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Metherall JP, Carroll RC, Coles SJ, Hall MJ, Probert MR. Advanced crystallisation methods for small organic molecules. Chem Soc Rev 2023; 52:1995-2010. [PMID: 36857636 DOI: 10.1039/d2cs00697a] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Molecular materials based on small organic molecules often require advanced structural analysis, beyond the capability of spectroscopic techniques, to fully characterise them. In such cases, diffraction methods such as single crystal X-ray diffraction (SCXRD), are one of the most powerful tools available to researchers, providing molecular and structural elucidation at atomic level resolution, including absolute stereochemistry. However SCXRD, and related diffraction methods, are heavily dependent on the availability of suitable, high-quality crystals, thus crystallisation often becomes the major bottleneck in preparing samples. Following a summary of classical methods for the crystallisation of small organic molecules, this review will focus on a number of recently developed advanced methods for crystalline material sample preparation for SCXRD. This review will cover two main areas of modern small organic molecule crystallisation, namely the inclusion of molecules within host complexes (e.g., "crystalline sponge" and tetraaryladamantane based inclusion chaperones) and the use of high-throughput crystallisation, employing "under-oil" approaches (e.g., microbatch under-oil and ENaCt). Representative examples have been included for each technique, together with a discussion of their relative advantages and limitations to aid the reader in selecting the most appropriate technique to overcome a specific analytical challenge.
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Affiliation(s)
- J P Metherall
- Newcastle University, Chemistry - School of Natural Environmental Sciences, Newcastle upon Tyne, NE1 7RU, UK.
| | - R C Carroll
- University of Southampton, School of Chemistry, Southampton, SO17 1BJ, UK
| | - S J Coles
- University of Southampton, School of Chemistry, Southampton, SO17 1BJ, UK
| | - M J Hall
- Newcastle University, Chemistry - School of Natural Environmental Sciences, Newcastle upon Tyne, NE1 7RU, UK.
| | - M R Probert
- Newcastle University, Chemistry - School of Natural Environmental Sciences, Newcastle upon Tyne, NE1 7RU, UK.
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2
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Chauhan P, Javed S. Crystallographic capture of caged diamondoids: Camphor and adamantanes’ guests‐encapsulation on specific recognition‐sites of host MOF. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Chauhan P, Javed S, Levendis DC, Fernandes M. Hydrophobicity directed guest-inclusion for structure-elucidation of enclatherated guests within a crystalline sponge by SC-XRD. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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4
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Zigon N, Duplan V, Wada N, Fujita M. Crystalline Sponge Method: X‐ray Structure Analysis of Small Molecules by Post‐Orientation within Porous Crystals—Principle and Proof‐of‐Concept Studies. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nicolas Zigon
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Vincent Duplan
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Naoki Wada
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Makoto Fujita
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Division of Advanced Molecular Science Institute for Molecular Science (IMS) 5-1 Higashiyama Myodaiji Okazaki Aichi 444-8787 Japan
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5
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Taniguchi Y, Miwa M, Kitada N. Crystalline sponge X-ray analysis coupled with supercritical fluid chromatography: a novel analytical platform for the rapid separation, isolation, and characterization of analytes. Analyst 2021; 146:5230-5235. [PMID: 34373868 DOI: 10.1039/d1an00948f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystalline sponge (CS) based X-ray diffraction (XRD) analysis allows for the observation of the structure of an analyte, including its absolute configuration. Herein we report a powerful analytical platform for the separation, isolation, and structural elucidation of a target analyte in a seamless way by coupling supercritical fluid chromatography (SFC) with CS-based XRD analysis (SFC-CSXRD). The efficacy of this methodology is demonstrated by the rapid characterization of regio- and stereoisomers using three types of CSs with differing tolerances to the solvents used in SFC and guest-soaking.
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Affiliation(s)
- Yoshimasa Taniguchi
- Kirin Central Research Institute, Research & Development Division, Kirin Holdings Company Ltd., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
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6
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Zigon N, Duplan V, Wada N, Fujita M. Crystalline Sponge Method: X-ray Structure Analysis of Small Molecules by Post-Orientation within Porous Crystals-Principle and Proof-of-Concept Studies. Angew Chem Int Ed Engl 2021; 60:25204-25222. [PMID: 34109717 DOI: 10.1002/anie.202106265] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Indexed: 01/05/2023]
Abstract
This Review discusses, along with the historical background, the principles as well as proof-of-concept studies of the crystalline sponge (CS) method, a new single-crystal X-ray diffraction (SCXRD) method for the analysis of the structures of small molecules without sample crystallization. The method uses single-crystalline porous coordination networks (crystalline sponges) that can absorb small guest molecules within their pores. The absorbed guest molecules are ordered in the pores through molecular recognition and become observable by conventional SCXRD analysis. The complex {[(ZnI2 )3 (tpt)2 ]⋅x(solvent)}n (tpt=tris(4-pyridyl)-1,3,5-triazine) was first proposed as a crystalline sponge and has been most generally used. Crystalline sponges developed later are also discussed here. The principle of the CS method can be described as "post-crystallization" of the absorbed guest, whose ordering is templated by the pre-latticed cavities. The method has been widely applied to synthetic chemistry as well as natural product studies, for which proof-of-concept examples will be shown here.
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Affiliation(s)
- Nicolas Zigon
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Vincent Duplan
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Naoki Wada
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Makoto Fujita
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Division of Advanced Molecular Science, Institute for Molecular Science (IMS), 5-1 Higashiyama Myodaiji, Okazaki, Aichi, 444-8787, Japan
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7
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Lunn RJ, Tocher DA, Sidebottom PJ, Montgomery MG, Keates AC, Carmalt CJ. Applying the Crystalline Sponge Method to Agrochemicals: Obtaining X-ray Structures of the Fungicide Metalaxyl-M and Herbicide S-Metolachlor. CRYSTAL GROWTH & DESIGN 2021; 21:3024-3036. [PMID: 34054355 PMCID: PMC8154245 DOI: 10.1021/acs.cgd.1c00196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/29/2021] [Indexed: 06/12/2023]
Abstract
The crystalline sponge method is a technique that provides the ability to elucidate the absolute structure of noncrystalline or hard to crystallize compounds through single-crystal X-ray diffraction by removing the need to obtain crystals of the target compound. In this study the crystalline sponges {[(ZnX2)3(2,4,6-tris(4-pyridyl)-1,3,5-trazine)2].x(solvent)} n (X = I, Br) were used to obtain X-ray structures of the agrochemical active ingredients metalaxyl-M and S-metolachlor. The effect of the temperature used during guest uptake and the influence of changing the host framework ZnX2 nodes on guest encapsulation were investigated. Additionally, three compounds containing chemical fragments similar to those of metalaxyl-M and S-metolachlor (phenylacetaldehyde, N-ethyl-o-toluidine, and methyl phenylacetate) were also encapsulated. This allowed for the effect of guest size on the position that guests occupy within the host frameworks to be examined. The disorder experienced by the guest compounds was documented, and an analysis of the intermolecular host-guest interactions (CH···π and π ···π) used for guest ordering within the host frameworks was also undertaken in this study.
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Affiliation(s)
- Richard
D. J. Lunn
- University
College London, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Derek A. Tocher
- University
College London, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Philip J. Sidebottom
- Syngenta,
Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, U.K.
| | - Mark G. Montgomery
- Syngenta,
Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, U.K.
| | - Adam C. Keates
- Syngenta,
Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, U.K.
| | - Claire J. Carmalt
- University
College London, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, U.K.
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8
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Cardenal A, Ramadhar TR. Application of Crystalline Matrices for the Structural Determination of Organic Molecules. ACS CENTRAL SCIENCE 2021; 7:406-414. [PMID: 33791424 PMCID: PMC8006175 DOI: 10.1021/acscentsci.0c01492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Indexed: 06/12/2023]
Abstract
While single-crystal X-ray diffraction (SC-XRD) is one of the most powerful structural determination techniques for organic molecules, the requirement of obtaining a suitable crystal for analysis limits its applicability, particularly for liquids and amorphous solids. The emergent use of preformed porous crystalline matrices that can absorb organic compounds and stabilize them via host-guest interactions for observation via SC-XRD offers a way to overcome this hindrance. A topical and current discussion of SC-XRD in organic chemistry and the use of preformed matrices for the in crystallo analysis of organic compounds, with a particular focus on the absolute structure determination of chiral molecules, is presented. Preformed crystalline matrices that are covered include metal-organic frameworks (MOFs) as used in the crystalline sponge method, metal-organic polyhedra (MOPs, coordination cages), porous organic materials (POMs)/porous organic molecular crystals (POMCs), and biological scaffolds. An outlook and perspective on the current technology and on its future directions is provided.
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Affiliation(s)
- Ashley
D. Cardenal
- Department of Chemistry, Howard University, Washington, DC 20059, United States
| | - Timothy R. Ramadhar
- Department of Chemistry, Howard University, Washington, DC 20059, United States
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9
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Taniguchi Y, Matsumoto R, Kadota T. An Expansion of Crystalline Sponge X-ray Analysis to Elucidate the Molecular Structure of Reactive Compounds via Ion Pair Formation. Chemistry 2020; 26:15799-15803. [PMID: 32729166 DOI: 10.1002/chem.202002504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/28/2020] [Indexed: 12/17/2022]
Abstract
The crystalline sponge (CS) method allows structural elucidation of a target compound (guest) in solution by single crystal X-ray diffraction through trapping the guest into the CS framework. In principle, the CS method is inapplicable to reactive compounds that break the CS framework, such as acidic, basic, or nucleophilic ones. Here, a solution to this problem is disclosed wherein an ion pair of the guest compound is formed during the guest-soaking step by adding a suitable reagent. The ion pair can be observed and does not damage the CS framework. Using the developed method, amino, guanidino, and amidino compounds have been successfully analyzed as ion pairs with sulfonic acids. Practical utility has been shown because the absolute configurations of optically resolved amine derivatives were revealed with only a few micrograms. This demonstrates that the ion-pair-soaking method is simple and expands the range of compounds applicable to the CS method.
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Affiliation(s)
- Yoshimasa Taniguchi
- Kirin Central Research Institute, Research & Development Division, Kirin Holdings Company, Ltd., 1-13-5, Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa, 236-0004, Japan
| | - Rie Matsumoto
- Kirin Central Research Institute, Research & Development Division, Kirin Holdings Company, Ltd., 1-13-5, Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa, 236-0004, Japan
| | - Tomoyuki Kadota
- Kirin Central Research Institute, Research & Development Division, Kirin Holdings Company, Ltd., 1-13-5, Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa, 236-0004, Japan
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10
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Young RJ, Huxley MT, Pardo E, Champness NR, Sumby CJ, Doonan CJ. Isolating reactive metal-based species in Metal-Organic Frameworks - viable strategies and opportunities. Chem Sci 2020; 11:4031-4050. [PMID: 34122871 PMCID: PMC8152792 DOI: 10.1039/d0sc00485e] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/19/2020] [Indexed: 02/01/2023] Open
Abstract
Structural insight into reactive species can be achieved via strategies such as matrix isolation in frozen glasses, whereby species are kinetically trapped, or by confinement within the cavities of host molecules. More recently, Metal-Organic Frameworks (MOFs) have been used as molecular scaffolds to isolate reactive metal-based species within their ordered pore networks. These studies have uncovered new reactivity, allowed observation of novel metal-based complexes and clusters, and elucidated the nature of metal-centred reactions responsible for catalysis. This perspective considers strategies by which metal species can be introduced into MOFs and highlights some of the advantages and limitations of each approach. Furthermore, the growing body of work whereby reactive species can be isolated and structurally characterised within a MOF matrix will be reviewed, including discussion of salient examples and the provision of useful guidelines for the design of new systems. Novel approaches that facilitate detailed structural analysis of reactive chemical moieties are of considerable interest as the knowledge garnered underpins our understanding of reactivity and thus guides the synthesis of materials with unprecedented functionality.
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Affiliation(s)
- Rosemary J Young
- Department of Chemistry, Centre for Advanced Nanomaterials, The University of Adelaide Adelaide Australia
- School of Chemistry, The University of Nottingham Nottingham UK
| | - Michael T Huxley
- Department of Chemistry, Centre for Advanced Nanomaterials, The University of Adelaide Adelaide Australia
| | - Emilio Pardo
- Institute of Molecular Science, University of Valencia Valencia Spain
| | | | - Christopher J Sumby
- Department of Chemistry, Centre for Advanced Nanomaterials, The University of Adelaide Adelaide Australia
| | - Christian J Doonan
- Department of Chemistry, Centre for Advanced Nanomaterials, The University of Adelaide Adelaide Australia
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11
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Schwartz HA, Laurenzen H, Kerschbaumer S, Werker M, Olthof S, Kopacka H, Huppertz H, Meerholz K, Ruschewitz U. High fatigue resistance of a photochromic dithienylethene embedded into the pores of a metal–organic framework (MOF). Photochem Photobiol Sci 2020; 19:1730-1740. [DOI: 10.1039/d0pp00002g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The incorporation of photochromic dyes into porous metal–organic frameworks (MOFs) is an attractive way to transfer the photochromic properties of the dye to a solid crystalline material.
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Affiliation(s)
- Heidi A. Schwartz
- Institute of Inorganic Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
- Institute of General, Inorganic, and Theoretical Chemistry
| | - Hannah Laurenzen
- Institute of Inorganic Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
| | - Samuel Kerschbaumer
- Institute of General, Inorganic, and Theoretical Chemistry
- University of Innsbruck
- Center for Chemistry and Biomedicine
- A-6020 Innsbruck
- Austria
| | - Melanie Werker
- Institute of Inorganic Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
| | - Selina Olthof
- Institute of Physical Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
| | - Holger Kopacka
- Institute of General, Inorganic, and Theoretical Chemistry
- University of Innsbruck
- Center for Chemistry and Biomedicine
- A-6020 Innsbruck
- Austria
| | - Hubert Huppertz
- Institute of General, Inorganic, and Theoretical Chemistry
- University of Innsbruck
- Center for Chemistry and Biomedicine
- A-6020 Innsbruck
- Austria
| | - Klaus Meerholz
- Institute of Physical Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
| | - Uwe Ruschewitz
- Institute of Inorganic Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
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12
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Schwartz HA, Schaniel D, Ruschewitz U. Tracking the light-induced isomerization processes and the photostability of spiropyrans embedded in the pores of crystalline nanoporous MOFs via IR spectroscopy. Photochem Photobiol Sci 2020; 19:1433-1441. [DOI: 10.1039/d0pp00267d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Difference IR spectroscopy of spiropyran@MOF systems to obtain the characteristic signatures of the spiropyran and merocyanine form at ambient conditions.
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Affiliation(s)
- Heidi A. Schwartz
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- A-6020 Innsbruck
- Austria
| | | | - Uwe Ruschewitz
- Department of Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
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13
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Poel W, Tinnemans P, Duchateau ALL, Honing M, Rutjes FPJT, Vlieg E, Gelder R. The Crystalline Sponge Method in Water. Chemistry 2019; 25:14999-15003. [DOI: 10.1002/chem.201904174] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Wester Poel
- Radboud UniversityInstitute for Molecules and Materials Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | - Paul Tinnemans
- Radboud UniversityInstitute for Molecules and Materials Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | | | - Maarten Honing
- Maastricht University, M4I Institute Universiteitssingel 50, 6229 ER Maastricht, The Netherlands & DSM, Resolve, Urmonderbaan 22 Geleen 6160 MD The Netherlands
| | - Floris P. J. T. Rutjes
- Radboud UniversityInstitute for Molecules and Materials Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | - Elias Vlieg
- Radboud UniversityInstitute for Molecules and Materials Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | - René Gelder
- Radboud UniversityInstitute for Molecules and Materials Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
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14
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Intermolecular Interactions in Functional Crystalline Materials: From Data to Knowledge. CRYSTALS 2019. [DOI: 10.3390/cryst9090478] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Intermolecular interactions of organic, inorganic, and organometallic compounds are the key to many composition–structure and structure–property networks. In this review, some of these relations and the tools developed by the Cambridge Crystallographic Data Center (CCDC) to analyze them and design solid forms with desired properties are described. The potential of studies supported by the Cambridge Structural Database (CSD)-Materials tools for investigation of dynamic processes in crystals, for analysis of biologically active, high energy, optical, (electro)conductive, and other functional crystalline materials, and for the prediction of novel solid forms (polymorphs, co-crystals, solvates) are discussed. Besides, some unusual applications, the potential for further development and limitations of the CCDC software are reported.
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15
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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16
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Du Q, Peng J, Wu P, He H. Review: Metal-organic framework based crystalline sponge method for structure analysis. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.02.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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17
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Abstract
The crystallography of supramolecular host-guest complexes is reviewed and discussed as a part of small molecule crystallography. In these complexes, the host binds the guests through weak supramolecular interactions, such as hydrogen and halogen bonding, cation-π, anion-π, C-H-π, π-π, C-H-anion interactions and the hydrophobic effect. As the guest often shows severe disorder, large thermal motion and low occupancies, the reliable crystallographic determination of the guest can be very demanding. The analysis of host-guest interactions using tools such as Hirshfeld and cavity volume surface analysis will help to look closely at the most important host-guest interactions. The jewel in the crown of utilizing host-guest interactions in the solid-state is the recently developed Crystalline Sponge Method (CSM) by Makoto Fujita. This method, when successful, gives an accurate and unambiguous 3-D structure of the structurally unknown guest molecule from only micro- or nanogram amounts of the guest molecule. In the case of an optically pure enantiomer, its absolute configuration can be determined.
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Affiliation(s)
- Kari Rissanen
- University of Jyvaskyla, Department of Chemistry, Nanoscience Center, Survontie 9 B, Jyvaskyla, 40014, Finland.
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18
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Gee WJ. The growing importance of crystalline molecular flasks and the crystalline sponge method. Dalton Trans 2018; 46:15979-15986. [PMID: 29106430 DOI: 10.1039/c7dt03136j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article showcases recent advancements made using crystalline molecular flasks and the widening list of prospective applications for the crystalline sponge method. This expansion has coincided with an increasing number of materials termed crystalline sponges, and a report of a predictive means of identifying candidates from crystallographic databases. The crystalline sponge method's primary application has been determination of absolute configuration, and this has evolved from the analysis of carefully chosen planar aromatic guests to more diverse identification of natural products, biological metabolites, and analysis of volatile chemical components. However with time-resolved X-ray crystallography providing arguably the most informative atomic scale insights of dynamic chemical processes, this application of the crystalline sponge method may soon eclipse structural determination in terms of importance.
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Affiliation(s)
- William J Gee
- School of Physical Sciences, University of Kent, Canterbury, Kent CT2 7NH, UK.
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19
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20
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Ramadhar TR, Zheng SL, Chen YS, Clardy J. The Crystalline Sponge Method: A Solvent-Based Strategy to Facilitate Noncovalent Ordered Trapping of Solid and Liquid Organic Compounds. CrystEngComm 2017; 19:4528-4534. [PMID: 29225511 PMCID: PMC5716803 DOI: 10.1039/c7ce00885f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A strategy that leverages solvent effects to noncovalently trap solid and unstable liquid organic compounds within a crystalline sponge ({[(ZnI2)3(tris(4-pyridyl)-1,3,5-triazine)2]·x(CHCl3)}n) in a simple, mild, and efficient fashion for target molecule structure determination via X-ray diffraction is disclosed. Host-guest structures were obtained using third-generation synchrotron radiation, and new beamline hardware allowed rapid data collection in ~5-24 minutes. This is 40-90% faster than previously reported crystalline sponge synchrotron datasets collected by us, and approximately a 150-720-fold decrease in time versus using a typical in-house diffractometer, effectively enabling the potential for high-throughput analysis. The new target molecule inclusion method using methyl tert-butyl ether (MTBE) solvent was demonstrated by trapping (E)-stilbene, vanillin, 4-(trifluoromethyl)phenyl azide, and (+)-artemisinin (an antimalarial drug). The potential of guests to maximize intermolecular interactions with the crystalline sponge framework at the expense of attenuating intramolecular interactions (e.g., π-conjugation) was observed for (E)-stilbene. Trapping of vanillin and (+)-artemisinin elicited single-crystal-to-single-crystal transformations where space group symmetry reduced from C2/c to P1̄ and C2, respectively, and the absolute configuration of (+)-artemisinin was determined through anomalous dispersion.
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Affiliation(s)
- Timothy R. Ramadhar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts, 02115, USA
| | - Shao-Liang Zheng
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts, 02138, USA
| | - Yu-Sheng Chen
- ChemMatCARS, Center for Advanced Radiation Sources, The University of Chicago c/o Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois, 60439, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts, 02115, USA
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