1
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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.
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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
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2
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Erriah B, Shtukenberg AG, Aronin R, McCarthy D, Brázda P, Ward MD, Kahr B. ROY Crystallization on Poly(ethylene) Fibers, a Model for Bed Net Crystallography. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2024; 36:2432-2440. [PMID: 38495899 PMCID: PMC10938503 DOI: 10.1021/acs.chemmater.3c03188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
Many long-lasting insecticidal bed nets for protection against disease vectors consist of poly(ethylene) fibers in which insecticide is incorporated during manufacture. Insecticide molecules diffuse from within the supersaturated polymers to surfaces where they become bioavailable to insects and often crystallize, a process known as blooming. Recent studies revealed that contact insecticides can be highly polymorphic. Moreover, insecticidal activity is polymorph-dependent, with forms having a higher crystal free energy yielding faster insect knockdown and mortality. Consequently, the crystallographic characterization of insecticide crystals that form on fibers is critical to understanding net function and improving net performance. Structural characterization of insecticide crystals on bed net fiber surfaces, let alone their polymorphs, has been elusive owing to the minute size of the crystals, however. Using the highly polymorphous compound ROY (5-methyl-2-[(2-nitrophenyl)-amino]thiophene-3-carbonitrile) as a proxy for insecticide crystallization, we investigated blooming and crystal formation on the surface of extruded poly(ethylene) fibers containing ROY. The blooming rates, tracked from the time of extrusion, were determined by UV-vis spectroscopy after successive washes. Six crystalline polymorphs (of the 13 known) were observed on poly(ethylene) fiber surfaces, and they were identified and characterized by Raman microscopy, scanning electron microscopy, and 3D electron diffraction. These observations reveal that the crystallization and phase behavior of polymorphs forming on poly(ethylene) fibers is complex and dynamic. The characterization of blooming and microcrystals underscores the importance of bed net crystallography for the optimization of bed net performance.
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Affiliation(s)
- Bryan Erriah
- Department
of Chemistry and Molecular Design Institute, New York University, New York, 29 Washington Place, New York City, New York 10003, United States
| | - Alexander G. Shtukenberg
- Department
of Chemistry and Molecular Design Institute, New York University, New York, 29 Washington Place, New York City, New York 10003, United States
| | - Reese Aronin
- Department
of Chemistry and Molecular Design Institute, New York University, New York, 29 Washington Place, New York City, New York 10003, United States
| | - Derik McCarthy
- Department
of Chemistry and Molecular Design Institute, New York University, New York, 29 Washington Place, New York City, New York 10003, United States
| | - Petr Brázda
- Department
of Structure Analysis, Institute of Physics, Czech Academy of Sciences, Na Slovance 2/1999, Prague 8 18221, Czech Republic
| | - Michael D. Ward
- Department
of Chemistry and Molecular Design Institute, New York University, New York, 29 Washington Place, New York City, New York 10003, United States
| | - Bart Kahr
- Department
of Chemistry and Molecular Design Institute, New York University, New York, 29 Washington Place, New York City, New York 10003, United States
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3
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Thomas M, Cleverley A, Beanland R. Parameterized absorptive electron scattering factors. Acta Crystallogr A Found Adv 2024; 80:146-150. [PMID: 38270202 PMCID: PMC10913675 DOI: 10.1107/s2053273323010963] [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: 09/23/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024] Open
Abstract
In electron diffraction, thermal atomic motion produces incoherent scattering over a relatively wide angular range, which appears as a diffuse background that is usually subtracted from measurements of Bragg spot intensities in structure solution methods. The transfer of electron flux from Bragg spots to diffuse scatter is modelled using complex scattering factors f + if' in the Bloch wave methodology. In a two-beam Einstein model the imaginary `absorptive' scattering factor f' can be obtained by the evaluation of an integral containing f over all possible scattering angles. While more sophisticated models of diffuse scatter are widely used in the electron microscopy community, it is argued in this paper that this simple model is appropriate for current structure solution and refinement methods. The two-beam model is a straightforward numerical calculation, but even this simplistic approach can become time consuming for simulations of materials with large numbers of atoms in the unit cell and/or many incident beam orientations. Here, a parameterized form of f' is provided for 103 elements as neutral, spherical atoms that reduces calculation time considerably.
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Affiliation(s)
- M. Thomas
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - A. Cleverley
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - R. Beanland
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
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4
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Elizebath D, Lim JH, Nishiyama Y, Vedhanarayanan B, Saeki A, Ogawa Y, Praveen VK. Nonclassical Crystal Growth of Supramolecular Polymers in Aqueous Medium. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2306175. [PMID: 37771173 DOI: 10.1002/smll.202306175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/08/2023] [Indexed: 09/30/2023]
Abstract
A mechanistic understanding of the principles governing the hierarchical organization of supramolecular polymers offers a paradigm for tailoring synthetic molecular architectures at the nano to micrometric scales. Herein, the unconventional crystal growth mechanism of a supramolecular polymer of superbenzene(coronene)-diphenylalanine conjugate (Cr-FFOEt ) is demonstrated. 3D electron diffraction (3D ED), a technique underexplored in supramolecular chemistry, is effectively utilized to gain a molecular-level understanding of the gradual growth of the initially formed poorly crystalline hairy, fibril-like supramolecular polymers into the ribbon-like crystallites. The further evolution of these nanosized flat ribbons into microcrystals by oriented attachment and lateral fusion is probed by time-resolved microscopy and electron diffraction. The gradual morphological and structural changes reveal the nonclassical crystal growth pathway, where the balance of strong and weak intermolecular interactions led to a structure beyond the nanoscale. The role of distinct π-stacking and H-bonding interactions that drive the nonclassical crystallization process of Cr-FFOEt supramolecular polymers is analyzed in comparison to analogous molecules, Py-FFOEt and Cr-FF forming helical and twisted fibers, respectively. Furthermore, the Cr-FFOEt crystals formed through nonclassical crystallization are found to improve the functional properties.
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Affiliation(s)
- Drishya Elizebath
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jia Hui Lim
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, 38000, France
| | | | - Balaraman Vedhanarayanan
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, 695019, India
| | - Akinori Saeki
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yu Ogawa
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, 38000, France
| | - Vakayil K Praveen
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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5
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Abstract
Twenty years ago, I wrote a Chem. Commun. feature article entitled "Crystal Engineering: where from? Where to?": an update is in order. In this Highlight I argue that molecular crystal engineering, one of the areas of fast development of the field, has definitely reached the stage of "delivering the goods": new functional materials assembled via non-covalent interactions and/or improved properties of existing materials. As a proof of concept, the crystal engineering approach to tackle two contemporary emergencies, namely, urea fertilizer degradation and development of antimicrobial resistance by pathogens, is discussed and application-driven examples are provided.
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Affiliation(s)
- Dario Braga
- Chemistry Department G. Ciamician, University of Bologna, Via F. Selmi 2, 4016 Bologna, Italy.
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6
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Schmidt EM, Klar PB, Krysiak Y, Svora P, Goodwin AL, Palatinus L. Quantitative three-dimensional local order analysis of nanomaterials through electron diffraction. Nat Commun 2023; 14:6512. [PMID: 37845256 PMCID: PMC10579245 DOI: 10.1038/s41467-023-41934-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023] Open
Abstract
Structure-property relationships in ordered materials have long been a core principle in materials design. However, the introduction of disorder into materials provides structural flexibility and thus access to material properties that are not attainable in conventional, ordered materials. To understand disorder-property relationships, the disorder - i.e., the local ordering principles - must be quantified. Local order can be probed experimentally by diffuse scattering. The analysis is notoriously difficult, especially if only powder samples are available. Here, we combine the advantages of three-dimensional electron diffraction - a method that allows single crystal diffraction measurements on sub-micron sized crystals - and three-dimensional difference pair distribution function analysis (3D-ΔPDF) to address this problem. In this work, we compare the 3D-ΔPDF from electron diffraction data with those obtained from neutron and x-ray experiments of yttria-stabilized zirconia (Zr0.82Y0.18O1.91) and demonstrate the reliability of the proposed approach.
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Affiliation(s)
- Ella Mara Schmidt
- Faculty of Geosciences and MAPEX Center for Materials and Processes, University of Bremen, Bremen, Germany.
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, United Kingdom.
| | - Paul Benjamin Klar
- Faculty of Geosciences and MAPEX Center for Materials and Processes, University of Bremen, Bremen, Germany
- Institute of Physics of the Czech Academy of Sciences, Prague, Czechia
| | - Yaşar Krysiak
- Institute of Physics of the Czech Academy of Sciences, Prague, Czechia
- Institute of Inorganic Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Petr Svora
- Institute of Physics of the Czech Academy of Sciences, Prague, Czechia
| | - Andrew L Goodwin
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Lukas Palatinus
- Institute of Physics of the Czech Academy of Sciences, Prague, Czechia
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7
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Thompson AL, White NG. Hydrogen atoms in supramolecular chemistry: a structural perspective. Where are they, and why does it matter? Chem Soc Rev 2023; 52:6254-6269. [PMID: 37599586 DOI: 10.1039/d3cs00516j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Hydrogen bonding interactions are ubiquitous across the biochemical and chemical sciences, and are of particular interest to supramolecular chemists. They have been used to assemble hydrogen bonded polymers, cages and frameworks, and are the functional motif in many host-guest systems. Single crystal X-ray diffraction studies are often used as a key support for proposed structures, although this presents challenges as hydrogen atoms interact only weakly with X-rays. In this Tutorial Review, we discuss the information that can be gleaned about hydrogen bonding interactions through crystallographic experiments, key limitations of the data, and emerging techniques to overcome these limitations.
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Affiliation(s)
- Amber L Thompson
- Chemical Crystallography, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK.
| | - Nicholas G White
- Research School of Chemistry, The Australian National University, Canberra 2601, ACT, Australia.
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8
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Cordova M, Moutzouri P, Nilsson Lill SO, Cousen A, Kearns M, Norberg ST, Svensk Ankarberg A, McCabe J, Pinon AC, Schantz S, Emsley L. Atomic-level structure determination of amorphous molecular solids by NMR. Nat Commun 2023; 14:5138. [PMID: 37612269 PMCID: PMC10447443 DOI: 10.1038/s41467-023-40853-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023] Open
Abstract
Structure determination of amorphous materials remains challenging, owing to the disorder inherent to these materials. Nuclear magnetic resonance (NMR) powder crystallography is a powerful method to determine the structure of molecular solids, but disorder leads to a high degree of overlap between measured signals, and prevents the unambiguous identification of a single modeled periodic structure as representative of the whole material. Here, we determine the atomic-level ensemble structure of the amorphous form of the drug AZD4625 by combining solid-state NMR experiments with molecular dynamics (MD) simulations and machine-learned chemical shifts. By considering the combined shifts of all 1H and 13C atomic sites in the molecule, we determine the structure of the amorphous form by identifying an ensemble of local molecular environments that are in agreement with experiment. We then extract and analyze preferred conformations and intermolecular interactions in the amorphous sample in terms of the stabilization of the amorphous form of the drug.
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Affiliation(s)
- Manuel Cordova
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- National Centre for Computational Design and Discovery of Novel Materials MARVEL, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pinelopi Moutzouri
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Sten O Nilsson Lill
- Data Science & Modelling, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Alexander Cousen
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Martin Kearns
- Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Stefan T Norberg
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - Anna Svensk Ankarberg
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - James McCabe
- Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Arthur C Pinon
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390, Gothenburg, Sweden
| | - Staffan Schantz
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden.
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
- National Centre for Computational Design and Discovery of Novel Materials MARVEL, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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9
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Herzberg M, Rekis T, Støttrup Larsen A, Gonzalez A, Rantanen J, Østergaard Madsen A. The structure of magnesium stearate trihydrate determined from a micrometre-sized single crystal using a microfocused synchrotron X-ray beam. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2023; 79:330-335. [PMID: 37427850 PMCID: PMC10410307 DOI: 10.1107/s2052520623005607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 06/25/2023] [Indexed: 07/11/2023]
Abstract
Crystalline magnesium stearate has been extensively used as an additive in pharmaceutical and other industries for decades. However, the lack of suitably large crystals has hindered the determination of the crystal structure and thereby a more fundamental understanding of the structure-functionality relationship. Presented here is the structure of magnesium stearate trihydrate as determined from X-ray diffraction data of a micrometre-sized single crystal measured at a fourth-generation synchrotron facility. Despite the small size of the single crystals and the weak diffraction, it was possible to determine the positions of the non-hydrogen atoms reliably. Periodic dispersion-corrected density functional theory calculations were used to obtain the positions of the hydrogen atoms playing an important role in the overall organization of the structure via a hydrogen-bond network.
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Affiliation(s)
- Mikkel Herzberg
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Toms Rekis
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Anders Støttrup Larsen
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Ana Gonzalez
- BioMAX, MAX IV, Fotongatan 2, 224 84 Lund, Sweden
| | - Jukka Rantanen
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Anders Østergaard Madsen
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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10
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Wang S, Yang T, Kumar K, Namvar S, Kim S, Ahmadiparidari A, Shahbazi H, Singh S, Hemmat Z, Berry V, Cabana J, Khalili-Araghi F, Huang Z, Salehi-Khojin A. Thermodynamics and Kinetics in Anisotropic Growth of One-Dimensional Midentropy Nanoribbons. ACS NANO 2023. [PMID: 37467377 DOI: 10.1021/acsnano.3c04178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
One-dimensional (1D) materials demonstrate anisotropic in-plane physical properties that enable a wide range of functionalities in electronics, photonics, valleytronics, optoelectronics, and catalysis. Here, we undertake an in-depth study of the growth mechanism for equimolar midentropy alloy of (NbTaTi)0.33S3 nanoribbons as a model system for 1D transition metal trichalcogenide structures. To understand the thermodynamic and kinetic effects in the growth process, the energetically preferred phases at different synthesis temperatures and times are investigated, and the phase evolution is inspected at a sequence of growth steps. It is uncovered that the dynamics of the growth process occurs at four different stages via preferential incorporation of chemical species at high-surface-energy facets. Also, a sequence of temperature and time dependent nonuniform to uniform phase evolutions has emerged in the composition and structure of (NbTaTi)0.33S3 which is described based on an anisotropic vapor-solid (V-S) mechanism. Furthermore, direct evidence for the 3D structure of the charge density wave (CDW) phase (width less than 100 nm) is provided by three-dimensional electron diffraction (3DED) in individual nanoribbons at cryogenic temperature, and detailed comparisons are made between the phases obtained before and after CDW transformation. This study provides important fundamental information for the design and synthesis of future 1D alloy structures.
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Affiliation(s)
- Shuxi Wang
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Taimin Yang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Khagesh Kumar
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Shahriar Namvar
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Sungjoon Kim
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Alireza Ahmadiparidari
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Hessam Shahbazi
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Sakshi Singh
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Zahra Hemmat
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Vikas Berry
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Jordi Cabana
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Fatemeh Khalili-Araghi
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Zhehao Huang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Amin Salehi-Khojin
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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11
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Zhou G, Yang T, Huang Z. Structure determination of a low-crystallinity covalent organic framework by three-dimensional electron diffraction. Commun Chem 2023; 6:116. [PMID: 37286771 DOI: 10.1038/s42004-023-00915-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023] Open
Abstract
Covalent organic frameworks (COFs) have been attracting intense research due to their permanent porosity, designable architecture, and high stability. However, COFs are challenging to crystallize and their synthesis often results in tiny crystal sizes and low crystallinities, which hinders an unambiguous structure determination. Herein, we demonstrate that the structure of low-crystallinity COF Py-1P nanocrystals can be solved by coupling three-dimensional electron diffraction (3DED) with simulated annealing (SA). The resulting model is comparable to that obtained from high-crystallinity samples by dual-space method. Moreover, for low-resolution 3DED data, the model obtained by SA shows a better framework than those provided by classic direct method, dual-space method, and charge flipping. We further simulate data with different resolutions to understand the reliability of SA under different crystal quality conditions. The successful determination of Py-1P structure by SA compared to other methods provides new knowledge for using 3DED to analyze low-crystallinity and nanosized materials.
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Affiliation(s)
- Guojun Zhou
- 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
| | - Zhehao Huang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden.
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12
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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 2023:10.1038/s41557-023-01186-1. [PMID: 37081207 DOI: 10.1038/s41557-023-01186-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [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.
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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.
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13
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Simoncic P, Romeijn E, Hovestreydt E, Steinfeld G, Santiso-Quiñones G, Merkelbach J. Electron crystallography and dedicated electron-diffraction instrumentation. Acta Crystallogr E Crystallogr Commun 2023; 79:410-422. [PMID: 37151820 PMCID: PMC10162091 DOI: 10.1107/s2056989023003109] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
Electron diffraction (known also as ED, 3D ED or microED) is gaining momentum in science and industry. The application of electron diffraction in performing nano-crystallography on crystals smaller than 1 µm is a disruptive technology that is opening up fascinating new perspectives for a wide variety of compounds required in the fields of chemical, pharmaceutical and advanced materials research. Electron diffraction enables the characterization of solid compounds complementary to neutron, powder X-ray and single-crystal X-ray diffraction, as it has the unique capability to measure nanometre-sized crystals. The recent introduction of dedicated instrumentation to perform ED experiments is a key aspect of the continued growth and success of this technology. In addition to the ultra-high-speed hybrid-pixel detectors enabling ED data collection in continuous rotation mode, a high-precision goniometer and horizontal layout have been determined as essential features of an electron diffractometer, both of which are embodied in the Eldico ED-1. Four examples of data collected on an Eldico ED-1 are showcased to demonstrate the potential and advantages of a dedicated electron diffractometer, covering selected applications and challenges of electron diffraction: (i) multiple reciprocal lattices, (ii) absolute structure of a chiral compound, and (iii) R-values achieved by kinematic refinement comparable to X-ray data.
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Affiliation(s)
- Petra Simoncic
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
- Correspondence e-mail:
| | - Eva Romeijn
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | - Eric Hovestreydt
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | - Gunther Steinfeld
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | | | - Johannes Merkelbach
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
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14
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Luo Y, Wang B, Smeets S, Sun J, Yang W, Zou X. High-throughput phase elucidation of polycrystalline materials using serial rotation electron diffraction. Nat Chem 2023; 15:483-490. [PMID: 36717616 PMCID: PMC10070184 DOI: 10.1038/s41557-022-01131-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/16/2022] [Indexed: 02/01/2023]
Abstract
Rapid phase elucidation of polycrystalline materials is essential for developing new materials of chemical, pharmaceutical and industrial interest. Yet, the size and quantity of many crystalline phases are too small for routine X-ray diffraction analysis. This has become a workflow bottleneck in materials development, especially in high-throughput synthesis screening. Here we demonstrate the application of serial rotation electron diffraction (SerialRED) for high-throughput phase identification of complex polycrystalline zeolite products. The products were prepared from a combination of multiple framework T atoms ([Si,Ge,Al] or [Si,Ge,B]) and a simple organic structure-directing agent. We show that using SerialRED, five zeolite phases can be identified from a highly complex mixture. This includes phases with ultra-low contents undetectable using X-ray diffraction and phases with identical crystal morphology and similar unit cell parameters. By automatically and rapidly examining hundreds of crystals, SerialRED enables high-throughput phase analysis and allows the exploration of complex synthesis systems. It provides new opportunities for rapid development of polycrystalline materials.
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Affiliation(s)
- Yi Luo
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Green Chemical Engineering and Industrial Catalysis, Sinopec Shanghai Research Institute of Petrochemical Technology, Shanghai, China
| | - Bin Wang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Stef Smeets
- Netherlands eScience Center, Amsterdam, Netherlands
| | - Junliang Sun
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Weimin Yang
- State Key Laboratory of Green Chemical Engineering and Industrial Catalysis, Sinopec Shanghai Research Institute of Petrochemical Technology, Shanghai, China.
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
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15
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Andrusenko I, Gemmi M. 3D
electron diffraction for structure determination of small‐molecule nanocrystals: A possible breakthrough for the pharmaceutical industry. WIRES 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] [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]
Affiliation(s)
- Iryna Andrusenko
- Center for Materials Interfaces, Electron Crystallography Istituto Italiano di Tecnologia Pontedera
| | - Mauro Gemmi
- Center for Materials Interfaces, Electron Crystallography Istituto Italiano di Tecnologia Pontedera
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16
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Ge M, Yang T, Xu H, Zou X, Huang Z. Direct Location of Organic Molecules in Framework Materials by Three-Dimensional Electron Diffraction. J Am Chem Soc 2022; 144:15165-15174. [PMID: 35950776 PMCID: PMC9434828 DOI: 10.1021/jacs.2c05122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Indexed: 11/30/2022]
Abstract
In the study of framework materials, probing interactions between frameworks and organic molecules is one of the most important tasks, which offers us a fundamental understanding of host-guest interactions in gas sorption, separation, catalysis, and framework structure formation. Single-crystal X-ray diffraction (SCXRD) is a conventional method to locate organic species and study such interactions. However, SCXRD demands large crystals whose quality is often vulnerable to, e.g., cracking on the crystals by introducing organic molecules, and this is a major challenge to use SCXRD for structural analysis. With the development of three-dimensional electron diffraction (3D ED), single-crystal structural analysis can be performed on very tiny crystals with sizes on the nanometer scale. Here, we analyze two framework materials, SU-8 and SU-68, with organic molecules inside their inorganic crystal structures. By applying 3D ED, with fast data collection and an ultralow electron dose (0.8-2.6 e- Å-2), we demonstrate for the first time that each nonhydrogen atom from the organic molecules can be ab initio located from structure solution, and they are shown as distinct and well-separated peaks in the difference electrostatic potential maps showing high accuracy and reliability. As a result, two different spatial configurations are identified for the same guest molecule in SU-8. We find that the organic molecules interact with the framework through strong hydrogen bonding, which is the key to immobilizing them at well-defined positions. In addition, we demonstrate that host-guest systems can be studied at room temperature. Providing high accuracy and reliability, we believe that 3D ED can be used as a powerful tool to study host-guest interactions, especially for nanocrystals.
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Affiliation(s)
- Meng Ge
- 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
| | - Hongyi Xu
- 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
| | - Zhehao Huang
- Department of Materials and
Environmental Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
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17
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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.
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18
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Wennmacher JTC, Mahmoudi S, Rzepka P, Sik Lee S, Gruene T, Paunović V, van Bokhoven JA. Electron Diffraction Enables the Mapping of Coke in ZSM-5 Micropores Formed during Methanol-to-Hydrocarbons Conversion. Angew Chem Int Ed Engl 2022; 61:e202205413. [PMID: 35513343 PMCID: PMC9401574 DOI: 10.1002/anie.202205413] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Indexed: 12/29/2022]
Abstract
Unveiling the coke formation in zeolites is an essential prerequisite for tackling the deactivation of these catalysts in the transformations of hydrocarbons. Herein, we present the direct mapping of coke in the micropores of ZSM-5 catalysts used in methanol-to-hydrocarbons conversion by single-crystal electron diffraction analysis. The latter technique revealed a polycyclic aromatic structure along the straight channel, wherein the high-quality data permit refinement of its occupancy to about 40 %. These findings were exploited to analyze the evolution of micropore coke during the reaction. Herein, coke-associated signals, which correlate with the activity loss, indicate that the nucleation of coke commences in the intersections of sinusoidal and straight channels, while the formation of coke in the straight pores occurs in the late stages of deactivation. The findings uncover an attractive method for analyzing coke deposition in the micropore domain.
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Affiliation(s)
- Julian T. C. Wennmacher
- Institute for Chemical and BioengineeringDepartment of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 18093ZurichSwitzerland
- Laboratory for Catalysis and Sustainable ChemistryPaul Scherrer InstituteForschungsstrasse 1115232Villigen PSISwitzerland
| | - Soheil Mahmoudi
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaWähringer Strasse 421090ViennaAustria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Strasse 421090ViennaAustria
| | - Przemyslaw Rzepka
- Institute for Chemical and BioengineeringDepartment of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 18093ZurichSwitzerland
- Laboratory for Catalysis and Sustainable ChemistryPaul Scherrer InstituteForschungsstrasse 1115232Villigen PSISwitzerland
| | - Sung Sik Lee
- Scientific Center of Optical and Electron MicroscopyETH ZurichOtto-Stern-Weg 38093ZurichSwitzerland
| | - Tim Gruene
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaWähringer Strasse 421090ViennaAustria
| | - Vladimir Paunović
- Institute for Chemical and BioengineeringDepartment of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 18093ZurichSwitzerland
- Laboratory for Catalysis and Sustainable ChemistryPaul Scherrer InstituteForschungsstrasse 1115232Villigen PSISwitzerland
| | - Jeroen A. van Bokhoven
- Institute for Chemical and BioengineeringDepartment of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 18093ZurichSwitzerland
- Laboratory for Catalysis and Sustainable ChemistryPaul Scherrer InstituteForschungsstrasse 1115232Villigen PSISwitzerland
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19
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Newman JA, Iuzzolino L, Tan M, Orth P, Bruhn J, Lee AY. From Powders to Single Crystals: A Crystallographer's Toolbox for Small-Molecule Structure Determination. Mol Pharm 2022; 19:2133-2141. [PMID: 35576503 PMCID: PMC10152450 DOI: 10.1021/acs.molpharmaceut.2c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although the crystal structures of small-molecule compounds are often determined from single-crystal X-ray diffraction (scXRD), recent advances in three-dimensional electron diffraction (3DED) and crystal structure prediction (CSP) methods promise to expand the structure elucidation toolbox available to the crystallographer. Herein, a comparative assessment of scXRD, 3DED, and CSP in combination with powder X-ray diffraction is carried out on two former drug candidate compounds and a multicomponent crystal of a key building block in the synthesis of gefapixant citrate.
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Affiliation(s)
- Justin A. Newman
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Luca Iuzzolino
- Department
of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Melissa Tan
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Peter Orth
- Department
of Computational and Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jessica Bruhn
- Nanoimaging
Services, San Diego, California 92121, United States
| | - Alfred Y. Lee
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
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20
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Bürgi HB. Crystal structures. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:283-289. [PMID: 35695099 DOI: 10.1107/s205252062200292x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/16/2022] [Indexed: 06/15/2023]
Abstract
A personal view is offered on various solved and open problems related to crystal structures: the present state of reconstructing the crystal electron density from X-ray diffraction data; characterization of atomic and molecular motion from a combination of atomic displacement parameters and quantum chemical calculations; Bragg diffraction and diffuse scattering: twins, but different; models of real (as opposed to ideal) crystal structures from diffuse scattering; exploiting unexplored neighbourhoods of crystallography to mathematics, physics and chemistry.
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Affiliation(s)
- Hans Beat Bürgi
- Department of Chemistry, Biochemistry and Pharmacy, University of Berne, Freiestrasse 12, Bern, CH-3012, Switzerland
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21
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Huo ZQ, Zhu F, Zhang XW, Zhang X, Liang HB, Yao JC, Liu Z, Zhang GM, Yao QQ, Qin GF. Approaches to Configuration Determinations of Flexible Marine Natural Products: Advances and Prospects. Mar Drugs 2022; 20:333. [PMID: 35621984 PMCID: PMC9143581 DOI: 10.3390/md20050333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023] Open
Abstract
Flexible marine natural products (MNPs), such as eribulin and bryostatin, play an important role in the development of modern marine drugs. However, due to the multiple chiral centers and geometrical uncertainty of flexible systems, configuration determinations of flexible MNPs face great challenges, which, in turn, have led to obstacles in druggability research. To resolve this issue, the comprehensive use of multiple methods is necessary. Additionally, configuration assignment methods, such as X-ray single-crystal diffraction (crystalline derivatives, crystallization chaperones, and crystalline sponges), NMR-based methods (JBCA and Mosher's method), circular dichroism-based methods (ECCD and ICD), quantum computational chemistry-based methods (NMR calculations, ECD calculations, and VCD calculations), and chemical transformation-based methods should be summarized. This paper reviews the basic principles, characteristics, and applicability of the methods mentioned above as well as application examples to broaden the research and applications of these methods and to provide a reference for the configuration determinations of flexible MNPs.
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Affiliation(s)
- Zong-Qing Huo
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
| | - Feng Zhu
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
| | - Xing-Wang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiao Zhang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
| | - Hong-Bao Liang
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
| | - Jing-Chun Yao
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
| | - Zhong Liu
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
| | - Gui-Min Zhang
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
| | - Qing-Qiang Yao
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China;
| | - Guo-Fei Qin
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
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22
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Electron Diffraction Enables the Mapping of Coke in ZSM‐5 Micropores Formed during Methanol‐to‐Hydrocarbons Conversion. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Pearce N, Reynolds KEA, Kayal S, Sun XZ, Davies ES, Malagreca F, Schürmann CJ, Ito S, Yamano A, Argent SP, George MW, Champness NR. Selective photoinduced charge separation in perylenediimide-pillar[5]arene rotaxanes. Nat Commun 2022; 13:415. [PMID: 35058440 PMCID: PMC8776946 DOI: 10.1038/s41467-022-28022-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
The ability to control photoinduced charge transfer within molecules represents a major challenge requiring precise control of the relative positioning and orientation of donor and acceptor groups. Here we show that such photoinduced charge transfer processes within homo- and hetero-rotaxanes can be controlled through organisation of the components of the mechanically interlocked molecules, introducing alternative pathways for electron donation. Specifically, studies of two rotaxanes are described: a homo[3]rotaxane, built from a perylenediimide diimidazolium rod that threads two pillar[5]arene macrocycles, and a hetero[4]rotaxane in which an additional bis(1,5-naphtho)-38-crown-10 (BN38C10) macrocycle encircles the central perylenediimide. The two rotaxanes are characterised by a combination of techniques including electron diffraction crystallography in the case of the hetero[4]rotaxane. Cyclic voltammetry, spectroelectrochemistry, and EPR spectroscopy are employed to establish the behaviour of the redox states of both rotaxanes and these data are used to inform photophysical studies using time-resolved infra-red (TRIR) and transient absorption (TA) spectroscopies. The latter studies illustrate the formation of a symmetry-breaking charge-separated state in the case of the homo[3]rotaxane in which charge transfer between the pillar[5]arene and perylenediimide is observed involving only one of the two macrocyclic components. In the case of the hetero[4]rotaxane charge separation is observed involving only the BN38C10 macrocycle and the perylenediimide leaving the pillar[5]arene components unperturbed.
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Affiliation(s)
- Nicholas Pearce
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | - Surajit Kayal
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Xue Z Sun
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - E Stephen Davies
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Ferdinando Malagreca
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | | | - Sho Ito
- Rigaku Corporation, 3-9-12, Matsubara, Akishima, Tokyo, 196-8666, Japan
| | - Akihito Yamano
- Rigaku Corporation, 3-9-12, Matsubara, Akishima, Tokyo, 196-8666, Japan
| | - Stephen P Argent
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Michael W George
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Neil R Champness
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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24
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Gorelik TE, Tehrani KHME, Gruene T, Monecke T, Niessing D, Kaiser U, Blankenfeldt W, Müller R. Crystal structure of natural product argyrin-D determined by 3D electron diffraction. CrystEngComm 2022. [DOI: 10.1039/d2ce00707j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystal structure of natural product argyrin D was determined from electron diffraction data.
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Affiliation(s)
- Tatiana E. Gorelik
- Electron Microscopy Group of Materials Science, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, Germany
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrucken, 66123, Germany
| | - Kamaleddin H. M. E. Tehrani
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrucken, 66123, Germany
| | - Tim Gruene
- Faculty of Chemistry, Department of Inorganic Chemistry, University of Vienna, AT-1090 Vienna, Austria
| | - Thomas Monecke
- Institute of Pharmaceutical Biotechnology, Ulm University, James-Franck-Ring N27, 89081 Ulm, Germany
| | - Dierk Niessing
- Institute of Pharmaceutical Biotechnology, Ulm University, James-Franck-Ring N27, 89081 Ulm, Germany
| | - Ute Kaiser
- Electron Microscopy Group of Materials Science, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrucken, 66123, Germany
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25
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Petersen H, Weidenthaler C. A review of recent developments for the in situ/operando characterization of nanoporous materials. Inorg Chem Front 2022. [DOI: 10.1039/d2qi00977c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This is a review on up-to-date in situ/operando methods for a comprehensive characterization of nanoporous materials. The group of nanoporous materials is constantly growing, and with it, the variety of...
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26
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Samperisi L, Zou X, Huang Z. Three-Dimensional Electron Diffraction: A Powerful Structural Characterization Technique for Crystal Engineering. CrystEngComm 2022. [DOI: 10.1039/d2ce00051b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding crystal structures and behaviors is crucial for constructing and engineering crystalline materials with various properties and functions. Recent advancement in three-dimensional electron diffraction (3D ED) and its application on...
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27
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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.
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28
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Anderson CL, Li H, Jones CG, Teat SJ, Settineri NS, Dailing EA, Liang J, Mao H, Yang C, Klivansky LM, Li X, Reimer JA, Nelson HM, Liu Y. Solution-processable and functionalizable ultra-high molecular weight polymers via topochemical synthesis. Nat Commun 2021; 12:6818. [PMID: 34819494 PMCID: PMC8613210 DOI: 10.1038/s41467-021-27090-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/01/2021] [Indexed: 01/25/2023] Open
Abstract
Topochemical polymerization reactions hold the promise of producing ultra-high molecular weight crystalline polymers. However, the totality of topochemical polymerization reactions has failed to produce ultra-high molecular weight polymers that are both soluble and display variable functionality, which are restrained by the crystal-packing and reactivity requirements on their respective monomers in the solid state. Herein, we demonstrate the topochemical polymerization reaction of a family of para-azaquinodimethane compounds that undergo facile visible light and thermally initiated polymerization in the solid state, allowing for the first determination of a topochemical polymer crystal structure resolved via the cryoelectron microscopy technique of microcrystal electron diffraction. The topochemical polymerization reaction also displays excellent functional group tolerance, accommodating both solubilizing side chains and reactive groups that allow for post-polymerization functionalization. The thus-produced soluble ultra-high molecular weight polymers display superior capacitive energy storage properties. This study overcomes several synthetic and characterization challenges amongst topochemical polymerization reactions, representing a critical step toward their broader application.
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Affiliation(s)
- Christopher L Anderson
- The Molecular Foundry, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - He Li
- The Molecular Foundry, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Christopher G Jones
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Simon J Teat
- Advanced Light Source, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Nicholas S Settineri
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
- Advanced Light Source, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Eric A Dailing
- The Molecular Foundry, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jiatao Liang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Haiyan Mao
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Chongqing Yang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Liana M Klivansky
- The Molecular Foundry, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Xinle Li
- The Molecular Foundry, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jeffrey A Reimer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Hosea M Nelson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Yi Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA.
- Materials Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA.
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29
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Gruene T, Mugnaioli E. 3D Electron Diffraction for Chemical Analysis: Instrumentation Developments and Innovative Applications. Chem Rev 2021; 121:11823-11834. [PMID: 34533919 PMCID: PMC8517952 DOI: 10.1021/acs.chemrev.1c00207] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 01/26/2023]
Abstract
In the past few years, many exciting papers reported results based on crystal structure determination by electron diffraction. The aim of this review is to provide general and practical information to structural chemists interested in stepping into this emerging field. We discuss technical characteristics of electron microscopes for research units that would like to acquire their own instrumentation, as well as those practical aspects that appear different between X-ray and electron crystallography. We also include a discussion about applications where electron crystallography provides information that is different, and possibly complementary, with respect to what is available from X-ray crystallography.
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Affiliation(s)
- Tim Gruene
- University
of Vienna, Faculty of Chemistry,
Department of Inorganic Chemistry, AT-1090 Vienna, Austria
| | - Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, IT-56127 Pisa, Italy
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