1
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Anyfanti G, Husanu E, Andrusenko I, Marchetti D, Gemmi M. The crystal structure of olanzapine form III. IUCRJ 2024; 11:843-848. [PMID: 39072705 PMCID: PMC11364035 DOI: 10.1107/s2052252524007383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
The antipsychotic drug olanzapine is well known for its complex polymorphism. Although widely investigated, the crystal structure of one of its anhydrous polymorphs, form III, is still unknown. Its appearance, always in concomitance with forms II and I, and the impossibility of isolating it from that mixture, have prevented its structure determination so far. The scenario has changed with the emerging field of 3D electron diffraction (3D ED) and its great advantages in the characterization of polyphasic mixtures of nanosized crystals. In this study, we show how the application of 3D ED allows the ab initio structure determination and dynamical refinement of this elusive crystal structure that remained unknown for more than 20 years. Olanzapine form III is monoclinic and shows a similar but shifted packing with respect to form II. It is remarkably different from the lowest-energy structures predicted by the energy-minimization algorithms of crystal structure prediction.
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Affiliation(s)
- Goulielmina Anyfanti
- Electron CrystallographyIstituto Italiano di Tecnologia (ITT)Viale Rianaldo Piaggio 34Pontedera56025Italy
| | - Elena Husanu
- Electron CrystallographyIstituto Italiano di Tecnologia (ITT)Viale Rianaldo Piaggio 34Pontedera56025Italy
| | - Iryna Andrusenko
- Electron CrystallographyIstituto Italiano di Tecnologia (ITT)Viale Rianaldo Piaggio 34Pontedera56025Italy
| | - Danilo Marchetti
- Electron CrystallographyIstituto Italiano di Tecnologia (ITT)Viale Rianaldo Piaggio 34Pontedera56025Italy
- Department of ChemistryUniversity of ParmaParco Area delle Scienze 17/AParma43124Italy
| | - Mauro Gemmi
- Electron CrystallographyIstituto Italiano di Tecnologia (ITT)Viale Rianaldo Piaggio 34Pontedera56025Italy
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2
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Jin ZB, Zhou G, Han Y, Huang Z, Gu ZG, Zhang J. Topochemical Polymerization at Diacetylene Metal-Organic Framework Thin Films for Tuning Nonlinear Optics. J Am Chem Soc 2024. [PMID: 39213506 DOI: 10.1021/jacs.4c07432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Developing the topochemical polymerization of metal-organic frameworks (MOFs) is of pronounced significance for expanding their functionalities but is still a challenge on third-order nonlinear optics (NLO). Here, we report diacetylene MOF (CAS-1-3) films prepared using a stepwise deposition method and film structural transformation approach, featuring dynamic structural diversity. The MOF structures were determined by the three-dimensional electron diffraction (3D ED) method from nanocrystals collected from the films, which provides a reliable strategy for determining the precise structure of unknown MOF films. We demonstrate the well-aligned diacetylene groups in the MOFs can promote topological polymerization to produce a highly conjugated system under thermal stimulation. As a result, the three MOF films have distinct NLO properties: the CAS-1 film exhibits saturable absorption (SA) while CAS-2 and CAS-3 films exhibit reverse saturable absorption (RSA). Interestingly, due to the topochemical polymerization of the MOF films, a transition from SA to RSA response was observed with increasing temperatures, and the optical limiting effect was significantly enhanced (∼46 times). This study provides a new strategy for preparing NLO materials and thermally regulation of nonlinear optics.
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Affiliation(s)
- Zhi-Bin Jin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Guojun Zhou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
| | - Yu Han
- Center for Electron Microscopy, School of Emergent Soft Matter, South China University of Technology, Guangzhou, 510006, China
| | - Zhehao Huang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
- Center for Electron Microscopy, School of Emergent Soft Matter, South China University of Technology, Guangzhou, 510006, China
| | - Zhi-Gang Gu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou, Fujian 350108, China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Jian Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou, Fujian 350108, China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
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3
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Yuan Z, Wang L, Wu M, Niu Y, Meng Y, Ruan X, He G, Jiang X. Confined liquid crystallization governed by electric field for API crystal polymorphism screening and massive preparation. J Colloid Interface Sci 2024; 664:74-83. [PMID: 38460386 DOI: 10.1016/j.jcis.2024.02.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/22/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024]
Abstract
Active pharmaceutical ingredients (APIs) crystal preparation is a significant issue for the pharmaceutical development attributed to the effect on anti-inflammatory, anti-bacteria, and anti-viral, etc. While, the massive preparation of API crystal with high polymorphism selectivity is still a pendent challenge. Here, we firstly proposed a criterion according to the molecular aggregation, molecular orientation, and hydrogen bond energy between INA molecules from molecular dynamics (MD) simulations, which predicted the hydrogen bond architecture in crystal under different electric fields, hinting the recognition of crystal polymorphism. Then, an electric field governing confined liquid crystallization was constructed to achieve the INA crystal polymorphism screening relying on the criterion. Further, magnifying confined liquid volume by 5000 times from 1.0 μL to 5.0 mL realized the massive preparation of INA crystal with high polymorphic purity (>98.4%), giving a unique pathway for crystal engineering and pharmaceutical industry on the development of innovative and generic API based drugs.
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Affiliation(s)
- Zhijie Yuan
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Lingfeng Wang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Mengyuan Wu
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Yuchao Niu
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Yingshuang Meng
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xuehua Ruan
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Gaohong He
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xiaobin Jiang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning 116024, China
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4
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Gemmi M. 3D ED/MicroED entering a new era. Acta Crystallogr C Struct Chem 2024; 80:177-178. [PMID: 38835200 DOI: 10.1107/s205322962400490x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/06/2024] Open
Abstract
Aragon et al. [Acta Cryst. (2024), C80, 179-189], by reporting the discussion and the final conclusions of a round table held during a symposium at the National Center for CryoEM Access and Training, well describe all the advances that have been made for the application of 3D ED/MicroED to pharmaceutical and macromolecular nanocrystals and propose possible future scenarios.
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Affiliation(s)
- Mauro Gemmi
- Electron Crystallography, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera, Italy
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5
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Nguyen DT, Zhu L, Gray DL, Woods TJ, Padhi C, Flatt KM, Mitchell DA, van der Donk WA. Biosynthesis of Macrocyclic Peptides with C-Terminal β-Amino-α-keto Acid Groups by Three Different Metalloenzymes. ACS CENTRAL SCIENCE 2024; 10:1022-1032. [PMID: 38799663 PMCID: PMC11117315 DOI: 10.1021/acscentsci.4c00088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 05/29/2024]
Abstract
Advances in genome sequencing and bioinformatics methods have identified a myriad of biosynthetic gene clusters (BGCs) encoding uncharacterized molecules. By mining genomes for BGCs containing a prevalent peptide-binding domain used for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), we uncovered a new compound class involving modifications installed by a cytochrome P450, a multinuclear iron-dependent non-heme oxidative enzyme (MNIO, formerly DUF692), a cobalamin- and radical S-adenosyl-l-methionine-dependent enzyme (B12-rSAM), and a methyltransferase. All enzymes were functionally expressed in Burkholderia sp. FERM BP-3421. Structural characterization demonstrated that the P450 enzyme catalyzed the formation of a biaryl C-C cross-link between two Tyr residues with the B12-rSAM generating β-methyltyrosine. The MNIO transformed a C-terminal Asp residue into aminopyruvic acid, while the methyltransferase acted on the β-carbon of this α-keto acid. Exciton-coupled circular dichroism spectroscopy and microcrystal electron diffraction (MicroED) were used to elucidate the stereochemical configuration of the atropisomer formed upon biaryl cross-linking. To the best of our knowledge, the MNIO featured in this pathway is the first to modify a residue other than Cys. This study underscores the utility of genome mining to isolate new macrocyclic RiPPs biosynthesized via previously undiscovered enzyme chemistry.
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Affiliation(s)
- Dinh T. Nguyen
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lingyang Zhu
- School
of Chemical Sciences NMR Laboratory, University
of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Danielle L. Gray
- School
of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials
Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Toby J. Woods
- School
of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials
Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chandrashekhar Padhi
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kristen M. Flatt
- Materials
Research Laboratory, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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6
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Lightowler M, Li S, Ou X, Cho J, Liu B, Li A, Hofer G, Xu J, Yang T, Zou X, Lu M, Xu H. Phase Identification and Discovery of an Elusive Polymorph of Drug-Polymer Inclusion Complex Using Automated 3D Electron Diffraction. Angew Chem Int Ed Engl 2024; 63:e202317695. [PMID: 38380831 DOI: 10.1002/anie.202317695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/22/2024]
Abstract
3D electron diffraction (3D ED) has shown great potential in crystal structure determination in materials, small organic molecules, and macromolecules. In this work, an automated, low-dose and low-bias 3D ED protocol has been implemented to identify six phases from a multiple-phase melt-crystallisation product of an active pharmaceutical ingredient, griseofulvin (GSF). Batch data collection under low-dose conditions using a widely available commercial software was combined with automated data analysis to collect and process over 230 datasets in three days. Accurate unit cell parameters obtained from 3D ED data allowed direct phase identification of GSF Forms III, I and the known GSF inclusion complex (IC) with polyethylene glycol (PEG) (GSF-PEG IC-I), as well as three minor phases, namely GSF Forms II, V and an elusive new phase, GSF-PEG IC-II. Their structures were then directly determined by 3D ED. Furthermore, we reveal how the stabilities of the two GSF-PEG IC polymorphs are closely related to their crystal structures. These results demonstrate the power of automated 3D ED for accurate phase identification and direct structure determination of complex, beam-sensitive crystallisation products, which is significant for drug development where solid form screening is crucial for the overall efficacy of the drug product.
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Affiliation(s)
- Molly Lightowler
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Shuting Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jungyoun Cho
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Binbin Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ao Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Gerhard Hofer
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Jiaoyan Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Taimin Yang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Ming Lu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
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7
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Krysiak Y, Plana-Ruiz S, Fink L, Alig E, Bahnmüller U, Kolb U, Schmidt MU. High Temperature Electron Diffraction on Organic Crystals: In Situ Crystal Structure Determination of Pigment Orange 34. J Am Chem Soc 2024; 146:9880-9887. [PMID: 38536667 PMCID: PMC11009952 DOI: 10.1021/jacs.3c14800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/23/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
Abstract
Small molecule structures and their applications rely on good knowledge of their atomic arrangements. However, the crystal structures of these compounds and materials, which are often composed of fine crystalline domains, cannot be determined with single-crystal X-ray diffraction. Three-dimensional electron diffraction (3D ED) is already becoming a reliable method for the structure analysis of submicrometer-sized organic materials. The reduction of electron beam damage is essential for successful structure determination and often prevents the analysis of organic materials at room temperature, not to mention high temperature studies. In this work, we apply advanced 3D ED methods at different temperatures enabling the accurate structure determination of two phases of Pigment Orange 34 (C34H28N8O2Cl2), a biphenyl pyrazolone pigment that has been industrially produced for more than 80 years and used for plastics application. The crystal structure of the high-temperature phase, which can be formed during plastic coloration, was determined at 220 °C. For the first time, we were able to observe a reversible phase transition in an industrial organic pigment in the solid state, even with atomic resolution, despite crystallites being submicrometer in size. By localizing hydrogen atoms, we were even able to detect the tautomeric state of the molecules at different temperatures. This demonstrates that precise, fast, and low-dose 3D ED measurements enable high-temperature studies the door for general in situ studies of nanocrystalline materials at the atomic level.
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Affiliation(s)
- Yaşar Krysiak
- Institute
of Inorganic Chemistry, Leibniz University
Hannover, Callinstraße 9, 30167 Hannover, Germany
| | - Sergi Plana-Ruiz
- Department
of Materials and Geoscience, Technische
Universität Darmstadt, Petersenstrasse 23, 64287 Darmstadt, Germany
- LENS,
MIND/IN2UB, Departament d’Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Catalonia, Spain
| | - Lothar Fink
- Institute
of Inorganic and Analytical Chemistry, Goethe
University Frankfurt am Main, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Edith Alig
- Institute
of Inorganic and Analytical Chemistry, Goethe
University Frankfurt am Main, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Ulrich Bahnmüller
- Institute
of Inorganic Chemistry, Leibniz University
Hannover, Callinstraße 9, 30167 Hannover, Germany
| | - Ute Kolb
- Department
of Materials and Geoscience, Technische
Universität Darmstadt, Petersenstrasse 23, 64287 Darmstadt, Germany
- Institute
of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Martin U. Schmidt
- Institute
of Inorganic and Analytical Chemistry, Goethe
University Frankfurt am Main, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
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8
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Lin J, Unge J, Gonen T. Distinct Conformations of Mirabegron Determined by MicroED. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304476. [PMID: 37847906 PMCID: PMC10700164 DOI: 10.1002/advs.202304476] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/31/2023] [Indexed: 10/19/2023]
Abstract
Mirabegron, commonly known as "Myrbetriq", has been widely prescribed as a medicine for overactive bladder syndrome for over a decade. However, the structure of the drug and what conformational changes it may undergo upon binding its receptor remain unknown. In this study, the authors employed microcrystal electron diffraction (MicroED) to reveal its elusive three-dimensional (3D) structure. They find that the drug adopts two distinct conformational states (conformers) within the asymmetric unit. Analysis of hydrogen bonding and packing demonstrated that the hydrophilic groups are embedded within the crystal lattice, resulting in a hydrophobic surface and low water solubility. Structural comparison revealed the presence of trans- and cis- forms in conformers 1 and 2, respectively. Comparison of the structures of Mirabegron alone with that of the drug bound to its receptor, the beta 3 adrenergic receptor (β3AR) suggests that the drug undergoes major conformational change to fit in the receptor agonist binding site. This research highlights the efficacy of MicroED in determining the unknown and polymorphic structures of active pharmaceutical ingredients (APIs) directly from powders.
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Affiliation(s)
- Jieye Lin
- Department of Biological ChemistryUniversity of California615 Charles E. Young Drive SouthLos AngelesCA90095USA
| | - Johan Unge
- Department of Biological ChemistryUniversity of California615 Charles E. Young Drive SouthLos AngelesCA90095USA
| | - Tamir Gonen
- Department of Biological ChemistryUniversity of California615 Charles E. Young Drive SouthLos AngelesCA90095USA
- Department of PhysiologyUniversity of California615 Charles E. Young Drive SouthLos AngelesCA90095USA
- Howard Hughes Medical InstituteUniversity of CaliforniaLos AngelesCA90095USA
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9
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Lin J, Unge J, Gonen T. Distinct Conformations of Mirabegron Determined by MicroED. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546957. [PMID: 37425799 PMCID: PMC10326998 DOI: 10.1101/2023.06.28.546957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Mirabegron, commonly known as "Myrbetriq", has been widely prescribed as a medicine for overactive bladder syndrome for over a decade. However, the structure of the drug and what conformational changes it may undergo upon binding its receptor remain unknown. In this study, we employed microcrystal electron diffraction (MicroED) to reveal its elusive three-dimensional (3D) structure. We find that the drug adopts two distinct conformational states (conformers) within the asymmetric unit. Analysis of hydrogen bonding and packing demonstrated that the hydrophilic groups were embedded within the crystal lattice, resulting in a hydrophobic surface and low water solubility. Structural comparison revealed the presence of trans- and cis- forms in conformers 1 and 2, respectively. Comparison of the structures of Mirabegron alone with that of the drug bound to its receptor,1 the beta 3 adrenergic receptor (β3AR) suggests that the drug undergoes major conformational change to fit in the receptor agonist binding site. This research highlights the efficacy of MicroED in determining the unknown and polymorphic structures of active pharmaceutical ingredients (APIs) directly from powders.
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Affiliation(s)
- Jieye Lin
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Johan Unge
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
- Department of Physiology, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
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10
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Simoncic P, Romeijn E, Hovestreydt E, Steinfeld G, Santiso-Quiñones G, Merkelbach J. Electron crystallography and dedicated electron-diffraction instrumentation. Acta Crystallogr E Crystallogr Commun 2023; 79:410-422. [PMID: 37151820 PMCID: PMC10162091 DOI: 10.1107/s2056989023003109] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
Electron diffraction (known also as ED, 3D ED or microED) is gaining momentum in science and industry. The application of electron diffraction in performing nano-crystallography on crystals smaller than 1 µm is a disruptive technology that is opening up fascinating new perspectives for a wide variety of compounds required in the fields of chemical, pharmaceutical and advanced materials research. Electron diffraction enables the characterization of solid compounds complementary to neutron, powder X-ray and single-crystal X-ray diffraction, as it has the unique capability to measure nanometre-sized crystals. The recent introduction of dedicated instrumentation to perform ED experiments is a key aspect of the continued growth and success of this technology. In addition to the ultra-high-speed hybrid-pixel detectors enabling ED data collection in continuous rotation mode, a high-precision goniometer and horizontal layout have been determined as essential features of an electron diffractometer, both of which are embodied in the Eldico ED-1. Four examples of data collected on an Eldico ED-1 are showcased to demonstrate the potential and advantages of a dedicated electron diffractometer, covering selected applications and challenges of electron diffraction: (i) multiple reciprocal lattices, (ii) absolute structure of a chiral compound, and (iii) R-values achieved by kinematic refinement comparable to X-ray data.
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Affiliation(s)
- Petra Simoncic
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
- Correspondence e-mail:
| | - Eva Romeijn
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | - Eric Hovestreydt
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | - Gunther Steinfeld
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | | | - Johannes Merkelbach
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
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11
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Romagnoli L, D’Annibale A, Blundo E, Patra A, Polimeni A, Meggiolaro D, Andrusenko I, Marchetti D, Gemmi M, Latini A. 4,4'-(Anthracene-9,10-diylbis(ethyne-2,1-diyl))bis(1-methyl-1-pyridinium) Lead Iodide C 30H 22N 2Pb 2I 6: A Highly Luminescent, Chemically and Thermally Stable One-Dimensional Hybrid Iodoplumbate. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2023; 35:1818-1826. [PMID: 36873626 PMCID: PMC9979375 DOI: 10.1021/acs.chemmater.2c03798] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/02/2023] [Indexed: 06/17/2023]
Abstract
A new one-dimensional hybrid iodoplumbate, namely, 4,4'-(anthracene-9,10-diylbis(ethyne-2,1-diyl))bis(1-methyl-1-pyridinium) lead iodide C30H22N2Pb2I6 (AEPyPbI), is reported here for the first time with its complete characterization. The material exhibits remarkable thermal stability (up to 300 °C), and it is unreactive under ambient conditions toward water and atmospheric oxygen, due to the quaternary nature of the nitrogen atoms present in the organic cation. The cation exhibits strong visible fluorescence under ultraviolet (UV) irradiation, and when its iodide is combined with PbI2, it forms AEPyPb2I6, an efficient light-emitting material, with a photoluminescence emission intensity comparable to that of high-quality InP epilayers. The structure determination was obtained using three-dimensional electron diffraction, and the material was extensively studied by using a wide range of techniques, such as X-ray powder diffraction, diffuse reflectance UV-visible spectroscopy, thermogravimetry-differential thermal analysis, elemental analysis, Raman and infrared spectroscopies, and photoluminescence spectroscopy. The emissive properties of the material were correlated with its electronic structure by using state-of-the-art theoretical calculations. The complex, highly conjugated electronic structure of the cation interacts strongly with that of the Pb-I network, giving rise to the peculiar optoelectronic properties of AEPyPb2I6. The material, considering its relatively easy synthesis and stability, shows promise for light-emitting and photovoltaic devices. The use of highly conjugated quaternary ammonium cations may be useful for the development of new hybrid iodoplumbates and perovskites with optoelectronic properties tailored for specific applications.
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Affiliation(s)
- Lorenza Romagnoli
- Dipartimento
di Chimica, Sapienza Università di
Roma, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Andrea D’Annibale
- Dipartimento
di Chimica, Sapienza Università di
Roma, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Elena Blundo
- Dipartimento
di Fisica, Sapienza Università di
Roma, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Atanu Patra
- Dipartimento
di Fisica, Sapienza Università di
Roma, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Antonio Polimeni
- Dipartimento
di Fisica, Sapienza Università di
Roma, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Daniele Meggiolaro
- Computational
Laboratory for Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Chimiche “Giulio Natta”
(CNR-SCITEC), Via Elce di Sotto 8, Perugia 06123, Italy
| | - Iryna Andrusenko
- Electron
Crystallography, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera 56025, Italy
| | - Danilo Marchetti
- Electron
Crystallography, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera 56025, Italy
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma (PR) 43124, Italy
| | - Mauro Gemmi
- Electron
Crystallography, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera 56025, Italy
| | - Alessandro Latini
- Dipartimento
di Chimica, Sapienza Università di
Roma, Piazzale Aldo Moro 5, Roma 00185, Italy
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12
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Direct structure determination of vemurafenib polymorphism from compact spherulites using 3D electron diffraction. Commun Chem 2023; 6:18. [PMID: 36697943 PMCID: PMC9871043 DOI: 10.1038/s42004-022-00804-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/22/2022] [Indexed: 01/25/2023] Open
Abstract
The spherulitic morphology is considered to be the most common morphology of crystalline materials and is particularly apparent in melt-crystallized products. Yet, historically, the polycrystalline nature of spherulites has hindered successful crystal structure determination. Here, we report the direct structure determination of a clinical drug, vemurafenib (VMN), in compact spherulite form using 3D electron diffraction (3D ED). VMN has four known polymorphs. We first solved the crystal structures of α-, β-, and γ-VMN from compact spherulites using 3D ED, and the resulting structures were highly consistent with those obtained by single-crystal X-ray diffraction. We then determined the crystal structure of δ-VMN-the least stable polymorph which cannot be cultivated as a single crystal-directly from the compact spherulite sample. We unexpectedly discovered a new polymorph during our studies, denoted as ε-VMN. Single crystals of ε-VMN are extremely thin and not suitable for study by X-ray diffraction. Again, we determined the structure of ε-VMN in a compact spherulite form. This successful structure elucidation of all five VMN polymorphs demonstrates the possibility of directly determining structures from melt-grown compact spherulite samples. Thereby, this discovery will improve the efficiency and broaden the scope of polymorphism research, especially within the field of melt crystallization.
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13
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Li X, Xu L, Wan Y, Li J, Qian X, Xia W, He Z, Zheng T, Xu S, Li Y. Urinary paracetamol (4-acetaminophenol) and its isomer 2-acetaminophenol of Chinese pregnant women: Exposure characteristics and association with oxidative stress biomarkers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158375. [PMID: 36049689 DOI: 10.1016/j.scitotenv.2022.158375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
N-Acetyl-4-aminophenol (NA4AP, paracetamol/acetaminophen), a widely used pharmaceutical, is ubiquitous in urine samples of general population, raising concern about human health risks; oxidative stress is considered to be a mechanism for its toxicities. N-Acetyl-2-aminophenol (NA2AP) is an isomer of NA4AP; until now, few studies characterized exposure characteristics of NA4AP and NA2AP in pregnant women. In this work, NA4AP and NA2AP concentrations in urine samples (n = 2124) collected at three different trimesters were measured to examine their internal body burden among Chinese pregnant women (n = 708) and their associations with three oxidative stress biomarkers (OSBs, 8-OHG, 8-OHdG, and HNE-MA). NA4AP was detected in 100% of the urine samples (median concentration: 7.96 ng/mL); NA2AP was detected in 94.9% of them (median: 3.05 ng/mL). The intraclass correlation coefficients of their concentrations across three trimesters were poor (<0.4); correlations of NA4AP and NA2AP were weak (r: 0.15-0.23). Pregnant women who had higher household income or urine samples provided in summer (vs. winter) had higher concentrations of NA4AP. Pregnant women who had a college degree or above (vs. less than a high school education) had higher concentrations of NA2AP but urine samples provided in summer (vs. winter) had lower concentrations of NA2AP. The 95th percentile estimated daily intake of NA4AP (2,331 ng/kg-bw/d) based on averaged concentrations of the three trimesters was 40 times lower than the cRfD for NA4AP (2.33 vs. 93 μg/kg-bw/d). Urinary concentrations of NA4AP and NA2AP were associated with higher levels of the selected OSBs. For example, an interquartile range increase in NA4AP was associated with a 26.5% (95% CI: 23.6-29.6%) increase in 8-OHG, a 27.5% (95% CI: 23.8-31.3%) increase in 8-OHdG, and a 33.4% (95% CI: 24.7-42.7%) increase in HNE-MA (p < 0.05). This is the first study to measure their concentrations repeatedly over three trimesters, examine their exposure characteristics, and reveal their associations with the selected OSBs in pregnant women. Further studies are needed to identify non-intentional exposure sources of NA4AP, NA2AP, and another isomer of them (i.e., N-acetyl-3-aminophenol), as well as more health risks related to their exposure.
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Affiliation(s)
- Xuejing Li
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection and State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China.
| | - Li Xu
- Institute of Environmental Health, Wuhan Centers for Disease Control & Prevention, Wuhan, Hubei 430024, PR China.
| | - Yanjian Wan
- Institute of Environmental Health, Wuhan Centers for Disease Control & Prevention, Wuhan, Hubei 430024, PR China.
| | - Juxiao Li
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection and State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China.
| | - Xi Qian
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection and State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China.
| | - Wei Xia
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection and State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China.
| | - Zhenyu He
- Institute of Environmental Health, Wuhan Centers for Disease Control & Prevention, Wuhan, Hubei 430024, PR China.
| | - Tongzhang Zheng
- School of Public Health, Brown University, Providence, RI 02903, USA.
| | - Shunqing Xu
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection and State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China.
| | - Yuanyuan Li
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection and State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China.
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14
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Abstract
Electron crystallography has a storied history which rivals that of its more established X-ray-enabled counterpart. Recent advances in data collection and analysis have sparked a renaissance in the field, opening a new chapter for this venerable technique. Burgeoning interest in electron crystallography has spawned innovative methods described by various interchangeable labels (3D ED, MicroED, cRED, etc.). This Review covers concepts and findings relevant to the practicing crystallographer, with an emphasis on experiments aimed at using electron diffraction to elucidate the atomic structure of three-dimensional molecular crystals.
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Affiliation(s)
- Ambarneil Saha
- UCLA−DOE
Institute for Genomics and Proteomics, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Shervin S. Nia
- UCLA−DOE
Institute for Genomics and Proteomics, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los
Angeles, California 90095, United States
| | - José A. Rodríguez
- UCLA−DOE
Institute for Genomics and Proteomics, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los
Angeles, California 90095, United States
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15
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Andrusenko I, Gemmi M. 3D electron diffraction for structure determination of small-molecule nanocrystals: A possible breakthrough for the pharmaceutical industry. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1810. [PMID: 35595285 PMCID: PMC9539612 DOI: 10.1002/wnan.1810] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 11/10/2022]
Abstract
Nanomedicine is among the most fascinating areas of research. Most of the newly discovered pharmaceutical polymorphs, as well as many new synthesized or isolated natural products, appear only in form of nanocrystals. The development of techniques that allow investigating the atomic structure of nanocrystalline materials is therefore one of the most important frontiers of crystallography. Some unique features of electrons, like their non-neutral charge and their strong interaction with matter, make this radiation suitable for imaging and detecting individual atoms, molecules, or nanoscale objects down to sub-angstrom resolution. In the recent years the development of three-dimensional (3D) electron diffraction (3D ED) has shown that electron diffraction can be successfully used to solve the crystal structure of nanocrystals and most of its limiting factors like dynamical scattering or limited completeness can be easily overcome. This article is a review of the state of the art of this method with a specific focus on how it can be applied to beam sensitive samples like small-molecule organic nanocrystals. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Iryna Andrusenko
- Center for Materials Interfaces, Electron CrystallographyIstituto Italiano di TecnologiaPontedera
| | - Mauro Gemmi
- Center for Materials Interfaces, Electron CrystallographyIstituto Italiano di TecnologiaPontedera
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16
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Two New Organic Co-Crystals Based on Acetamidophenol Molecules. Symmetry (Basel) 2022. [DOI: 10.3390/sym14030431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Herein we present two new organic co-crystals obtained through a simple solution growth process based on an acetamidophenol molecule, either paracetamol or metacetamol, and on 7,7,8,8-tetracyanoquinodimethane (TCNQ). These co-crystals are part of a family of potential organic charge transfer complexes, where the acetamidophenol molecule behaves as an electron donor and TCNQ behaves as an electron acceptor. Due to the sub-micron size of the crystalline domains, 3D electron diffraction was employed for the structure characterization of both systems. Paracetamol-TCNQ structure was solved by standard direct methods, while the analysis of metacetamol-TCNQ was complicated by the low resolution of the available diffraction data and by the low symmetry of the system. The structure determination of metacetamol-TCNQ was eventually achieved after merging two data sets and combining direct methods with simulated annealing. Our study reveals that both paracetamol-TCNQ and metacetamol-TCNQ systems crystallize in a 1:1 stoichiometry, assembling in a mixed-stack configuration and adopting a non-centrosymmetric P1 symmetry. It appears that paracetamol and metacetamol do not form a strong structural scaffold based on hydrogen bonding, as previously observed for orthocetamol-TCNQ and orthocetamol-TCNB (1,2,4,5-tetracyanobenzene) co-crystals.
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17
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Lightowler M, Li S, Ou X, Zou X, Lu M, Xu H. Indomethacin Polymorph δ Revealed To Be Two Plastically Bendable Crystal Forms by 3D Electron Diffraction: Correcting a 47-Year-Old Misunderstanding. Angew Chem Int Ed Engl 2022; 61:e202114985. [PMID: 34902212 PMCID: PMC9306882 DOI: 10.1002/anie.202114985] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Indexed: 11/24/2022]
Abstract
Indomethacin is a clinically classical non-steroidal anti-inflammatory drug that has been marketed since 1965. The third polymorph, Form δ, was discovered by both melt and solution crystallization in 1974. δ-indomethacin cannot be cultivated as large single crystals suitable for X-ray crystallography and, therefore, its crystal structure has not yet been determined. Here, we report the structure elucidation of δ-indomethacin by 3D electron diffraction and reveal the truth that melt-crystallized and solution-crystallized δ-indomethacin are in fact two polymorphs with different crystal structures. We propose to keep the solution-crystallized polymorph as Form δ and name the melt-crystallized polymorph as Form θ. Intriguingly, both structures display plastic flexibility based on a slippage mechanism, making indomethacin the first drug to have two plastic polymorphs. This discovery and correction of a 47-year-old misunderstanding signify that 3D electron diffraction has become a powerful tool for polymorphic structural studies.
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Affiliation(s)
- Molly Lightowler
- Department of Materials and Environmental ChemistryStockholm UniversityStockholmSE-106 91Sweden
| | - Shuting Li
- School of Pharmaceutical SciencesSun Yat-sen UniversityGuangzhou510006China
| | - Xiao Ou
- School of Pharmaceutical SciencesSun Yat-sen UniversityGuangzhou510006China
| | - Xiaodong Zou
- Department of Materials and Environmental ChemistryStockholm UniversityStockholmSE-106 91Sweden
| | - Ming Lu
- School of Pharmaceutical SciencesSun Yat-sen UniversityGuangzhou510006China
| | - Hongyi Xu
- Department of Materials and Environmental ChemistryStockholm UniversityStockholmSE-106 91Sweden
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18
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Lightowler M, Li S, Ou X, Zou X, Lu M, Xu H. Indomethacin Polymorph δ Revealed To Be Two Plastically Bendable Crystal Forms by 3D Electron Diffraction: Correcting a 47‐Year‐Old Misunderstanding**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Molly Lightowler
- Department of Materials and Environmental Chemistry Stockholm University Stockholm SE-106 91 Sweden
| | - Shuting Li
- School of Pharmaceutical Sciences Sun Yat-sen University Guangzhou 510006 China
| | - Xiao Ou
- School of Pharmaceutical Sciences Sun Yat-sen University Guangzhou 510006 China
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry Stockholm University Stockholm SE-106 91 Sweden
| | - Ming Lu
- School of Pharmaceutical Sciences Sun Yat-sen University Guangzhou 510006 China
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry Stockholm University Stockholm SE-106 91 Sweden
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19
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Svensson Grape E, Willhammar T, Inge AK. Triple helix and rod structures of the antiseptic drug bibrocathol revealed by electron crystallography. Chem Commun (Camb) 2022; 58:10695-10698. [DOI: 10.1039/d2cc04209f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bibrocathol is an active pharmaceutical ingredient that has been used to treat eyelid diseases for over a century, yet its structure has remained unknown. 3D electron diffraction on crystals from...
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20
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Samperisi L, Zou X, Huang Z. Three-Dimensional Electron Diffraction: A Powerful Structural Characterization Technique for Crystal Engineering. CrystEngComm 2022. [DOI: 10.1039/d2ce00051b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding crystal structures and behaviors is crucial for constructing and engineering crystalline materials with various properties and functions. Recent advancement in three-dimensional electron diffraction (3D ED) and its application on...
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21
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Microcrystal electron diffraction in macromolecular and pharmaceutical structure determination. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 37:93-105. [PMID: 34895659 DOI: 10.1016/j.ddtec.2020.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 02/05/2023]
Abstract
Microcrystal electron diffraction (MicroED) has recently shown to be a promising technique for structure determination in structural biology and pharmaceutical chemistry. Here, we discuss the unique properties of electrons and motivate its use for diffraction experiments. We review the latest developments in MicroED, and illustrate its applications in macromolecular crystallography, fragment screening and structure guided drug discovery. We discuss the perspectives of MicroED in synthetic chemistry and pharmaceutical development. We anticipate that the rapid advances MicroED showcased here will promote further development of electron crystallography and open up new opportunities for drug discovery.
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22
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Andrusenko I, Hamilton V, Lanza AE, Hall CL, Mugnaioli E, Potticary J, Buanz A, Gaisford S, Piras AM, Zambito Y, Hall SR, Gemmi M. Structure determination, thermal stability and dissolution rate of δ-indomethacin. Int J Pharm 2021; 608:121067. [PMID: 34481012 DOI: 10.1016/j.ijpharm.2021.121067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 11/17/2022]
Abstract
The structure solution of the δ-polymorph of indomethacin was obtained using three-dimensional electron diffraction. This form shows a significantly enhanced dissolution rate compared with the more common and better studied α- and γ-polymorphs, indicating better biopharmaceutical properties for medicinal applications. The structure was solved in non-centrosymmetric space group P21 and comprises two molecules in the asymmetric unit. Packing and molecule conformation closely resemble indomethacin methyl ester and indomethacin methanol solvate. Knowledge of the structure allowed the rational interpretation of spectroscopic IR and Raman data for δ-polymorph and a tentative interpretation for still unsolved indomethacin polymorphs. Finally, we observed a solid-solid transition from δ-polymorph to α-polymorph that can be driven by similarities in molecular conformation.
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Affiliation(s)
- Iryna Andrusenko
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa 56127, Italy
| | - Victoria Hamilton
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Arianna E Lanza
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa 56127, Italy
| | - Charlie L Hall
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Enrico Mugnaioli
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa 56127, Italy
| | - Jason Potticary
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Asma Buanz
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Simon Gaisford
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Anna M Piras
- Department of Pharmacy, University of Pisa, Via Bonanno 33, Pisa 56126, Italy
| | - Ylenia Zambito
- Department of Pharmacy, University of Pisa, Via Bonanno 33, Pisa 56126, Italy.
| | - Simon R Hall
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa 56127, Italy.
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23
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Gruene T, Mugnaioli E. 3D Electron Diffraction for Chemical Analysis: Instrumentation Developments and Innovative Applications. Chem Rev 2021; 121:11823-11834. [PMID: 34533919 PMCID: PMC8517952 DOI: 10.1021/acs.chemrev.1c00207] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 01/26/2023]
Abstract
In the past few years, many exciting papers reported results based on crystal structure determination by electron diffraction. The aim of this review is to provide general and practical information to structural chemists interested in stepping into this emerging field. We discuss technical characteristics of electron microscopes for research units that would like to acquire their own instrumentation, as well as those practical aspects that appear different between X-ray and electron crystallography. We also include a discussion about applications where electron crystallography provides information that is different, and possibly complementary, with respect to what is available from X-ray crystallography.
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Affiliation(s)
- Tim Gruene
- University
of Vienna, Faculty of Chemistry,
Department of Inorganic Chemistry, AT-1090 Vienna, Austria
| | - Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, IT-56127 Pisa, Italy
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24
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Hall CL, Andrusenko I, Potticary J, Gao S, Liu X, Schmidt W, Marom N, Mugnaioli E, Gemmi M, Hall SR. 3D Electron Diffraction Structure Determination of Terrylene, a Promising Candidate for Intermolecular Singlet Fission. Chemphyschem 2021; 22:1631-1637. [PMID: 34117821 PMCID: PMC8457070 DOI: 10.1002/cphc.202100320] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/05/2021] [Indexed: 12/13/2022]
Abstract
Herein we demonstrate the prowess of the 3D electron diffraction approach by unveiling the structure of terrylene, the third member in the series of peri‐condensed naphthalene analogues, which has eluded structure determination for 65 years. The structure was determined by direct methods using electron diffraction data and corroborated by dispersion‐inclusive density functional theory optimizations. Terrylene crystalizes in the monoclinic space group P21/a, arranging in a sandwich‐herringbone packing motif, similar to analogous compounds. Having solved the crystal structure, we use many‐body perturbation theory to evaluate the excited‐state properties of terrylene in the solid‐state. We find that terrylene is a promising candidate for intermolecular singlet fission, comparable to tetracene and rubrene.
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Affiliation(s)
- Charlie L Hall
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Iryna Andrusenko
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation@NEST, Pisa, 56127, Italy
| | - Jason Potticary
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Siyu Gao
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Xingyu Liu
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | | | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Enrico Mugnaioli
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation@NEST, Pisa, 56127, Italy
| | - Mauro Gemmi
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation@NEST, Pisa, 56127, Italy
| | - Simon R Hall
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
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25
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Gruene T, Holstein JJ, Clever GH, Keppler B. Establishing electron diffraction in chemical crystallography. Nat Rev Chem 2021; 5:660-668. [PMID: 37118416 DOI: 10.1038/s41570-021-00302-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
The emerging field of 3D electron diffraction (3D ED) opens new opportunities for structure determination from sub-micrometre-sized crystals. Although the foundations of this technology emerged earlier, the past decade has seen developments in cryo-electron microscopy and (X-ray) crystallography that particularly enable the widespread use of 3D ED. This Perspective describes to chemists and chemical crystallographers just how similar electron and X-ray diffraction are and discusses their complementary aspects. We wish to establish 3D ED in the broader chemistry community, such that electron crystallography becomes a common part of the analytical chemistry toolkit. With a suitable instrument at their disposal, every skilled crystallographer can quickly learn to perform structure determinations using 3D ED.
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26
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Danelius E, Halaby S, van der Donk WA, Gonen T. MicroED in natural product and small molecule research. Nat Prod Rep 2021; 38:423-431. [PMID: 32939523 PMCID: PMC7965795 DOI: 10.1039/d0np00035c] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Covering: 2013 to 2020The electron cryo-microscopy (cryo-EM) method Microcrystal Electron Diffraction (MicroED) allows the collection of high-resolution structural data from vanishingly small crystals that appear like amorphous powders or very fine needles. Since its debut in 2013, data collection and analysis schemes have been fine-tuned, and there are currently close to 100 structures determined by MicroED. Although originally developed to study proteins, MicroED is also very powerful for smaller systems, with some recent and very promising examples from the field of natural products. Herein, we review what has been achieved so far and provide examples of natural product structures, as well as demonstrate the expected future impact of MicroED to the field of natural product and small molecule research.
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Affiliation(s)
- Emma Danelius
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA 90095, USA.
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27
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Woollam GR, Das PP, Mugnaioli E, Andrusenko I, Galanis AS, van de Streek J, Nicolopoulos S, Gemmi M, Wagner T. Structural analysis of metastable pharmaceutical loratadine form II, by 3D electron diffraction and DFT+D energy minimisation. CrystEngComm 2020. [DOI: 10.1039/d0ce01216e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coupling 3D electron diffraction and density functional theory provided the metastable pharmaceutical crystal structure within nanometre range, under ambient conditions.
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Affiliation(s)
| | | | - Enrico Mugnaioli
- Center for Nanotechnology Innovation@NEST
- Istituto Italiano di Tecnologia
- 56127 Pisa
- Italy
| | - Iryna Andrusenko
- Center for Nanotechnology Innovation@NEST
- Istituto Italiano di Tecnologia
- 56127 Pisa
- Italy
| | | | | | | | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST
- Istituto Italiano di Tecnologia
- 56127 Pisa
- Italy
| | - Trixie Wagner
- Novartis Institutes for BioMedical Research
- Basel 4002
- Switzerland
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Broadhurst ET, Xu H, Clabbers MTB, Lightowler M, Nudelman F, Zou X, Parsons S. Polymorph evolution during crystal growth studied by 3D electron diffraction. IUCRJ 2020; 7:5-9. [PMID: 31949899 PMCID: PMC6949601 DOI: 10.1107/s2052252519016105] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/29/2019] [Indexed: 05/24/2023]
Abstract
3D electron diffraction (3DED) has been used to follow polymorph evolution in the crystallization of glycine from aqueous solution. The three polymorphs of glycine which exist under ambient conditions follow the stability order β < α < γ. The least stable β polymorph forms within the first 3 min, but this begins to yield the α-form after only 1 min more. Both structures could be determined from continuous rotation electron diffraction data collected in less than 20 s on crystals of thickness ∼100 nm. Even though the γ-form is thermodynamically the most stable polymorph, kinetics favour the α-form, which dominates after prolonged standing. In the same sample, some β and one crystallite of the γ polymorph were also observed.
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Affiliation(s)
- Edward T. Broadhurst
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh EH9 3FJ, UK
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
| | - Max T. B. Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
| | - Molly Lightowler
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
| | - Fabio Nudelman
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh EH9 3FJ, UK
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
| | - Simon Parsons
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh EH9 3FJ, UK
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29
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Zemtsova VM, Fedorov AY, Fedorova EA, Boa C, Arkhipov SG, Rychkov DA, Minkov VS, Pulham CR, Boldyreva EV. A novel crystal form of metacetamol: the first example of a hydrated form. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2019; 75:1465-1470. [PMID: 31686655 DOI: 10.1107/s2053229619012981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/19/2019] [Indexed: 02/05/2023]
Abstract
We report the crystal structure and crystallization conditions of a first hydrated form of metacetamol (a hemihydrate), C8H9NO2·0.5H2O. It crystallizes from metacetamol-saturated 1:1 (v/v) water-ethanol solutions in a monoclinic structure (space group P21/n) and contains eight metacetamol and four water molecules per unit cell. The conformations of the molecules are the same as in polymorph II of metacetamol, which ensures the formation of hydrogen-bonded dimers and R22(16) ring motifs in its crystal structure similar to those in polymorph II. Unlike in form II, however, these dimers in the hemihydrate are connected through water molecules into infinite hydrogen-bonded molecular chains. Different chains are linked to each other by metacetamol-water and metacetamol-metacetamol hydrogen bonds, the latter type being also present in polymorph I. The overall noncovalent network of the hemihydrate is well developed and several types of hydrogen bonds are responsible for its formation.
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Affiliation(s)
- Viktoria M Zemtsova
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russian Federation
| | - Alexey Yu Fedorov
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russian Federation
| | - Elizaveta A Fedorova
- Boreskov Institute of Catalysis SB RAS, Lavrentiev Ave. 5, Novosibirsk 630090, Russian Federation
| | - Callum Boa
- The University of Edinburgh, School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, Scotland
| | - Sergey G Arkhipov
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russian Federation
| | - Denis A Rychkov
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russian Federation
| | - Vasily S Minkov
- Max-Planck Institute for Chemistry, Hahn-Meitner-Weg 1, Mainz 55128, Germany
| | - Colin R Pulham
- The University of Edinburgh, School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, Scotland
| | - Elena V Boldyreva
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russian Federation
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30
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Gemmi M, Mugnaioli E, Gorelik TE, Kolb U, Palatinus L, Boullay P, Hovmöller S, Abrahams JP. 3D Electron Diffraction: The Nanocrystallography Revolution. ACS CENTRAL SCIENCE 2019; 5:1315-1329. [PMID: 31482114 PMCID: PMC6716134 DOI: 10.1021/acscentsci.9b00394] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Indexed: 05/20/2023]
Abstract
Crystallography of nanocrystalline materials has witnessed a true revolution in the past 10 years, thanks to the introduction of protocols for 3D acquisition and analysis of electron diffraction data. This method provides single-crystal data of structure solution and refinement quality, allowing the atomic structure determination of those materials that remained hitherto unknown because of their limited crystallinity. Several experimental protocols exist, which share the common idea of sampling a sequence of diffraction patterns while the crystal is tilted around a noncrystallographic axis, namely, the goniometer axis of the transmission electron microscope sample stage. This Outlook reviews most important 3D electron diffraction applications for different kinds of samples and problematics, related with both materials and life sciences. Structure refinement including dynamical scattering is also briefly discussed.
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Affiliation(s)
- Mauro Gemmi
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, 56127 Pisa, Italy
| | - Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, 56127 Pisa, Italy
| | - Tatiana E. Gorelik
- University
of Ulm, Central Facility for Electron Microscopy, Electron Microscopy
Group of Materials Science (EMMS), Albert Einstein Allee 11, 89081 Ulm, Germany
| | - Ute Kolb
- Institut
für Anorganische Chemie und Analytische Chemie, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany
- Institut
für Angewandte Geowissenschaften, Technische Universität Darmstadt, Schnittspahnstraße 9, 64287 Darmstadt, Germany
| | - Lukas Palatinus
- Department
of Structure Analysis, Institute of Physics
of the CAS, Na Slovance 2, 182 21 Prague 8, Czechia
| | - Philippe Boullay
- CRISMAT,
Normandie Université, ENSICAEN, UNICAEN, CNRS UMR 6508, 6 Bd Maréchal Juin, F-14050 Cedex Caen, France
| | - Sven Hovmöller
- Inorganic
and Structural Chemistry, Department of Materials and Environmental
Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Jan Pieter Abrahams
- Center
for Cellular Imaging and NanoAnalytics (C−CINA), Biozentrum, Basel University, Mattenstrasse 26, CH-4058 Basel, Switzerland
- Department
of Biology and Chemistry, Paul Scherrer
Institut (PSI), CH-5232 Villigen PSI, Switzerland
- Leiden
Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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31
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Gemmi M, Serravalle E, Roberti di Sarsina P. A New Method Based on Electron Diffraction for Detecting Nanoparticles in Injectable Medicines. J Pharm Sci 2019; 109:891-899. [PMID: 31348938 DOI: 10.1016/j.xphs.2019.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/13/2019] [Accepted: 07/17/2019] [Indexed: 10/26/2022]
Abstract
A new method for detecting and characterizing nanoparticles in an injectable pharmaceutical solution is presented. The method is based on the simultaneous use, on those nanoparticles that are crystalline, of three-dimensional electron diffraction tomography and energy dispersive X-ray spectrometry. With three-dimensional electron diffraction tomography, the unit cell and the crystal symmetry of the nanoparticles are determined, while with energy dispersive X-ray spectrometry, the chemical composition is derived. With these data, through an inspection of a crystallographic database, it is possible to determine the crystal phase of the nanoparticles. The knowledge of the crystal phase is a valuable element for understanding the provenance and the formation of the nanoparticles, helping the researcher in solving any quality control issue related to the presence of nanoparticles in an injectable solution.
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Affiliation(s)
- Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy.
| | - Eugenio Serravalle
- AsSIS, Associazione di Studi e Informazione sulla Salute, Via Firenze 8, Pisa, Italy
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