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Reilly AM, Tkatchenko A. Role of dispersion interactions in the polymorphism and entropic stabilization of the aspirin crystal. PHYSICAL REVIEW LETTERS 2014; 113:055701. [PMID: 25126928 DOI: 10.1103/physrevlett.113.055701] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Indexed: 05/29/2023]
Abstract
Aspirin has been used and studied for over a century but has only recently been shown to have an additional polymorphic form, known as form II. Since the two observed solid forms of aspirin are degenerate in terms of lattice energy, kinetic effects have been suggested to determine the metastability of the less abundant form II. Here, first-principles calculations provide an alternative explanation based on free-energy differences at room temperature. The explicit consideration of many-body van der Waals interactions in the free energy demonstrates that the stability of the most abundant form of aspirin is due to a subtle coupling between collective electronic fluctuations and quantized lattice vibrations. In addition, a systematic analysis of the elastic properties of the two forms of aspirin rules out mechanical instability of form II as making it metastable.
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Affiliation(s)
- Anthony M Reilly
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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52
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Pantelides CC, Adjiman CS, Kazantsev AV. General Computational Algorithms for Ab Initio Crystal Structure Prediction for Organic Molecules. Top Curr Chem (Cham) 2014; 345:25-58. [DOI: 10.1007/128_2013_497] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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53
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Zhang Y, Maginn EJ. Toward Fully in Silico Melting Point Prediction Using Molecular Simulations. J Chem Theory Comput 2013; 9:1592-9. [DOI: 10.1021/ct301095j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yong Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556,
United States
| | - Edward J. Maginn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556,
United States
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Braun DE, Bhardwaj RM, Florence AJ, Tocher DA, Price SL. Complex Polymorphic System of Gallic Acid-Five Monohydrates, Three Anhydrates, and over 20 Solvates. CRYSTAL GROWTH & DESIGN 2013; 13:19-23. [PMID: 23378823 PMCID: PMC3557919 DOI: 10.1021/cg301506x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 11/16/2012] [Indexed: 05/25/2023]
Abstract
We report the structure of the fifth monohydrate of gallic acid and two additional anhydrate polymorphs and evidence of at least 22 other solvates formed, many containing water and another solvent. This unprecedented number of monohydrate polymorphs and diversity of solid forms is consistent with the anhydrate and monohydrate crystal energy landscapes, showing both a wide range of packing motifs and also some structures differing only in proton positions. By aiding the solution of structures from powder X-ray diffraction data and guiding the screening, the computational studies help explain the complex polymorphism of gallic acid. This is industrially relevant, as the three anhydrates are stable at ambient conditions but hydration/dehydration behavior is very dependent on relative humidity and phase purity.
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Affiliation(s)
- Doris E. Braun
- Department of Chemistry, University College London, 20 Gordon Street, London
WC1H 0AJ, U.K
- Institute
of Pharmacy, University of Innsbruck, Innrain
52c, 6020 Innsbruck,
Austria
| | - Rajni M. Bhardwaj
- Strathclyde Institute
of Pharmacy
and Biomedical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, U.K
| | - Alastair J. Florence
- Strathclyde Institute
of Pharmacy
and Biomedical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, U.K
| | - 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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55
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Wu H, Habgood M, Parker JE, Reeves-McLaren N, Cockcroft JK, Vickers M, West AR, Jones AG. Crystal structure determination by combined synchrotronpowder X-ray diffraction and crystal structure prediction: 1 : 1 l-ephedrined-tartrate. CrystEngComm 2013. [DOI: 10.1039/c2ce26097b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Vasileiadis M, Kazantsev AV, Karamertzanis PG, Adjiman CS, Pantelides CC. The polymorphs of ROY: application of a systematic crystal structure prediction technique. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2012; 68:677-85. [PMID: 23165604 DOI: 10.1107/s0108768112045636] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 11/05/2012] [Indexed: 11/11/2022]
Abstract
We investigate the ability of current ab initio crystal structure prediction techniques to identify the polymorphs of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, also known as ROY because of the red, orange and yellow colours of its polymorphs. We use a methodology combining the generation of a large number of structures based on a computationally inexpensive model using the CrystalPredictor global search algorithm, and the further minimization of the most promising of these structures using the CrystalOptimizer local minimization algorithm which employs an accurate, yet efficiently constructed, model based on isolated-molecule quantum-mechanical calculations. We demonstrate that this approach successfully predicts the seven experimentally resolved structures of ROY as lattice-energy minima, with five of these structures being within the 12 lowest energy structures predicted. Some of the other low-energy structures identified are likely candidates for the still unresolved polymorphs of this molecule. The relative stability of the predicted structures only partially matches that of the experimentally resolved polymorphs. The worst case is that of polymorph ON, whose relative energy with respect to Y is overestimated by 6.65 kJ mol(-1). This highlights the need for further developments in the accuracy of the energy calculations.
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Affiliation(s)
- Manolis Vasileiadis
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
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57
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Habgood M. Intermolecular electrostatics via molecular fragmentation: an application to crystal structure prediction. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2012.696110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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58
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Habgood M. Solution and nanoscale structure selection: implications for the crystal energy landscape of tetrolic acid. Phys Chem Chem Phys 2012; 14:9195-203. [DOI: 10.1039/c2cp40644f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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59
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Issa N, Barnett SA, Mohamed S, Braun DE, Copley RCB, Tocher DA, Price SL. Screening for cocrystals of succinic acid and 4-aminobenzoic acid. CrystEngComm 2012. [DOI: 10.1039/c2ce06325e] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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60
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Spencer J, Patel H, Deadman JJ, Palmer RA, Male L, Coles SJ, Uzoh OG, Price SL. The unexpected but predictable tetrazole packing in flexible 1-benzyl-1H-tetrazole. CrystEngComm 2012. [DOI: 10.1039/c2ce25940k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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61
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Bardwell DA, Adjiman CS, Arnautova YA, Bartashevich E, Boerrigter SXM, Braun DE, Cruz-Cabeza AJ, Day GM, Della Valle RG, Desiraju GR, van Eijck BP, Facelli JC, Ferraro MB, Grillo D, Habgood M, Hofmann DWM, Hofmann F, Jose KVJ, Karamertzanis PG, Kazantsev AV, Kendrick J, Kuleshova LN, Leusen FJJ, Maleev AV, Misquitta AJ, Mohamed S, Needs RJ, Neumann MA, Nikylov D, Orendt AM, Pal R, Pantelides CC, Pickard CJ, Price LS, Price SL, Scheraga HA, van de Streek J, Thakur TS, Tiwari S, Venuti E, Zhitkov IK. Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test. ACTA CRYSTALLOGRAPHICA. SECTION B, STRUCTURAL SCIENCE 2011; 67:535-51. [PMID: 22101543 PMCID: PMC3222142 DOI: 10.1107/s0108768111042868] [Citation(s) in RCA: 247] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 10/16/2011] [Indexed: 12/04/2022]
Abstract
Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories - a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.
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Affiliation(s)
- David A Bardwell
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England.
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62
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Jones JTA, Hasell T, Wu X, Bacsa J, Jelfs KE, Schmidtmann M, Chong SY, Adams DJ, Trewin A, Schiffman F, Cora F, Slater B, Steiner A, Day GM, Cooper AI. Modular and predictable assembly of porous organic molecular crystals. Nature 2011; 474:367-71. [DOI: 10.1038/nature10125] [Citation(s) in RCA: 410] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 04/18/2011] [Indexed: 11/09/2022]
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Braun DE, Karamertzanis PG, Price SL. Which, if any, hydrates will crystallise? Predicting hydrate formation of two dihydroxybenzoic acids. Chem Commun (Camb) 2011; 47:5443-5. [PMID: 21475750 PMCID: PMC3175531 DOI: 10.1039/c1cc10762c] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A study of two dihydroxybenzoic acid isomers shows that computational methods can be used to predict hydrate formation, the compound:water ratio and hydrate crystal structures. The calculations also help identify a novel hydrate found in the solid form screening that validates this study.
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Affiliation(s)
- Doris E Braun
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
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64
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Hartke B. Global optimization. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.70] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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65
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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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66
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Price SL, Leslie M, Welch GWA, Habgood M, Price LS, Karamertzanis PG, Day GM. Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials. Phys Chem Chem Phys 2010; 12:8478-90. [PMID: 20607186 DOI: 10.1039/c004164e] [Citation(s) in RCA: 202] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state. The calculated terahertz frequency k = 0 rigid-body lattice modes and elastic tensor can be used to estimate free energies. The program uses a distributed multipole electrostatic model (Q, t = 00,...,44s) for the electrostatic fields, and can use anisotropic atom-atom repulsion models, damped isotropic dispersion up to R(-10), as well as a range of empirically fitted isotropic exp-6 atom-atom models with different definitions of atomic types. A new feature is that an accurate model for the induction energy contribution to the lattice energy has been implemented that uses atomic anisotropic dipole polarizability models (alpha, t = (10,10)...(11c,11s)) to evaluate the changes in the molecular charge density induced by the electrostatic field within the crystal. It is demonstrated, using the four polymorphs of the pharmaceutical carbamazepine C(15)H(12)N(2)O, that whilst reproducing crystal structures is relatively easy, calculating the polymorphic energy differences to the accuracy of a few kJ mol(-1) required for applications is very demanding of assumptions made in the modelling. Thus DMACRYS enables the comparison of both known and hypothetical crystal structures as an aid to the development of pharmaceuticals and other speciality organic materials, and provides a tool to develop the modelling of the intermolecular forces involved in molecular recognition processes.
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Affiliation(s)
- Sarah L Price
- Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, UK.
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67
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Cruz-Cabeza AJ, Karki S, Fábián L, Friščić T, Day GM, Jones W. Predicting stoichiometry and structure of solvates. Chem Commun (Camb) 2010; 46:2224-6. [DOI: 10.1039/b922955h] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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68
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Day GM, Cooper TG. Crystal packing predictions of the alpha-amino acids: methods assessment and structural observations. CrystEngComm 2010. [DOI: 10.1039/c002213f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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69
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Karamertzanis PG, Kazantsev AV, Issa N, Welch GW, Adjiman CS, Pantelides CC, Price SL. Can the Formation of Pharmaceutical Cocrystals Be Computationally Predicted? 2. Crystal Structure Prediction. J Chem Theory Comput 2009; 5:1432-48. [DOI: 10.1021/ct8004326] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Panagiotis G. Karamertzanis
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, SW7 2AZ, United Kingdom, and Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
| | - Andrei V. Kazantsev
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, SW7 2AZ, United Kingdom, and Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
| | - Nizar Issa
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, SW7 2AZ, United Kingdom, and Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
| | - Gareth W.A. Welch
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, SW7 2AZ, United Kingdom, and Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
| | - Claire S. Adjiman
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, SW7 2AZ, United Kingdom, and Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
| | - Constantinos C. Pantelides
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, SW7 2AZ, United Kingdom, and Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
| | - Sarah L. Price
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, SW7 2AZ, United Kingdom, and Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
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Karamertzanis PG, Day GM, Welch GWA, Kendrick J, Leusen FJJ, Neumann MA, Price SL. Modeling the interplay of inter- and intramolecular hydrogen bonding in conformational polymorphs. J Chem Phys 2008; 128:244708. [PMID: 18601366 DOI: 10.1063/1.2937446] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The predicted stability differences of the conformational polymorphs of oxalyl dihydrazide and ortho-acetamidobenzamide are unrealistically large when the modeling of intermolecular energies is solely based on the isolated-molecule charge density, neglecting charge density polarization. Ab initio calculated crystal electron densities showed qualitative differences depending on the spatial arrangement of molecules in the lattice with the greatest variations observed for polymorphs that differ in the extent of inter- and intramolecular hydrogen bonding. We show that accounting for induction dramatically alters the calculated stability order of the polymorphs and reduces their predicted stability differences to be in better agreement with experiment. Given the challenges in modeling conformational polymorphs with marked differences in hydrogen bonding geometries, we performed an extensive periodic density functional study with a range of exchange-correlation functionals using both atomic and plane wave basis sets. Although such electronic structure methods model the electrostatic and polarization contributions well, the underestimation of dispersion interactions by current exchange-correlation functionals limits their applicability. The use of an empirical dispersion-corrected density functional method consistently reduces the structural deviations between the experimental and energy minimized crystal structures and achieves plausible stability differences. Thus, we have established which types of models may give worthwhile relative energies for crystal structures and other condensed phases of flexible molecules with intra- and intermolecular hydrogen bonding capabilities, advancing the possibility of simulation studies on polymorphic pharmaceuticals.
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72
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Price SL. From crystal structure prediction to polymorph prediction: interpreting the crystal energy landscape. Phys Chem Chem Phys 2008; 10:1996-2009. [DOI: 10.1039/b719351c] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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73
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Polito M, D'Oria E, Maini L, Karamertzanis PG, Grepioni F, Braga D, Price SL. The crystal structures of chloro and methyl ortho-benzoic acids and their co-crystal: rationalizing similarities and differences. CrystEngComm 2008. [DOI: 10.1039/b811438b] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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