatures. J Phys Chem A 2009; 113:1934-45. [DOI: 10.1021/jp807796c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Valeriy V. Smirnov
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Michael P. Lanci
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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16
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de la Lande A, Parisel O, Gérard H, Moliner V, Reinaud O. Theoretical Exploration of the Oxidative Properties of a [(trenMe1)CuO2]+Adduct Relevant to Copper Monooxygenase Enzymes: Insights into Competitive Dehydrogenation versus Hydroxylation Reaction Pathways. Chemistry 2008; 14:6465-73. [DOI: 10.1002/chem.200701595] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Valero R, Costa R, de P. R. Moreira I, Truhlar DG, Illas F. Performance of the M06 family of exchange-correlation functionals for predicting magnetic coupling in organic and inorganic molecules. J Chem Phys 2008; 128:114103. [DOI: 10.1063/1.2838987] [Citation(s) in RCA: 186] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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18
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Gourlaouen C, Gérard H, Piquemal JP, Parisel O. Understanding Lead Chemistry from Topological Insights: The Transition between Holo- and Hemidirected Structures within the [Pb(CO)n]2+ Model Series. Chemistry 2008; 14:2730-43. [DOI: 10.1002/chem.200701265] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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de la Lande A, Martí S, Parisel O, Moliner V. Long Distance Electron-Transfer Mechanism in Peptidylglycine α-Hydroxylating Monooxygenase: A Perfect Fitting for a Water Bridge. J Am Chem Soc 2007; 129:11700-7. [PMID: 17764178 DOI: 10.1021/ja070329l] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The active sites of copper enzymes have been the subject of many theoretical and experimental investigations from a number of years. Such studies have embraced topics devoted to the modeling of the first coordination sphere at the metallic cations up to the development of biomimetic, or bioinspired, catalytic systems. At least from the theoretical viewpoint, fewer efforts have been dedicated to elucidate how the two copper cations act concertedly in noncoupled dicopper enzymes such as peptidylglycine alpha-hydroxylating monooxygenase (PHM) and dopamine beta-monooxygenase (DbetaM). In these metalloenzymes, an electronic transfer is assumed between the two distant copper cations (11 A). Recent experimental results suggest that this transfer occurs through water molecules, a phenomenon which has been theoretically evidenced to be of high efficiency in the case of cytochrome b5 (Science, 2005, 310, 1311). In the present contribution dedicated to PHM, we overpass the common theoretical approaches dedicated to the electronic and geometrical structures of sites CuM or CuH restricted to their first coordination spheres and aim at directly comparing theoretical results to the experimentally measured activity of the PHM enzyme. To achieve this goal, molecular dynamics simulations were performed on wild-type and various mutants of PHM. More precisely, we provide an estimate of the electron-transfer efficiency between the CuM and CuH sites by means of such molecular dynamics simulations coupled to Marcus theory joined to the Beratan model to approximate the required coupling matrix elements. The theoretical results are compared to the kinetics measurements performed on wild and mutated PHM. The present work, the dynamic aspects of which are essential, accounts for the experimental results issued from mutagenesis. It supports the conclusion that an electronic transfer can occur between two copper(I) sites along a bridge involving a set of hydrogen and chemical bonds. Residue Gln170 is evidenced to be the keystone of this water-mediated pathway.
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Affiliation(s)
- Aurélien de la Lande
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
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Cramer CJ, Tolman WB. Mononuclear Cu-O2 complexes: geometries, spectroscopic properties, electronic structures, and reactivity. Acc Chem Res 2007; 40:601-8. [PMID: 17458929 PMCID: PMC2593863 DOI: 10.1021/ar700008c] [Citation(s) in RCA: 321] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Using interwoven experimental and theoretical methods, detailed studies of several structurally defined 1:1 Cu-O 2 complexes have provided important fundamental chemical information useful for understanding the nature of intermediates involved in aerobic oxidations in synthetic and enzymatic copper-mediated catalysis. In particular, these studies have shed new light on the factors that influence the mode of O 2 coordination (end-on vs side-on) and the electronic structure, which can vary between Cu(II)-superoxo and Cu(III)-peroxo extremes.
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Affiliation(s)
- Christopher J Cramer
- Department of Chemistry, Supercomputer Institute, and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55410, USA.
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