101
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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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102
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Whittleton SR, Otero-de-la-Roza A, Johnson ER. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction II: Nonplanar Molecules. J Chem Theory Comput 2017; 13:5332-5342. [PMID: 28933853 DOI: 10.1021/acs.jctc.7b00715] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structure prediction (CSP) of a given compound from its molecular diagram is a fundamental challenge in computational chemistry with implications in relevant technological fields. A key component of CSP is the method to calculate the lattice energy of a crystal, which allows the ranking of candidate structures. This work is the second part of our investigation to assess the potential of the exchange-hole dipole moment (XDM) dispersion model for crystal structure prediction. In this article, we study the relatively large, nonplanar, mostly flexible molecules in the first five blind tests held by the Cambridge Crystallographic Data Centre. Four of the seven experimental structures are predicted as the energy minimum, and thermal effects are demonstrated to have a large impact on the ranking of at least another compound. As in the first part of this series, delocalization error affects the results for a single crystal (compound X), in this case by detrimentally overstabilizing the π-conjugated conformation of the monomer. Overall, B86bPBE-XDM correctly predicts 16 of the 21 compounds in the five blind tests, a result similar to the one obtained using the best CSP method available to date (dispersion-corrected PW91 by Neumann et al.). Perhaps more importantly, the systems for which B86bPBE-XDM fails to predict the experimental structure as the energy minimum are mostly the same as with Neumann's method, which suggests that similar difficulties (absence of vibrational free energy corrections, delocalization error,...) are not limited to B86bPBE-XDM but affect GGA-based DFT-methods in general. Our work confirms B86bPBE-XDM as an excellent option for crystal energy ranking in CSP and offers a guide to identify crystals (organic salts, conjugated flexible systems) where difficulties may appear.
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Affiliation(s)
- Sarah R Whittleton
- Department of Chemistry, Dalhousie University , 6274 Coburg Road, Halifax, Nova Scotia, Canada B3H 4R2
| | - A Otero-de-la-Roza
- Department of Chemistry, University of British Columbia , Okanagan, 3247 University Way, Kelowna, British Columbia, Canada VIV 1V7
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University , 6274 Coburg Road, Halifax, Nova Scotia, Canada B3H 4R2
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103
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Schrode B, Bodak B, Riegler H, Zimmer A, Christian P, Werzer O. Solvent Vapor Annealing of Amorphous Carbamazepine Films for Fast Polymorph Screening and Dissolution Alteration. ACS OMEGA 2017; 2:5582-5590. [PMID: 28983522 PMCID: PMC5623942 DOI: 10.1021/acsomega.7b00783] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/24/2017] [Indexed: 06/07/2023]
Abstract
Solubility enhancement and thus higher bioavailability are of great importance and a constant challenge in pharmaceutical research whereby polymorph screening and selection is one of the most important tasks. A very promising approach for polymorph screening is solvent vapor annealing where a sample is exposed to an atmosphere saturated with molecules of a specific chemical/solvent. In this work, amorphous carbamazepine thin films were prepared by spin coating, and the transformation into crystalline forms under exposure to solvent vapors was investigated. Employing grazing incidence X-ray diffraction, four distinct carbamazepine polymorphs, a solvate, and hydrates could be identified, while optical microscopy showed mainly spherulitic morphologies. In vitro dissolution experiments revealed different carbamazepine release from the various thin-film samples containing distinct polymorphic compositions: heat treatment of amorphous samples at 80 °C results in an immediate release; samples exposed to EtOH vapors show a drug release about 5 times slower than this immediate one; and all the others had intermediate release profiles. Noteworthy, even the sample of slowest release has a manifold faster release compared to a standard powder sample demonstrating the capabilities of thin-film preparation for faster drug release in general. Despite the small number of samples in this screening experiment, the results clearly show how solvent vapor annealing can assist in identifying potential polymorphs and allows for estimating their impact on properties like bioavailability.
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Affiliation(s)
- Benedikt Schrode
- Institute
of Pharmaceutical Sciences, NAWI Graz, Department of Pharmaceutical
Technology, University Graz, Universtitätsplatz 1, 8010 Graz, Austria
- Institute
for Solid State Physics, NAWI Graz, Graz
University of Technology, Petersgasse 16, 8010 Graz, Austria
| | - Brigitta Bodak
- Institute
of Pharmaceutical Sciences, NAWI Graz, Department of Pharmaceutical
Technology, University Graz, Universtitätsplatz 1, 8010 Graz, Austria
| | - Hans Riegler
- Institute
of Pharmaceutical Sciences, NAWI Graz, Department of Pharmaceutical
Technology, University Graz, Universtitätsplatz 1, 8010 Graz, Austria
| | - Andreas Zimmer
- Institute
of Pharmaceutical Sciences, NAWI Graz, Department of Pharmaceutical
Technology, University Graz, Universtitätsplatz 1, 8010 Graz, Austria
| | - Paul Christian
- Institute
for Solid State Physics, NAWI Graz, Graz
University of Technology, Petersgasse 16, 8010 Graz, Austria
| | - Oliver Werzer
- Institute
of Pharmaceutical Sciences, NAWI Graz, Department of Pharmaceutical
Technology, University Graz, Universtitätsplatz 1, 8010 Graz, Austria
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104
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Iuzzolino L, Reilly AM, McCabe P, Price SL. Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules. J Chem Theory Comput 2017; 13:5163-5171. [PMID: 28892623 DOI: 10.1021/acs.jctc.7b00623] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information from the crystal structures in the Cambridge Structural Database (CSD) to facilitate this task. The conformations produced by the CSD Conformer Generator are reduced in number by considering the underlying rotamer distributions, an analysis of changes in molecular shape, and a minimal number of molecular ab initio calculations. This method is tested for five pharmaceutical-like molecules where an extensive CSP study has already been performed. The CSD informatics-derived set of crystal structure searches generates almost all the low-energy crystal structures previously found, including all experimental structures. The workflow effectively combines information on individual torsion angles and then eliminates the combinations that are too high in energy to be found in the solid state, reducing the resources needed to cover the solid-state conformational space of a molecule. This provides insights into how the low-energy solid-state and isolated-molecule conformations are related to the properties of the individual flexible torsion angles.
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Affiliation(s)
- Luca Iuzzolino
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, England
| | - Anthony M Reilly
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Patrick McCabe
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Sarah L Price
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, England
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105
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Johnston A, Bhardwaj-Miglani R, Gurung R, Vassileiou AD, Florence AJ, Johnston BF. Combined Chemoinformatics Approach to Solvent Library Design Using clusterSim and Multidimensional Scaling. J Chem Inf Model 2017; 57:1807-1815. [PMID: 28666389 DOI: 10.1021/acs.jcim.7b00038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reported here is a rational approach for the selection of solvents intended for use in physical form screening based on a novel chemoinformatics analysis of solvent properties. A comprehensive assessment of eight clustering methods was carried out on a series of 94 solvents described by calculated molecular descriptors using the clusterSim package in R. The effectiveness of clustering methods was evaluated using a range of statistical measures as well as increasing efficiency of solid form discovery using a cluster-based solvent selection approach. Multidimensional scaling was used to illustrate cluster analysis on a two-dimensional solvent map. The map presented here is a valuable tool to aid efficient solvent selection in physical form screens. This tool is equally applicable to any scientific area which requires a solubility dependent decision on solvent choice.
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Affiliation(s)
- Andrea Johnston
- EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Crystallisation and ‡EPSRC Doctoral Training Centre in Continuous Manufacturing and Crystallisation c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde , Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Rajni Bhardwaj-Miglani
- EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Crystallisation and ‡EPSRC Doctoral Training Centre in Continuous Manufacturing and Crystallisation c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde , Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Rajesh Gurung
- EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Crystallisation and ‡EPSRC Doctoral Training Centre in Continuous Manufacturing and Crystallisation c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde , Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Antony D Vassileiou
- EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Crystallisation and ‡EPSRC Doctoral Training Centre in Continuous Manufacturing and Crystallisation c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde , Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Alastair J Florence
- EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Crystallisation and ‡EPSRC Doctoral Training Centre in Continuous Manufacturing and Crystallisation c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde , Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Blair F Johnston
- EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Crystallisation and ‡EPSRC Doctoral Training Centre in Continuous Manufacturing and Crystallisation c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde , Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, United Kingdom
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106
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Alcolea V, Garnica P, Palop JA, Sanmartín C, González-Peñas E, Durán A, Lizarraga E. Antitumoural Sulphur and Selenium Heteroaryl Compounds: Thermal Characterization and Stability Evaluation. Molecules 2017; 22:molecules22081314. [PMID: 28786948 PMCID: PMC6152329 DOI: 10.3390/molecules22081314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/04/2017] [Indexed: 11/29/2022] Open
Abstract
The physicochemical properties of a compound play a crucial role in the cancer development process. In this context, polymorphism can become an important obstacle for the pharmaceutical industry because it frequently leads to the loss of therapeutic effectiveness of some drugs. Stability under manufacturing conditions is also critical to ensure no undesired degradations or transformations occur. In this study, the thermal behaviour of 40 derivatives of a series of sulphur and selenium heteroaryl compounds with potential antitumoural activity were studied. In addition, the most promising cytotoxic derivatives were analysed by a combination of differential scanning calorimetry, X-ray diffraction and thermogravimetric techniques in order to investigate their polymorphism and thermal stability. Moreover, stability under acid, alkaline and oxidative media was tested. Degradation under stress conditions as well as the presence of polymorphism was found for the compounds VA6E and VA7J, which might present a hurdle to carrying on with formulation. On the contrary, these obstacles were not found for derivative VA4J.
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Affiliation(s)
- Verónica Alcolea
- Department of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy and Nutrition, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain.
| | - Pablo Garnica
- Department of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy and Nutrition, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain.
| | - Juan A Palop
- Department of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy and Nutrition, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain.
| | - Carmen Sanmartín
- Department of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy and Nutrition, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain.
| | - Elena González-Peñas
- Department of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy and Nutrition, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain.
| | - Adrián Durán
- Department of Chemistry, Faculty of Sciences, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain.
| | - Elena Lizarraga
- Department of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy and Nutrition, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain.
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107
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Pindelska E, Sokal A, Kolodziejski W. Pharmaceutical cocrystals, salts and polymorphs: Advanced characterization techniques. Adv Drug Deliv Rev 2017; 117:111-146. [PMID: 28931472 DOI: 10.1016/j.addr.2017.09.014] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/21/2017] [Accepted: 09/14/2017] [Indexed: 12/11/2022]
Abstract
The main goal of a novel drug development is to obtain it with optimal physiochemical, pharmaceutical and biological properties. Pharmaceutical companies and scientists modify active pharmaceutical ingredients (APIs), which often are cocrystals, salts or carefully selected polymorphs, to improve the properties of a parent drug. To find the best form of a drug, various advanced characterization methods should be used. In this review, we have described such analytical methods, dedicated to solid drug forms. Thus, diffraction, spectroscopic, thermal and also pharmaceutical characterization methods are discussed. They all are necessary to study a solid API in its intrinsic complexity from bulk down to the molecular level, gain information on its structure, properties, purity and possible transformations, and make the characterization efficient, comprehensive and complete. Furthermore, these methods can be used to monitor and investigate physical processes, involved in the drug development, in situ and in real time. The main aim of this paper is to gather information on the current advancements in the analytical methods and highlight their pharmaceutical relevance.
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108
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109
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Granero-García R, Falenty A, Fabbiani FPA. Dense Semi-Clathrates at High Pressure: A Study of the Water-tert-Butylamine System. Chemistry 2017; 23:3691-3698. [PMID: 28092417 DOI: 10.1002/chem.201605090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 11/06/2022]
Abstract
In situ high-pressure crystallization and diffraction techniques have been applied to obtain two very structurally distinct semi-clathrates of the tert-butylamine-water system with hydration numbers 5.65 and 5.8, respectively, thereby considerably reducing a notable hydration gap between the monohydrate and the 71/4 -hydrate that results when crystallization space is explored by temperature alone. Both structures can be considered as an intriguing solid-state example of hydrophobic hydration, in which the water network creates wide tert-butylamine-filled channels stabilized by cross-linking hydrogen bonds. The existence of interconnected channels might also add low hydration structures to a list of potential targets for hydrogen storage. A detailed analysis of the topology of host water and host-guest interactions is reported and extended to those of other hydrates of the compound. This analysis offers new insight into properties of the tert-butylamine-water system and provides some clues as to the occurrence of the sizable number of hydrates of this compound.
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Affiliation(s)
- Rubén Granero-García
- GZG, Abt. Kristallographie, Georg-August-Universität Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Andrzej Falenty
- GZG, Abt. Kristallographie, Georg-August-Universität Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Francesca P A Fabbiani
- GZG, Abt. Kristallographie, Georg-August-Universität Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
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110
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Li X, Neumann MA, van de Streek J. The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine. IUCRJ 2017; 4:175-184. [PMID: 28250956 PMCID: PMC5330528 DOI: 10.1107/s2052252517001415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/27/2017] [Indexed: 05/04/2023]
Abstract
Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more attention to anisotropic chemical shifts and development of the method of solid-state NMR calculations.
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Affiliation(s)
- Xiaozhou Li
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Marcus A. Neumann
- Avant-garde Materials Simulation Deutschland GmbH, Rosa-Luxemberg-Strasse 14, Freiburg D-79100, Germany
| | - Jacco van de Streek
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
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111
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Abstract
Existing methods to compute free-energy differences between polymorphs use harmonic approximations, advanced non-Boltzmann bias sampling techniques, and/or multistage free-energy perturbations. This work demonstrates how Bennett's diabat interpolation method ( J. Comput. Phys. 1976, 22, 245 ) can be combined with energy gaps from lattice-switch Monte Carlo techniques ( Phys. Rev. E 2000, 61, 906 ) to swiftly estimate polymorph free-energy differences. The new method requires only two unbiased molecular dynamics simulations, one for each polymorph. To illustrate the new method, we compute the free-energy difference between face-centered cubic and body-centered cubic polymorphs for a Gaussian core solid. We discuss the justification for parabolic models of the free-energy diabats and similarities to methods that have been used in studies of electron transfer.
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Affiliation(s)
- Kartik Kamat
- Department of Chemical Engineering and ‡Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
| | - Baron Peters
- Department of Chemical Engineering and ‡Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
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112
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Rychkov DA, Stare J, Boldyreva EV. Pressure-driven phase transition mechanisms revealed by quantum chemistry: l-serine polymorphs. Phys Chem Chem Phys 2017; 19:6671-6676. [PMID: 28210731 DOI: 10.1039/c6cp07721h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present study delivers a computational approach for the understanding of the mechanism of phase transitions between polymorphs of small organic molecules.
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Affiliation(s)
- Denis A. Rychkov
- Institute of Solid State Chemistry and Mechanochemistry
- Siberian Branch of Russian Academy of Sciences
- Novosibirsk 630128
- Russian Federation
- Novosibirsk State University
| | - Jernej Stare
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Elena V. Boldyreva
- Institute of Solid State Chemistry and Mechanochemistry
- Siberian Branch of Russian Academy of Sciences
- Novosibirsk 630128
- Russian Federation
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113
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Sugden I, Adjiman CS, Pantelides CC. Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:864-874. [PMID: 27910837 PMCID: PMC5134761 DOI: 10.1107/s2052520616015122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/26/2016] [Indexed: 05/14/2023]
Abstract
The global search stage of crystal structure prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II [Habgood et al. (2015). J. Chem. Theory Comput. 11, 1957-1969] program is presented, where the most efficient use of computational effort is ensured via the use of adaptive local approximate model (LAM) placement. The entire search space of the relevant molecule's conformations is initially evaluated using a coarse, low accuracy grid. Additional LAM points are then placed at appropriate points determined via an automated process, aiming to minimize the computational effort expended in high-energy regions whilst maximizing the accuracy in low-energy regions. As the size, complexity and flexibility of molecules increase, the reduction in computational cost becomes marked. This improvement is illustrated with energy calculations for benzoic acid and the ROY molecule, and a CSP study of molecule (XXVI) from the sixth blind test [Reilly et al. (2016). Acta Cryst. B72, 439-459], which is challenging due to its size and flexibility. Its known experimental form is successfully predicted as the global minimum. The computational cost of the study is tractable without the need to make unphysical simplifying assumptions.
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Affiliation(s)
- Isaac Sugden
- Molecular Systems Engineering Group Centre for Process Systems Engineering Department of Chemical Engineering, Imperial College London, London SW7 2AZ, England
| | - Claire S. Adjiman
- Molecular Systems Engineering Group Centre for Process Systems Engineering Department of Chemical Engineering, Imperial College London, London SW7 2AZ, England
| | - Constantinos C. Pantelides
- Molecular Systems Engineering Group Centre for Process Systems Engineering Department of Chemical Engineering, Imperial College London, London SW7 2AZ, England
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114
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Beran GJO, Hartman JD, Heit YN. Predicting Molecular Crystal Properties from First Principles: Finite-Temperature Thermochemistry to NMR Crystallography. Acc Chem Res 2016; 49:2501-2508. [PMID: 27754668 DOI: 10.1021/acs.accounts.6b00404] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties. First, it describes the coupling of fragment electronic structure models with quasi-harmonic techniques for modeling the thermal expansion of molecular crystals, and what effects this expansion has on thermochemical and mechanical properties. Excellent agreement with experiment is demonstrated for the molar volume, sublimation enthalpy, entropy, and free energy, and the bulk modulus of phase I carbon dioxide when large basis second-order Møller-Plesset perturbation theory (MP2) or coupled cluster theories (CCSD(T)) are used. In addition, physical insight is offered into how neglect of thermal expansion affects these properties. Zero-point vibrational motion leads to an appreciable expansion in the molar volume; in carbon dioxide, it accounts for around 30% of the overall volume expansion between the electronic structure energy minimum and the molar volume at the sublimation point. In addition, because thermal expansion typically weakens the intermolecular interactions, neglecting thermal expansion artificially stabilizes the solid and causes the sublimation enthalpy to be too large at higher temperatures. Thermal expansion also frequently weakens the lower-frequency lattice phonon modes; neglecting thermal expansion causes the entropy of sublimation to be overestimated. Interestingly, the sublimation free energy is less significantly affected by neglecting thermal expansion because the systematic errors in the enthalpy and entropy cancel somewhat. Second, because solid state nuclear magnetic resonance (NMR) plays an increasingly important role in molecular crystal studies, this Account discusses how fragment methods can be used to achieve higher-accuracy chemical shifts in molecular crystals. Whereas widely used plane wave density functional theory models are largely restricted to generalized gradient approximation (GGA) functionals like PBE in practice, fragment methods allow the routine use of hybrid density functionals with only modest increases in computational cost. In extensive molecular crystal benchmarks, hybrid functionals like PBE0 predict chemical shifts with 20-30% higher accuracy than GGAs, particularly for 1H, 13C, and 15N nuclei. Due to their higher sensitivity to polarization effects, 17O chemical shifts prove slightly harder to predict with fragment methods. Nevertheless, the fragment model results are still competitive with those from GIPAW. The improved accuracy achievable with fragment approaches and hybrid density functionals increases discrimination between different potential assignments of individual shifts or crystal structures, which is critical in NMR crystallography applications. This higher accuracy and greater discrimination are highlighted in application to the solid state NMR of different acetaminophen and testosterone crystal forms.
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Affiliation(s)
- Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Joshua D. Hartman
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yonaton N. Heit
- Department of Chemistry, University of California, Riverside, California 92521, United States
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115
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Mandal T, Marson RL, Larson RG. Coarse-grained modeling of crystal growth and polymorphism of a model pharmaceutical molecule. SOFT MATTER 2016; 12:8246-8255. [PMID: 27714373 DOI: 10.1039/c6sm01817c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We describe a systematic coarse-graining method to study crystallization and predict possible polymorphs of small organic molecules. In this method, a coarse-grained (CG) force field is obtained by inverse-Boltzmann iteration from the radial distribution function of atomistic simulations of the known crystal. With the force field obtained by this method, we show that CG simulations of the drug phenytoin predict growth of a crystalline slab from a melt of phenytoin, allowing determination of the fastest-growing surface, as well as giving the correct lattice parameters and crystal morphology. By applying meta-dynamics to the coarse-grained model, a new crystalline form of phenytoin (monoclinic, space group P21) was predicted which is different from the experimentally known crystal structure (orthorhombic, space group Pna21). Atomistic simulations and quantum calculations then showed the polymorph to be meta-stable at ambient temperature and pressure, and thermodynamically more stable than the conventional orthorhombic crystal at high pressure. The results suggest an efficient route to study crystal growth of small organic molecules that could also be useful for identification of possible polymorphs as well.
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Affiliation(s)
- Taraknath Mandal
- Department of Chemical Engineering and Biointerfaces Institute, University of Michigan, Ann Arbor, MI-48109, USA.
| | - Ryan L Marson
- Department of Chemical Engineering and Biointerfaces Institute, University of Michigan, Ann Arbor, MI-48109, USA.
| | - Ronald G Larson
- Department of Chemical Engineering and Biointerfaces Institute, University of Michigan, Ann Arbor, MI-48109, USA.
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116
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Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED. Proc Natl Acad Sci U S A 2016; 113:11232-11236. [PMID: 27647903 DOI: 10.1073/pnas.1606287113] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods.
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117
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Reilly AM, Cooper RI, Adjiman CS, Bhattacharya S, Boese AD, Brandenburg JG, Bygrave PJ, Bylsma R, Campbell JE, Car R, Case DH, Chadha R, Cole JC, Cosburn K, Cuppen HM, Curtis F, Day GM, DiStasio Jr RA, Dzyabchenko A, van Eijck BP, Elking DM, van den Ende JA, Facelli JC, Ferraro MB, Fusti-Molnar L, Gatsiou CA, Gee TS, de Gelder R, Ghiringhelli LM, Goto H, Grimme S, Guo R, Hofmann DWM, Hoja J, Hylton RK, Iuzzolino L, Jankiewicz W, de Jong DT, Kendrick J, de Klerk NJJ, Ko HY, Kuleshova LN, Li X, Lohani S, Leusen FJJ, Lund AM, Lv J, Ma Y, Marom N, Masunov AE, McCabe P, McMahon DP, Meekes H, Metz MP, Misquitta AJ, Mohamed S, Monserrat B, Needs RJ, Neumann MA, Nyman J, Obata S, Oberhofer H, Oganov AR, Orendt AM, Pagola GI, Pantelides CC, Pickard CJ, Podeszwa R, Price LS, Price SL, Pulido A, Read MG, Reuter K, Schneider E, Schober C, Shields GP, Singh P, Sugden IJ, Szalewicz K, Taylor CR, Tkatchenko A, Tuckerman ME, Vacarro F, Vasileiadis M, Vazquez-Mayagoitia A, Vogt L, Wang Y, Watson RE, de Wijs GA, Yang J, Zhu Q, Groom CR. Report on the sixth blind test of organic crystal structure prediction methods. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:439-59. [PMID: 27484368 PMCID: PMC4971545 DOI: 10.1107/s2052520616007447] [Citation(s) in RCA: 298] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/04/2016] [Indexed: 05/05/2023]
Abstract
The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.
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Affiliation(s)
- Anthony M. Reilly
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Richard I. Cooper
- Chemical Crystallography, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England
| | - Claire S. Adjiman
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | - Saswata Bhattacharya
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - A. Daniel Boese
- Department of Chemistry, Institute of Physical and Theoretical Chemistry, University of Graz, Heinrichstraße 28/IV, 8010 Graz, Austria
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Peter J. Bygrave
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Rita Bylsma
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Josh E. Campbell
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Roberto Car
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - David H. Case
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Renu Chadha
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Jason C. Cole
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Katherine Cosburn
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Department of Physics, University of Toronto, Toronto, Canada M5S 1A7
| | - Herma M. Cuppen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Farren Curtis
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Graeme M. Day
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Robert A. DiStasio Jr
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Dennis M. Elking
- OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508, USA
| | - Joost A. van den Ende
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Julio C. Facelli
- Center for High Performance Computing, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, USA
- Department of Biomedical Informatics, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, USA
| | - Marta B. Ferraro
- Departamento de Física and Ifiba (CONICET) Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina
| | - Laszlo Fusti-Molnar
- OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508, USA
| | - Christina-Anna Gatsiou
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | - Thomas S. Gee
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - René de Gelder
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Luca M. Ghiringhelli
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Hitoshi Goto
- Educational Programs on Advanced Simulation Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
- Department of Computer Science and Engineering, Graduate School of Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Rui Guo
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Detlef W. M. Hofmann
- CRS4, Parco Scientifico e Tecnologico, POLARIS, Edificio 1, 09010 PULA, Italy
- FlexCryst, Schleifweg 23, 91080 Uttenreuth, Germany
| | - Johannes Hoja
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Rebecca K. Hylton
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Luca Iuzzolino
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Wojciech Jankiewicz
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Daniël T. de Jong
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - John Kendrick
- Faculty of Life Sciences, University of Bradford, Richmond Road, Bradford BD7 1DP, England
| | - Niek J. J. de Klerk
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hsin-Yu Ko
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | | | - Xiayue Li
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Sanjaya Lohani
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
| | - Frank J. J. Leusen
- Faculty of Life Sciences, University of Bradford, Richmond Road, Bradford BD7 1DP, England
| | - Albert M. Lund
- OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508, USA
- Department of Chemistry, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, USA
| | - Jian Lv
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, People’s Republic of China
| | - Yanming Ma
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, People’s Republic of China
| | - Noa Marom
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Department of Materials Science and Engineering and Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Artëm E. Masunov
- NanoScience Technology Center, University of Central Florida, 12424 Research Parkway, PAV400, Orlando, FL 32826, USA
- Department of Chemistry, University of Central Florida, 4111 Libra Drive PSB225, Orlando, FL 32816, USA
- Department of Physics, University of Central Florida, 4111 Libra Drive PSB430, Orlando, FL 32816, USA
- Department of Condensed Matter Physics, National Research Nuclear University MEPhI, Kashirskoye shosse 31, Moscow 115409, Russia
| | - Patrick McCabe
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - David P. McMahon
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Hugo Meekes
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Michael P. Metz
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
| | - Alston J. Misquitta
- School of Physics and Astronomy, Queen Mary University of London, London E1 4NS, England
| | | | - Bartomeu Monserrat
- Cavendish Laboratory, 19, J. J. Thomson Avenue, Cambridge CB3 0HE, England
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854-8019, USA
| | - Richard J. Needs
- Cavendish Laboratory, 19, J. J. Thomson Avenue, Cambridge CB3 0HE, England
| | | | - Jonas Nyman
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Shigeaki Obata
- Educational Programs on Advanced Simulation Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Artem R. Oganov
- Department of Geosciences, Center for Materials by Design, and Institute for Advanced Computational Science, SUNY Stony Brook, NY 11794-2100, USA
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Centers, Bldg. 3, Moscow Region, 143026, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny City, Moscow Region 141700, Russia
- International Center for Materials Discovery, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi’an 710072, China
| | - Anita M. Orendt
- Center for High Performance Computing, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, USA
| | - Gabriel I. Pagola
- Departamento de Física and Ifiba (CONICET) Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina
| | - Constantinos C. Pantelides
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | - Chris J. Pickard
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, England
- Department of Physics and Astronomy, University College London, Gower St., London WC1E 6BT, England
| | - Rafal Podeszwa
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Louise S. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Sarah L. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Angeles Pulido
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Murray G. Read
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Elia Schneider
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Christoph Schober
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Gregory P. Shields
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Pawanpreet Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Isaac J. Sugden
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
| | | | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg
| | - Mark E. Tuckerman
- Department of Chemistry, New York University, New York, NY 10003, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
| | - Francesca Vacarro
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Department of Chemistry, Loyola University, New Orleans, LA 70118, USA
| | - Manolis Vasileiadis
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | | | - Leslie Vogt
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Yanchao Wang
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, People’s Republic of China
| | - Rona E. Watson
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Gilles A. de Wijs
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jack Yang
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Qiang Zhu
- Department of Geosciences, Center for Materials by Design, and Institute for Advanced Computational Science, SUNY Stony Brook, NY 11794-2100, USA
| | - Colin R. Groom
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
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118
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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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119
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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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120
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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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121
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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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122
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Grzybowska K, Capaccioli S, Paluch M. Recent developments in the experimental investigations of relaxations in pharmaceuticals by dielectric techniques at ambient and elevated pressure. Adv Drug Deliv Rev 2016; 100:158-82. [PMID: 26705851 DOI: 10.1016/j.addr.2015.12.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/05/2015] [Accepted: 12/09/2015] [Indexed: 10/22/2022]
Abstract
In recent years, there is a growing interest in improving the physicochemical stability of amorphous pharmaceutical solids due to their very promising applications to manufacture medicines characterized by a better water solubility, and consequently by a higher dissolution rate than those of their crystalline counterparts. In this review article, we show that the molecular mobility investigated both in the supercooled liquid and glassy states is the crucial factor required to understand molecular mechanisms that govern the physical stability of amorphous drugs. We demonstrate that pharmaceuticals can be thoroughly examined by means of the broadband dielectric spectroscopy, which is a very useful experimental technique to explore different relaxation processes and crystallization kinetics as well. Such studies conducted in the wide temperature and pressure ranges provide data needed in searching correlations between properties of molecular dynamics and crystallization process, which are aimed at developing effective and efficient methods for stabilizing amorphous drugs.
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123
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Abstract
Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
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124
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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: 61] [Impact Index Per Article: 7.6] [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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125
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Céolin R, Rietveld IB. X-ray crystallography, an essential tool for the determination of thermodynamic relationships between crystalline polymorphs. ANNALES PHARMACEUTIQUES FRANÇAISES 2016; 74:12-20. [DOI: 10.1016/j.pharma.2015.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/15/2015] [Accepted: 10/19/2015] [Indexed: 11/28/2022]
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126
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Zakharov BA, Seryotkin YV, Tumanov NA, Paliwoda D, Hanfland M, Kurnosov AV, Boldyreva EV. The role of fluids in high-pressure polymorphism of drugs: different behaviour of β-chlorpropamide in different inert gas and liquid media. RSC Adv 2016. [DOI: 10.1039/c6ra17750f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Compression of β-chlorpropamide gives different phases depending on the choice of non-dissolving pressure-transmitting fluid (paraffin, neon and helium).
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Affiliation(s)
- B. A. Zakharov
- Institute of Solid State Chemistry and Mechanochemistry SB RAS
- Novosibirsk 630128
- Russia
- Novosibirsk State University
- Novosibirsk 630090
| | - Y. V. Seryotkin
- Institute of Solid State Chemistry and Mechanochemistry SB RAS
- Novosibirsk 630128
- Russia
- Novosibirsk State University
- Novosibirsk 630090
| | - N. A. Tumanov
- Institute of Condensed Matter and Nanosciences
- Université catholique de Louvain
- Louvain-la-Neuve 1348
- Belgium
- Université de Namur
| | - D. Paliwoda
- European Synchrotron Radiation Facility
- Grenoble 38000
- France
| | - M. Hanfland
- European Synchrotron Radiation Facility
- Grenoble 38000
- France
| | - A. V. Kurnosov
- Bayerisches Geoinstitut
- Universität Bayreuth
- Bayreuth D-95447
- Germany
| | - E. V. Boldyreva
- Institute of Solid State Chemistry and Mechanochemistry SB RAS
- Novosibirsk 630128
- Russia
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127
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Zakharov BA, Goryainov SV, Boldyreva EV. Unusual seeding effect in the liquid-assisted high-pressure polymorphism of chlorpropamide. CrystEngComm 2016. [DOI: 10.1039/c6ce00711b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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128
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Fabbiani FPA, Bergantin S, Gavezzotti A, Rizzato S, Moret M. X-ray diffraction and computational studies of the pressure-dependent tetrachloroethane solvation of diphenylanthracene. CrystEngComm 2016. [DOI: 10.1039/c6ce00055j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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129
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Patyk E, Jenczak A, Katrusiak A. Giant strain geared to transformable H-bonded network in compressed β-d-mannose. Phys Chem Chem Phys 2016; 18:11474-9. [DOI: 10.1039/c6cp01286h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The clearly visible shape change of β-d-mannose crystals is associated with pressure-induced isostructural phase transition.
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Affiliation(s)
- Ewa Patyk
- Department of Materials Chemistry
- Faculty of Chemistry
- Adam Mickiewicz University
- Poznań
- Poland
| | - Anna Jenczak
- Department of Materials Chemistry
- Faculty of Chemistry
- Adam Mickiewicz University
- Poznań
- Poland
| | - Andrzej Katrusiak
- Department of Materials Chemistry
- Faculty of Chemistry
- Adam Mickiewicz University
- Poznań
- Poland
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130
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Ruiz-Palomero C, Kennedy SR, Soriano ML, Jones CD, Valcárcel M, Steed JW. Pharmaceutical crystallization with nanocellulose organogels. Chem Commun (Camb) 2016; 52:7782-5. [DOI: 10.1039/c6cc03088b] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A carboxylated nanocellulose organogel facilitates crystallization of pharmaceutical solid forms including a new sulfapyridine solvate.
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Affiliation(s)
| | - Stuart R. Kennedy
- Department of Chemistry
- Durham University
- University Science Laboratories
- Durham
- UK
| | - M. Laura Soriano
- Department of Analytical Chemistry
- University of Córdoba
- E-14071 Córdoba
- Spain
| | | | - Miguel Valcárcel
- Department of Analytical Chemistry
- University of Córdoba
- E-14071 Córdoba
- Spain
| | - Jonathan W. Steed
- Department of Chemistry
- Durham University
- University Science Laboratories
- Durham
- UK
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131
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Structural Elucidation of α-Cyclodextrin-Succinic Acid Pseudo Dodecahydrate: Expanding the Packing Types of α-Cyclodextrin Inclusion Complexes. CRYSTALS 2015. [DOI: 10.3390/cryst6010002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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