Supramolecular structure of five-coordinate  [(4-methyl-2,6-dinitrophenolato)(octaethylporphinato)iron(III)] heme complex

Saifon A. Kohnhorst

doi:10.59796/jcst.V13N2.2023.1752

Authors

Saifon A. Kohnhorst Chemistry Program, Faculty of Science and Technology, Nakhon Ratchasima Rajabhat University, Nakhon Ratchasima 30000, Thailand

DOI:

https://doi.org/10.59796/jcst.V13N2.2023.1752

Keywords:

dinitrophenol, heme, hydrogen bond, Iron porphyrin, malaria, phenolate, supramolecular

Abstract

The crystallographic and spectroscopic characterization of the phenolate complex of [(4-methyl-2,6-dinitrophenolato)(2,3,7,8,12,13,17,18-octaethylporphinato)Fe(III)], [Fe^III(OEP)(DNOC)] is reported. The 4-methyl-2,6-dinitrophenol (DNOC) ligand was coordinating with the Fe^III(OEP) moiety through the phenylato-O-atom. The complex crystallizes in the triclinic P-1 with Z=2. The crystallographic information showed the average Fe—Np distance of 2.053(18) Å, with the Fe displacement from the 24 atoms porphyrin plane of 0.41(6) Å, and the Fe—O distance of 1.881(15) Å showing a five-coordinate square-pyramidal geometry. The characteristic of the formation of the Fe—O bond was found near 537 cm^-1 for IR spectra and the n₄ band was near 534 cm^-1 for Raman spectra. The major supramolecular interactions involved an intermolecular hydrogen bond C—H···O with a minimum distance of 2.732(5) Å, and the shortest plane-plane contact distance of 3.689(3) Å. The FT-IR characteristic showed the new band near 3400 cm^-1, which was broadened due to the formation of hydrogen bonds. The role of these weak C—H···O hydrogen bonds concerted to stabilized the crystal packing in the heme complex. Thus, the number of excellent hydrogen bond acceptors of the axial ligand contributes to its supramolecular structure.

References

Bernstein, J., Davis, R. E., Shimoni, L., & Chang, N.-L. (1995). Patterns in hydrogen bonding: Functionality and graph set analysis in Crystals. Angewandte Chemie International Edition in English, 34(15), 1555–1573. https://doi.org/10.1002/anie.199515551

Bhowmik, S., Dey, S., Sahoo, D., & Rath, S. P. (2013). Unusual stabilization of an intermediate spin state of iron upon the axial phenoxide coordination of a diiron(III)-bisporphyrin: Effect of heme-heme interactions. Chemistry - A European Journal, 19(41), 13732–13744. https://doi.org/10.1002/chem.201301242

Bondi, A. (1966). Van der Waals volumes and radii of metals in covalent compounds. The Journal of Physical Chemistry, 70(9), 3006–3007. https://doi.org/10.1021/j100881a503

Brémard, C., Kowalewski, P., Merlin, J. C., & Moreau, S. (1992). Resonance Raman enhancement of the oxo-bridged dinuclear iron center: Vibrational modes in iron(iii) physiological-type porphyrin complexes. Journal of Raman Spectroscopy, 23(6), 325–333. https://doi.org/10.1002/jrs.1250230603

Bruker. (2016). APEX4, SAINT and SADABS; Bruker AXS Inc.: Madison, WI, USA.

Bruker. (2021). SAINT V8.40B. Bruker AXS Inc. Madison, WI, USA.

Chaudhary, A., Patra, R., & Rath, S. P. (2010). Binding of catechols to iron(iii)–octaethylporphyrin: An experimental and DFT investigation. European Journal of Inorganic Chemistry, 2010(33), 5211–5221. https://doi.org/10.1002/ejic.201000707

Corwin, A. H. (1965). Porphyrins and metalloporphyrins; their general, physical and Coordination Chemistry, and laboratory methods. Journal of the Amarican Society, 87(5), 1154–1155. ttps://doi.org/10.1021/ja01083a061

Das, R. R. (1975). Absorption and emission spectral studies on the dimerization of free porphyrin and its zinc(ii), copper(ii) and nickel(ii) derivatives in aqueous solution. Journal of Inorganic and Nuclear Chemistry, 37(1), 153–157. https://doi.org/10.1016/0022-1902(75)80143-6

Dhifaoui, S., Hajji, M., Nasri, S., Guerfel, T., Daran, J. C., & Nasri, H. (2018b). A new high-spin iron(iii) bis(aqua) complex with the Meso-tetra(para-chlorophenyl)porphyrin: X-ray crystallography, Hirshfeld surface analysis, magnetic, EPR and electrochemical properties. Research on Chemical Intermediates, 44(12), 7259–7276. https://doi.org/10.1007/s11164-018-3555-1

Dhifaoui, S., Mchiri, C., Quatremare, P., Marvaud, V., Bujacz, A., & Nasri, H. (2018a). Molecular structure, magnetic properties, cyclic voltammetry of the low-spin iron(iii) bis(4-ethylaniline) complex with the para -chloro substituted Meso -tetraphenylporphyrin. Journal of Molecular Structure, 1153, 353–359. https://doi.org/10.1016/j.molstruc.2017.10.023

Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A., & Puschmann, H. (2009). OLEX2: a complete structure solution, refinement and analysis program. Journal of applied crystallography, 42(2), 339-341. https://doi.org/10.1107/s0021889808042726

Edwards, S. L., Xuong, N. H., Hamlin, R. C., & Kraut, J. (1987). Crystal structure of cytochrome c peroxidase compound I. Biochemistry, 26(6), 1503-1511. https://doi.org/10.1021/bi00380a002

Etter, M. C., MacDonald, J. C., & Bernstein, J. (1990). Graph-set analysis of hydrogen-bond patterns in organic crystals. Acta Crystallographica Section B: Structural Science, 46(2), 256-262. https://doi.org/10.1107/s0108768189012929

Facchin, A., Zerbetto, M., Gennaro, A., Vittadini, A., Forrer, D., & Durante, C. (2021). Oxygen Reduction Reaction at Single‐Site Catalysts: A Combined Electrochemical Scanning Tunnelling Microscopy and DFT Investigation on Iron Octaethylporphyrin Chloride on HOPG. ChemElectroChem, 8(15), 2825-2835. https://doi.org/10.1002/celc.202100543

Farrugia, L. J. (1997). ORTEP-3 for windows - a version of ORTEP-iii with a graphical user interface (GUI). Journal of Applied Crystallography, 30(5), 565–565. https://doi.org/10.1107/s0021889897003117

Hersleth, H.-P., Ryde, U., Rydberg, P., Görbitz, C. H., & Andersson, K. K. (2006). Structures of the high-valent metal-ion haem–oxygen intermediates in peroxidases, oxygenases and catalases. Journal of Inorganic Biochemistry, 100(4), 460–476. https://doi.org/10.1016/j.jinorgbio.2006.01.018

Hu, C., Noll, B. C., Schulz, C. E., & Scheidt, W. R. (2018). Hydrogen-bonding effects in five-coordinate high-spin imidazole-ligated iron(ii) porphyrinates. Inorganic Chemistry, 57(2), 793–803. https://doi.org/10.1021/acs.inorgchem.7b02744

Hu, S., Smith, K. M., & Spiro, T. G. (1996). Assignment of Protoheme Resonance Raman Spectrum by heme labeling in myoglobin. Journal of the American Chemical Society, 118(50), 12638–12646. https://doi.org/10.1021/ja962239e

Hübschle, C. B. (2011). ShelXle: A Qt graphical user interface for SHEXL. Acta Crystallographica Section A Foundations and Advances, 44, 1281-1284. https://doi.org/10.1107/S0021889811043202

Kanamori, D., Yamada, Y., Onoda, A., Okamura, T.-aki, Adachi, S., Yamamoto, H., & Ueyama, N. (2005). Structures and properties of octaethylporphinato(phenolate)iron(iii) complexes with NH⋯O hydrogen bonds: Modulation of Fe–O bond character by the hydrogen bond. Inorganica Chimica Acta, 358(2), 331–338. https://doi.org/10.1016/j.ica.2004.09.014

Kingsbury, C. J., & Senge, M. O. (2021). The shape of Porphyrins. Coordination Chemistry Reviews, 431, 213760. https://doi.org/10.1016/j.ccr.2020.213760

Kirkman, H. N., & Gaetani, G. F. (2007). Mammalian catalase: A venerable enzyme with New Mysteries. Trends in Biochemical Sciences, 32(1), 44–50. https://doi.org/10.1016/j.tibs.2006.11.003

Kohnhorst, S. A., & Haller, K. J. (2014). Chlorido(2,3,7,8,12,13,17,18-octaethylporphyrinato)iron(iii): A new triclinic polymorph of Fe(OEP)Cl. Acta Crystallographica Section C Structural Chemistry, 70(4), 368–374. https://doi.org/10.1107/s2053229614005002

Lee, H., Lee, D., Kim, I., Lee, E., & Jang, W.-D. (2020). Formation of supramolecular polymers from porphyrin tripods. Macromolecules, 53(18), 8060–8067. https://doi.org/10.1021/acs.macromol.0c01446

Macrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T., McCabe, P., Pidcock, E., ... & Wood, P. A. (2020). Mercury 4.0: From visualization to analysis, design and prediction. Journal of applied crystallography, 53(1), 226-235. https://doi.org/10.1107/s1600576719014092

Martin, D. J., Johnson, S. I., Mercado, B. Q., Raugei, S., & Mayer, J. M. (2020). Intramolecular electrostatic effects on O2, CO2, and acetate binding to a cationic iron porphyrin. Inorganic Chemistry, 59(23), 17402–17414. https://doi.org/10.1021/acs.inorgchem.0c02703

Mchiri, C., Dhifaoui, S., Ezzayani, K., Guergueb, M., Roisnel, T., Loiseau, F., & Nasri, H. (2019). Insights into the new cadmium(ii) metalloporphyrin: Synthesis, X-ray crystal structure, Hirshfeld surface analysis, photophysical and cyclic voltammetry characterization of the (morpholine){(meso-tetra(para-chloro-phenyl)porphyrinato}cadmium(ii). Polyhedron, 171, 10–19. https://doi.org/10.1016/j.poly.2019.06.055

Norvaiša, K., Flanagan, K. J., Gibbons, D., & Senge, M. O. (2019). Conformational RE‐engineering of porphyrins as receptors with switchable N−H⋅⋅⋅X‐type binding modes. Angewandte Chemie International Edition, 58(46), 16553–16557. https://doi.org/10.1002/anie.201907929

Norvaiša, K., Kielmann, M., & Senge, M. O. (2020). Porphyrins as colorimetric and photometric biosensors in modern bioanalytical systems. ChemBioChem, 21(13), 1793–1807. https://doi.org/10.1002/cbic.202000067

Norvaiša, K., Maguire, S., Donohoe, C., O'Brien, J. E., Twamley, B., Gomes‐da‐Silva, L. C., & Senge, M. O. (2021). Steric repulsion induced conformational switch in supramolecular structures. Chemistry – A European Journal, 28(4), e202103879. https://doi.org/10.1002/chem.202103879

Panyanon, C., Dungkaew, W., & Chainok, K. (2021, January). Synthesis and structural characterization of (Na6F(H2O)18[(VO4)2] •2H3O•2HF. Journal of Current Science and Technology, 11(1), 32-39. https://doi.org/10.14456/jcst.2021.6

Park, J. M., Hong, K.-I., Lee, H., & Jang, W.-D. (2021). Bioinspired applications of porphyrin derivatives. Accounts of Chemical Research, 54(9), 2249–2260. https://doi.org/10.1021/acs.accounts.1c00114

Puntharod, R. (2008). Synthesis and structural studies of malaria pigment model systems. [Doctroal dissertation, Suranaree University of Technology]. http://sutir.sut.ac.th:8080/jspui/handle/123456789/3385

Puntharod, R., Haller, K. J., Robertson, E. G., Gwee, E. S., Izgorodina, E. I., & Wood, B. R. (2017). An improved model for malaria pigment and β‐hematin: Fe(OEP)Picrate. Journal of Raman Spectroscopy, 48(9), 1148–1157. https://doi.org/10.1002/jrs.5176

Puntharod, R., Webster, G. T., Asghari-Khiavi, M., Bambery, K. R., Safinejad, F., Rivadehi, S., ... & Wood, B. R. (2010). Supramolecular interactions playing an integral role in the near-infrared Raman “excitonic” enhancement observed in β-hematin (malaria pigment) and other related heme derivatives. The Journal of Physical Chemistry B, 114(37), 12104-12115. https://doi.org/10.1021/jp102307s

Rani, J., Raveendran, A., Sushila, Chaudhary, A., Panda, M. K., & Patra, R. (2018). Polymorphism in Sn (IV)-tetrapyridyl porphyrins with a halogenated axial ligand: Structural, photophysical, and morphological study. Crystal Growth & Design, 18(3), 1437-1447. https://doi.org/10.1021/acs.cgd.7b01357

Sahoo, D., Quesne, M. G., de Visser, S. P., & Rath, S. P. (2015). Hydrogen-bonding interactions trigger a spin-flip in iron(III) porphyrin complexes. Angewandte Chemie International Edition, 54, 4796–4800. https://onlinelibrary.wiley.com/doi/10.1002/anie.201411399

Scheidt, W. R., & Lee, Y. J. (1987). Recent advances in the stereochemistry of metallotetrapyrroles. Structure and Bonding, 1–70. https://doi.org/10.1007/bfb0036789

Scheidt, W. R., Geiger, D. K., Lee, Y. J., Reed, C. A., & Lang, G. (1985). Characterization of five-coordinate mono (imidazole)(porphinato) iron (II) complexes. Journal of the American Chemical Society, 107(20), 5693-5699. https://doi.org/10.1021/ja00306a015

Sheldrick, G. M. (2015). Crystal structure refinement with SHELXL. Acta Crystallographica Section C Structural Chemistry, 71(1), 3–8. https://doi.org/10.1107/s2053229614024218

Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D., & Spackman, M. A. (2021). CrystalExplorer: A program for Hirshfeld Surface Analysis, visualization and quantitative analysis of molecular crystals. Journal of Applied Crystallography, 54(3), 1006–1011. https://doi.org/10.1107/s1600576721002910

Steiner, T. (2003). C–H···O hydrogen bonding in Crystals. Crystallography Reviews, 9(2-3), 177–228. https://doi.org/10.1080/08893110310001621772

Sujatha, S., & Arunkumar, C. (2016). Fluorinated porphyrinic crystalline solids: Structural elucidation and study of intermolecular interactions. Crystalline and Non-Crystalline Solids, 57. https://doi.org/10.5772/62946

Sumner, J. B. (1926). The isolation and crystallization of the enzyme urease. Journal of Biological Chemistry, 69(2), 435–441. https://doi.org/10.1016/s0021-9258(18)84560-4

Sumner, J. B., & Dounce, A. L. (1937). Crystalline catalase. Science, 85(2206), 366–367. https://doi.org/10.1126/science.85.2206.366

Uno, T., Hatano, K., Nishimura, Y., & Arata, Y. (1990). Spectrophotometric and resonance Raman studies on the formation of phenolate and thiolate complexes of (octaethylporphinato)iron(iii). Inorganic Chemistry, 29(15), 2803–2807. https://doi.org/10.1021/ic00340a018

Wang, Z., Johnson, S. I., Wu, G., & Ménard, G. (2021). Multiple N–H and C–H Hydrogen Atom Abstractions Through Coordination-Induced Bond Weakening at Fe-Amine Complexes. Inorganic Chemistry, 60(11), 8242-8251. https://doi.org/10.1021/acs.inorgchem.1c00923

Watanabe, Y., Nakajima, H., & Ueno, T. (2007). Reactivities of oxo and peroxo intermediates studied by hemoprotein mutants. ChemInform, 38(41). https://doi.org/10.1002/chin.200741272

Westrip, S. P. (2010). publcif: Software for editing, validating and formatting crystallographic information files. Journal of Applied Crystallography, 43(4), 920–925. https://doi.org/10.1107/s0021889810022120

Wood, B. R., Langford, S. J., Cooke, B. M., Glenister, F. K., Lim, J., & McNaughton, D. (2003). Raman imaging of Hemozoin within the food vacuole of plasmodium falciparum trophozoites. FEBS Letters, 554(3), 247–252. https://doi.org/10.1016/s0014-5793(03)00975-x

Wood, B. R., Langford, S. J., Cooke, B. M., Lim, J., Glenister, F. K., Duriska, M., Unthank, J. K., & McNaughton, D. (2004). Resonance Raman spectroscopy reveals new insight into the electronic structure of β-hematin and malaria pigment. Journal of the American Chemical Society, 126(30), 9233–9239. https://doi.org/10.1021/ja038691x