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American Mineralogist

Journal of Earth and Planetary Materials

Ed. by Baker, Don / Xu, Hongwu / Swainson, Ian


IMPACT FACTOR 2018: 2.631

CiteScore 2018: 2.55

SCImago Journal Rank (SJR) 2018: 1.355
Source Normalized Impact per Paper (SNIP) 2018: 1.103

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1945-3027
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Volume 102, Issue 5

Issues

Crystal structure of abelsonite, the only known crystalline geoporphyrin

Daniel R. Hummer / Bruce C. Noll / Robert M. Hazen / Robert T. Downs
Published Online: 2017-05-06 | DOI: https://doi.org/10.2138/am-2017-5927

Abstract

The crystal structure of the unique nickel porphyrin mineral abelsonite, NiC31H32N4, has been solved using direct methods with 2195 independent reflections to a final R1 = 0.0406. Abelsonite crystallizes in the triclinic space group P 1¯, with Z = 1 and unit-cell parameters a = 8.4416(5) Å, b = 10.8919(7) Å, c = 7.2749(4) Å, α = 90.465(2)°, β = 113.158(2)°, and γ = 78.080(2)° at the measurement condition of 100 K, in very good agreement with previous unit-cell parameters reported from powder diffraction. The structure consists of nearly planar, covalently bonded porphyrin molecules stacked approximately parallel to (1 1¯ 1), and held together by weak intermolecular Van der Waals forces. The molecules within a layer are slightly tilted such that molecular planes do not overlap, and an up-turned ethyl group on one molecule sits adjacent to a down-turned ethyl group on a neighboring molecule of the same layer. Layers are stacked along a vector normal to (1 1¯ 1) such that an aromatic ring at one corner of the molecule lies directly above the opposite aromatic ring of the molecule below. Although a single molecule does not quite possess 1¯ symmetry, matching ethyl groups at roughly opposite ends of the molecule enable orientational disorder, in which molecules can randomly adopt one of two different orientations while still stacking in the same manner. The aggregate of these two random orientations produces an overall symmetry of P 1¯.

Keywords: Abelsonite; crystal structure; porphyrin; geoporphyrin; organic; orientational disorder

References cited

  • Cheng, R.J., Chen, P.Y., Lovell, T., Liu, T., Noodleman, L., and Case, D.A. (2003) Symmetry and bonding in metalloporphyrins. A modern implementation for the bonding analysis of five- and six-coordinated high-spin iron(III)-porphyrin complexes through density functional calculation and NMR spectroscopy. Journal of the American Chemical Society, 125, 6774–6783.Google Scholar

  • Hazen, R.M., Hoering, T.C., and Hofmeister, A.M. (1987) Compressibility and high pressure phase transition of a metalloporphyrin: (5,10,15,20-Tetraphenyl-21H,23H-porphinato)cobalt(II). Journal of Physical Chemistry, 91, 5042–5045.Google Scholar

  • Hunter, S.C., Smith, B.A., Hoffmann, C.M., Wang, X., Chen, Y.S., McIntyre, G.J., and Xue, Z.L. (2014) Intermolecular interactions in solid-state metalloporphyrins and their impact on crystal and molecular structures. Inorganic Chemistry, 53, 11552–11562.Google Scholar

  • Mason, G.M., Trudell, L.G., and Branthaver, J.F. (1989) Review of the stratigraphic distribution and diagenetic history of abelsonite. Organic Geochemistry, 14, 585–594.Google Scholar

  • Milton, C., Dwornik, E.J., Estep-Barnes, P.A., Finkelman, R.B., Pabst, A., and Palmer, S. (1978) Abelsonite, nickel porphyrin, a new mineral from the Green River Formation, Utah. American Mineralogist, 63, 930–937.Google Scholar

  • Pettersen, R.C. (1969) The crystal and molecular structure of vanadyldeoxophylloerythroetioporphyrin-1,2-dichloroethane solvate: an analogue of chlorophyll. Acta Crystallographica, B25, 2527–2539.Google Scholar

  • Pettersen, R.C. (1971) Crystal structure of nickel(II) deoxophylloerythrin methyl ester 1,2-dichloroethane solvate. A carbocyclic porphyrin. Journal of the American Chemical Society, 93, 5629–5634.Google Scholar

  • Sheldrick, G.M. (2008) A short history of SHELX. Acta Crystallographica, A64, 112–122.Google Scholar

  • Sheldrick, G.M. (2015) Crystal structure refinement with SHELXL. Acta Crystallographica, C71, 3–8.Google Scholar

  • Stevens, E.D. (1981) Electronic structure of metalloporphyrins. 1. Experimental electron density distribution of (meso-tetraphenylporphinato)cobalt(II). Journal of the American Chemical Society, 103, 5087–5095.Google Scholar

  • Storm, C.B., Krane, J., Skjetne, T., Telnaes, N., Branthaver, J.F., and Baker, E.W. (1984) The structure of abelsonite. Science, 223, 1075–1076.Google Scholar

  • Trudell, L. (1970) Lithologic description of Western Oil Shale Corporation project Utah EX-1. Laramie Petroleum Research Center.Google Scholar

  • Zhang, B., and Lash, T.D. (2003) Total synthesis of the porphyrin mineral abelsonite and related petroporphyrins with five-membered exocyclic rings. Tetrahedron Letters, 44, 7253–7256.Google Scholar

About the article

* Present address: Department of Geology, Southern Illinois University, Carbondale, Illinois 62901, U.S.A.


Received: 2016-08-04

Accepted: 2017-01-24

Published Online: 2017-05-06

Published in Print: 2017-05-24


Citation Information: American Mineralogist, Volume 102, Issue 5, Pages 1129–1132, ISSN (Online) 1945-3027, ISSN (Print) 0003-004X, DOI: https://doi.org/10.2138/am-2017-5927.

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© 2017 by Walter de Gruyter Berlin/Boston.

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