1
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Bicknell J, Agarwal SA, Petersen KJ, Loya JD, Lutz N, Sittinger PM, Teat SJ, Settineri NS, Campillo-Alvarado G. Engineering Lipophilic Aggregation of Adapalene and Adamantane-Based Cocrystals via van der Waals Forces and Hydrogen Bonding. CRYSTAL GROWTH & DESIGN 2024; 24:5222-5230. [PMID: 38911135 PMCID: PMC11191584 DOI: 10.1021/acs.cgd.4c00457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024]
Abstract
Lipophilic aggregation using adamantanes is a widely exploited molecular property in medicinal and materials chemistry. Adamantanes are traditionally installed to molecular units via covalent bonds. However, the noncovalent installation of adamantanes has been relatively underexplored and presents the potential to bring properties associated with adamantanes to molecules without affecting their intrinsic properties (e.g., pharmacophores). Here, we systematically study a series of adamantanecarboxylic acids with varying substitution levels of methyl groups and their cocrystals with bipyridines. Specifically, single-crystal X-ray diffraction shows that while the directionality of single-component adamantanes is notably sensitive to changes in methyl substitution, hydrogen-bonded cocrystals with bipyridines show consistent and robust packing due to π-stacking predominance. Our observations are supported by Hirshfeld surface and energy framework analyses. The applicability of cocrystal formation of adamantanes bearing carboxylic acids was used to generate the first cocrystals of adapalene, an adamantane-bearing retinoid used for treating acne vulgaris. We envisage our study to inspire noncovalent (i.e., cocrystal) installation of adamantanes to generate lipophilic aggregation in multicomponent systems.
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Affiliation(s)
- Josephine Bicknell
- Department
of Chemistry, Reed College, Portland, Oregon 97202-8199, United
States
| | - Sidhaesh A. Agarwal
- Department
of Chemistry, Reed College, Portland, Oregon 97202-8199, United
States
| | - Kyle J. Petersen
- Department
of Chemistry, Reed College, Portland, Oregon 97202-8199, United
States
| | - Jesus Daniel Loya
- Department
of Chemistry, Reed College, Portland, Oregon 97202-8199, United
States
| | - Nicholas Lutz
- Department
of Chemistry, Reed College, Portland, Oregon 97202-8199, United
States
| | - Paulina M. Sittinger
- Department
of Chemistry, Reed College, Portland, Oregon 97202-8199, United
States
- Institut
für Chemie und Biochemie, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Simon J. Teat
- Advanced
Light Source, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Nicholas S. Settineri
- Advanced
Light Source, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720-1460, United States
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2
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A data-driven and topological mapping approach for the a priori prediction of stable molecular crystalline hydrates. Proc Natl Acad Sci U S A 2022; 119:e2204414119. [PMID: 36252020 DOI: 10.1073/pnas.2204414119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Predictions of the structures of stoichiometric, fractional, or nonstoichiometric hydrates of organic molecular crystals are immensely challenging due to the extensive search space of different water contents, host molecular placements throughout the crystal, and internal molecular conformations. However, the dry frameworks of these hydrates, especially for nonstoichiometric or isostructural dehydrates, can often be predicted from a standard anhydrous crystal structure prediction (CSP) protocol. Inspired by developments in the field of drug binding, we introduce an efficient data-driven and topologically aware approach for predicting organic molecular crystal hydrate structures through a mapping of water positions within the crystal structure. The method does not require a priori specification of water content and can, therefore, predict stoichiometric, fractional, and nonstoichiometric hydrate structures. This approach, which we term a mapping approach for crystal hydrates (MACH), establishes a set of rules for systematic determination of favorable positions for water insertion within predicted or experimental crystal structures based on considerations of the chemical features of local environments and void regions. The proposed approach is tested on hydrates of three pharmaceutically relevant compounds that exhibit diverse crystal packing motifs and void environments characteristic of hydrate structures. Overall, we show that our mapping approach introduces an advance in the efficient performance of hydrate CSP through generation of stable hydrate stoichiometries at low cost and should be considered an integral component for CSP workflows.
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3
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Taylor CR, Mulvee MT, Perenyi DS, Probert MR, Day GM, Steed JW. Minimizing Polymorphic Risk through Cooperative Computational and Experimental Exploration. J Am Chem Soc 2020; 142:16668-16680. [PMID: 32897065 PMCID: PMC7586337 DOI: 10.1021/jacs.0c06749] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
We
combine state-of-the-art computational crystal structure prediction
(CSP) techniques with a wide range of experimental crystallization
methods to understand and explore crystal structure in pharmaceuticals
and minimize the risk of unanticipated late-appearing polymorphs.
Initially, we demonstrate the power of CSP to rationalize the difficulty
in obtaining polymorphs of the well-known pharmaceutical isoniazid
and show that CSP provides the structure of the recently obtained,
but unsolved, Form III of this drug despite there being only a single
resolved form for almost 70 years. More dramatically, our blind CSP
study predicts a significant risk of polymorphism for the related
iproniazid. Employing a wide variety of experimental techniques, including
high-pressure experiments, we experimentally obtained the first three
known nonsolvated crystal forms of iproniazid, all of which were successfully
predicted in the CSP procedure. We demonstrate the power of CSP methods
and free energy calculations to rationalize the observed elusiveness
of the third form of iproniazid, the success of high-pressure experiments
in obtaining it, and the ability of our synergistic computational-experimental
approach to “de-risk” solid form landscapes.
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Affiliation(s)
- Christopher R Taylor
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton SO17 1NX, U.K
| | - Matthew T Mulvee
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Domonkos S Perenyi
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Michael R Probert
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, U.K
| | - Graeme M Day
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton SO17 1NX, U.K
| | - Jonathan W Steed
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
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4
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Surampudi AVSD, Rajendrakumar S, Nanubolu JB, Balasubramanian S, Surov AO, Voronin AP, Perlovich GL. Influence of crystal packing on the thermal properties of cocrystals and cocrystal solvates of olanzapine: insights from computations. CrystEngComm 2020. [DOI: 10.1039/d0ce00914h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A multicomponent supramolecular host with adaptive guest accommodation abilities is observed in the cocrystal solvates of the olanzapine–hydroquinone system.
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Affiliation(s)
- Anuja Venkata Sai Durga Surampudi
- Centre for X-ray Crystallography
- Department of Analytical & Structural Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad-500007
- India
| | - Satyasree Rajendrakumar
- Centre for X-ray Crystallography
- Department of Analytical & Structural Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad-500007
- India
| | - Jagadeesh Babu Nanubolu
- Centre for X-ray Crystallography
- Department of Analytical & Structural Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad-500007
- India
| | - Sridhar Balasubramanian
- Centre for X-ray Crystallography
- Department of Analytical & Structural Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad-500007
- India
| | - Artem O. Surov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | - Alexander P. Voronin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | - German L. Perlovich
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
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5
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Braun DE. Supramolecular organisation of sulphate salt hydrates exemplified with brucine sulphate. CrystEngComm 2020. [DOI: 10.1039/c9ce01762c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The frequency of hydrate formation among organic sulphate salts is unravelled. Interconversion of the hydrates of brucine sulphate occurs with small changes in the relative humidity.
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Affiliation(s)
- Doris E. Braun
- Institute of Pharmacy
- University of Innsbruck
- 6020 Innsbruck
- Austria
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6
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McMahon DP, Stephenson A, Chong SY, Little MA, Jones JTA, Cooper AI, Day GM. Computational modelling of solvent effects in a prolific solvatomorphic porous organic cage. Faraday Discuss 2018; 211:383-399. [PMID: 30083695 PMCID: PMC6208051 DOI: 10.1039/c8fd00031j] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 03/22/2018] [Indexed: 11/21/2022]
Abstract
Crystal structure prediction methods can enable the in silico design of functional molecular crystals, but solvent effects can have a major influence on relative lattice energies, sometimes thwarting predictions. This is particularly true for porous solids, where solvent included in the pores can have an important energetic contribution. We present a Monte Carlo solvent insertion procedure for predicting the solvent filling of porous structures from crystal structure prediction landscapes, tested using a highly solvatomorphic porous organic cage molecule, CC1. Using this method, we can understand why the predicted global energy minimum structure for CC1 is never observed from solvent crystallisation. We also explain the formation of three different solvatomorphs of CC1 from three structurally-similar chlorinated solvents. Calculated solvent stabilisation energies are found to correlate with experimental results from thermogravimetric analysis, suggesting a future computational framework for a priori materials design that factors in solvation effects.
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Affiliation(s)
- David P. McMahon
- Computational Systems Chemistry
, School of Chemistry
, University of Southampton
,
SO17 1BJ
, UK
.
| | - Andrew Stephenson
- Department of Chemistry and Materials Innovation Factory
, University of Liverpool
,
Crown St.
, Liverpool L69 7ZD
, UK
.
| | - Samantha Y. Chong
- Department of Chemistry and Materials Innovation Factory
, University of Liverpool
,
Crown St.
, Liverpool L69 7ZD
, UK
.
| | - Marc A. Little
- Department of Chemistry and Materials Innovation Factory
, University of Liverpool
,
Crown St.
, Liverpool L69 7ZD
, UK
.
| | - James T. A. Jones
- Department of Chemistry and Materials Innovation Factory
, University of Liverpool
,
Crown St.
, Liverpool L69 7ZD
, UK
.
| | - Andrew I. Cooper
- Department of Chemistry and Materials Innovation Factory
, University of Liverpool
,
Crown St.
, Liverpool L69 7ZD
, UK
.
| | - Graeme M. Day
- Computational Systems Chemistry
, School of Chemistry
, University of Southampton
,
SO17 1BJ
, UK
.
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7
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Day GM, Cooper AI. Energy-Structure-Function Maps: Cartography for Materials Discovery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1704944. [PMID: 29205536 DOI: 10.1002/adma.201704944] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/20/2017] [Indexed: 06/07/2023]
Abstract
Some of the most successful approaches to structural design in materials chemistry have exploited strong directional bonds, whose geometric reliability lends predictability to solid-state assembly. For example, metal-organic frameworks are an important design platform in materials chemistry. By contrast, the structure of molecular crystals is defined by a balance of weaker intermolecular forces, and small changes to the molecular building blocks can lead to large changes in crystal packing. Hence, empirical rules are inherently less reliable for engineering the structures of molecular solids. Energy-structure-function (ESF) maps are a new approach for the discovery of functional organic crystals. These maps fuse crystal-structure prediction with the computation of physical properties to allow researchers to choose the most promising molecule for a given application, prior to its synthesis. ESF maps were used recently to discover a highly porous molecular crystal that has a high methane deliverable capacity and the lowest density molecular crystal reported to date (r = 0.41 g cm-3 , SABET = 3425 m2 g-1 ). Progress in this field is reviewed, with emphasis on the future opportunities and challenges for a design strategy based on computed ESF maps.
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Affiliation(s)
- Graeme M Day
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Andrew I Cooper
- Department of Chemistry and Materials Innovation Factory, Leverhulme Centre for Functional Materials Design, 51 Oxford Street, Liverpool, L7 3NY, UK
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8
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Mohamed S, Li L. From serendipity to supramolecular design: assessing the utility of computed crystal form landscapes in inferring the risks of crystal hydration in carboxylic acids. CrystEngComm 2018. [DOI: 10.1039/c8ce00758f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Calculated structural descriptors for predicted anhydrate polymorphs are used to assess the risks of crystal hydration in carboxylic acids.
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Affiliation(s)
- Sharmarke Mohamed
- Department of Chemistry
- Khalifa University of Science and Technology
- Abu Dhabi
- United Arab Emirates
| | - Liang Li
- Central Technology Platforms
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
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9
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Braun D, Lingireddy SR, Beidelschies MD, Guo R, Müller P, Price SL, Reutzel-Edens SM. Unraveling Complexity in the Solid Form Screening of a Pharmaceutical Salt: Why so Many Forms? Why so Few? CRYSTAL GROWTH & DESIGN 2017; 17:5349-5365. [PMID: 29018305 PMCID: PMC5629560 DOI: 10.1021/acs.cgd.7b00842] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/28/2017] [Indexed: 06/07/2023]
Abstract
The solid form landscape of 5-HT2a antagonist 3-(4-(benzo[d]isoxazole-3-yl)piperazin-1-yl)-2,2-dimethylpropanoic acid hydrochloride (B5HCl) proved difficult to establish. Many crystalline materials were produced by solid form screening, but few forms readily grew high quality crystals to afford a clear picture or understanding of the solid form landscape. Careful control of crystallization conditions, a range of experimental methods, computational modeling of solvate structures, and crystal structure prediction were required to see potential arrangements of the salt in its crystal forms. Structural diversity in the solid form landscape of B5HCl was apparent in the layer structures for the anhydrate polymorphs (Forms I and II), dihydrate and a family of solvates with alcohols. The alcohol solvates, which provided a distinct packing from the neat forms and the dihydrate, form layers with conserved hydrogen bonding between B5HCl and the solvent, as well as stacking of the aromatic rings. The ability of the alcohol hydrocarbon moieties to efficiently pack between the layers accounted for the difficulty in growing some solvate crystals and the inability of other solvates to crystallize altogether. Through a combination of experiment and computation, the crystallization problems, form stability, and desolvation pathways of B5HCl have been rationalized at a molecular level.
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Affiliation(s)
- Doris
E. Braun
- Institute
of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | | | - Mark D. Beidelschies
- Eurofins
Lancaster Laboratories, PSS, Indianapolis, Indiana 46285, United States
| | - Rui Guo
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Peter Müller
- X-Ray Diffraction
Facility, MIT Department of Chemistry, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sarah L. Price
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
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10
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Slater AG, Reiss PS, Pulido A, Little MA, Holden DL, Chen L, Chong SY, Alston BM, Clowes R, Haranczyk M, Briggs ME, Hasell T, Day GM, Cooper AI. Computationally-Guided Synthetic Control over Pore Size in Isostructural Porous Organic Cages. ACS CENTRAL SCIENCE 2017; 3:734-742. [PMID: 28776015 PMCID: PMC5532722 DOI: 10.1021/acscentsci.7b00145] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Indexed: 05/28/2023]
Abstract
The physical properties of 3-D porous solids are defined by their molecular geometry. Hence, precise control of pore size, pore shape, and pore connectivity are needed to tailor them for specific applications. However, for porous molecular crystals, the modification of pore size by adding pore-blocking groups can also affect crystal packing in an unpredictable way. This precludes strategies adopted for isoreticular metal-organic frameworks, where addition of a small group, such as a methyl group, does not affect the basic framework topology. Here, we narrow the pore size of a cage molecule, CC3, in a systematic way by introducing methyl groups into the cage windows. Computational crystal structure prediction was used to anticipate the packing preferences of two homochiral methylated cages, CC14-R and CC15-R, and to assess the structure-energy landscape of a CC15-R/CC3-S cocrystal, designed such that both component cages could be directed to pack with a 3-D, interconnected pore structure. The experimental gas sorption properties of these three cage systems agree well with physical properties predicted by computational energy-structure-function maps.
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Affiliation(s)
- Anna G. Slater
- Department of Chemistry
and Materials Innovation Factory, University
of Liverpool, Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Paul S. Reiss
- Department of Chemistry
and Materials Innovation Factory, University
of Liverpool, Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Angeles Pulido
- School of
Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Marc A. Little
- Department of Chemistry
and Materials Innovation Factory, University
of Liverpool, Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Daniel L. Holden
- Department of Chemistry
and Materials Innovation Factory, University
of Liverpool, Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Linjiang Chen
- Department of Chemistry
and Materials Innovation Factory, University
of Liverpool, Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Samantha Y. Chong
- Department of Chemistry
and Materials Innovation Factory, University
of Liverpool, Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Ben M. Alston
- Department of Chemistry
and Materials Innovation Factory, University
of Liverpool, Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Rob Clowes
- Department of Chemistry
and Materials Innovation Factory, University
of Liverpool, Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Maciej Haranczyk
- Computational Research Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Michael E. Briggs
- Department of Chemistry
and Materials Innovation Factory, University
of Liverpool, Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Tom Hasell
- Department of Chemistry
and Materials Innovation Factory, University
of Liverpool, Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Graeme M. Day
- School of
Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Andrew I. Cooper
- Department of Chemistry
and Materials Innovation Factory, University
of Liverpool, Crown Street, Liverpool L69 7ZD, United Kingdom
| |
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11
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Pulido A, Chen L, Kaczorowski T, Holden D, Little MA, Chong SY, Slater BJ, McMahon DP, Bonillo B, Stackhouse CJ, Stephenson A, Kane CM, Clowes R, Hasell T, Cooper AI, Day GM. Functional materials discovery using energy-structure-function maps. Nature 2017; 543:657-664. [PMID: 28329756 PMCID: PMC5458805 DOI: 10.1038/nature21419] [Citation(s) in RCA: 247] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 01/20/2017] [Indexed: 12/24/2022]
Abstract
Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.
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Affiliation(s)
- Angeles Pulido
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, UK
| | - Linjiang Chen
- Department of Chemistry, University of Liverpool, Liverpool, UK
| | | | - Daniel Holden
- Department of Chemistry, University of Liverpool, Liverpool, UK
| | - Marc A Little
- Department of Chemistry, University of Liverpool, Liverpool, UK
| | | | | | - David P McMahon
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, UK
| | | | | | | | | | - Rob Clowes
- Department of Chemistry, University of Liverpool, Liverpool, UK
| | - Tom Hasell
- Department of Chemistry, University of Liverpool, Liverpool, UK
| | - Andrew I Cooper
- Department of Chemistry, University of Liverpool, Liverpool, UK
| | - Graeme M Day
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, UK
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12
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Selent M, Nyman J, Roukala J, Ilczyszyn M, Oilunkaniemi R, Bygrave PJ, Laitinen R, Jokisaari J, Day GM, Lantto P. Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129 Xe NMR Spectroscopy. Chemistry 2017; 23:5258-5269. [PMID: 28111848 PMCID: PMC5763392 DOI: 10.1002/chem.201604797] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Indexed: 11/09/2022]
Abstract
An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o- and m-fluorophenol, whose previously unknown clathrate structures have been studied by 129 Xe NMR spectroscopy. The high sensitivity of the 129 Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures.
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Affiliation(s)
- Marcin Selent
- NMR Research Unit, Faculty of Science, University of Oulu, 90014, Oulu, Finland.,Faculty of Chemistry, Wrocław University, Joliot Curie 14, 50-383, Wrocław, Poland
| | - Jonas Nyman
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, UK
| | - Juho Roukala
- NMR Research Unit, Faculty of Science, University of Oulu, 90014, Oulu, Finland
| | - Marek Ilczyszyn
- Faculty of Chemistry, Wrocław University, Joliot Curie 14, 50-383, Wrocław, Poland
| | - Raija Oilunkaniemi
- Laboratory of Inorganic Chemistry, University of Oulu, 90014, Oulu, Finland
| | - Peter J Bygrave
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, UK
| | - Risto Laitinen
- Laboratory of Inorganic Chemistry, University of Oulu, 90014, Oulu, Finland
| | - Jukka Jokisaari
- NMR Research Unit, Faculty of Science, University of Oulu, 90014, Oulu, Finland
| | - Graeme M Day
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, UK
| | - Perttu Lantto
- NMR Research Unit, Faculty of Science, University of Oulu, 90014, Oulu, Finland
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13
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Bernabei M, Pérez-Soto R, Gómez García I, Haranczyk M. Towards stable porous crystalline phases of molecular belts. CrystEngComm 2017. [DOI: 10.1039/c7ce01679d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A chemical modification of a molecular belt (M1) renders the molecule (M2) into a stable supramolecular nanotube porous crystal.
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Affiliation(s)
| | | | - Ismael Gómez García
- IMDEA Materials Institute
- 28096 Getafe
- Spain
- Departamento de Materiales
- Universidad Carlos III de Madrid
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14
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Evans JD, Jelfs KE, Day GM, Doonan CJ. Application of computational methods to the design and characterisation of porous molecular materials. Chem Soc Rev 2017; 46:3286-3301. [DOI: 10.1039/c7cs00084g] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Composed from discrete units, porous molecular materials (PMMs) possess properties not observed for conventional, extended solids. Molecular simulations provide crucial understanding for the design and characterisation of these unique materials.
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Affiliation(s)
- Jack D. Evans
- Chimie ParisTech
- PSL Research University
- CNRS
- Institut de Recherche de Chimie Paris
- 75005 Paris
| | - Kim E. Jelfs
- Department of Chemistry
- Imperial College London
- South Kensington
- London
- UK
| | - Graeme M. Day
- Computational Systems Chemistry
- School of Chemistry
- University of Southampton
- Highfield
- Southampton
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15
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Reticular synthesis of porous molecular 1D nanotubes and 3D networks. Nat Chem 2016; 9:17-25. [DOI: 10.1038/nchem.2663] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 09/29/2016] [Indexed: 02/08/2023]
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16
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Braun DE, Griesser UJ. Why do Hydrates (Solvates) Form in Small Neutral Organic Molecules? Exploring the Crystal Form Landscapes of the Alkaloids Brucine and Strychnine. CRYSTAL GROWTH & DESIGN 2016; 16:6405-6418. [PMID: 28670205 PMCID: PMC5486441 DOI: 10.1021/acs.cgd.6b01078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Computational methods were used to generate and explore the crystal structure landscapes of the two alkaloids strychnine and brucine. The computed structures were analyzed and rationalized by correlating the modelling results to a rich pool of available experimental data. Despite their structural similarity, the two compounds show marked differences in the formation of solid forms. For strychnine only one anhydrous form is reported in the literature and two new solvates from 1,4-dioxane were detected in the course of this work. In contrast, 22 solid forms are so far known to exist for brucine, comprising two anhydrates, four hydrates (HyA - HyC and a 5.25-hydrate), twelve solvates (alcohols and acetone) and four heterosolvates (mixed solvates with water and alcohols). For strychnine it is hard to produce any solid form other than the stable anhydrate while the formation of specific solid state forms of brucine is governed by a complex interplay between temperature and relative humidity/water activity and it is rather a challenging to avoid hydrate formation. Differences in crystal packing and the high tendency for brucine to form hydrates are not intuitive from the molecular structure alone, as both molecules have hydrogen bond acceptor groups but lack hydrogen bond donor groups. Only the evaluation of the crystal energy landscapes, in particular the close-packed crystal structures and high-energy open frameworks containing voids of molecular (water) dimensions, allowed us to unravel the diverse solid state behavior of the two alkaloids at a molecular level. In this study we demonstrate that expanding the analysis of anhydrate crystal energy landscapes to higher energy structures and calculating the solvent-accessible volume can be used to estimate non-stoichiometric or channel hydrate (solvate) formation, without explicitly computing the hydrate/solvate crystal energy landscapes.
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Affiliation(s)
- Doris E. Braun
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - Ulrich J. Griesser
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
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17
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Mayorquín-Torres MC, Arcos-Ramos R, Flores-Álamo M, Iglesias-Arteaga MA. Crystalline arrays of side chain modified bile acids derivatives. Two novel self-assemblies based on π-π and belly-to-belly interactions. Steroids 2016; 115:169-176. [PMID: 27644146 DOI: 10.1016/j.steroids.2016.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/10/2016] [Accepted: 09/13/2016] [Indexed: 11/16/2022]
Abstract
Crystalline derivatives of side chain modified bile acids were efficiently prepared from the naturally occurring steroids by palladium-catalyzed cross coupling reaction as a key step. The solvent-free crystalline bile acids derivatives 2b-e are readily accessed by slow evaporation from selected solvents. A variety of steroidal scaffolds were found and elucidated by SXRD studies. The crystal packing of the title compounds are dominated by hydrogen-bonding interactions established between differently positioned acetyl protecting groups, which in the case of 2b and 2e take advantage of the facial amphiphilicity producing two novel steroidal supramolecular self-assemblies combining π-π and strong facial interactions. Thus, these crystalline arrays of side chain modified bile acids represent promising scaffolds for research and implementation in biomolecular materials or inclusion phenomena.
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Affiliation(s)
- Martha C Mayorquín-Torres
- Facultad de Química, Departamento de Química Orgánica, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Rafael Arcos-Ramos
- Instituto de Ciencias Nucleares, Departamento de Química de Radiaciones y Radioquímica, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Marcos Flores-Álamo
- Facultad de Química, Departamento de Química Orgánica, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Martín A Iglesias-Arteaga
- Facultad de Química, Departamento de Química Orgánica, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico.
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18
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Mohamed S, Karothu DP, Naumov P. Using crystal structure prediction to rationalize the hydration propensities of substituted adamantane hydrochloride salts. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2016; 72:551-61. [DOI: 10.1107/s2052520616006326] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/14/2016] [Indexed: 12/31/2022]
Abstract
The crystal energy landscapes of the salts of two rigid pharmaceutically active molecules reveal that the experimental structure of amantadine hydrochloride is the most stable structure with the majority of low-energy structures adopting a chain hydrogen-bond motif and packings that do not have solvent accessible voids. By contrast, memantine hydrochloride which differs in the substitution of two methyl groups on the adamantane ring has a crystal energy landscape where all structures within 10 kJ mol−1of the global minimum have solvent-accessible voids ranging from 3 to 14% of the unit-cell volume including the lattice energy minimum that was calculated after removing water from the hydrated memantine hydrochloride salt structure. The success in using crystal structure prediction (CSP) to rationalize the different hydration propensities of these substituted adamantane hydrochloride salts allowed us to extend the model to predict under blind test conditions the experimental crystal structures of the previously uncharacterized 1-(methylamino)adamantane base and its corresponding hydrochloride salt. Although the crystal structure of 1-(methylamino)adamantane was correctly predicted as the second ranked structure on the static lattice energy landscape, the crystallization of aZ′ = 3 structure of 1-(methylamino)adamantane hydrochloride reveals the limits of applying CSP when the contents of the crystallographic asymmetric unit are unknown.
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19
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Price SL, Braun DE, Reutzel-Edens SM. Can computed crystal energy landscapes help understand pharmaceutical solids? Chem Commun (Camb) 2016; 52:7065-77. [PMID: 27067116 PMCID: PMC5486446 DOI: 10.1039/c6cc00721j] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Computational crystal structure prediction (CSP) methods can now be applied to the smaller pharmaceutical molecules currently in drug development. We review the recent uses of computed crystal energy landscapes for pharmaceuticals, concentrating on examples where they have been used in collaboration with industrial-style experimental solid form screening. There is a strong complementarity in aiding experiment to find and characterise practically important solid forms and understanding the nature of the solid form landscape.
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Affiliation(s)
- Sarah L Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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20
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Price SL, Reutzel-Edens SM. The potential of computed crystal energy landscapes to aid solid-form development. Drug Discov Today 2016; 21:912-23. [DOI: 10.1016/j.drudis.2016.01.014] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/04/2015] [Accepted: 01/26/2016] [Indexed: 11/29/2022]
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21
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Braun DE, Gelbrich T, Wurst K, Griesser UJ. Computational and Experimental Characterization of Five Crystal Forms of Thymine: Packing Polymorphism, Polytypism/Disorder and Stoichiometric 0.8-Hydrate. CRYSTAL GROWTH & DESIGN 2016; 16:3480-3496. [PMID: 28663717 PMCID: PMC5486440 DOI: 10.1021/acs.cgd.6b00459] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
New polymorphs of thymine emerged in an experimental search for solid forms, which was guided by the computationally generated crystal energy landscape. Three of the four anhydrates (AH) are homeoenergetic (A° - C) and their packing modes differ only in the location of oxygen and hydrogen atoms. AHs A° and B are ordered phases, whereas AH C shows disorder (X-ray diffuse scattering). Anhydrates AHs A° and B are ordered phases, whereas AH C shows disorder (X-ray diffuse scattering). Analysis of the crystal energy landscape for alternative AH C hydrogen bonded ribbon motifs identified a number of different packing modes, whose 3D structures were calculated to deviate by less than 0.24 kJ mol-1 in lattice energy. These structures provide models for stacking faults. The three anhydrates A° - C show strong similarity in their powder X-ray diffraction, thermoanalytical and spectroscopic (IR and Raman) characteristics. The already known anhydrate AH A° was identified as the thermodynamically most stable form at ambient conditions; AH B and AH C are metastable but show high kinetic stability. The hydrate of thymine is stable only at water activities (aw) > 0.95 at temperatures ≤ 25 °C. It was found to be a stoichiometric hydrate despite being a channel hydrate with an unusual water:thymine ratio of 0.8:1. Depending on the dehydration conditions, either AH C or AH D is obtained. The hydrate is the only known precursor to AH D. This study highlights the value and complementarity of simultaneous explorations of computationally and experimentally generated solid form landscapes of a small molecule anhydrate ↔ hydrate system.
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Affiliation(s)
- Doris E. Braun
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - Thomas Gelbrich
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - Klaus Wurst
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Ulrich J. Griesser
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
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22
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Case D, Campbell JE, Bygrave PJ, Day GM. Convergence Properties of Crystal Structure Prediction by Quasi-Random Sampling. J Chem Theory Comput 2016; 12:910-24. [PMID: 26716361 PMCID: PMC4750085 DOI: 10.1021/acs.jctc.5b01112] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Indexed: 12/05/2022]
Abstract
Generating sets of trial structures that sample the configurational space of crystal packing possibilities is an essential step in the process of ab initio crystal structure prediction (CSP). One effective methodology for performing such a search relies on low-discrepancy, quasi-random sampling, and our implementation of such a search for molecular crystals is described in this paper. Herein we restrict ourselves to rigid organic molecules and, by considering their geometric properties, build trial crystal packings as starting points for local lattice energy minimization. We also describe a method to match instances of the same structure, which we use to measure the convergence of our packing search toward completeness. The use of these tools is demonstrated for a set of molecules with diverse molecular characteristics and as representative of areas of application where CSP has been applied. An important finding is that the lowest energy crystal structures are typically located early and frequently during a quasi-random search of phase space. It is usually the complete sampling of higher energy structures that requires extended sampling. We show how the procedure can first be refined, through targetting the volume of the generated crystal structures, and then extended across a range of space groups to make a full CSP search and locate experimentally observed and lists of hypothetical polymorphs. As the described method has also been created to lie at the base of more involved approaches to CSP, which are being developed within the Global Lattice Energy Explorer (Glee) software, a few of these extensions are briefly discussed.
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Affiliation(s)
- David
H. Case
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Josh E. Campbell
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Peter J. Bygrave
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Graeme M. Day
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
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23
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Braun DE, Gelbrich T, Kahlenberg V, Griesser UJ. Solid state forms of 4-aminoquinaldine - From void structures with and without solvent inclusion to close packing. CrystEngComm 2015; 17:2504-2516. [PMID: 26726294 PMCID: PMC4693969 DOI: 10.1039/c5ce00118h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Polymorphs of 4-aminoquinaldine (4-AQ) have been predicted in silico and experimentally identified and characterised. The two metastable forms, AH (anhydrate) II and AH III, crystallise in the trigonal space group [Formula: see text] and are less densely packed than the thermodynamically most stable phase AH I° (P21/c ). AH II can crystallise and exist both, as a solvent inclusion compound and as an unsolvated phase. The third polymorph, AH III, is exclusively obtained by desolvation of a carbon tetrachloride solvate. Theoretical calculations correctly estimated the experimental 0K stability order, confirmed that AH II can exist without solvents, gave access to the AH III structure, and identified that there exists a subtle balance between close packing and number of hydrogen bonding interactions in the solid state of anhydrous 4-AQ. Furthermore, the prevalence of void space and solvent inclusion in [Formula: see text] structures is discussed.
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Affiliation(s)
- Doris E. Braun
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - Thomas Gelbrich
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - Volker Kahlenberg
- Institute of Mineralogy and Petrography, University of Innsbruck, Innrain 52, 6020 Innsbruck, Austria
| | - Ulrich J. Griesser
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
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24
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Steed KM, Steed JW. Packing problems: high Z' crystal structures and their relationship to cocrystals, inclusion compounds, and polymorphism. Chem Rev 2015; 115:2895-933. [PMID: 25675105 DOI: 10.1021/cr500564z] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kirsty M Steed
- †SAgE Faculty, Newcastle University, Devonshire Building, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Jonathan W Steed
- ‡Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
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25
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Braun DE, Gelbrich T, Kahlenberg V, Griesser UJ. Insights into hydrate formation and stability of morphinanes from a combination of experimental and computational approaches. Mol Pharm 2014; 11:3145-63. [PMID: 25036525 PMCID: PMC4685752 DOI: 10.1021/mp500334z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
Morphine, codeine, and ethylmorphine
are important drug compounds
whose free bases and hydrochloride salts form stable hydrates. These
compounds were used to systematically investigate the influence of
the type of functional groups, the role of water molecules, and the
Cl– counterion on molecular aggregation and solid
state properties. Five new crystal structures have been determined.
Additionally, structure models for anhydrous ethylmorphine and morphine
hydrochloride dihydrate, two phases existing only in a very limited
humidity range, are proposed on the basis of computational dehydration
modeling. These match the experimental powder X-ray diffraction patterns
and the structural information derived from infrared spectroscopy.
All 12 structurally characterized morphinane forms (including structures
from the Cambridge Structural Database) crystallize in the orthorhombic
space group P212121. Hydrate formation results in higher dimensional hydrogen bond networks.
The salt structures of the different compounds exhibit only little
structural variation. Anhydrous polymorphs were detected for all compounds
except ethylmorphine (one anhydrate) and its hydrochloride salt (no
anhydrate). Morphine HCl forms a trihydrate and dihydrate. Differential
scanning and isothermal calorimetry were employed to estimate the
heat of the hydrate ↔ anhydrate phase transformations, indicating
an enthalpic stabilization of the respective hydrate of 5.7 to 25.6
kJ mol–1 relative to the most stable anhydrate.
These results are in qualitative agreement with static 0 K lattice
energy calculations for all systems except morphine hydrochloride,
showing the need for further improvements in quantitative thermodynamic
prediction of hydrates having water···water interactions.
Thus, the combination of a variety of experimental techniques, covering
temperature- and moisture-dependent stability, and computational modeling
allowed us to generate sufficient kinetic, thermodynamic and structural
information to understand the principles of hydrate formation of the
model compounds. This approach also led to the detection of several
new crystal forms of the investigated morphinanes.
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Affiliation(s)
- Doris E Braun
- Institute of Pharmacy, University of Innsbruck , Innrain 52c, 6020 Innsbruck, Austria
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26
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Thompson HPG, Day GM. Which conformations make stable crystal structures? Mapping crystalline molecular geometries to the conformational energy landscape. Chem Sci 2014. [DOI: 10.1039/c4sc01132e] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Flexible organic molecules often do not adopt their lowest energy conformer in crystal structures. We find that there is a preference for molecules to crystallise with high surface area conformers.
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Affiliation(s)
| | - Graeme M. Day
- School of Chemistry
- University of Southampton
- Southampton, UK
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27
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Pyzer-Knapp EO, Thompson HPG, Schiffmann F, Jelfs KE, Chong SY, Little MA, Cooper AI, Day GM. Predicted crystal energy landscapes of porous organic cages. Chem Sci 2014. [DOI: 10.1039/c4sc00095a] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Computational methods predict the crystal packing of porous organic cage molecules, allowing crystal structure and porosity to be predicted starting from the chemical diagram alone.
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Affiliation(s)
| | | | | | - Kim E. Jelfs
- Department of Chemistry
- Imperial College London
- London, UK
| | - Samantha Y. Chong
- Department of Chemistry and Centre for Materials Discovery
- University of Liverpool
- Liverpool, UK
| | - Marc A. Little
- Department of Chemistry and Centre for Materials Discovery
- University of Liverpool
- Liverpool, UK
| | - Andrew I. Cooper
- Department of Chemistry and Centre for Materials Discovery
- University of Liverpool
- Liverpool, UK
| | - Graeme M. Day
- School of Chemistry
- University of Southampton
- Southampton, UK
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28
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Natarajan R, Bridgland L, Sirikulkajorn A, Lee JH, Haddow MF, Magro G, Ali B, Narayanan S, Strickland P, Charmant JPH, Orpen AG, McKeown N, Bezzu CG, Davis AP. Tunable porous organic crystals: structural scope and adsorption properties of nanoporous steroidal ureas. J Am Chem Soc 2013; 135:16912-25. [PMID: 24147834 PMCID: PMC3880060 DOI: 10.1021/ja405701u] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Indexed: 01/22/2023]
Abstract
Previous work has shown that certain steroidal bis-(N-phenyl)ureas, derived from cholic acid, form crystals in the P6(1) space group with unusually wide unidimensional pores. A key feature of the nanoporous steroidal urea (NPSU) structure is that groups at either end of the steroid are directed into the channels and may in principle be altered without disturbing the crystal packing. Herein we report an expanded study of this system, which increases the structural variety of NPSUs and also examines their inclusion properties. Nineteen new NPSU crystal structures are described, to add to the six which were previously reported. The materials show wide variations in channel size, shape, and chemical nature. Minimum pore diameters vary from ~0 up to 13.1 Å, while some of the interior surfaces are markedly corrugated. Several variants possess functional groups positioned in the channels with potential to interact with guest molecules. Inclusion studies were performed using a relatively accessible tris-(N-phenyl)urea. Solvent removal was possible without crystal degradation, and gas adsorption could be demonstrated. Organic molecules ranging from simple aromatics (e.g., aniline and chlorobenzene) to the much larger squalene (M(w) = 411) could be adsorbed from the liquid state, while several dyes were taken up from solutions in ether. Some dyes gave dichroic complexes, implying alignment of the chromophores in the NPSU channels. Notably, these complexes were formed by direct adsorption rather than cocrystallization, emphasizing the unusually robust nature of these organic molecular hosts.
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Affiliation(s)
| | - Lydia Bridgland
- School
of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | | | - Ji-Hun Lee
- School
of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Mairi F. Haddow
- School
of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Germinal Magro
- School
of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Bakhat Ali
- School
of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Sampriya Narayanan
- School
of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Peter Strickland
- School
of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | | | - A. Guy Orpen
- School
of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Neil
B. McKeown
- School
of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - C. Grazia Bezzu
- School
of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Anthony P. Davis
- School
of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
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29
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Braun DE, Bhardwaj RM, Arlin JB, Florence AJ, Kahlenberg V, Griesser UJ, Tocher DA, Price SL. Absorbing a Little Water: The Structural, Thermodynamic, and Kinetic Relationship between Pyrogallol and Its Tetarto-Hydrate. CRYSTAL GROWTH & DESIGN 2013; 13:4071-4083. [PMID: 24027438 PMCID: PMC3767201 DOI: 10.1021/cg4009015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/22/2013] [Indexed: 05/11/2023]
Abstract
The anhydrate and the stoichiometric tetarto-hydrate of pyrogallol (0.25 mol water per mol pyrogallol) are both storage stable at ambient conditions, provided that they are phase pure, with the system being at equilibrium at aw (water activity) = 0.15 at 25 °C. Structures have been derived from single crystal and powder X-ray diffraction data for the anhydrate and hydrate, respectively. It is notable that the tetarto-hydrate forms a tetragonal structure with water in channels, a framework that although stabilized by water, is found as a higher energy structure on a computationally generated crystal energy landscape, which has the anhydrate crystal structure as the most stable form. Thus, a combination of slurry experiments, X-ray diffraction, spectroscopy, moisture (de)sorption, and thermo-analytical methods with the computationally generated crystal energy landscape and lattice energy calculations provides a consistent picture of the finely balanced hydration behavior of pyrogallol. In addition, two monotropically related dimethyl sulfoxide monosolvates were found in the accompanying solid form screen.
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Affiliation(s)
- Doris E. Braun
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck,
Austria
- Department
of Chemistry, University College London, 20 Gordon
Street, London WC1H 0AJ, U.K
| | - Rajni M. Bhardwaj
- Strathclyde Institute of Pharmacy
and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, U.K
| | - Jean-Baptiste Arlin
- Institut Charles
Sadron (UPR22-CNRS), 23 rue du Loess, BP 84047, 67034
Strassbourg, Cedex, France
| | - Alastair J. Florence
- Strathclyde Institute of Pharmacy
and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, U.K
| | - Volker Kahlenberg
- Institute of Mineralogy and
Petrography, University of Innsbruck, Innrain
52, 6020 Innsbruck, Austria
| | - Ulrich J. Griesser
- Institute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck,
Austria
| | - Derek A. Tocher
- Department
of Chemistry, University College London, 20 Gordon
Street, London WC1H 0AJ, U.K
| | - Sarah L. Price
- Department
of Chemistry, University College London, 20 Gordon
Street, London WC1H 0AJ, U.K
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30
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Price SL. Why don't we find more polymorphs? ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2013; 69:313-28. [PMID: 23873056 DOI: 10.1107/s2052519213018861] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 07/08/2013] [Indexed: 05/11/2023]
Abstract
Crystal structure prediction (CSP) studies are not limited to being a search for the most thermodynamically stable crystal structure, but play a valuable role in understanding polymorphism, as shown by interdisciplinary studies where the crystal energy landscape has been explored experimentally and computationally. CSP usually produces more thermodynamically plausible crystal structures than known polymorphs. This article illustrates some reasons why: because (i) of approximations in the calculations, particularly the neglect of thermal effects (see §1.1); (ii) of the molecular rearrangement during nucleation and growth (see §1.2); (iii) the solid-state structures observed show dynamic or static disorder, stacking faults, other defects or are not crystalline and so represent more than one calculated structure (see §1.3); (iv) the structures are metastable relative to other molecular compositions (see §1.4); (v) the right crystallization experiment has not yet been performed (see §1.5) or (vi) cannot be performed (see §1.6) and the possibility (vii) that the polymorphs are not detected or structurally characterized (see §1.7). Thus, we can only aspire to a general predictive theory for polymorphism, as this appears to require a quantitative understanding of the kinetic factors involved in all possible multi-component crystallizations. For a specific molecule, analysis of the crystal energy landscape shows the potential complexity of its crystallization behaviour.
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Affiliation(s)
- Sarah L Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England.
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31
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Jelfs KE, Eden EB, Culshaw JL, Shakespeare S, Pyzer-Knapp EO, Thompson HPG, Bacsa J, Day GM, Adams DJ, Cooper AI. In silico design of supramolecules from their precursors: odd-even effects in cage-forming reactions. J Am Chem Soc 2013; 135:9307-10. [PMID: 23745577 PMCID: PMC3697021 DOI: 10.1021/ja404253j] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Indexed: 01/23/2023]
Abstract
We synthesize a series of imine cage molecules where increasing the chain length of the alkanediamine precursor results in an odd-even alternation between [2 + 3] and [4 + 6] cage macrocycles. A computational procedure is developed to predict the thermodynamically preferred product and the lowest energy conformer, hence rationalizing the observed alternation and the 3D cage structures, based on knowledge of the precursors alone.
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Affiliation(s)
- Kim E. Jelfs
- Department of Chemistry and
Centre for Materials Discovery, University of Liverpool, Liverpool, L69 7ZD, U.K
| | - Edward
G. B. Eden
- Department of Chemistry and
Centre for Materials Discovery, University of Liverpool, Liverpool, L69 7ZD, U.K
| | - Jamie L. Culshaw
- Department of Chemistry and
Centre for Materials Discovery, University of Liverpool, Liverpool, L69 7ZD, U.K
| | - Stephen Shakespeare
- Department of Chemistry and
Centre for Materials Discovery, University of Liverpool, Liverpool, L69 7ZD, U.K
| | - Edward O. Pyzer-Knapp
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge,
CB2 1EW, U.K
| | - Hugh P. G. Thompson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge,
CB2 1EW, U.K
| | - John Bacsa
- Department of Chemistry and
Centre for Materials Discovery, University of Liverpool, Liverpool, L69 7ZD, U.K
| | - Graeme M. Day
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge,
CB2 1EW, U.K
- Chemistry, University
of Southampton, Southampton, SO17 1BJ, U.K
| | - Dave J. Adams
- Department of Chemistry and
Centre for Materials Discovery, University of Liverpool, Liverpool, L69 7ZD, U.K
| | - Andrew I. Cooper
- Department of Chemistry and
Centre for Materials Discovery, University of Liverpool, Liverpool, L69 7ZD, U.K
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Frampton CS, Ketuly KA, Hadi AHA, Gall JH, Macnicol DD. Engineering robust polar chiral clathrate crystals. Chem Commun (Camb) 2013; 49:7198-200. [PMID: 23799369 DOI: 10.1039/c3cc43012j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Christopher S Frampton
- SAFC Pharmorphix®, A Sigma Aldrich Company, 250 Cambridge Science Park, Milton Road, Cambridge, CB4 0WE, UK.
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Mastalerz M. Permanent Porous Materials from Discrete Organic Molecules-Towards Ultra-High Surface Areas. Chemistry 2012; 18:10082-91. [DOI: 10.1002/chem.201201351] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Mastalerz M, Oppel IM. Rationale Herstellung eines extrinsisch porösen Molekülkristalls mit einer außergewöhnlich großen spezifischen Oberfläche. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201174] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Mastalerz M, Oppel IM. Rational Construction of an Extrinsic Porous Molecular Crystal with an Extraordinary High Specific Surface Area. Angew Chem Int Ed Engl 2012; 51:5252-5. [DOI: 10.1002/anie.201201174] [Citation(s) in RCA: 380] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Indexed: 11/11/2022]
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Galcera J, Friščić T, Hejczyk KE, Fábián L, Clarke SM, Day GM, Molins E, Jones W. Isostructural organic binary-host frameworks with tuneable and diversely decorated inclusion cavities. CrystEngComm 2012. [DOI: 10.1039/c2ce25550b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mastalerz M. Rational Design of Multifunctional Nanopores by Mixing Matching Molecules. Angew Chem Int Ed Engl 2011; 51:584-6. [DOI: 10.1002/anie.201107828] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Indexed: 11/12/2022]
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Mastalerz M. Rationales Design multifunktionaler Nanoporen durch Mischen passender Moleküle. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201107828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Natarajan R, Magro G, Bridgland LN, Sirikulkajorn A, Narayanan S, Ryan LE, Haddow MF, Orpen AG, Charmant JPH, Hudson AJ, Davis AP. Nanoporous Organic Alloys. Angew Chem Int Ed Engl 2011; 50:11386-90. [DOI: 10.1002/anie.201105216] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Indexed: 11/06/2022]
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Natarajan R, Magro G, Bridgland LN, Sirikulkajorn A, Narayanan S, Ryan LE, Haddow MF, Orpen AG, Charmant JPH, Hudson AJ, Davis AP. Nanoporous Organic Alloys. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201105216] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Kazantsev AV, Karamertzanis PG, Adjiman CS, Pantelides CC, Price SL, Galek PTA, Day GM, Cruz-Cabeza AJ. Successful prediction of a model pharmaceutical in the fifth blind test of crystal structure prediction. Int J Pharm 2011; 418:168-78. [PMID: 21497184 DOI: 10.1016/j.ijpharm.2011.03.058] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 03/10/2011] [Accepted: 03/24/2011] [Indexed: 10/18/2022]
Abstract
The range of target structures in the fifth international blind test of crystal structure prediction was extended to include a highly flexible molecule, (benzyl-(4-(4-methyl-5-(p-tolylsulfonyl)-1,3-thiazol-2-yl)phenyl)carbamate, as a challenge representative of modern pharmaceuticals. Two of the groups participating in the blind test independently predicted the correct structure. The methods they used are described and contrasted, and the implications of the capability to tackle molecules of this complexity are discussed.
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Affiliation(s)
- Andrei V Kazantsev
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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Saint Martin S, Marre S, Guionneau P, Cansell F, Renouard J, Marchetto V, Aymonier C. Host-Guest Inclusion Compound from Nitramine Crystals Exposed to Condensed Carbon Dioxide. Chemistry 2010; 16:13473-8. [DOI: 10.1002/chem.201001600] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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