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Hartman JD, Capistran D. Predicting 51V nuclear magnetic resonance observables in molecular crystals. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:416-428. [PMID: 38114304 DOI: 10.1002/mrc.5420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy and quantum chemical density functional theory (DFT) calculations are widely used to characterize vanadium centers in biological and pharmaceutically relevant compounds. Several techniques have been recently developed to improve the accuracy of predicted NMR parameters obtained from DFT. Fragment-based and planewave-corrected methods employing hybrid density functionals are particularly effective tools for solid-state applications. A recent benchmark study involving molecular crystal compounds found that fragment-based NMR calculations using hybrid density functionals improve the accuracy of predicted 51V chemical shieldings by 20% relative to traditional planewave methods. This work extends the previous study, including a careful analysis of 51V chemical shift anisotropy, electric field gradient calculations, and a more extensive test set. The accuracy of planewave-corrected techniques and recently developed fragment-based methods using electrostatic embedding based on the polarized continuum model (PCM) are found to be highly competitive with previous methods. Planewave-corrected methods achieve a 34% improvement in the errors of predicted 51V chemical shieldings relative to planewave. Additionally, planewave-corrected and fragment-based calculations were performed using PCM embedding, improving the accuracy of predicted 51V chemical shielding (CS) tensor principal values by 30% andC q values by 15% relative to traditional planewave methods. The performance of these methods is further examined using a redox-active oxovandium complex and a common 51V NMR reference compound.
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Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
| | - Daniel Capistran
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
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2
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Recent development of biomimetic halogenation inspired by vanadium dependent haloperoxidase. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214404] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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3
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Pessoa JC, Santos MF, Correia I, Sanna D, Sciortino G, Garribba E. Binding of vanadium ions and complexes to proteins and enzymes in aqueous solution. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214192] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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4
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Mathews A, Hartman JD. Accurate fragment-based 51-V chemical shift predictions in molecular crystals. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 114:101733. [PMID: 34082261 DOI: 10.1016/j.ssnmr.2021.101733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy plays a crucial role in determining molecular structure for complex biological and pharmaceutical compounds. NMR investigations are increasingly reliant on computation for mapping spectral features to chemical structures. Here we benchmark the accuracy of fragment-based 51V chemical shielding tensor calculations using a training set comprised of 10 biologically and pharmaceutically relevant oxovanadium complexes. Using our self-consistent reproduction of the Madelung potential (SCRMP) electrostatic embedding model, we demonstrate comparable performance between fragment methods and computationally demanding cluster-based techniques. Specifically, fragment methods employing hybrid density functionals are capable of reproducing the experimental 51V isotropic chemical shifts with a training set rms error of ~9 ppm, representing a 20% improvement over traditional plane wave techniques. We provide training set-derived linear regression models for mapping the absolute shieldings obtained from computation to the experimentally determined chemical shifts using four common density functionals; PBE0, B3LYP, PBE, and BLYP. Finally, we establish the utility of fragment methods and the reported regression parameters examining four oxovanadium structures excluded from the training set including the tetracoordinate oxovanadium silicate [Formula: see text] , VO15NGlySalbz which contains redox-active ligands, and the solid-state form of the common 51V NMR reference compound VOCl3.
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Affiliation(s)
- Amanda Mathews
- Department of Chemistry, Mt. San Jacinto College, Menifee, CA, USA
| | - Joshua D Hartman
- Department of Chemistry, Mt. San Jacinto College, Menifee, CA, USA.
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5
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Mubarak MQE, Gérard EF, Blanford CF, Hay S, de Visser SP. How Do Vanadium Chloroperoxidases Generate Hypochlorite from Hydrogen Peroxide and Chloride? A Computational Study. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03490] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- M. Qadri E. Mubarak
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Emilie F. Gérard
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Christopher F. Blanford
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Materials, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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6
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Anderson GA, Behera RN, Gomatam R. Calculation of higher protonation states and of a new resting state for vanadium chloroperoxidase using QM/MM, with an Atom-in-Molecules analysis. J Mol Graph Model 2020; 99:107624. [PMID: 32388271 DOI: 10.1016/j.jmgm.2020.107624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/12/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022]
Abstract
Earlier QM/MM studies of the resting state of vanadium chloroperoxidase (VCPO) focused on the diprotonated states of the vanadate cofactor. Herein, we report a new extensive QM/MM study that includes the tri- and quadprotonated states of VCPO at neutral pH. We identify certain di- and triprotonated states as being candidates for the resting state based on a comparison of relative energies. The quadprotonated states as well as some of the triprotonated states are ruled out as the resting state. An Atoms-in-Molecules (AIM) analysis of the complex hydrogen bonding around the vanadate cofactor helps to explain the relative energies of the protonation states considered herein, and it also indicates new hydrogen bonding which has not been recognized previously. A Natural Bond Orbital (NBO) study is presented to give a better understanding of the electronic structure of the vanadate co-factor.
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Affiliation(s)
| | - Raghu Nath Behera
- Department of Chemistry, Birla Institute of Technology and Science, Pilani - Goa Campus, Zuarinagar, Goa, 403726, India.
| | - Ravi Gomatam
- Bhaktivedanta Institute and Institute of Semantic Information Sciences and Technology, Juhu Road, Juhu, Mumbai, 400049, India
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7
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Mubarak MQE, de Visser SP. Second-Coordination Sphere Effect on the Reactivity of Vanadium–Peroxo Complexes: A Computational Study. Inorg Chem 2019; 58:15741-15750. [DOI: 10.1021/acs.inorgchem.9b01778] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Qadri E. Mubarak
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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8
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Single and double fluorine migration in third row transition metal dialkylaminodifluorosulfane complexes. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.10.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Duncan Lyngdoh RH, Schaefer HF, King RB. Metal-Metal (MM) Bond Distances and Bond Orders in Binuclear Metal Complexes of the First Row Transition Metals Titanium Through Zinc. Chem Rev 2018; 118:11626-11706. [PMID: 30543419 DOI: 10.1021/acs.chemrev.8b00297] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This survey of metal-metal (MM) bond distances in binuclear complexes of the first row 3d-block elements reviews experimental and computational research on a wide range of such systems. The metals surveyed are titanium, vanadium, chromium, manganese, iron, cobalt, nickel, copper, and zinc, representing the only comprehensive presentation of such results to date. Factors impacting MM bond lengths that are discussed here include (a) the formal MM bond order, (b) size of the metal ion present in the bimetallic core (M2) n+, (c) the metal oxidation state, (d) effects of ligand basicity, coordination mode and number, and (e) steric effects of bulky ligands. Correlations between experimental and computational findings are examined wherever possible, often yielding good agreement for MM bond lengths. The formal bond order provides a key basis for assessing experimental and computationally derived MM bond lengths. The effects of change in the metal upon MM bond length ranges in binuclear complexes suggest trends for single, double, triple, and quadruple MM bonds which are related to the available information on metal atomic radii. It emerges that while specific factors for a limited range of complexes are found to have their expected impact in many cases, the assessment of the net effect of these factors is challenging. The combination of experimental and computational results leads us to propose for the first time the ranges and "best" estimates for MM bond distances of all types (Ti-Ti through Zn-Zn, single through quintuple).
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Affiliation(s)
| | - Henry F Schaefer
- Centre for Computational Quantum Chemistry , University of Georgia , Athens , Georgia 30602 , United States
| | - R Bruce King
- Centre for Computational Quantum Chemistry , University of Georgia , Athens , Georgia 30602 , United States
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10
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A Comparative Review on the Catalytic Mechanism of Nonheme Iron Hydroxylases and Halogenases. Catalysts 2018. [DOI: 10.3390/catal8080314] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Enzymatic halogenation and haloperoxidation are unusual processes in biology; however, a range of halogenases and haloperoxidases exist that are able to transfer an aliphatic or aromatic C–H bond into C–Cl/C–Br. Haloperoxidases utilize hydrogen peroxide, and in a reaction with halides (Cl−/Br−), they react to form hypohalides (OCl−/OBr−) that subsequently react with substrate by halide transfer. There are three types of haloperoxidases, namely the iron-heme, nonheme vanadium, and flavin-dependent haloperoxidases that are reviewed here. In addition, there are the nonheme iron halogenases that show structural and functional similarity to the nonheme iron hydroxylases and form an iron(IV)-oxo active species from a reaction of molecular oxygen with α-ketoglutarate on an iron(II) center. They subsequently transfer a halide (Cl−/Br−) to an aliphatic C–H bond. We review the mechanism and function of nonheme iron halogenases and hydroxylases and show recent computational modelling studies of our group on the hectochlorin biosynthesis enzyme and prolyl-4-hydroxylase as examples of nonheme iron halogenases and hydroxylases. These studies have established the catalytic mechanism of these enzymes and show the importance of substrate and oxidant positioning on the stereo-, chemo- and regioselectivity of the reaction that takes place.
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11
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Xu L, Li QS, King RB. Unsaturated trinuclear iron fluoroborylene complexes. J Mol Model 2017; 23:123. [PMID: 28315080 DOI: 10.1007/s00894-017-3301-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/27/2017] [Indexed: 11/28/2022]
Abstract
The unsaturated trinuclear iron fluoroborylene complexes Fe3(BF)3(CO) n (n = 7, 6) have been studied using density functional theory (DFT). Relatively complicated potential energy surfaces are found with nine and eight structures within 15 kcal mol-1 of the lowest energy structures for the Fe3(BF)3(CO)7 and Fe3(BF)3(CO)6 systems, respectively. In each of these low-energy structures all three BF groups are either edge-bridging or face-bridging but never terminal groups. Some, but not all, of the low-energy structures also have edge-bridging and/or face-bridging CO groups leading to some structures with as many as five bridging groups. The relatively narrow range of Fe-Fe distances in the central Fe3 triangles of the Fe3(BF)3(CO) n (n = 7, 6) structures, mainly between 2.37 and 2.55 Å, suggests considerable delocalization in these unsaturated systems. Graphical Abstract The lowest energy Fe3(BF)3(CO)7 and Fe3(BF)3(CO)6 structures have a face-bridging μ3-BF group with the two remaining BF groups bridging edges. The lowest energy Fe3(BF)3(CO)6 structure also has one four-electron donor bridging η2-μ-CO group.
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Affiliation(s)
- Liancai Xu
- Department of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, People's Republic of China.
| | - Qian-Shu Li
- Center for Computational Quantum Chemistry, South China Normal University, Guangzhou, 510631, People's Republic of China.,Institute of Chemical Physics, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - R Bruce King
- Center for Computational Quantum Chemistry, South China Normal University, Guangzhou, 510631, People's Republic of China. .,Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, GA, 30602, USA.
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12
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Rana S, Pandey B, Dey A, Haque R, Rajaraman G, Maiti D. A Doubly Biomimetic Synthetic Transformation: Catalytic Decarbonylation and Halogenation at Room Temperature by Vanadium Pentoxide. ChemCatChem 2016. [DOI: 10.1002/cctc.201600843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sujoy Rana
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Bhawana Pandey
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Aniruddha Dey
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Rameezul Haque
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Gopalan Rajaraman
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Debabrata Maiti
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
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13
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Gupta R, Yehl J, Li M, Polenova T. 51V magic angle spinning NMR spectroscopy and quantum chemical calculations in vanadium bio-inorganic systems: current perspective. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0557] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In recent years, 51V magic angle spinning (MAS) NMR spectroscopy has been widely used to characterize vanadium centers in biology, biomimetic complexes, and inorganic compounds of medicinal and industrial relevance. It has been demonstrated that 51V NMR parameters are sensitive probes of the coordination geometry and chemical environment of the metal center, beyond the first coordination sphere. To establish the relationships between NMR parameters and structure of the vanadium centers, over the past decade a large series of coordination complexes have been analyzed by MAS NMR spectroscopy. It has been demonstrated that the interpretation of the NMR parameters requires the use of theoretical methods, such as density functional (DFT) theory, whereby the experimental NMR observables are linked to the electronic and structural properties of a molecule. DFT calculations have been successfully employed to not only predict NMR parameters but to also yield valuable information regarding the structure and function of various vanadium compounds. In this report, we review the current state of the field, and present a survey of bioinorganic vanadium complexes as well as vanadium-dependent haloperoxidases analyzed using 51V MAS NMR spectroscopy and DFT calculations, to illustrate the rich information content available from such a combined approach.
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Affiliation(s)
- Rupal Gupta
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Jenna Yehl
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Mingyue Li
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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14
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Enzymatic Halogenases and Haloperoxidases: Computational Studies on Mechanism and Function. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 100:113-51. [PMID: 26415843 DOI: 10.1016/bs.apcsb.2015.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Despite the fact that halogenated compounds are rare in biology, a number of organisms have developed processes to utilize halogens and in recent years, a string of enzymes have been identified that selectively insert halogen atoms into, for instance, a CH aliphatic bond. Thus, a number of natural products, including antibiotics, contain halogenated functional groups. This unusual process has great relevance to the chemical industry for stereoselective and regiospecific synthesis of haloalkanes. Currently, however, industry utilizes few applications of biological haloperoxidases and halogenases, but efforts are being worked on to understand their catalytic mechanism, so that their catalytic function can be upscaled. In this review, we summarize experimental and computational studies on the catalytic mechanism of a range of haloperoxidases and halogenases with structurally very different catalytic features and cofactors. This chapter gives an overview of heme-dependent haloperoxidases, nonheme vanadium-dependent haloperoxidases, and flavin adenine dinucleotide-dependent haloperoxidases. In addition, we discuss the S-adenosyl-l-methionine fluoridase and nonheme iron/α-ketoglutarate-dependent halogenases. In particular, computational efforts have been applied extensively for several of these haloperoxidases and halogenases and have given insight into the essential structural features that enable these enzymes to perform the unusual halogen atom transfer to substrates.
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15
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Gupta R, Hou G, Renirie R, Wever R, Polenova T. 51V NMR Crystallography of Vanadium Chloroperoxidase and Its Directed Evolution P395D/L241V/T343A Mutant: Protonation Environments of the Active Site. J Am Chem Soc 2015; 137:5618-28. [DOI: 10.1021/jacs.5b02635] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Rupal Gupta
- Department
of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Guangjin Hou
- Department
of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Rokus Renirie
- Van’t
Hoff Institute for Molecular Science, University of Amsterdam, POSTBUS
94157, 1090 GD, Amsterdam, The Netherlands
| | - Ron Wever
- Van’t
Hoff Institute for Molecular Science, University of Amsterdam, POSTBUS
94157, 1090 GD, Amsterdam, The Netherlands
| | - Tatyana Polenova
- Department
of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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16
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Wu P, Zeng Y, Feng H, Xie Y, King RB. Cyclic versus acyclic structures of six-carbon ligands in binuclear cobalt carbonyl derivatives: Some thermochemical observations. Inorganica Chim Acta 2015. [DOI: 10.1016/j.ica.2015.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Senn HM. Insights into enzymatic halogenation from computational studies. Front Chem 2014; 2:98. [PMID: 25426489 PMCID: PMC4227530 DOI: 10.3389/fchem.2014.00098] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/20/2014] [Indexed: 12/15/2022] Open
Abstract
The halogenases are a group of enzymes that have only come to the fore over the last 10 years thanks to the discovery and characterization of several novel representatives. They have revealed the fascinating variety of distinct chemical mechanisms that nature utilizes to activate halogens and introduce them into organic substrates. Computational studies using a range of approaches have already elucidated many details of the mechanisms of these enzymes, often in synergistic combination with experiment. This Review summarizes the main insights gained from these studies. It also seeks to identify open questions that are amenable to computational investigations. The studies discussed herein serve to illustrate some of the limitations of the current computational approaches and the challenges encountered in computational mechanistic enzymology.
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Affiliation(s)
- Hans M. Senn
- WestCHEM School of Chemistry, University of GlasgowGlasgow, UK
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18
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Binuclear allyliron carbonyls: Fragile dimers and diverse types of allyl groups. Polyhedron 2012. [DOI: 10.1016/j.poly.2012.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Sun Q, Li Z, Lan Z, Pfisterer C, Doerr M, Fischer S, Smith SC, Thiel W. Isomerization mechanism of the HcRed fluorescent protein chromophore. Phys Chem Chem Phys 2012; 14:11413-24. [PMID: 22801745 DOI: 10.1039/c2cp41217a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To understand how the protein achieves fluorescence, the isomerization mechanism of the HcRed chromophore is studied both under vacuum and in the solvated red fluorescent protein. Quantum mechanical (QM) and quantum mechanical/molecular mechanical (QM/MM) methods are applied both for the ground and the first excited state. The photoinduced processes in the chromophore mainly involve torsions around the imidazolinone-bridge bond (τ) and the phenoxy-bridge bond (φ). Under vacuum, the isomerization of the cis-trans chromophore essentially proceeds by τ twisting, while the radiationless decay requires φ torsion. By contrast, the isomerization of the cis-trans chromophore in HcRed occurs via simultaneous τ and φ twisting. The protein environment significantly reduces the barrier of this hula twist motion compared with vacuum. The excited-state isomerization barrier via the φ rotation of the cis-coplanar conformer in HcRed is computed to be significantly higher than that of the trans-non-coplanar conformer. This is consistent with the experimental observation that the cis-coplanar-conformation of the chromophore is related to the fluorescent properties of HcRed, while the trans-non-planar conformation is weakly fluorescent or non-fluorescent. Our study shows how the protein modifies the isomerization mechanism, notably by interactions involving the nearby residue Ile197, which keeps the chromophore coplanar and blocks the twisting motion that leads to photoinduced radiationless decay.
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Affiliation(s)
- Qiao Sun
- Centre for Computational Molecular Science, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Qld 4072, Brisbane, Australia.
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20
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Xu L, Li QS, King RB. Fluoroborylene ligands in binuclear ruthenium carbonyls: Comparison with their iron analogues. Polyhedron 2012. [DOI: 10.1016/j.poly.2012.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Liao RZ, Thiel W. Comparison of QM-Only and QM/MM Models for the Mechanism of Tungsten-Dependent Acetylene Hydratase. J Chem Theory Comput 2012; 8:3793-803. [DOI: 10.1021/ct3000684] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
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22
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Binuclear dimethylaminoborole iron carbonyls: iron–iron multiple bonding versus nitrogen → iron dative bonding. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1090-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Chen X, Jin R, Du Q, Feng H, Xie Y, King RB. Five-electron donor versus seven-electron donor bridging phospholyl rings in binuclear cobalt carbonyl derivatives. J Organomet Chem 2012. [DOI: 10.1016/j.jorganchem.2011.10.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Binuclear heptalene iron carbonyl complexes: Comparison with related azulene and pentalene complexes. J Organomet Chem 2012. [DOI: 10.1016/j.jorganchem.2011.10.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Quintal S, Viegas A, Erhardt S, Cabrita EJ, Farrell NP. Platinated DNA affects zinc finger conformation. Interaction of a platinated single-stranded oligonucleotide and the C-terminal zinc finger of nucleocapsid protein HIVNCp7. Biochemistry 2012; 51:1752-61. [PMID: 22303928 DOI: 10.1021/bi201834g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper describes for the first time the intimate molecular details of the association between a platinated oligonucleotide and a zinc finger peptide. Site-specific platination of the guanine in a single-stranded hexanucleotide gave {[Pt(dien)d(5'-TACGCC-3')], Pt(dien)(6-mer)} (II) characterized by mass spectrometry and (1)H nuclear magnetic resonance (NMR) spectroscopy. The work extends the study of platinum-nucleobase complex-zinc finger interactions using small molecules such as [Pt(dien)(9-EtGua)](2+) (I). The structure of the (34-52) C-terminal finger of HIV nucleocapsid protein HIVNCp7 (ZF1) was characterized by (1)H NMR spectroscopy and compared with that of the N-terminal single finger and the two-finger "intact" NCp7. Interaction of II with ZF1 results in significant changes in comparison to the "free" uncomplexed hexanucleotide; the major changes occurring for Trp37 resonances that are broadened and moved upfield, and other major shifts are for Gln45 (Hε21, Hγ3, Qβ), Met46 (NH, Hγ2), Lys47 (NH, Qγ), and Glu50 (Hγ2, Hγ3). The Zn-Cys/His chemical shifts show only marginal deviations. The solution structures of ZF1 and the 6-mer-ZF1 and II-ZF1 adducts were calculated from the nuclear Overhauser effect spectroscopy-derived distance constraints. The DNA position in the II-ZF1 adduct is completely different than in the absence of platinum. Major differences are the appearance of new Met46-Cyt6 H5 and Trp37-Cyt5 H5 contacts but severe weakening of the Trp37-Gua4 contact, attributed to the steric effects caused by Gua4 platination, accompanied by a change in the position of the aromatic ring. The results demonstrate the feasibility of targeting specific ZF motifs with DNA-tethered coordination compounds, such as Pt compounds and Co macrocycles, with implications for drug targetting and indeed the intimate mechanisms of DNA repair of platinated DNA.
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Affiliation(s)
- Susana Quintal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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Ramalho TC, Pereira DH, Thiel W. Thermal and solvent effects on NMR indirect spin-spin coupling constants of a prototypical Chagas disease drug. J Phys Chem A 2011; 115:13504-12. [PMID: 21995614 DOI: 10.1021/jp201576u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
NMR J-couplings across hydrogen bonds reflect the static and dynamic character of hydrogen bonding. They are affected by thermal and solvent effects and can therefore be used to probe such effects. We have applied density functional theory (DFT) to compute the NMR (n)J(N,H) scalar couplings of a prototypical Chagas disease drug (metronidazole). The calculations were done for the molecule in vacuo, in microsolvated cluster models with one or few water molecules, in snapshots obtained from molecular dynamics simulations with explicit water solvent, and in a polarizable dielectric continuum. Hyperconjugative and electrostatic effects on spin-spin coupling constants were assessed through DFT calculations using natural bond orbital (NBO) analysis and atoms in molecules (AIM) theory. In the calculations with explicit solvent molecules, special attention was given to the nature of the hydrogen bonds formed with the solvent molecules. The results highlight the importance of properly incorporating thermal and solvent effects into NMR calculations in the condensed phase.
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Affiliation(s)
- Teodorico C Ramalho
- Department of Chemistry, Federal University of Lavras, Lavras, Minas Gerais, Brazil.
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Coordination asymmetry in μ-oxido divanadium complexes: Development of synthetic protocols. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2011.02.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Fenn A, Wächtler M, Breitzke H, Buchholz A, Lippold I, Plass W, Buntkowsky G. A simple method for analyzing 51V solid-state NMR spectra of complex systems. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2011; 40:60-65. [PMID: 21601435 DOI: 10.1016/j.ssnmr.2011.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 02/14/2011] [Accepted: 05/03/2011] [Indexed: 05/30/2023]
Abstract
Five vanadium complexes as models for biological systems were investigated using (51)V-MAS-NMR spectroscopy. All spectra show an uncommon line shape, which can be attributed to a shorter relaxation time of the satellite transition in contrast to the central one. A method for the reliable analysis of such kind of spectra is presented for the first time and the most important NMR parameters of the investigated complexes (quadrupolar coupling constant C(Q), asymmetry of the EFG tensor η(Q), isotropic chemical shift δ(iso), chemical shift anisotropy δ(σ) and asymmetry of the CSA tensor η(σ)) are presented. These results are of particular importance with respect to the analysis of the (51)V-MAS-NMR spectra of vanadium moieties in biological matrices such as vanadium chloroperoxidase, which show hitherto unexplained low intensity of the satellite sideband pattern.
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Affiliation(s)
- Annika Fenn
- Institut für Physikalische Chemie, Friedrich-Schiller-Universität Jena, Jena, Germany
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Li H, Feng H, Sun W, Fan Q, Xie Y, King RB. Binuclear Carbonylheptalenechromium Complexes: Partition of Heptalene into a Complexed Heptafulvene Subunit and an Uncomplexed 1,3‐Diene Subunit for Coordination to a Multiply Bonded Pair of Chromium Atoms. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201001329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Huidong Li
- School of Physics and Chemistry, Research Center for Advanced Computation, Xihua University, Chengdu 610039, China
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, Sichuan 610065, China
| | - Hao Feng
- School of Physics and Chemistry, Research Center for Advanced Computation, Xihua University, Chengdu 610039, China
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, Sichuan 610065, China
| | - Weiguo Sun
- School of Physics and Chemistry, Research Center for Advanced Computation, Xihua University, Chengdu 610039, China
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, Sichuan 610065, China
| | - Qunchao Fan
- School of Physics and Chemistry, Research Center for Advanced Computation, Xihua University, Chengdu 610039, China
| | - Yaoming Xie
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - R. Bruce King
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, USA
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Feng X, Chen L, Lei J, Jiang Y, Xie Y, Bruce King R. Unsaturation in binuclear cyclopentadienylrhodium carbonyls: Comparison with their cobalt analogs. J Organomet Chem 2011. [DOI: 10.1016/j.jorganchem.2011.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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31
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Bühl M, van Mourik T. NMR spectroscopy: quantum-chemical calculations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.63] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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32
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Li H, Feng H, Sun W, Xie Y, King RB, Schaefer HF. Binuclear Pentalene Iron Carbonyl Complexes. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201100155] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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33
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Pu MP, Li QS, Xie Y, King RB, Schaefer HF. Mononuclear Homoleptic Allyl Complexes of the First Row Transition Metals: Species with Unusual Metal Electronic Configurations. J Phys Chem A 2011; 115:4491-504. [DOI: 10.1021/jp1119712] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mao Ping Pu
- Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, People's Republic of China
| | - Qian-shu Li
- Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, People's Republic of China
- Institute of Chemical Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Yaoming Xie
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - R. Bruce King
- Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, People's Republic of China
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Henry F. Schaefer
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
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34
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Zhai X, Li G, Li QS, Xie Y, King RB, Schaefer HF. Binuclear Cyclopentadienylmetal Cyclooctatetraene Derivatives of the First Row Transition Metals: Effects of Ring Conformation on the Bonding of an Eight-Membered Carbocyclic Ring to a Pair of Metal Atoms. J Phys Chem A 2011; 115:3133-43. [DOI: 10.1021/jp112077j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiuming Zhai
- Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, People's Republic of China
| | - Guoliang Li
- Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, People's Republic of China
| | - Qian-shu Li
- Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, People's Republic of China
- Institute of Chemical Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Yaoming Xie
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - R. Bruce King
- Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, People's Republic of China
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Henry F. Schaefer
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
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Chen J, Chen S, Zhong L, Feng H, Xie Y, King RB. Binuclear Methylborole Iron Carbonyls: Iron−Iron Multiple Bonds and Perpendicular Structures. Inorg Chem 2011; 50:1351-60. [DOI: 10.1021/ic101956z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jianlin Chen
- School of Physics and Chemistry, Research Center for Advanced Computation, Xihua University, Chengdu, China 610039
| | - Shaolin Chen
- School of Physics and Chemistry, Research Center for Advanced Computation, Xihua University, Chengdu, China 610039
| | - Liu Zhong
- School of Physics and Chemistry, Research Center for Advanced Computation, Xihua University, Chengdu, China 610039
| | - Hao Feng
- School of Physics and Chemistry, Research Center for Advanced Computation, Xihua University, Chengdu, China 610039
| | - Yaoming Xie
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - R. Bruce King
- School of Physics and Chemistry, Research Center for Advanced Computation, Xihua University, Chengdu, China 610039
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
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36
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Bjornsson R, Früchtl H, Bühl M. 51V NMR parameters of VOCl3: static and dynamic density functional study from the gas phase to the bulk. Phys Chem Chem Phys 2011; 13:619-27. [DOI: 10.1039/c0cp01176b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Li H, Feng H, Sun W, Xie Y, King RB, Schaefer III HF. Mononuclear bis(pentalene) sandwich compounds of the first-row transition metals: variable hapticity of the pentalene rings and intramolecular coupling reactions. NEW J CHEM 2011. [DOI: 10.1039/c1nj20144a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Chen X, Du Q, Jin R, Feng H, Xie Y, Bruce King R. Analogies between binuclear phospholyl and cyclopentadienyl manganese carbonyl complexes: seven-electron donor bridging phospholyl rings. NEW J CHEM 2011. [DOI: 10.1039/c0nj00470g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Gong X, Li QS, Xie Y, King RB, Schaefer HF. Boronyl Ligand as a Member of the Isoelectronic Series BO− → CO → NO+: Viable Cobalt Carbonyl Boronyl Derivatives? Inorg Chem 2010; 49:10820-32. [DOI: 10.1021/ic101215v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaoli Gong
- College of Electronic Information, Hangzhou Dianzi University, Hangzhou 310018, P.R. China
| | - Qian-shu Li
- Institute of Chemical Physics, Beijing Institute of Technology, Beijing 100081, P.R. China
- Center for Computational Quantum Chemistry, School of Chemistry and Environment, South China Normal University, Guangzhou 510631, P.R. China
| | - Yaoming Xie
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - R. Bruce King
- Center for Computational Quantum Chemistry, School of Chemistry and Environment, South China Normal University, Guangzhou 510631, P.R. China
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Henry F. Schaefer
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
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40
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Li N, Xie Y, King RB, Schaefer HF. Diverse roles of hydrogen in rhenium carbonyl chemistry: hydrides, dihydrogen complexes, and a formyl derivative. J Phys Chem A 2010; 114:11670-80. [PMID: 20942474 DOI: 10.1021/jp103267v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rhenium carbonyl hydride chemistry dates back to the 1959 synthesis of HRe(CO)₅ by Hieber and Braun. The binuclear H₂Re₂(CO)₈ was subsequently synthesized as a stable compound with a central Re₂(μ-H)₂ unit analogous to the B₂(μ-H)₂ unit in diborane. The complete series of HRe(CO)(n) (n = 5, 4, 3) and H₂Re₂(CO)(n) (n = 9, 8, 7, 6) derivatives have now been investigated by density functional theory. In contrast to the corresponding manganese derivatives, all of the triplet rhenium structures are found to lie at relatively high energies compared with the corresponding singlet structures consistent with the higher ligand field splitting of rhenium relative to manganese. The lowest energy HRe(CO)₅ structure is the expected octahedral structure. Low-energy structures for HRe(CO)(n) (n = 4, 3) are singlet structures derived from the octahedral HRe(CO)₅ structure by removal of one or two carbonyl groups. For H₂Re₂(CO)₉ a structure HRe₂(CO)₉(μ-H), with one terminal and one bridging hydrogen atom, lies within 3 kcal/mol of the structure Re₂(CO)₉(η²-H₂), similar to that of Re₂(CO)₁₀. For H₂Re₂(CO)(n) (n = 8, 7, 6) the only low-energy structures are doubly bridged singlet Re₂(μ-H)₂(CO)(n) structures. Higher energy dihydrogen complex structures are also found.
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Affiliation(s)
- Nan Li
- School of Chemical Engineering & the Environment, Beijing Institute of Technology, Beijing 100081, China
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41
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Wang H, Sun Z, Xie Y, King RB, Schaefer HF. Chromium-Chromium Bonding in Binuclear Azulene Chromium Carbonyl Complexes. Eur J Inorg Chem 2010. [DOI: 10.1002/ejic.201000737] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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42
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Variable hapticity of the cyclooctatetraene ring in sandwich compounds of the first row transition metals. J Organomet Chem 2010. [DOI: 10.1016/j.jorganchem.2010.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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43
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44
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Yang HQ, Li QS, Xie Y, Bruce King R, Schaefer HF. The quest for trifluorophosphine as a bridging ligand in homoleptic binuclear and tetranuclear cobalt complexes. Mol Phys 2010. [DOI: 10.1080/00268976.2010.505214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Hua-Qing Yang
- a Center for Computational Quantum Chemistry, South China Normal University , Guangzhou 510631 , P.R. China
| | - Qian-Shu Li
- a Center for Computational Quantum Chemistry, South China Normal University , Guangzhou 510631 , P.R. China
- b Institute of Chemical Physics, Beijing Institute of Technology , Beijing 100081 , P.R. China
| | - Yaoming Xie
- c Department of Chemistry and Center for Computational Chemistry , University of Georgia , Athens , Georgia 30602 , USA
| | - R. Bruce King
- a Center for Computational Quantum Chemistry, South China Normal University , Guangzhou 510631 , P.R. China
- c Department of Chemistry and Center for Computational Chemistry , University of Georgia , Athens , Georgia 30602 , USA
| | - Henry F. Schaefer
- c Department of Chemistry and Center for Computational Chemistry , University of Georgia , Athens , Georgia 30602 , USA
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45
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Chen HL, Li QS, Xie Y, Bruce King R, Schaefer HF. Unsaturation in trinuclear cobalt carbonyl compounds of the type ECo3(CO)n (E=CH, CF, P, As; n=9, 8, 7, 6) with Co3E tetrahedrane structures. Polyhedron 2010. [DOI: 10.1016/j.poly.2010.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Decarbonylation of As2Co2(CO)6, a binuclear cobalt carbonyl derivative of diarsenic. Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2010.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Renirie R, Charnock JM, Garner CD, Wever R. Vanadium K-edge XAS studies on the native and peroxo-forms of vanadium chloroperoxidase from Curvularia inaequalis. J Inorg Biochem 2010; 104:657-64. [DOI: 10.1016/j.jinorgbio.2010.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 02/11/2010] [Accepted: 02/23/2010] [Indexed: 11/29/2022]
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48
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Zou R, Li QS, Xie Y, King RB, Schaefer HF. Metal-metal bonding in binuclear metal carbonyls with three bridging methylaminobis(difluorophosphine) ligands: iron, cobalt, and nickel derivatives. Inorg Chem 2010; 49:2280-9. [PMID: 20108929 DOI: 10.1021/ic902133g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The [CH3N(PF2)2]3M2(CO)n (M = Fe, Co, Ni; n = 2, 1, 0) derivatives, in which a metal-metal bond is bridged by three CH3N(PF2)2 groups similar to the known very stable [CH3N(PF2)2]3Co2(CO)2, have been investigated by density functional theory. The lowest energy structures for the dicarbonyls [CH3N(PF2)2]3M2(CO)2 (M = Ni, Co, Fe) are predicted to be closed-shell singlets with metal-metal distances of approximately 3.94 A, approximately 2.80 A, and approximately 2.63 A, respectively, corresponding to the metal-metal bonds of orders 0, 1, and 2, required to give both metal atoms the favored 18-electron configurations. For the monocarbonyls [CH3N(PF2)2]3M2(CO) (M = Ni, Co, Fe), unsymmetrical structures with a carbonyl group terminally bonded to one metal are greatly preferred energetically over structures in which the carbonyl group bridges the pair of metal atoms. The lowest energy structures for [CH3N(PF2)2]3M2(CO) (M = Ni, Co, Fe) are singlet, triplet, and singlet states, respectively, with metal-metal distances of approximately 2.77 A, approximately 2.38 A, and approximately 2.13 A, respectively. These distances correspond to the metal-metal dative bonds of orders 1, 2, and 3, required to give both metal atoms the favored 18-electron configuration. Among the carbonyl-free species the iron compound [CH3N(PF2)2]3Fe2 is of particular interest since its very short Fe[double double bonds]Fe distance of approximately 2.02 A suggests the formal quadruple bond required to give both iron atoms the favored 18-electron configuration.
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Affiliation(s)
- Rong Zou
- Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, P.R. China
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49
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Pacios LF, Gálvez O. Active Site, Catalytic Cycle, and Iodination Reactions of Vanadium Iodoperoxidase: A Computational Study. J Chem Theory Comput 2010; 6:1738-52. [DOI: 10.1021/ct100041x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Luis F. Pacios
- Departamento de Biotecnología, Unidad de Química y Bioquímica, E.TSI Montes, Universidad Politécnica de Madrid, 28040 Madrid, Spain, and Departamento de Física Molecular, Instituto de Estructura de la Materia, C.S.I.C., Serrano 121, 28006 Madrid, Spain
| | - Oscar Gálvez
- Departamento de Biotecnología, Unidad de Química y Bioquímica, E.TSI Montes, Universidad Politécnica de Madrid, 28040 Madrid, Spain, and Departamento de Física Molecular, Instituto de Estructura de la Materia, C.S.I.C., Serrano 121, 28006 Madrid, Spain
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50
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Wang H, Xie Y, Silaghi-Dumitrescu† I, Bruce King R, Schaefer HF. The mixed sandwich compounds C5H5MC7H7of the first row transition metals: variable hapticity of the seven-membered ring. Mol Phys 2010. [DOI: 10.1080/00268970903530807] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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