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Domes R, Frosch T. Molecular Interactions Identified by Two-Dimensional Analysis-Detailed Insight into the Molecular Interactions of the Antimalarial Artesunate with the Target Structure β-Hematin by Means of 2D Raman Correlation Spectroscopy. Anal Chem 2023; 95:12719-12731. [PMID: 37586701 PMCID: PMC10469332 DOI: 10.1021/acs.analchem.3c01415] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
A thorough understanding of the interaction of endoperoxide antimalarial agents with their biological target structures is of utmost importance for the tailored design of future efficient antimalarials. Detailed insights into molecular interactions between artesunate and β-hematin were derived with a combination of resonance Raman spectroscopy, two-dimensional correlation analysis, and density functional theory calculations. Resonance Raman spectroscopy with three distinct laser wavelengths enabled the specific excitation of different chromophore parts of β-hematin. The resonance Raman spectra of the artesunate-β-hematin complexes were thoroughly analyzed with the help of high-resolution and highly sensitive two-dimensional correlation spectroscopy. Spectral changes in the peak properties were found with increasing artesunate concentration. Changes in the low-frequency, morphology-sensitive Raman bands indicated a loss in crystallinity of the drug-target complexes. Differences in the high-wavenumber region were assigned to increased distortions of the planarity of the structure of the target molecule due to the appearance of various coexisting alkylation species. Evidence for the appearance of high-valent ferryl-oxo species could be observed with the help of differences in the peak properties of oxidation-state sensitive Raman modes. To support those findings, the relaxed ground-state structures of ten possible covalent mono- and di-meso(Cm)-alkylated hematin-dihydroartemisinyl complexes were calculated using density functional theory. A very good agreement with the experimental peak properties was achieved, and the out-of-plane displacements along the lowest-frequency normal coordinates were investigated by normal coordinate structural decomposition analysis. The strongest changes in all data were observed in vibrations with a high participation of Cm-parts of β-hematin.
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Affiliation(s)
- Robert Domes
- Leibniz
Institute of Photonic Technology, Albert Einstein Strasse 9, D-07745 Jena, Germany
| | - Torsten Frosch
- Biophotonics and
Biomedical Engineering Group, Technical
University Darmstadt, Merckstraße 25, 64283 Darmstadt, Germany
- Leibniz
Institute of Photonic Technology, Albert Einstein Strasse 9, D-07745 Jena, Germany
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2
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Krumsieck J, Bröring M. PorphyStruct: A Digital Tool for the Quantitative Assignment of Non-Planar Distortion Modes in Four-Membered Porphyrinoids. Chemistry 2021; 27:11580-11588. [PMID: 34061410 PMCID: PMC8453524 DOI: 10.1002/chem.202101243] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Indexed: 11/20/2022]
Abstract
PorphyStruct, a new digital tool for the analysis of non‐planar distortion modes of different porphyrinoids, and its application to corrole structures is reported. The program makes use of the normal‐coordinate structure decomposition technique (NSD) and employs sets of normal modes equivalent to those established for porphyrins in order to describe the out‐of‐plane dislocation pattern of perimeter atoms from corroles, norcorroles, porphycenes and other porphyrinoids quantitatively and in analogy to the established terminology. A comparative study of 17 porphyrin structures shows very similar results to the original NSD analysis and no systematic error. Application to corroles is successful and reveals the necessity to implement an extended basis of normal modes for a large share of experimental structures. The results frequently show the concomitant occurence of several modes but remain interpretable. For group XI metal corroles the phenomenon of supersaddling was unravelled, allowing for more in‐depths discussions of structure‐function correlations.
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Affiliation(s)
- Jens Krumsieck
- Institute for Inorganic and Analytical Chemistry, TU Braunschweig, Hagenring 30, 38102, Braunschweig, Germany
| | - Martin Bröring
- Institute for Inorganic and Analytical Chemistry, TU Braunschweig, Hagenring 30, 38102, Braunschweig, Germany
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3
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Thuita D, Guberman‐Pfeffer MJ, Brückner C. S
N
Ar Reaction Toward the Synthesis of Fluorinated Quinolino[2,3,4‐at]porphyrins. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Damaris Thuita
- Department of Chemistry University of Connecticut, Unit 3060 Storrs CT 06268-3060 U.S.A
| | - Matthew J. Guberman‐Pfeffer
- Department of Chemistry University of Connecticut, Unit 3060 Storrs CT 06268-3060 U.S.A
- Current address: Department of Molecular Biophysics and Biochemistry and the Microbial Science Institute Yale University New Haven CT 06520 U.S.A
| | - Christian Brückner
- Department of Chemistry University of Connecticut, Unit 3060 Storrs CT 06268-3060 U.S.A
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4
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Influence of heme c attachment on heme conformation and potential. J Biol Inorg Chem 2018; 23:1073-1083. [PMID: 30143872 DOI: 10.1007/s00775-018-1603-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
Heme c is characterized by its covalent attachment to a polypeptide. The attachment is typically to a CXXCH motif in which the two Cys form thioether bonds with the heme, "X" can be any amino acid other than Cys, and the His serves as a heme axial ligand. Some cytochromes c, however, contain heme attachment motifs with three or four intervening residues in a CX3CH or CX4CH motif. Here, the impacts of these variations in the heme attachment motif on heme ruffling and electronic structure are investigated by spectroscopically characterizing CX3CH and CX4CH variants of Hydrogenobacter thermophilus cytochrome c552. In addition, a novel CXCH variant is studied. 1H and 13C NMR, EPR, and resonance Raman spectra of the protein variants are analyzed to deduce the extent of ruffling using previously reported relationships between these spectral data and heme ruffling. In addition, the reduction potentials of these protein variants are measured using protein film voltammetry. The CXCH and CX4CH variants are found to have enhanced heme ruffling and lower reduction potentials. Implications of these results for the use of these noncanonical motifs in nature, and for the engineering of novel heme peptide structures, are discussed.
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5
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Hong J, Kelley MS, Shelby ML, Hayes DK, Hadt RG, Rimmerman D, Zhang X, Chen LX. The Nature of the Long-Lived Excited State in a Ni II Phthalocyanine Complex Investigated by X-Ray Transient Absorption Spectroscopy. CHEMSUSCHEM 2018; 11:2421-2428. [PMID: 29851241 DOI: 10.1002/cssc.201800777] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/24/2018] [Indexed: 06/08/2023]
Abstract
The nature of the photoexcited state of octabutoxy nickel(II) phthalocyanine (NiPcOBu8 ) with a 500 ps lifetime was investigated by X-ray transient absorption (XTA) spectroscopy. Previous optical, vibrational, and computational studies have suggested that this photoexcited state has a ligand-to-metal charge transfer (LMCT) nature. By using XTA, which provides unambiguous information on the local electronic and nuclear configuration around the Ni center, the nature of the excited state of NiPcOBu8 was reassessed. Using X-ray probe pulses from a synchrotron source, the ground- and excited-state X-ray absorption spectra of NiPcOBu8 were measured. Based on the results, we identified that the excited state exhibits spectral features that are characteristic of a Ni1, 3 (3dz2 ,3dx2-y2 ) state rather than a LMCT state with a transiently reduced Ni center. This state resembles the (d,d) state of nickel(II) tetramesitylphorphyrin. The XTA features are rationalized based on the inherent cavity sizes of the macrocycles. These results may provide useful guidance for the design of photocatalysts in the future.
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Affiliation(s)
- Jiyun Hong
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston IL, 60208, USA
| | - Matthew S Kelley
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston IL, 60208, USA
| | - Megan L Shelby
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston IL, 60208, USA
| | - Dugan K Hayes
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Ryan G Hadt
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Dolev Rimmerman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston IL, 60208, USA
| | - Xiaoyi Zhang
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Lin X Chen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston IL, 60208, USA
- Division of Chemical Sciences and Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
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6
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Sterically induced distortions of nickel(II) porphyrins – Comprehensive investigation by DFT calculations and resonance Raman spectroscopy. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2017.12.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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7
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Zhang Q, Zheng X, Kuang G, Wang W, Zhu L, Pang R, Shi X, Shang X, Huang X, Liu PN, Lin N. Single-Molecule Investigations of Conformation Adaptation of Porphyrins on Surfaces. J Phys Chem Lett 2017; 8:1241-1247. [PMID: 28248110 DOI: 10.1021/acs.jpclett.7b00007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The porphyrin macrocyclic core features dynamic conformational transformations in free space because of its structural flexibility. Once attached to a substrate, the molecule-substrate interaction often restricts this flexibility and stabilizes the porphyrin in a specific conformation. Here using molecular dynamic and density-functional theory simulations and scanning tunneling microscopy and spectroscopy, we investigated the conformation relaxation and stabilization processes of two porphyrin derivatives (5,15-dibromophenyl-10,20-diphenylporphyrin, Br2TPP, and 5,15-diphenylporphyrin, DPP) adsorbed on Au(111) and Pb(111) surfaces. We found that Br2TPP adopts either dome or saddle conformations on Au(111) but only the saddle conformation on Pb(111), whereas DPP deforms to a ruffled conformation on Au(111). We also resolved the structural transformation pathway of Br2TPP from the free-space conformations to the surface-anchored conformations. These findings provide unprecedented insights revealing the conformation adaptation process. We anticipate that our results may be useful for controlling the conformation of surface-anchored porphyrin molecules.
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Affiliation(s)
- Qiushi Zhang
- Department of Physics, The Hong Kong University of Science and Technology , Hong Kong, China
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction , Hong Kong, China
| | - Xiaoyan Zheng
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction , Hong Kong, China
- Department of Chemistry, The Hong Kong University of Science and Technology , Hong Kong, China
| | - Guowen Kuang
- Department of Physics, The Hong Kong University of Science and Technology , Hong Kong, China
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction , Hong Kong, China
| | - Weihua Wang
- Department of Physics, The Hong Kong University of Science and Technology , Hong Kong, China
| | - Lizhe Zhu
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction , Hong Kong, China
- Department of Chemistry, The Hong Kong University of Science and Technology , Hong Kong, China
| | - Rui Pang
- Department of Physics, South University of Science and Technology of China , Nanshan District, Shenzhen, Guangdong 518055, China
| | - Xingqiang Shi
- Department of Physics, South University of Science and Technology of China , Nanshan District, Shenzhen, Guangdong 518055, China
| | - Xuesong Shang
- Shanghai Key Laboratory of Functional Materials Chemistry and Institute of Fine Chemicals, East China University of Science and Technology , Meilong Road 130, Shanghai, China
| | - Xuhui Huang
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction , Hong Kong, China
- Department of Chemistry, The Hong Kong University of Science and Technology , Hong Kong, China
| | - Pei Nian Liu
- Shanghai Key Laboratory of Functional Materials Chemistry and Institute of Fine Chemicals, East China University of Science and Technology , Meilong Road 130, Shanghai, China
| | - Nian Lin
- Department of Physics, The Hong Kong University of Science and Technology , Hong Kong, China
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction , Hong Kong, China
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8
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Noori M, Aragonès AC, Di Palma G, Darwish N, Bailey SWD, Al-Galiby Q, Grace I, Amabilino DB, González-Campo A, Díez-Pérez I, Lambert CJ. Tuning the electrical conductance of metalloporphyrin supramolecular wires. Sci Rep 2016; 6:37352. [PMID: 27869128 PMCID: PMC5116753 DOI: 10.1038/srep37352] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/21/2016] [Indexed: 12/29/2022] Open
Abstract
In contrast with conventional single-molecule junctions, in which the current flows parallel to the long axis or plane of a molecule, we investigate the transport properties of M(II)-5,15-diphenylporphyrin (M-DPP) single-molecule junctions (M=Co, Ni, Cu, or Zn divalent metal ions), in which the current flows perpendicular to the plane of the porphyrin. Novel STM-based conductance measurements combined with quantum transport calculations demonstrate that current-perpendicular-to-the-plane (CPP) junctions have three-orders-of-magnitude higher electrical conductances than their current-in-plane (CIP) counterparts, ranging from 2.10−2 G0 for Ni-DPP up to 8.10−2 G0 for Zn-DPP. The metal ion in the center of the DPP skeletons is strongly coordinated with the nitrogens of the pyridyl coated electrodes, with a binding energy that is sensitive to the choice of metal ion. We find that the binding energies of Zn-DPP and Co-DPP are significantly higher than those of Ni-DPP and Cu-DPP. Therefore when combined with its higher conductance, we identify Zn-DPP as the favoured candidate for high-conductance CPP single-molecule devices.
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Affiliation(s)
- Mohammed Noori
- Department of Physics, Lancaster University, Lancaster, LA1 4YB, UK.,Department of Physics, Collage of Science, Thi-Qar University, Iraq
| | - Albert C Aragonès
- Department of Physical Chemistry, University of Barcelona, Diagonal 645, Spain.,Institute for Bioengineering of Catalonia (IBEC) Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain.,Centro Investigación Biomédica en Red (CIBER-BBN). Campus Río Ebro-Edificio I+D, Poeta Mariano Esquillor s/n, 50018 Zaragoza, Spain
| | - Giuseppe Di Palma
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus Universitari, 08193 Bellaterra, Catalonia, Spain
| | - Nadim Darwish
- Department of Physical Chemistry, University of Barcelona, Diagonal 645, Spain.,Institute for Bioengineering of Catalonia (IBEC) Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain
| | | | - Qusiy Al-Galiby
- Department of Physics, Lancaster University, Lancaster, LA1 4YB, UK.,Physics Department, College of Education, Al-Qadisiyah University, Iraq
| | - Iain Grace
- Department of Physics, Lancaster University, Lancaster, LA1 4YB, UK
| | - David B Amabilino
- School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Arántzazu González-Campo
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus Universitari, 08193 Bellaterra, Catalonia, Spain
| | - Ismael Díez-Pérez
- Department of Physical Chemistry, University of Barcelona, Diagonal 645, Spain.,Institute for Bioengineering of Catalonia (IBEC) Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain.,Centro Investigación Biomédica en Red (CIBER-BBN). Campus Río Ebro-Edificio I+D, Poeta Mariano Esquillor s/n, 50018 Zaragoza, Spain
| | - Colin J Lambert
- Department of Physics, Lancaster University, Lancaster, LA1 4YB, UK
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9
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Schindler J, Kupfer S, Zedler L, Wächtler M, Gräfe S, Ryan AA, Senge MO, Dietzek B. Spectroelectrochemical Investigation of the One-Electron Reduction of Nonplanar Nickel(II) Porphyrins. Chemphyschem 2016; 17:3480-3493. [PMID: 27526952 DOI: 10.1002/cphc.201600698] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Indexed: 11/06/2022]
Abstract
The electrochemical reduction of a series of nickel porphyrins with an increasing number of substituents was investigated in acetonitrile. A one-electron reduction of [5,15-bis(1-ethylpropyl)porphyrinato]nickel(II) leads to π-anion radicals and to efficient formation of phlorin anions, presumably by disproportionation and subsequent protonation of the doubly reduced species. The phlorin anion was identified by using cyclic voltammetry and UV/Vis and resonance Raman spectroelectrochemistry, complemented by quantum-chemical calculations to assign the spectral signatures. The theoretical analysis of the potential-energy landscape of the singly reduced species suggests a thermally activated intersystem crossing that populates the quartet state and thus lowers the energy barrier towards disproportionation channels. Structure-reactivity correlations are investigated by considering different substitution patterns of the investigated nickel(II) porphyrin cores, that is, for the porphyrin with additional β-aryl ([5,15-bis(1-ethylpropyl)-2,8,12,18-tetra(p-tolyl)porphyrinato]nickel(II)) and meso-alkyl substitution ([5,10,15,20-tetrakis(1-ethylpropyl)porphyrinato]nickel(II)), no phlorin anion formation was observed under electrochemical conditions. This observation is correlated either to kinetic inhibition of the disproportionation reaction or to lower reactivity of the subsequently formed doubly reduced species towards protonation.
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Affiliation(s)
- Julian Schindler
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,Leibniz Institute of Photonic Technology Jena (IPHT), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Stephan Kupfer
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
| | - Linda Zedler
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,Leibniz Institute of Photonic Technology Jena (IPHT), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Maria Wächtler
- Leibniz Institute of Photonic Technology Jena (IPHT), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Stefanie Gräfe
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
| | - Aoife A Ryan
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Science Institute, 152-160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Mathias O Senge
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Science Institute, 152-160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Benjamin Dietzek
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,Leibniz Institute of Photonic Technology Jena (IPHT), Albert-Einstein-Straße 9, 07745, Jena, Germany
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10
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Senge MO, MacGowan SA, O'Brien JM. Conformational control of cofactors in nature - the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles. Chem Commun (Camb) 2016; 51:17031-63. [PMID: 26482230 DOI: 10.1039/c5cc06254c] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tetrapyrrole-containing proteins are one of the most fundamental classes of enzymes in nature and it remains an open question to give a chemical rationale for the multitude of biological reactions that can be catalyzed by these pigment-protein complexes. There are many fundamental processes where the same (i.e., chemically identical) porphyrin cofactor is involved in chemically quite distinct reactions. For example, heme is the active cofactor for oxygen transport and storage (hemoglobin, myoglobin) and for the incorporation of molecular oxygen in organic substrates (cytochrome P450). It is involved in the terminal oxidation (cytochrome c oxidase) and the metabolism of H2O2 (catalases and peroxidases) and catalyzes various electron transfer reactions in cytochromes. Likewise, in photosynthesis the same chlorophyll cofactor may function as a reaction center pigment (charge separation) or as an accessory pigment (exciton transfer) in light harvesting complexes (e.g., chlorophyll a). Whilst differences in the apoprotein sequences alone cannot explain the often drastic differences in physicochemical properties encountered for the same cofactor in diverse protein complexes, a critical factor for all biological functions must be the close structural interplay between bound cofactors and the respective apoprotein in addition to factors such as hydrogen bonding or electronic effects. Here, we explore how nature can use the same chemical molecule as a cofactor for chemically distinct reactions using the concept of conformational flexibility of tetrapyrroles. The multifaceted roles of tetrapyrroles are discussed in the context of the current knowledge on distorted porphyrins. Contemporary analytical methods now allow a more quantitative look at cofactors in protein complexes and the development of the field is illustrated by case studies on hemeproteins and photosynthetic complexes. Specific tetrapyrrole conformations are now used to prepare bioengineered designer proteins with specific catalytic or photochemical properties.
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Affiliation(s)
- Mathias O Senge
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland and Medicinal Chemistry, Institute of Molecular Medicine, Trinity Centre for Health Sciences, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland.
| | - Stuart A MacGowan
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Jessica M O'Brien
- Medicinal Chemistry, Institute of Molecular Medicine, Trinity Centre for Health Sciences, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland.
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11
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Soman R, Sujatha S, Arunkumar C. Structural elucidation and study of intermolecular interactions in meso-tetratolylporphyrins. J PORPHYR PHTHALOCYA 2016. [DOI: 10.1142/s1088424616501017] [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
Synthesis and crystal structure analysis of meso-tetratolylporphyrins, 1–5 combined with computational Hirshfeld surface analysis were investigated. The crystal packing of porphyrins 1, 3 and 4 are arranged in an “orthogonal fashion” whereas 2 and 5 are in a “slip-stack or off-set fashion” through various intermolecular interactions. Compound 2 exhibits saddle geometry whereas 5 showed a domed geometry as evident from the single crystal X-ray diffraction studies. The enhancement of non-planarity in 2 is probably due to the presence of numerous intermolecular interactions caused by the presence of trifluoroacetate anions on both faces of the porphyrin in addition to the bulky bromine groups at the [Formula: see text]-pyrrole positions. In 5, the non-planarity is merely due to the metal coordination at the porphyrin core as pentacoordinated Mn[Formula: see text] center with a chloro ligand in the axial position. Hirshfeld surface analysis was performed in order to analyze the various intermolecular interactions present in these porphyrins and the result was discussed.
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Affiliation(s)
- Rahul Soman
- Bioinorganic Materials Research Laboratory, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673 601, India
| | - Subramaniam Sujatha
- Bioinorganic Materials Research Laboratory, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673 601, India
| | - Chellaiah Arunkumar
- Bioinorganic Materials Research Laboratory, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673 601, India
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12
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Conformational and structural studies of meso monosubstituted metalloporphyrins—Edge-on molecular interactions of porphyrins in crystals. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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van der Salm H, Wagner P, Wagner K, Officer DL, Wallace GG, Gordon KC. Flexible Tuning of Unsaturated β-Substituents on Zn Porphyrins: A Synthetic, Spectroscopic and Computational Study. Chemistry 2015; 21:15622-32. [DOI: 10.1002/chem.201501938] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Indexed: 11/07/2022]
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14
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Koo BT, Berard PG, Clancy P. A Kinetic Monte Carlo Study of Fullerene Adsorption within a Pc-PBBA Covalent Organic Framework and Implications for Electron Transport. J Chem Theory Comput 2015; 11:1172-80. [PMID: 26579766 DOI: 10.1021/ct501044u] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Two-dimensional covalent organic frameworks (COFs), with their predictable assembly into ordered porous crystalline materials, tunable composition, and high charge carrier mobility, offer the possibility of creating ordered bulk heterojunction solar cells given a suitable electron-transporting material to fill the pores. The photoconductive (hole-transporting) properties of many COFs have been reported, including the recent creation of a TT-COF/PCBM solar cell by Dogru et al. Although a prototype device has been fabricated, its poor solar efficiency suggests a potential issue with electron transport caused by the interior packing of the fullerenes. Such packing information is absent and cannot be obtained experimentally. In this paper, we use Kinetic Monte Carlo (KMC) simulations to understand the dominant pore-filling mechanisms and packing configurations of C60 molecules in a Pc-PBBA COF that are similar to the COF fabricated experimentally. The KMC simulations thus offer more realistic filling conditions than our previously used Monte Carlo (MC) techniques. We found persistently large separation distances between C60 molecules that are absent in the more tractable MC simulations and which are likely to hinder electron transport significantly. We attribute the looser fullerene packing to the existence of stable motifs with pairwise distances that are mismatched with the underlying adsorption lattice of the COF. We conclude that larger pore COFs may be necessary to optimize electron transport and hence produce higher efficiency devices.
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Affiliation(s)
- Brian T Koo
- School of Chemical and Biomolecular Engineering, Cornell University , Ithaca, New York 14850, United States
| | - Philip G Berard
- School of Chemical and Biomolecular Engineering, Cornell University , Ithaca, New York 14850, United States
| | - Paulette Clancy
- School of Chemical and Biomolecular Engineering, Cornell University , Ithaca, New York 14850, United States
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15
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Suzuki M, Ishii S, Hoshino T, Neya S. Syntheses of Highly Distorted meso-Trifluoromethyl-substituted β-Octaalkylporphyrins. CHEM LETT 2014. [DOI: 10.1246/cl.140561] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Masaaki Suzuki
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Shuto Ishii
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Saburo Neya
- Graduate School of Pharmaceutical Sciences, Chiba University
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Shelby ML, Mara MW, Chen LX. New insight into metalloporphyrin excited state structures and axial ligand binding from X-ray transient absorption spectroscopic studies. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.05.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Ishida T, Aono S. A model theoretical study on ligand exchange reactions of CooA. Phys Chem Chem Phys 2013; 15:6139-48. [DOI: 10.1039/c3cp43253j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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18
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Senge MO. [5,15-Bis(2-methyl-prop-yl)porphyrinato]nickel(II). Acta Crystallogr Sect E Struct Rep Online 2012; 68:m1191-2. [PMID: 22969482 PMCID: PMC3435609 DOI: 10.1107/s1600536812035726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 08/14/2012] [Indexed: 12/03/2022]
Abstract
The title compound, [Ni(C(28)H(28)N(4))], crystallizes with two independent mol-ecules in the unit cell, one of which is located on an inversion center. Both macrocycles exhibit a planar conformation with average deviation from the least-squares-plane of the 24 macrocycle atoms of Δ24 = 0.043 Å for the first mol-ecule and 0.026 Å for the mol-ecule located on an inversion center. The average Ni-N bond lengths are 1.955 (2) and 1.956 (2) Å in the two mol-ecules. The mol-ecules form π-π dimers of inter-mediary strength with a mean plane separation of 3.36 (2) Å.
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Affiliation(s)
- Mathias O Senge
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, Dublin 2, Ireland
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19
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Abstract
An overview of the use of classical mechanical molecular simulations of porphyrins, hydroporphyrins and heme proteins is given. The topics cover molecular mechanics calculations of structures and conformer energies of porphyrins, energies of barriers for interconversion between stable conformers, molecular dynamics of porphyrins and heme proteins, and normal-coordinate structural analysis of experimental and calculated porphyrin structures. Molecular mechanics and dynamics are currently a fertile area of research on porphyrins. In the future, other computational methods such as Monte Carlo simulations, which have yet to be applied to porphyrins, will come into use and open new avenues of research into molecular simulations of porphyrins.
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Affiliation(s)
- JOHN A. SHELNUTT
- Biomolecular Materials and Interfaces Department, Sandia National Laboratories, Albuquerque, NM 87185-1349, USA
- Department of Chemistry, The University of New Mexico, Albuquerque, NM 87131, USA
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20
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Haddad R, Lu Y, Quirke JME, Berget P, Sun L, Fettinger JC, Leung K, Qiu Y, Schore NE, van Swol F, Medforth CJ, Shelnutt JA. Steric bulkiness of pyrrole substituents and the out-of-plane deformations of porphyrins: nickel(II) octaisopropylporphyrin and its meso-nitro derivative. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424611003707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sterically bulky substituents at the β-carbons of the pyrrole rings of porphyrins are sufficient to cause large out-of-plane porphyrin distortions even in the absence of substituent groups at the meso carbons. It is well established that substituents at the meso-positions only or at both the β-pyrrole and the meso-positions are sufficiently bulky to result in large non-planar distortions of the macrocycle. However, no systematic studies of the effects of bulky β-pyrrole substituents alone have been reported. Herein, molecular simulations and X-ray crystallography of nickel(II) 2,3,7,8,12,13,17,18-octa(isopropyl)porphyrin reveal that large out-of-plane distortions (>1.5 Å) are induced by the steric repulsion of the β-isopropyl groups but fail to lead to a single strongly energetically favored conformer. The molecular simulations indicate that multiple conformers differing in the orientation of the isopropyl groups and the macrocycle conformation coexist in solution and this is confirmed by resonance Raman spectroscopy. Large downshifts in the structure-sensitive lines result from the non-planar distortion, and line broadenings result from structural heterogeneity. The heterogeneity originates from tradeoffs between energy contributions from steric repulsion and macrocycle distortion. Simulations for 5-nitro-2,3,7,8,12,13,17,18-octa(isopropyl)porphyrin suggest two possible orientations of the nitro group with respect to the macrocycle mean plane — one nearly vertical (as in the crystal structure) and another that is nearly parallel. INDO/S semiempirical calculations indicate an orbital of the NO2 group resides between the porphyrin frontier orbitals with significant mixing of the nitro and porphyrin orbitals.KEYWORDS: porphyrin, non-planar, resonance Raman, X-ray crystallography, crystal structure, isopropyl, nitro, conformer, molecular mechanics, molecular simulations, density functional theory, steric crowding, conformational heterogeneity.
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Affiliation(s)
- Raid Haddad
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, NM 87185-1349, USA
- Departments of Chemistry & Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - Yi Lu
- Departments of Chemistry & Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - J. Martin E. Quirke
- Department of Chemistry, Florida International University, Miami, FL 33199, USA
| | - Patrick Berget
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Lisong Sun
- Departments of Chemistry & Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | | | - Kevin Leung
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, NM 87185-1349, USA
| | - Yan Qiu
- Departments of Chemistry & Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - Neil E. Schore
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Frank van Swol
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, NM 87185-1349, USA
- Departments of Chemistry & Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - Craig J. Medforth
- Departments of Chemistry & Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - John A. Shelnutt
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, NM 87185-1349, USA
- Department of Chemistry, University of Georgia, Athens, GA 30607, USA
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21
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Valicsek Z, Lendvay G, Horváth O. Equilibrium, photophysical, photochemical and quantum chemical examination of anionic mercury(I) porphyrins. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424609001261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Hg22+ ion and 5,10,15,20-tetrakis(parasulphonato-phenyl)porphyrin anion can form 2:1 (2 clusters:1 porphyrin) and 2:2 complexes, while the formation of the 1:1 species is not observable: it is only an intermediate, similarly to the cases of other large metal ions of small charge-density. The differences between mercury(I) and mercury(II) porphyrins in the composition of monoporphyrins (2:1 vs. 1:1), in the stability and the Soret absorption based on the arrangement of 2:2 complexes (asymmetric vs. probably symmetric sandwich-structure), in the kinetic behavior (molecularities and the special dimerization of HgIIP4-), in the product of the photoinduced dissociations of 2:2 bisporphyrins (free-base ligand vs. 1:1 complex) can prove that no mercury(II) porphyrins can form due to the possible disproportion of dimercury(I) ions. However, the similarities in the absorption, photophysical and photochemical features (also to other out-of-plane metalloporphyrins) suggest that the out-of-plane position of metal center and the distorted structure of complexes may be responsible for these common properties, the so-called sitting-atop characteristics. Moreover, the calculated structural data of the theoretically studied 1:1 mercury(I) porphyrin are very similar to those of Hg II P as a consequence of the charge separation in the cluster based on the strength of metal-nitrogen bonds. In the case of the 2:2 species, neither the increased distance (because of the Hg-Hg bond), nor the absence of 45° rotation of the two ligands can significantly modify the π-π interaction because its both measured and calculated absorption spectra are similar to those of Hg II2 P 2.
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Affiliation(s)
- Zsolt Valicsek
- Department of General and Inorganic Chemistry, Institute of Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - György Lendvay
- Department of General and Inorganic Chemistry, Institute of Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
- Institute of Structural Chemistry, Chemical Research Center, Hungarian Academy of Sciences, P.O. Box 17, H-1525 Budapest, Hungary
| | - Ottó Horváth
- Department of General and Inorganic Chemistry, Institute of Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
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Zakavi S, Rahiminezhad H, Alizadeh R. Hydrogen bond controlled adduct formation of meso-tetra(4-sulfonatophenyl)porphyrin with protic acids: a UV-vis spectroscopic study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 77:994-997. [PMID: 20863746 DOI: 10.1016/j.saa.2010.08.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 08/22/2010] [Accepted: 08/23/2010] [Indexed: 05/29/2023]
Abstract
Interaction of meso-tetra(4-sulfonatophenyl)porphyrin (H2tppS4) with weak and strong protic acid have been studied by UV-vis spectroscopy in water, dichloromethane and methanol. Different shifts of the Soret and Q(0,0) bands in the three solvents, the aggregation of diprotonated species and the stability of porphyrin-acid adducts in the solution, may be explained by the inter- and intramolecular hydrogen bonds. Whilst, the addition of excess amounts of tetra-n-butylammonium chloride to H2tppS4(Cl)2 in dichloromethane has little to no effect on the UV-vis spectrum of the dication, gradual addition of tetra-n-butylammonium hydrogen sulfate to the dichloromethane solution of H2tppS4(H2SO4)2 leads to the degradation of adducts and the release of porphryin. The results of this study clearly show the crucial role played by hydrogen bonds between the porphyrin diprotonated species and the counter ion in the stability of porphyrin diacids in solution.
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Affiliation(s)
- Saeed Zakavi
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Gava Zang, Zanjan 45137-66731, Iran.
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23
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Zhang YH, Zhao W, Jiang P, Zhang LJ, Zhang T, Wang J. Structural parameters and vibrational spectra of a series of zinc meso-phenylporphyrins: a DFT and experimental study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 75:880-890. [PMID: 20042362 DOI: 10.1016/j.saa.2009.12.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 10/14/2009] [Accepted: 12/07/2009] [Indexed: 05/28/2023]
Abstract
The influences of meso-phenyl substitution on the geometric structure and vibrational spectra have been studied by DFT calculation (B3LYP/6-31G(d)) and experiment on a series of zinc porphyrins (ZnTPP: zinc 5,10,15,20-tetraphenylporphyrin; ZnTrPP: zinc 5,10,15-triphenylporphryin; ZnDPP: zinc 5,15-dipenylporphyirn; ZnMPP: zinc 5-monophenylporphyrin; ZnP: zinc porphine). Calculation indicates that meso-phenyl substitution gives rise to slight out-of-plane distortion but significant in-plane distortion, especially for the configuration around C(m) atom, to zinc porphyrin. The assignment of experimental vibrational spectra was proposed mainly on the basis of calculation. Different shifting tendency upon meso-phenyl substitution is observed for different structure-sensitive bands, such as the shifting of nu(2), nu(3), nu(6), and nu(8) modes toward higher frequencies and nu(4) and nu(28) modes toward lower frequencies, upon meso-phenyl substitution. This is attributed primarily to in-plane nuclear reorganization effect (IPNR), though the contribution from out-of-plane distortion cannot be excluded completely. Analysis on vibrational structure reveals that asymmetric meso-phenyl substitution, especially the 5,15-diphenyl substitution of ZnDPP, brings about asymmetric vibrational displacement, or even splitting of vibrational structure to normal modes involving mainly the motion of meso-C(m). This is ascribed to the reduction of symmetry of porphyrin skeleton caused by asymmetric meso-phenyl substitution.
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Affiliation(s)
- Ying-Hui Zhang
- Department of Chemistry, Nankai University, Weijin Road 94, Tianjin 300071, People's Republic of China.
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24
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Zhang YH, Zhao W, Wang J, Jiang P. Experimental and theoretical study on vibrational spectra of nickel and zinc complexes of 5,10-diphenylporphyrin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 75:499-506. [PMID: 20022802 DOI: 10.1016/j.saa.2009.09.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Revised: 08/13/2009] [Accepted: 09/12/2009] [Indexed: 05/28/2023]
Abstract
The vibrational spectra of nickel and zinc 5,10-diphenylporphyrin (NiDaPP and ZnDaPP) have been studied by density functional theory (B3LYP/6-31G(d)) and experimental measurement. The assignment of observed Raman and IR bands are proposed based on theoretical calculation. Theoretical study indicates that 5,10-diphenyl substitution together with out-of-plane distortion diversify the structure of four pyrrole rings and the environment around C(m) atoms, which lowers the symmetry of porphyrin skeleton and brings about some variation to vibrational spectra. The first is the activation of all normal modes both in Raman and IR spectra. The second is the lifting of original degenerate E(u) representation and its splitting into two A modes in NiDaPP (C(1) group point) and A'/A'' presentation in ZnDaPP (C(s) group point), respectively. Furthermore, one or both of the two split components, especially for some vibration involving the motion of C(m) atom, undergoes further mixing with original non-degenerate mode (A(1g), A(2g), B(1g), or B(2g)) of same vibration. This produces new modes involving only partial motion of original mode. Besides general increasing frequency of NiDaPP with respect to ZnDaPP, different vibrational structure is also indicated by calculation for some structure-sensitive bands, especially nu(8) mode that couples with gamma(6) mode and split into two modes for NiDaPP but not for ZnDaPP.
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Affiliation(s)
- Ying-Hui Zhang
- Department of Chemistry, Nankai University, Tianjin 300071, People's Republic of China.
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Le Moigne C, Picaud T, Boussac A, Loock B, Momenteau M, Desbois A. Redox effects on the coordination geometry and heme conformation of bis(N-methylimidazole) complexes of superstructured Fe-porphyrins. A spectroscopic study. Inorg Chem 2010; 48:10084-92. [PMID: 19852518 DOI: 10.1021/ic9010604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electronic absorption, electron paramagnetic resonance (EPR), and Soret-excited resonance Raman (RR) spectra are reported for bis(N-alkylimidazole) complexes of various iron(III)-"basket-handle" (Fe(III)BHP(+)) and "picket-fence" (Fe(III)PFP(+)) porphyrins in methylene chloride. The Fe(III)BHP(+) derivatives consist of four cross-trans (CT) and two adjacent-cis (AC) -linked in which the composition and the length of the handles are variable (CT Fe(III)[(C(11)Im)(2)(+)], CT and AC Fe(III)[((C(4))(2)phi)(2)](+), CT Fe(III)[((C(3))(2)phi)(C(12))](+), CT and AC Fe(III)[((C(3))(2)phi)(2)](+)). The meso-alphaalpha betabeta and meso-alphabeta alphabeta atropisomers of Fe(III)-tetrakis(o-pivalamidophenyl)-porphyrins represents the Fe(III)PFP(+) derivatives (Fe(III)alphaalpha betabeta-T(piv)PP(+) and Fe(III)alphabeta alphabeta-T(piv)PP(+), respectively). The absorption and RR data obtained for these ferric compounds were compared to those previously published for the homologous ferrous complexes (Picaud, T., Le Moigne, C., Loock, B., Momenteau, M. and Desbois, A. J. Am. Chem. Soc. 2003, 125, 11616 and Le Moigne, C., Picaud, T., Boussac, A., Loock, B., Momenteau, M. and Desbois, A. Inorg. Chem. 2003, 42, 6081). The Soret band position of the eight investigated ferric compounds is observed between 417 and 424 nm, indicating that none of the complexes possesses a planar heme. The EPR spectra show that most of the Fe(III)BHP(+) complexes and all the Fe(III)PFP(+) complexes are rhombic B-type hemichromes (g(max) = 2.86-2.96). Notable exceptions concern the bis(N-methylimidazole) complexes of two CT Fe(III)BHP(+). The Fe(III)BHP(+) with the shortest handles (Fe(III)[((C(3))(2)phi)(2)](+)) exhibits a g value at 2.80. When the handles are lengthened by two methylene units (Fe(III)[((C(3))(2)phi)(2)](+)), the EPR spectrum corresponds to a mixture of two "highly anisotropic low-spin " or "large g(max)" type I EPR signals, a major species at g = 3.17 and a minor species at g = 3.77. All these EPR data were converted in terms of dihedral angle formed by the rings of the axial ligands. The RR spectra of the Fe(III)BHP(+) and Fe(III)PFP(+) complexes exhibited variable frequencies for the structure-sensitive nu(2) and nu(8) lines (1558-1563 cm(-1) and 386-401 cm(-1), respectively). In considering the ability of the different superstructures to stabilize particular out-of-plane distortions, this vibrational information was analyzed in terms of heme structure through changes in core size and Fe-N(pyrrole) bond length, in relation to changes in coordination geometry. The bis(N-methylimidazole) complex of Fe(III)[((C(3))(2)phi)(2)](+) was found to be the most distorted with a strongly ruffled tetrapyrrole. Because of a handle asymmetry, the heme conformation of the bis(N-methylimidazole) complex of Fe(III)[((C(3))(2)phi)(C(12))](+) was deduced to be a composition of ruffled and domed structures. The heme structure of the other complexes is a mixture of ruffled and saddled or ruffled and waved conformations. Taking into account our previous data on the ferrous series, this investigation provides information about the reorganization of the heme structure upon iron oxidation. The general trend is a decrease of either the core-size, or the Fe-N(pyrrole) bond length, or both. However, we demonstrated that the heme superstructures precisely control the nature and the extent of the tetrapyrrole reshaping. These results point out similar possible effect in the heme proteins, considering both an analogy between porphyrin superstructures and amino acids forming the heme sites and the diversity of the heme environments in the proteins.
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Affiliation(s)
- Carole Le Moigne
- Service de Bioénergétique, Biologie Structurale et Mécanismes (SB2SM) et URA CNRS 2096, Institut de Biologie et Technologie de Saclay (iBiTec-S), CEA/Saclay, F-91191 Gif-sur-Yvette Cedex, France
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Li M, Neal TJ, Ehlinger N, Schulz CE, Scheidt WR. Inter-Ring Interactions in [Fe(TalkylP)(Cl)] (alkyl = ethyl, n-propyl, n-hexyl) Complexes: Control by meso-Substituted Groups. J PORPHYR PHTHALOCYA 2010; 14:115-122. [PMID: 20526455 PMCID: PMC2879655 DOI: 10.1142/s1088424610001714] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Syntheses, molecular structures and magnetic susceptibilities of three meso-substituted high-spin iron(III) porphyrinate complexes ([Fe(TEtP)(Cl)], [Fe(TPrP)(Cl)], and [Fe(THexP)(Cl)]) are described. It was determined that the inter-ring interactions within each dimeric unit change upon alteration of the alkyl groups at the meso-positions. Magnetic exchange couplings between iron centers of the dimers are in accord with the trends in structural inter-ring geometries. Crystal data for [Fe(TEtP)(Cl)]: a = 10.1710(5) Å, b = 11.309(3) Å, c = 12.170(3) Å, α = 91.774(9) °, β = 113.170(14) °, γ = 112.149(9) °, V = 1165.2(4) Å(3), triclinic, P1̄, Z = 2, R(1) = 0.0844 and ωR(2) = 0.2073 for observed data. Crystal data for [Fe([Fe(TPrP)(Cl)])(Cl)]: a = 13.040(2) Å, b = 15.221(2) Å, c = 14.6681(9) Å, β = 109.997(11) °, V = 2735.9(7) Å(3), monoclinic, P2(1)/n, Z = 4, R(1) = 0.0477 and ωR(2) = 0.1176 for observed data. Crystal data for [Fe(THexP)(Cl)]: a = 10.246(7) Å, b = 12.834(4) Å, c = 17.420(15) Å, α = 69.74(3) °, β = 87.52(4) °, γ, = 84.89(3) °, V = 2140(2) Å(3), triclinic, P1̄, Z = 2, R(1) = 0.1024 and ωR(2) = 0.2659 for observed data.
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Affiliation(s)
- Ming Li
- The Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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Chen LX, Zhang X, Wasinger EC, Lockard JV, Stickrath AB, Mara MW, Attenkofer K, Jennings G, Smolentsev G, Soldatov A. X-ray snapshots for metalloporphyrin axial ligation. Chem Sci 2010. [DOI: 10.1039/c0sc00323a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Li ZY, Lu TT, He TJ, Liu FC, Chen DM. Resonance Raman Study of AggregatedMeso-tetra(4-pyridinium)porphyrin Diacid. CHINESE J CHEM PHYS 2009. [DOI: 10.1088/1674-0068/22/04/346-352] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Valicsek Z, Lendvay G, Horváth O. Equilibrium, photophysical, photochemical, and quantum chemical examination of anionic mercury(II) mono- and bisporphyrins. J Phys Chem B 2008; 112:14509-24. [PMID: 18954102 DOI: 10.1021/jp804039s] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mercury(II) ion and 5,10,15,20-tetrakis(parasulfonato-phenyl)porphyrin anion can form 1:1, 2:2, and 3:2 (metal ion/porphyrin) out-of-plane (OOP) complexes, from which Hg2P2(8-) has not been identified until now. Identification of this species significantly promoted the confirmation of the composition and the precise elucidation of the equilibrium of Hg3P2(6-). Since the formation of each complex is too fast, their kinetic behavior was studied from the side of dissociation. The rate-determining step in dissociations, as well as in the formation of the 2:2 complex, that is, the dimerization of 1:1 complex, proved to be virtually first-order under these conditions, while the consecutive formations of HgP(4-) and Hg3P2(6-) are second-order reactions. The equilibria can be spectrophotometrically investigated because the Soret- as well as the Q-absorption bands of the free-base ligand are more and more red-shifted in the series of 1:1, 2:2, and 3:2 complexes, and the split of Q-bands disappears as the singlet-1 excited states become degenerate; in the case of bisporphyrins, the bands broaden, especially in the longer-wavelength region of the spectra. The quantum yield and the lifetime of S1-fluorescence from the macrocycle is decreased by the insertion of a mercury(II) ion due to distortion, and in bisporphyrins the luminescence totally ceases because their more complicated structure promotes other ways of energy dissipation. The lifetime of the triplet excited-state is also reduced by metalation. The transient absorption measured upon excitation of Hg3P2(6-) probably originates from Hg2P2(8-) formed by efficient photodissocation during the laser pulse. This photoinduced dissociation is characteristic to out-of-plane complexes, but in metallo-monoporphyrins it needs the energetically higher Soret-excitation; in bisporphyrins, it can take place during irradiation at the longer Q-wavelengths. Investigation of the intramolecular photoredox reactions has proved that for the increased efficiency of the indirect photoinduced LMCT, not the redox potential, but the position of the metal center is responsible. The two orders of magnitude higher photoredux quantum yield for the 3:2 complex, compared to that of the 2:2 species, can be explained by the repulsive effect of the inner mercury(II) ion pushing the other two farther out of the ligand cavity. In bisporphyrins the second excited states are photochemically more reactive than the first ones, while most of the photochemical processes of HgP(4-) originate from the first excited state. According to our quantum chemical calculations, the mercury(II) ion causes the expansion of the porphyrin-cavity; therefore its out-of-plane position is smaller than the value expected based on its ionic radius. In the hitherto unknown 2:2 dimer two 1:1 saucer-shaped monomers are kept together by secondary forces, mostly by pi-pi interaction, but their relative arrangement was not unequivocally determined by the two DFT functionals used. The arrangements with a symmetry axis or plane perpendicular to both rings are not favored; instead, the two monomers are shifted along the porphyrin planes, either in a Hg-P-Hg-P or a Hg-P-P-Hg order. Our time-dependent density functional theory (TD-DFT) calculations indicate that the electronic spectra are not very sensitive to the structure of the dimer, even though the environment of the porphyrin rings is quite different if one of the metal ions is between or outside of both macrocycles. The calculated spectral shifts agree only partially with the experimental data. The TD-DFT calculations suggest that the chromophores are not fully independent in the bisporphyrins and that the observed spectral shift cannot be uniquely assigned to the geometrical distortion of the porphyrin macrocyle.
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Affiliation(s)
- Zsolt Valicsek
- Department of General and Inorganic Chemistry, Institute of Chemistry, University of Pannonia, H-8201 Veszprem, P.O. Box 158, Hungary.
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31
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Zhang X, Wasinger EC, Muresan AZ, Attenkofer K, Jennings G, Lindsey JS, Chen LX. Ultrafast Stimulated Emission and Structural Dynamics in Nickel Porphyrins. J Phys Chem A 2007; 111:11736-42. [DOI: 10.1021/jp0751763] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaoyi Zhang
- Chemistry Division and X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Erik C. Wasinger
- Chemistry Division and X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Ana Z. Muresan
- Chemistry Division and X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Klaus Attenkofer
- Chemistry Division and X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Guy Jennings
- Chemistry Division and X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Jonathan S. Lindsey
- Chemistry Division and X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Lin X. Chen
- Chemistry Division and X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208
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32
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Interaction of para-substituted meso-tetraphenylporphyrins and meso-tetra(n-propyl)porphyrin with weak and strong carboxylic acids: A UV–Vis spectroscopic study. Polyhedron 2007. [DOI: 10.1016/j.poly.2006.12.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Mathai S, Smith TA, Ghiggino KP. Singlet oxygen quantum yields of potential porphyrin-based photosensitisers for photodynamic therapy. Photochem Photobiol Sci 2007; 6:995-1002. [PMID: 17721599 DOI: 10.1039/b705853e] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The singlet oxygen formation quantum yield (Phi(Delta)) for solutions of the di-cation, free-base and metallated forms of hematoporphyrin derivative (HpD), hematoporphyrin IX (Hp9) and a boronated protoporphyrin (BOPP) are reported using the method of direct detection of the characteristic phosphorescence following polychromatic excitation. Values of Phi(Delta) for the free-base form of all the porphyrins and the di-cation forms of Hp9 and HpD are in the range of 0.44 to 0.85 in the solvents investigated. Incorporation of zinc ions into the macrocycle reduces Phi(Delta) for all three porphyrins. BOPP facilitates the coordination of certain transition metals (Mn, Co and Cu) compared to Hp9 and HpD and results in a dramatic decrease in Phi(Delta). The experimental data suggest the introduction of low energy charge transfer states associated with the disruption of the planarity of the macrocyclic ring provides alternative non-radiative deactivation pathways. In BOPP, this non-planarity is augmented by the large closo-carborane peripheral substituent groups.
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Affiliation(s)
- Sean Mathai
- School of Chemistry, The University of Melbourne, VIC, 3010, Australia
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34
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Zhang YH, Li ZY, Wu Y, Zhu YZ, Zheng JY. DFT study on the geometric, electronic structure and Raman spectra of 5,15-diphenylporphine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2005; 62:83-91. [PMID: 16257697 DOI: 10.1016/j.saa.2004.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2004] [Revised: 10/30/2004] [Accepted: 12/04/2004] [Indexed: 05/05/2023]
Abstract
The ground state geometric, electronic structure and Raman spectra of 5,15-diphenylporphine (H(2)DPP) have been studied using B3LYP/6-31G(d) method and compared with that of well-studied free base porphine (H(2)P) and meso-tetraphenylporphine (H(2)TPP). Calculation shows that 5,15-substitution causes remarkable in-plane distortion, whereas the resulting out-of-plane distortion is negligible. The calculated electronic structure of H(2)DPP is consistent with the absorption spectra compared with H(2)P and H(2)TPP. The calculated vibrational frequencies of H(2)DPP scaled with a single factor of 0.971 agree well with experimental data (the rms error is 8.0 cm(-1)). The assignment of experimental Raman bands of H(2)DPP was discussed on the basis of theoretical calculation and the comparison with that of H(2)P and H(2)TPP. The splitting of some vibrational modes involving the motion of C(m) atom, such as nu(1), nu(8), and nu(10), was observed and was attributed to the diversification of the environment around C(m) atoms. As the shift of absorption peaks, the shift of some structure-sensitive Raman bands of H(2)DPP form that of H(2)TPP and H(2)P was attributed to the in-plane nuclear reorganization (IPNR) induced by phenyl-substitution, though the contribution of nonplanarity mechanism could not be excluded completely.
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Affiliation(s)
- Ying-Hui Zhang
- Department of Chemistry, Nankai University, Tianjin 300071, People's Republic of China.
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35
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Senge MO. Exercises in molecular gymnastics--bending, stretching and twisting porphyrins. Chem Commun (Camb) 2005:243-56. [PMID: 16391725 DOI: 10.1039/b511389j] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The functional versatility of tetrapyrroles as natural cofactors is related to their conformational flexibility where manipulation of the macrocycle conformation allows a fine-tuning of their physicochemical properties. This feature article gives a personal account of the synthesis and solid state structural characterization of highly substituted, non-planar porphyrins. Their conformational analysis identifies sterically strained tetrapyrroles as a versatile class of biomimetic compounds with tailor-made properties.
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Affiliation(s)
- Mathias O Senge
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland.
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36
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Medaković VB, Milcić MK, Bogdanović GA, Zarić SD. C-H. . .pi interactions in the metal-porphyrin complexes with chelate ring as the H acceptor. J Inorg Biochem 2005; 98:1867-73. [PMID: 15522414 DOI: 10.1016/j.jinorgbio.2004.08.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Revised: 07/27/2004] [Accepted: 08/09/2004] [Indexed: 11/22/2022]
Abstract
Specific C-H. . .pi interactions with the pi-system of porphyrinato chelate ring were found in crystal structures of transition metal complexes from the Cambridge Structural Database and statistical analysis of geometrical parameters for intramolecular and intermolecular interactions was done. By density functional theory calculations on a model system it was evaluated that an interaction energy is above 1.5 kcal/mol and that the strongest interaction occurs when the distance between hydrogen atom and the center of the chelate ring is 2.6 A. This prediction is in good agreement with the distances for intermolecular interactions found in the crystal structures. In many cases the intramolecular interaction distances are much shorter than 2.6 A, and these short distances are caused by geometrical constrains. The C-H. . .pi interactions with chelate ring of porphyrinato ligand can influence the structure, contribute to its stability, and play some role in the function of biomolecules with metalo porphyrins.
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Affiliation(s)
- Vesna B Medaković
- Department of Chemistry, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia and Montenegro
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37
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Modified porphyrinoids from carbazates and hydrazones and the first crystal structure of a di-iminoporphodimethene. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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38
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Zhang YH, Ruan WJ, Li ZY, Wu Y, Zheng JY. DFT study on the influence of meso-phenyl substitution on the geometric, electronic structure and vibrational spectra of free base porphyrin. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2005.04.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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39
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Bondarenko V, Wang J, Kalish H, Balch AL, La Mar GN. Solution 1H NMR study of the accommodation of the side chain of n-butyl-etiohemin-I incorporated into the active site of cyano-metmyoglobin. J Biol Inorg Chem 2005; 10:283-93. [PMID: 15821940 DOI: 10.1007/s00775-005-0640-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Accepted: 03/01/2005] [Indexed: 11/24/2022]
Abstract
In order to identify the most readily deformable portion of the heme pocket in myoglobin, equine myoglobin was reconstituted with a meso-n-butyl substituent on centrosymmetric etiohemin-I. Solution 1H NMR data for the low-spin iron(III) cyanide complex of oxidized myoglobin that include 2D nuclear Overhauser enhancement spectroscopy contacts, paramagnetic relaxation, and dipolar shifts resulting from magnetic anisotropy show that the heme binds uniquely to the iron in a manner that arranges the methyl and ethyl substituents on a given pyrrole in a clockwise manner when viewed from the proximal side, and with the n-butyl group seated at the canonical alpha-meso position of native protohemin-IX. The butyl group is oriented sharply toward the proximal side and its protein contacts demonstrate that it is oriented largely into the "xenon hole" in myoglobin. The location of the n-butyl group on the proximal side near the vacancies places it within the region found to be most flexible in molecular dynamics simulation. A small, counterclockwise rotation of the pyrrole N-Fe-N vector of n-butyl-etiohemin-I relative to that for native protohemin, indicated by both the prosthetic group methyl contact shift pattern and the prosthetic group contacts to heme pocket residues, is proposed to allow the xenon hole to accommodate better the n-butyl group. In contrast to previous work, which showed that a bulky polar substituent on etiohemin-I preferentially seats at the canonical gamma-meso position, the nonpolar n-butyl group selects the alpha-meso position.
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Affiliation(s)
- Vasyl Bondarenko
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
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40
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Miljacic L, Sarkisov L, Ellis DE, Snurr RQ. Structural analysis of porphyrin molecular squares using molecular mechanics and density-functional methods. J Chem Phys 2004; 121:7228-36. [PMID: 15473790 DOI: 10.1063/1.1793951] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
"Molecular squares" formed from Re(CO)(3)Cl corners and porphyrin sides have potential applications as hosts for catalytic sites and as building blocks for membranes. In these materials, knowledge of the conformations of the squares is important. Molecular-mechanics (MM) and density-functional (DF) calculations have been used iteratively in this work to find the minimum-energy configurations of several porphyrin molecular squares. MM predicts that the steric and torsional interactions at connecting junctures of the square framework determine the overall geometry. Torsional degrees of freedom around these junctures were therefore analyzed using DF methods, giving further insight and helping choose among MM force-field options. Single-point DF calculations on the entire squares showed that the energy and conformation of the entire square could be reliably obtained by performing DF calculations on the critical elements of the square and then piecing them together. This "piecewise" strategy allows for both the major torsional motions and the most important local relaxations of large supramolecular species such as molecular squares.
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Affiliation(s)
- Ljubomir Miljacic
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA
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41
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Tsai HH(G, Simpson MC. Isolated Impact of Ruffling on the Vibrational Spectrum of Ni Porphyrins. Diagnosing Out-of-Plane Distortions. J Phys Chem A 2004. [DOI: 10.1021/jp036880w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hui-Hsu (Gavin) Tsai
- Center for Chemical Dynamics, Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - M. Cather Simpson
- Center for Chemical Dynamics, Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
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42
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Le Moigne C, Picaud T, Boussac A, Loock B, Momenteau M, Desbois A. Absorption and resonance Raman investigations of ligand rotation and nonplanar heme distortion in bis-base low-spin iron(II)-tetrakis(o-pivalamidophenyl)porphyrin complexes. Inorg Chem 2003; 42:6081-8. [PMID: 12971780 DOI: 10.1021/ic034449f] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The absorption and resonance Raman (RR) spectra of the bis-N-methylimidazole, bis-1,5-dicyclohexylimidazole, and bis-pyridine complexes of the meso-alphaalphabetabeta and meso-alphabetaalphabeta atropisomers of Fe(II)-tetrakis(o-pivalamidophenyl)porphyrins (Fe(II)TpivPP) were obtained in methylene chloride. The different spatial arrangements of the o-pivalamide pickets in these two Fe(II)TpivPP compounds are expected to control the absolute and relative positions of the axial ligand rings with respect to the Fe-N(pyrrole) bonds. In particular, the spectroscopic data obtained for the bis-N-methylimidazole and bis-dicyclohexylimidazole complexes of the Fe(II)[alphabetaalphabeta-TpivPP] derivative showed the most important differences. Redshifts of the B and Q absorption bands (+ 4-5 nm) as well as an upshift of the low frequency nu(8) RR mode (+ 5 cm(-)(1)) were observed. No shift of the skeletal high frequency modes was detected. These spectral effects were associated with a change in relative position of the axial imidazole rings from nearly parallel in the bis-N-methylimidazole complex to nearly perpendicular in the bis-dicyclohexylimidazole complex. On the basis of stereochemical considerations as well as previous spectroscopic investigations, the data were interpreted in terms of change in porphyrin structure from planar to saddled. Complementing to a parallel study on bis-base Fe(II) "basket handle" porphyrin complexes, this spectroscopic investigation provides an additional means to distinguish planar, ruffled, and saddled conformations for ferrous hemes included in proteins.
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Affiliation(s)
- Carole Le Moigne
- Département de Biologie Joliot-Curie, CEA et URA 2096, CEA/Saclay, F-91191 Gif-sur-Yvette Cedex, France
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43
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Medforth CJ, Haddad RE, Muzzi CM, Dooley NR, Jaquinod L, Shyr DC, Nurco DJ, Olmstead MM, Smith KM, Ma JG, Shelnutt JA. Unusual aryl-porphyrin rotational barriers in peripherally crowded porphyrins. Inorg Chem 2003; 42:2227-41. [PMID: 12665356 DOI: 10.1021/ic010958a] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previous studies of 5,10,15,20-tetraarylporphyrins have shown that the barrier for meso aryl-porphyrin rotation (DeltaG++(ROT)) varies as a function of the core substituent M and is lower for a small metal (M = Ni) compared to a large metal (M = Zn) and for a dication (M = 4H(2+)) versus a free base porphyrin (M = 2H). This has been attributed to changes in the nonplanar distortion of the porphyrin ring and the deformability of the macrocycle caused by the core substituent. In the present work, X-ray crystallography, molecular mechanics (MM) calculations, and variable temperature (VT) (1)H NMR spectroscopy are used to examine the relationship between the aryl-porphyrin rotational barrier and the core substituent M in some novel 2,3,5,7,8,10,12,13,15,17,18,20-dodecaarylporphyrins (DArPs), and specifically in some 5,10,15,20-tetraaryl-2,3,7,8,12,13,17,18-octaphenylporphyrins (TArOPPs), where steric crowding of the peripheral groups always results in a very nonplanar macrocycle. X-ray structures of DArPs indicate differences in the nonplanar conformation of the macrocycle as a function of M, with saddle conformations being observed for M = Zn, 2H or M = 4H(2+) and saddle and/or ruffle conformations for M = Ni. VT NMR studies show that the effect of protonation in the TArOPPs is to increase DeltaG++(ROT), which is the opposite of the effect seen for the TArPs, and MM calculations also predict a strikingly high barrier for the TArOPPs when M = 4H(2+). These and other findings suggest that the aryl-porphyrin rotational barriers in the DArPs are closely linked to the deformability of the macrocycle along a nonplanar distortion mode which moves the substituent being rotated out of the porphyrin plane.
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Affiliation(s)
- Craig J Medforth
- Department of Chemistry, University of California, Davis, California 95616, USA.
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44
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Renner MW, Barkigia KM, Melamed D, Gisselbrecht JP, Nelson NY, Smith KM, Fajer J. Conformational control of oxidation sites, spin states and orbital occupancy in nickel porphyrins. RESEARCH ON CHEMICAL INTERMEDIATES 2002. [DOI: 10.1163/15685670260469393] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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45
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Gruden M, Grubišić S, Coutsolelos A, Niketić S. Conformational analysis of octa- and tetrahalogenated tetraphenylporphyrins and their metal derivatives. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(01)00550-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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46
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Schweitzer-Stenner R, Lemke C, Haddad R, Qiu Y, Shelnutt JA, Quirke JME, Dreybrodt W. Conformational Distortions of Metalloporphyrins with Electron-Withdrawing NO2Substituents at Different Meso Positions. A Structural Analysis by Polarized Resonance Raman Dispersion Spectroscopy and Molecular Mechanics Calculations. J Phys Chem A 2001. [DOI: 10.1021/jp010936+] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Göller A, Clark T. SAM1 semiempirical calculations on the mechanism of cytochrome P450 metabolism. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(00)00810-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Zimmer M. Molecular mechanics evaluation of the proposed mechanisms for the degradation of urea by urease. J Biomol Struct Dyn 2000; 17:787-97. [PMID: 10798524 DOI: 10.1080/07391102.2000.10506568] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A thorough conformational search of all the conformations available to oxygen-bound urea within wild-type urease was carried out. Identical low energy urea conformations were obtained by a Ramachandran type plot for the NHis272-Ni1-O-Curea, and Ni1-O-Curea-Nurea dihedral angles. Ramachandran plots, with active sites and protonation states modified to model the different urease mechanisms, were used to evaluate the different mechanisms. Based upon the low energy conformations available to urea in the active site of wild-type urease one can conclude that the traditional "His320 acts as a base" mechanism is unlikely. while the N,O urea bridged and the reverse protonation mechanisms cannot be ruled out. A consensus hydrogen-bonding network that does not favor any of the mechanisms has been reconfirmed by the extensive conformational search.
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Affiliation(s)
- M Zimmer
- Chemistry Department, Connecticut College, New London 06320, USA.
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49
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Nemykin VN, Kobayashi N, Nonomura T, Luk’yanets EA. Low Symmetrical Phthalocyanines Having Spectroscopic and Electrochemical Properties Characteristic of Unexpected Accidental S1State Degeneracy and Non-Planar Distortions. CHEM LETT 2000. [DOI: 10.1246/cl.2000.184] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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50
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Csiki C, Zimmer M. A molecular mechanical analysis of the active site of urease with a special emphasis on determining the binding conformations available to oxygen-bound urea. J Biomol Struct Dyn 1999; 17:121-31. [PMID: 10496427 DOI: 10.1080/07391102.1999.10508346] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In order to model the active site of urease which contains two nickel ions with differing coordination geometries new parameters were derived for the AMBER* force field. These parameters were obtained by structure based optimization and use a single set of parameters with points on a sphere approach to model nickel(II) high-spin in all its coordination geometries. The force field was successfully used to model the active site of urease and to predict that a bridging water between the two nickel ions in urease was missing from the solid state structure of urease. A thorough conformational search was undertaken to find the conformations available to urea within urease. All the low energy conformations found were used to determine a consensus urea binding model.
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Affiliation(s)
- C Csiki
- Chemistry Department, Connecticut College, New London 06320, USA
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