1
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Beran GJO. Frontiers of molecular crystal structure prediction for pharmaceuticals and functional organic materials. Chem Sci 2023; 14:13290-13312. [PMID: 38033897 PMCID: PMC10685338 DOI: 10.1039/d3sc03903j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
The reliability of organic molecular crystal structure prediction has improved tremendously in recent years. Crystal structure predictions for small, mostly rigid molecules are quickly becoming routine. Structure predictions for larger, highly flexible molecules are more challenging, but their crystal structures can also now be predicted with increasing rates of success. These advances are ushering in a new era where crystal structure prediction drives the experimental discovery of new solid forms. After briefly discussing the computational methods that enable successful crystal structure prediction, this perspective presents case studies from the literature that demonstrate how state-of-the-art crystal structure prediction can transform how scientists approach problems involving the organic solid state. Applications to pharmaceuticals, porous organic materials, photomechanical crystals, organic semi-conductors, and nuclear magnetic resonance crystallography are included. Finally, efforts to improve our understanding of which predicted crystal structures can actually be produced experimentally and other outstanding challenges are discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
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2
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Riaz M, Ali A, Ashfaq M, Ibrahim M, Akram N, Tahir MN, Kuznetsov A, Rodríguez L, Sameeh MY, Assiri MA, Torre AFDL. Polymorphs of Substituted p-Toluenesulfonanilide: Synthesis, Single-Crystal Analysis, Hirshfeld Surface Exploration, and Theoretical Investigation. ACS OMEGA 2023; 8:35307-35320. [PMID: 37779999 PMCID: PMC10536877 DOI: 10.1021/acsomega.3c04957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023]
Abstract
Polymorphism is an exciting feature of chemical systems where a compound can exist in different crystal forms. The present investigation is focused on the two polymorphic forms, triclinic (MSBT) and monoclinic (MSBM), of ethyl 3-iodo-4-((4-methylphenyl)sulfonamido)benzoate prepared from ethyl 4-amino-3-iodobenzoate. The prepared polymorphs were unambiguously confirmed by single-crystal X-ray diffraction (SC-XRD) analysis. According to the SC-XRD results, the molecular configurations of both structures are stabilized by intramolecular N-H···I and C-H···O bonding. The crystal packing of MSBT is different as compared to the crystal packing of MSBM because MSBT is crystallized in the triclinic crystal system with the space group P1̅, whereas MSBM is crystallized in the monoclinic crystal system with the space group P21/c. The molecules of MSBT are interlinked in the form of dimers through N-H···O bonding to form R22(8) loops, while the MSBM molecules are connected with each other in the form of an infinite chain through C-H···O bonding. The crystal packing of both compounds is further stabilized by off-set π···π stacking interactions between phenyl rings, which is found stronger in MSBM as compared to in MSBT. Moreover, Hirshfeld surface exploration of the polymorphs was carried out, and the results were compared with the closely related literature structure. Accordingly, the supramolecular assembly of these polymorphs is mainly stabilized by noncovalent interactions or intermolecular interactions. Furthermore, a density functional theory (DFT) study was also carried out, which provided good support for the SC-XRD and Hirshfeld studies, suggesting the formation of both intramolecular and intermolecular interactions for both compounds.
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Affiliation(s)
- Mehreen Riaz
- Department
of Applied Chemistry, Government College
University Faisalabad, 38000 Faisalabad, Pakistan
| | - Akbar Ali
- Department
of Chemistry, Government College University
Faisalabad, 38000 Faisalabad, Pakistan
| | - Muhammad Ashfaq
- Department
of Physics, University of Sargodha, 40100 Sargodha, Pakistan
| | - Muhammad Ibrahim
- Department
of Applied Chemistry, Government College
University Faisalabad, 38000 Faisalabad, Pakistan
| | - Nadia Akram
- Department
of Chemistry, Government College University
Faisalabad, 38000 Faisalabad, Pakistan
| | | | - Aleksey Kuznetsov
- Departamento
de Química, Campus Santiago Vitacura, Universidad Técnica Federico Santa María, Vitacura 7660251, Chile
| | - Lyanne Rodríguez
- Department
of Clinical Biochemistry and Immunohaematology, Thrombosis Research
Center, Medical Technology School, Faculty of Health Sciences, Universidad de Talca, Talca 3460000, Chile
| | - Manal Y. Sameeh
- Chemistry
Department, Faculty of Applied Sciences, Al-Leith University College, Umm Al-Qura University, Makkah 24831, Saudi Arabia
| | - Mohammed A. Assiri
- Research
center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61514, Saudi Arabia
- Department
of Chemistry, Faculty of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
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3
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Wilson CG, Cervenka T, Wood PA, Parsons S. Behavior of Occupied and Void Space in Molecular Crystal Structures at High Pressure. CRYSTAL GROWTH & DESIGN 2022; 22:2328-2341. [PMID: 35431662 PMCID: PMC9007411 DOI: 10.1021/acs.cgd.1c01427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/10/2022] [Indexed: 06/14/2023]
Abstract
We report a Monte Carlo algorithm for calculation of occupied ("network") and unoccupied ("void") space in crystal structures. The variation of the volumes of the voids and the network of intermolecular contacts with pressure sensitively reveals discontinuities associated with first- and second-order phase transitions, providing insights into the effect of compression (and, in principle, other external stimuli) at a level between those observed in individual contact distances and the overall unit cell dimensions. The method is shown to be especially useful for the correlation of high-pressure crystallographic and spectroscopic data, illustrated for naphthalene, where a phase transition previously detected by vibrational spectroscopy, and debated in the literature for over 80 years, has been revealed unambiguously in crystallographic data for the first time. Premonitory behavior before a phase transition and crystal collapse at the end of a compression series has also been detected. The network and void volumes for 129 high-pressure studies taken from the Cambridge Structural Database (CSD) were fitted to equation of state to show that networks typically have bulk moduli between 40 and 150 GPa, while those of voids fall into a much smaller range, 2-5 GPa. These figures are shown to reproduce the narrow range of overall bulk moduli of molecular solids (ca. 5-20 GPa). The program, called CellVol, has been written in Python using the CSD Python API and can be run through the command line or through the Cambridge Crystallographic Data Centre's Mercury interface.
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Affiliation(s)
- Cameron
J. G. Wilson
- Centre
for Science at Extreme Conditions, School of Chemistry, The University of Edinburgh, King’s Buildings, West Mains
Road, Edinburgh EH9 3FJ, U.K.
| | - Tomas Cervenka
- Centre
for Science at Extreme Conditions, School of Chemistry, The University of Edinburgh, King’s Buildings, West Mains
Road, Edinburgh EH9 3FJ, U.K.
| | - Peter A. Wood
- The
Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K.
| | - Simon Parsons
- Centre
for Science at Extreme Conditions, School of Chemistry, The University of Edinburgh, King’s Buildings, West Mains
Road, Edinburgh EH9 3FJ, U.K.
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4
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Broadhurst ET, Wilson CJG, Zissimou GA, Nudelman F, Constantinides CP, Koutentis PA, Parsons S. A first-order phase transition in Blatter's radical at high pressure. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:107-116. [PMID: 35411850 DOI: 10.1107/s2052520622000191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
The crystal structure of Blatter's radical (1,3-diphenyl-1,4-dihydrobenzo[e][1,2,4]triazin-4-yl) has been investigated between ambient pressure and 6.07 GPa. The sample remains in a compressed form of the ambient-pressure phase up to 5.34 GPa, the largest direction of strain being parallel to the direction of π-stacking interactions. The bulk modulus is 7.4 (6) GPa, with a pressure derivative equal to 9.33 (11). As pressure increases, the phenyl groups attached to the N1 and C3 positions of the triazinyl moieties of neighbouring pairs of molecules approach each other, causing the former to begin to rotate between 3.42 to 5.34 GPa. The onset of this phenyl rotation may be interpreted as a second-order phase transition which introduces a new mode for accommodating pressure. It is premonitory to a first-order isosymmetric phase transition which occurs on increasing pressure from 5.34 to 5.54 GPa. Although the phase transition is driven by volume minimization, rather than relief of unfavourable contacts, it is accompanied by a sharp jump in the orientation of the rotation angle of the phenyl group. DFT calculations suggest that the adoption of a more planar conformation by the triazinyl moiety at the phase transition can be attributed to relief of intramolecular H...H contacts at the transition. Although no dimerization of the radicals occurs, the π-stacking interactions are compressed by 0.341 (3) Å between ambient pressure and 6.07 GPa.
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Affiliation(s)
- Edward T Broadhurst
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Cameron J G Wilson
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Georgia A Zissimou
- Department of Chemistry, University of Cyprus, PO Box 20537, 1678 Nicosia, Cyprus
| | - Fabio Nudelman
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Christos P Constantinides
- Department of Natural Sciences, University of Michigan-Dearborn, 4901 Evergreen Road, Dearborn, Michigan, 48128-1491, USA
| | | | - Simon Parsons
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, EH9 3FJ, United Kingdom
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5
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Beran GJO, Sugden IJ, Greenwell C, Bowskill DH, Pantelides CC, Adjiman CS. How many more polymorphs of ROY remain undiscovered. Chem Sci 2022; 13:1288-1297. [PMID: 35222912 PMCID: PMC8809489 DOI: 10.1039/d1sc06074k] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022] Open
Abstract
With 12 crystal forms, 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecabonitrile (a.k.a. ROY) holds the current record for the largest number of fully characterized organic crystal polymorphs. Four of these polymorph structures have been reported since 2019, raising the question of how many more ROY polymorphs await future discovery. Employing crystal structure prediction and accurate energy rankings derived from conformational energy-corrected density functional theory, this study presents the first crystal energy landscape for ROY that agrees well with experiment. The lattice energies suggest that the seven most stable ROY polymorphs (and nine of the twelve lowest-energy forms) on the Z' = 1 landscape have already been discovered experimentally. Discovering any new polymorphs at ambient pressure will likely require specialized crystallization techniques capable of trapping metastable forms. At pressures above 10 GPa, however, a new crystal form is predicted to become enthalpically more stable than all known polymorphs, suggesting that further high-pressure experiments on ROY may be warranted. This work highlights the value of high-accuracy crystal structure prediction for solid-form screening and demonstrates how pragmatic conformational energy corrections can overcome the limitations of conventional density functionals for conformational polymorphs.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
| | - Isaac J Sugden
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
| | - Chandler Greenwell
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
| | - David H Bowskill
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
| | - Constantinos C Pantelides
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
| | - Claire S Adjiman
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
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6
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Novelli G, Kamenev KV, Maynard-Casely HE, Parsons S, McIntyre GJ. Use of a miniature diamond-anvil cell in a joint X-ray and neutron high-pressure study on copper sulfate pentahydrate. IUCRJ 2022; 9:73-85. [PMID: 35059212 PMCID: PMC8733890 DOI: 10.1107/s2052252521010708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/15/2021] [Indexed: 06/14/2023]
Abstract
Single-crystal X-ray and neutron diffraction data are usually collected using separate samples. This is a disadvantage when the sample is studied at high pressure because it is very difficult to achieve exactly the same pressure in two separate experiments, especially if the neutron data are collected using Laue methods where precise absolute values of the unit-cell dimensions cannot be measured to check how close the pressures are. In this study, diffraction data have been collected under the same conditions on the same sample of copper(II) sulfate pentahydrate, using a conventional laboratory diffractometer and source for the X-ray measurements and the Koala single-crystal Laue diffractometer at the ANSTO facility for the neutron measurements. The sample, of dimensions 0.40 × 0.22 × 0.20 mm3 and held at a pressure of 0.71 GPa, was contained in a miniature Merrill-Bassett diamond-anvil cell. The highly penetrating diffracted neutron beams passing through the metal body of the miniature cell as well as through the diamonds yielded data suitable for structure refinement, and compensated for the low completeness of the X-ray measurements, which was only 24% on account of the triclinic symmetry of the sample and the shading of reciprocal space by the cell. The two data-sets were combined in a single 'XN' structure refinement in which all atoms, including H atoms, were refined with anisotropic displacement parameters. The precision of the structural parameters was improved by a factor of up to 50% in the XN refinement compared with refinements using the X-ray or neutron data separately.
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Affiliation(s)
- Giulia Novelli
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh EH9 3FJ, United Kingdom
| | - Konstantin V. Kamenev
- School of Engineering and Centre for Science at Extreme Conditions, University of Edinburgh, Erskine Williamson Building, King’s Buildings, Edinburgh EH9 3FD, United Kingdom
| | - Helen E. Maynard-Casely
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights NSW 2234, Australia
| | - Simon Parsons
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh EH9 3FJ, United Kingdom
| | - Garry J. McIntyre
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights NSW 2234, Australia
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7
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Warren LR, McGowan E, Renton M, Morrison CA, Funnell NP. Direct evidence for distinct colour origins in ROY polymorphs. Chem Sci 2021; 12:12711-12718. [PMID: 34703557 PMCID: PMC8494124 DOI: 10.1039/d1sc04051k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/27/2021] [Indexed: 11/21/2022] Open
Abstract
ROY is one of the most well-studied families of crystal structures owing to it being the most polymorphic organic material on record. The various red, orange, and yellow colours of its crystal structures are widely-believed to originate from molecular conformation, though the orange needle (ON) polymorph is thought to be an exception. We report high-pressure, single-crystal X-ray measurements which provide direct experimental evidence that the colour origin in ON is intermolecular, revealing that the molecule undergoes minimal deformation but still exhibits a pronounced, reversible, pale orange → dark red colour change between ambient pressure and 4.18 GPa. Our experimental data are rationalised with band structures, calculated using an accurate hybrid DFT approach, where we are able to account for the variation in colour for five polymorphs of ROY. We highlight the outlier behaviour of ON which shows marked π⋯π stacking interactions that are directly modified through application of pressure. Band structure calculations confirm these intermolecular interactions as the origin of the colour change.
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Affiliation(s)
- Lisette R Warren
- University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK +44 (0)131 650 4725
| | - Evana McGowan
- University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK +44 (0)131 650 4725
| | - Margaret Renton
- University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK +44 (0)131 650 4725
| | - Carole A Morrison
- University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK +44 (0)131 650 4725
| | - Nicholas P Funnell
- ISIS Neutron and Muon Facility, Rutherford Appleton Laboratory Didcot OX11 0QX UK +44 (0)1235 445385
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8
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Chen Z, Gui Y, Cui K, Schmit JR, Yu L. Prolific Polymorph Generator ROY in Its Liquid and Glass: Two Conformational Populations Mirroring the Crystalline-State Distribution. J Phys Chem B 2021; 125:10304-10311. [PMID: 34464152 DOI: 10.1021/acs.jpcb.1c05834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5-Methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, dubbed ROY for its numerous crystal polymorphs of red, orange, and yellow colors, has been studied in its liquid and glassy state by infrared spectroscopy. Two populations of conformers are observed, whose equilibrium is characterized by ΔH = 2.4 kJ/mol and ΔS = 8.0 J/K/mol. The two populations correspond to the global and local minima of the torsional energy surface and to the conformational preference of the 13 crystal polymorphs. The local minimum features a more coplanar arrangement of the two aromatic rings, greater π conjugation, and lower CN stretch frequency. In the gas phase, the lowest-energy path between the two minima has an energy barrier 3.9 kJ/mol above the global minimum, consistent with the rapid equilibration between the two populations. The relevance of our result for understanding the prolific polymorphism of ROY is discussed.
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Affiliation(s)
- Zhenxuan Chen
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Yue Gui
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Kai Cui
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - J R Schmit
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lian Yu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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9
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Boström HLB, Collings IE, Daisenberger D, Ridley CJ, Funnell NP, Cairns AB. Probing the Influence of Defects, Hydration, and Composition on Prussian Blue Analogues with Pressure. J Am Chem Soc 2021; 143:3544-3554. [PMID: 33629831 PMCID: PMC8028041 DOI: 10.1021/jacs.0c13181] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
The vast compositional
space of Prussian blue analogues (PBAs),
formula AxM[M′(CN)6]y·nH2O, allows
for a diverse range of functionality. Yet, the interplay between composition
and physical properties—e.g., flexibility and propensity for
phase transitions—is still largely unknown, despite its fundamental
and industrial relevance. Here we use variable-pressure X-ray and
neutron diffraction to explore how key structural features, i.e.,
defects, hydration, and composition, influence the compressibility
and phase behavior of PBAs. Defects enhance the flexibility, manifesting
as a remarkably low bulk modulus (B0 ≈
6 GPa) for defective PBAs. Interstitial water increases B0 and enables a pressure-induced phase transition
in defective systems. Conversely, hydration does not alter the compressibility
of stoichiometric MnPt(CN)6, but changes the high-pressure
phase transitions, suggesting an interplay between low-energy distortions.
AMnCo(CN)6 (AI = Rb, Cs) transition from F4̅3m to P4̅n2 upon compression due to octahedral tilting, and the critical
pressure can be tuned by the A-site cation. At 1 GPa, the symmetry
of Rb0.87Mn[Co(CN)6]0.91 is further
lowered to the polar space group Pn by an improper
ferroelectric mechanism. These fundamental insights aim to facilitate
the rational design of PBAs for applications within a wide range of
fields.
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Affiliation(s)
- Hanna L B Boström
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569 Stuttgart, Germany.,Department of Inorganic Chemistry, Ångström Laboratory, Uppsala University, Box 538, SE-751 21 Uppsala, Sweden.,Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, U.K
| | - Ines E Collings
- Centre for X-ray Analytics, EMPA - Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | | | - Christopher J Ridley
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K
| | - Nicholas P Funnell
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K
| | - Andrew B Cairns
- Department of Materials, Imperial College London, Royal School of Mines, Exhibition Road, London SW7 2AZ, U.K.,London Centre for Nanotechnology, Imperial College London, London SW7 2AZ, U.K
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10
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Reeves MG, Wood PA, Parsons S. MrPIXEL: automated execution of Pixel calculations via the Mercury interface. J Appl Crystallogr 2020; 53:1154-1162. [PMID: 32788907 PMCID: PMC7401789 DOI: 10.1107/s1600576720008444] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/23/2020] [Indexed: 12/04/2022] Open
Abstract
A program is described that enables the energetics of crystal packing to be analysed quickly and easily through a user interface, using Pixel, Python scripts and the widely known visualizer Mercury. The interpretation of crystal structures in terms of intermolecular interaction energies enables phase stability and polymorphism to be rationalized in terms of quantitative thermodynamic models, while also providing insight into the origin of physical and chemical properties including solubility, compressibility and host–guest formation. The Pixel method is a semi-empirical procedure for the calculation of intermolecular interactions and lattice energies based only on crystal structure information. Molecules are represented as blocks of undistorted ab initio molecular electron and nuclear densities subdivided into small volume elements called pixels. Electrostatic, polarization, dispersion and Pauli repulsion terms are calculated between pairs of pixels and nuclei in different molecules, with the accumulated sum equating to the intermolecular interaction energy, which is broken down into physically meaningful component terms. The MrPIXEL procedure enables Pixel calculations to be carried out with minimal user intervention from the graphical interface of Mercury, which is part of the software distributed with the Cambridge Structural Database (CSD). Following initial setup of a crystallographic model, one module assigns atom types and writes necessary input files. A second module then submits the required electron-density calculation either locally or to a remote server, downloads the results, and submits the Pixel calculation itself. Full lattice energy calculations can be performed for structures with up to two molecules in the crystallographic asymmetric unit. For more complex cases, only molecule–molecule energies are calculated. The program makes use of the CSD Python API, which is also distributed with the CSD.
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Affiliation(s)
- Matthew G Reeves
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3FJ, Scotland
| | - Peter A Wood
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Simon Parsons
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3FJ, Scotland
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11
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Lévesque A, Maris T, Wuest JD. ROY Reclaims Its Crown: New Ways To Increase Polymorphic Diversity. J Am Chem Soc 2020; 142:11873-11883. [PMID: 32510946 DOI: 10.1021/jacs.0c04434] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical compounds that exist in multiple crystalline forms are said to exhibit polymorphism. Polymorphs have the same composition, but their structures and properties can vary markedly. In many fields, conditions for crystallizing compounds of interest are screened exhaustively to generate as many polymorphs as possible, from which the most advantageous form can be selected. We report new ways to search for polymorphs and increase polymorphic diversity, based on crystallization induced by suitably designed mixed-crystal seeds. The potential of the strategy has been demonstrated by using it to produce new polymorphs of the benchmark compound ROY as single crystals structurally characterized by X-ray diffraction. This allows ROY to reclaim its crown as the most polymorphic compound in the Cambridge Structural Database. More generally, the methods promise to become valuable tools for polymorphic screening in all fields where crystalline solids are used.
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Affiliation(s)
- Alexandre Lévesque
- Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Thierry Maris
- Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - James D Wuest
- Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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12
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Giordano N, Beavers CM, Campbell BJ, Eigner V, Gregoryanz E, Marshall WG, Peña-Álvarez M, Teat SJ, Vennari CE, Parsons S. High-pressure polymorphism in pyridine. IUCRJ 2020; 7:58-70. [PMID: 31949905 PMCID: PMC6949594 DOI: 10.1107/s2052252519015616] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
Single crystals of the high-pressure phases II and III of pyridine have been obtained by in situ crystallization at 1.09 and 1.69 GPa, revealing the crystal structure of phase III for the first time using X-ray diffraction. Phase II crystallizes in P212121 with Z' = 1 and phase III in P41212 with Z' = ½. Neutron powder diffraction experiments using pyridine-d5 establish approximate equations of state of both phases. The space group and unit-cell dimensions of phase III are similar to the structures of other simple compounds with C 2v molecular symmetry, and the phase becomes stable at high pressure because it is topologically close-packed, resulting in a lower molar volume than the topologically body-centred cubic phase II. Phases II and III have been observed previously by Raman spectroscopy, but have been mis-identified or inconsistently named. Raman spectra collected on the same samples as used in the X-ray experiments establish the vibrational characteristics of both phases unambiguously. The pyridine molecules interact in both phases through CH⋯π and CH⋯N interactions. The nature of individual contacts is preserved through the phase transition between phases III and II, which occurs on decompression. A combination of rigid-body symmetry mode analysis and density functional theory calculations enables the soft vibrational lattice mode which governs the transformation to be identified.
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Affiliation(s)
- Nico Giordano
- Centre for Science at Extreme Conditions and EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkley, CA 94720, USA
| | - Christine M. Beavers
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, CA 95064, USA
- Diamond Light Source, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
| | - Branton J. Campbell
- Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602, USA
| | - Václav Eigner
- Centre for Science at Extreme Conditions and EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
- Institute of Physics of the AS CR, v.v.i., Cukrovarnicka 10, 162 00 Prague 6, Czech Republic
| | - Eugene Gregoryanz
- School of Physics and Astronomy and the Centre for Science at Extreme Conditions, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - Willliam G. Marshall
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot OX11 0QX, UK
| | - Miriam Peña-Álvarez
- School of Physics and Astronomy and the Centre for Science at Extreme Conditions, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - Simon J. Teat
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkley, CA 94720, USA
| | - Cara E. Vennari
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Simon Parsons
- Centre for Science at Extreme Conditions and EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
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Giordano N, Beavers CM, Kamenev KV, Love JB, Pankhurst JR, Teat SJ, Parsons S. Pressure-induced inclusion of neon in the crystal structure of a molecular Cu 2(pacman) complex at 4.67 GPa. Chem Commun (Camb) 2020; 56:3449-3452. [DOI: 10.1039/c9cc09884d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Crystals of Cu2(pacman) inflate on taking up neon at 46 000 atm through a switch in the ligand conformation.
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Affiliation(s)
- Nico Giordano
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions
- The University of Edinburgh
- Edinburgh
- UK
- Advanced Light Source
| | - Christine M. Beavers
- Advanced Light Source
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
- Department of Earth & Planetary Sciences
| | - Konstantin V. Kamenev
- Centre for Science at Extreme Conditions and School of Engineering
- The University of Edinburgh
- Edinburgh
- UK
| | - Jason B. Love
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions
- The University of Edinburgh
- Edinburgh
- UK
| | - James R. Pankhurst
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions
- The University of Edinburgh
- Edinburgh
- UK
| | - Simon J. Teat
- Advanced Light Source
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
| | - Simon Parsons
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions
- The University of Edinburgh
- Edinburgh
- UK
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14
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Giordano N, Afanasjevs S, Beavers CM, Hobday CL, Kamenev KV, O'Bannon EF, Ruiz-Fuertes J, Teat SJ, Valiente R, Parsons S. The Effect of Pressure on Halogen Bonding in 4-Iodobenzonitrile. Molecules 2019; 24:molecules24102018. [PMID: 31137795 PMCID: PMC6572472 DOI: 10.3390/molecules24102018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 11/16/2022] Open
Abstract
The crystal structure of 4-iodobenzonitrile, which is monoclinic (space group I2/a) under ambient conditions, contains chains of molecules linked through C≡N···I halogen-bonds. The chains interact through CH···I, CH···N and π-stacking contacts. The crystal structure remains in the same phase up to 5.0 GPa, the b axis compressing by 3.3%, and the a and c axes by 12.3 and 10.9 %. Since the chains are exactly aligned with the crystallographic b axis these data characterise the compressibility of the I···N interaction relative to the inter-chain interactions, and indicate that the halogen bond is the most robust intermolecular interaction in the structure, shortening from 3.168(4) at ambient pressure to 2.840(1) Å at 5.0 GPa. The π∙∙∙π contacts are most sensitive to pressure, and in one case the perpendicular stacking distance shortens from 3.6420(8) to 3.139(4) Å. Packing energy calculations (PIXEL) indicate that the π∙∙∙π interactions have been distorted into a destabilising region of their potentials at 5.0 GPa. The structure undergoes a transition to a triclinic ( P 1 ¯ ) phase at 5.5 GPa. Over the course of the transition, the initially colourless and transparent crystal darkens on account of formation of microscopic cracks. The resistance drops by 10% and the optical transmittance drops by almost two orders of magnitude. The I···N bond increases in length to 2.928(10) Å and become less linear [<C-I∙∙∙N = 166.2(5)°]; the energy stabilises by 2.5 kJ mol-1 and the mixed C-I/I..N stretching frequency observed by Raman spectroscopy increases from 249 to 252 cm-1. The driving force of the transition is shown to be relief of strain built-up in the π∙∙∙π interactions rather than minimisation of the molar volume. The triclinic phase persists up to 8.1 GPa.
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Affiliation(s)
- Nico Giordano
- Centre for Science at Extreme Conditions and EaStCHEM School of Chemistry, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, Scotland EH9 3FD, UK.
- Advanced Light Source, 1 Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Sergejs Afanasjevs
- Centre for Science at Extreme Conditions and School of Engineering, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, Scotland EH9 3FD, UK.
| | - Christine M Beavers
- Advanced Light Source, 1 Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
- Department of Earth & Planetary Sciences, University of California, Santa Cruz, 1156 High Street Santa Cruz, CA 95064, USA.
- Present address: Diamond Light Source, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Harwell Oxford, Didcot OX11 0QX, UK.
| | - Claire L Hobday
- Centre for Science at Extreme Conditions and EaStCHEM School of Chemistry, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, Scotland EH9 3FD, UK.
| | - Konstantin V Kamenev
- Centre for Science at Extreme Conditions and School of Engineering, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, Scotland EH9 3FD, UK.
| | - Earl F O'Bannon
- Advanced Light Source, 1 Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
- Department of Earth & Planetary Sciences, University of California, Santa Cruz, 1156 High Street Santa Cruz, CA 95064, USA.
- Present address: Physical and Life Sciences, Physics Division, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.
| | - Javier Ruiz-Fuertes
- Dpto. DCITIMAC, Facultad de Ciencias, Universidad de Cantabria, 39005 Santander, Spain.
| | - Simon J Teat
- Advanced Light Source, 1 Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Rafael Valiente
- Dpto. Física Aplicada, Facultad de Ciencias, Universidad de Cantabria-IDIVAL, 39005 Santander, Spain.
| | - Simon Parsons
- Centre for Science at Extreme Conditions and EaStCHEM School of Chemistry, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, Scotland EH9 3FD, UK.
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