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Reyes-Gasga J, Tehuacanero-Núñez S, Sánchez-Ochoa F. An approach to investigate the crystallographic unit cell of human tooth enamel. Acta Crystallogr B Struct Sci Cryst Eng Mater 2023; 79:399-407. [PMID: 37703288 DOI: 10.1107/s2052520623006777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/02/2023] [Indexed: 09/15/2023]
Abstract
Human tooth enamel (HTE) is the hardest tissue in the human body and its structural organization shows a hierarchical composite material. At the nanometric level, HTE is composed of approximately 97% hydroxyapatite [HAP, Ca10(PO4)6(OH)2] as inorganic phase, and of 3% as organic phase and water. However, it is still controversial whether the hexagonal HAP phase crystallizes in P63/m or another space group. The observance in HTE of Ca2+, Mg2+ and Na+ ions using X-ray characteristic energy-dispersive spectroscopy in the scanning electron microscope has been explained by substitutions in the HAP unit cell. Thus, Ca2+ can be replaced by Na+ and Mg2+ ions; the PO43- group can be replaced by CO32- ions; and the OH- ions can also be replaced by CO32-. A unit-cell model of the hexagonal structure of HTE is not fully defined yet. In this work, density functional theory calculations are performed to study the hexagonal HAP unit cell when substitution by OH-, CO32-, Mg2+ and Na+ ions are carried out. An approach is presented to study the crystallographic unit cell of HTE by examining the changes resulting from the inclusion of these different ions in the unit cell of HAP. Enthalpies of formation and crystallographic characteristics of the electron diffraction patterns are analysed in each case. The results show an enhancement in structural stability of HAP with OH defects, atomic substitution of Mg2+, carbonate and interstitial Na+. Simulated electron diffraction patterns of the generated structures show similar characteristics to those of human tooth enamel. Hence, the results explain the indiscernible structural changes shown in experimental X-ray diffractograms and electron diffraction patterns.
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Affiliation(s)
- Jose Reyes-Gasga
- Departamento Materia Condensada, Instituto de Física, Universidad Nacional Autónoma de México, Circuito de la Investigación, Cd. Universitaria, Mexico City, CDMX 04510, Mexico
| | - Samuel Tehuacanero-Núñez
- Departamento Materia Condensada, Instituto de Física, Universidad Nacional Autónoma de México, Circuito de la Investigación, Cd. Universitaria, Mexico City, CDMX 04510, Mexico
| | - Francisco Sánchez-Ochoa
- Departamento Materia Condensada, Instituto de Física, Universidad Nacional Autónoma de México, Circuito de la Investigación, Cd. Universitaria, Mexico City, CDMX 04510, Mexico
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Gorelik TE, Bekő SL, Teteruk J, Heyse W, Schmidt MU. Analysis of diffuse scattering in electron diffraction data for the crystal structure determination of Pigment Orange 13, C 32H 24Cl 2N 8O 2. Acta Crystallogr B Struct Sci Cryst Eng Mater 2023; 79:122-137. [PMID: 36920875 PMCID: PMC10088482 DOI: 10.1107/s2052520623000720] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/26/2023] [Indexed: 03/05/2023]
Abstract
The crystallographic study of two polymorphs of the industrial pyrazolone Pigment Orange 13 (P.O.13) is reported. The crystal structure of the β phase was determined using single-crystal X-ray analysis of a tiny needle. The α phase was investigated using three-dimensional electron diffraction. The electron diffraction data contain sharp Bragg reflections and strong diffuse streaks, associated with severe stacking disorder. The structure was solved by careful analysis of the diffuse scattering, and similarities of the unit-cell parameters with the β phase. The structure solution is described in detail and this provides a didactic example of solving molecular crystal structures in the presence of diffuse scattering. Several structural models were constructed and optimized by lattice-energy minimization with dispersion-corrected DFT. A four-layer model was found, which matches the electron diffraction data, including the diffuse scattering, and agrees with X-ray powder data. Additionally, five further phases of P.O.13 are described.
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Affiliation(s)
- Tatiana E Gorelik
- Ulm University, Central Facility of Electron Microscopy, Materials Science Electron Microscopy, Albert Einstein Allee 11, 89069 Ulm, Germany
| | - Sàndor L Bekő
- Goethe University, Institute of Inorganic and Analytical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Jaroslav Teteruk
- Goethe University, Institute of Inorganic and Analytical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Winfried Heyse
- Sanofi, R&D / PDP / TIDES Analytical Sciences, Building H770, 65926 Frankfurt am Main, Germany
| | - Martin U Schmidt
- Goethe University, Institute of Inorganic and Analytical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
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Schlesinger C, Fitterer A, Buchsbaum C, Habermehl S, Chierotti MR, Nervi C, Schmidt MU. Ambiguous structure determination from powder data: four different structural models of 4,11-di-fluoro-quinacridone with similar X-ray powder patterns, fit to the PDF, SSNMR and DFT-D. IUCrJ 2022; 9:406-424. [PMID: 35844476 PMCID: PMC9252154 DOI: 10.1107/s2052252522004237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/20/2022] [Indexed: 05/31/2023]
Abstract
Four different structural models, which all fit the same X-ray powder pattern, were obtained in the structure determination of 4,11-di-fluoro-quinacridone (C20H10N2O2F2) from unindexed X-ray powder data by a global fit. The models differ in their lattice parameters, space groups, Z, Z', molecular packing and hydrogen bond patterns. The molecules form a criss-cross pattern in models A and B, a layer structure built from chains in model C and a criss-cross arrangement of dimers in model D. Nevertheless, all models give a good Rietveld fit to the experimental powder pattern with acceptable R-values. All molecular geometries are reliable, except for model D, which is slightly distorted. All structures are crystallochemically plausible, concerning density, hydrogen bonds, intermolecular distances etc. All models passed the checkCIF test without major problems; only in model A a missed symmetry was detected. All structures could have probably been published, although 3 of the 4 structures were wrong. The investigation, which of the four structures is actually the correct one, was challenging. Six methods were used: (1) Rietveld refinements, (2) fit of the crystal structures to the pair distribution function (PDF) including the refinement of lattice parameters and atomic coordinates, (3) evaluation of the colour, (4) lattice-energy minimizations with force fields, (5) lattice-energy minimizations by two dispersion-corrected density functional theory methods, and (6) multinuclear CPMAS solid-state NMR spectroscopy (1H, 13C, 19F) including the comparison of calculated and experimental chemical shifts. All in all, model B (perhaps with some disorder) can probably be considered to be the correct one. This work shows that a structure determination from limited-quality powder data may result in totally different structural models, which all may be correct or wrong, even if they are chemically sensible and give a good Rietveld refinement. Additionally, the work is an excellent example that the refinement of an organic crystal structure can be successfully performed by a fit to the PDF, and the combination of computed and experimental solid-state NMR chemical shifts can provide further information for the selection of the most reliable structure among several possibilities.
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Affiliation(s)
- Carina Schlesinger
- Institute of Inorganic and Analytical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Arnd Fitterer
- Institute of Inorganic and Analytical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Christian Buchsbaum
- Institute of Inorganic and Analytical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Stefan Habermehl
- Institute of Inorganic and Analytical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Michele R. Chierotti
- Department of Chemistry and NIS centre, University of Torino, V. Giuria 7, Torino 10125, Italy
| | - Carlo Nervi
- Department of Chemistry and NIS centre, University of Torino, V. Giuria 7, Torino 10125, Italy
| | - Martin U. Schmidt
- Institute of Inorganic and Analytical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
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Schlesinger C, Hammer SM, Gorelik TE, Schmidt MU. Orientational disorder of monomethyl-quinacridone investigated by Rietveld refinement, structure refinement to the pair distribution function and lattice-energy minimizations. Acta Crystallogr B Struct Sci Cryst Eng Mater 2020; 76:353-365. [PMID: 32831256 DOI: 10.1107/s2052520620003984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/19/2020] [Indexed: 06/11/2023]
Abstract
The crystal structure of the organic pigment 2-monomethyl-quinacridone (Pigment Red 192, C21H14N2O2) was solved from X-ray powder diffraction data. The resulting average structure is described in space group P\overline 1, Z = 1 with the molecule on the inversion centre. The molecules are arranged in chains. The molecules, which have no inversion symmetry, show orientational head-to-tail disorder. In the average structure, the methyl group is disordered and found on both ends of the molecule with an occupancy of 0.5 each. The disorder and the local structure were investigated using various ordered structural models. All models were analysed by three approaches: Rietveld refinement, structure refinement to the pair distribution function (PDF) and lattice-energy minimization. All refinements converged well. The Rietveld refinement provided the average structure and gave no indication of a long-range ordering. The refinement to the PDF turned out to be very sensitive to small structural details, giving insight into the local structure. The lattice-energy minimizations revealed a significantly preferred local ordering of neighbouring molecules along the [0\bar 11] direction. In conclusion, all methods indicate a statistical orientational disorder with a preferred parallel orientation of molecules in one direction. Additionally, electron diffraction revealed twinning and faint diffuse scattering.
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Affiliation(s)
- Carina Schlesinger
- Institut für Anorganische und Analytische Chemie, Goethe Universität, Max-von-Laue-Strasse 7, Frankfurt am Main, 60438, Germany
| | - Sonja M Hammer
- Institut für Anorganische und Analytische Chemie, Goethe Universität, Max-von-Laue-Strasse 7, Frankfurt am Main, 60438, Germany
| | - Tatiana E Gorelik
- Central Facility for Electron Microscopy, Electron Microscopy Group of Materials Science (EMMS), Ulm University, Albert Einstein Allee 11, Ulm, 89081, Germany
| | - Martin U Schmidt
- Institut für Anorganische und Analytische Chemie, Goethe Universität, Max-von-Laue-Strasse 7, Frankfurt am Main, 60438, Germany
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Czech C, Kalinowsky L, Schmidt MU. Local structure and stacking disorder of chloro(phthalocyaninato)aluminium. Acta Crystallogr B Struct Sci Cryst Eng Mater 2017; 73:744-755. [PMID: 28762984 DOI: 10.1107/s2052520617005017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/31/2017] [Indexed: 06/07/2023]
Abstract
Chloro(phthalocyaninato)aluminium [(C32H16N8)AlCl, Pigment Blue 79] is a molecular compound which crystallizes in a layer structure with stacking disorder. Order-disorder theory was applied to analyse and explain the stacking disorder and to determine the symmetry operations, which generate subsequent layers from a given one. Corresponding ordered structural models were constructed and optimized by force field and dispersion-corrected density functional theory methods. The superposition of the four lowest-energy stackings lead to a structure in which every second double layer looks to be ordered; in the other double layers the molecules occupy one of two lateral positions. This calculated superposition structure agrees excellently with an (incomplete) experimental structure determined from single-crystal data. From the optimized ordered models, the stacking probabilities and the preferred local arrangements were derived. Packing effects such as the distortion of the molecules depending on the arrangement of neighbouring molecules could also be determined.
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Affiliation(s)
- Christian Czech
- Institut für Anorganische und Analytische Chemie der Goethe-Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Lena Kalinowsky
- Institut für Anorganische und Analytische Chemie der Goethe-Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Martin U Schmidt
- Institut für Anorganische und Analytische Chemie der Goethe-Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
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Teteruk JL, Glinnemann J, Gorelik TE, Linden A, Schmidt MU. Explanation of the stacking disorder in the β-phase of Pigment Red 170. Acta Crystallogr B Struct Sci Cryst Eng Mater 2014; 70:296-305. [PMID: 24675599 DOI: 10.1107/s2052520613031636] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 11/20/2013] [Indexed: 06/03/2023]
Abstract
The β-phase of Pigment Red 170, C26H22N4O4, which is used industrially for the colouration of plastics, crystallizes in a layer structure with stacking disorder. The disorder is characterized by a lateral translational shift between the layers with a component ty of either +0.421 or -0.421. Order-disorder (OD) theory is used to derive the possible stacking sequences. Extensive lattice-energy minimizations were carried out on a large set of structural models with different stacking sequences, containing up to 2688 atoms. These calculations were used to determine the actual local structures and to derive the stacking probabilities. It is shown that local structures and energies depend not only on the arrangement of neighbouring layers, but also next-neighbouring layers. Large models with 100 layers were constructed according to the derived stacking probabilities. The diffraction patterns simulated from those models are in good agreement with the experimental single-crystal and powder diffraction patterns. Electron diffraction investigation on a nanocrystalline industrial sample revealed the same disorder. Hence the lattice-energy minimizations are able to explain the disorder and the diffuse scattering.
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Affiliation(s)
- Jaroslav L Teteruk
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Jürgen Glinnemann
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Tatiana E Gorelik
- Institut für Physikalische Chemie, Gutenberg-Universität, Welderweg 11, D-55128 Mainz, Germany
| | - Anthony Linden
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Martin U Schmidt
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
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