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Mackintosh MJ, Lodowski P, Kozlowski PM. Photoproduct formation in coenzyme B 12-dependent CarH photoreceptor via a triplet pathway. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 245:112751. [PMID: 37441852 DOI: 10.1016/j.jphotobiol.2023.112751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
CarH is a cobalamin-based photoreceptor which has attracted significant interest due to its complex mechanism involving its organometallic coenzyme-B12 chromophore. While several experimental and computational studies have sought to understand CarH's mechanism of action, there are still many aspects of the mechanism which remain unclear. While light is needed to activate the Co-C5' bond, it is not entirely clear whether reaction pathway involves singlet or triplet diradical states. A recent experimental study implicated triplet pathway and importance of intersystem crossing (ISC) as a viable mechanistic route for photoproduct formation in CarH. Herein, a combined quantum mechanics/molecular mechanics approach (QM/MM) was used to explore the involvement of triplet states in CarH. Two possibilities were explored. The first possibility involved photo-induced homolytic cleavage of the Co-C5' where the radical pair (RP) would deactivate to a triplet state (T0) on the ground state potential energy surface (PES). However, a pathway for the formation of the photoproduct, 4',5'-anhydroadenosine (anhAdo), on the triplet ground state PES was not energetically feasible. The second possibility involved exploring a manifold of low-lying triplet excited states computed using TD-DFT within the QM/MM framework. Viable crossings of triplet excited states with singlet excited states were identified using semiclassical Landau-Zener theory and the effectiveness of spin-orbit coupling by El-Sayed rules. Several candidates along both the Co-NIm potential energy curve (PEC) and Co-C5'/Co-NIm PES were identified, which appear to corroborate experimental findings and implicate the possible role of triplet states in CarH.
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Affiliation(s)
- Megan J Mackintosh
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States
| | - Piotr Lodowski
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States.
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2
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Farcaş AA, Bende A. Theoretical modeling of the singlet-triplet spin transition in different Ni(II)-diketo-pyrphyrin-based metal-ligand octahedral complexes. Phys Chem Chem Phys 2021; 23:4784-4795. [PMID: 33599640 DOI: 10.1039/d0cp05366j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structural stability, charge transfer effects and strength of the spin-orbit couplings in different Ni(ii)-ligand complexes have been studied at the DFT (B3LYP and CAM-B3LYP) and coupled cluster (DLPNO-CCSD(T)) levels of theory. Accordingly, two different, porphyrin- and diketo-pyrphyrin-based four-coordination macrocycles as planar ligands as well as pyridine (or pyrrole) and mesylate anion molecular groups as vertical ligands were considered in order to build metal-organic complexes with octahedral coordination configurations. For each molecular system, the identification of equilibrium geometries and the intersystem crossing (the minimum energy crossing) points between the potential energy surfaces of the singlet and triplet spin states is followed by computing the spin-orbit couplings between the two spin states. Structures, based on the diketo-pyrphyrin macrocycle as the planar ligand, show stronger six-coordination metal-organic complexes due to the extra electrostatic interaction between the positively charged central metal cation and the negatively charged vertical ligands. The results also show that the magnitude of the spin-orbit coupling is influenced by the atomic positions of deprotonations of the ligands, and implicitly the direction of the charge transfer between the ligand and the central metal ion.
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Affiliation(s)
- Alex-Adrian Farcaş
- Faculty of Physics, "Babeş-Bolyai" University, Mihail Kogalniceanu Street No. 1, Ro-400084 Cluj-Napoca, Romania
| | - Attila Bende
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Donat Street, No. 67-103, Ro-400293 Cluj-Napoca, Romania.
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3
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Yamamoto Y, Hasegawa K, Shibata T, Momotake A, Ogura T, Yanagisawa S, Neya S, Suzuki A, Kobayashi Y, Saito M, Seto M, Ohta T. Effect of the Electron Density of the Heme Fe Atom on the Nature of Fe-O 2 Bonding in Oxy Myoglobin. Inorg Chem 2021; 60:1021-1027. [PMID: 33356193 DOI: 10.1021/acs.inorgchem.0c03123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mössbauer spectroscopy has been used to characterize oxygenated myoglobins (oxy Mbs) reconstituted with native and chemically modified 57Fe-enriched heme cofactors with different electron densities of the heme Fe atom (ρFe) and to elucidate the effect of a change in the ρFe on the nature of the bond between heme Fe and oxygen (O2), i.e., the Fe-O2 bond, in the protein. Quadrupole splitting (ΔEQ) was found to decrease with decreasing ρFe, and the observed ρFe-dependent ΔEQ confirmed an increase in the contribution of the ferric-superoxide (Fe3+-O2-) form to the resonance hybrid of the Fe-O2 fragment with decreasing ρFe. These observations explicitly accounted for the lowering of O2 affinity of the protein due to an increase in the O2 dissociation rate and a decrease in the autoxidation reaction rate of oxy Mb through decreasing H+ affinity of the bound ligand with decreasing ρFe. Therefore, the present study demonstrated the mechanism underlying the electronic control of O2 affinity and the autoxidation of the protein through the heme electronic structure. Carbon monoxide (CO) adducts of reconstituted Mbs (CO-Mbs) were similarly characterized, and we found that the resonance between the two canonical forms of the Fe-CO fragment was also affected by a change in ρFe. Thus, the nature of the Fe-ligand bond in the protein was found to be affected by the ρFe.
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Affiliation(s)
- Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Kazuyasu Hasegawa
- Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba 305-8571, Japan
| | - Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Takashi Ogura
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Sachiko Yanagisawa
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Saburo Neya
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Akihiro Suzuki
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Yasuhiro Kobayashi
- Department of Material Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Makina Saito
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Makoto Seto
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Takehiro Ohta
- Department of Applied Chemistry, Faculty of Engineering, Sanyo-Onoda City University, Sanyo-Onoda, Yamaguchi 756-0884, Japan
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4
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Saito K, Watabe Y, Miyazaki T, Takayanagi T, Hasegawa JY. Spin-inversion mechanisms in O 2 binding to a model heme compound: A perspective from nonadiabatic wave packet calculations. J Comput Chem 2020; 41:2527-2537. [PMID: 32841410 DOI: 10.1002/jcc.26409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/18/2020] [Accepted: 08/08/2020] [Indexed: 12/13/2022]
Abstract
Spin-inversion dynamics in O2 binding to a model heme complex, which consisted of Fe(II)-porphyrin and imidazole, were studied using nonadiabatic wave packet dynamics calculations. We considered three active nuclear degrees of freedom in the dynamics, including the motions along the Fe-O distance, Fe-O-O angle, and Fe out-of-plane distance. Spin-free potential energy surfaces for the singlet, triplet, quintet, and septet states were developed using density functional theory calculations, and spin-orbit coupling elements were obtained from CASSCF-level electronic structure calculations. The spin-inversion mainly occurred between the singlet state and one of the triplet states due to large spin-orbit couplings and the contributions of other states were extremely small. The present quantum dynamics calculations suggested that the narrow crossing region model plays a dominant role in the O2 binding dynamics. In addition, the one-dimensional Landau-Zener model underestimated the nonadiabatic transition probability.
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Affiliation(s)
- Kohei Saito
- Department of Chemistry, Saitama University, Saitama City, Saitama, Japan
| | - Yuya Watabe
- Department of Chemistry, Saitama University, Saitama City, Saitama, Japan
| | - Takaaki Miyazaki
- Department of Chemistry, Saitama University, Saitama City, Saitama, Japan
| | | | - Jun-Ya Hasegawa
- Institute for Catalysis, Hokkaido University, Sapporo, Hokkaido, Japan
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5
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Saito K, Watabe Y, Fujihara T, Takayanagi T, Hasegawa JY. Spin-inversion mechanisms in O 2 binding to a model heme complex revisited by density function theory calculations. J Comput Chem 2020; 41:1130-1138. [PMID: 32020659 DOI: 10.1002/jcc.26159] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/12/2020] [Accepted: 01/16/2020] [Indexed: 01/10/2023]
Abstract
Spin-inversion mechanisms in O2 binding to a model heme complex, consisting of Fe(II)-porphyrin and imidazole, were investigated using density-functional theory calculations. First, we applied the recently proposed mixed-spin Hamiltonian method to locate spin-inversion structures between different total spin multiplicities. Nine spin-inversion structures were successfully optimized for the singlet-triplet, singlet-quintet, triplet-quintet, and quintet-septet spin-inversion processes. We found that the singlet-triplet spin-inversion points are located around the potential energy surface region at short Fe-O distances, whereas the singlet-quintet and quintet-septet spin-inversion points are located at longer Fe-O distances. This suggests that both narrow and broad crossing models play roles in O2 binding to the Fe-porphyrin complex. To further understand spin-inversion mechanisms, we performed on-the-fly Born-Oppenheimer molecular dynamics calculations. The reaction coordinates, which are correlated to the spin-inversion dynamics between different spin multiplicities, are also discussed.
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Affiliation(s)
- Kohei Saito
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Yuya Watabe
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Takashi Fujihara
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Jun-Ya Hasegawa
- Instituteof Catalysis, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0021, Japan
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6
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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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7
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Mamun AA, Toda MJ, Kozlowski PM. Can photolysis of the Co C bond in coenzyme B12-dependent enzymes be used to mimic the native reaction? JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 191:175-184. [DOI: 10.1016/j.jphotobiol.2018.12.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 12/22/2022]
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8
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Meuwly M. Reactive molecular dynamics: From small molecules to proteins. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1386] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Markus Meuwly
- Department of Chemistry University of Basel Basel Switzerland
- Department of Chemistry Brown University Providence Rhode Island
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9
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Ostojić B, Schwerdtfeger P, Đorđević D. Modeling the hydrogen sulfide binding to heme. J Inorg Biochem 2018; 184:108-114. [DOI: 10.1016/j.jinorgbio.2018.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 04/14/2018] [Accepted: 04/17/2018] [Indexed: 10/17/2022]
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10
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Lábas A, Menyhárd DK, Harvey JN, Oláh J. First Principles Calculation of the Reaction Rates for Ligand Binding to Myoglobin: The Cases of NO and CO. Chemistry 2018; 24:5350-5358. [PMID: 29285802 DOI: 10.1002/chem.201704867] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Indexed: 12/12/2022]
Abstract
Ligand binding by proteins is among the most fundamental processes in nature. Among these processes the binding of small gas molecules, such as O2 , CO and NO to heme proteins has traditionally received vivid interest, which was further boosted by their recently recognized significant role in gas sensing in the body. At the heart of the binding of these ligands to the heme group is the spinforbidden reaction between high-spin iron(II) and the ligand yielding a low-spin adduct. We use computational means to address the complete mechanism of CO and NO binding by myoglobin. Considering that it involves several steps occurring on different time scales, molecular dynamics simulations were performed to address the diffusion of the ligand through the enzyme, and DFT calculations in combination with statistical rate calculation to investigate the spin-forbidden reaction. The calculations yielded rate constants in qualitative agreement with experiments and revealed that the bottleneck of NO and CO binding is different; for NO, diffusion was found to be rate-limiting, whereas for CO, the spin-forbidden step is the slowest.
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Affiliation(s)
- Anikó Lábas
- Department of Inorganic Chemistry, Budapest University of Technology and Economics, H-1111, Budapest, Szent Gellért tér 4., Hungary
| | - Dóra K Menyhárd
- MTA-ELTE Protein Modelling Research Group, H-1117, Budapest, Pázmány Péter st. 1/A, Hungary
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, B-3001, Leuven Celestijnenlaan 200F- box 2404, Belgium
| | - Julianna Oláh
- Department of Inorganic Chemistry, Budapest University of Technology and Economics, H-1111, Budapest, Szent Gellért tér 4., Hungary
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11
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Kepp KP. Heme isomers substantially affect heme's electronic structure and function. Phys Chem Chem Phys 2018; 19:22355-22362. [PMID: 28805222 DOI: 10.1039/c7cp03285d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Inspection of heme protein structures in the protein data bank reveals four isomers of heme characterized by different relative orientations of the vinyl side chains; remarkably, all these have been reported in multiple protein structures. Density functional theory computations explain this as due to similar energy of the isomers but with a sizable (25 kJ mol-1) barrier to interconversion arising from restricted rotation around the conjugated bonds. The four isomers, EE, EZ, ZE, and ZZ, were then investigated as 4-coordinate hemes, as 5-coordinate deoxyhemes, in 6-coordinate O2-adducts of globins and as compound I intermediates typical of heme peroxidases. Substantial differences were observed in electronic properties relevant to heme function: notably, the spin state energy gap of O2-heme adducts, important for fast reversible binding of O2, depends on the isomer state, and O2-binding enthalpies change by up to 16 kJ mol-1; redox potentials change by up to 0.2 V depending on the isomer, and the doublet-quartet energy splitting of compound I, central to "two-state" reactivity, is affected by up to ∼15 kJ mol-1. These effects are consistently seen with three distinct density functionals, i.e. the effects are not method-dependent. Thus, the nature of the isomer state is an important but overlooked feature of heme chemistry and function, and previous and future studies of hemes may be reconsidered in this new context.
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Affiliation(s)
- Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, DK, Denmark.
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12
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Bie L, Liu F, Li Y, Dong T, Gao J, Du L, Yuan Q. Spin crossover dynamics studies on the thermally activated molecular oxygen binding mechanism on a model copper complex. Phys Chem Chem Phys 2018; 20:15852-15862. [DOI: 10.1039/c8cp02482k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The theoretical description of the primary dioxygen (O2) binding and activation step in many copper or iron enzymes, suffers from the instrinsically electronic non-adiabaticity of the spin flip events of the triplet dioxygen molecule (3O2), mediated by spin–orbit couplings.
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Affiliation(s)
- Lihua Bie
- Hubei Key Laboratory of Agricultural Bioinformatics
- College of Informatics
- Huazhong Agricultural University
- Wuhan
- P. R. China
| | - Fang Liu
- Hubei Key Laboratory of Agricultural Bioinformatics
- College of Informatics
- Huazhong Agricultural University
- Wuhan
- P. R. China
| | - Yanwei Li
- Environment Research Institute
- Shandong University
- Jinan
- P. R. China
| | - Tiange Dong
- Hubei Key Laboratory of Agricultural Bioinformatics
- College of Informatics
- Huazhong Agricultural University
- Wuhan
- P. R. China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics
- College of Informatics
- Huazhong Agricultural University
- Wuhan
- P. R. China
| | - Likai Du
- Hubei Key Laboratory of Agricultural Bioinformatics
- College of Informatics
- Huazhong Agricultural University
- Wuhan
- P. R. China
| | - Qiaoxia Yuan
- College of Engineering
- Huazhong Agricultural University
- Wuhan 430070
- P. R. China
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13
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Shafizadeh N, Soorkia S, Grégoire G, Broquier M, Crestoni ME, Soep B. Dioxygen Binding to Protonated Heme in the Gas Phase, an Intermediate Between Ferric and Ferrous Heme. Chemistry 2017; 23:13493-13500. [DOI: 10.1002/chem.201702615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Niloufar Shafizadeh
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud; Université Paris-Saclay; 91405 Orsay France
| | - Satchin Soorkia
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud; Université Paris-Saclay; 91405 Orsay France
| | - Gilles Grégoire
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud; Université Paris-Saclay; 91405 Orsay France
| | - Michel Broquier
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud; Université Paris-Saclay; 91405 Orsay France
- Centre Laser de l'Université Paris-Sud (CLUPS/LUMAT), Université Paris-Sud, CNRS, IOGS, Université Paris-Saclay; 91405 Orsay France
| | - Maria-Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco; Università degli Studi di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Benoît Soep
- LIDYL, CEA, CNRS; Université Paris-Saclay, CEA Saclay; 91191 Gif-sur-Yvette France
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15
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Shibata T, Kanai Y, Nishimura R, Xu L, Moritaka Y, Suzuki A, Neya S, Nakamura M, Yamamoto Y. Characterization of Ground State Electron Configurations of High-Spin Quintet Ferrous Heme Iron in Deoxy Myoglobin Reconstituted with Trifluoromethyl Group-Substituted Heme Cofactors. Inorg Chem 2016; 55:12128-12136. [DOI: 10.1021/acs.inorgchem.6b01360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Yuki Kanai
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryu Nishimura
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Liyang Xu
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Yuki Moritaka
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, Nagaoka National College of Technology, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of
Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Mikio Nakamura
- Department
of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
- Life Science
Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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16
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Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins. Methods Enzymol 2016. [PMID: 27498633 DOI: 10.1016/bs.mie.2016.05.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed.
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17
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Garabato BD, Lodowski P, Jaworska M, Kozlowski PM. Mechanism of Co-C photodissociation in adenosylcobalamin. Phys Chem Chem Phys 2016; 18:19070-82. [PMID: 27356617 DOI: 10.1039/c6cp02136k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A mechanism of Co-C bond photodissociation in the base-on form of adenosylcobalamin (AdoCbl) was investigated by time-dependent density functional theory (TD-DFT). The key mechanistic step involves singlet radical pair (RP) generation from the first electronically excited state (S1). To connect TD-DFT calculations with ultra-fast excited state dynamics, the potential energy surface (PES) of the S1 state was constructed using Co-C and Co-NIm axial coordinates. The S1 PES can be characterized by two minima separated by a seam resulting from the crossing of two surfaces, of metal-to-ligand charge transfer (MLCT) character near the minimum, and a shallow ligand field (LF) surface at elongated axial bond distances. Only one possible pathway for photolysis (path A) was identified based on energetic grounds. This pathway is characterized by the first elongation of the Co-C bond, followed by photolysis from an LF state where the axial base is partially detached. A new perspective on the photolysis of AdoCbl is then gained by connecting TD-DFT results with available experimental observations.
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Affiliation(s)
- Brady D Garabato
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40202, USA.
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18
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Andruniów T, Lodowski P, Garabato BD, Jaworska M, Kozlowski PM. The role of spin-orbit coupling in the photolysis of methylcobalamin. J Chem Phys 2016; 144:124305. [DOI: 10.1063/1.4943184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Tadeusz Andruniów
- Department of Chemistry, Advanced Materials Engineering and Modelling Group, Wroclaw University of Technology, 50-370 Wroclaw, Poland
| | - Piotr Lodowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland
| | - Brady D. Garabato
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, USA
| | - 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, 2320 South Brook Street, Louisville, Kentucky 40292, USA
- Department of Food Sciences, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
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Abstract
Iron complexes are important spin crossover (SCO) systems with vital roles in oxidative metabolism and promising technological potential. The SCO tendency depends on the free energy balance of high- and low-spin states, which again depends on physical effects such as dispersion, relativistic effects, and vibrational entropy. This work studied 30 different iron SCO systems with experimentally known thermochemical data, using 12 different density functionals. Remarkably general entropy-enthalpy compensation across SCO systems was identified (R = 0.82, p = 0.002) that should be considered in rational SCO design. Iron(II) complexes displayed higher ΔH and ΔS values than iron(III) complexes and also less steep compensation effects. First-coordination sphere ΔS values computed from numerical frequencies reproduce most of the experimental entropy and should thus be included when modeling spin-state changes in inorganic chemistry (R = 0.52, p = 3.4 × 10(-3); standard error in TΔS ≈ 4.4 kJ/mol at 298 K vs 16 kJ/mol of total TΔS on average). Zero-point energies favored high-spin states by 9 kJ/mol on average. Interestingly, dispersion effects are surprisingly large for the SCO process (average: 9 kJ/mol, but up to 33 kJ/mol) and favor the more compact low-spin state. Relativistic effects favor low-spin by ∼9 kJ/mol on average, but up to 24 kJ/mol. B3LYP*, TPSSh, B2PLYP, and PW6B95 performed best for the typical calculation scheme that includes ZPE. However, if relativistic and dispersion effects are included, only B3LYP* remained accurate. On average, high-spin was favored by LYP by 11-15 kJ/mol relative to other correlation functionals, and by 4.2 kJ/mol per 1% HF exchange in hybrids. 13% HF exchange was optimal without dispersion, and 15% was optimal with all effects included for these systems.
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Affiliation(s)
- Kasper P Kepp
- DTU Chemistry, Technical University of Denmark , Building 206, Lyngby DK-2800, Denmark
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20
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Bustamante JP, Szretter ME, Sued M, Martí MA, Estrin DA, Boechi L. A quantitative model for oxygen uptake and release in a family of hemeproteins. Bioinformatics 2016; 32:1805-13. [PMID: 27153569 DOI: 10.1093/bioinformatics/btw083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/30/2016] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Hemeproteins have many diverse functions that largely depend on the rate at which they uptake or release small ligands, like oxygen. These proteins have been extensively studied using either simulations or experiments, albeit only qualitatively and one or two proteins at a time. RESULTS We present a physical-chemical model, which uses data obtained exclusively from computer simulations, to describe the uptake and release of oxygen in a family of hemeproteins, called truncated hemoglobins (trHbs). Through a rigorous statistical analysis we demonstrate that our model successfully recaptures all the reported experimental oxygen association and dissociation kinetic rate constants, thus allowing us to establish the key factors that determine the rates at which these hemeproteins uptake and release oxygen. We found that internal tunnels as well as the distal site water molecules control ligand uptake, whereas oxygen stabilization by distal site residues controls ligand release. Because these rates largely determine the functions of these hemeproteins, these approaches will also be important tools in characterizing the trHbs members with unknown functions. CONTACT lboechi@ic.fcen.uba.ar SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Juan P Bustamante
- Departamento de Química Inorgánica, Analítica Y Química Física, INQUIMAE-CONICET, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - María E Szretter
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires Departamento De Matemática, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Mariela Sued
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Marcelo A Martí
- Departamento De Química Biológica E Instituto De Química Biológica De La Facultad De Ciencias Exactas Y Naturales (IQUIBICEN), Universidad De Buenos Aires, Buenos Aires, Argentina
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica Y Química Física, INQUIMAE-CONICET, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Leonardo Boechi
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
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21
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Kitagawa Y, Chen Y, Nakatani N, Nakayama A, Hasegawa J. A DFT and multi-configurational perturbation theory study on O2 binding to a model heme compound via the spin-change barrier. Phys Chem Chem Phys 2016; 18:18137-44. [DOI: 10.1039/c6cp02329k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Potential energy surface of the O2 binding to a model heme compound via minimum energy intersystem crossing point (MEISCP) was investigated with DFT and MS-CASPT2. The porphyrin's symmetric shrinking vibration mode contributes to reach the MESICP from the T1 minimum.
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Affiliation(s)
- Y. Kitagawa
- Institute for Catalysis
- Hokkaido University
- Hokkaido 001-0021
- Japan
| | - Y. Chen
- Institute for Catalysis
- Hokkaido University
- Hokkaido 001-0021
- Japan
| | - N. Nakatani
- Institute for Catalysis
- Hokkaido University
- Hokkaido 001-0021
- Japan
| | - A. Nakayama
- Institute for Catalysis
- Hokkaido University
- Hokkaido 001-0021
- Japan
| | - J. Hasegawa
- Institute for Catalysis
- Hokkaido University
- Hokkaido 001-0021
- Japan
- JST-CREST
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22
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Mebs S, Braun B, Kositzki R, Limberg C, Haumann M. Abrupt versus Gradual Spin-Crossover in Fe(II)(phen)2(NCS)2 and Fe(III)(dedtc)3 Compared by X-ray Absorption and Emission Spectroscopy and Quantum-Chemical Calculations. Inorg Chem 2015; 54:11606-24. [PMID: 26624918 DOI: 10.1021/acs.inorgchem.5b01822] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular spin-crossover (SCO) compounds are attractive for information storage and photovoltaic technologies. We compared two prototypic SCO compounds with Fe(II)N6 (1, [Fe(phen)2(NCS)2], with phen = 1,10-phenanthroline) or Fe(III)S6 (2, [Fe(dedtc)3], with dedtc = N,N'-diethyldithiocarbamate) centers, which show abrupt (1) or gradual (2) thermally induced SCO, using K-edge X-ray absorption and Kβ emission spectroscopy (XAS/XES) in a 8-315 K temperature range, single-crystal X-ray diffraction (XRD), and density functional theory (DFT). Core-to-valence and valence-to-core electronic transitions in the XAS/XES spectra and bond lengths change from XRD provided benchmark data, verifying the adequacy of the TPSSh/TZVP DFT approach for the description of low-spin (LS) and high-spin (HS) species. Determination of the spin densities, charge distributions, bonding descriptors, and valence-level configurations, as well as similar experimental and calculated enthalpy changes (ΔH), suggested that the varying metal-ligand bonding properties and deviating electronic structures converge to similar enthalpic contributions to the free-energy change (ΔG) and thus presumably are not decisive for the differing SCO behavior of 1 and 2. Rather, SCO seems to be governed by vibrational contributions to the entropy changes (ΔS) in both complexes. Intra- and intermolecular interactions in crystals of 1 and 2 were identified by atoms-in-molecules analysis. Thermal excitation of individual dedtc ligand vibrations accompanies the gradual SCO in 2. In contrast, extensive inter- and intramolecular phen/NCS vibrational mode coupling may be an important factor in the cooperative SCO behavior of 1.
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Affiliation(s)
- Stefan Mebs
- Institut für Experimentalphysik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Beatrice Braun
- Institut für Chemie, Humboldt-Universität zu Berlin , 12489 Berlin, Germany
| | - Ramona Kositzki
- Institut für Experimentalphysik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Christian Limberg
- Institut für Chemie, Humboldt-Universität zu Berlin , 12489 Berlin, Germany
| | - Michael Haumann
- Institut für Experimentalphysik, Freie Universität Berlin , 14195 Berlin, Germany
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23
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Lodowski P, Jaworska M, Garabato BD, Kozlowski PM. Mechanism of Co–C Bond Photolysis in Methylcobalamin: Influence of Axial Base. J Phys Chem A 2015; 119:3913-28. [DOI: 10.1021/jp5120674] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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
| | - Maria Jaworska
- Department
of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland
| | - Brady D. Garabato
- 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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Samanta S, Demesko S, Dechert S, Meyer F. A two-in-one pincer ligand and its diiron(II) complex showing spin state switching in solution through reversible ligand exchange. Angew Chem Int Ed Engl 2015; 54:583-7. [PMID: 25412962 DOI: 10.1002/anie.201408966] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 11/09/2022]
Abstract
A novel pyrazolate-bridged ligand providing two {PNN} pincer-type compartments has been synthesized. Its diiron(II) complex LFe2(OTf)3(CH3CN) (1; Tf = triflate) features, in solid state, two bridging triflate ligands, with a terminal triflate and a MeCN ligand completing the octahedral coordination spheres of the two high-spin metal ions. In MeCN solution, 1 is shown to undergo a sequential, reversible, and complete spin transition to the low-spin state upon cooling. Detailed UV/Vis and (19)F NMR spectroscopic studies as well as magnetic measurements have unraveled that spin state switching correlates with a rapid multistep triflate/MeCN ligand exchange equilibrium. The spin transition temperature can be continuously tuned by varying the triflate concentration in solution.
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Affiliation(s)
- Subhas Samanta
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany) http://www.meyer.chemie.uni-goettingen.de
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25
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Lodowski P, Jaworska M, Andruniów T, Garabato BD, Kozlowski PM. Mechanism of Co–C Bond Photolysis in the Base-On Form of Methylcobalamin. J Phys Chem A 2014; 118:11718-34. [DOI: 10.1021/jp508513p] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [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
| | - 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
| | - Brady D. Garabato
- 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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26
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Samanta S, Demesko S, Dechert S, Meyer F. A Two-in-one Pincer Ligand and its Diiron(II) Complex Showing Spin State Switching in Solution through Reversible Ligand Exchange. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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27
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Kepp KP. Co-C dissociation of adenosylcobalamin (coenzyme B12): role of dispersion, induction effects, solvent polarity, and relativistic and thermal corrections. J Phys Chem A 2014; 118:7104-17. [PMID: 25116644 DOI: 10.1021/jp503607k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantum-chemical cluster modeling is challenged in the limit of large, soft systems by the effects of dispersion and solvent, and well as other physical interactions. Adenosylcobalamin (AdoCbl, coenzyme B12), as one of the most complex cofactors in life, constitutes such a challenge. The cleavage of its unique organometallic Co-C bond has inspired multiple studies of this cofactor. This paper reports the fully relaxed potential energy surface of Co-C cleavage of AdoCbl, including for the first time all side-chain interactions with the dissociating Ado group. Various methods and corrections for dispersion, relativistic effects, solvent polarity, basis set superposition error, and thermal and vibrational effects were investigated, totaling more than 550 single-point energies for the large model. The results show immense variability depending on method, including solvation, functional type, and dispersion, challenging the conceived accuracy of methods used for such systems. In particular, B3LYP-D3 seems to severely underestimate the Co-C bond strength, consistent with previous results, and BP86 remains accurate for cobalamins when dispersion interactions are accounted for.
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Affiliation(s)
- Kasper P Kepp
- DTU Chemistry, Technical University of Denmark , Building 206, Kgs. Lyngby, DK-2800, Denmark
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