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Ramos DR, Furtmüller PG, Obinger C, Peña-Gallego Á, Pérez-Juste I, Santaballa JA. Common Reactivity and Properties of Heme Peroxidases: A DFT Study of Their Origin. Antioxidants (Basel) 2023; 12:antiox12020303. [PMID: 36829861 PMCID: PMC9952403 DOI: 10.3390/antiox12020303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/06/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Electronic structure calculations using the density-functional theory (DFT) have been performed to analyse the effect of water molecules and protonation on the heme group of peroxidases in different redox (ferric, ferrous, compounds I and II) and spin states. Shared geometries, spectroscopic properties at the Soret region, and the thermodynamics of peroxidases are discussed. B3LYP and M06-2X density functionals with different basis sets were employed on a common molecular model of the active site (Fe-centred porphine and proximal imidazole). Computed Gibbs free energies indicate that the corresponding aquo complexes are not thermodynamically stable, supporting the five-coordinate Fe(III) centre in native ferric peroxidases, with a water molecule located at a non-bonding distance. Protonation of the ferryl oxygen of compound II is discussed in terms of thermodynamics, Fe-O bond distances, and redox properties. It is demonstrated that this protonation is necessary to account for the experimental data, and computed Gibbs free energies reveal pKa values of compound II about 8.5-9.0. Computation indicates that the general oxidative properties of peroxidase intermediates, as well as their reactivity towards water and protons and Soret bands, are mainly controlled by the iron porphyrin and its proximal histidine ligand.
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Affiliation(s)
- Daniel R. Ramos
- Chemical Reactivity & Photoreactivity Group (React!), Department of Chemistry, CICA & Faculty of Sciences, Universidade da Coruña, Campus da Zapateira, E-15071 A Coruña, Spain
- Departamento de Química Física, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, E-36310 Vigo, Spain
- Correspondence: (D.R.R.); (J.A.S.)
| | - Paul G. Furtmüller
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Christian Obinger
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Ángeles Peña-Gallego
- Departamento de Química Física, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, E-36310 Vigo, Spain
| | - Ignacio Pérez-Juste
- Departamento de Química Física, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, E-36310 Vigo, Spain
| | - J. Arturo Santaballa
- Chemical Reactivity & Photoreactivity Group (React!), Department of Chemistry, CICA & Faculty of Sciences, Universidade da Coruña, Campus da Zapateira, E-15071 A Coruña, Spain
- Correspondence: (D.R.R.); (J.A.S.)
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2
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Eschenbach P, Neugebauer J. Subsystem density-functional theory: A reliable tool for spin-density based properties. J Chem Phys 2022; 157:130902. [PMID: 36209003 DOI: 10.1063/5.0103091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Subsystem density-functional theory compiles a set of features that allow for efficiently calculating properties of very large open-shell radical systems such as organic radical crystals, proteins, or deoxyribonucleic acid stacks. It is computationally less costly than correlated ab initio wave function approaches and can pragmatically avoid the overdelocalization problem of Kohn-Sham density-functional theory without employing hard constraints on the electron-density. Additionally, subsystem density-functional theory calculations commonly start from isolated fragment electron densities, pragmatically preserving a priori specified subsystem spin-patterns throughout the calculation. Methods based on subsystem density-functional theory have seen a rapid development over the past years and have become important tools for describing open-shell properties. In this Perspective, we address open questions and possible developments toward challenging future applications in connection with subsystem density-functional theory for spin-dependent properties.
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Affiliation(s)
- Patrick Eschenbach
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Simulation, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Simulation, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
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Abstract
We introduce a computational approach to study porphyrin-like transition metal complexes, bridging density functional theory and exact many-body techniques, such as the density matrix renormalization group (DMRG). We first derive a multi-orbital Anderson impurity Hamiltonian starting from first principles considerations that qualitatively reproduce generalized gradient approximation (GGA)+U results when ignoring inter-orbital Coulomb repulsion U ′ and Hund exchange J. An exact canonical transformation is used to reduce the dimensionality of the problem and make it amenable to DMRG calculations, including all many-body terms (both intra- and inter-orbital), which are treated in a numerically exact way. We apply this technique to FeN 4 centers in graphene and show that the inclusion of these terms has dramatic effects: as the iron orbitals become single occupied due to the Coulomb repulsion, the inter-orbital interaction further reduces the occupation, yielding a non-monotonic behavior of the magnetic moment as a function of the interactions, with maximum polarization only in a small window at intermediate values of the parameters. Furthermore, U ′ changes the relative position of the peaks in the density of states, particularly on the iron d z 2 orbital, which is expected to affect the binding of ligands greatly.
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4
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Theoretical Study on Electronic Structural Properties of Catalytically Reactive Metalloporphyrin Intermediates. Catalysts 2020. [DOI: 10.3390/catal10020224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Metalloporphyrins have attracted great attention in the potential application of biomimetic catalysis. Especially, they were widely investigated as green catalysts in the chemical oxidation of various hydrocarbons through the catalytic activation of molecular oxygen. The structural properties of active central metal ions were reported to play a decisive role in catalytic activity. However, those delicate structural changes are difficult to be experimentally captured or elucidated in detail. Herein, we explored the electronic structural properties of metalloporphyrins (metal porphyrin (PMII, PMIIICl)) and their corresponding catalytically active intermediates (metal(III)-peroxo(PMIII-O2), metal(III)-hydroperoxo(PMIII-OH), and metal(IV)-oxo(PMIV=O), (M=Fe, Mn, and Co)) through the density functional theory method. The ground states of these intermediates were determined based on the assessment of relative energy and the corresponding geometric structures of ground states also further confirmed the stability of energy. Furthermore, our analyses of Mulliken charges and frontier molecular orbitals revealed the potential catalytic behavior of reactive metalloporphyrin intermediates.
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5
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Pimachev A, Nielsen RD, Karanovich A, Dahnovsky Y. Ferromagnetism in 2D organic iron hemoglobin crystals based on nitrogenated conjugated micropore materials. Phys Chem Chem Phys 2019; 21:25820-25825. [PMID: 31728472 DOI: 10.1039/c9cp04509k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we study a low-cost two-dimensional ferromagnetic semiconductor with possible applications in biomedicine, solar cells, spintronics, and energy and hydrogen storage. From first principle calculations we describe the unique electronic, transport, optical, and magnetic properties of a π-conjugated micropore polymer (CMP) with three iron atoms placed in the middle of an isolated pore locally resembling heme complexes. This material exhibits strong Fe-localized dz2 bands. The bandgap is direct and equal to 0.28 eV. The valence band is doubly degenerate at the Γ-point and for larger k-wavevectors the HOMO band becomes flat with low contribution to charge mobility. The absorption coefficient is roughly isotropic. The conductivity is also isotropic with the nonzero contribution in the energy range 0.3-8 eV. The xy-component of the imaginary part of the dielectric tensor determines the magneto-optical Faraday and Kerr rotation. Nonvanishing rotation is observed in the interval of 0.5-5.0 eV. This material is found to be a ferromagnet of an Ising type with long-range exchange interactions with a very high magnetic moment per unit cell, m = 6 μB. The exchange integral is calculated by two independent methods: (a) from the energy difference between ferromagnetic and antiferromagnetic states and (b) from a magnon dispersion curve. In the former case Jnn = 27 μeV. In the latter case the magnon dispersion is fitted by the Ising model with the nearest and next-nearest neighbor spin interactions. From these estimations we find that Jnn = 19.5 μeV and Jnnn = -3 μeV. Despite the different nature of the calculations, the exchange integrals are only within 28% difference.
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Affiliation(s)
- Artem Pimachev
- Aerospace Mechanics Research Center, University of Colorado Boulder, Boulder, CO 80309, USA
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Kabay N, Bozer BD, Kiraz AÖ, Baygu Y, Kara İ, Gök Y. Synthesis, characterization and structural computational investigation of novel Zn(II) phthalocyanines containing peripheral anthracene moieties. J PORPHYR PHTHALOCYA 2019. [DOI: 10.1142/s1088424619500913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
New zinc(II) phthalocyanines (ZnPc-I and ZnPc-II) containing four peripheral anthracene pendant groups were synthesized by cyclotetramerization of (E)-4-(3-(4-((anthracen-9-yl-methylene)amino)phenoxy)propoxy)phthalonitrile and 4-(3-(4-((anthracen-9-ylmethyl)amino)phenoxy)propoxy)phthalonitrile. All compounds were characterized using a combination of analytical and spectroscopic techniques such 1H, [Formula: see text]C NMR, FT-IR, UV-vis and MS spectral data. The molecular geometry and gauge including atomic orbital (GIAO) 1H and [Formula: see text]C chemical shift values of the compounds in the ground state have also been calculated using B3LYP with the 6–31G([Formula: see text] basis set. The chemical shift of the optimized molecular structure is compared with the experimental chemical shift values.
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Affiliation(s)
- Nilgün Kabay
- Department of Biomedical Engineering, Pamukkale University, Denizli, Turkey
| | - Burak Doğan Bozer
- Department of Biomedical Engineering, Pamukkale University, Denizli, Turkey
| | | | - Yasemin Baygu
- Tavas Vocational School of Higher Education, Pamukkale University, Denizli, Turkey
| | - İzzet Kara
- Department of Physical Education, Pamukkale University, Denizli, Turkey
| | - Yaşar Gök
- Department of Chemical Engineering, Uşak University, Uşak, Turkey
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7
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Khazaei S, Eskandari M, Zakavi S. Computational and experimental insights into the oxidative stability of iron porphyrins: A mono-ortho-substituted iron porphyrin with unusually high oxidative stability. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3869] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Saeede Khazaei
- Institute for Advanced Studies in Basic Sciences (IASBS); Zanjan Iran
| | - Mortaza Eskandari
- Institute for Advanced Studies in Basic Sciences (IASBS); Zanjan Iran
| | - Saeed Zakavi
- Institute for Advanced Studies in Basic Sciences (IASBS); Zanjan Iran
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8
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Atay ÇK, Kara Y, Gökalp M, Kara I, Tilki T, Karci F. Disazo dyes containing pyrazole and indole moieties: Synthesis, characterization, absorption characteristics, theoretical calculations, structural and electronic properties. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.01.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Bayrakdar A, Kart HH, Elcin S, Deligoz H, Karabacak M. Synthesis and DFT calculation of a novel 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:607-617. [PMID: 25448961 DOI: 10.1016/j.saa.2014.09.074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 09/17/2014] [Accepted: 09/19/2014] [Indexed: 06/04/2023]
Abstract
In this study, 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene has been synthesized from 2-aminoantracene and 25,27-dihydroxy-26,28-diethylacetate calix[4]arene. In order to identify the molecular structure and vibrational features of the prepared azocalix[4]arene, FT-IR and (1)H NMR spectral data have been used. FT-IR spectrum of the studied molecule is recorded in the region 4000-400 cm(-1). (1)H NMR spectrum is recorded for 0.1-0.2 M solutions in DMSO-d6 solution. The molecular geometry, infrared spectrum are calculated by the density functional method employing B3LYP level with different basis sets, including 6-31G(d) and LanL2DZ. The chemical shifts calculation for (1)H NMR of the title molecule is calculated by using by Gauge-Invariant Atomic Orbital method by utilizing the same basis sets. The total density of state, the partial density of state and the overlap population density of state diagram analysis are done via GaussSum 3.0 program. Frontier molecular orbital (HOMO-LUMO) and molecular electrostatic potential surface on the title molecule are carried out for various intramolecular interactions that are responsible for the stabilization of the molecule. The experimental results and theoretical calculations have been compared, and they are found to be in good agreement.
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Affiliation(s)
- A Bayrakdar
- Pamukkale University, Faculty of Science-Arts, Department of Physics, 20070 Denizli, Turkey
| | - H H Kart
- Pamukkale University, Faculty of Science-Arts, Department of Physics, 20070 Denizli, Turkey
| | - S Elcin
- Pamukkale University, Faculty of Engineering, Department of Chemical Engineering, 20017 Denizli, Turkey
| | - H Deligoz
- Pamukkale University, Faculty of Engineering, Department of Chemical Engineering, 20017 Denizli, Turkey
| | - M Karabacak
- Department of Mechatronics Engineering, H.F.T. Technology Faculty, Celal Bayar University, Turgutlu, Manisa, Turkey.
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10
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Radoń M. Spin-State Energetics of Heme-Related Models from DFT and Coupled Cluster Calculations. J Chem Theory Comput 2014; 10:2306-21. [DOI: 10.1021/ct500103h] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Mariusz Radoń
- Faculty of Chemistry, Jagiellonian University in Kraków, ul. Ingardena 3, 30-060 Kraków, Poland
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11
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Abstract
By analysing the properties of the electron density in the structurally simple perhalogenated ethanes, X3C-CY3 (X, Y = F, Cl), a previously overlooked non-covalent attraction between halogens attached to opposite carbon atoms is found. Quantum chemical calculations extrapolated towards the full solution of the Schrödinger equation reveal the complex nature of the interaction. When at least one of the halogens is a chlorine, the strength of the interaction is comparable to that of hydrogen bonds. Further analysis shows that the bond character is quite different from standard non-covalent halogen bonds and hydrogen bonds; no bond critical points are found between the halogens, and the σ-holes of the halogens are not utilised for bonding. Thus, the nature of the intramolecular halogen···halogen bonding studied here appears to be of an unusually strong van der Waals type.
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Affiliation(s)
- Mikael P Johansson
- Institut de Química Computational i Catàlisi and Departament de Química, Universitat de Girona, Campus Montilivi, ES-17071 Girona, Spain
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12
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Charkin OP. Theoretical study of the structure and stability of oxo heme derivatives. RUSS J INORG CHEM+ 2013. [DOI: 10.1134/s0036023613030042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Ab initio, density functional theory, and semi-empirical calculations. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 924:3-27. [PMID: 23034743 DOI: 10.1007/978-1-62703-017-5_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This chapter introduces the theory and applications of commonly used methods of electronic structure calculation, with particular emphasis on methods applicable for modelling biomolecular systems. This chapter is sectioned as follows. We start by presenting ab initio methods, followed by a treatment of density functional theory (DFT) and some recent advances in semi-empirical methods. Treatment of excited states as well as basis sets are also presented.
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14
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Johansson MP, Swart M. Subtle effects control the polymerisation mechanism in α-diimine iron catalysts. Dalton Trans 2011; 40:8419-28. [DOI: 10.1039/c1dt10045a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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15
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Panchmatia PM, Ali ME, Sanyal B, Oppeneer PM. Halide Ligated Iron Porphines: A DFT+U and UB3LYP Study. J Phys Chem A 2010; 114:13381-7. [DOI: 10.1021/jp106358m] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pooja M. Panchmatia
- Department of Physics and Astronomy, Uppsala University, Box 516, S-751 20 Uppsala, Sweden, Department of Chemistry, University of Bath, Bath, BA2 7AY, U.K., and Theoretische Chemie, Ruhr-Universität, Bochum, D-44780, Bochum, Germany
| | - Md. Ehesan Ali
- Department of Physics and Astronomy, Uppsala University, Box 516, S-751 20 Uppsala, Sweden, Department of Chemistry, University of Bath, Bath, BA2 7AY, U.K., and Theoretische Chemie, Ruhr-Universität, Bochum, D-44780, Bochum, Germany
| | - Biplab Sanyal
- Department of Physics and Astronomy, Uppsala University, Box 516, S-751 20 Uppsala, Sweden, Department of Chemistry, University of Bath, Bath, BA2 7AY, U.K., and Theoretische Chemie, Ruhr-Universität, Bochum, D-44780, Bochum, Germany
| | - Peter M. Oppeneer
- Department of Physics and Astronomy, Uppsala University, Box 516, S-751 20 Uppsala, Sweden, Department of Chemistry, University of Bath, Bath, BA2 7AY, U.K., and Theoretische Chemie, Ruhr-Universität, Bochum, D-44780, Bochum, Germany
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16
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Johansson MP, Swart M. Magnetizabilities at Self-Interaction-Corrected Density Functional Theory Level. J Chem Theory Comput 2010; 6:3302-11. [DOI: 10.1021/ct100235b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mikael P. Johansson
- Institut de Química Computacional, Universitat de Girona, Campus Montilivi, ES-17071 Girona, Spain and Laboratory for Instruction in Swedish, Department of Chemistry, University of Helsinki, FI-00014 Helsinki, Finland
| | - Marcel Swart
- Institut de Química Computacional, Universitat de Girona, Campus Montilivi, ES-17071 Girona, Spain and Laboratory for Instruction in Swedish, Department of Chemistry, University of Helsinki, FI-00014 Helsinki, Finland
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17
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Takano Y, Nakamura H. Electronic structures of heme a of cytochrome c oxidase in the redox states--charge density migration to the propionate groups of heme a. J Comput Chem 2010; 31:954-62. [PMID: 19645053 DOI: 10.1002/jcc.21379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The electronic structures of heme a of cytochrome c oxidase in the redox states were studied, using hybrid density functional theory with a polarizable continuum model and a point charge model. We found that the most stable electronic configurations of the d electrons of the Fe ion are determined by the orbital interactions of the d orbitals of the Fe ion with the pi orbitals of the porphyrin ring and the His residues. The redox reaction of the Fe ion influences the charge density on the formyl group through the pi conjugation of the porphyrin ring. In addition, we found the charge transfer from the Fe ion to the propionate group of heme a in the redox change despite the lack of the pi-conjugation. We elucidated that the charge propagation originates from the heme a structure itself and that the origin of the charge delocalization to the heme propionate is the orbital interactions between the d orbital of the Fe ion and the p orbitals of the carboxylate part of the heme propionate via the pi conjugation of the porphyrin ring and the sigma* orbital of the C-C bond of the propionate group. The electrostatic effect by surrounding proteins enhances the charge transfer from the Fe ion to the propionate group. These results indicate that heme propionate groups serve electron mediators in electron transfer as well as electrostatic anchors, and that proteins surrounding the active site reinforce the congenital abilities of the cofactors.
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Affiliation(s)
- Yu Takano
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
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18
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Shubina TE. Computational Studies on Properties, Formation, and Complexation of M(II)-Porphyrins. ADVANCES IN INORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0898-8838(10)62007-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Send R, Sundholm D, Johansson MP, Pawłowski F. Excited State Potential Energy Surfaces of Polyenes and Protonated Schiff Bases. J Chem Theory Comput 2009; 5:2401-14. [DOI: 10.1021/ct900240s] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robert Send
- Institut für Physikalische Chemie, Universität Karlsruhe, Kaiserstrasse 12, D-76128 Karlsruhe, Germany
| | - Dage Sundholm
- Department of Chemistry, P.O. Box 55 (A.I. Virtanens plats 1), University of Helsinki, FI-00014 Helsinki, Finland
| | - Mikael P. Johansson
- Lundbeck Foundation Centre for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Århus C, Denmark
| | - Filip Pawłowski
- Physics Institute, Kazimierz Wielki University, Plac Weyssenhoffa 11, PL-85-072 Bydgoszcz, Poland
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20
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Kamiya K, Yamamoto S, Shiraishi K, Oshiyama A. Significant change in electronic structures of heme upon reduction by strong Coulomb repulsion between Fe d electrons. J Phys Chem B 2009; 113:6866-72. [PMID: 19371055 DOI: 10.1021/jp809405s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report total-energy electronic-structure calculations based on the density functional theory performed on a low-spin heme. We have found that the high-lying occupied and low-lying unoccupied states having Fe d and/or porphyrin pi orbital character are significantly rearranged upon the reduction of the heme. An analysis of these states shows that the remarkable elevation of the Fe d levels takes place due to the strong Coulombic repulsion between accommodated d electrons. Due to a peculiarity of the heme, this elevation could be controlled by lower-lying empty porphyrin pi states, leading to electron transfer from Fe d orbitals to the porphyrin pi ones in order to reduce the Coulomb-energy cost. This self-limiting mechanism provides a natural explanation not only for the present calculated results, but also for general electron delocalization appearing under various physiological conditions, regardless of the types of the hemes.
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Affiliation(s)
- Katsumasa Kamiya
- Institute of Picobiology, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan.
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21
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Lehtonen O, Sundholm D, Send R, Johansson MP. Coupled-cluster and density functional theory studies of the electronic excitation spectra of trans-1,3-butadiene and trans-2-propeniminium. J Chem Phys 2009; 131:024301. [DOI: 10.1063/1.3158990] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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22
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Kaila VRI, Johansson MP, Sundholm D, Laakkonen L, Wiström M. The chemistry of the CuB site in cytochrome c oxidase and the importance of its unique His-Tyr bond. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:221-33. [PMID: 19388139 DOI: 10.1016/j.bbabio.2009.01.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The CuB metal center is at the core of the active site of the heme-copper oxidases, comprising a copper atom ligating three histidine residues one of which is covalently bonded to a tyrosine residue. Using quantum chemical methodology, we have studied the CuB site in several redox and ligand states proposed to be intermediates of the catalytic cycle. The importance of the His-Tyr crosslink was investigated by comparing energetics, charge, and spin distributions between systems with and without the crosslink. The His-Tyr bond was shown to decrease the proton affinity and increase the electron affinity of both Tyr-244 and the copper. A previously unnoticed internal electronic equilibrium between the copper atom and the tyrosine was observed, which seems to be coupled to the unique structure of the system. In certain states the copper and Tyr-244 compete for the unpaired electron, the localization of which is determined by the oxygenous ligand of the copper. This electronic equilibrium was found to be sensitive to the presence of a positive charge 10 A away from the center, simulating the effect of Lys-319 in the K-pathway of proton transfer. The combined results provide an explanation for why the heme-copper oxidases need two pathways of proton uptake, and why the K-pathway is active only in the second half of the reaction cycle.
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Affiliation(s)
- Ville R I Kaila
- Helsinki Bioenergetics Group, Programme of Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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23
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Kara I, Kart HH, Kolsuz N, Karakuş ÖÖ, Deligöz H. Ab initio studies of NMR chemical shifts for calix[4]arene and its derivatives. Struct Chem 2009. [DOI: 10.1007/s11224-009-9414-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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24
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Yamasaki H, Takano Y, Nakamura H. Theoretical Investigation of the Electronic Asymmetry of the Special Pair Cation Radical in the Photosynthetic Type-II Reaction Center. J Phys Chem B 2008; 112:13923-33. [DOI: 10.1021/jp806309p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Hideki Yamasaki
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yu Takano
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
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25
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Johansson MP, Kaila VRI, Laakkonen L. Charge parameterization of the metal centers in cytochrome c oxidase. J Comput Chem 2008; 29:753-67. [PMID: 17876762 DOI: 10.1002/jcc.20835] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Reliable atomic point charges are of key importance for a correct description of the electrostatic interactions when performing classical, force field based simulations. Here, we present a systematic procedure for point charge derivation, based on quantum mechanical methodology suited for the systems at hand. A notable difference to previous procedures is to include an outer region around the actual system of interest. At the cost of increasing the system sizes, here up to 265 atoms, including the surroundings achieves near-neutrality for the systems as well as structural stability, important factors for reliable charge distributions. In addition, the common problem of converting between C--H bonds and C--C bonds at the border vanishes. We apply the procedure to the four redox-active metal centers of cytochrome c oxidase: Cu(A), haem a, haem a(3), and Cu(B). Several relevant charge and ligand states are considered. Charges for two different force fields, CHARMM and AMBER, are presented.
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Affiliation(s)
- Mikael P Johansson
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland.
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26
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Panchmatia PM, Sanyal B, Oppeneer PM. GGA+U modeling of structural, electronic, and magnetic properties of iron porphyrin-type molecules. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.10.030] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Theoretical analysis of the electronic asymmetry of the special pair in the photosynthetic reaction center: Effect of structural asymmetry and protein environment. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.08.101] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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28
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Bach RD, Dmitrenko O. The “Somersault” Mechanism for the P-450 Hydroxylation of Hydrocarbons. The Intervention of Transient Inverted Metastable Hydroperoxides. J Am Chem Soc 2006; 128:1474-88. [PMID: 16448118 DOI: 10.1021/ja052111+] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of model theoretical calculations are described that suggest a new mechanism for the oxidation step in enzymatic cytochrome P450 hydroxylation of saturated hydrocarbons. A new class of metastable metal hydroperoxides is described that involves the rearrangement of the ground-state metal hydroperoxide to its inverted isomeric form with a hydroxyl radical hydrogen bonded to the metal oxide (MO-OH --> MO....HO). The activation energy for this somersault motion of the FeO-OH group is 20.3 kcal/mol for the P450 model porphyrin iron(III) hydroperoxide [Por(SH)Fe(III)-OOH(-)] to produce the isomeric ferryl oxygen hydrogen bonded to an *OH radical [Por(SH)Fe(III)-O....HO(-)]. This isomeric metastable hydroperoxide, the proposed primary oxidant in the P450 hydroxylation reaction, is calculated to be 17.8 kcal/mol higher in energy than the ground-state iron(III) hydroperoxide Cpd 0. The first step of the proposed mechanism for isobutane oxidation is abstraction of a hydrogen atom from the C-H bond of isobutane by the hydrogen-bonded hydroxyl radical to produce a water molecule strongly hydrogen bonded to anionic Cpd II. The hydroxylation step involves a concerted but nonsynchronous transfer of a hydrogen atom from this newly formed, bound, water molecule to the ferryl oxygen with a concomitant rebound of the incipient *OH radical to the carbon radical of isobutane to produce the C-O bond of the final product, tert-butyl alcohol. The TS for the oxygen rebound step is 2 kcal/mol lower in energy than the hydrogen abstraction TS (DeltaE() = 19.5 kcal/mol). The overall proposed new mechanism is consistent with a lot of the ancillary experimental data for this enzymatic hydroxylation reaction.
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Affiliation(s)
- Robert D Bach
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
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29
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Semi-empirical AM1 and PM3 calculations of five- and six-coordinate oxo iron (IV) porphyrin complexes. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.04.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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30
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Remenyi C, Kaupp M. Where Is the Spin? Understanding Electronic Structure and g-Tensors for Ruthenium Complexes with Redox-Active Quinonoid Ligands. J Am Chem Soc 2005; 127:11399-413. [PMID: 16089469 DOI: 10.1021/ja051811b] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the bonding in transition metal complexes with redox-active ligands is a major challenge, for example in redox catalysis or in bioinorganic chemistry. In this work, electronic g-tensors, spin-density distributions, and electronic structure have been studied by different density functional methods for an extended series of complexes [Ru(acac)2(L)]n (n = -1, 0, +1; L = redox-active o-quinonoid ligand). Comparison is made with experimental g-tensors and g-tensor-based oxidation-state assignments for a number of experimentally studied examples, using both gradient-corrected (BP86) and hybrid functionals (B3LYP, BHLYP) representing a range of exact-exchange admixtures. Reasonable, albeit not perfect, agreement with experimental g-tensors is obtained in one-component DFT calculations with hybrid functionals. Analyses of spin densities confirm the assignment of the cationic complexes as predominantly d5-Ru(III) with a neutral quinonoid ligand. However, this conclusion is obtained only after inclusion of the appreciable spin polarization of the unrestricted determinant, while the singly occupied molecular orbital (SOMO) is localized more on the acac ligands. The anionic complexes turn out to be approximately halfway between a d6-Ru(II)/semiquinone and a d5-Ru(III)/catecholate formulation, but again only after taking into account the extensive spin polarization. Even the previous assignment of the neutral parent systems as d5-Ru(III)/semiquinone is not accurate, as a d6-Ru(II)/quinone resonance structure contributes to some extent. Very unusual trends in the spin contamination of the Kohn-Sham determinant with increasing exact-exchange admixture in some of the cationic complexes have been traced to an interplay between spin delocalization and spin polarization.
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Affiliation(s)
- Christian Remenyi
- Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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