1
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Pavlova A, Parks JM, Gumbart JC. Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations. J Chem Theory Comput 2018; 14:784-798. [PMID: 29334459 DOI: 10.1021/acs.jctc.7b01236] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co3+, Co2+, and Co1+, and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.
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Affiliation(s)
- Anna Pavlova
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States.,School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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2
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Morita Y, Oohora K, Sawada A, Kamachi T, Yoshizawa K, Hayashi T. Redox Potentials of Cobalt Corrinoids with Axial Ligands Correlate with Heterolytic Co–C Bond Dissociation Energies. Inorg Chem 2017; 56:1950-1955. [DOI: 10.1021/acs.inorgchem.6b02482] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoshitsugu Morita
- Department of Applied
Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
- Institute for Materials Chemistry and Engineering
and IRCCS, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Koji Oohora
- Department of Applied
Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
- PRESTO, JST, Kawaguchi 332-0012, Japan
- Frontier Research Base for Global Young Researchers,
Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Akiyoshi Sawada
- Institute for Materials Chemistry and Engineering
and IRCCS, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takashi Kamachi
- Institute for Materials Chemistry and Engineering
and IRCCS, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
- Elements Strategy Initiative for Catalysts and Batteries
(ESICB), Kyoto University, Nishikyo-ku, Kyoto 615-8520, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering
and IRCCS, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
- Elements Strategy Initiative for Catalysts and Batteries
(ESICB), Kyoto University, Nishikyo-ku, Kyoto 615-8520, Japan
| | - Takashi Hayashi
- Department of Applied
Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
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3
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Morita Y, Oohora K, Mizohata E, Sawada A, Kamachi T, Yoshizawa K, Inoue T, Hayashi T. Crystal Structures and Coordination Behavior of Aqua- and Cyano-Co(III) Tetradehydrocorrins in the Heme Pocket of Myoglobin. Inorg Chem 2016; 55:1287-95. [DOI: 10.1021/acs.inorgchem.5b02598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoshitsugu Morita
- Department of Applied Chemistry, Graduate
School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Koji Oohora
- Department of Applied Chemistry, Graduate
School of Engineering, Osaka University, Suita 565-0871, Japan
- Frontier Research Base for Global Young
Researchers, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate
School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Akiyoshi Sawada
- Institute
for Materials Chemistry and Engineering and International Research
Center for Molecular Systems, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takashi Kamachi
- Institute
for Materials Chemistry and Engineering and International Research
Center for Molecular Systems, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Institute
for Materials Chemistry and Engineering and International Research
Center for Molecular Systems, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
- Elements
Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Nishikyo-ku, Kyoto 615-8520, Japan
| | - Tsuyoshi Inoue
- Department of Applied Chemistry, Graduate
School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate
School of Engineering, Osaka University, Suita 565-0871, Japan
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4
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Morita Y, Oohora K, Sawada A, Doitomi K, Ohbayashi J, Kamachi T, Yoshizawa K, Hisaeda Y, Hayashi T. Intraprotein transmethylation via a CH3–Co(iii) species in myoglobin reconstituted with a cobalt corrinoid complex. Dalton Trans 2016; 45:3277-84. [DOI: 10.1039/c5dt04109k] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A cobalt corrinoid complex bound in the myoglobin heme pocket demonstrates the formation of a CH3–Co(iii) bond and subsequent transmethylation.
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Affiliation(s)
- Yoshitsugu Morita
- Department of Applied Chemistry
- Graduate School of Engineering
- Osaka University
- Suita 565-0871
- Japan
| | - Koji Oohora
- Department of Applied Chemistry
- Graduate School of Engineering
- Osaka University
- Suita 565-0871
- Japan
| | - Akiyoshi Sawada
- Institute for Materials Chemistry and Engineering and International Research Centre for Molecular Systems
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Kazuki Doitomi
- Institute for Materials Chemistry and Engineering and International Research Centre for Molecular Systems
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Jun Ohbayashi
- Department of Applied Chemistry
- Graduate School of Engineering
- Osaka University
- Suita 565-0871
- Japan
| | - Takashi Kamachi
- Institute for Materials Chemistry and Engineering and International Research Centre for Molecular Systems
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering and International Research Centre for Molecular Systems
- Kyushu University
- Fukuoka 819-0395
- Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB)
| | - Yoshio Hisaeda
- Department of Chemistry and Biochemistry
- Graduate School of Engineering
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Takashi Hayashi
- Department of Applied Chemistry
- Graduate School of Engineering
- Osaka University
- Suita 565-0871
- Japan
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5
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Majumdar S, Stauber JM, Palluccio TD, Cai X, Velian A, Rybak-Akimova EV, Temprado M, Captain B, Cummins CC, Hoff CD. Role of Axial Base Coordination in Isonitrile Binding and Chalcogen Atom Transfer to Vanadium(III) Complexes. Inorg Chem 2014; 53:11185-96. [DOI: 10.1021/ic5017005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Subhojit Majumdar
- Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables Florida 33021, United States
| | - Julia M. Stauber
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Taryn D. Palluccio
- Department of Chemistry, Tufts University, 62
Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Xiaochen Cai
- Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables Florida 33021, United States
| | - Alexandra Velian
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Elena V. Rybak-Akimova
- Department of Chemistry, Tufts University, 62
Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Manuel Temprado
- Department of Analytical Chemistry, Physical Chemistry and Chemical
Engineering, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, Madrid, 28871, Spain
| | - Burjor Captain
- Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables Florida 33021, United States
| | - Christopher C. Cummins
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Carl D. Hoff
- Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables Florida 33021, United States
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6
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Brunk E, Kellett W, Richards NGJ, Rothlisberger U. A mechanochemical switch to control radical intermediates. Biochemistry 2014; 53:3830-8. [PMID: 24846280 PMCID: PMC4067147 DOI: 10.1021/bi500050k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 05/17/2014] [Indexed: 12/24/2022]
Abstract
B₁₂-dependent enzymes employ radical species with exceptional prowess to catalyze some of the most chemically challenging, thermodynamically unfavorable reactions. However, dealing with highly reactive intermediates is an extremely demanding task, requiring sophisticated control strategies to prevent unwanted side reactions. Using hybrid quantum mechanical/molecular mechanical simulations, we follow the full catalytic cycle of an AdoB₁₂-dependent enzyme and present the details of a mechanism that utilizes a highly effective mechanochemical switch. When the switch is "off", the 5'-deoxyadenosyl radical moiety is stabilized by releasing the internal strain of an enzyme-imposed conformation. Turning the switch "on," the enzyme environment becomes the driving force to impose a distinct conformation of the 5'-deoxyadenosyl radical to avoid deleterious radical transfer. This mechanochemical switch illustrates the elaborate way in which enzymes attain selectivity of extremely chemically challenging reactions.
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Affiliation(s)
- Elizabeth Brunk
- Laboratory
of Computational Chemistry and Biochemistry, EPFL, Lausanne, Switzerland 1015
| | - Whitney
F. Kellett
- Indiana
University-Purdue University, Indianapolis, Indiana 46202, United States
| | - Nigel G. J. Richards
- Indiana
University-Purdue University, Indianapolis, Indiana 46202, United States
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, EPFL, Lausanne, Switzerland 1015
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7
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Liu H, Kornobis K, Lodowski P, Jaworska M, Kozlowski PM. TD-DFT insight into photodissociation of the Co-C bond in coenzyme B12. Front Chem 2014; 1:41. [PMID: 24790969 PMCID: PMC3982521 DOI: 10.3389/fchem.2013.00041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/24/2013] [Indexed: 11/30/2022] Open
Abstract
Coenzyme B12 (AdoCbl) is one of the most biologically active forms of vitamin B12, and continues to be a topic of active research interest. The mechanism of Co-C bond cleavage in AdoCbl, and the corresponding enzymatic reactions are however, not well understood at the molecular level. In this work, time-dependent density functional theory (TD-DFT) has been applied to investigate the photodissociation of coenzyme B12. To reduce computational cost, while retaining the major spectroscopic features of AdoCbl, a truncated model based on ribosylcobalamin (RibCbl) was used to simulate Co-C photodissociation. Equilibrium geometries of RibCbl were obtained by optimization at the DFT/BP86/TZVP level of theory, and low-lying excited states were calculated by TD-DFT using the same functional and basis set. The calculated singlet states, and absorption spectra were simulated in both the gas phase, and water, using the polarizable continuum model (PCM). Both spectra were in reasonable agreement with experimental data, and potential energy curves based on vertical excitations were plotted to explore the nature of Co-C bond dissociation. It was found that a repulsive 3(σCo−C → σ*Co−C) triplet state became dissociative at large Co-C bond distance, similar to a previous observation for methylcobalamin (MeCbl). Furthermore, potential energy surfaces (PESs) obtained as a function of both Co-CRib and Co-NIm distances, identify the S1 state as a key intermediate generated during photoexcitation of RibCbl, attributed to a mixture of a metal-to-ligand charge transfer (MLCT) and a σ bonding-ligand charge transfer (SBLCT) states.
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Affiliation(s)
- Hui Liu
- Department of Chemistry, University of Louisville Louisville, KY, USA
| | - Karina Kornobis
- Department of Chemistry, University of Louisville Louisville, KY, USA
| | - Piotr Lodowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia Katowice, Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia Katowice, Poland
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville Louisville, KY, USA
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8
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 436] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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9
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Eisenberg AS, Likhtina IV, Znamenskiy VS, Birke RL. Electronic Spectroscopy and Computational Studies of Glutathionylco(III)balamin. J Phys Chem A 2012; 116:6851-69. [DOI: 10.1021/jp301294x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Azaria S. Eisenberg
- Department of Chemistry, The City
College of New York,
and The Graduate School and University Center, The City University of New York, New York, New York 10031, United
States
| | - Iya V. Likhtina
- Department of Chemistry, The City
College of New York,
and The Graduate School and University Center, The City University of New York, New York, New York 10031, United
States
| | - Vasiliy S. Znamenskiy
- Department of Chemistry, The City
College of New York,
and The Graduate School and University Center, The City University of New York, New York, New York 10031, United
States
| | - Ronald L. Birke
- Department of Chemistry, The City
College of New York,
and The Graduate School and University Center, The City University of New York, New York, New York 10031, United
States
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10
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Kozlowski PM, Kumar M, Piecuch P, Li W, Bauman NP, Hansen JA, Lodowski P, Jaworska M. The Cobalt–Methyl Bond Dissociation in Methylcobalamin: New Benchmark Analysis Based on Density Functional Theory and Completely Renormalized Coupled-Cluster Calculations. J Chem Theory Comput 2012; 8:1870-94. [DOI: 10.1021/ct300170y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pawel M. Kozlowski
- Department of Chemistry, University
of Louisville,
2320 South Brook St., Louisville, Kentucky 40292, United States
| | - Manoj Kumar
- Department of Chemistry, University
of Louisville,
2320 South Brook St., Louisville, Kentucky 40292, United States
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Wei Li
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Nicholas P. Bauman
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Jared A. Hansen
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Piotr Lodowski
- Institute
of Chemistry, University of Silesia, Szkolna
9, PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Institute
of Chemistry, University of Silesia, Szkolna
9, PL-40 006 Katowice, Poland
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11
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Kozlowski PM, Kamachi T, Kumar M, Yoshizawa K. Reductive elimination pathway for homocysteine to methionine conversion in cobalamin-dependent methionine synthase. J Biol Inorg Chem 2012; 17:611-9. [DOI: 10.1007/s00775-012-0881-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 02/02/2012] [Indexed: 12/20/2022]
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12
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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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13
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Brunk E, Neri M, Tavernelli I, Hatzimanikatis V, Rothlisberger U. Integrating computational methods to retrofit enzymes to synthetic pathways. Biotechnol Bioeng 2011; 109:572-82. [PMID: 21928337 DOI: 10.1002/bit.23334] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/23/2011] [Accepted: 09/06/2011] [Indexed: 11/07/2022]
Abstract
Microbial production of desired compounds provides an efficient framework for the development of renewable energy resources. To be competitive to traditional chemistry, one requirement is to utilize the full capacity of the microorganism to produce target compounds with high yields and turnover rates. We use integrated computational methods to generate and quantify the performance of novel biosynthetic routes that contain highly optimized catalysts. Engineering a novel reaction pathway entails addressing feasibility on multiple levels, which involves handling the complexity of large-scale biochemical networks while respecting the critical chemical phenomena at the atomistic scale. To pursue this multi-layer challenge, our strategy merges knowledge-based metabolic engineering methods with computational chemistry methods. By bridging multiple disciplines, we provide an integral computational framework that could accelerate the discovery and implementation of novel biosynthetic production routes. Using this approach, we have identified and optimized a novel biosynthetic route for the production of 3HP from pyruvate.
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Affiliation(s)
- Elizabeth Brunk
- Laboratory of Computational Chemistry and Biochemistry, EPFL, CH-1015 Lausanne, Switzerland
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14
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Hirao H. Which DFT Functional Performs Well in the Calculation of Methylcobalamin? Comparison of the B3LYP and BP86 Functionals and Evaluation of the Impact of Empirical Dispersion Correction. J Phys Chem A 2011; 115:9308-13. [DOI: 10.1021/jp2052807] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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15
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Kumar N, Alfonso-Prieto M, Rovira C, Lodowski P, Jaworska M, Kozlowski PM. Role of the Axial Base in the Modulation of the Cob(I)alamin Electronic Properties: Insight from QM/MM, DFT, and CASSCF Calculations. J Chem Theory Comput 2011; 7:1541-51. [PMID: 26610143 DOI: 10.1021/ct200065s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantum chemical computations are used to study the electronic and structural properties of the cob(I)alamin intermediate of the cobalamin-dependent methionine synthase (MetH). QM(DFT)/MM calculations on the methylcobalamin (MeCbl) binding domain of MetH reveal that the transfer of the methyl group to the substrate is associated with the displacement of the histidine axial base (His759). The axial base oscillates between a His-on form in the Me-cob(III)lamin:MetH resting state, where the Co-N(His759) distance is 2.27 Å, and a His-off form in the cob(I)alamin:MetH intermediate (2.78 Å). Furthermore, QM/MM and gas phase DFT calculations based on an unrestricted formalism show that the cob(I)alamin intermediate exhibits a complex electronic structure, intermediate between the Co(I) and Co(II)-radical corrin states. To understand this complexity, the electronic structure of Im···[Cob(I)alamin] is investigated using multireference CASSCF/QDPT2 calculations on gas phase models where the axial histidine is modeled by imidazole (Im). It is found that the correlated ground state wave function consists of a closed-shell Co(I) (d(8)) configuration and a diradical contribution, which can be described as a Co(II) (d(7))-radical corrin (π*)(1) configuration. Moreover, the contribution of these two configurations depends on the Co-NIm distance. At short Co-NIm distances (<2.5 Å), the dominant electronic configuration is the diradical state, while for longer distances it is the closed-shell state. The implications of this finding are discussed in the context of the methyl transfer reaction between the Me-H4folate substrate and cob(I)alamin.
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Affiliation(s)
- Neeraj Kumar
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40292, United States
| | - Mercedes Alfonso-Prieto
- Institut de Química Teòrica i Computacional (IQTCUB) and Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain.,Institute for Computational Molecular Science, Temple University , 1900 North 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - Carme Rovira
- Institut de Química Teòrica i Computacional (IQTCUB) and Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA)
| | - Piotr Lodowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia , Szkolna 9, PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia , Szkolna 9, PL-40 006 Katowice, Poland
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40292, United States
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16
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Chen SL, Blomberg MRA, Siegbahn PEM. How Is a Co-Methyl Intermediate Formed in the Reaction of Cobalamin-Dependent Methionine Synthase? Theoretical Evidence for a Two-Step Methyl Cation Transfer Mechanism. J Phys Chem B 2011; 115:4066-77. [DOI: 10.1021/jp105729e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, Department of Chemistry, School of Science, Beijing Institute of Technology, Beijing 100081, P. R. China
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden
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17
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Alfonso-Prieto M, Biarnés X, Kumar M, Rovira C, Kozlowski PM. Reductive cleavage mechanism of Co-C bond in cobalamin-dependent methionine synthase. J Phys Chem B 2011; 114:12965-71. [PMID: 20853870 DOI: 10.1021/jp1043738] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The key step in the catalytic cycle of methionine synthase (MetH) is the transfer of a methyl group from the methylcobalamin (MeCbl) cofactor to homocysteine (Hcy). This mechanism has been traditionally viewed as an S(N)2-type reaction, but a different mechanism based on one-electron reduction of the cofactor (reductive cleavage) has been recently proposed. In this work, we analyze whether this mechanism is plausible from a theoretical point of view. By means of a combination of gas-phase as well as hybrid QM/MM calculations, we show that cleavage of the Co-C bond in a MeCbl···Hcy complex (Hcy = methylthiolate substrate (Me-S(-)), a structural mimic of deprotonated homocysteine) proceeds via a [Co(III)(corrin(*-))]-Me···*S-Me diradical configuration, involving electron transfer (ET) from a π*(corrin)-type state to a σ*(Co-C) one, and the methyl transfer displays an energy barrier ≤8.5 kcal/mol. This value is comparable to the one previously computed for the alternative S(N)2 reaction pathway (10.5 kcal/mol). However, the ET-based reductive cleavage pathway does not impose specific geometrical and distance constraints with respect to substrate and cofactor, as does the S(N)2 pathway. This might be advantageous from the enzymatic point of view because in that case, a methyl group can be transferred efficiently at longer distances.
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Affiliation(s)
- Mercedes Alfonso-Prieto
- Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
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Marino N, Rabideau AE, Doyle RP. Trifluoracetic acid-assisted crystallization of vitamin B12 results in protonation of the phosphate group of the nucleotide loop: insight into the influence of crystal packing forces on vitamin B12 structures. Inorg Chem 2010; 50:220-30. [PMID: 21128680 DOI: 10.1021/ic101810v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In the course of experiments concerning our ongoing project on the synthesis of vitamin B(12) (cyanocobalamin, CNCbl) bioconjugates for drug-delivery purposes, we observed the formation of well-shaped red parallelepipeds from a concentrated aqueous solution of the HPLC-purified vitamin. The X-ray structural investigation (MoK(α)) at 98 K on these crystals revealed a CNCbl-TFA salt of formula [CNCbl(H)](TFAc)·14H(2)O (1, where TFA = trifluoracetic acid; TFAc(-) = trifluoracetate anion), in which a proton transfer from the trifluoracetic acid to the phosphate-O4P oxygen atoms is observed. 1 crystallizes in the standard orthorhombic P2(1)2(1)2(1) space group, a = 16.069(2) Å, b = 20.818(2) Å, c = 24.081(2) Å, Z = 4. The final full-matrix least-squares refinements on F(2) converged with R(1) = 4.1% for the 18957 significant reflections, a very low crystallographic residual for cobalamins, which facilitated the analysis of the extensive network of hydrogen bonds within the lattice. To the best of our knowledge, this is the first cobalamin structure to show protonation of the phosphate group of the cobalamin nucleotide loop. In this work, the crystal structure of 1 is analyzed and compared to other CNCbls reported in the literature, namely, CNCbl·3PrOH·12H(2)O (2, PrOH = propyl alcohol), CNCbl·acetone·20H(2)O (3), CNCbl·2LiCl·10.2H(2)O (4), and CNCbl·2KCl·10.6H(2)O (5). The analysis confirmed that protonation of the phosphate leaves the major CNCbl structural parameters unaffected, so that 1 can be considered an "unmodified" Cbl solvate. However, comparison between 1-5 led to interesting findings. In fact, although the cobalt(III) coordination sphere in 1-5 is similar, significant differences could be noted in the upward fold angle of the corrin macrocycle, a parameter commonly related to the steric hindrance of the axial lower "α" nucleotide-base and the electronic trans influence of the upper "β" substituent. This suggests that crystal-packing forces may influence the corrin deformation as well. Herein we explore, on the basis of the newly acquired structure and reported crystallographic data, whether the incongruities among 1-5 have to be attributed to random crystal packing effects or if it is possible to associate them with specific crystal packing (clusters).
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Affiliation(s)
- Nadia Marino
- Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100, USA
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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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20
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Lodowski P, Jaworska M, Andruniów T, Kumar M, Kozlowski PM. Photodissociation of Co−C Bond in Methyl- and Ethylcobalamin: An Insight from TD-DFT Calculations. J Phys Chem B 2009; 113:6898-909. [DOI: 10.1021/jp810223h] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Piotr Lodowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland; Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland; and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Maria Jaworska
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland; Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland; and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Tadeusz Andruniów
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland; Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland; and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Manoj Kumar
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland; Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland; and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Pawel M. Kozlowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland; Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland; and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
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21
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Andruniów T, Jaworska M, Lodowski P, Zgierski MZ, Dreos R, Randaccio L, Kozlowski PM. Time-dependent density functional theory study of cobalt corrinoids: Electronically excited states of methylcobalamin. J Chem Phys 2008; 129:085101. [DOI: 10.1063/1.2956836] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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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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23
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Qi XJ, Li Z, Fu Y, Guo QX, Liu L. anti-Spin-Delocalization Effect in Co−C Bond Dissociation Enthalpies. Organometallics 2008. [DOI: 10.1021/om701135c] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Xiu-Juan Qi
- Joint Laboratory of Green Synthetic Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zhe Li
- Joint Laboratory of Green Synthetic Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yao Fu
- Joint Laboratory of Green Synthetic Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qing-Xiang Guo
- Joint Laboratory of Green Synthetic Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Lei Liu
- Joint Laboratory of Green Synthetic Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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24
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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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25
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Kuta J, Patchkovskii S, Zgierski MZ, Kozlowski PM. Performance of DFT in modeling electronic and structural properties of cobalamins. J Comput Chem 2007; 27:1429-37. [PMID: 16807975 DOI: 10.1002/jcc.20454] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Computational modeling of the enzymatic activity of B12-dependent enzymes requires a detailed understanding of the factors that influence the strength of the Co--C bond and the limits associated with a particular level of theory. To address this issue, a systematic analysis of the electronic and structural properties of coenzyme B12 models has been performed to establish the performance of three different functionals including B3LYP, BP86, and revPBE. In particular the cobalt-carbon bond dissociation energies, axial bond lengths, and selected stretching frequencies have been analyzed in detail. Current analysis shows that widely used B3LYP functional significantly underestimates the strength of the Co--C bond while the nonhybrid BP86 functional produces very consistent results in comparison to experimental data. To explain such different performance of these functionals molecular orbital analysis associated with axial bonds has been performed to show differences in axial bonding provided by hybrid and nonhybrid functionals.
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Affiliation(s)
- Jadwiga Kuta
- Department of Chemistry, University of Louisville, 2320 S. Brook Street, Louisville, Kentucky 40292, USA
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26
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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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27
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Kozlowski PM, Andruniow T, Jarzecki AA, Zgierski MZ, Spiro TG. DFT analysis of co-alkyl and co-adenosyl vibrational modes in B12-cofactors. Inorg Chem 2007; 45:5585-90. [PMID: 16813422 PMCID: PMC2773831 DOI: 10.1021/ic052069j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory (DFT)-based normal mode calculations have been carried out on models for B12-cofactors to assign reported isotope-edited resonance Raman spectra, which isolate vibrations of the organo-Co group. Interpretation is straightforward for alkyl-Co derivatives, which display prominent Co-C stretching vibrational bands. DFT correctly reproduces Co-C distances and frequencies for the methyl and ethyl derivatives. However, spectra are complex for adenosyl derivatives, due to mixing of Co-C stretching with a ribose deformation coordinate and to activation of modes involving Co-C-C bending and Co-adenosyl torsion. Despite this complexity, the computed spectra provide a satisfactory re-assignment of the experimental data. Reported trends in adenosyl-cobalamin spectra upon binding to the methylmalonyl CoA mutase enzyme, as well as on subsequent binding of substrates and inhibitors, provide support for an activation mechanism involving substrate-induced deformation of the adenosyl ligand.
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Affiliation(s)
- Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
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28
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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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Spataru T, Birke RL. Carbon−Cobalt Bond Distance and Bond Cleavage in One-Electron Reduced Methylcobalamin: A Failure of the Conventional DFT Method. J Phys Chem A 2006; 110:8599-604. [PMID: 16836419 DOI: 10.1021/jp062741d] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Geometry optimizations at the HF, B3LYP, and CASSCF levels of electronic structure theory have been performed for methylcobalamin (MeCbl) model compounds in both the Co(III) (MeCbl(III)) and Co(II) (MeCbl(II)) formal oxidation states. Since the HOMO-LUMO and C-Co sigma-sigma MO gaps are significantly smaller in the MeCbl(II) compounds compared with MeCbl(III), a pseudo-Jahn Teller effect is possible. CASSCF calculations show that there is strong coupling between C-Co sigma-sigma MOs for the MeCbl(II) models leading to strong state mixing with significant total charge density transfer (approximately 0.4 e-), mainly from the C-Co sigma MO to C-Co sigma MO (approximately 0.3 e-). CASSCF(9:7) calculations show that the strong state mixing leads to an increase in the C-Co bond length for MeCbl(II) model compounds from 1.969 A (DFT and HF calculations) to 2.164 A in the base-on MeCbl(II) model and from 1.938 A to 2.144 A in the base-off MeCbl(II) model. Concomitantly, the Co-N axial bond length increases from 2.121 A (DFT) to 2.344 A in the CASSCF calculation. This coupling interaction between states can be used to explain the much lower Co-C bond dissociation enthalpy and much faster bond cleavage rate for the one-electron reduced methylcobalamin radical anion compared to MeCbl(III). It may also be important for axial bond distances in other Co(II) compounds.
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