1
|
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.
Collapse
Affiliation(s)
- Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
| |
Collapse
|
2
|
Methyl transfer reactions catalyzed by cobalamin-dependent enzymes: Insight from molecular docking. J Mol Graph Model 2020; 104:107831. [PMID: 33529932 DOI: 10.1016/j.jmgm.2020.107831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 11/22/2022]
Abstract
Methyl transfer reactions, mediated by methyltransferases (MeTrs), such as methionine synthase (MetH) or monomethylamine: CoM (MtmBC), constitute one of the most important classes of vitamin B12-dependent reactions. The challenge in exploring the catalytic function of MeTrs is related to their modular structure. From the crystallographic point of view, the structure of each subunit has been determined, but there is a lack of understanding of how each subunit interacts with each other. So far, theoretical studies of methyl group transfer were carried out for the structural models of the active site of each subunit. However, those studies do not include the effect of the enzymatic environment, which is crucial for a comprehensive understanding of enzyme-mediated methyl transfer reactions. Herein, to explore how two subunits interact with each other and how the methyl transfer reaction is catalyzed by MeTrs, molecular docking of the functional units of MetH and MtmBC was carried out. Along with the interactions of the functional units, the reaction coordinates, including the Co-C bond distance for methylation of cob(I)alamin (CoICbl) and the C-S bond distance in demethylation reaction of cob(III)alamin (CoIIICbl), were considered. The functional groups should be arranged so that there is an appropriate distance to transfer a methyl group and present results indicate that steric interactions can limit the number of potential arrangements. This calls into question the possibility of SN2-type mechanism previously proposed for MeTrs. Further, it leads to the conclusion that the methyl transfer reaction involves some spatial changes of modules suggesting an alternate radical-based pathway for MeTrs-mediated methyl transfer reactions. The calculations also showed that changes in torsion angles induce a change in reaction coordinates, namely Co-C and C-S bond distances, for the methylation and demethylation reactions catalyzed both by MetH and MtmBC.
Collapse
|
3
|
Kumar M, Francisco JS. Evidence of the Elusive Gold-Induced Non-classical Hydrogen Bonding in Aqueous Environments. J Am Chem Soc 2020; 142:6001-6006. [PMID: 32126169 DOI: 10.1021/jacs.9b05493] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The ability of a gold ion to act as a proton acceptor in hydrogen bonding continues to remain an open question. Heavy-atom effects and secondary competitive interactions in gold complexes make it challenging to precisely establish the identity of gold-ion-induced hydrogen bonding via experimental techniques. In such situations, computational chemistry may play an important role. Herein we have performed Born-Oppenheimer molecular dynamics simulations to study the behavior of [Au(CH3)2)]- in bulk and interfacial aqueous environments. The simulation results suggest that the [Au(CH3)2)]- complex forms one and two gold-ion-induced hydrogen bonds with the water molecules in interfacial and bulk environments, respectively. The calculated probabilities of key hydrogen-bonded configurations of [Au(CH3)2)]-, combined distribution functions, and diffusion coefficients further support this unusual hydrogen-bonding interaction. In summary, the present results suggest that gold-ion-induced hydrogen bonding in an actual solvent environment may be feasible. These results will improve our understanding about the role of weak interactions in transition metal complexes and, thus, will have implications in catalysis and supramolecular assemblies.
Collapse
Affiliation(s)
- Manoj Kumar
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Joseph S Francisco
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| |
Collapse
|
4
|
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
| |
Collapse
|
5
|
Electronic and structural properties of Cob(I)alamin: Ramifications for B 12 -dependent processes. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
6
|
Lawrence MAW, Celestine MJ, Artis ET, Joseph LS, Esquivel DL, Ledbetter AJ, Cropek DM, Jarrett WL, Bayse CA, Brewer MI, Holder AA. Computational, electrochemical, and spectroscopic studies of two mononuclear cobaloximes: the influence of an axial pyridine and solvent on the redox behaviour and evidence for pyridine coordination to cobalt(i) and cobalt(ii) metal centres. Dalton Trans 2016; 45:10326-42. [PMID: 27244471 PMCID: PMC5973836 DOI: 10.1039/c6dt01583b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
[Co(dmgBF2)2(H2O)2] (where dmgBF2 = difluoroboryldimethylglyoximato) was used to synthesize [Co(dmgBF2)2(H2O)(py)]·0.5(CH3)2CO (where py = pyridine) in acetone. The formulation of complex was confirmed by elemental analysis, high resolution MS, and various spectroscopic techniques. The complex [Co(dmgBF2)2(solv)(py)] (where solv = solvent) was readily formed in situ upon the addition of pyridine to complex . A spectrophotometric titration involving complex and pyridine proved the formation of such a species, with formation constants, log K = 5.5, 5.1, 5.0, 4.4, and 3.1 in 2-butanone, dichloromethane, acetone, 1,2-difluorobenzene/acetone (4 : 1, v/v), and acetonitrile, respectively, at 20 °C. In strongly coordinating solvents, such as acetonitrile, the lower magnitude of K along with cyclic voltammetry, NMR, and UV-visible spectroscopic measurements indicated extensive dissociation of the axial pyridine. In strongly coordinating solvents, [Co(dmgBF2)2(solv)(py)] can only be distinguished from [Co(dmgBF2)2(solv)2] upon addition of an excess of pyridine, however, in weakly coordinating solvents the distinctions were apparent without the need for excess pyridine. The coordination of pyridine to the cobalt(ii) centre diminished the peak current at the Epc value of the Co(I/0) redox couple, which was indicative of the relative position of the reaction equilibrium. Herein we report the first experimental and theoretical (59)Co NMR spectroscopic data for the formation of Co(i) species of reduced cobaloximes in the presence and absence of py (and its derivatives) in CD3CN. From spectroelectrochemical studies, it was found that pyridine coordination to a cobalt(i) metal centre is more favourable than coordination to a cobalt(ii) metal centre as evident by the larger formation constant, log K = 4.6 versus 3.1, respectively, in acetonitrile at 20 °C. The electrosynthesis of hydrogen by complexes and in various solvents demonstrated the dramatic effects of the axial ligand and the solvent on the turnover number of the respective catalyst.
Collapse
Affiliation(s)
- Mark A W Lawrence
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Michael J Celestine
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Edward T Artis
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Lorne S Joseph
- University of the Virgin Islands, #2 John Brewers Bay, Charlotte Amalie, VI 00802, USA
| | - Deisy L Esquivel
- Johnson C. Smith University, 100 Beatties Ford Road, Charlotte, NC 28216, USA
| | | | - Donald M Cropek
- U.S. Army Corps of Engineers, Construction Engineering Research Laboratory, Champaign, IL 61822, USA
| | - William L Jarrett
- School of Polymers and High-Performance Materials, The University of Southern Mississippi, 118 College Drive, #5050, Hattiesburg, MS 39406-0076, USA
| | - Craig A Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Matthew I Brewer
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Alvin A Holder
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| |
Collapse
|
7
|
|
8
|
Garabato BD, Kumar N, Lodowski P, Jaworska M, Kozlowski PM. Electronically excited states of cob(ii)alamin: insights from CASSCF/XMCQDPT2 and TD-DFT calculations. Phys Chem Chem Phys 2016; 18:4513-26. [DOI: 10.1039/c5cp06439b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The low-lying excited states of cob(ii)alamin were investigated using time-dependent density functional theory (TD-DFT), and multiconfigurational CASSCF/XMCQDPT2 methodology, to help understand their role in B12-mediated reactions.
Collapse
Affiliation(s)
| | - Neeraj Kumar
- Department of Chemistry
- University of Louisville
- Louisville
- USA
- Pacific Northwest National Laboratory
| | - Piotr Lodowski
- Department of Theoretical Chemistry
- Institute of Chemistry
- University of Silesia
- PL-40 006 Katowice
- Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry
- Institute of Chemistry
- University of Silesia
- PL-40 006 Katowice
- Poland
| | - Pawel M. Kozlowski
- Department of Chemistry
- University of Louisville
- Louisville
- USA
- Visiting Professor at the Department of Food Sciences
| |
Collapse
|
9
|
Dereven'kov IA, Salnikov DS, Makarov SV, Boss GR, Koifman OI. Kinetics and mechanism of oxidation of super-reduced cobalamin and cobinamide species by thiosulfate, sulfite and dithionite. Dalton Trans 2014; 42:15307-16. [PMID: 23999614 DOI: 10.1039/c3dt51714d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We studied the kinetics of reactions of cob(I)alamin and cob(I)inamide with thiosulfate, sulfite, and dithionite by UV-Visible (UV-Vis) and stopped-flow spectroscopy. We found that the two Co(I) species were oxidized by these sulfur-containing compounds to Co(II) forms: oxidation by excess thiosulfate leads to penta-coordinate complexes and oxidation by excess sulfite or dithionite leads to hexa-coordinate Co(II)-SO2(-) complexes. The net scheme involves transfer of three electrons in the case of oxidation by thiosulfate and one electron for oxidation by sulfite and dithionite. On the basis of kinetic data, the nature of the reactive oxidants was suggested, i.e., HS2O3(-) (for oxidation by thiosulfate), S2O5(2-), HSO3(-), and aquated SO2 (for oxidation by sulfite), and S2O4(2-) and SO2(-) (for oxidation by dithionite). No difference was observed in kinetics with cob(i)alamin or cob(i)inamide as reductants.
Collapse
Affiliation(s)
- Ilia A Dereven'kov
- State University of Chemistry and Technology, Sheremetevskiy str. 7, 153000 Ivanovo, Russia.
| | | | | | | | | |
Collapse
|
10
|
Demissie TB, Repisky M, Liu H, Ruud K, Kozlowski PM. Cob(II)alamin: Relativistic DFT Analysis of the EPR Parameters. J Chem Theory Comput 2014; 10:2125-36. [DOI: 10.1021/ct400769t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Taye B. Demissie
- Centre for Theoretical and Computational
Chemistry, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Michal Repisky
- Centre for Theoretical and Computational
Chemistry, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Hui Liu
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
| | - Kenneth Ruud
- Centre for Theoretical and Computational
Chemistry, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
| |
Collapse
|
11
|
Can the local enzyme scaffold act as an H-donor for a Co(I)H bond formation? The curious case of methionine synthase-bound cob(I)alamin. J Inorg Biochem 2013; 126:26-34. [DOI: 10.1016/j.jinorgbio.2013.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Revised: 04/19/2013] [Accepted: 04/20/2013] [Indexed: 11/19/2022]
|
12
|
Bergès J, Fourré I, Pilmé J, Kozelka J. Quantum Chemical Topology Study of the Water-Platinum(II) Interaction. Inorg Chem 2013; 52:1217-27. [DOI: 10.1021/ic301512c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jacqueline Bergès
- Laboratoire de Chimie Théorique,
UMR 7616 CNRS, Université Pierre et Marie Curie, Sorbonne Universités, Case Courier 137, 4 place Jussieu,
75252 Paris Cedex 05, France
- Université Paris Descartes, 75270
Paris, France
| | - Isabelle Fourré
- Laboratoire de Chimie Théorique,
UMR 7616 CNRS, Université Pierre et Marie Curie, Sorbonne Universités, Case Courier 137, 4 place Jussieu,
75252 Paris Cedex 05, France
| | - Julien Pilmé
- Laboratoire de Chimie Théorique,
UMR 7616 CNRS, Université Pierre et Marie Curie, Sorbonne Universités, Case Courier 137, 4 place Jussieu,
75252 Paris Cedex 05, France
| | - Jiri Kozelka
- Laboratoire
de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR-CNRS 8601, 75270
Paris, France
- Institute
of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 2, 61137
Brno, Czech Republic
| |
Collapse
|
13
|
Affiliation(s)
- Sergei V. Makarov
- a Department of Food Chemistry and Biotechnology , State University of Chemistry and Technology , Engels Street 7, Ivanovo , 153000 , Russia
| | - Radu Silaghi-Dumitrescu
- b Faculty of Chemistry and Chemical Engineering , “Babes-Bolyai” University , 11 Arany Janos Street, Cluj-Napoca , RO-400028 , Romania
| |
Collapse
|
14
|
Kocak A, Austein-Miller G, Pearson WL, Altinay G, Metz RB. Dissociation Energy and Electronic and Vibrational Spectroscopy of Co+(H2O) and Its Isotopomers. J Phys Chem A 2012; 117:1254-64. [DOI: 10.1021/jp305673t] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Abdulkadir Kocak
- Department of Chemistry, University of Massachusetts—Amherst, Amherst,
Massachusetts 01003, United States
| | - Geoff Austein-Miller
- Department of Chemistry, University of Massachusetts—Amherst, Amherst,
Massachusetts 01003, United States
| | - Wright L. Pearson
- Department of Chemistry, University of Massachusetts—Amherst, Amherst,
Massachusetts 01003, United States
| | - Gokhan Altinay
- Department of Chemistry, University of Massachusetts—Amherst, Amherst,
Massachusetts 01003, United States
| | - Ricardo B. Metz
- Department of Chemistry, University of Massachusetts—Amherst, Amherst,
Massachusetts 01003, United States
| |
Collapse
|