1
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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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2
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Haymaker A, Nannenga BL. Advances and applications of microcrystal electron diffraction (MicroED). Curr Opin Struct Biol 2024; 84:102741. [PMID: 38086321 PMCID: PMC10882645 DOI: 10.1016/j.sbi.2023.102741] [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: 01/01/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 02/08/2024]
Abstract
Microcrystal electron diffraction, commonly referred to as MicroED, has become a powerful tool for high-resolution structure determination. The method makes use of cryogenic transmission electron microscopes to collect electron diffraction data from crystals that are several orders of magnitude smaller than those used by other conventional diffraction techniques. MicroED has been used on a variety of samples including soluble proteins, membrane proteins, small organic molecules, and materials. Here we will review the MicroED method and highlight recent advancements to the methodology, as well as describe applications of MicroED within the fields of structural biology and chemical crystallography.
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Affiliation(s)
- Alison Haymaker
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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3
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Yörük E, Klein H, Kodjikian S. Dose symmetric electron diffraction tomography (DS-EDT): Implementation of a dose-symmetric tomography scheme in 3D electron diffraction. Ultramicroscopy 2024; 255:113857. [PMID: 37797486 DOI: 10.1016/j.ultramic.2023.113857] [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: 06/22/2023] [Revised: 08/30/2023] [Accepted: 09/14/2023] [Indexed: 10/07/2023]
Abstract
Beam sensitive nanomaterials such as zeolites or metal-organic frameworks (MOF) represent a great challenge for crystallographic structure determination and refinement. The strong electron-matter interaction and the high spatial resolution achievable make electron diffraction the technique of choice for particles of sizes below a micrometer and many different 3-dimensional electron diffraction (3D ED) techniques have been developed in recent years. Nevertheless, beam sensitivity of the samples can lead to the crystal structure being damaged during the data acquisition impeding the determination of its structure. A simple way to reduce beam damage is to lower the dose during the experiment. However, this implies weaker diffraction intensities which can become problematic for the exploitation of the data. In order to obtain complete data sets with strong intensities without damaging the crystals, we developed the dose symmetric electron diffraction tomography (DS-EDT) method, combining the low-dose electron diffraction tomography (LD-EDT) technique with the dose-symmetric tomography scheme known from cryo-EM. In order to reduce the dose on an individual crystal and still obtain enough data for a structure solution and refinement, we partition the dose over several crystals. The individual datasets are then merged in order to achieve the necessary completeness. On two test structures we first show that merging of data from small domains of the reciprocal space is indeed sufficient to obtain reliable data for structure solution and refinement. Second, we show on the beam sensitive manganese formate that high-quality data can be obtained on a few frames while the frames that have suffered from beam damage can still be used to determine the orientation matrix and the unit cell of the crystals. The results from the dynamical refinement on the obtained data show a high accuracy of the atom positions. In this way, DS-EDT can reduce the total dose on an individual crystal by an order of magnitude with respect to the already very dose-efficient LD-EDT.
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Affiliation(s)
- Emre Yörük
- Institut Néel, Université Grenoble-Alpes and CNRS, Grenoble 38000, France.
| | - Holger Klein
- Institut Néel, Université Grenoble-Alpes and CNRS, Grenoble 38000, France
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4
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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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5
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Li S, Lightowler M, Ou X, Huang S, Jiang Y, Li X, Zou X, Xu H, Lu M. 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] [Grants] [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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Affiliation(s)
- Shuting Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Molly Lightowler
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Xiao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Siyong Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yifan Jiang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xizhen Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Ming Lu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
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6
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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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7
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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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8
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Studying membrane proteins with MicroED. Biochem Soc Trans 2022; 50:231-239. [PMID: 35191473 PMCID: PMC9022970 DOI: 10.1042/bst20210911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 12/27/2022]
Abstract
The structural investigation of biological macromolecules is indispensable in understanding the molecular mechanisms underlying diseases. Several structural biology techniques have been introduced to unravel the structural facets of biomolecules. Among these, the electron cryomicroscopy (cryo-EM) method microcrystal electron diffraction (MicroED) has produced atomic resolution structures of important biological and small molecules. Since its inception in 2013, MicroED established a demonstrated ability for solving structures of difficult samples using vanishingly small crystals. However, membrane proteins remain the next big frontier for MicroED. The intrinsic properties of membrane proteins necessitate improved sample handling and imaging techniques to be developed and optimized for MicroED. Here, we summarize the milestones of electron crystallography of two-dimensional crystals leading to MicroED of three-dimensional crystals. Then, we focus on four different membrane protein families and discuss representatives from each family solved by MicroED.
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9
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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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10
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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: 17] [Impact Index Per Article: 8.5] [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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11
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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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12
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Gorelik TE, Tehrani KHME, Gruene T, Monecke T, Niessing D, Kaiser U, Blankenfeldt W, Müller R. Crystal structure of natural product argyrin-D determined by 3D electron diffraction. CrystEngComm 2022. [DOI: 10.1039/d2ce00707j] [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
Crystal structure of natural product argyrin D was determined from electron diffraction data.
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Affiliation(s)
- Tatiana E. Gorelik
- Electron Microscopy Group of Materials Science, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, Germany
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrucken, 66123, Germany
| | - Kamaleddin H. M. E. Tehrani
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrucken, 66123, Germany
| | - Tim Gruene
- Faculty of Chemistry, Department of Inorganic Chemistry, University of Vienna, AT-1090 Vienna, Austria
| | - Thomas Monecke
- Institute of Pharmaceutical Biotechnology, Ulm University, James-Franck-Ring N27, 89081 Ulm, Germany
| | - Dierk Niessing
- Institute of Pharmaceutical Biotechnology, Ulm University, James-Franck-Ring N27, 89081 Ulm, Germany
| | - Ute Kaiser
- Electron Microscopy Group of Materials Science, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrucken, 66123, Germany
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13
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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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14
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Clark LJ, Bu G, Nannenga BL, Gonen T. MicroED for the study of protein–ligand interactions and the potential for drug discovery. Nat Rev Chem 2021; 5:853-858. [PMID: 37117388 DOI: 10.1038/s41570-021-00332-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2021] [Indexed: 12/18/2022]
Abstract
Microcrystal electron diffraction (MicroED) is an electron cryo-microscopy (cryo-EM) technique used to determine molecular structures with crystals that are a millionth the size needed for traditional single-crystal X-ray crystallography. An exciting use of MicroED is in drug discovery and development, where it can be applied to the study of proteins and small molecule interactions, and for structure determination of natural products. The structures are then used for rational drug design and optimization. In this Perspective, we discuss the current applications of MicroED for structure determination of protein-ligand complexes and potential future applications in drug discovery.
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15
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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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16
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Chen J. Advanced Electron Microscopy of Nanophased Synthetic Polymers and Soft Complexes for Energy and Medicine Applications. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:2405. [PMID: 34578720 PMCID: PMC8470047 DOI: 10.3390/nano11092405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/02/2021] [Accepted: 09/10/2021] [Indexed: 11/23/2022]
Abstract
After decades of developments, electron microscopy has become a powerful and irreplaceable tool in understanding the ionic, electrical, mechanical, chemical, and other functional performances of next-generation polymers and soft complexes. The recent progress in electron microscopy of nanostructured polymers and soft assemblies is important for applications in many different fields, including, but not limited to, mesoporous and nanoporous materials, absorbents, membranes, solid electrolytes, battery electrodes, ion- and electron-transporting materials, organic semiconductors, soft robotics, optoelectronic devices, biomass, soft magnetic materials, and pharmaceutical drug design. For synthetic polymers and soft complexes, there are four main characteristics that differentiate them from their inorganic or biomacromolecular counterparts in electron microscopy studies: (1) lower contrast, (2) abundance of light elements, (3) polydispersity or nanomorphological variations, and (4) large changes induced by electron beams. Since 2011, the Center for Nanophase Materials Sciences (CNMS) at Oak Ridge National Laboratory has been working with numerous facility users on nanostructured polymer composites, block copolymers, polymer brushes, conjugated molecules, organic-inorganic hybrid nanomaterials, organic-inorganic interfaces, organic crystals, and other soft complexes. This review crystalizes some of the essential challenges, successes, failures, and techniques during the process in the past ten years. It also presents some outlooks and future expectations on the basis of these works at the intersection of electron microscopy, soft matter, and artificial intelligence. Machine learning is expected to automate and facilitate image processing and information extraction of polymer and soft hybrid nanostructures in aspects such as dose-controlled imaging and structure analysis.
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Affiliation(s)
- Jihua Chen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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17
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Halaby S, Martynowycz M, Zhu Z, Tretiak S, Zhugayevych A, Gonen T, Seifrid M. Microcrystal Electron Diffraction for Molecular Design of Functional Non-Fullerene Acceptor Structures. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2021; 33:966-977. [PMID: 36942096 PMCID: PMC10024952 DOI: 10.1021/acs.chemmater.0c04111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Understanding the relationship between molecular structure and solid-state arrangement informs about the design of new organic semiconductor (OSC) materials with improved optoelectronic properties. However, determining their atomic structure remains challenging. Here, we report the lattice organization of two non-fullerene acceptors (NFAs) determined using microcrystal electron diffraction (MicroED) from crystals not traceable by X-ray crystallography. The MicroED structure of o-IDTBR was determined from a powder without crystallization, and a new polymorph of ITIC-Th is identified with the most distorted backbone of any NFA. Electronic structure calculations elucidate the relationships between molecular structures, lattice arrangements, and charge-transport properties for a number of NFA lattices. The high dimensionality of the connectivity of the 3D wire mesh topology is the best for robust charge transport within NFA crystals. However, some examples suffer from uneven electronic coupling. MicroED combined with advanced electronic structure modeling is a powerful new approach for structure determination, exploring polymorphism and guiding the design of new OSCs and NFAs.
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Affiliation(s)
- Steve Halaby
- Howard Hughes Medical Institute, David Geffen School of Medicine, Department of Biological Chemistry and Physiology, University of California, Los Angeles, California 90095, United States
| | - Michael Martynowycz
- Howard Hughes Medical Institute, David Geffen School of Medicine, Department of Biological Chemistry and Physiology, University of California, Los Angeles, California 90095, United States
| | - Ziyue Zhu
- Center for Polymers and Organic Solids, Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Sergei Tretiak
- Physics and Chemistry of Materials, Theoretical Division and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States; Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | | | - Tamir Gonen
- Howard Hughes Medical Institute, David Geffen School of Medicine, Department of Biological Chemistry and Physiology, University of California, Los Angeles, California 90095, United States
| | - Martin Seifrid
- Center for Polymers and Organic Solids, Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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18
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Gleason PR, Nannenga BL, Mills JH. Rapid Structural Analysis of a Synthetic Non-canonical Amino Acid by Microcrystal Electron Diffraction. Front Mol Biosci 2021; 7:609999. [PMID: 33490105 PMCID: PMC7821094 DOI: 10.3389/fmolb.2020.609999] [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: 09/24/2020] [Accepted: 12/07/2020] [Indexed: 02/03/2023] Open
Abstract
Structural characterization of small molecules is a crucial component of organic synthesis. In this work, we applied microcrystal electron diffraction (MicroED) to analyze the structure of the product of an enzymatic reaction that was intended to produce the unnatural amino acid 2,4-dihydroxyphenylalanine (24DHF). Characterization of our isolated product with nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) suggested that an isomer of 24DHF had been formed. Microcrystals present in the isolated product were then used to determine its structure to 0.62 Å resolution, which confirmed its identity as 2-amino-2-(2,4-dihydroxyphenyl)propanoic acid (24DHPA). Moreover, the MicroED structural model indicated that both enantiomeric forms of 24DHPA were present in the asymmetric unit. Notably, the entire structure determination process including setup, data collection, and refinement was completed in ~1 h. The MicroED data not only bolstered previous results obtained using NMR and MS but also immediately provided information about the stereoisomers present in the product, which is difficult to achieve using NMR and MS alone. Our results therefore demonstrate that MicroED methods can provide useful structural information on timescales that are similar to many commonly used analytical methods and can be added to the existing suite of small molecule structure determination tools in future studies.
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Affiliation(s)
- Patrick R. Gleason
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Brent L. Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, United States,*Correspondence: Brent L. Nannenga
| | - Jeremy H. Mills
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States,Jeremy H. Mills
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19
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Sun T, Hughes CE, Guo L, Wei L, Harris KDM, Zhang Y, Ma Y. Direct‐Space Structure Determination of Covalent Organic Frameworks from 3D Electron Diffraction Data. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tu Sun
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
| | | | - Linshuo Guo
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
| | - Lei Wei
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
| | - Kenneth D. M. Harris
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
- School of Chemistry Cardiff University Cardiff CF10 3AT UK
| | - Yue‐Biao Zhang
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
| | - Yanhang Ma
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
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20
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Andrusenko I, Potticary J, Hall SR, Gemmi M. A new olanzapine cocrystal obtained from volatile deep eutectic solvents and determined by 3D electron diffraction. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:1036-1044. [PMID: 33289715 DOI: 10.1107/s2052520620012779] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/20/2020] [Indexed: 06/12/2023]
Abstract
A previously unknown cocrystal of olanzapine and phenol was identified from a volatile deep eutectic solvent as the intermediate species in the crystallization of olanzapine. This new nanocrystalline phase was investigated by electron diffraction, powder X-ray diffraction and differential scanning calorimetry. The structure was determined by simulated annealing using 3D electron diffraction data and confirmed using DFT-D optimizations. Olanzapine and phenol cocrystallize in the triclinic space group P1, supporting the hypothesis of a dimeric growth unit, where a centrosymmetric dimer is stabilized by multiple weak C-H...π interactions and forms double N-H...N hydrogen bonding with adjacent dimers.
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Affiliation(s)
- Iryna Andrusenko
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
| | - Jason Potticary
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom
| | - Simon R Hall
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
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21
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Sun T, Hughes CE, Guo L, Wei L, Harris KDM, Zhang YB, Ma Y. Direct-Space Structure Determination of Covalent Organic Frameworks from 3D Electron Diffraction Data. Angew Chem Int Ed Engl 2020; 59:22638-22644. [PMID: 32885575 DOI: 10.1002/anie.202009922] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Indexed: 02/06/2023]
Abstract
Structure determination of covalent organic frameworks (COFs) with atomic precision is a bottleneck that hinders the development of COF chemistry. Although three-dimensional electron diffraction (3D-ED) data has been used to solve structures of sub-micrometer-sized COFs, successful structure solution is not guaranteed as the data resolution is usually low. We demonstrate that the direct-space strategy for structure solution, implemented using a genetic algorithm (GA), is a successful approach for structure determination of COF-300 from 3D-ED data. Structural models with different geometric constraints were considered in the GA calculations, with successful structure solution achieved from room-temperature 3D-ED data with a resolution as low as ca. 3.78 Å. The generality of this strategy was further verified for different phases of COF-300. This study demonstrates a viable strategy for structure solution of COF materials from 3D-ED data of limited resolution, which may facilitate the discovery of new COF materials in the future.
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Affiliation(s)
- Tu Sun
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Colan E Hughes
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Linshuo Guo
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Lei Wei
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Kenneth D M Harris
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China.,School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Yue-Biao Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
| | - Yanhang Ma
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
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22
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Sun T, Lei W, Ma Y, Zhang Y. Unravelling Crystal Structures of Covalent Organic Frameworks by Electron Diffraction Tomography. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000120] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tu Sun
- School of Physical Science and Technology, ShanghaiTech University Shanghai 201210 China
| | - Wei Lei
- School of Physical Science and Technology, ShanghaiTech University Shanghai 201210 China
| | - Yanhang Ma
- School of Physical Science and Technology, ShanghaiTech University Shanghai 201210 China
| | - Yue‐Biao Zhang
- School of Physical Science and Technology, ShanghaiTech University Shanghai 201210 China
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23
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Das PP, Guzzinati G, Coll C, Gomez Perez A, Nicolopoulos S, Estrade S, Peiro F, Verbeeck J, Zompra AA, Galanis AS. Reliable Characterization of Organic & Pharmaceutical Compounds with High Resolution Monochromated EEL Spectroscopy. Polymers (Basel) 2020; 12:polym12071434. [PMID: 32605004 PMCID: PMC7408036 DOI: 10.3390/polym12071434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 11/16/2022] Open
Abstract
Organic and biological compounds (especially those related to the pharmaceutical industry) have always been of great interest for researchers due to their importance for the development of new drugs to diagnose, cure, treat or prevent disease. As many new API (active pharmaceutical ingredients) and their polymorphs are in nanocrystalline or in amorphous form blended with amorphous polymeric matrix (known as amorphous solid dispersion—ASD), their structural identification and characterization at nm scale with conventional X-Ray/Raman/IR techniques becomes difficult. During any API synthesis/production or in the formulated drug product, impurities must be identified and characterized. Electron energy loss spectroscopy (EELS) at high energy resolution by transmission electron microscope (TEM) is expected to be a promising technique to screen and identify the different (organic) compounds used in a typical pharmaceutical or biological system and to detect any impurities present, if any, during the synthesis or formulation process. In this work, we propose the use of monochromated TEM-EELS, to analyze selected peptides and organic compounds and their polymorphs. In order to validate EELS for fingerprinting (in low loss/optical region) and by further correlation with advanced DFT, simulations were utilized.
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Affiliation(s)
- Partha Pratim Das
- NanoMegas SPRL, Boulevard Edmond Machtens 79, B1080 Brussels, Belgium; (A.G.P.); (A.S.G.)
- Electron Crystallography Solutions SL, Calle Orense 8, 28020 Madrid, Spain
- Correspondence: (P.P.D.); (S.N.)
| | - Giulio Guzzinati
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; (G.G.); (J.V.)
| | - Catalina Coll
- LENS-MIND, Department of Electronics and Biomedical Engineering, Universitat de Barcelona, 08028 Barcelona, Spain; (C.C.); (S.E.); (F.P.)
- Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Alejandro Gomez Perez
- NanoMegas SPRL, Boulevard Edmond Machtens 79, B1080 Brussels, Belgium; (A.G.P.); (A.S.G.)
| | - Stavros Nicolopoulos
- NanoMegas SPRL, Boulevard Edmond Machtens 79, B1080 Brussels, Belgium; (A.G.P.); (A.S.G.)
- Correspondence: (P.P.D.); (S.N.)
| | - Sonia Estrade
- LENS-MIND, Department of Electronics and Biomedical Engineering, Universitat de Barcelona, 08028 Barcelona, Spain; (C.C.); (S.E.); (F.P.)
- Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Francesca Peiro
- LENS-MIND, Department of Electronics and Biomedical Engineering, Universitat de Barcelona, 08028 Barcelona, Spain; (C.C.); (S.E.); (F.P.)
- Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Johan Verbeeck
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; (G.G.); (J.V.)
| | | | - Athanassios S. Galanis
- NanoMegas SPRL, Boulevard Edmond Machtens 79, B1080 Brussels, Belgium; (A.G.P.); (A.S.G.)
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24
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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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25
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Nannenga BL. MicroED methodology and development. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:014304. [PMID: 32071929 PMCID: PMC7018523 DOI: 10.1063/1.5128226] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
Microcrystal electron diffraction, or MicroED, is a method that is capable of determining structure from very small and thin 3D crystals using a transmission electron microscope. MicroED has been successfully used on microcrystalline samples, including proteins, peptides, and small organic molecules, in many cases to very high resolutions. In this work, the MicroED workflow will be briefly described and areas of future method development will be highlighted. These areas include improvements in sample preparation, data collection, and structure determination.
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Affiliation(s)
- Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA and Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, USA
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26
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Brázda P, Palatinus L, Babor M. Electron diffraction determines molecular absolute configuration in a pharmaceutical nanocrystal. Science 2019; 364:667-669. [PMID: 31097664 DOI: 10.1126/science.aaw2560] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/03/2019] [Indexed: 01/19/2023]
Abstract
Determination of the absolute configuration of organic molecules is essential in drug development and the subsequent approval process. We show that this determination is possible through electron diffraction using nanocrystalline material. Ab initio structure determination by electron diffraction has so far been limited to compounds that maintain their crystallinity after a dose of one electron per square angstrom or more. We present a complete structure analysis of a pharmaceutical cocrystal of sofosbuvir and l-proline, which is about one order of magnitude less stable. Data collection on multiple positions of a crystal and an advanced-intensity extraction procedure enabled us to solve the structure ab initio. We further show that dynamical diffraction effects are strong enough to permit unambiguous determination of the absolute structure of material composed of light scatterers.
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Affiliation(s)
- Petr Brázda
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 18200 Prague 8, Czech Republic.
| | - Lukáš Palatinus
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 18200 Prague 8, Czech Republic
| | - Martin Babor
- University of Chemistry and Technology, Technická 3, 16628 Prague 6, Czech Republic.,Zentiva, U Kabelovny 130, 10237 Prague 10, Czech Republic
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27
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Jones CG, Asay M, Kim LJ, Kleinsasser JF, Saha A, Fulton TJ, Berkley KR, Cascio D, Malyutin AG, Conley MP, Stoltz BM, Lavallo V, Rodríguez JA, Nelson HM. Characterization of Reactive Organometallic Species via MicroED. ACS CENTRAL SCIENCE 2019; 5:1507-1513. [PMID: 31572777 PMCID: PMC6764211 DOI: 10.1021/acscentsci.9b00403] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Indexed: 06/10/2023]
Abstract
Here we apply microcrystal electron diffraction (MicroED) to the structural determination of transition-metal complexes. We find that the simultaneous use of 300 keV electrons, very low electron doses, and an ultrasensitive camera allows for the collection of data without cryogenic cooling of the stage. This technique reveals the first crystal structures of the classic zirconocene hydride, colloquially known as "Schwartz's reagent", a novel Pd(II) complex not amenable to solution-state NMR or X-ray crystallography, and five other paramagnetic and diamagnetic transition-metal complexes.
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Affiliation(s)
- Christopher G. Jones
- Department of Chemistry and Biochemistry and
UCLA-DOE Institute for Genomics & Proteomics,
University of California, Los Angeles, California 90095,
United States
| | - Matthew Asay
- Department of Chemistry and Biochemistry and
UCLA-DOE Institute for Genomics & Proteomics,
University of California, Los Angeles, California 90095,
United States
| | - Lee Joon Kim
- Department of Chemistry and Biochemistry and
UCLA-DOE Institute for Genomics & Proteomics,
University of California, Los Angeles, California 90095,
United States
| | - Jack F. Kleinsasser
- Department of Chemistry, University of
California, Riverside, California 92521, United
States
| | - Ambarneil Saha
- Department of Chemistry and Biochemistry and
UCLA-DOE Institute for Genomics & Proteomics,
University of California, Los Angeles, California 90095,
United States
| | - Tyler J. Fulton
- The Warren and Katharine Schlinger Laboratory for
Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering and
Beckman Institute, California Institute of
Technology, Pasadena, California 91125, United
States
| | - Kevin R. Berkley
- Department of Chemistry, University of
California, Riverside, California 92521, United
States
| | - Duilio Cascio
- Department of Chemistry and Biochemistry and
UCLA-DOE Institute for Genomics & Proteomics,
University of California, Los Angeles, California 90095,
United States
| | - Andrey G. Malyutin
- The Warren and Katharine Schlinger Laboratory for
Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering and
Beckman Institute, California Institute of
Technology, Pasadena, California 91125, United
States
| | - Matthew P. Conley
- Department of Chemistry, University of
California, Riverside, California 92521, United
States
| | - Brian M. Stoltz
- The Warren and Katharine Schlinger Laboratory for
Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering and
Beckman Institute, California Institute of
Technology, Pasadena, California 91125, United
States
| | - Vincent Lavallo
- Department of Chemistry, University of
California, Riverside, California 92521, United
States
| | - José A. Rodríguez
- Department of Chemistry and Biochemistry and
UCLA-DOE Institute for Genomics & Proteomics,
University of California, Los Angeles, California 90095,
United States
| | - Hosea M. Nelson
- Department of Chemistry and Biochemistry and
UCLA-DOE Institute for Genomics & Proteomics,
University of California, Los Angeles, California 90095,
United States
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28
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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: 227] [Impact Index Per Article: 45.4] [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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29
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Kolb U, Krysiak Y, Plana-Ruiz S. Automated electron diffraction tomography - development and applications. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:463-474. [PMID: 32830704 PMCID: PMC6690130 DOI: 10.1107/s2052520619006711] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/10/2019] [Indexed: 06/10/2023]
Abstract
Electron diffraction tomography (EDT) has gained increasing interest, starting with the development of automated electron diffraction tomography (ADT) which enables the collection of three-dimensional electron diffraction data from nano-sized crystals suitable for ab initio structure analysis. A basic description of the ADT method, nowadays recognized as a reliable and established method, as well as its special features and general applicability to different transmission electron microscopes is provided. In addition, the usability of ADT for crystal structure analysis of single nano-sized crystals with and without special crystallographic features, such as twinning, modulations and disorder is demonstrated.
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Affiliation(s)
- Ute Kolb
- Institut für Anorganische Chemie und Analytische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, Mainz, 55128, Germany
- Institut für Angewandte Geowissenchaften, Technische Universität Darmstadt, Schnittspahnstrasse 9, Darmstadt, 64287, Germany
| | - Yaşar Krysiak
- Institut für Anorganische Chemie und Analytische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, Mainz, 55128, Germany
| | - Sergi Plana-Ruiz
- Institut für Angewandte Geowissenchaften, Technische Universität Darmstadt, Schnittspahnstrasse 9, Darmstadt, 64287, Germany
- LENS-MIND, Departament d’Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, Martí i Franquès 1, Barcelona, 08028, Spain
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30
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Gemmi M, Lanza AE. 3D electron diffraction techniques. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:495-504. [PMID: 32830707 DOI: 10.1107/s2052520619007510] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/23/2019] [Indexed: 06/11/2023]
Abstract
3D electron diffraction is an emerging technique for the structural analysis of nanocrystals. The challenges that 3D electron diffraction has to face for providing reliable data for structure solution and the different ways of overcoming these challenges are described. The route from zone axis patterns towards 3D electron diffraction techniques such as precession-assisted electron diffraction tomography, rotation electron diffraction and continuous rotation is also discussed. Finally, the advantages of the new hybrid detectors with high sensitivity and fast readout are demonstrated with a proof of concept experiment of continuous rotation electron diffraction on a natrolite nanocrystal.
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Affiliation(s)
- Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, 56127, Italy
| | - Arianna E Lanza
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, 56127, Italy
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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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32
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Lanza AE, Gemmi M, Bindi L, Mugnaioli E, Paar WH. Daliranite, PbHgAs2S5: determination of the incommensurately modulated structure and revision of the chemical formula. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2019; 75:711-716. [DOI: 10.1107/s2052520619007340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/20/2019] [Indexed: 01/16/2023]
Abstract
The incommensurately modulated crystal structure of the mineral daliranite has been determined using 3D electron diffraction data obtained on nanocrystalline domains. Daliranite is orthorhombic with a = 21, b = 4.3, c = 9.5 Å and shows modulation satellites along c. The solution of the average structure in the Pnma space group together with energy-dispersive X-ray spectroscopy data obtained on the same domains indicate a chemical formula of PbHgAs2S5, which has one S fewer than previously reported. The crystal structure of daliranite is built from columns of face-sharing PbS8 bicapped trigonal prisms laterally connected by [2+4]Hg polyhedra and (As3+
2S5)4− groups. The excellent quality of the electron diffraction data allows a structural model to be built for the modulated structure in superspace, which shows that the modulation is due to an alternated occupancy of a split As site.
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33
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Andrusenko I, Hamilton V, Mugnaioli E, Lanza A, Hall C, Potticary J, Hall SR, Gemmi M. The Crystal Structure of Orthocetamol Solved by 3D Electron Diffraction. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904564] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Iryna Andrusenko
- Center for Nanotechnology Innovation@NESTIstituto Italiano di Tecnologia Piazza San Silvestro 12 Pisa Italy
| | - Victoria Hamilton
- Complex Functional Materials GroupSchool of ChemistryUniversity of Bristol Bristol BS8 1TS UK
- Bristol Centre for Functional NanomaterialsCentre for Nanoscience and Quantum Information Tyndall Avenue Bristol BS8 1FD UK
| | - Enrico Mugnaioli
- Center for Nanotechnology Innovation@NESTIstituto Italiano di Tecnologia Piazza San Silvestro 12 Pisa Italy
| | - Arianna Lanza
- Center for Nanotechnology Innovation@NESTIstituto Italiano di Tecnologia Piazza San Silvestro 12 Pisa Italy
| | - Charlie Hall
- Complex Functional Materials GroupSchool of ChemistryUniversity of Bristol Bristol BS8 1TS UK
- Centre for Doctoral Training in Condensed Matter PhysicsHH Wills Physics Laboratory Tyndall Avenue Bristol BS8 1TL UK
| | - Jason Potticary
- Complex Functional Materials GroupSchool of ChemistryUniversity of Bristol Bristol BS8 1TS UK
| | - Simon R. Hall
- Complex Functional Materials GroupSchool of ChemistryUniversity of Bristol Bristol BS8 1TS UK
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NESTIstituto Italiano di Tecnologia Piazza San Silvestro 12 Pisa Italy
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34
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Andrusenko I, Hamilton V, Mugnaioli E, Lanza A, Hall C, Potticary J, Hall SR, Gemmi M. The Crystal Structure of Orthocetamol Solved by 3D Electron Diffraction. Angew Chem Int Ed Engl 2019; 58:10919-10922. [PMID: 31210373 DOI: 10.1002/anie.201904564] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/14/2019] [Indexed: 12/11/2022]
Abstract
Orthocetamol is a regioisomer of the well-known pain medication paracetamol and a promising analgesic and an anti-arthritic medicament itself. However, orthocetamol cannot be grown as single crystals suitable for X-ray diffraction, so its crystal structure has remained a mystery for more than a century. Here, we report the ab-initio structure determination of orthocetamol obtained by 3D electron diffraction, combining a low-dose acquisition method and a dedicated single-electron detector for recording the diffracted intensities. The structure is monoclinic, with a pseudo-tetragonal cell that favors multiple twinning on a scale of a few tens of nanometers. The successful application of 3D electron diffraction to orthocetamol introduces a new gold standard of total structure solution in all cases where X-ray diffraction and electron-microscope imaging methods fail.
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Affiliation(s)
- Iryna Andrusenko
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
| | - Victoria Hamilton
- Complex Functional Materials Group, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,Bristol Centre for Functional Nanomaterials, Centre for Nanoscience and Quantum Information, Tyndall Avenue, Bristol, BS8 1FD, UK
| | - Enrico Mugnaioli
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
| | - Arianna Lanza
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
| | - Charlie Hall
- Complex Functional Materials Group, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,Centre for Doctoral Training in Condensed Matter Physics, HH Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
| | - Jason Potticary
- Complex Functional Materials Group, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Simon R Hall
- Complex Functional Materials Group, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
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35
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Hofstetter A, Balodis M, Paruzzo FM, Widdifield CM, Stevanato G, Pinon AC, Bygrave PJ, Day GM, Emsley L. Rapid Structure Determination of Molecular Solids Using Chemical Shifts Directed by Unambiguous Prior Constraints. J Am Chem Soc 2019; 141:16624-16634. [PMID: 31117663 PMCID: PMC7540916 DOI: 10.1021/jacs.9b03908] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
NMR-based crystallography approaches involving the combination of crystal structure prediction methods, ab initio calculated chemical shifts and solid-state NMR experiments are powerful methods for crystal structure determination of microcrystalline powders. However, currently structural information obtained from solid-state NMR is usually included only after a set of candidate crystal structures has already been independently generated, starting from a set of single-molecule conformations. Here, we show with the case of ampicillin that this can lead to failure of structure determination. We propose a crystal structure determination method that includes experimental constraints during conformer selection. In order to overcome the problem that experimental measurements on the crystalline samples are not obviously translatable to restrict the single-molecule conformational space, we propose constraints based on the analysis of absent cross-peaks in solid-state NMR correlation experiments. We show that these absences provide unambiguous structural constraints on both the crystal structure and the gas-phase conformations, and therefore can be used for unambiguous selection. The approach is parametrized on the crystal structure determination of flutamide, flufenamic acid, and cocaine, where we reduce the computational cost by around 50%. Most importantly, the method is then shown to correctly determine the crystal structure of ampicillin, which would have failed using current methods because it adopts a high-energy conformer in its crystal structure. The average positional RMSE on the NMR powder structure is ⟨rav⟩ = 0.176 Å, which corresponds to an average equivalent displacement parameter Ueq = 0.0103 Å2.
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Affiliation(s)
- Albert Hofstetter
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Martins Balodis
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Federico M Paruzzo
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Cory M Widdifield
- Department of Chemistry, Mathematics and Science Center , Oakland University , 146 Library Drive , Rochester , Michigan 48309-4479 , United States
| | - Gabriele Stevanato
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Arthur C Pinon
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Peter J Bygrave
- School of Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , United Kingdom
| | - Graeme M Day
- School of Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , United Kingdom
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
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36
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Nicolopoulos S, Das PP, Pérez AG, Zacharias N, Cuapa ST, Alatorre JAA, Mugnaioli E, Gemmi M, Rauch EF. Novel TEM Microscopy and Electron Diffraction Techniques to Characterize Cultural Heritage Materials: From Ancient Greek Artefacts to Maya Mural Paintings. SCANNING 2019; 2019:4870695. [PMID: 31263516 PMCID: PMC6556332 DOI: 10.1155/2019/4870695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
To understand in-depth material properties, manufacturing, and conservation in cultural heritage artefacts, there is a strong need for advanced characterization tools that enable analysis down to the nanometric scale. Transmission electron microscopy (TEM) and electron diffraction (ED) techniques, like 3D precession electron diffraction tomography and ASTAR phase/orientation mapping, are proposed to study cultural heritage materials at nanoscale. In this work, we show how electron crystallography in TEM helps to determine precise structural information and phase/orientation distribution of various pigments in cultural heritage materials from various historical periods like Greek amphorisks, Roman glass tesserae, and pre-Hispanic Maya mural paintings. Such TEM-based methods can be an alternative to synchrotron techniques and can allow distinguishing accurately different crystalline phases even in cases of identical or very close chemical compositions at the nanometric scale.
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Affiliation(s)
| | - Partha P. Das
- NanoMEGAS Sprl, Blvd Edmond Machtens 79, B-1080 Brussels, Belgium
- Electron Crystallography Solutions SL, Calle Orense 8, 28020 Madrid, Spain
| | | | - Nikolaos Zacharias
- Department of History, Archaeology and Cultural Resources Management, University of the Peloponnese, 24100 Kalamata, Greece
| | - Samuel Tehuacanero Cuapa
- Instituto de Física, Circuito de la Investigación s/n, UNAM, Cd. Universitaria, Coyoacán, 04510 México D.F., Mexico
| | - Jesús Angel Arenas Alatorre
- Instituto de Física, Circuito de la Investigación s/n, UNAM, Cd. Universitaria, Coyoacán, 04510 México D.F., Mexico
| | - Enrico Mugnaioli
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Edgar F. Rauch
- SIMaP, Grenoble INP CNRS UJF, BP 46, 38402 Saint-Martin-d'Hères Cedex, France
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