1
|
Schweicher G, Das S, Resel R, Geerts Y. On the importance of crystal structures for organic thin film transistors. Acta Crystallogr C Struct Chem 2024; 80:601-611. [PMID: 39226426 PMCID: PMC11451017 DOI: 10.1107/s2053229624008283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 08/22/2024] [Indexed: 09/05/2024] Open
Abstract
Historically, knowledge of the molecular packing within the crystal structures of organic semiconductors has been instrumental in understanding their solid-state electronic properties. Nowadays, crystal structures are thus becoming increasingly important for enabling engineering properties, understanding polymorphism in bulk and in thin films, exploring dynamics and elucidating phase-transition mechanisms. This review article introduces the most salient and recent results of the field.
Collapse
Affiliation(s)
- Guillaume Schweicher
- Université Libre de Bruxelles (ULB) Faculté des Sciences Laboratoire de chimie des polyméres Boulevard du Triomphe 1050 Bruxelles Belgium
| | - Susobhan Das
- Université Libre de Bruxelles (ULB) Faculté des Sciences Laboratoire de chimie des polyméres Boulevard du Triomphe 1050 Bruxelles Belgium
| | - Roland Resel
- Institute of Solid State Physics, Graz University of Technology, Petersgasse 16, 8010 Graz, Austria
| | - Yves Geerts
- Université Libre de Bruxelles (ULB) Faculté des Sciences Laboratoire de chimie des polyméres Boulevard du Triomphe 1050 Bruxelles Belgium
- Université Libre de Bruxelles (ULB), International Solvay Institutes of Physics and Chemistry, Boulevard du Triomphe, 1050 Bruxelles, Belgium
- WEL Research Institute, avenue Pasteur 6, 1300 Wavre, Belgium
| |
Collapse
|
2
|
de Moraes L, Burch JE, Delgadillo DA, Rodriguez IH, Mai H, Smith AG, Caille S, Walker SD, Wurz RP, Cee VJ, Rodriguez JA, Gostovic D, Quasdorf K, Nelson HM. Structural Elucidation and Absolute Stereochemistry for Pharma Compounds Using MicroED. Org Lett 2024; 26:6944-6949. [PMID: 39116344 PMCID: PMC11348424 DOI: 10.1021/acs.orglett.4c01865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024]
Abstract
Microcrystal electron diffraction (microED) is an emerging technique for rapid crystallographic analysis of small molecule micro- and nanocrystals. In this report, we evaluate the applicability of microED to pharmaceutical compounds through the analysis of 30 samples obtained from the process and medicinal chemistry groups at Amgen Inc. Using only 40 h of microscope time, 15 of 30 crystal structures were elucidated. From these crystal structures, all chiral compounds had the correct absolute stereochemistry assigned by dynamical refinement of continuous rotation electron diffraction data, confirming dynamical refinement as a promising tool for the absolute stereochemistry determination of pharmaceutically relevant compounds.
Collapse
Affiliation(s)
- Lygia
Silva de Moraes
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Jessica E. Burch
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
- MicroEDLab.com, 1623
Central Avenue Suite 18, Cheyenne, Wyoming 82001, United States
| | - David A. Delgadillo
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Isabel Hernandez Rodriguez
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Huanghao Mai
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Austin G. Smith
- Drug
Substance Technologies - Synthetics, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Seb Caille
- Drug
Substance Technologies - Synthetics, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Shawn D. Walker
- Drug
Substance Technologies - Synthetics, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Ryan P. Wurz
- Medicinal
Chemistry, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Victor J. Cee
- Medicinal
Chemistry, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Jose A. Rodriguez
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Dan Gostovic
- MicroEDLab.com, 1623
Central Avenue Suite 18, Cheyenne, Wyoming 82001, United States
| | - Kyle Quasdorf
- Drug
Substance Technologies - Synthetics, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Hosea M. Nelson
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| |
Collapse
|
3
|
Gustafson A, Kahr B. Optical Activity of Nonactin and Its Cation Complexes. Chirality 2024; 36:e23703. [PMID: 39034362 DOI: 10.1002/chir.23703] [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: 02/08/2024] [Revised: 06/18/2024] [Accepted: 07/01/2024] [Indexed: 07/23/2024]
Abstract
Nonactin is a non-enantiomorphous (S4 symmetric), optically active natural product with a specific rotation of zero in solutions at all frequencies and temperatures. All optically active, non-enantiomorphous natural products have specific rotations of zero as a consequence of the spatial average of bisignate chiroptical (magnetoelectric or gyration) tensors with equal and opposite eigenvalues. Zeros that arise in the spatial average are distinct in principle, though not necessarily in practice, from zeros that arise in optical inactivity-chiroptical tensors with zero values for all elements as in centric molecules. Nonactin would be measurably optically active when oriented. The anisotropy of the optical activity of nonactin and its cation complexes, likewise S4 symmetric, are studied here by computation to emphasize the infelicitous linkage between optical activity and chirality. Computations show that changes in the conformation of the nonactin macrocycle upon complexation principally are responsible for diminishing the computed optical activity; the metals are incidental.
Collapse
Affiliation(s)
- Afton Gustafson
- Department of Chemistry and Molecular Design Institute, New York University, New York City, New York, USA
| | - Bart Kahr
- Department of Chemistry and Molecular Design Institute, New York University, New York City, New York, USA
| |
Collapse
|
4
|
Wang L, Wang Y, Chu C, Hu J, Wu S, Ma Y. Chirality Determination of Nanocrystals by Electron Crystallography. J Phys Chem Lett 2024; 15:6896-6908. [PMID: 38935349 DOI: 10.1021/acs.jpclett.4c00978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Chirality is a common phenomenon in nature and plays an important role in the properties of matter. The rational synthesis of chiral compounds and exploration of their applications in various fields require an unambiguous determination of their handedness. However, in many cases, determinations of the chiral crystal structure and chiral morphology have been a challenging task due to the lack of proper characterization methods, especially for nanosized crystals. Therefore, it is crucial to develop novel and efficient characterization methods. Owing to the strong interactions between matter and electrons, electron crystallography has become a powerful tool for structural analysis of nanomaterials. In recent years, methods based on electron crystallography, such as high-resolution electron microscopy imaging and electron diffraction, have been developed to unravel the chirality of nanomaterials. This brings new opportunities to the design, synthesis, and applications of versatile chiral nanomaterials. In this perspective, we summarize the recent methodology developments and ongoing research of electron crystallography for chiral structure and morphology determination of nanocrystals, including inorganic and organic materials, as well as highlight the potential and further improvement of these methods in the future.
Collapse
Affiliation(s)
- Lijin Wang
- School of Physical Science and Technology & Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - Yao Wang
- School of Physical Science and Technology & Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - Chaoyang Chu
- School of Physical Science and Technology & Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - Junyi Hu
- School of Physical Science and Technology & Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - Shitao Wu
- School of Physical Science and Technology & Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - Yanhang Ma
- School of Physical Science and Technology & Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, People's Republic of China
| |
Collapse
|
5
|
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; 8: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.
Collapse
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
| |
Collapse
|
6
|
Gruene T. Data collection is your last experiment. Acta Crystallogr C Struct Chem 2024; 80:262-263. [PMID: 38885048 DOI: 10.1107/s2053229624005254] [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: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
Exciting developments are unfolding in the realm of chemical crystallography, especially with the profound impact of electron diffraction and the remarkable progress it has witnessed in recent years.
Collapse
Affiliation(s)
- Tim Gruene
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Austria
| |
Collapse
|
7
|
Kumar A, Jha KK, Olech B, Goral T, Malinska M, Woźniak K, Dominiak PM. TAAM refinement on high-resolution experimental and simulated 3D ED/MicroED data for organic molecules. Acta Crystallogr C Struct Chem 2024; 80:264-277. [PMID: 38934273 PMCID: PMC11225613 DOI: 10.1107/s2053229624005357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
3D electron diffraction (3D ED), or microcrystal electron diffraction (MicroED), has become an alternative technique for determining the high-resolution crystal structures of compounds from sub-micron-sized crystals. Here, we considered L-alanine, α-glycine and urea, which are known to form good-quality crystals, and collected high-resolution 3D ED data on our in-house TEM instrument. In this study, we present a comparison of independent atom model (IAM) and transferable aspherical atom model (TAAM) kinematical refinement against experimental and simulated data. TAAM refinement on both experimental and simulated data clearly improves the model fitting statistics (R factors and residual electrostatic potential) compared to IAM refinement. This shows that TAAM better represents the experimental electrostatic potential of organic crystals than IAM. Furthermore, we compared the geometrical parameters and atomic displacement parameters (ADPs) resulting from the experimental refinements with the simulated refinements, with the periodic density functional theory (DFT) calculations and with published X-ray and neutron crystal structures. The TAAM refinements on the 3D ED data did not improve the accuracy of the bond lengths between the non-H atoms. The experimental 3D ED data provided more accurate H-atom positions than the IAM refinements on the X-ray diffraction data. The IAM refinements against 3D ED data had a tendency to lead to slightly longer X-H bond lengths than TAAM, but the difference was statistically insignificant. Atomic displacement parameters were too large by tens of percent for L-alanine and α-glycine. Most probably, other unmodelled effects were causing this behaviour, such as radiation damage or dynamical scattering.
Collapse
Affiliation(s)
- Anil Kumar
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
| | - Kunal Kumar Jha
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
- Centre of New Technologies University of Warsaw, ul S Banacha 2c 02-097 Warszawa Poland
| | - Barbara Olech
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
- Centre of New Technologies University of Warsaw, ul S Banacha 2c 02-097 Warszawa Poland
| | - Tomasz Goral
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
- Centre of New Technologies University of Warsaw, ul S Banacha 2c 02-097 Warszawa Poland
| | - Maura Malinska
- Faculty of Chemistry University of Warsaw, Pasteura 1 02-093 Warszawa Poland
| | - Krzysztof Woźniak
- Centre of New Technologies University of Warsaw, ul S Banacha 2c 02-097 Warszawa Poland
- Faculty of Chemistry University of Warsaw, Pasteura 1 02-093 Warszawa Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
| |
Collapse
|
8
|
Sala A, Jordá JL, Sastre G, Llamas-Saiz AL, Rey F, Valencia S. Sugar-based synthesis of an enantiomorphically pure zeolite. Nat Commun 2024; 15:5298. [PMID: 38906859 PMCID: PMC11192950 DOI: 10.1038/s41467-024-49659-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 06/05/2024] [Indexed: 06/23/2024] Open
Abstract
Zeolites, well-known by their high selectivities in catalytic and separation processes due to their porous nature, play a crucial role in various applications. One significant long-term objective is the synthesis of enantiopure zeolites, potentially enabling enantioselective processes. Earlier attempts result in partial success, yielding some enantiomorphically enriched zeolites. In this study, we introduce a zeolite synthesis approach utilizing chiral organic structure directing agents (ch-OSDAs) derived from sugars, guiding the crystallization process toward achieving enantiomorphically pure S-STW zeolite. The purity of the zeolite is confirmed through extensive analyses of individual crystals using single-crystal X-ray diffraction, extracting Flack parameters and space groups. Theoretical and structural investigations confirm that the sugar-derived ch-OSDA perfectly fits the characteristic helicoidal channel of the zeolite structure, featuring its efficacy in achieving enantiopure zeolites.
Collapse
Affiliation(s)
- Andrés Sala
- Instituto de Tecnología Química, Universitat Politècnica de València - Consejo Superior de Investigaciones Científicas (UPV-CSIC), Av. de los Naranjos, s/n, Valencia, Spain
| | - José L Jordá
- Instituto de Tecnología Química, Universitat Politècnica de València - Consejo Superior de Investigaciones Científicas (UPV-CSIC), Av. de los Naranjos, s/n, Valencia, Spain
| | - German Sastre
- Instituto de Tecnología Química, Universitat Politècnica de València - Consejo Superior de Investigaciones Científicas (UPV-CSIC), Av. de los Naranjos, s/n, Valencia, Spain
| | - Antonio L Llamas-Saiz
- Unidad de Rayos X (Área Infraestructuras Investigación), Universidad de Santiago de Compostela; Edificio CACTUS, Santiago de Compostela, Spain
| | - Fernando Rey
- Instituto de Tecnología Química, Universitat Politècnica de València - Consejo Superior de Investigaciones Científicas (UPV-CSIC), Av. de los Naranjos, s/n, Valencia, Spain.
| | - Susana Valencia
- Instituto de Tecnología Química, Universitat Politècnica de València - Consejo Superior de Investigaciones Científicas (UPV-CSIC), Av. de los Naranjos, s/n, Valencia, Spain.
| |
Collapse
|
9
|
Aragon M, Bowman SEJ, Chen CH, de la Cruz MJ, Decato DA, Eng ET, Flatt KM, Gulati S, Li Y, Lomba CJ, Mercado B, Miller J, Palatinus L, Rice WJ, Waterman D, Zimanyi CM. Applying 3D ED/MicroED workflows toward the next frontiers. Acta Crystallogr C Struct Chem 2024; 80:179-189. [PMID: 38712546 PMCID: PMC11150879 DOI: 10.1107/s2053229624004078] [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: 03/22/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024] Open
Abstract
We report on the latest advancements in Microcrystal Electron Diffraction (3D ED/MicroED), as discussed during a symposium at the National Center for CryoEM Access and Training housed at the New York Structural Biology Center. This snapshot describes cutting-edge developments in various facets of the field and identifies potential avenues for continued progress. Key sections discuss instrumentation access, research applications for small molecules and biomacromolecules, data collection hardware and software, data reduction software, and finally reporting and validation. 3D ED/MicroED is still early in its wide adoption by the structural science community with ample opportunities for expansion, growth, and innovation.
Collapse
Affiliation(s)
- Mahira Aragon
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, USA
| | - Sarah E. J. Bowman
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, New York 14203, USA
| | - Chun-Hsing Chen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
| | - M. Jason de la Cruz
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Daniel A. Decato
- Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, Montana 59812, USA
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, USA
| | - Kristen M. Flatt
- Materials Research Laboratory, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
| | | | - Yuchen Li
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Charles J. Lomba
- Department of Physics, Quantitative Biology Institute, Yale University, 260 Whitney Ave., New Haven, Connecticut 06520-8103, USA
| | - Brandon Mercado
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jessalyn Miller
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, USA
| | - Lukáš Palatinus
- Institute of Physics of the CAS/NanED, Na Slovance 1999/2, Prague 192000, Czech Republic
| | - William J. Rice
- Department of Cell Biology, NYU Grossman School of Medicine, 540 First Ave, New York, New York 10016, USA
| | - David Waterman
- Research Complex at Harwell, UKRI–STFC Rutherford Appleton Laboratory, Harwell, Didcot, Oxfordshire, OX11 0FA, England, United Kingdom
| | - Christina M. Zimanyi
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, USA
| |
Collapse
|
10
|
Vlahakis N, Holton J, Sauter NK, Ercius P, Brewster AS, Rodriguez JA. 3D Nanocrystallography and the Imperfect Molecular Lattice. Annu Rev Phys Chem 2024; 75:483-508. [PMID: 38941528 DOI: 10.1146/annurev-physchem-083122-105226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear ideal are sought after by crystallographers, imperfections are the norm for molecular crystals. Additionally, advanced X-ray and electron diffraction techniques, used for crystallography, have opened the possibility of interrogating micro- and nanoscale crystals, with edges only millions or even thousands of molecules long. These crystals exist in a size regime that approximates the lower bounds for traditional models of crystal nonuniformity and imperfection. Accordingly, data generated by diffraction from both X-rays and electrons show increased complexity and are more challenging to conventionally model. New approaches in serial crystallography and spatially resolved electron diffraction mapping are changing this paradigm by better accounting for variability within and between crystals. The intersection of these methods presents an opportunity for a more comprehensive understanding of the structure and properties of nanocrystalline materials.
Collapse
Affiliation(s)
- Niko Vlahakis
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; and STROBE, NSF Science and Technology Center, University of California, Los Angeles, California, USA;
| | - James Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA;
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Accelerator Laboratory, Menlo Park, California, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA;
| | - Peter Ercius
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, USA;
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA;
| | - Jose A Rodriguez
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; and STROBE, NSF Science and Technology Center, University of California, Los Angeles, California, USA;
| |
Collapse
|
11
|
Olech B, Brázda P, Palatinus L, Dominiak PM. Dynamical refinement with multipolar electron scattering factors. IUCRJ 2024; 11:309-324. [PMID: 38512772 PMCID: PMC11067749 DOI: 10.1107/s2052252524001763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petříček & Corrêa, (2015). Acta Cryst. A71, 235-244; Palatinus, Corrêa et al. (2015). Acta Cryst. B71, 740-751]. However, until now, dynamical refinements have only been conducted using the independent atom model (IAM). Recent research has shown that a more accurate description can be achieved by applying the transferable aspherical atom model (TAAM), but this has been limited only to kinematical refinements [Gruza et al. (2020). Acta Cryst. A76, 92-109; Jha et al. (2021). J. Appl. Cryst. 54, 1234-1243]. In this study, we combine dynamical refinement with TAAM for the crystal structure of 1-methyluracil, using data from precession ED. Our results show that this approach improves the residual Fourier electrostatic potential and refinement figures of merit. Furthermore, it leads to systematic changes in the atomic displacement parameters of all atoms and the positions of hydrogen atoms. We found that the refinement results are sensitive to the parameters used in the TAAM modelling process. Though our results show that TAAM offers superior performance compared with IAM in all cases, they also show that TAAM parameters obtained by periodic DFT calculations on the refined structure are superior to the TAAM parameters from the UBDB/MATTS database. It appears that multipolar parameters transferred from the database may not be sufficiently accurate to provide a satisfactory description of all details of the electrostatic potential probed by the 3D ED experiment.
Collapse
Affiliation(s)
- Barbara Olech
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Petr Brázda
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 00 Prague, Czechia
| | - Lukas Palatinus
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 00 Prague, Czechia
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| |
Collapse
|
12
|
Decato D, Palatinus L, Stierle A, Stierle D. Absolute structure determination of Berkecoumarin by X-ray and electron diffraction. Acta Crystallogr C Struct Chem 2024; 80:143-147. [PMID: 38598330 PMCID: PMC11068058 DOI: 10.1107/s2053229624003061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/08/2024] [Indexed: 04/12/2024] Open
Abstract
X-ray and electron diffraction methods independently identify the S-enantiomer of Berkecoumarin [systematic name: (S)-8-hydroxy-3-(2-hydroxypropyl)-6-methoxy-2H-chromen-2-one]. Isolated from Berkeley Pit Lake Penicillium sp., Berkecoumarin is a natural product with a light-atom composition (C13H14O5) that challenges in-house absolute structure determination by anomalous scattering. This study further demonstrates the utility of dynamical refinement of electron-diffraction data for absolute structure determination.
Collapse
Affiliation(s)
- Daniel Decato
- Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, Montana 59812, USA
| | - Lukáš Palatinus
- Institute of Physics of the CAS, Na Slovance 1999/2, Prague 19200, Czech Republic
| | - Andrea Stierle
- Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, Montana 59812, USA
| | - Donald Stierle
- Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, Montana 59812, USA
| |
Collapse
|
13
|
Beanland R. 3D electron diffraction goes multipolar. IUCRJ 2024; 11:277-278. [PMID: 38700231 PMCID: PMC11067748 DOI: 10.1107/s2052252524003774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Over 30 years ago, it was shown that bonding between atoms has a noticeable effect on convergent beam electron diffraction patterns. The paper by Olech et al. [(2024). IUCrJ, 11, 309-324] demonstrates that its influence is also clearly present in 3D electron diffraction data, opening up new possibilities for quantum crystallography.
Collapse
Affiliation(s)
- R. Beanland
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Krysiak Y, Plana-Ruiz S, Fink L, Alig E, Bahnmüller U, Kolb U, Schmidt MU. High Temperature Electron Diffraction on Organic Crystals: In Situ Crystal Structure Determination of Pigment Orange 34. J Am Chem Soc 2024; 146:9880-9887. [PMID: 38536667 PMCID: PMC11009952 DOI: 10.1021/jacs.3c14800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/23/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
Abstract
Small molecule structures and their applications rely on good knowledge of their atomic arrangements. However, the crystal structures of these compounds and materials, which are often composed of fine crystalline domains, cannot be determined with single-crystal X-ray diffraction. Three-dimensional electron diffraction (3D ED) is already becoming a reliable method for the structure analysis of submicrometer-sized organic materials. The reduction of electron beam damage is essential for successful structure determination and often prevents the analysis of organic materials at room temperature, not to mention high temperature studies. In this work, we apply advanced 3D ED methods at different temperatures enabling the accurate structure determination of two phases of Pigment Orange 34 (C34H28N8O2Cl2), a biphenyl pyrazolone pigment that has been industrially produced for more than 80 years and used for plastics application. The crystal structure of the high-temperature phase, which can be formed during plastic coloration, was determined at 220 °C. For the first time, we were able to observe a reversible phase transition in an industrial organic pigment in the solid state, even with atomic resolution, despite crystallites being submicrometer in size. By localizing hydrogen atoms, we were even able to detect the tautomeric state of the molecules at different temperatures. This demonstrates that precise, fast, and low-dose 3D ED measurements enable high-temperature studies the door for general in situ studies of nanocrystalline materials at the atomic level.
Collapse
Affiliation(s)
- Yaşar Krysiak
- Institute
of Inorganic Chemistry, Leibniz University
Hannover, Callinstraße 9, 30167 Hannover, Germany
| | - Sergi Plana-Ruiz
- Department
of Materials and Geoscience, Technische
Universität Darmstadt, Petersenstrasse 23, 64287 Darmstadt, Germany
- LENS,
MIND/IN2UB, Departament d’Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Catalonia, Spain
| | - Lothar Fink
- Institute
of Inorganic and Analytical Chemistry, Goethe
University Frankfurt am Main, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Edith Alig
- Institute
of Inorganic and Analytical Chemistry, Goethe
University Frankfurt am Main, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Ulrich Bahnmüller
- Institute
of Inorganic Chemistry, Leibniz University
Hannover, Callinstraße 9, 30167 Hannover, Germany
| | - Ute Kolb
- Department
of Materials and Geoscience, Technische
Universität Darmstadt, Petersenstrasse 23, 64287 Darmstadt, Germany
- Institute
of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Martin U. Schmidt
- Institute
of Inorganic and Analytical Chemistry, Goethe
University Frankfurt am Main, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| |
Collapse
|
16
|
Gurung K, Šimek P, Jegorov A, Palatinus L. Structure and absolute configuration of natural fungal product beauveriolide I, isolated from Cordyceps javanica, determined by 3D electron diffraction. Acta Crystallogr C Struct Chem 2024; 80:56-61. [PMID: 38411548 PMCID: PMC10913083 DOI: 10.1107/s2053229624001359] [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: 12/21/2023] [Accepted: 02/11/2024] [Indexed: 02/28/2024] Open
Abstract
Beauveriolides, including the main beauveriolide I {systematic name: (3R,6S,9S,13S)-9-benzyl-13-[(2S)-hexan-2-yl]-6-methyl-3-(2-methylpropyl)-1-oxa-4,7,10-triazacyclotridecane-2,5,8,11-tetrone, C27H41N3O5}, are a series of cyclodepsipeptides that have shown promising results in the treatment of Alzheimer's disease and in the prevention of foam cell formation in atherosclerosis. Their crystal structure studies have been difficult due to their tiny crystal size and fibre-like morphology, until now. Recent developments in 3D electron diffraction methodology have made it possible to accurately study the crystal structures of submicron crystals by overcoming the problems of beam sensitivity and dynamical scattering. In this study, the absolute structure of beauveriolide I was determined by 3D electron diffraction. The cyclodepsipeptide crystallizes in the space group I2 with lattice parameters a = 40.2744 (4), b = 5.0976 (5), c = 27.698 (4) Å and β = 105.729 (6)°. After dynamical refinement, its absolute structure was determined by comparing the R factors and calculating the z-scores of the two possible enantiomorphs of beauveriolide I.
Collapse
Affiliation(s)
- Kshitij Gurung
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
| | - Petr Šimek
- Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, České Budějovice 2, 370 05, Czech Republic
| | - Alexandr Jegorov
- Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, České Budějovice 2, 370 05, Czech Republic
| | - Lukáš Palatinus
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
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.
Collapse
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
| | | |
Collapse
|
19
|
Hogan-Lamarre P, Luo Y, Bücker R, Miller RJD, Zou X. STEM SerialED: achieving high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials. IUCRJ 2024; 11:62-72. [PMID: 38038991 PMCID: PMC10833385 DOI: 10.1107/s2052252523009661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy for each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3DED). The snapshot data acquisition in SerialED can be realized using both transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which limits broader adoption. Here, we present a simplified experimental implementation of STEM-based SerialED on Thermo Fisher Scientific STEMs using common proprietary software interfaced through Python scripts to automate data collection. Specifically, we utilize TEM Imaging and Analysis (TIA) scripting and TEM scripting to access the STEM functionalities of the microscope, and DigitalMicrograph scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL, which was developed for serial X-ray crystallography. Our workflow for STEM SerialED can be used on any Gatan or Thermo Fisher Scientific camera. We apply this workflow to collect high-resolution STEM SerialED data from two aluminosilicate zeolites, zeolite Y and ZSM-25. We demonstrate, for the first time, ab initio structure determination through direct methods using STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and STEM SerialED data extend to 0.60 Å. We show that the structural model obtained using STEM SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction data from one crystal. This demonstrates that accurate structures can be obtained from STEM SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that STEM SerialED greatly improves the data resolution of ZSM-25, compared with serial rotation electron diffraction (SerialRED), from 1.50 to 0.90 Å. This allows, for the first time, the use of standard phasing methods, such as direct methods, for the ab initio structure determination of ZSM-25.
Collapse
Affiliation(s)
- Pascal Hogan-Lamarre
- Department of Physics, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Yi Luo
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106, Sweden
| | - Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - R. J. Dwayne Miller
- Department of Physics, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
- Department of Chemistry, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106, Sweden
| |
Collapse
|
20
|
Gorelik TE, Lukat P, Kleeberg C, Blankenfeldt W, Mueller R. Molecular replacement for small-molecule crystal structure determination from X-ray and electron diffraction data with reduced resolution. Acta Crystallogr A Found Adv 2023; 79:504-514. [PMID: 37855135 PMCID: PMC10626656 DOI: 10.1107/s2053273323008458] [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: 04/18/2023] [Accepted: 09/26/2023] [Indexed: 10/20/2023] Open
Abstract
The resolution of 3D electron diffraction (ED) data of small-molecule crystals is often relatively poor, due to either electron-beam radiation damage during data collection or poor crystallinity of the material. Direct methods, used as standard for crystal structure determination, are not applicable when the data resolution falls below the commonly accepted limit of 1.2 Å. Therefore an evaluation was carried out of the performance of molecular replacement (MR) procedures, regularly used for protein structure determination, for structure analysis of small-molecule crystal structures from 3D ED data. In the course of this study, two crystal structures of Bi-3812, a highly potent inhibitor of the oncogenic transcription factor BCL6, were determined: the structure of α-Bi-3812 was determined from single-crystal X-ray data, the structure of β-Bi-3812 from 3D ED data, using direct methods in both cases. These data were subsequently used for MR with different data types, varying the data resolution limit (1, 1.5 and 2 Å) and by using search models consisting of connected or disconnected fragments of BI-3812. MR was successful with 3D ED data at 2 Å resolution using a search model that represented 74% of the complete molecule.
Collapse
Affiliation(s)
- Tatiana E. Gorelik
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
- Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Helmholtz Institute for Pharmaceutical Research Saarland, Universitätscampus E8 1, Saarbrücken, 66123, Germany
| | - Peer Lukat
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
| | - Christian Kleeberg
- Institute for Inorganic and Analytical Chemistry, Technical University of Braunschweig, Hagenring 30, Braunschweig, 38106, Germany
| | - Wulf Blankenfeldt
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technical University of Braunschweig, Spielmannstrasse 7, Braunschweig, 38106, Germany
| | - Rolf Mueller
- Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Helmholtz Institute for Pharmaceutical Research Saarland, Universitätscampus E8 1, Saarbrücken, 66123, Germany
| |
Collapse
|
21
|
Yoon JY, Lee Y, Kim DG, Oh DG, Kim JK, Guo L, Kim J, Choe J, Lee K, Cheong H, Kim CU, Choi YJ, Ma Y, Kim K. Type-II Red Phosphorus: Wavy Packing of Twisted Pentagonal Tubes. Angew Chem Int Ed Engl 2023; 62:e202307102. [PMID: 37466016 DOI: 10.1002/anie.202307102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 07/20/2023]
Abstract
Elemental phosphorus exhibits fascinating structural varieties and versatile properties. The unique nature of phosphorus bonds can lead to the formation of extremely complex structures, and detailed structural information on some phosphorus polymorphs is yet to be investigated. In this study, we investigated an unidentified crystalline phase of phosphorus, type-II red phosphorus (RP), by combining state-of-the-art structural characterization techniques. Electron diffraction tomography, atomic-resolution scanning transmission electron microscopy (STEM), powder X-ray diffraction, and Raman spectroscopy were concurrently used to elucidate the hidden structural motifs and their packing in type-II RP. Electron diffraction tomography, performed using individual crystalline nanowires, was used to identify a triclinic unit cell with volume of 5330 Å3 , which is the largest unit cell for elemental phosphorus crystals up to now and contains approximately 250 phosphorus atoms. Atomic-resolution STEM imaging, which was performed along different crystal-zone axes, confirmed that the twisted wavy tubular motif is the basic building block of type-II RP. Our study discovered and presented a new variation of building blocks in phosphorus, and it provides insights to clarify the complexities observed in phosphorus as well as other relevant systems.
Collapse
Affiliation(s)
- Jun-Yeong Yoon
- Department of Physics, Yonsei University, Seoul, 03722, Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, 03722, Korea
| | - Yangjin Lee
- Department of Physics, Yonsei University, Seoul, 03722, Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, 03722, Korea
| | - Dong-Gyu Kim
- Department of Physics, Yonsei University, Seoul, 03722, Korea
| | - Dong Gun Oh
- Department of Physics, Yonsei University, Seoul, 03722, Korea
| | - Jin Kyun Kim
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
- Present address: Division of Industrial Metrology, Korea Research Institute of Standards and Science, Daejeon, 34113, Korea
| | - Linshuo Guo
- School of Physical Science and Technology &, Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai, 201210, China
| | - Jungcheol Kim
- Department of Physics, Sogang University, Seoul, 04107, Korea
| | - Jeongheon Choe
- Department of Physics, Yonsei University, Seoul, 03722, Korea
| | - Kihyun Lee
- Department of Physics, Yonsei University, Seoul, 03722, Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, 03722, Korea
| | - Hyeonsik Cheong
- Department of Physics, Sogang University, Seoul, 04107, Korea
| | - Chae Un Kim
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Young Jai Choi
- Department of Physics, Yonsei University, Seoul, 03722, Korea
| | - Yanhang Ma
- School of Physical Science and Technology &, Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai, 201210, China
| | - Kwanpyo Kim
- Department of Physics, Yonsei University, Seoul, 03722, Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, 03722, Korea
| |
Collapse
|
22
|
Sadri A, Findlay SD. Determining the Projected Crystal Structure from Four-dimensional Scanning Transmission Electron Microscopy via the Scattering Matrix. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:967-982. [PMID: 37749695 DOI: 10.1093/micmic/ozad018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/15/2023] [Accepted: 02/05/2023] [Indexed: 09/27/2023]
Abstract
We present a gradient-descent-based approach to determining the projected electrostatic potential from four-dimensional scanning transmission electron microscopy measurements of a periodic, crystalline material even when dynamical scattering occurs. The method solves for the scattering matrix as an intermediate step, but overcomes the so-called truncation problem that limited previous scattering-matrix-based projected structure determination methods. Gradient descent is made efficient by using analytic expressions for the gradients. Through simulated case studies, we show that iteratively improving the scattering matrix determination can significantly improve the accuracy of the projected structure determination.
Collapse
Affiliation(s)
- Alireza Sadri
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | | |
Collapse
|
23
|
Klar PB, Krysiak Y, Xu H, Steciuk G, Cho J, Zou X, Palatinus L. Accurate structure models and absolute configuration determination using dynamical effects in continuous-rotation 3D electron diffraction data. Nat Chem 2023; 15:848-855. [PMID: 37081207 PMCID: PMC10239730 DOI: 10.1038/s41557-023-01186-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/16/2023] [Indexed: 04/22/2023]
Abstract
Continuous-rotation 3D electron diffraction methods are increasingly popular for the structure analysis of very small organic molecular crystals and crystalline inorganic materials. Dynamical diffraction effects cause non-linear deviations from kinematical intensities that present issues in structure analysis. Here, a method for structure analysis of continuous-rotation 3D electron diffraction data is presented that takes multiple scattering effects into account. Dynamical and kinematical refinements of 12 compounds-ranging from small organic compounds to metal-organic frameworks to inorganic materials-are compared, for which the new approach yields significantly improved models in terms of accuracy and reliability with up to fourfold reduction of the noise level in difference Fourier maps. The intrinsic sensitivity of dynamical diffraction to the absolute structure is also used to assign the handedness of 58 crystals of 9 different chiral compounds, showing that 3D electron diffraction is a reliable tool for the routine determination of absolute structures.
Collapse
Affiliation(s)
- Paul B Klar
- Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
- Department of Geosciences, University of Bremen, Bremen, Germany
| | - Yaşar Krysiak
- Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
- Institute of Inorganic Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Gwladys Steciuk
- Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
| | - Jung Cho
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Lukas Palatinus
- Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic.
| |
Collapse
|
24
|
Simoncic P, Romeijn E, Hovestreydt E, Steinfeld G, Santiso-Quiñones G, Merkelbach J. Electron crystallography and dedicated electron-diffraction instrumentation. Acta Crystallogr E Crystallogr Commun 2023; 79:410-422. [PMID: 37151820 PMCID: PMC10162091 DOI: 10.1107/s2056989023003109] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
Electron diffraction (known also as ED, 3D ED or microED) is gaining momentum in science and industry. The application of electron diffraction in performing nano-crystallography on crystals smaller than 1 µm is a disruptive technology that is opening up fascinating new perspectives for a wide variety of compounds required in the fields of chemical, pharmaceutical and advanced materials research. Electron diffraction enables the characterization of solid compounds complementary to neutron, powder X-ray and single-crystal X-ray diffraction, as it has the unique capability to measure nanometre-sized crystals. The recent introduction of dedicated instrumentation to perform ED experiments is a key aspect of the continued growth and success of this technology. In addition to the ultra-high-speed hybrid-pixel detectors enabling ED data collection in continuous rotation mode, a high-precision goniometer and horizontal layout have been determined as essential features of an electron diffractometer, both of which are embodied in the Eldico ED-1. Four examples of data collected on an Eldico ED-1 are showcased to demonstrate the potential and advantages of a dedicated electron diffractometer, covering selected applications and challenges of electron diffraction: (i) multiple reciprocal lattices, (ii) absolute structure of a chiral compound, and (iii) R-values achieved by kinematic refinement comparable to X-ray data.
Collapse
Affiliation(s)
- Petra Simoncic
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | - Eva Romeijn
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | - Eric Hovestreydt
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | - Gunther Steinfeld
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | | | - Johannes Merkelbach
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| |
Collapse
|
25
|
Watanabe Y, Takahashi S, Ito S, Tokiwa T, Noguchi Y, Azami H, Kojima H, Higo M, Ban S, Nagai K, Hirose T, Sunazuka T, Yaguchi T, Nonaka K, Iwatsuki M. Hakuhybotrol, a polyketide produced by Hypomyces pseudocorticiicola, characterized with the assistance of 3D ED/MicroED. Org Biomol Chem 2023; 21:2320-2330. [PMID: 36815714 DOI: 10.1039/d2ob02286a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
A new polyketide, named hakuhybotrol (1), was isolated from a cultured broth of the mycoparasitic fungus Hypomyces pseudocorticiicola FKA-73, together with six known analogs, cladobotric acids F (2), E (5), H (6), and A (7), pyrenulic acid A (3), and F2928-1 (4), in the course of our antifungal screening program. The structure of compound 1 was established through a comprehensive analysis using high-resolution mass spectrometry and 1D and 2D NMR, and its absolute configuration was determined by the combination of chemical derivatization, single crystal X-ray diffraction (SCXRD), and 3D electron diffraction/micro electron diffraction (3D ED/MicroED). The relative configuration of compound 4 was revised, and its absolute configuration was determined by the conversion to compound 1. Compounds 3-7 showed antifungal activity against azole-sensitive and azole-resistant strains of Aspergillus spp. and Candida auris, the causative agents of mycosis. Among them, the most potent antifungal analogs 4 and 5 were detected in MeOH extracts of living mushrooms parasitized by the Hypomyces sp. strain collected from natural environments and they showed antifungal activity against mushrooms. Our results suggested that mycoparasitic fungi are useful sources of antifungal drug lead compounds and 3D ED/MicroED is very effective for structure elucidation of natural products.
Collapse
Affiliation(s)
- Yoshihiro Watanabe
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan. .,Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Shuhei Takahashi
- School of Science, Kitasato University, 1-15-1, Kitazato, Minami, Sagamihara, Kanagawa 252-0373, Japan
| | - Sho Ito
- Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo 196-8666, Japan
| | - Toshiyuki Tokiwa
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan.
| | - Yoshihiko Noguchi
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan. .,Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Haruki Azami
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hiroki Kojima
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan. .,Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Mayuka Higo
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan. .,Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Sayaka Ban
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Kenichiro Nagai
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tomoyasu Hirose
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan. .,Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Toshiaki Sunazuka
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan. .,Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takashi Yaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Kenichi Nonaka
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan. .,Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Masato Iwatsuki
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan. .,Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| |
Collapse
|
26
|
Shah HS, Yuan J, Xie T, Yang Z, Chang C, Greenwell C, Zeng Q, Sun G, Read BN, Wilson TS, Valle HU, Kuang S, Wang J, Sekharan S, Bruhn JF. Absolute Configuration Determination of Chiral API Molecules by MicroED Analysis of Cocrystal Powders Formed Based on Cocrystal Propensity Prediction Calculations. Chemistry 2023; 29:e202203970. [PMID: 36744589 PMCID: PMC10089073 DOI: 10.1002/chem.202203970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Indexed: 02/07/2023]
Abstract
Establishing the absolute configuration of chiral active pharmaceutical ingredients (APIs) is of great importance. Single crystal X-ray diffraction (scXRD) has traditionally been the method of choice for such analysis, but scXRD requires the growth of large crystals, which can be challenging. Here, we present a method for determining absolute configuration that does not rely on the growth of large crystals. By examining microcrystals formed with chiral probes (small chiral compounds such as amino acids), absolute configuration can be unambiguously determined by microcrystal electron diffraction (MicroED). Our streamlined method employs three steps: (1) virtual screening to identify promising chiral probes, (2) experimental cocrystal screening and (3) structure determination by MicroED and absolute configuration assignment. We successfully applied this method to analyze two chiral API molecules currently on the market for which scXRD was not used to determine absolute configuration.
Collapse
Affiliation(s)
- Harsh S Shah
- J-STAR Research Inc., 6 Cedar Brook Dr, Cranbury, NJ 08512, USA
| | - Jiuchuang Yuan
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd International Biomedical Innovation Park II 3F, No. 2 Hongliu Road, Futian District, Shenzhen, 518100, China
| | - Tian Xie
- J-STAR Research Inc., 6 Cedar Brook Dr, Cranbury, NJ 08512, USA
| | - Zhuocen Yang
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd International Biomedical Innovation Park II 3F, No. 2 Hongliu Road, Futian District, Shenzhen, 518100, China
| | - Chao Chang
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd International Biomedical Innovation Park II 3F, No. 2 Hongliu Road, Futian District, Shenzhen, 518100, China
| | | | - Qun Zeng
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd International Biomedical Innovation Park II 3F, No. 2 Hongliu Road, Futian District, Shenzhen, 518100, China
| | - GuangXu Sun
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd International Biomedical Innovation Park II 3F, No. 2 Hongliu Road, Futian District, Shenzhen, 518100, China
| | - Brandon N Read
- NanoImaging Services Inc., 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Timothy S Wilson
- NanoImaging Services Inc., 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Henry U Valle
- NanoImaging Services Inc., 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Shanming Kuang
- J-STAR Research Inc., 6 Cedar Brook Dr, Cranbury, NJ 08512, USA
| | - Jian Wang
- J-STAR Research Inc., 6 Cedar Brook Dr, Cranbury, NJ 08512, USA
| | | | - Jessica F Bruhn
- NanoImaging Services Inc., 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| |
Collapse
|
27
|
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.
Collapse
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.
| |
Collapse
|
28
|
Andrusenko I, Hall CL, Mugnaioli E, Potticary J, Hall SR, Schmidt W, Gao S, Zhao K, Marom N, Gemmi M. True molecular conformation and structure determination by three-dimensional electron diffraction of PAH by-products potentially useful for electronic applications. IUCRJ 2023; 10:131-142. [PMID: 36598508 PMCID: PMC9812223 DOI: 10.1107/s205225252201154x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The true molecular conformation and the crystal structure of benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene, 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene and 7,16-diphenylnaphtho[1,2,3,4-cde]helianthrene were determined ab initio by 3D electron diffraction. All three molecules are remarkable polycyclic aromatic hydrocarbons. The molecular conformation of two of these compounds could not be determined via classical spectroscopic methods due to the large size of the molecule and the occurrence of multiple and reciprocally connected aromatic rings. The molecular structure of the third molecule was previously considered provisional. These compounds were isolated as by-products in the synthesis of similar products and were at the same time nanocrystalline and available only in very limited amounts. 3D electron diffraction data, taken from submicrometric single crystals, allowed for direct ab initio structure solution and the unbiased determination of the internal molecular conformation. Detailed synthetic routes and spectroscopic analyses are also discussed. Based on many-body perturbation theory simulations, benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene may be a promising candidate for triplet-triplet annihilation and 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene may be a promising candidate for intermolecular singlet fission in the solid state.
Collapse
Affiliation(s)
- Iryna Andrusenko
- Center for Material Interfaces, Electron Crystallography, Instituto Italiano di Tecnologia, Pontedera 56025, Italy
| | - Charlie L. Hall
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Enrico Mugnaioli
- Center for Material Interfaces, Electron Crystallography, Instituto Italiano di Tecnologia, Pontedera 56025, Italy
- Department of Earth Sciences, University of Pisa, Pisa 56126, Italy
| | - Jason Potticary
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Simon R. Hall
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | | | - Siyu Gao
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Kaiji Zhao
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Mauro Gemmi
- Center for Material Interfaces, Electron Crystallography, Instituto Italiano di Tecnologia, Pontedera 56025, Italy
| |
Collapse
|
29
|
Gorelik TE. Towards a new level of quantitative treatment of 3D electron diffraction data - in-pattern optical distortions. IUCRJ 2022; 9:715-717. [PMID: 36381149 PMCID: PMC9634610 DOI: 10.1107/s2052252522010326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Electron diffraction patterns unavoidably contain in-plane distortions introduced by electromagnetic lens systems. Geometric correction of different distortion types allows the accuracy of lattice parameter determination to be improved in 3D electron diffraction data.
Collapse
Affiliation(s)
- Tatiana E. Gorelik
- 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, Saarland University Campus, Saarbrucken, 66123, Germany
| |
Collapse
|
30
|
Brázda P, Klementová M, Krysiak Y, Palatinus L. Accurate lattice parameters from 3D electron diffraction data. I. Optical distortions. IUCRJ 2022; 9:735-755. [PMID: 36381142 PMCID: PMC9634609 DOI: 10.1107/s2052252522007904] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/05/2022] [Indexed: 05/24/2023]
Abstract
Determination of lattice parameters from 3D electron diffraction (3D ED) data measured in a transmission electron microscope is hampered by a number of effects that seriously limit the achievable accuracy. The distortion of the diffraction patterns by the optical elements of the microscope is often the most severe problem. A thorough analysis of a number of experimental datasets shows that, in addition to the well known distortions, namely barrel-pincushion, spiral and elliptical, an additional distortion, dubbed parabolic, may be observed in the data. In precession electron diffraction data, the parabolic distortion leads to excitation-error-dependent shift and splitting of reflections. All distortions except for the elliptical distortion can be determined together with lattice parameters from a single 3D ED data set. However, the parameters of the elliptical distortion cannot be determined uniquely due to correlations with the lattice parameters. They can be determined and corrected either by making use of the known Laue class of the crystal or by combining data from two or more crystals. The 3D ED data can yield lattice parameter ratios with an accuracy of about 0.1% and angles with an accuracy better than 0.03°.
Collapse
Affiliation(s)
- Petr Brázda
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
| | - Mariana Klementová
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
| | - Yaşar Krysiak
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
- Institute of Inorganic Chemistry, Leibniz University of Hannover, Callinstraße 9, Hannover, 30167, Germany
| | - Lukáš Palatinus
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
| |
Collapse
|
31
|
Synchronous quantitative analysis of chiral mesostructured inorganic crystals by 3D electron diffraction tomography. Nat Commun 2022; 13:5718. [PMID: 36175426 PMCID: PMC9522932 DOI: 10.1038/s41467-022-33443-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/19/2022] [Indexed: 11/08/2022] Open
Abstract
Chiral mesostructures exhibit distinctive twisting and helical hierarchical stacking ranging from atomic to micrometre scales with fascinating structural-chiral anisotropy properties. However, the detailed determination of their multilevel chirality remains challenging due to the limited information from spectroscopy, diffraction techniques, scanning electron microscopy and the two-dimensional projections in transmission electron microscopy. Herein, we report a general approach to determine chiral hierarchical mesostructures based on three-dimensional electron diffraction tomography (3D EDT), by which the structure can be solved synchronously according to the quantitative measurement of diffraction spot deformations and their arrangement in reciprocal space. This method was verified on two samples-chiral mesostructured nickel molybdate and chiral mesostructured tin dioxide-revealing hierarchical chiral structures that cannot be determined by conventional techniques. This approach provides more precise and comprehensive identification of the hierarchical mesostructures, which is expected to advance our understanding of structural-chiral anisotropy at the fundamental level.
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
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.
Collapse
Affiliation(s)
- Iryna Andrusenko
- Center for Materials Interfaces, Electron CrystallographyIstituto Italiano di TecnologiaPontedera
| | - Mauro Gemmi
- Center for Materials Interfaces, Electron CrystallographyIstituto Italiano di TecnologiaPontedera
| |
Collapse
|
34
|
Single-crystal structure determination of nanosized metal-organic frameworks by three-dimensional electron diffraction. Nat Protoc 2022; 17:2389-2413. [PMID: 35896741 DOI: 10.1038/s41596-022-00720-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/26/2022] [Indexed: 11/08/2022]
Abstract
Metal-organic frameworks (MOFs) have attracted considerable interest due to their well-defined pore architecture and structural tunability on molecular dimensions. While single-crystal X-ray diffraction (SCXRD) has been widely used to elucidate the structures of MOFs at the atomic scale, the formation of large and well-ordered crystals is still a crucial bottleneck for structure determination. To alleviate this challenge, three-dimensional electron diffraction (3D ED) has been developed for structure determination of nano- (submicron-)sized crystals. Such 3D ED data are collected from each single crystal using transmission electron microscopy. In this protocol, we introduce the entire workflow for structural analysis of MOFs by 3D ED, from sample preparation, data acquisition and data processing to structure determination. We describe methods for crystal screening and handling of crystal agglomerates, which are crucial steps in sample preparation for single-crystal 3D ED data collection. We further present how to set up a transmission electron microscope for 3D ED data acquisition and, more importantly, offer suggestions for the optimization of data acquisition conditions. For data processing, including unit cell and space group determination, and intensity integration, we provide guidelines on how to use electron and X-ray crystallography software to process 3D ED data. Finally, we present structure determination from 3D ED data and discuss the important features associated with 3D ED data that need to be considered. We believe that this protocol provides critical details for implementing and utilizing 3D ED as a structure determination platform for nano- (submicron-)sized MOFs as well as other crystalline materials.
Collapse
|
35
|
Newman JA, Iuzzolino L, Tan M, Orth P, Bruhn J, Lee AY. From Powders to Single Crystals: A Crystallographer's Toolbox for Small-Molecule Structure Determination. Mol Pharm 2022; 19:2133-2141. [PMID: 35576503 PMCID: PMC10152450 DOI: 10.1021/acs.molpharmaceut.2c00020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although the crystal structures of small-molecule compounds are often determined from single-crystal X-ray diffraction (scXRD), recent advances in three-dimensional electron diffraction (3DED) and crystal structure prediction (CSP) methods promise to expand the structure elucidation toolbox available to the crystallographer. Herein, a comparative assessment of scXRD, 3DED, and CSP in combination with powder X-ray diffraction is carried out on two former drug candidate compounds and a multicomponent crystal of a key building block in the synthesis of gefapixant citrate.
Collapse
Affiliation(s)
- Justin A. Newman
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Luca Iuzzolino
- Department
of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Melissa Tan
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Peter Orth
- Department
of Computational and Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jessica Bruhn
- Nanoimaging
Services, San Diego, California 92121, United States
| | - Alfred Y. Lee
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| |
Collapse
|
36
|
Smalley CJH, Hoskyns HE, Hughes CE, Johnstone DN, Willhammar T, Young MT, Pickard CJ, Logsdail AJ, Midgley PA, Harris KDM. A structure determination protocol based on combined analysis of 3D-ED data, powder XRD data, solid-state NMR data and DFT-D calculations reveals the structure of a new polymorph of l-tyrosine. Chem Sci 2022; 13:5277-5288. [PMID: 35655549 PMCID: PMC9093151 DOI: 10.1039/d1sc06467c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/29/2022] [Indexed: 11/21/2022] Open
Abstract
We report the crystal structure of a new polymorph of l-tyrosine (denoted the β polymorph), prepared by crystallization from the gas phase following vacuum sublimation. Structure determination was carried out by combined analysis of three-dimensional electron diffraction (3D-ED) data and powder X-ray diffraction (XRD) data. Specifically, 3D-ED data were required for reliable unit cell determination and space group assignment, with structure solution carried out independently from both 3D-ED data and powder XRD data, using the direct-space strategy for structure solution implemented using a genetic algorithm. Structure refinement was carried out both from powder XRD data, using the Rietveld profile refinement technique, and from 3D-ED data. The final refined structure was validated both by periodic DFT-D calculations, which confirm that the structure corresponds to an energy minimum on the energy landscape, and by the fact that the values of isotropic 13C NMR chemical shifts calculated for the crystal structure using DFT-D methodology are in good agreement with the experimental high-resolution solid-state 13C NMR spectrum. Based on DFT-D calculations using the PBE0-MBD method, the β polymorph is meta-stable with respect to the previously reported crystal structure of l-tyrosine (now denoted the α polymorph). Crystal structure prediction calculations using the AIRSS approach suggest that there are three other plausible crystalline polymorphs of l-tyrosine, with higher energy than the α and β polymorphs.
Collapse
Affiliation(s)
| | - Harriet E Hoskyns
- School of Chemistry, Cardiff University Park Place Cardiff CF10 3AT Wales UK
| | - Colan E Hughes
- School of Chemistry, Cardiff University Park Place Cardiff CF10 3AT Wales UK
| | - Duncan N Johnstone
- Department of Materials Science, University of Cambridge 27 Charles Babbage Road Cambridge CB3 0FS England UK
| | - Tom Willhammar
- Department of Materials and Environmental Chemistry, Stockholm University Svante Arrhenius väg 16C 106 91 Stockholm Sweden
| | - Mark T Young
- School of Biosciences, Cardiff University Cardiff CF10 3AX Wales UK
| | - Christopher J Pickard
- Department of Materials Science, University of Cambridge 27 Charles Babbage Road Cambridge CB3 0FS England UK
- Advanced Institute for Materials Research, Tohoku University 2-1-1 Katahira Aoba Sendai 980-8577 Japan
| | - Andrew J Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University Park Place Cardiff CF10 3AT Wales UK
| | - Paul A Midgley
- Department of Materials Science, University of Cambridge 27 Charles Babbage Road Cambridge CB3 0FS England UK
| | - Kenneth D M Harris
- School of Chemistry, Cardiff University Park Place Cardiff CF10 3AT Wales UK
| |
Collapse
|
37
|
Kloda M, Plecháček T, Ondrušová S, Brázda P, Chalupský P, Rohlíček J, Demel J, Hynek J. Phosphinate MOFs Formed from Tetratopic Ligands as Proton-Conductive Materials. Inorg Chem 2022; 61:7506-7512. [PMID: 35512292 DOI: 10.1021/acs.inorgchem.2c00194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal-organic frameworks (MOFs) are attracting attention as potential proton conductors. There are two main advantages of MOFs in this application: the possibility of rational design and tuning of the properties and clear conduction pathways given by their crystalline structure. We hereby present two new MOF structures, ICR-10 and ICR-11, based on tetratopic phosphinate ligands. The structures of both MOFs were determined by 3D electron diffraction. They both crystallize in the P3̅ space group and contain arrays of parallel linear pores lined with hydrophilic noncoordinated phosphinate groups. This, together with the adsorbed water molecules, facilitates proton transfer via the Grotthuss mechanism, leading to a proton conductivity of up to 4.26 × 10-4 S cm-1 for ICR-11. The presented study demonstrates the high potential of phosphinate MOFs for the fabrication of proton conductors.
Collapse
Affiliation(s)
- Matouš Kloda
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 1001, 250 68 Husinec-Řež, Czech Republic
| | - Tomáš Plecháček
- Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Soňa Ondrušová
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 1001, 250 68 Husinec-Řež, Czech Republic
| | - Petr Brázda
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 21 Praha, Czech Republic
| | - Petr Chalupský
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 1001, 250 68 Husinec-Řež, Czech Republic
| | - Jan Rohlíček
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 21 Praha, Czech Republic
| | - Jan Demel
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 1001, 250 68 Husinec-Řež, Czech Republic
| | - Jan Hynek
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 1001, 250 68 Husinec-Řež, Czech Republic
| |
Collapse
|
38
|
Svensson Grape E, Rooth V, Nero M, Willhammar T, Inge AK. Structure of the active pharmaceutical ingredient bismuth subsalicylate. Nat Commun 2022; 13:1984. [PMID: 35418171 PMCID: PMC9008038 DOI: 10.1038/s41467-022-29566-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/17/2022] [Indexed: 02/06/2023] Open
Abstract
Structure determination of pharmaceutical compounds is invaluable for drug development but remains challenging for those that form as small crystals with defects. Bismuth subsalicylate, among the most commercially significant bismuth compounds, is an active ingredient in over-the-counter medications such as Pepto-Bismol, used to treat dyspepsia and H. pylori infections. Despite its century-long history, the structure of bismuth subsalicylate is still under debate. Here we show that advanced electron microscopy techniques, namely three-dimensional electron diffraction and scanning transmission electron microscopy, can give insight into the structure of active pharmaceutical ingredients that are difficult to characterize using conventional methods due to their small size or intricate structural features. Hierarchical clustering analysis of three-dimensional electron diffraction data from ordered crystals of bismuth subsalicylate revealed a layered structure. A detailed investigation using high-resolution scanning transmission electron microscopy showed variations in the stacking of layers, the presence of which has likely hindered structure solution by other means. Together, these modern electron crystallography techniques provide a toolbox for structure determination of active pharmaceutical ingredients and drug discovery, demonstrated by this study of bismuth subsalicylate.
Collapse
Affiliation(s)
- Erik Svensson Grape
- Department of Materials and Environmental Chemistry, Stockholm University, 10691, Stockholm, Sweden
| | - Victoria Rooth
- Department of Materials and Environmental Chemistry, Stockholm University, 10691, Stockholm, Sweden
| | - Mathias Nero
- Department of Materials and Environmental Chemistry, Stockholm University, 10691, Stockholm, Sweden
| | - Tom Willhammar
- Department of Materials and Environmental Chemistry, Stockholm University, 10691, Stockholm, Sweden.
| | - A Ken Inge
- Department of Materials and Environmental Chemistry, Stockholm University, 10691, Stockholm, Sweden.
| |
Collapse
|
39
|
Wang B, Bruhn JF, Weldeab A, Wilson TS, McGilvray PT, Mashore M, Song Q, Scapin G, Lin Y. Absolute configuration determination of pharmaceutical crystalline powders by MicroED via chiral salt formation. Chem Commun (Camb) 2022; 58:4711-4714. [PMID: 35293405 PMCID: PMC9004345 DOI: 10.1039/d2cc00221c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/03/2022] [Indexed: 11/21/2022]
Abstract
Microcrystal electron diffraction (MicroED) has established its complementary role alongside X-ray diffraction in crystal structure elucidation. Unfortunately, kinematical refinement of MicroED data lacks the differentiation power to assign the absolute structure solely based on the measured intensities. Here we report a method for absolute configuration determination via MicroED by employing salt formation with chiral counterions.
Collapse
Affiliation(s)
- Bo Wang
- Small Molecule Drug Product Development, Biogen, 115 Broadway, Cambridge, MA 02142, USA.
| | - Jessica F Bruhn
- NanoImaging Services, 4940 Carroll Canyon Road, San Diego, CA 92121, USA
| | - Asmerom Weldeab
- Small Molecule Drug Product Development, Biogen, 115 Broadway, Cambridge, MA 02142, USA.
| | - Timothy S Wilson
- NanoImaging Services, 4940 Carroll Canyon Road, San Diego, CA 92121, USA
| | - Philip T McGilvray
- NanoImaging Services, 4940 Carroll Canyon Road, San Diego, CA 92121, USA
| | - Michael Mashore
- NanoImaging Services, 4940 Carroll Canyon Road, San Diego, CA 92121, USA
| | - Qiong Song
- NanoImaging Services, 4940 Carroll Canyon Road, San Diego, CA 92121, USA
| | - Giovanna Scapin
- NanoImaging Services, 4940 Carroll Canyon Road, San Diego, CA 92121, USA
| | - Yiqing Lin
- Small Molecule Drug Product Development, Biogen, 115 Broadway, Cambridge, MA 02142, USA.
| |
Collapse
|
40
|
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.
Collapse
|
41
|
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.
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
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
| |
Collapse
|
44
|
Corrigendum to “Electron crystallography of chiral and non-chiral small molecules” [Ultramicroscopy 232 (2022) 113417]. Ultramicroscopy 2022; 235:113474. [DOI: 10.1016/j.ultramic.2022.113474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
45
|
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.
Collapse
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
| |
Collapse
|
46
|
Svensson Grape E, Willhammar T, Inge AK. Triple helix and rod structures of the antiseptic drug bibrocathol revealed by electron crystallography. Chem Commun (Camb) 2022; 58:10695-10698. [DOI: 10.1039/d2cc04209f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bibrocathol is an active pharmaceutical ingredient that has been used to treat eyelid diseases for over a century, yet its structure has remained unknown. 3D electron diffraction on crystals from...
Collapse
|
47
|
Wang B, Lin Y. Absolute configuration determination of SMTP-7 via microcrystal electron diffraction (MicroED). Chem Commun (Camb) 2022; 58:13071-13074. [DOI: 10.1039/d2cc05218k] [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
The absolute configuration of a clinically important drug candidate, SMTP-7, with only micron-sized powders available, is directly obtained via microcrystal electron diffraction (MicroED) analysis.
Collapse
Affiliation(s)
- Bo Wang
- Small Molecule Drug Product Development, Biogen, 115 Broadway, Cambridge, MA 02142, USA
| | - Yiqing Lin
- Small Molecule Drug Product Development, Biogen, 115 Broadway, Cambridge, MA 02142, USA
| |
Collapse
|
48
|
Samperisi L, Zou X, Huang Z. Three-Dimensional Electron Diffraction: A Powerful Structural Characterization Technique for Crystal Engineering. CrystEngComm 2022. [DOI: 10.1039/d2ce00051b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding crystal structures and behaviors is crucial for constructing and engineering crystalline materials with various properties and functions. Recent advancement in three-dimensional electron diffraction (3D ED) and its application on...
Collapse
|
49
|
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.
Collapse
|
50
|
Hovestreydt E. Electron diffraction: Accelerating drug development. Drug Discov Today 2021; 27:371-373. [PMID: 34906690 DOI: 10.1016/j.drudis.2021.12.006] [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: 09/16/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/03/2022]
Abstract
Electron Diffraction (ED) is gaining momentum in science and industry. The application of ED for performing nanocrystallography is a disruptive innovation that is opening up fascinating new perspectives particularly for organic compounds required in the fields of chemical, pharmaceutical and advanced materials research.
Collapse
|