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Zhang X, Su M, Meng W, Zhao J, Huang M, Zhang J, Qian S, Gao Y, Wei Y. Trace polymer coated clarithromycin spherulites: Formation mechanism, improvement in pharmaceutical properties and development of high-drug-loading direct compression tablets. Int J Pharm 2024; 654:123944. [PMID: 38403089 DOI: 10.1016/j.ijpharm.2024.123944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 02/12/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Clarithromycin (CLA) is a high dose antibiotic drug exhibiting poor flowability and tabletability, making the tablet development challenging. This study aims to develop spherulitic CLA by introducing trace amount of polymer in crystallization solution. Its formation mechanism, physicochemical properties and potential for the direct compression (DC) tablets development were also investigated. Morphological analyses and the in situ observation on crystallization process revealed that the CLA spherulites are formed by fractal branching growth from both sides of the threadlike precursor fibers. 1H NMR analysis and nucleation time monitoring indicated that the existence of hydroxypropyl cellulose in solution slowed down the crystal nucleation and growth rate by forming hydrogen bonding interactions with CLA molecules, making the system maintain high supersaturation, providing high driving forces for CLA spherulitic growth. In comparison to commercial CLA, the CLA spherulites exhibit profoundly improved flowability, tabletability and dissolution behaviors. XPS, contact angle and Raman mapping analysis confirmed the presence of a thin HPC layer on the surfaces and interior of CLA spherulitic particles, resulting in increasing powder plasticity, interparticulate bonding strength and powder wettability, thus better tabletability and dissolution performances. The improved flowability and tabletability of CLA spherulites also enabled the successful development of DC tablet formulation with a high CLA loading (82.8 wt%) and similar dissolution profiles to reference listed drug. This study provides a novel solid form of CLA with superior manufacturability for further development.
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Affiliation(s)
- Xiaohua Zhang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China; Nanjing Chia-Tai Tianqing Pharmaceutical Company, Nanjing 210046, PR China
| | - Meiling Su
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Wenhui Meng
- Nanjing Chia-Tai Tianqing Pharmaceutical Company, Nanjing 210046, PR China; School of Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Jiyun Zhao
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Maoli Huang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Jianjun Zhang
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Shuai Qian
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Yuan Gao
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China.
| | - Yuanfeng Wei
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China.
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2
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Bravetti F, Tapmeyer L, Skorodumov K, Alig E, Habermehl S, Hühn R, Bordignon S, Gallo A, Nervi C, Chierotti MR, Schmidt MU. Leucopterin, the white pigment in butterfly wings: structural analysis by PDF fit, FIDEL fit, Rietveld refinement, solid-state NMR and DFT-D. IUCRJ 2023; 10:448-463. [PMID: 37335768 PMCID: PMC10324491 DOI: 10.1107/s2052252523004281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/16/2023] [Indexed: 06/21/2023]
Abstract
Leucopterin (C6H5N5O3) is the white pigment in the wings of Pieris brassicae butterflies, and other butterflies; it can also be found in wasps and other insects. Its crystal structure and its tautomeric form in the solid state were hitherto unknown. Leucopterin turned out to be a variable hydrate, with 0.5 to about 0.1 molecules of water per leucopterin molecule. Under ambient conditions, the preferred state is the hemihydrate. Initially, all attempts to grow single crystals suitable for X-ray diffraction were to no avail. Attempts to determine the crystal structure by powder diffraction using the direct-space method failed, because the trials did not include the correct, but rare, space group P2/c. Attempts were made to solve the crystal structure by a global fit to the pair distribution function (PDF-Global-Fit), as described by Prill and co-workers [Schlesinger et al. (2021). J. Appl. Cryst. 54, 776-786]. The approach worked well, but the correct structure was not found, because again the correct space group was not included. Finally, tiny single crystals of the hemihydrate could be obtained, which allowed at least the determination of the crystal symmetry and the positions of the C, N and O atoms. The tautomeric state of the hemihydrate was assessed by multinuclear solid-state NMR spectroscopy. 15N CPMAS spectra showed the presence of one NH2 and three NH groups, and one unprotonated N atom, which agreed with the 1H MAS and 13C CPMAS spectra. Independently, the tautomeric state was investigated by lattice-energy minimizations with dispersion-corrected density functional theory (DFT-D) on 17 different possible tautomers, which also included the prediction of the corresponding 1H, 13C and 15N chemical shifts in the solid. All methods showed the presence of the 2-amino-3,5,8-H tautomer. The DFT-D calculations also confirmed the crystal structure. Heating of the hemihydrate results in a slow release of water between 130 and 250 °C, as shown by differential thermal analysis and thermogravimetry (DTA-TG). Temperature-dependent powder X-ray diffraction (PXRD) showed an irreversible continuous shift of the reflections upon heating, which reveals that leucopterin is a variable hydrate. This observation was also confirmed by PXRD of samples obtained under various synthetic and drying conditions. The crystal structure of a sample with about 0.2 molecules of water per leucopterin was solved by a fit with deviating lattice parameters (FIDEL), as described by Habermehl et al. [Acta Cryst. (2022), B78, 195-213]. A local fit, starting from the structure of the hemihydrate, as well as a global fit, starting from random structures, were performed, followed by Rietveld refinements. Despite dehydration, the space group remains P2/c. In both structures (hemihydrate and variable hydrate), the leucopterin molecules are connected by 2-4 hydrogen bonds into chains, which are connected by further hydrogen bonds to neighbouring chains. The molecular packing is very efficient. The density of leucopterin hemihydrate is as high as 1.909 kg dm-3, which is one of the highest densities for organic compounds consisting of C, H, N and O only. The high density might explain the good light-scattering and opacity properties of the wings of Pieris brassicae and other butterflies.
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Affiliation(s)
- Federica Bravetti
- Dipartimento di Chimica e Centro di Eccellenza NIS, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Lukas Tapmeyer
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
- F.K.M. Buster Altöl- und Reststoff-Entsorgung GmbH, Holländerstrasse 18, 68219 Mannheim, Germany
| | - Kathrin Skorodumov
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
- Institut für Organische Chemie und Chemische Biologie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Edith Alig
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Stefan Habermehl
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Robert Hühn
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Simone Bordignon
- Dipartimento di Chimica e Centro di Eccellenza NIS, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Angelo Gallo
- Dipartimento di Chimica e Centro di Eccellenza NIS, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Carlo Nervi
- Dipartimento di Chimica e Centro di Eccellenza NIS, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Michele R. Chierotti
- Dipartimento di Chimica e Centro di Eccellenza NIS, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Martin U. Schmidt
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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3
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Insights into the ethanol solvate form of clarithromycin. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Newman JA, Iuzzolino L, Tan M, Orth P, Bruhn J, Lee AY. From Powders to Single Crystals: A Crystallographer's Toolbox for Small-Molecule Structure Determination. Mol Pharm 2022; 19:2133-2141. [PMID: 35576503 PMCID: PMC10152450 DOI: 10.1021/acs.molpharmaceut.2c00020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although the crystal structures of small-molecule compounds are often determined from single-crystal X-ray diffraction (scXRD), recent advances in three-dimensional electron diffraction (3DED) and crystal structure prediction (CSP) methods promise to expand the structure elucidation toolbox available to the crystallographer. Herein, a comparative assessment of scXRD, 3DED, and CSP in combination with powder X-ray diffraction is carried out on two former drug candidate compounds and a multicomponent crystal of a key building block in the synthesis of gefapixant citrate.
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Affiliation(s)
- Justin A. Newman
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Luca Iuzzolino
- Department
of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Melissa Tan
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Peter Orth
- Department
of Computational and Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jessica Bruhn
- Nanoimaging
Services, San Diego, California 92121, United States
| | - Alfred Y. Lee
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
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5
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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] [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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6
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Habermehl S, Schlesinger C, Schmidt MU. Structure determination from unindexed powder data from scratch by a global optimization approach using pattern comparison based on cross-correlation functions. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:195-213. [PMID: 35411858 PMCID: PMC9004021 DOI: 10.1107/s2052520622001500] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/08/2022] [Indexed: 06/02/2023]
Abstract
A method of ab initio crystal structure determination from powder diffraction data for organic and metal-organic compounds, which does not require prior indexing of the powder pattern, has been developed. Only a reasonable molecular geometry is required, needing knowledge of neither unit-cell parameters nor space group. The structures are solved from scratch by a global fit to the powder data using the new program FIDEL-GO (`FIt with DEviating Lattice parameters - Global Optimization'). FIDEL-GO uses a similarity measure based on cross-correlation functions, which allows the comparison of simulated and experimental powder data even if the unit-cell parameters deviate strongly. The optimization starts from large sets of random structures in various space groups. The unit-cell parameters, molecular position and orientation, and selected internal degrees of freedom are fitted simultaneously to the powder pattern. The optimization proceeds in an elaborate multi-step procedure with built-in clustering of duplicate structures and iterative adaptation of parameter ranges. The best structures are selected for an automatic Rietveld refinement. Finally, a user-controlled Rietveld refinement is performed. The procedure aims for the analysis of a wide range of `problematic' powder patterns, in particular powders of low crystallinity. The method can also be used for the clustering and screening of a large number of possible structure candidates and other application scenarios. Examples are presented for structure determination from unindexed powder data of the previously unknown structures of the nanocrystalline phases of 4,11-difluoro-, 2,9-dichloro- and 2,9-dichloro-6,13-dihydro-quinacridone, which were solved from powder patterns with 14-20 peaks only, and of the coordination polymer dichloro-bis(pyridine-N)copper(II).
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Affiliation(s)
- Stefan Habermehl
- Institute of Inorganic and Analytical Chemistry, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Carina Schlesinger
- Institute of Inorganic and Analytical Chemistry, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Martin U. Schmidt
- Institute of Inorganic and Analytical Chemistry, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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7
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Watts TA, Price LS, Price SL, Niederberger SM, Bertke JA, Swift JA. The Crystal Structure of 5‐Aminouracil and the Ambiguity of Alternative Polymorphs. Isr J Chem 2021. [DOI: 10.1002/ijch.202100062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Taylor A. Watts
- Department of Chemistry Georgetown University 37th and O Sts NW Washington DC 20057–1227 USA
| | - Louise S. Price
- Department of Chemistry University College London 20 Gordon Street London WC1H 0AJ UK
| | - Sarah L. Price
- Department of Chemistry University College London 20 Gordon Street London WC1H 0AJ UK
| | - Sara M. Niederberger
- Department of Chemistry Georgetown University 37th and O Sts NW Washington DC 20057–1227 USA
| | - Jeffery A. Bertke
- Department of Chemistry Georgetown University 37th and O Sts NW Washington DC 20057–1227 USA
| | - Jennifer A. Swift
- Department of Chemistry Georgetown University 37th and O Sts NW Washington DC 20057–1227 USA
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8
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Schlesinger C, Habermehl S, Prill D. Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing. J Appl Crystallogr 2021; 54:776-786. [PMID: 34188612 PMCID: PMC8202035 DOI: 10.1107/s1600576721002569] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/08/2021] [Indexed: 11/20/2022] Open
Abstract
A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called 'PDF-Global-Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross-correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF-Global-Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF-Global-Fit is in excellent agreement with the published crystal structure data.
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Affiliation(s)
- Carina Schlesinger
- Institut für Anorganische und Analytische Chemie, Goethe Universität, Max-von-Laue-Strasse 7, Frankfurt am Main, 60437, Germany
| | - Stefan Habermehl
- Institut für Anorganische und Analytische Chemie, Goethe Universität, Max-von-Laue-Strasse 7, Frankfurt am Main, 60437, Germany
| | - Dragica Prill
- Institut für Anorganische und Analytische Chemie, Goethe Universität, Max-von-Laue-Strasse 7, Frankfurt am Main, 60437, Germany
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9
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Habermehl S, Schlesinger C, Prill D. Comparison and evaluation of pair distribution functions, using a similarity measure based on cross-correlation functions. J Appl Crystallogr 2021; 54:612-623. [PMID: 33953658 PMCID: PMC8056768 DOI: 10.1107/s1600576721001722] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/11/2021] [Indexed: 11/10/2022] Open
Abstract
An approach for the comparison of pair distribution functions (PDFs) has been developed using a similarity measure based on cross-correlation functions. The PDF is very sensitive to changes in the local structure, i.e. small deviations in the structure can cause large signal shifts and significant discrepancies between the PDFs. Therefore, a comparison based on pointwise differences (e.g. R values and difference curves) may lead to the assumption that the investigated PDFs as well as the corresponding structural models are not in agreement at all, whereas a careful visual inspection of the investigated structural models and corresponding PDFs may reveal a relatively good match. To quantify the agreement of different PDFs for those cases an alternative approach is introduced: the similarity measure based on cross-correlation functions. In this paper, the power of this application of the similarity measure to the analysis of PDFs is highlighted. The similarity measure is compared with the classical R wp values as representative of the comparison based on pointwise differences as well as with the Pearson product-moment correlation coefficient, using polymorph IV of barbituric acid as an example.
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Affiliation(s)
- Stefan Habermehl
- Institute of Inorganic and Analytical Chemistry, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Carina Schlesinger
- Institute of Inorganic and Analytical Chemistry, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Dragica Prill
- Institute of Inorganic and Analytical Chemistry, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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10
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Bowskill DH, Sugden IJ, Konstantinopoulos S, Adjiman CS, Pantelides CC. Crystal Structure Prediction Methods for Organic Molecules: State of the Art. Annu Rev Chem Biomol Eng 2021; 12:593-623. [PMID: 33770462 DOI: 10.1146/annurev-chembioeng-060718-030256] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The prediction of the crystal structures that a given organic molecule is likely to form is an important theoretical problem of significant interest for the pharmaceutical and agrochemical industries, among others. As evidenced by a series of six blind tests organized over the past 2 decades, methodologies for crystal structure prediction (CSP) have witnessed substantial progress and have now reached a stage of development where they can begin to be applied to systems of practical significance. This article reviews the state of the art in general-purpose methodologies for CSP, placing them within a common framework that highlights both their similarities and their differences. The review discusses specific areas that constitute the main focus of current research efforts toward improving the reliability and widening applicability of these methodologies, and offers some perspectives for the evolution of this technology over the next decade.
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Affiliation(s)
- David H Bowskill
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
| | - Isaac J Sugden
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
| | - Stefanos Konstantinopoulos
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
| | - Claire S Adjiman
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
| | - Constantinos C Pantelides
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
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11
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Sacchi P, Lusi M, Cruz-Cabeza AJ, Nauha E, Bernstein J. Same or different – that is the question: identification of crystal forms from crystal structure data. CrystEngComm 2020. [DOI: 10.1039/d0ce00724b] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An analysis of the CSD with structural comparison tools shows that differentiating between polymorphism and redeterminations is not always straight forward and requires of complementary tools at the hands of an expert practitioner.
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Affiliation(s)
- Pietro Sacchi
- Department of Chemical Engineering and Analytical Science
- University of Manchester
- Manchester
- UK
| | - Matteo Lusi
- SSPC
- The SFI Research Centre for Pharmaceuticals
- Bernal Institute
- Department of Chemical Sciences
- University of Limerick
| | - Aurora J. Cruz-Cabeza
- Department of Chemical Engineering and Analytical Science
- University of Manchester
- Manchester
- UK
| | - Elisa Nauha
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
| | - Joel Bernstein
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
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12
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Bhardwaj RM, McMahon JA, Nyman J, Price LS, Konar S, Oswald IDH, Pulham CR, Price SL, Reutzel-Edens SM. A Prolific Solvate Former, Galunisertib, under the Pressure of Crystal Structure Prediction, Produces Ten Diverse Polymorphs. J Am Chem Soc 2019; 141:13887-13897. [DOI: 10.1021/jacs.9b06634] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajni M. Bhardwaj
- Small Molecule Design & Development, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Jennifer A. McMahon
- Small Molecule Design & Development, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Jonas Nyman
- Small Molecule Design & Development, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
- School of Pharmacy, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Louise S. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Sumit Konar
- School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Iain D. H. Oswald
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral St, Glasgow G4 0RE, U.K
| | - Colin R. Pulham
- School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Sarah L. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Susan M. Reutzel-Edens
- Small Molecule Design & Development, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
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13
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Abstract
A novel pumpkin-orange polymorph of ROY was matched to a predicted structure and refined to PXRD data.
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Affiliation(s)
| | - Jonas Nyman
- Small Molecule Design & Development
- Eli Lilly and Company
- Indianapolis
- USA
- School of Pharmacy
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14
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Nyman J, Yu L, Reutzel-Edens SM. Accuracy and reproducibility in crystal structure prediction: the curious case of ROY. CrystEngComm 2019. [DOI: 10.1039/c8ce01902a] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Because of excessive electron delocalization, the polymorphs of ROY constitute a surprisingly challenging system for crystal structure prediction.
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Affiliation(s)
- Jonas Nyman
- School of Pharmacy
- University of Wisconsin – Madison
- Madison
- USA
- Small Molecule Design & Development
| | - Lian Yu
- School of Pharmacy
- University of Wisconsin – Madison
- Madison
- USA
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15
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Schlesinger C, Bolte M, Schmidt MU. Challenging structure determination from powder diffraction data: two pharmaceutical salts and one cocrystal with Z′ = 2. ACTA ACUST UNITED AC 2018. [DOI: 10.1515/zkri-2018-2093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Structure solution of molecular crystals from powder diffraction data by real-space methods becomes challenging when the total number of degrees of freedom (DoF) for molecular position, orientation and intramolecular torsions exceeds a value of 20. Here we describe the structure determination from powder diffraction data of three pharmaceutical salts or cocrystals, each with four molecules per asymmetric unit on general position: Lamivudine camphorsulfonate (1, P 21, Z=4, Z′=2; 31 DoF), Theophylline benzamide (2, P 41, Z=8, Z′=2; 23 DoF) and Aminoglutethimide camphorsulfonate hemihydrate [3, P 21, Z=4, Z′=2; 31 DoF (if the H2O molecule is ignored)]. In the salts 1 and 3 the cations and anions have two intramolecular DoF each. The molecules in the cocrystal 2 are rigid. The structures of 1 and 2 could be solved without major problems by DASH using simulated annealing. For compound 3, indexing, space group determination and Pawley fit proceeded without problems, but the structure could not be solved by the real-space method, despite extensive trials. By chance, a single crystal of 3 was obtained and the structure was determined by single-crystal X-ray diffraction. A post-analysis revealed that the failure of the real-space method could neither be explained by common sources of error such as incorrect indexing, wrong space group, phase impurities, preferred orientation, spottiness or wrong assumptions on the molecular geometry or other user errors, nor by the real-space method itself. Finally, is turned out that the structure solution failed because of problems in the extraction of the integrated reflection intensities in the Pawley fit. With suitable extracted reflection intensities the structure of 3 could be determined in a routine way.
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Affiliation(s)
- Carina Schlesinger
- Institut für Anorganische und Analytische Chemie , Goethe-Universität , Max-von-Laue-Str. 7 , 60438 Frankfurt am Main , Germany
| | - Michael Bolte
- Institut für Anorganische und Analytische Chemie , Goethe-Universität , Max-von-Laue-Str. 7 , 60438 Frankfurt am Main , Germany
| | - Martin U. Schmidt
- Institut für Anorganische und Analytische Chemie , Goethe-Universität , Max-von-Laue-Str. 7 , 60438 Frankfurt am Main , Germany
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16
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Price SL. Control and prediction of the organic solid state: a challenge to theory and experiment †. Proc Math Phys Eng Sci 2018; 474:20180351. [PMID: 30333710 PMCID: PMC6189584 DOI: 10.1098/rspa.2018.0351] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/15/2018] [Indexed: 11/12/2022] Open
Abstract
The ability of theoretical chemists to quantitatively model the weak forces between organic molecules is being exploited to predict their crystal structures and estimate their physical properties. Evolving crystal structure prediction methods are increasingly being used to aid the design of organic functional materials and provide information about thermodynamically plausible polymorphs of speciality organic materials to aid, for example, pharmaceutical development. However, the increasingly sophisticated experimental studies for detecting the range of organic solid-state behaviours provide many challenges for improving quantitative theories that form the basis for the computer modelling. It is challenging to calculate the relative thermodynamic stability of different organic crystal structures, let alone understand the kinetic effects that determine which polymorphs can be observed and are practically important. However, collaborations between experiment and theory are reaching the stage of devising experiments to target the first crystallization of new polymorphs or create novel organic molecular materials.
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Affiliation(s)
- Sarah L. Price
- Department of Chemistry, University College London, 20 Gordon St, London WC1H 0AJ, UK
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17
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Guccione P, Palin L, Milanesio M, Belviso BD, Caliandro R. Improved multivariate analysis for fast and selective monitoring of structural dynamics by in situ X-ray powder diffraction. Phys Chem Chem Phys 2018; 20:2175-2187. [PMID: 29104977 DOI: 10.1039/c7cp06326a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The development of two solid-state reactions, Xe absorption into MFI and molecular complex formation, where samples are affected by changes of crystal lattice due to temperature or pressure variation was structurally monitored through in situ or in operando X-ray powder diffraction experiments. Consequent variations of the peak positions prevent collective analysis of measured patterns, aiming at investigating structural changes occurring within the crystal cell. Moreover, an intrinsic and variable error in peak position is unavoidable when using the Bragg-Brentano geometry and, in some cases (sticky, bulky, aggregate samples) the sample mounting can increase the error within a dataset. Here we present a general multivariate analysis method to process in a fast and automatic way in situ XRPD data collected on charge transfer complexes and porous materials, with the capacity of disentangling peak shifts from intensity and shape variations in diffraction signals, thus allowing an efficient separation of the contribution of crystal lattice changes from structural changes. The peak shift correction allowed an improved PCA analysis that turned out to be more sensible than the traditional single pattern Rietveld analysis. The developed algorithms allowed, with respect to the traditional approach, the location of two new Xe positions into MFI with a better interpretation of the experimental data, while a much faster and more efficient recovery of the reaction coordinate was achieved in the molecular complex formation reaction.
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Affiliation(s)
- Pietro Guccione
- Dipartimento di Ingegneria Elettrica e dell'Informazione, Politecnico di Bari, via Orabona 4, Bari, 70125, Italy
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18
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Price SL. Is zeroth order crystal structure prediction (CSP_0) coming to maturity? What should we aim for in an ideal crystal structure prediction code? Faraday Discuss 2018; 211:9-30. [PMID: 30051901 DOI: 10.1039/c8fd00121a] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystal structure prediction based on searching for the global minimum in the lattice energy (CSP_0) is growing in use for guiding the discovery of new materials, for example, new functional materials, new phases of interest to planetary scientists and new polymorphs relevant to pharmaceutical development. This Faraday Discussion can assess the progress of CSP_0 over the range of types of materials to which CSP is currently and could be applied, which depends on our ability to model the variety of interatomic forces in crystals. The basic hypothesis, that the outcome of crystallisation is determined by thermodynamics, needs examining by considering methods of modelling relative thermodynamic stability not only as a function of pressure and temperature, but also of size, solvent and the presence of heterogeneous templates or impurities (CSP_thd). Given that many important materials persist, and indeed may be formed, when they are not the most thermodynamically stable structure, we need to define what would be required of an ideal CSP code (CSP_aim).
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Affiliation(s)
- Sarah L Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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19
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Heine M, Fink L, Schmidt MU. 3-Cyanopyridine as a bridging and terminal ligand in coordination polymers. CrystEngComm 2018. [DOI: 10.1039/c8ce01568f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystal structures of [MIIBr2(3-CNpy)x](n) with M = Mn, Fe, Co, Ni and x = 1, 2, 4 were determined by powder diffraction. For x = 1, the 3-cyanopyridine ligand is bridging two metal atoms.
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Affiliation(s)
- Miriam Heine
- Institute of Inorganic and Analytical Chemistry
- Goethe University
- 60438 Frankfurt am Main
- Germany
| | - Lothar Fink
- Institute of Inorganic and Analytical Chemistry
- Goethe University
- 60438 Frankfurt am Main
- Germany
| | - Martin U. Schmidt
- Institute of Inorganic and Analytical Chemistry
- Goethe University
- 60438 Frankfurt am Main
- Germany
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20
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Brandenburg JG, Potticary J, Sparkes HA, Price SL, Hall SR. Thermal Expansion of Carbamazepine: Systematic Crystallographic Measurements Challenge Quantum Chemical Calculations. J Phys Chem Lett 2017; 8:4319-4324. [PMID: 28841023 DOI: 10.1021/acs.jpclett.7b01944] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report systematic temperature-dependent X-ray measurements on the most stable carbamazepine polymorph. This active pharmaceutical ingredient is used to demonstrate how the thermal expansion can probe certain intermolecular interactions resulting in anisotropic expansion behavior. We show that most structural features can be captured by electronic structure calculations at the quasi-harmonic approximation (QHA) provided a dispersion-corrected density functional based method is employed. The impact of thermal expansion on the phonon modes and hence free energy contributions is large enough to impact the relative stability of different polymorphs.
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Affiliation(s)
- Jan Gerit Brandenburg
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AH, United Kingdom
- School of Chemistry, University of Bristol , Cantocks Close, Bristol BS8 1TS, United Kingdom
| | - Jason Potticary
- Thomas Young Centre, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Hazel A Sparkes
- Thomas Young Centre, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Sarah L Price
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AH, United Kingdom
- School of Chemistry, University of Bristol , Cantocks Close, Bristol BS8 1TS, United Kingdom
| | - Simon R Hall
- Thomas Young Centre, University College London , Gower Street, London WC1E 6BT, United Kingdom
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21
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Kurta RP, Altarelli M, Vartanyants IA. STRUCTURAL ANALYSIS BY X-RAY INTENSITY ANGULAR CROSS CORRELATIONS. ADVANCES IN CHEMICAL PHYSICS 2016. [DOI: 10.1002/9781119290971.ch1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | | | - Ivan A. Vartanyants
- Deutsches Elektronen-Synchrotron; DESY; Hamburg Germany
- National Research Nuclear University ‘MEPhI’ (Moscow Engineering Physics Institute); Moscow Russia
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22
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Price SL, Braun DE, Reutzel-Edens SM. Can computed crystal energy landscapes help understand pharmaceutical solids? Chem Commun (Camb) 2016; 52:7065-77. [PMID: 27067116 PMCID: PMC5486446 DOI: 10.1039/c6cc00721j] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Computational crystal structure prediction (CSP) methods can now be applied to the smaller pharmaceutical molecules currently in drug development. We review the recent uses of computed crystal energy landscapes for pharmaceuticals, concentrating on examples where they have been used in collaboration with industrial-style experimental solid form screening. There is a strong complementarity in aiding experiment to find and characterise practically important solid forms and understanding the nature of the solid form landscape.
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Affiliation(s)
- Sarah L Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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23
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Price SL, Reutzel-Edens SM. The potential of computed crystal energy landscapes to aid solid-form development. Drug Discov Today 2016; 21:912-23. [DOI: 10.1016/j.drudis.2016.01.014] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/04/2015] [Accepted: 01/26/2016] [Indexed: 11/29/2022]
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