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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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Lv ZP, Srivastava D, Conley K, Ruoko TP, Xu H, Lightowler M, Hong X, Cui X, Huang Z, Yang T, Wang HY, Karttunen AJ, Bergström L. Visualizing Noncovalent Interactions and Property Prediction of Submicron-Sized Charge-Transfer Crystals from ab-initio Determined Structures. SMALL METHODS 2024:e2301229. [PMID: 38528393 DOI: 10.1002/smtd.202301229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 03/03/2024] [Indexed: 03/27/2024]
Abstract
The charge-transfer (CT) interactions between organic compounds are reflected in the (opto)electronic properties. Determining and visualizing crystal structures of CT complexes are essential for the design of functional materials with desirable properties. Complexes of pyranine (PYR), methyl viologen (MV), and their derivatives are the most studied water-based CT complexes. Nevertheless, very few crystal structures of CT complexes have been reported so far. In this study, the structures of two PYRs-MVs CT crystals and a map of the noncovalent interactions using 3D electron diffraction (3DED) are reported. Physical properties, e.g., band structure, conductivity, and electronic spectra of the CT complexes and their crystals are investigated and compared with a range of methods, including solid and liquid state spectroscopies and highly accurate quantum chemical calculations based on density functional theory (DFT). The combination of 3DED, spectroscopy, and DFT calculation can provide important insight into the structure-property relationship of crystalline CT materials, especially for submicrometer-sized crystals.
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Affiliation(s)
- Zhong-Peng Lv
- Department of Applied Physics, Aalto University, Espoo, FI 02150, Finland
| | - Divya Srivastava
- Department of Chemistry and Materials Science, Aalto University, Espoo, FI 02150, Finland
| | - Kevin Conley
- Department of Chemistry and Materials Science, Aalto University, Espoo, FI 02150, Finland
| | - Tero-Petri Ruoko
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, FI-33720, Finland
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE 10691, Sweden
| | - Molly Lightowler
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE 10691, Sweden
| | - Xiaodan Hong
- Department of Applied Physics, Aalto University, Espoo, FI 02150, Finland
| | - Xiaoqi Cui
- Department of Electronics and Nanoengineering, Aalto University, Espoo, FI 02150, Finland
| | - Zhehao Huang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE 10691, Sweden
| | - Taimin Yang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE 10691, Sweden
| | - Hai-Ying Wang
- School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, P. R. China
| | - Antti J Karttunen
- Department of Chemistry and Materials Science, Aalto University, Espoo, FI 02150, Finland
| | - Lennart Bergström
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE 10691, Sweden
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3
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Yonekura K, Maki-Yonekura S, Takaba K. Applications and limitations of electron 3D crystallography. Structure 2023; 31:1328-1334. [PMID: 37797620 DOI: 10.1016/j.str.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/27/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
Three-dimensional electron diffraction (3D ED) is a measurement and analysis technique in transmission electron microscopy that is used for determining atomic structures from small crystals. Diverse targets such as proteins, polypeptides, and organic compounds, whose crystals exist in aqueous solutions and organic solvents, or as dried powders, can be studied with 3D ED. We have been involved in the development of this technique, which can now rapidly process a large number of data collected through AI control, enabling efficient structure determination. Here, we introduce this method and describe our recent results. These include the structures and pathogenic mechanisms of wild-type and mutant polypeptides associated with the debilitating disease amyotrophic lateral sclerosis (ALS), the double helical structure of nanographene promoting nanofiber formation, and the structural properties of an organic semiconductor containing disordered regions. We also discuss the limitations and prospects of 3D ED compared to microcrystallography with X-ray free electron lasers.
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Affiliation(s)
- Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan.
| | - Saori Maki-Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Kiyofumi Takaba
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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4
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Wang S, Yang T, Kumar K, Namvar S, Kim S, Ahmadiparidari A, Shahbazi H, Singh S, Hemmat Z, Berry V, Cabana J, Khalili-Araghi F, Huang Z, Salehi-Khojin A. Thermodynamics and Kinetics in Anisotropic Growth of One-Dimensional Midentropy Nanoribbons. ACS NANO 2023. [PMID: 37467377 DOI: 10.1021/acsnano.3c04178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
One-dimensional (1D) materials demonstrate anisotropic in-plane physical properties that enable a wide range of functionalities in electronics, photonics, valleytronics, optoelectronics, and catalysis. Here, we undertake an in-depth study of the growth mechanism for equimolar midentropy alloy of (NbTaTi)0.33S3 nanoribbons as a model system for 1D transition metal trichalcogenide structures. To understand the thermodynamic and kinetic effects in the growth process, the energetically preferred phases at different synthesis temperatures and times are investigated, and the phase evolution is inspected at a sequence of growth steps. It is uncovered that the dynamics of the growth process occurs at four different stages via preferential incorporation of chemical species at high-surface-energy facets. Also, a sequence of temperature and time dependent nonuniform to uniform phase evolutions has emerged in the composition and structure of (NbTaTi)0.33S3 which is described based on an anisotropic vapor-solid (V-S) mechanism. Furthermore, direct evidence for the 3D structure of the charge density wave (CDW) phase (width less than 100 nm) is provided by three-dimensional electron diffraction (3DED) in individual nanoribbons at cryogenic temperature, and detailed comparisons are made between the phases obtained before and after CDW transformation. This study provides important fundamental information for the design and synthesis of future 1D alloy structures.
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Affiliation(s)
- Shuxi Wang
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Taimin Yang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Khagesh Kumar
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Shahriar Namvar
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Sungjoon Kim
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Alireza Ahmadiparidari
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Hessam Shahbazi
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Sakshi Singh
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Zahra Hemmat
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Vikas Berry
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Jordi Cabana
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Fatemeh Khalili-Araghi
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Zhehao Huang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Amin Salehi-Khojin
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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Yang T, Xu H, Zou X. Improving data quality for three-dimensional electron diffraction by a post-column energy filter and a new crystal tracking method. J Appl Crystallogr 2022; 55:1583-1591. [PMID: 36570655 PMCID: PMC9721325 DOI: 10.1107/s1600576722009633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022] Open
Abstract
Three-dimensional electron diffraction (3D ED) has become an effective technique to determine the structures of submicrometre- (nanometre-)sized crystals. In this work, energy-filtered 3D ED was implemented using a post-column energy filter in both STEM mode and TEM mode [(S)TEM denoting (scanning) transmission electron microscope]. The setups for performing energy-filtered 3D ED on a Gatan imaging filter are described. The technique and protocol improve the accessibility of energy-filtered 3D ED post-column energy filters, which are available in many TEM laboratories. In addition, a crystal tracking method in STEM mode using high-angle annular dark-field imaging is proposed. This method enables the user to monitor the crystal position while collecting 3D ED data at the same time, allowing a larger tilt range without foregoing any diffraction frames or imposing extra electron dose. In order to compare the differences between energy-filtered and unfiltered 3D ED data sets, three well known crystallized inorganic samples have been studied in detail. For these samples, the final R 1 values improved by 10-30% for the energy-filtered data sets compared with the unfiltered data sets, and the structures became more chemically reasonable. Possible reasons for improvement are also discussed.
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Affiliation(s)
- Taimin Yang
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16 C, Stockholm, SE-10691, Sweden,Correspondence e-mail: ,
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16 C, Stockholm, SE-10691, Sweden,Correspondence e-mail: ,
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16 C, Stockholm, SE-10691, Sweden
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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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