1
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Marques HM. The inorganic chemistry of the cobalt corrinoids - an update. J Inorg Biochem 2023; 242:112154. [PMID: 36871417 DOI: 10.1016/j.jinorgbio.2023.112154] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B12, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B12-dependent enzymes is also given for the reader's convenience.
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Affiliation(s)
- Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
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2
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Ji L, Zhang H, Ding W, Song R, Han Y, Yu H, Paneth P. Theoretical Kinetic Isotope Effects in Establishing the Precise Biodegradation Mechanisms of Organic Pollutants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4915-4929. [PMID: 36926881 DOI: 10.1021/acs.est.2c04755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Compound-specific isotope analysis (CSIA) for natural isotope ratios has been recognized as a promising tool to elucidate biodegradation pathways of organic pollutants by microbial enzymes by relating reported kinetic isotope effects (KIEs) to apparent KIEs (AKIEs) derived from bulk isotope fractionations (εbulk). However, for many environmental reactions, neither are the reference KIE ranges sufficiently narrow nor are the mechanisms elucidated to the point that rate-determining steps have been identified unequivocally. In this work, besides providing reference KIEs and rationalizing AKIEs, good relationships have been explained by DFT computations for diverse biodegradation pathways with known enzymatic models between the theoretical isotope fractionations (εbulk') from intrinsic KIEs on the rate-determining steps and the observed εbulk. (1) To confirm the mechanistic details of previously reported pathway-dependent CSIA, it includes isotope changes in MTBE biodegradation between hydroxylation by CYP450 and SN2 reaction by cobalamin-dependent methyltransferase, the regioselectivity of toluene biodegradation by CYP450, and the rate-determining step in toluene biodegradation by benzylsuccinate synthase. (2) To yield new fundamental insights into some unclear biodegradation pathways, it consists of the oxidative function of toluene dioxygenase in biodegradation of TCE, the epoxidation mode in biodegradation of TCE by toluene 4-monooxygenase, and the weighted average mechanism in biodegradation of cDCE by CYP450.
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Affiliation(s)
- Li Ji
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Huanni Zhang
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Wen Ding
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Runqian Song
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Ye Han
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Haiying Yu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland
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3
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Heckel B, McNeill K, Elsner M. Chlorinated Ethene Reactivity with Vitamin B12 Is Governed by Cobalamin Chloroethylcarbanions as Crossroads of Competing Pathways. ACS Catal 2018. [DOI: 10.1021/acscatal.7b02945] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Benjamin Heckel
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, D-81377 Munich, Germany
| | - Kristopher McNeill
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zurich, CH-8092 Zurich, Switzerland
| | - Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, D-81377 Munich, Germany
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4
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Ji L, Wang C, Ji S, Kepp KP, Paneth P. Mechanism of Cobalamin-Mediated Reductive Dehalogenation of Chloroethylenes. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00540] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Li Ji
- College
of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Chenchen Wang
- College
of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Shujing Ji
- College
of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Kasper P. Kepp
- DTU
Chemistry, Technical University of Denmark, Building 206, Kgs. Lyngby DK-2800, Denmark
| | - Piotr Paneth
- Institute
of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
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5
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Luo J, Hu J, Wei X, Fu L, Li L. Dehalogenation of persistent halogenated organic compounds: A review of computational studies and quantitative structure-property relationships. CHEMOSPHERE 2015; 131:17-33. [PMID: 25765260 DOI: 10.1016/j.chemosphere.2015.02.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 12/20/2014] [Accepted: 02/03/2015] [Indexed: 06/04/2023]
Abstract
Dehalogenation is one of the highly important degradation reactions for halogenated organic compounds (HOCs) in the environment, which is also being developed as a potential type of the remediation technologies. In combination with the experimental results, intensive efforts have recently been devoted to the development of efficient theoretical methodologies (e.g. multi-scale simulation) to investigate the mechanisms for dehalogenation of HOCs. This review summarizes the structural characteristics of neutral molecules, anionic species and excited states of HOCs as well as their adsorption behavior on the surface of graphene and the Fe cluster. It discusses the key physiochemical properties (e.g. frontier orbital energies and thermodynamic properties) calculated at various levels of theory (e.g. semiempirical, ab initio, density functional theory (DFT) and the periodic DFT) as well as their connections to the reactivity and reaction pathway for the dehalogenation. This paper also reviews the advances in the linear and nonlinear quantitative structure-property relationship models for the dehalogenation kinetics of HOCs and in the mathematical modeling of the dehalogenation processes. Furthermore, prospects of further expansion and exploration of the current research fields are described in this article.
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Affiliation(s)
- Jin Luo
- Guizhou Provincial Key Laboratory for Information Systems of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang 550001, PR China
| | - Jiwei Hu
- Guizhou Provincial Key Laboratory for Information Systems of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang 550001, PR China.
| | - Xionghui Wei
- Department of Applied Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PR China
| | - Liya Fu
- Guizhou Provincial Key Laboratory for Information Systems of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang 550001, PR China
| | - Lingyun Li
- Guizhou Provincial Key Laboratory for Information Systems of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang 550001, PR China
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6
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Parthasarathy A, Stich TA, Lohner ST, Lesnefsky A, Britt RD, Spormann AM. Biochemical and EPR-spectroscopic investigation into heterologously expressed vinyl chloride reductive dehalogenase (VcrA) from Dehalococcoides mccartyi strain VS. J Am Chem Soc 2015; 137:3525-32. [PMID: 25686300 PMCID: PMC4516053 DOI: 10.1021/ja511653d] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reductive dehalogenases play a critical role in the microbial detoxification of aquifers contaminated with chloroethenes and chlorethanes by catalyzing the reductive elimination of a halogen. We report here the first heterologous production of vinyl chloride reductase VcrA from Dehalococcoides mccartyi strain VS. Heterologously expressed VcrA was reconstituted to its active form by addition of hydroxocobalamin/adenosylcobalamin, Fe(3+), and sulfide in the presence of mercaptoethanol. The kinetic properties of reconstituted VcrA catalyzing vinyl chloride reduction with Ti(III)-citrate as reductant and methyl viologen as mediator were similar to those obtained previously for VcrA as isolated from D. mccartyi strain VS. VcrA was also found to catalyze a novel reaction, the environmentally important dihaloelimination of 1,2-dichloroethane to ethene. Electron paramagnetic resonance (EPR) spectroscopic studies with reconstituted VcrA in the presence of mercaptoethanol revealed the presence of Cob(II)alamin. Addition of Ti(III)-citrate resulted in the appearance of a new signal characteristic of a reduced [4Fe-4S] cluster and the disappearance of the Cob(II)alamin signal. UV-vis absorption spectroscopy of Ti(III)citrate-treated samples revealed the formation of two new absorption maxima characteristic of Cob(I)alamin. No evidence for the presence of a [3Fe-4S] cluster was found. We postulate that during the reaction cycle of VcrA, a reduced [4Fe-4S] cluster reduces Co(II) to Co(I) of the enzyme-bound cobalamin. Vinyl chloride reduction to ethene would be initiated when Cob(I)alamin transfers an electron to the substrate, generating a vinyl radical as a potential reaction intermediate.
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Affiliation(s)
- Anutthaman Parthasarathy
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Troy A. Stich
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Svenja T. Lohner
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Ann Lesnefsky
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - R. David Britt
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Alfred M. Spormann
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
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7
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Abstract
Nitrosylcobalamin (NOCbl) is readily formed when Co(II)balamin reacts with nitric oxide (NO) gas. NOCbl has been implicated in the inhibition of various B12-dependent enzymes, as well as in the modulation of blood pressure and of the immunological response. Previous studies revealed that among the known biologically relevant cobalamin species, NOCbl possesses the longest bond between the Co ion and the axially bound 5,6-dimethylbenzimidazole base, which was postulated to result from a strong trans influence exerted by the NO ligand. In this study, various spectroscopic (electronic absorption, circular dichroism, magnetic circular dichroism, and resonance Raman) and computational (density functional theory (DFT) and time-dependent DFT) techniques were used to generate experimentally validated electronic structure descriptions for the "base-on" and "base-off" forms of NOCbl. Further insights into the principal Co-ligand bonding interactions were obtained by carrying out natural bond orbital analyses. Collectively, our results indicate that the formally unoccupied Co 3dz(2) orbital engages in a highly covalent bonding interaction with the filled NO π* orbital and that the Co-NO bond is strengthened further by sizable π-backbonding interactions that are not present in any other Co(III)Cbl characterized to date. Because of the substantial NO(-) to Co(III) charge donation, NOCbl is best described as a hybrid of Co(III)-NO(-) and Co(II)-NO(•) resonance structures. In contrast, our analogous computational characterization of a related species, superoxocobalamin, reveals that in this case a Co(III)-O2(-) description is adequate due to the larger oxidizing power of O2 versus NO. The implications of our results with respect to the unusual structural features and thermochromism of NOCbl and the proposed inhibition mechanisms of B12-dependent enzymes by NOCbl are discussed.
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Affiliation(s)
- Ivan G. Pallares
- Department of Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Thomas C. Brunold
- Department of Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
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8
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Goris B, Guzzinati G, Fernández-López C, Pérez-Juste J, Liz-Marzán LM, Trügler A, Hohenester U, Verbeeck J, Bals S, Van Tendeloo G. Plasmon Mapping in Au@Ag Nanocube Assemblies. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2014; 118:15356-15362. [PMID: 25067991 PMCID: PMC4106270 DOI: 10.1021/jp502584t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 06/27/2014] [Indexed: 05/15/2023]
Abstract
Surface plasmon modes in metallic nanostructures largely determine their optoelectronic properties. Such plasmon modes can be manipulated by changing the morphology of the nanoparticles or by bringing plasmonic nanoparticle building blocks close to each other within organized assemblies. We report the EELS mapping of such plasmon modes in pure Ag nanocubes, Au@Ag core-shell nanocubes, and arrays of Au@Ag nanocubes. We show that these arrays enable the creation of interesting plasmonic structures starting from elementary building blocks. Special attention will be dedicated to the plasmon modes in a triangular array formed by three nanocubes. Because of hybridization, a combination of such nanotriangles is shown to provide an antenna effect, resulting in strong electrical field enhancement at the narrow gap between the nanotriangles.
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Affiliation(s)
- Bart Goris
- EMAT, University
of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Giulio Guzzinati
- EMAT, University
of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | | | - Jorge Pérez-Juste
- Departamento de Química Física, Universidade de Vigo, 36310 Vigo, Spain
| | - Luis M. Liz-Marzán
- Departamento de Química Física, Universidade de Vigo, 36310 Vigo, Spain
- BioNanoPlasmonics
Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia - San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Andreas Trügler
- Institut
für Physik, Karl-Franzens-Universität
Graz, Universitätsplatz
5, 8010 Graz, Austria
| | - Ulrich Hohenester
- Institut
für Physik, Karl-Franzens-Universität
Graz, Universitätsplatz
5, 8010 Graz, Austria
| | - Jo Verbeeck
- EMAT, University
of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Sara Bals
- EMAT, University
of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
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9
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Zhou J, Riccardi D, Beste A, Smith JC, Parks JM. Mercury methylation by HgcA: theory supports carbanion transfer to Hg(II). Inorg Chem 2013; 53:772-7. [PMID: 24377658 DOI: 10.1021/ic401992y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many proteins use corrinoid cofactors to facilitate methyl transfer reactions. Recently, a corrinoid protein, HgcA, has been shown to be required for the production of the neurotoxin methylmercury by anaerobic bacteria. A strictly conserved Cys residue in HgcA was predicted to be a lower-axial ligand to Co(III), which has never been observed in a corrinoid protein. Here, we use density functional theory to study homolytic and heterolytic Co-C bond dissociation and methyl transfer to Hg(II) substrates with model methylcobalamin complexes containing a lower-axial Cys or His ligand to cobalt, the latter of which is commonly found in other corrinoid proteins. We find that Cys thiolate coordination to Co facilitates both methyl radical and methyl carbanion transfer to Hg(II) substrates, but carbanion transfer is more favorable overall in the condensed phase. Thus, our findings are consistent with HgcA representing a new class of corrinoid protein capable of transferring methyl groups to electrophilic substrates.
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Affiliation(s)
- Jing Zhou
- Graduate School of Genome Science and Technology, University of Tennessee , Knoxville, Tennessee 37996, United States
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10
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Kumar N, Kuta J, Galezowski W, Kozlowski PM. Electronic Structure of One-Electron-Oxidized Form of the Methylcobalamin Cofactor: Spin Density Distribution and Pseudo-Jahn–Teller Effect. Inorg Chem 2013; 52:1762-71. [DOI: 10.1021/ic3013443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Neeraj Kumar
- Department of Chemistry, University of Louisville,
Louisville, Kentucky 40292, United States
| | - Jadwiga Kuta
- Department of Chemistry, University of Louisville,
Louisville, Kentucky 40292, United States
| | - Wlodzimierz Galezowski
- Department of Chemistry, A. Mickiewicz University,
Umultowska 89b, 61-614 Poznan, Poland
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville,
Louisville, Kentucky 40292, United States
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11
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Reig AJ, Conrad KS, Brunold TC. Combined spectroscopic/computational studies of vitamin B12 precursors: geometric and electronic structures of cobinamides. Inorg Chem 2012; 51:2867-79. [PMID: 22332807 DOI: 10.1021/ic202052g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vitamin B(12) (cyanocobalamin) and its biologically active derivatives, methylcobalamin and adenosylcobalamin, are members of the family of corrinoids, which also includes cobinamides. As biological precursors to cobalamins, cobinamides possess the same structural core, consisting of a low-spin Co(3+) ion that is ligated equatorially by the four nitrogens of a highly substituted tetrapyrrole macrocycle (the corrin ring), but differ with respect to the lower axial ligation. Specifically, cobinamides possess a water molecule instead of the nucleotide loop that coordinates axially to Co(3+)cobalamins via its dimethylbenzimidazole (DMB) base. Compared to the cobalamin species, cobinamides have proven much more difficult to study experimentally, thus far eluding characterization by X-ray crystallography. In this study, we have utilized combined quantum mechanics/molecular mechanics (QM/MM) computations to generate complete structural models of a representative set of cobinamide species with varying upper axial ligands. To validate the use of this approach, analogous QM/MM geometry optimizations were carried out on entire models of the cobalamin counterparts for which high-resolution X-ray structural data are available. The accuracy of the cobinamide structures was assessed further by comparing electronic absorption spectra computed using time-dependent density functional theory to those obtained experimentally. Collectively, the results obtained in this study indicate that the DMB → H(2)O lower axial ligand switch primarily affects the energies of the Co 3d(z(2))-based molecular orbital (MO) and, to a lesser extent, the other Co 3d-based MOs as well as the corrin π-based highest energy MO. Thus, while the energy of the lowest-energy electronic transition of cobalamins changes considerably as a function of the upper axial ligand, it is nearly invariant for the cobinamides.
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Affiliation(s)
- Amanda J Reig
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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12
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Plymale NT, Dassanayake RS, Hassanin HA, Brasch NE. Kinetic and Mechanistic Studies on the Reactions of the Reduced Vitamin B12 Complex Cob(I)alamin with Nitrite and Nitrate. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201100992] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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13
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Hannibal L, Smith CA, Smith JA, Axhemi A, Miller A, Wang S, Brasch NE, Jacobsen DW. High resolution crystal structure of the methylcobalamin analogues ethylcobalamin and butylcobalamin by X-ray synchrotron diffraction. Inorg Chem 2010; 48:6615-22. [PMID: 19545130 DOI: 10.1021/ic900590p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The X-ray crystal structures of the methylcobalamin (MeCbl) analogues ethylcobalamin (EtCbl) and butylcobalamin (BuCbl) are reported. The X-ray crystal structures of EtCbl and BuCbl were obtained with some of the lowest crystallographic residuals ever achieved for cobalamins (R = 0.0468 and 0.0438, respectively). The Co-C bond distances for EtCbl and BuCbl are 2.023(2) and 2.028(4) A, whereas the Co-alpha-5,6-dimethylbenzimidazole (Co-N3B) bond distances were 2.232(1) and 2.244(1) A, respectively. Although EtCbl and BuCbl displayed a longer Co-N3B bond than that observed in the naturally occurring methylcobalamin, the orientation of the alpha-5,6-dimethylbenzimidazole moiety with respect to the corrin ring did not vary substantially among the structures. The lengthening of both Co-C and Co-N3B bonds in EtCbl and BuCbl can be attributed to the "inverse" trans influence exerted by the sigma-donating alkyl groups, typically observed in alkylcobalamins. Analysis of the molecular surface maps showed that the alkyl ligands in EtCbl and BuCbl are directed toward the hydrophobic side of the corrin ring. The corrin fold angles in EtCbl and BuCbl were determined to be 14.7 degrees and 13.1 degrees, respectively. A rough correlation exists between the corrin fold angle and the length of the Co-N3B bond, and both alkylcobalamins follow the same trend.
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Affiliation(s)
- Luciana Hannibal
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
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14
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Kliegman S, McNeill K. Reconciling disparate models of the involvement of vinyl radicals in cobalamin-mediated dechlorination reactions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2009; 43:8961-8967. [PMID: 19943673 DOI: 10.1021/es902267j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Inner-sphere (nonradical) and outer-sphere (radical-based) mechanisms have been suggested for cobalamin-mediated dechlorination of tetrachloroethylene (PCE) and trichloroethylene (TCE). In this study, the role of free vinyl radicals was investigated using deuterated radical traps: d(8)-isopropanol and d(8)-tetrahydrofuran. For both substrates, addition of trap resulted in production of deuterated dechlorination products, and higher concentrations of trap resulted in increased amounts of deuterated products. However, only a finite proportion of the products were trappable: 8% of the PCE-derived products and 86% of the TCE-derived products result from free radicals. The data show that the reaction does not proceed solely by either an inner-sphere or an outer-sphere mechanism and led to the hypothesis that caged radical intermediates were involved in the mechanism. The untrappable fraction of products are hypothesized to result from in-cage reactions. This hypothesis was investigated using d(5)-glycerol as a radical trap and viscogen. Although increased viscosity resulted in decreased formation of free-radical-derived products, consistent with the cage hypothesis, these data were inconclusive. The role of d(8)-isopropanol in enhancing the production of radicals in this system via an acetone ketyl radical chain mechanism was also investigated, and no evidence for such an effect was found.
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Affiliation(s)
- Sarah Kliegman
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
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15
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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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16
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Degtyarenko I, Biarnés X, Nieminen RM, Rovira C. Density-functional molecular dynamics studies of biologically relevant iron and cobalt complexes with macrocyclic ligands. Coord Chem Rev 2008. [DOI: 10.1016/j.ccr.2007.10.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Galezowski W, Kuta J, Kozlowski PM. DFT Study of Co−C Bond Cleavage in the Neutral and One-Electron-Reduced Alkyl−Cobalt(III) Phthalocyanines. J Phys Chem B 2008; 112:3177-83. [PMID: 18271575 DOI: 10.1021/jp0769678] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wlodzimierz Galezowski
- Department of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland, and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Jadwiga Kuta
- Department of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland, and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Pawel M. Kozlowski
- Department of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland, and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
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18
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Kliegman S, McNeill K. Dechlorination of chloroethylenes by cob(i)alamin and cobalamin model complexes. Dalton Trans 2008:4191-201. [DOI: 10.1039/b801679h] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kozlowski PM, Kuta J, Galezowski W. Reductive Cleavage Mechanism of Methylcobalamin: Elementary Steps of Co−C Bond Breaking. J Phys Chem B 2007; 111:7638-45. [PMID: 17567060 DOI: 10.1021/jp066972w] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory has been applied to the investigation of the reductive cleavage mechanism of methylcobalamin (MeCbl). In the reductive cleavage of MeCbl, the Co-C bond is cleaved homolytically, and formation of the anion radical ([MeCbl]*-) reduces the dissociation energy by approximately 50%. Such dissociation energy lowering in [MeCbl]*- arises from the involvement of two electronic states: the initial state, which is formed upon electron addition, has dominant pi*corrin character, but when the Co-C bond is stretched the unpaired electron moves to the sigma*Co-C state, and the final cleavage involves the three-electron (sigma)2(sigma*)1 bond. The pi*corrin-sigma*Co-C states crossing does not take place at the equilibrium geometry of [MeCbl]*- but only when the Co-C bond is stretched to 2.3 A. In contrast to the neutral cofactor, the most energetically efficient cleavage of the Co-C bond is from the base-off form. The analysis of thermodynamic and kinetic data provides a rationale as to why Co-C cleavage in reduced form requires prior departure of the axial base. Finally, the possible connection of present work to B12 enzymatic catalysis and the involvement of anion-radical-like [MeCbl]*- species in relevant methyl transfer reactions is discussed.
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Affiliation(s)
- Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA.
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20
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Rovira C, Kozlowski PM. First Principles Study of Coenzyme B12. Crystal Packing Forces Effect on Axial Bond Lengths. J Phys Chem B 2007; 111:3251-7. [PMID: 17388442 DOI: 10.1021/jp0660029] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work we analyze the structure of coenzyme B12 (AdoCbl) by means of periodic density functional theory (DFT) in order to elucidate the influence of the corrin side chains and the crystalline environment on the properties of axial bonds. The Co-Nax axial bond is very weak and its strength of less than 8 kcal/mol is four times smaller than Co-C which in solution is approximately 31 kcal/mol. The proper description of the Co-Nax distance has been problematic in previous DFT calculations and the source of disagreement between experiment and theory remained unexplained. To resolve this discrepancy, periodic DFT calculations within the Car-Parrinello molecular dynamics (CPMD) framework were carried out on three different structural models of increased complexity. The simplest model (DBI-Ado+) contains the naked corrin ring with a total of 96 atoms. The second model is the full coenzyme B12 (AdoCbl) with 209 atoms which has been taken from crystallographic analysis. To understand the extent to which the crystal packing forces influence the structural properties of AdoCbl the complete crystal consisting of four AdoCbl molecules plus 48 water molecules periodically repeated in space was analyzed (1008 atoms). The results show that the properties associated with the Co-C bond can be well reproduced using truncated models. This does not apply to the Co-Nax axial bond and the presence of the local environment appears to be essential for the correct prediction of its bond length. The most interesting outcome of the present analysis is the finding that the actual length of the Co-Nax bond (2.262 A) is largely influenced by crystal packing forces.
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Affiliation(s)
- Carme Rovira
- Centre de Recerca en Química Teorica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain.
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21
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Bühl M, Vrček IV, Kabrede H. Dehalogenation of Chloroalkenes at Cobalt Centers. A Model Density Functional Study. Organometallics 2007. [DOI: 10.1021/om070027s] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael Bühl
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany, and Faculty of Pharmacy and Biochemistry, University of Zagreb, HR-10000, Zagreb, Croatia
| | - Ivana Vinković Vrček
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany, and Faculty of Pharmacy and Biochemistry, University of Zagreb, HR-10000, Zagreb, Croatia
| | - Hendrik Kabrede
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany, and Faculty of Pharmacy and Biochemistry, University of Zagreb, HR-10000, Zagreb, Croatia
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22
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Follett AD, McNabb KA, Peterson AA, Scanlon JD, Cramer CJ, McNeill K. Characterization of Co−C Bonding in Dichlorovinylcobaloxime Complexes. Inorg Chem 2007; 46:1645-54. [PMID: 17286398 DOI: 10.1021/ic0618293] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study combines theory and experiment in an examination of Co-C bonding and reductive Co-C cleavage in cobalt dichlorovinyl complexes. It is motivated by the role of dichlorovinyl complexes as intermediates in the dechlorination of trichloroethylene by cobalamin and cobalamin model complexes. A series of seven cis-1,2-dichlorovinyl(L)cobaloxime complexes were prepared (L = m- and p-substituted pyridines; cobaloxime = bis(dimethylglyoximato)cobalt). The complexes were characterized using 1H NMR, 13C NMR, cyclic voltammetry, and X-ray crystallography. Examination of the metrical parameters of the Co-C=C unit across the series shows very little change in the C=C bond length and a slight increase in the Co-C bond length with increasing electron-donating ability of the pyridine ligand. These structural changes along with electronic structure calculations indicate that Co-C pi-bonding is not important in these complexes. The stronger Co-C bonds of vinylcobaloximes compared to those of alkylcobaloximes are best explained by the higher s character at C. Changes in the reduction potential across the series indicate that the pyridine-bound form is the primary electrochemically active species. Theoretical examination of the Co-C cleavage following reduction supports the direct formation of the cis-1,2-dichlorovinyl anion and not the cis-1,2-dichlorovinyl radical.
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Affiliation(s)
- Angela D Follett
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
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23
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Abstract
This Perspective provides an overview of the progress in two of the original programs in my research group focused on the biosynthesis of the antibiotics nisin, lacticin 481, fosfomycin, and bialaphos. The path from start-up funds to tenure and beyond offers insights into the opportunities realized and missed along the road.
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Affiliation(s)
- Wilfred A van der Donk
- Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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24
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Liptak MD, Brunold TC. Spectroscopic and Computational Studies of Co1+Cobalamin: Spectral and Electronic Properties of the “Superreduced” B12Cofactor. J Am Chem Soc 2006; 128:9144-56. [PMID: 16834388 DOI: 10.1021/ja061433q] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 4-coordinate, low-spin cob(I)alamin (Co1+Cbl) species, which can be obtained by heterolytic cleavage of the Co-C bond in methylcobalamin or the two-electron reduction of vitamin B12, is one of the most powerful nucleophiles known to date. The supernucleophilicity of Co1+Cbl has been harnessed by a number of cobalamin-dependent enzymes, such as the B12-dependent methionine synthase, and by enzymes involved in the biosynthesis of B12, including the human adenosyltransferase. The nontoxic nature of the Co1+Cbl supernucleophile also makes it an attractive target for the in situ bioremediation of halogenated waste. To gain insight into the geometric, electronic, and vibrational properties of this highly reactive species, electronic absorption, circular dichroism (CD), magnetic CD, and resonance Raman (rR) spectroscopies have been employed in conjunction with density functional theory (DFT), time-dependent DFT, and combined quantum mechanics/molecular mechanics computations. Collectively, our results indicate that the supernucleophilicity of Co1+Cbl can be attributed to the large destabilization of the Co 3dz2-based HOMO and its favorable orientation with respect to the corrin macrocycle, which minimizes steric repulsion during nucleophilic attack. An intense feature in the CD spectrum and a prominent peak in the rR spectra of Co1+Cbl have been identified that may serve as excellent probes of the nucleophilic character, and thus the reactivity, of Co1+Cbl in altered environments, including enzyme active sites. The implications of our results with respect to the enzymatic formation and reactivity of Co1+Cbl are discussed, and spectroscopic trends along the series from Co3+Cbls to Co2+Cbl and Co1+Cbl are explored.
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Affiliation(s)
- Mathew D Liptak
- University of Wisconsin-Madison, Department of Chemistry, 1101 University Avenue, Madison, Wisconsin 53706, USA
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Follett AD, McNeill K. Evidence for the Formation of a cis-Dichlorovinyl Anion upon Reduction of cis-1,2-Dichlorovinyl(pyridine)cobaloxime. Inorg Chem 2006; 45:2727-32. [PMID: 16529497 DOI: 10.1021/ic052020d] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reduction of cis-1,2-dichlorovinyl(pyridine)cobaloxime, a model complex for the organometallic intermediate proposed in the dechlorination of trichloroethylene by cobalamin, was studied. Two mechanisms were considered for the Co-C bond cleavage following reduction. In the first, the Co-C bond cleaves to produce Co(I) and a chlorovinyl radical, while the second pathway results in the formation of Co(II) and a chlorovinyl anion. Four reducing agents, cobaltocene, decamethylcobaltocene, cob(I)alamin, and chromium(II), were used in the presence of H atom and proton donor species to identify the presence of chlorovinyl radical or chlorovinyl anion intermediates. Mechanistic conclusions were based on comparisons of the final product ratios of cis-dichloroethylene (cDCE) and chloroacetylene, which were found to have a direct relationship to the amount of proton donor available, with increased proton donor leading to increased cDCE production. The results support the intermediacy of a cis-1,2-dichlorovinyl anion.
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Affiliation(s)
- Angela D Follett
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
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Fritsch JM, Retka ND, McNeill K. Synthesis, Structure, and Unusual Reactivity of β-Halovinyl Cobalt Porphyrin Complexes. Inorg Chem 2006; 45:2288-95. [PMID: 16499395 DOI: 10.1021/ic0518834] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The preparation, structures, and reactivity of tetraphenylporphyrin (TPP) cobalt halovinyl complexes are reported. Beta-halovinyl complexes of (TPP)Co(E-CHCHX) (X = Br and I) were prepared from the insertion of acetylene into the cobalt halide bonds of the corresponding halide complexes. The reactivity of these compounds and of the previously reported (TPP)Co(E-CHCHCl), was studied in depth, and it was found that complex reactivity increased with the leaving group ability of the halide. A trans-dichlorovinyl cobalt porphyrin complex, (TPP)Co(Z-CClCHCl), was also prepared through the reaction of (TPP)CoNa and TCE. The structures of (TPP)Co(E-CHCHBr), (TPP)Co(Z-CClCHCl), and (TPP)Co(C(2)H) are reported. The C-C bond length of the vinyl group was found to vary for the beta-halovinyl complexes (TPP)Co(E-CHCHX) from 1.211 A for X = Br to 1.234 A for X = Cl and 1.320 A for (TPP)Co(Z-CClCHCl). A comparison of these structures to many chlorovinyl cobalt complexes shows that trans-2-halo substitution results in a dramatically decreased vinyl C-C bond length. The mechanism of halide substitution for the beta-halovinyl complexes was investigated with kinetic experiments that indicated a dissociative mechanism and supported the intermediacy of a cobalt acetylene complex.
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Affiliation(s)
- Joseph M Fritsch
- Department of Chemistry, University of Minnesota, 225 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
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Pratt DA, van der Donk WA. On the role of alkylcobalamins in the vitamin B12-catalyzed reductive dehalogenation of perchloroethylene and trichloroethylene. Chem Commun (Camb) 2005:558-60. [PMID: 16432582 DOI: 10.1039/b513624e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Theoretical studies are presented on the structures and reactivity of chlorinated ethylcobalamins, potential intermediates in the vitamin B12-catalyzed reductive dehalogenation of the environmental pollutants perchloroethylene and trichloroethylene; the results suggest an alternative mechanism of catalysis.
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Affiliation(s)
- Derek A Pratt
- Department of Chemistry, Queen's University, 90 Bader Crescent, Kingston, Ontario, Canada K7L 3N6.
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Dölker N, Morreale A, Maseras F. Computational study on the difference between the Co–C bond dissociation energy in methylcobalamin and adenosylcobalamin. J Biol Inorg Chem 2005; 10:509-17. [PMID: 15986217 DOI: 10.1007/s00775-005-0662-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Accepted: 05/16/2005] [Indexed: 10/25/2022]
Abstract
The bond dissociation energies of the Co-C bonds in the cobalamin cofactors methylcobalamin and adenosylcobalamin were calculated using the hybrid quantum mechanics/molecular mechanics method IMOMM (integrated molecular orbital and molecular mechanics). Calculations were performed on models of differing complexities as well as on the full systems. We investigated the origin of the different experimental values for the Co-C bond dissociation energies in methylcobalamin and adenosylcobalamin, and have provided an explanation for the difficulties encountered when we attempt to reproduce this difference in quantum chemistry. Additional calculations have been performed using the Miertus-Scrocco-Tomasi method in order to estimate the influence of solvent effects on the homolytic Co-C bond cleavage. Introduction of these solvation effects is shown to be necessary for the correct reproduction of experimental trends in bond dissociation energies in solution, which consequently have no direct correlation with dissociation processes in the enzyme.
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Affiliation(s)
- Nicole Dölker
- Unitat de Química Física, Edifici C.n, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain.
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