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Elmendorf LD, Brunold TC. Vibronic Coupling in Vitamin B 12: A Combined Spectroscopic and Computational Study. Inorg Chem 2023; 62:12762-12772. [PMID: 37463115 DOI: 10.1021/acs.inorgchem.3c01305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Understanding the diverse reactivities of vitamin B12 and its derivatives, collectively called cobalamins, requires detailed knowledge of their geometric and electronic structures. Electronic absorption (Abs) and resonance Raman (rR) spectroscopies have proven invaluable in this area, particularly when used in concert with computational techniques such as density functional theory (DFT). There remain, however, lingering uncertainties in the computational description of electronic excited states of cobalamins, particularly surrounding the vibronic coupling that impacts the Abs bandshapes and gives rise to rR enhancement of vibrational modes. Past computational analyses of the vibrational spectra of cobalamins have either neglected rR enhancement or calculated rR enhancement for only a small number of modes. In the present study, we used the recently developed ORCA_ASA computational tool in conjunction with the popular B3LYP and BP86 functionals to predict Abs bandshapes and rR spectra for vitamin B12. The ORCA_ASA/B3LYP-computed Abs envelope in the visible spectral region and rR spectra of vitamin B12 agree remarkably well with our experimental data, while BP86 fails to reproduce both. This finding represents a significant advance in our understanding of how these two commonly used density functionals differently model the electronic properties of cobalamins. Guided by the computed frequencies for the Co-C stretching and Co-C-N bending modes, we identified, for the first time, isotope-sensitive features in our rR spectra of 12CNCbl and 13CNCbl that can be assigned to these modes. A normal coordinate analysis of the experimentally determined Co-C stretching and Co-C-N bending frequencies indicates that the Co-C force constant for vitamin B12 is 2.67 mdyn/Å, considerably larger than the Co-C force constants reported for alkylcobalamins.
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Affiliation(s)
- Laura D Elmendorf
- Department of Chemistry, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
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2
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Elmendorf LD, Brunold TC. Electronic structure studies of free and enzyme-bound B 12 species by magnetic circular dichroism and complementary spectroscopic techniques. Methods Enzymol 2022; 669:333-365. [PMID: 35644179 DOI: 10.1016/bs.mie.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Electronic absorption (Abs) and circular dichroism (CD) spectroscopic techniques have been used successfully for over half a century in studies of free and enzyme-bound B12 species. More recently, magnetic circular dichroism (MCD) spectroscopy and other complementary techniques have provided an increasingly detailed understanding of the electronic structure of cobalamins. While CD spectroscopy measures the difference in the absorption of left- and right-circularly polarized light, MCD spectroscopy adds the application of a magnetic field parallel to the direction of light propagation. Transitions that are formally forbidden according to the Abs and CD selection rules, such as ligand field (or d→d) transitions, can gain MCD intensity through spin-orbit coupling. As such, MCD spectroscopy provides a uniquely sensitive probe of the different binding modes, Co oxidation states, and axial ligand environments of B12 species in enzyme active sites, and thus the distinct reactivities displayed by these species. This chapter summarizes representative MCD studies of free and enzyme-bound B12 species, including those present in adenosyltransferases, isomerases, and reductive dehalogenases. Complementary spectroscopic and computational data are also presented and discussed where appropriate.
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Affiliation(s)
- Laura D Elmendorf
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States.
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3
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Nguyen HT, Bui TQ, Nhat PV, Lan DTP, Nhung NTA. A DFT study of the molecular and electronic structures of cis-dioxidomolybdenum (VI) complex of 8-hydroxyquinoline and 4-benzoyl-3-methyl-1-phenyl-2-pyrazolin-5-one with water. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02868-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Toda MJ, Lodowski P, Mamun AA, Kozlowski PM. Electronic and photolytic properties of hydridocobalamin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2021; 224:112295. [PMID: 34548209 DOI: 10.1016/j.jphotobiol.2021.112295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/06/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Hydridocobalamin (HCbl), is a known member of the B12 family of molecules (cobalamins, Cbls) yet unlike other well-studied Cbls, little is known of the electronic and photolytic properties of this species. Interest in HCbl has increased significantly in recent years when at least three experimentally proposed mechanisms implicate HCbl as an intermediary in the photoreaction of coenzyme B12-dependent photoreceptor CarH. Specifically, cleavage of the Co-C5' bond of coenzyme B12 could lead to a β-hydride or β‑hydrogen elimination reaction to form HCbl. HCbl is known to be a transient species where the oxidation state of the Co is variable; Co(I)-H+ ↔ Co(II)-H ↔ Co(III)-H-. Further, HCbl is a very unstable with a pKa of ~1. This complicates experimental studies and to the best of our knowledge there are no available crystal structures of HCbl - either for the isolated molecule or bound to an enzyme. In this study, the electronic structure, photolytic properties, and reactivity of HCbl were explored to determine the preferred oxidation state as well as its potential role in the formation of the photoproduct in CarH. Natural bond orbital (NBO) analysis was performed to determine the oxidation state of Co in isolated HCbl. Based on the NBO analysis of HCbl, Co clearly had excess negative charge, which is in stark contrast to other alkylCbls where the Co ion is marked by significant positive charge. In sum, NBO results indicate that the CoH bond is strongly polarized and almost ionic. It can be described as protonated Co(I). In addition, DFT was used to explore the bond dissociation energy of HCbl based on homolytic cleavage of the CoH bond. TD-DFT calculations were used to compare computed electronic transitions to the experimentally determined absorption spectrum. The photoreaction of CarH was explored using an isolated model system and a pathway for hydrogen transfer was found. Finally, quantum mechanics/molecular mechanics (QM/MM) calculations were employed to investigate the formation of HCbl in CarH.
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Affiliation(s)
- Megan J Toda
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States
| | - Piotr Lodowski
- Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Abdullah Al Mamun
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States.
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5
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Tok GC, Reiter S, Freiberg ATS, Reinschlüssel L, Gasteiger HA, de Vivie-Riedle R, Hess CR. H 2 Evolution from Electrocatalysts with Redox-Active Ligands: Mechanistic Insights from Theory and Experiment vis-à-vis Co-Mabiq. Inorg Chem 2021; 60:13888-13902. [PMID: 34297556 DOI: 10.1021/acs.inorgchem.1c01157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electrocatalytic hydrogen production via transition metal complexes offers a promising approach for chemical energy storage. Optimal platforms to effectively control the proton and electron transfer steps en route to H2 evolution still need to be established, and redox-active ligands could play an important role in this context. In this study, we explore the role of the redox-active Mabiq (Mabiq = 2-4:6-8-bis(3,3,4,4-tetramethlyldihydropyrrolo)-10-15-(2,2-biquinazolino)-[15]-1,3,5,8,10,14-hexaene1,3,7,9,11,14-N6) ligand in the hydrogen evolution reaction (HER). Using spectro-electrochemical studies in conjunction with quantum chemical calculations, we identified two precatalytic intermediates formed upon the addition of two electrons and one proton to [CoII(Mabiq)(THF)](PF6) (CoMbq). We further examined the acid strength effect on the generation of the intermediates. The generation of the first intermediate, CoMbq-H1, involves proton addition to the bridging imine-nitrogen atom of the ligand and requires strong proton activity. The second intermediate, CoMbq-H2, acquires a proton at the diketiminate carbon for which a weaker proton activity is sufficient. We propose two decoupled H2 evolution pathways based on these two intermediates, which operate at different overpotentials. Our results show how the various protonation sites of the redox-active Mabiq ligand affect the energies and activities of HER intermediates.
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Affiliation(s)
- G Ceren Tok
- Department of Chemistry and Catalysis Research Center, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Sebastian Reiter
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Anna T S Freiberg
- Department of Chemistry and Catalysis Research Center, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Leonhard Reinschlüssel
- Department of Chemistry and Catalysis Research Center, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Hubert A Gasteiger
- Department of Chemistry and Catalysis Research Center, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Regina de Vivie-Riedle
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Corinna R Hess
- Department of Chemistry and Catalysis Research Center, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
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Resonance Raman Optical Activity Spectroscopy in Probing Structural Changes Invisible to Circular Dichroism Spectroscopy: A Study on Truncated Vitamin B 12 Derivatives. Molecules 2020; 25:molecules25194386. [PMID: 32987678 PMCID: PMC7584048 DOI: 10.3390/molecules25194386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 01/04/2023] Open
Abstract
This work demonstrates resonance Raman optical activity (RROA) spectra of three truncated vitamin B12 derivatives modified within the nucleotide loop. Since truncated cobalamins possess sufficiently high rotational strength in the range of ROA excitation (532 nm), it was possible to record their spectra in the resonance condition. They showed several distinct spectral features allowing for the distinguishing of studied compounds, in contrast to other methods, i.e., UV-Vis absorption, electronic circular dichroism, and resonance Raman spectroscopy. The improved capacity of the RROA method is based here on the excitation of molecules via more than two electronic states, giving rise to the bisignate RROA spectrum, significantly distinct from a parent Raman spectrum. This observation is an important step in the dissemination of using RROA spectroscopy in studying the complex structure of corrinoids which may prove crucial for a better understanding of their biological role.
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Toda MJ, Lodowski P, Mamun AA, Jaworska M, Kozlowski PM. Photolytic properties of the biologically active forms of vitamin B12. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2018.12.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wiley TE, Miller NA, Miller WR, Sofferman DL, Lodowski P, Toda MJ, Jaworska M, Kozlowski PM, Sension RJ. Off to the Races: Comparison of Excited State Dynamics in Vitamin B12 Derivatives Hydroxocobalamin and Aquocobalamin. J Phys Chem A 2018; 122:6693-6703. [DOI: 10.1021/acs.jpca.8b06103] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Theodore E. Wiley
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Nicholas A. Miller
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - William R. Miller
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Danielle L. Sofferman
- Applied Physics, University of Michigan, 450 Church Street, Ann Arbor, Michigan 48109-1040, United States
| | - Piotr Lodowski
- Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Megan J. Toda
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
| | - Maria Jaworska
- Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
- Department of Food Sciences, Medical University of Gdansk, Al. Gen J. Hallera, 107, 80-416 Gdansk, Poland
| | - Roseanne J. Sension
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Physics, University of Michigan, 450 Church Street, Ann Arbor, Michigan 48109-1040, United States
- Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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9
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Lodowski P, Toda MJ, Ciura K, Jaworska M, Kozlowski PM. Photolytic Properties of Antivitamins B12. Inorg Chem 2018; 57:7838-7850. [DOI: 10.1021/acs.inorgchem.8b00956] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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 in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Megan J. Toda
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
| | - Karolina Ciura
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
- Department of Food Sciences, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
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Abo Dena AS, Abdel Gaber SA. In vitro drug interaction of levocetirizine and diclofenac: Theoretical and spectroscopic studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 181:239-248. [PMID: 28371723 DOI: 10.1016/j.saa.2017.03.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/14/2017] [Accepted: 03/17/2017] [Indexed: 06/07/2023]
Abstract
Levocetirizine dihydrochloride is known to interact with some anti-inflammatory drugs. We report here a comprehensive integrated theoretical and experimental study for the in vitro drug interaction between levocetirizine dihydrochloride (LEV) and diclofenac sodium (DIC). The interaction of the two drugs was confirmed by the molecular ion peak obtained from the mass spectrum of the product. Moreover, FTIR and 1HNMR spectra of the individual drugs and their interaction product were inspected to allocate the possible sites of interaction. In addition, quantum mechanical DFT calculations were performed to search for the interaction sites and to verify the types of interactions deduced from the spectroscopic studies such as charge-transfer and non-bonding π-π interactions. It was found that the studied drugs interact with each other in aqueous solution via four types of interactions, namely, ion-pair formation, three weak hydrogen bonds, non-bonding π-π interactions and charge-transfer from DIC to LEV.
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Affiliation(s)
- Ahmed S Abo Dena
- National Organization for Drug Control and Research (NODCAR), P.O. Box 29, Giza, Egypt; Faculty of Oral and Dental Medicine, Future University in Egypt (FUE), New Cairo, Egypt.
| | - Sara A Abdel Gaber
- Faculty of Pharmacy and Biotechnology, German University in Cairo (GUC), New Cairo, Egypt
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11
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Bag A, Ghorai PK. Enhancement of biocompatibility and photoacoustic contrast activity of metal clusters. J Mol Graph Model 2017; 75:220-232. [PMID: 28601707 DOI: 10.1016/j.jmgm.2017.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/12/2017] [Accepted: 05/16/2017] [Indexed: 01/23/2023]
Abstract
Organometallic carbonyl clusters (OMCC) of group VIII elements are water soluble, bio-compatible and stable high-contrast photoacoustic agents for live cell imaging. But, they have limited application due to weak absorption within 700-1000nm wavelength which is known as the biological window of absorption. In this article, we report that hexa-nuclear iron (Fe6) carbonyl cluster derivatized with sodium thio-propanoate has very good absorption within 700-1600nm wave length. This modeled compound is water soluble and bio-compatible. The bio-compatibility of this compound is tested through cytotoxicity, LogP and metabolic probability at CYP450-2D6 enzyme.
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Affiliation(s)
- Arijit Bag
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, WB, India
| | - Pradip Kr Ghorai
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, WB, India.
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12
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Effect of ascorbic acid on the photolysis of cyanocobalamin and aquocobalamin/hydroxocobalamin in aqueous solution: A kinetic study. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2016.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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13
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14
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Rury AS, Wiley TE, Sension RJ. Energy cascades, excited state dynamics, and photochemistry in cob(III)alamins and ferric porphyrins. Acc Chem Res 2015; 48:860-7. [PMID: 25741574 DOI: 10.1021/ar5004016] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Porphyrins and the related chlorins and corrins contain a cyclic tetrapyrrole with the ability to coordinate an active metal center and to perform a variety of functions exploiting the oxidation state, reactivity, and axial ligation of the metal center. These compounds are used in optically activated applications ranging from light harvesting and energy conversion to medical therapeutics and photodynamic therapy to molecular electronics, spintronics, optoelectronic thin films, and optomagnetics. Cobalt containing corrin rings extend the range of applications through photolytic cleavage of a unique axial carbon-cobalt bond, permitting spatiotemporal control of drug delivery. The photochemistry and photophysics of cyclic tetrapyrroles are controlled by electronic relaxation dynamics including internal conversion and intersystem crossing. Typically the electronic excitation cascades through ring centered ππ* states, ligand to metal charge transfer (LMCT) states, metal to ligand charge transfer (MLCT) states, and metal centered states. Ultrafast transient absorption spectroscopy provides a powerful tool for the investigation of the electronic state dynamics in metal containing tetrapyrroles. The UV-visible spectrum is sensitive to the oxidation state, electronic configuration, spin state, and axial ligation of the central metal atom. Ultrashort broadband white light probes spanning the range from 270 to 800 nm, combined with tunable excitation pulses, permit the detailed unravelling of the time scales involved in the electronic energy cascade. State-of-the-art theoretical calculations provide additional insight required for precise assignment of the states. In this Account, we focus on recent ultrafast transient absorption studies of ferric porphyrins and corrin containing cob(III)alamins elucidating the electronic states responsible for ultrafast energy cascades, excited state dynamics, and the resulting photoreactivity or photostability of these compounds. Iron tetraphenyl porphyrin chloride (Fe((III))TPPCl) exhibits picosecond decay to a metal centered d → d* (4)T state. This state decays on a ca. 16 ps time scale in room temperature solution but persists for much longer in a cryogenic glass. The photoreactivity of the (4)T state may lead to novel future applications for these compounds. In contrast, the nonplanar cob(III)alamins contain two axial ligands to the central cobalt atom. The upper axial ligand can be an alkyl group as in the two biologically active coenzymes or a nonalkyl ligand such as -CN in cyanocobalamin (vitamin B12) or -OH in hydroxocobalamin. The electronic structure, energy cascade, and bond cleavage of these compounds is sensitive to the details of the axial ligand. Nonalkylcobalamins exhibit ultrafast internal conversion to a low-lying state of metal to ligand or ligand to metal charge transfer character. The compounds are generally photostable with ground state recovery complete on a time scale of 2-7 ps in room temperature aqueous solution. Alkylcobalamins exhibit ultrafast internal conversion to an S1 state of d/π → π* character. Most compounds undergo bond cleavage from this state with near unit quantum yield within ∼100 ps. Recent theoretical calculations provide a potential energy surface accounting for these observations. Conformation dependent mixing of the corrin π and cobalt d orbitals plays a significant role in the observed photochemistry and photophysics.
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Affiliation(s)
- Aaron S. Rury
- Department of Chemistry and
Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Theodore E. Wiley
- Department of Chemistry and
Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Roseanne J. Sension
- Department of Chemistry and
Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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15
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Bag A, Ghorai PK. Computational investigation of the ligand field effect to improve the photoacoustic properties of organometallic carbonyl clusters. RSC Adv 2015. [DOI: 10.1039/c5ra01757b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Organometallic nitrosyl carbonyl clusters are stable and better high-contrast photoacoustic contrast agents (PACAs) than organometallic carbonyl clusters.
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Affiliation(s)
- Arijit Bag
- Indian Institute of Science Education and Research Kolkata
- India
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16
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Bhattacharjee A, Chavarot-Kerlidou M, Dempsey JL, Gray HB, Fujita E, Muckerman JT, Fontecave M, Artero V, Arantes GM, Field MJ. Theoretical modeling of low-energy electronic absorption bands in reduced cobaloximes. Chemphyschem 2014; 15:2951-8. [PMID: 25113847 PMCID: PMC4530012 DOI: 10.1002/cphc.201402398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/08/2014] [Indexed: 11/07/2022]
Abstract
The reduced Co(I) states of cobaloximes are powerful nucleophiles that play an important role in the hydrogen-evolving catalytic activity of these species. In this work we analyze the low-energy electronic absorption bands of two cobaloxime systems experimentally and use a variety of density functional theory and molecular orbital ab initio quantum chemical approaches. Overall we find a reasonable qualitative understanding of the electronic excitation spectra of these compounds but show that obtaining quantitative results remains a challenging task.
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Affiliation(s)
- Anirban Bhattacharjee
- Dynamo Team, DYNAMOP Group, UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale — Jean-Pierre Ebel, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
| | - Murielle Chavarot-Kerlidou
- Laboratoire de Chimie et Biologie des Métaux, UMR 5249, Université Grenoble 1, CNRS, CEA, DSV/iRTSV, CEA-Grenoble, 17 rue des Martyrs F-38054 Grenoble Cedex 9, France
| | - Jillian L. Dempsey
- Beckman Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| | - Etsuko Fujita
- Chemistry Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - James T. Muckerman
- Chemistry Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Marc Fontecave
- Laboratoire de Chimie et Biologie des Métaux, UMR 5249, Université Grenoble 1, CNRS, CEA, DSV/iRTSV, CEA-Grenoble, 17 rue des Martyrs F-38054 Grenoble Cedex 9, France
- Collège de France, 11 place Marcellin-Berthelot, 75005 Paris, France
| | - Vincent Artero
- Laboratoire de Chimie et Biologie des Métaux, UMR 5249, Université Grenoble 1, CNRS, CEA, DSV/iRTSV, CEA-Grenoble, 17 rue des Martyrs F-38054 Grenoble Cedex 9, France
| | - Guilherme M. Arantes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo Av. Lineu Prestes 748, 05508-900, São Paulo, SP, Brazil
| | - Martin J. Field
- Dynamo Team, DYNAMOP Group, UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale — Jean-Pierre Ebel, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
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17
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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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18
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DFT Studies of Trans and Cis Influences in the Homolysis of the Co–C Bond in Models of the Alkylcobalamins. J Phys Chem A 2013; 117:3057-68. [DOI: 10.1021/jp311788t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Kornobis K, Ruud K, Kozlowski PM. Cob(I)alamin: insight into the nature of electronically excited states elucidated via quantum chemical computations and analysis of absorption, CD and MCD data. J Phys Chem A 2013; 117:863-76. [PMID: 23281629 DOI: 10.1021/jp310446c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The nature of electronically excited states of the super-reduced form of vitamin B(12) (i.e., cob(I)alamin or B(12s)), a ubiquitous B(12) intermediate, was investigated by performing quantum-chemical calculations within the time-dependent density functional theory (TD-DFT) framework and by establishing their correspondence to experimental data. Using response theory, the electronic absorption (Abs), circular dichroism (CD) and magnetic CD (MCD) spectra of cob(I)alamin were simulated and directly compared with experiment. Several issues have been taken into considerations while performing the TD-DFT calculations, such as strong dependence on the applied exchange-correlation (XC) functional or structural simplification imposed on the cob(I)alamin. In addition, the low-lying transitions were also validated by performing CASSCF/MC-XQDPT2 calculations. By comparing computational results with existing experimental data a new level of understanding of electronic excitations has been established at the molecular level. The present study extends and confirms conclusions reached for other cobalamins. In particular, the better performance of the BP86 functional, rather than hybrid-type, was observed in terms of the excitations associated with both Co d and corrin π localized transitions. In addition, the lowest energy band was associated with multiple metal-to-ligand charge transfer excitations as opposed to the commonly assumed view of a single π → π* transition followed by vibrational progression. Finally, the use of the full cob(I)alamin structure, instead of simplified molecular models, shed new light on the spectral analyses of cobalamin systems and revealed new challenges of this approach related to long-range charge transfer excitations involving side chains.
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Affiliation(s)
- Karina Kornobis
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
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20
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Kornobis K, Kumar N, Lodowski P, Jaworska M, Piecuch P, Lutz JJ, Wong BM, Kozlowski PM. Electronic structure of the S1state in methylcobalamin: Insight from CASSCF/MC-XQDPT2, EOM-CCSD, and TD-DFT calculations. J Comput Chem 2013; 34:987-1004. [DOI: 10.1002/jcc.23204] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 10/25/2012] [Accepted: 11/19/2012] [Indexed: 11/12/2022]
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21
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Navizet I, Perry CB, Govender PP, Marques HM. cis Influence in Models of Cobalt Corrins by DFT and TD-DFT Studies. J Phys Chem B 2012; 116:8836-45. [DOI: 10.1021/jp304007a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Isabelle Navizet
- Molecular Sciences
Institute, School of Chemistry, University of Witwatersrand, P.O. Wits, Johannesburg, 2050 South
Africa
| | - Christopher B. Perry
- Molecular Sciences
Institute, School of Chemistry, University of Witwatersrand, P.O. Wits, Johannesburg, 2050 South
Africa
| | - Penny P. Govender
- Molecular Sciences
Institute, School of Chemistry, University of Witwatersrand, P.O. Wits, Johannesburg, 2050 South
Africa
- Department
of Applied
Chemistry, University of Johannesburg, P.O. Box 17011, Doornfontein, Johannesburg, 2028 South Africa
| | - Helder M. Marques
- Molecular Sciences
Institute, School of Chemistry, University of Witwatersrand, P.O. Wits, Johannesburg, 2050 South
Africa
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22
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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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23
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Kumar N, Jaworska M, Lodowski P, Kumar M, Kozlowski PM. Electronic Structure of Cofactor−Substrate Reactant Complex Involved in the Methyl Transfer Reaction Catalyzed by Cobalamin-Dependent Methionine Synthase. J Phys Chem B 2011; 115:6722-31. [DOI: 10.1021/jp200945a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Neeraj Kumar
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Maria Jaworska
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland
| | - Piotr Lodowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland
| | - Manoj Kumar
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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24
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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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25
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Kornobis K, Kumar N, Wong BM, Lodowski P, Jaworska M, Andruniów T, Ruud K, Kozlowski PM. Electronically Excited States of Vitamin B12: Benchmark Calculations Including Time-Dependent Density Functional Theory and Correlated ab Initio Methods. J Phys Chem A 2011; 115:1280-92. [DOI: 10.1021/jp110914y] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Karina Kornobis
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Neeraj Kumar
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Bryan M. Wong
- Materials Chemistry Department, Sandia National Laboratories, Livermore, California 94551, United States
| | - 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
| | - Tadeusz Andruniów
- Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, 9037 Tromsø, Norway
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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26
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Solheim H, Kornobis K, Ruud K, Kozlowski PM. Electronically Excited States of Vitamin B12 and Methylcobalamin: Theoretical Analysis of Absorption, CD, and MCD Data. J Phys Chem B 2010; 115:737-48. [DOI: 10.1021/jp109793r] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Harald Solheim
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, 9037 Tromsø, Norway, and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Karina Kornobis
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, 9037 Tromsø, Norway, and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, 9037 Tromsø, Norway, and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Pawel M. Kozlowski
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, 9037 Tromsø, Norway, and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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27
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Peng J, Tang KC, McLoughlin K, Yang Y, Forgach D, Sension RJ. Ultrafast Excited-State Dynamics and Photolysis in Base-Off B12 Coenzymes and Analogues: Absence of the trans-Nitrogenous Ligand Opens a Channel for Rapid Nonradiative Decay. J Phys Chem B 2010; 114:12398-405. [DOI: 10.1021/jp104641u] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Jian Peng
- Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Kuo-Chun Tang
- Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Kaitlin McLoughlin
- Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Yang Yang
- Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Danika Forgach
- Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Roseanne J. Sension
- Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1055
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28
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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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29
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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 coenzyme B[sub 12]. J Chem Phys 2009. [DOI: 10.1063/1.3190326] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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