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Osadchuk I, Luts HE, Norvaiša K, Borovkov V, Senge MO. Supramolecular Chirogenesis in a Sterically Hindered Porphyrin: A Critical Theoretical Analysis. Chemistry 2023; 29:e202301408. [PMID: 37227167 DOI: 10.1002/chem.202301408] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 05/26/2023]
Abstract
The determination of molecular stereochemistry and absolute configuration is an important part of modern chemistry, pharmacology, and biology. Electronic circular dichroism (ECD) spectroscopy is a widely used tool for chirality assignment, especially with porphyrin macrocycles employed as reporter chromophores. However, the mechanisms of induced ECD in porphyrin complexes are yet to be comprehensively rationalized. In this work, the ECD spectra of a sterically hindered hexa-cationic porphyrin with two camphorsulfonic acids in dichloromethane and chloroform were experimentally measured and computationally analyzed. The influence of geometric factors such as the position of chiral guest molecules, distortion of the porphyrin macrocycle, and orientation of aromatic and non-aromatic peripheral substituents on the ECD spectra was theoretically studied. Various potential pitfalls, such as a lack of significant conformations and accidental agreement of experimental and simulated spectra, are considered and discussed.
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Affiliation(s)
- Irina Osadchuk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Hanna-Eliisa Luts
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Karolis Norvaiša
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, D02R590, Dublin, Ireland
| | - Victor Borovkov
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Mathias O Senge
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, D02R590, Dublin, Ireland
- Institute for Advanced Study (TUM-IAS), Technical University of Munich, Lichtenberg Str. 2a, 85748, Garching, Germany
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2
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Mirmarghabi P, Bahrami H. Theoretical investigation of five-coordinated manganese(III) oxophlorin with different axial ligands at various spin states using different DFT methods. J PORPHYR PHTHALOCYA 2022. [DOI: 10.1142/s1088424622500043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Mn(III)-oxophlorin complexes with imidazole, pyridine and t-butylcyanide as axial ligands have been studied using B3LYP, Bv86p, and M06-2X methods. All of the possible optimized geometries are specified, while the M06-2X is employed. Results obtained show that the isomers of Mn(III)-oxophlorin with imidazole or pyridine are the most stable at quintet state, compared to singlet and triplet spin states. Besides, there are two and four [Formula: see text]-electrons on manganese in each of these complexes at triplet and quintet states, respectively. Also, Mn(III)-oxophlorin with t-butylcyanide as axial ligand is only stable at singlet state. Non-specific solvent effects show that dispersion and London forces have the basic role in stability of complexes in a solvent. Note that latter interactions can occur in medium with dielectric constant ([Formula: see text]) of [Formula: see text]8, such as [Formula: see text] for position of oxophlorin in heme oxygenase enzyme. NBO analysis show that there is no degeneracy between d orbitals of Mn in the five-coordinated Mn(III)-oxophlorin at singlet and triplet spin states, but two d orbitals of manganese are degenerated in latter complexes at quintet state. Such degeneracy of d orbitals is observed in a complex with square pyramid structure. Then five-coordinated Mn(III)-oxophlorin with imidazole or pyridine is the most stable at quintet spin state, because of its geometry corresponding to square pyramid configuration of atoms. Also, nonbounding interaction between Mn and the ring of oxophlorin or Mn and ligand are more effective in Mn(III)-oxophlorin with imidazole as axial ligand, compared to pyridine and t-butylcyanide.
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Affiliation(s)
| | - Homayoon Bahrami
- Department of Chemistry, Lorestan University, Khoramabad 68135-465, Iran
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3
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Tasharofi H, Jamaat PR, Asli MD. Investigation of different substitutions, structure, charge and multiplicity spin of the iron verdoheme-rat heme oxygenase complex: a DFT study. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s108842462150084x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Heme oxygenase-1 (HO-1) is an inducible stress protein that degrades heme to carbon monoxide, iron and biliverdin, which subsequently reduces to bilirubin. Many parameters of verdoheme–rat heme oxygenase complex structure and their role and function on heme degradation were unknown. In this work the structure of iron verdoheme in complex with rat heme oxygenase was studied by density functional theory based B3LYP method and 6-31G basis set. The main goal is to obtain structural and energetic information for various transition states and intermediates on reaction pathways. The charge of verdoheme and iron as the central metal, electron distribution, spin multiplicity of the molecule and proximal substituents effect on the verdoheme ring stabilization and their arrangement are discussed. Gas phase computation has shown that the central metal of the five coordinated rat-verdohemeas ferrous (Fe[Formula: see text] (from 1a-1i) and ferric (Fe[Formula: see text] (from 1j–1q). The Mulliken and NBO charge and spin calculation show that iron is considered as ferrous in all of the optimized structures. Assessment results can gain valuable chemical insight into the electronic reorganization during the reactions.
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Affiliation(s)
- Hamideh Tasharofi
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran, Postal code: 1467686831, Iran
| | - Parisa Rajabali Jamaat
- Department of Chemistry, East Tehran Branch, Islamic Azad University, Tehran, Iran, Postal code: 1866113118, Iran
| | - Maryam Daghighi Asli
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran, Postal code: 1467686831, Iran
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4
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Gheidi M, Safari N, Zahedi M. Density functional theory studies on the conversion of hydroxyheme to iron-verdoheme in the presence of dioxygen. Dalton Trans 2018; 46:2146-2158. [PMID: 28120965 DOI: 10.1039/c6dt04250c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Detailed insight into the second step of heme degradation by heme oxygenase, oxophlorin to verdoheme and biliverdin, is presented. Density functional theory methods are reported for the conversion of oxophlorin to verdoheme. Since it is currently unclear whether dioxygen binding to iron oxophlorin is followed by a reduction or not, in this work we have focused on the difference in reactivity between [(Im)(O2˙)FeIII(PO˙)] (PO˙ is the oxophlorin dianion radical) and [(Im)(O2˙)FeIII(PO)]- (PO is the oxophlorin trianion). Thus, we have shown that in [(Im)(O2˙)FeIII(PO˙)] and [(Im)(O2˙)FeIII(PO)]-, the mechanisms are stepwise with an initial C-O bond activation to form a ring-structure where the oxophlorin is distorted from planarity. This is followed by homolytic dioxygen bond breaking that directly leads to iron-oxo verdoheme products. The [(Im)(O2˙)FeIII(PO˙)] mechanism proceeds via two-state-reactivity patterns on the adjacent doublet and quartet spin state surfaces, whereas the [(Im)(O2˙)FeIII(PO)]- route shows single-state-reactivity on a triplet spin state surface. In both, the rate determining step is the C-O bond activation, with substantially lower barriers on the [(Im)(O2˙)FeIII(PO˙)] surface of 12.15 kcal mol-1 in the gas phase compared to 22.55 kcal mol-1 for the intermediate-spin of [(Im)(O2˙)FeIII(PO)]-. The complete active space self-consistent-field wave functions with second-order multi-reference perturbation theory were also studied. Finally, the effects of the solvent and the medium on the reaction barriers were tested and shown to be considerable.
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Affiliation(s)
- Mahin Gheidi
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, G. C., Evin, 19839-63113, Tehran, Iran.
| | - Nasser Safari
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, G. C., Evin, 19839-63113, Tehran, Iran.
| | - Mansour Zahedi
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, G. C., Evin, 19839-63113, Tehran, Iran.
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Balasekaran SM, Hagenbach A, Abram U. Tetrafluoridonitridotechnetate(VI) - Reactions and Structures. Z Anorg Allg Chem 2018. [DOI: 10.1002/zaac.201800206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Adelheid Hagenbach
- Institute of Chemistry and Biochemistry; Freie Universität Berlin; Fabeckstr. 34/36 14195 Berlin Germany
| | - Ulrich Abram
- Institute of Chemistry and Biochemistry; Freie Universität Berlin; Fabeckstr. 34/36 14195 Berlin Germany
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6
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Alavi FS, Gheidi M, Zahedi M, Safari N, Ryde U. A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations. Dalton Trans 2018; 47:8283-8291. [DOI: 10.1039/c8dt00064f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Heme degradation by heme oxygenase enzymes is important for maintaining iron homeostasis and prevention of oxidative stress.
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Affiliation(s)
- Fatemeh Sadat Alavi
- Department of Chemistry
- Faculty of Sciences
- Shahid Beheshti University
- Tehran
- Iran
| | - Mahin Gheidi
- Department of Chemistry
- Faculty of Sciences
- Shahid Beheshti University
- Tehran
- Iran
| | - Mansour Zahedi
- Department of Chemistry
- Faculty of Sciences
- Shahid Beheshti University
- Tehran
- Iran
| | - Nasser Safari
- Department of Chemistry
- Faculty of Sciences
- Shahid Beheshti University
- Tehran
- Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
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7
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Alavi FS, Zahedi M, Safari N, Ryde U. QM/MM Study of the Conversion of Oxophlorin into Verdoheme by Heme Oxygenase. J Phys Chem B 2017; 121:11427-11436. [PMID: 29090581 DOI: 10.1021/acs.jpcb.7b08332] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heme oxygenase is an enzyme that degrades heme, thereby recycling iron in most organisms, including humans. Pervious density functional theory (DFT) calculations have suggested that iron(III) hydroxyheme, an intermediate generated in the first step of heme degradation by heme oxygenase, is converted to iron(III) superoxo oxophlorin in the presence of dioxygen. In this article, we have studied the detailed mechanism of conversion of iron(III) superoxo oxophlorin to verdoheme by using combined quantum mechanics and molecular mechanics (QM/MM) calculations. The calculations employed the B3LYP method and the def2-QZVP basis set, considering dispersion effects with the DFT-D3 approach, obtaining accurate energies with large QM regions of almost 1000 atoms. The reaction was found to be exothermic by -35 kcal/mol, with a rate-determining barrier of 19 kcal/mol in the doublet state. The protein environment and especially water in the enzyme pocket significantly affects the reaction by decreasing the reaction activation energies and changing the structures by providing strategic hydrogen bonds.
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Affiliation(s)
- Fatemeh Sadat Alavi
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University , G.C., Evin, 19839-6313 Tehran, Iran
| | - Mansour Zahedi
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University , G.C., Evin, 19839-6313 Tehran, Iran
| | - Nasser Safari
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University , G.C., Evin, 19839-6313 Tehran, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University , Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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Esdaile LJ, Rintoul L, Goh MS, Merahi K, Parizel N, Wellard RM, Choua S, Arnold DP. Nickel(II)
meso
‐Hydroxyporphyrin Complexes Revisited: Palladium‐Catalysed Synthesis, Electronic Structures of Derived Oxy Radicals, and Oxidative Coupling to a Dioxoporphodimethene Dyad. Chemistry 2016; 22:3430-3446. [DOI: 10.1002/chem.201504252] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/01/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Louisa J. Esdaile
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology GPO Box 2434 Brisbane 4001 Australia
| | - Llew Rintoul
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology GPO Box 2434 Brisbane 4001 Australia
| | - Mean See Goh
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology GPO Box 2434 Brisbane 4001 Australia
| | - Khalissa Merahi
- Institut de Chimie Université de Strasbourg 4 rue Blaise Pascal, BP 296 R8 67008 Strasbourg Cedex France
| | - Nathalie Parizel
- Institut de Chimie Université de Strasbourg 4 rue Blaise Pascal, BP 296 R8 67008 Strasbourg Cedex France
| | - R. Mark Wellard
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology GPO Box 2434 Brisbane 4001 Australia
| | - Sylvie Choua
- Institut de Chimie Université de Strasbourg 4 rue Blaise Pascal, BP 296 R8 67008 Strasbourg Cedex France
| | - Dennis P. Arnold
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology GPO Box 2434 Brisbane 4001 Australia
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Mesbahi E, Safari N, Gheidi M. Investigation of axial ligand effects on catalytic activity of manganese porphyrin, evidence for the importance of hydrogen bonding in cytochrome-P450 model reactions. J PORPHYR PHTHALOCYA 2014. [DOI: 10.1142/s1088424614500102] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Various nitrogenous bases, such as imidazoles, pyridines and amines were employed as axial ligands in epoxidation reaction of cyclooctene bytetra-n-butylammonium hydrogen monopersulfate (n- Bu 4 NHSO 5), in the presence of Mn ( III )-tetrakis(2,3-dimethoxyphenyl)porphyrin-acetate ( T (2,3- OMeP ) PorMnOAc ). T (2,3- OMeP ) PorMnOAc is a fairly stable catalyst, with the ability of producing hydrogen bonding. High epoxidation yield of 85 ± 6% was obtained in the presence of imidazole axial ligand with 100% selectivity in 30 min. Higher conversion of around 100% was obtained by pyridine axial base, while selectivity was reduced to 69%. Further epoxidation reactions were also performed using Mn ( III )-Tetrakis(2,3-dihydroxyphenyl)porphyrin-acetate ( T (2,3- OHP ) PorMnOAc ) as catalyst. In addition to the usual electronic and steric effects, it is proposed that the catalytic activity depends on the existence and kind of hydrogen bonding between the axial base and the ortho-methoxy or hydroxy groups on the phenyl rings of manganese porphyrin. The cis to trans ratio of cis-stilbene oxide formed by imidazole and pyridine axial bases were obtained as 7.5 and 2.5 respectively. In addition GC-Ms and UV-vis studies were employed to find the nature of active species and product formation. Our DFT calculations disclosed that pyridine hydrogen bonding with moiety of the macrocycle rings strongly affects the relative energies of S/Q spin states in [ T (2,3- OMeP ) PorMn V ( O )( Py )]+, in that it results in the longer Mn – O bond and reactivity toward substrates.
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Affiliation(s)
- Elnaz Mesbahi
- Chemistry Department, Shahid Beheshti University, G.C, Evin, Tehran 19839-63113, Iran
| | - Nasser Safari
- Chemistry Department, Shahid Beheshti University, G.C, Evin, Tehran 19839-63113, Iran
| | - Mahin Gheidi
- Chemistry Department, Shahid Beheshti University, G.C, Evin, Tehran 19839-63113, Iran
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Gheidi M, Safari N, Zahedi M. Chameleonic Nature of Hydroxyheme in Heme Oxygenase and Its Reactivity: A Density Functional Theory Study. Inorg Chem 2014; 53:2766-75. [DOI: 10.1021/ic402754y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mahin Gheidi
- Department of Chemistry, Faculty
of Sciences, Shahid Beheshti University, G. C. Evin, 19839-63113 Tehran, Iran
| | - Nasser Safari
- Department of Chemistry, Faculty
of Sciences, Shahid Beheshti University, G. C. Evin, 19839-63113 Tehran, Iran
| | - Mansour Zahedi
- Department of Chemistry, Faculty
of Sciences, Shahid Beheshti University, G. C. Evin, 19839-63113 Tehran, Iran
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11
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Gheidi M, Safari N, Zahedi M. Structure and Redox Behavior of Iron Oxophlorin and Role of Electron Transfer in the Heme Degradation Process. Inorg Chem 2012; 51:12857-66. [DOI: 10.1021/ic3017497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mahin Gheidi
- Department
of Chemistry, Faculty of Sciences, Shahid
Beheshti University, G. C., Evin, 19839-63113, Tehran, Iran
| | - Nasser Safari
- Department
of Chemistry, Faculty of Sciences, Shahid
Beheshti University, G. C., Evin, 19839-63113, Tehran, Iran
| | - Mansour Zahedi
- Department
of Chemistry, Faculty of Sciences, Shahid
Beheshti University, G. C., Evin, 19839-63113, Tehran, Iran
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