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Beran GJO, Wright SE, Greenwell C, Cruz-Cabeza AJ. The interplay of intra- and intermolecular errors in modeling conformational polymorphs. J Chem Phys 2022; 156:104112. [DOI: 10.1063/5.0088027] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Conformational polymorphs of organic molecular crystals represent a challenging test for quantum chemistry because they require careful balancing of the intra- and intermolecular interactions. This study examines 54 molecular conformations from 20 sets of conformational polymorphs, along with the relative lattice energies and 173 dimer interactions taken from six of the polymorph sets. These systems are studied with a variety of van der Waals-inclusive density functionals theory models; dispersion-corrected spin-component-scaled second-order Møller–Plesset perturbation theory (SCS-MP2D); and domain local pair natural orbital coupled cluster singles, doubles, and perturbative triples [DLPNO-CCSD(T)]. We investigate how delocalization error in conventional density functionals impacts monomer conformational energies, systematic errors in the intermolecular interactions, and the nature of error cancellation that occurs in the overall crystal. The density functionals B86bPBE-XDM, PBE-D4, PBE-MBD, PBE0-D4, and PBE0-MBD are found to exhibit sizable one-body and two-body errors vs DLPNO-CCSD(T) benchmarks, and the level of success in predicting the relative polymorph energies relies heavily on error cancellation between different types of intermolecular interactions or between intra- and intermolecular interactions. The SCS-MP2D and, to a lesser extent, ωB97M-V models exhibit smaller errors and rely less on error cancellation. Implications for crystal structure prediction of flexible compounds are discussed. Finally, the one-body and two-body DLPNO-CCSD(T) energies taken from these conformational polymorphs establish the CP1b and CP2b benchmark datasets that could be useful for testing quantum chemistry models in challenging real-world systems with complex interplay between intra- and intermolecular interactions, a number of which are significantly impacted by delocalization error.
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Affiliation(s)
- Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Sarah E. Wright
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
| | - Chandler Greenwell
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Aurora J. Cruz-Cabeza
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
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2
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Dudek MK, Druzbicki K. Along the road to Crystal Structure Prediction (CSP) of pharmaceutical-like molecules. CrystEngComm 2022. [DOI: 10.1039/d1ce01564h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational methods used for predicting crystal structures of organic compounds are mature enough to be routinely used with many rigid and semi-rigid organic molecules. The usefulness of Crystal Structure Prediction...
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3
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Glutathione Disulfide as a Reducing, Capping, and Mass-Separating Agent for the Synthesis and Enrichment of Gold Nanoclusters. NANOMATERIALS 2021; 11:nano11092258. [PMID: 34578574 PMCID: PMC8472339 DOI: 10.3390/nano11092258] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/26/2021] [Accepted: 08/28/2021] [Indexed: 12/20/2022]
Abstract
Water-soluble nanoclusters, which are facilely enrichable without changes in the original properties, are highly demanded in many disciplines. In this contribution, a new class of gold nanoclusters (AuNCs) was synthesized using glutathione disulfide (GSSG) as a reducing and capping agent under intermittent heating mode. The as-prepared GSSG–AuNCs had a higher quantum yield (4.1%) compared to the conventional glutathione-protected AuNCs (1.8%). Moreover, by simply introducing the GSSG–AuNC solution to acetonitrile at a volume ratio of 1:7, a new bottom phase was formed, in which GSSG–AuNCs could be 400-fold enriched without changes in properties, with a percentage recovery higher than 99%. The enrichment approach did not need additional instruments and was potentially suitable for large-scale enrichment of nanoclusters. Further, density functional theory calculations indicated that the hydrogen bonding between GSSG and acetonitrile plays a key role for the bottom phase formation. Our work suggests that the highly emissive GSSG–AuNCs possess great potential not only in fluorescent measurements but also in other scenarios in which high-concentration AuNCs may be needed, such as catalysis, drug delivery, and electronic and optical industries.
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4
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Broadband Terahertz Spectroscopy of Glutathione. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60053-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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5
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Greenwell C, McKinley JL, Zhang P, Zeng Q, Sun G, Li B, Wen S, Beran GJO. Overcoming the difficulties of predicting conformational polymorph energetics in molecular crystals via correlated wavefunction methods. Chem Sci 2020; 11:2200-2214. [PMID: 32190277 PMCID: PMC7059316 DOI: 10.1039/c9sc05689k] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 01/13/2020] [Indexed: 11/21/2022] Open
Abstract
Molecular crystal structure prediction is increasingly being applied to study the solid form landscapes of larger, more flexible pharmaceutical molecules. Despite many successes in crystal structure prediction, van der Waals-inclusive density functional theory (DFT) methods exhibit serious failures predicting the polymorph stabilities for a number of systems exhibiting conformational polymorphism, where changes in intramolecular conformation lead to different intermolecular crystal packings. Here, the stabilities of the conformational polymorphs of o-acetamidobenzamide, ROY, and oxalyl dihydrazide are examined in detail. DFT functionals that have previously been very successful in crystal structure prediction perform poorly in all three systems, due primarily to the poor intramolecular conformational energies, but also due to the intermolecular description in oxalyl dihydrazide. In all three cases, a fragment-based dispersion-corrected second-order Møller-Plesset perturbation theory (MP2D) treatment of the crystals overcomes these difficulties and predicts conformational polymorph stabilities in good agreement with experiment. These results highlight the need for methods which go beyond current-generation DFT functionals to make crystal polymorph stability predictions truly reliable.
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Affiliation(s)
- Chandler Greenwell
- Department of Chemistry , University of California , Riverside , California 92521 , USA . ; Tel: +1-951-827-7869
| | - Jessica L McKinley
- Department of Chemistry , University of California , Riverside , California 92521 , USA . ; Tel: +1-951-827-7869
| | - Peiyu Zhang
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Qun Zeng
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Guangxu Sun
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Bochen Li
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Shuhao Wen
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Gregory J O Beran
- Department of Chemistry , University of California , Riverside , California 92521 , USA . ; Tel: +1-951-827-7869
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Toader AM, Zarić SD, Zalaru CM, Ferbinteanu M. The Structural Details of Aspirin Molecules and Crystals. Curr Med Chem 2020; 27:99-120. [PMID: 30381068 DOI: 10.2174/0929867325666181031132823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 01/29/2018] [Accepted: 02/06/2018] [Indexed: 11/22/2022]
Abstract
We revisit, in the key of structural chemistry, one of the most known and important drugs: the aspirin. Although apparently simple, the factors determining the molecular structure and supramolecular association in crystals are not trivial. We addressed the problem from experimental and theoretical sides, considering issues from X-ray measurements and results of first-principle reconstruction of molecule and lattices by ab initio calculations. Some puzzling problems can give headaches to specialists and intrigue the general public. Thus, the reported polymorphism of aspirin is disputed, a so-called form II being alleged as a result of misinterpretation. At the same time, were presented evidences that the structure of common form I can be disrupted by domains where the regular packing is changed to the pattern of form II. The problems appear even at the level of independent molecule: the most stable conformation computed by various techniques of electronic structure differs from those encountered in crystals. Because the energy difference between the related conformational isomers (computed as most stable vs. the experimental structure) is small, about 1 kcal/mol, comprised in the error bars of used methods, the unresting question is whether the modelling is imprecise, or the supramolecular factors are mutating the conformational preferences. By a detective following of the issue, the intermolecular effects were made responsible for the conformation of the molecule in crystal. The presented problems were gathered from literature results, debates, glued with modelling and analysis redone by ourselves, in order to secure the unitary view of the considered prototypic topic.
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Affiliation(s)
| | - Snezana D Zarić
- Department of Chemistry, University of Belgrade, Belgrade, Serbia.,Department of Chemistry, Texas A&M University at Qatar, Doha, Qatar
| | - Christina M Zalaru
- Department of Organic Chemistry, Biochemistry and Catalysis, Faculty of Chemistry, University of Bucharest, Bucharest, Romania
| | - Marilena Ferbinteanu
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Bucharest, Bucharest, Romania
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Ruggiero MT, Zeitler JA, Erba A. Intermolecular anharmonicity in molecular crystals: interplay between experimental low-frequency dynamics and quantum quasi-harmonic simulations of solid purine. Chem Commun (Camb) 2017; 53:3781-3784. [DOI: 10.1039/c7cc00509a] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined experimental spectroscopic and theoretical quasi-harmonic investigation of intermolecular anharmonicity in crystalline purine.
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Affiliation(s)
- Michael T. Ruggiero
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Cambridge
- UK
| | - J. Axel Zeitler
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Cambridge
- UK
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Elking DM, Fusti-Molnar L, Nichols A. Crystal structure prediction of rigid molecules. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2016; 72:488-501. [DOI: 10.1107/s2052520616010118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/21/2016] [Indexed: 11/11/2022]
Abstract
A non-polarizable force field based on atomic multipoles fit to reproduce experimental crystal properties andab initiogas-phase dimers is described. The Ewald method is used to calculate both long-range electrostatic and 1/r6dispersion energies of crystals. The dispersion energy of a crystal calculated by a cutoff method is shown to converge slowly to the exact Ewald result. A method for constraining space-group symmetry during unit-cell optimization is derived. Results for locally optimizing 4427 unit cells including volume, cell parameters, unit-cell r.m.s.d. and CPU timings are given for both flexible and rigid molecule optimization. An algorithm for randomly generating rigid molecule crystals is described. Using the correct experimentally determined space group, the average and maximum number of random crystals needed to find the correct experimental structure is given for 2440 rigid single component crystals. The force field energy rank of the correct experimental structure is presented for the same set of 2440 rigid single component crystals assuming the correct space group. A complete crystal prediction is performed for two rigid molecules by searching over the 32 most probable space groups.
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9
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Brandenburg JG, Grimme S. Organic crystal polymorphism: a benchmark for dispersion-corrected mean-field electronic structure methods. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:502-513. [PMID: 27484372 DOI: 10.1107/s2052520616007885] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/13/2016] [Indexed: 06/06/2023]
Abstract
We analyze the energy landscape of the sixth crystal structure prediction blind test targets with various first principles and semi-empirical quantum chemical methodologies. A new benchmark set of 59 crystal structures (termed POLY59) for testing quantum chemical methods based on the blind test target crystals is presented. We focus on different means to include London dispersion interactions within the density functional theory (DFT) framework. We show the impact of pairwise dispersion corrections like the semi-empirical D2 scheme, the Tkatchenko-Scheffler (TS) method, and the density-dependent dispersion correction dDsC. Recent methodological progress includes higher-order contributions in both the many-body and multipole expansions. We use the D3 correction with Axilrod-Teller-Muto type three-body contribution, the TS based many-body dispersion (MBD), and the nonlocal van der Waals density functional (vdW-DF2). The density functionals with D3 and MBD correction provide an energy ranking of the blind test polymorphs in excellent agreement with the experimentally found structures. As a computationally less demanding method, we test our recently presented minimal basis Hartree-Fock method (HF-3c) and a density functional tight-binding Hamiltonian (DFTB). Considering the speed-up of three to four orders of magnitudes, the energy ranking provided by the low-cost methods is very reasonable. We compare the computed geometries with the corresponding X-ray data where TPSS-D3 performs best. The importance of zero-point vibrational energy and thermal effects on crystal densities is highlighted.
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Affiliation(s)
- Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstrasse 4-6, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstrasse 4-6, 53115 Bonn, Germany
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10
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Andersson O, Johari GP. Thermal conductivity of Glycerol's liquid, glass, and crystal states, glass-liquid-glass transition, and crystallization at high pressures. J Chem Phys 2016; 144:064504. [PMID: 26874494 DOI: 10.1063/1.4941335] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To investigate the effects of local density fluctuations on phonon propagation in a hydrogen bonded structure, we studied the thermal conductivity κ of the crystal, liquid, and glassy states of pure glycerol as a function of the temperature, T, and the pressure, p. We find that the following: (i) κcrystal is 3.6-times the κliquid value at 140 K at 0.1 MPa and 2.2-times at 290 K, and it varies with T according to 138 × T(-0.95); (ii) the ratio κliquid (p)/κliquid (0.1 MPa) is 1.45 GPa(-1) at 280 K, which, unexpectedly, is about the same as κcrystal (p)/κcrystal (0.1 MPa) of 1.42 GPa(-1) at 298 K; (iii) κglass is relatively insensitive to T but sensitive to the applied p (1.38 GPa(-1) at 150 K); (iv) κglass-T plots show an enhanced, pressure-dependent peak-like feature, which is due to the glass to liquid transition on heating; (v) continuous heating cold-crystallizes ultraviscous glycerol under pressure, at a higher T when p is high; and (vi) glycerol formed by cooling at a high p and then measured at a low p has a significantly higher κ than the glass formed by cooling at a low p. On heating at a fixed low p, its κ decreases before its glass-liquid transition range at that p is reached. We attribute this effect to thermally assisted loss of the configurational and vibrational instabilities of a glass formed at high p and recovered at low p, which is different from the usual glass-aging effect. While the heat capacity, entropy, and volume of glycerol crystal are less than those for its glass and liquid, κcrystal of glycerol, like its elastic modulus and refractive index, is higher. We discuss these findings in terms of the role of fluctuations in local density and structure, and the relations between κ and the thermodynamic quantities.
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Affiliation(s)
- Ove Andersson
- Department of Physics, Umeå University, 901 87 Umeå, Sweden
| | - G P Johari
- Department of Materials Science and Engineering, McMaster University, Hamilton, Ontario L8S 4L7, Canada
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11
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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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12
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Habgood M, Sugden IJ, Kazantsev AV, Adjiman CS, Pantelides CC. Efficient Handling of Molecular Flexibility in Ab Initio Generation of Crystal Structures. J Chem Theory Comput 2015; 11:1957-69. [DOI: 10.1021/ct500621v] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Matthew Habgood
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Isaac J. Sugden
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrei V. Kazantsev
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Claire S. Adjiman
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Constantinos C. Pantelides
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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14
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A review of the effect of multiple conformers on crystallization from solution and strategies for crystallizing slow inter-converting conformers. Chem Eng Sci 2014. [DOI: 10.1016/j.ces.2013.11.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Baias M, Dumez JN, Svensson PH, Schantz S, Day GM, Emsley L. De novo determination of the crystal structure of a large drug molecule by crystal structure prediction-based powder NMR crystallography. J Am Chem Soc 2013; 135:17501-7. [PMID: 24168679 DOI: 10.1021/ja4088874] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structure of form 4 of the drug 4-[4-(2-adamantylcarbamoyl)-5-tert-butyl-pyrazol-1-yl]benzoic acid is determined using a protocol for NMR powder crystallography at natural isotopic abundance combining solid-state (1)H NMR spectroscopy, crystal structure prediction, and density functional theory chemical shift calculations. This is the first example of NMR crystal structure determination for a molecular compound of previously unknown structure, and at 422 g/mol this is the largest compound to which this method has been applied so far.
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Affiliation(s)
- Maria Baias
- Centre de RMN à Très Hauts Champs, CNRS/ENS-Lyon/UCB Lyon 1, Université de Lyon , 5 rue de la Doua, 69100 Villeurbanne, France
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Baias M, Widdifield CM, Dumez JN, Thompson HPG, Cooper TG, Salager E, Bassil S, Stein RS, Lesage A, Day GM, Emsley L. Powder crystallography of pharmaceutical materials by combined crystal structure prediction and solid-state 1H NMR spectroscopy. Phys Chem Chem Phys 2013; 15:8069-80. [PMID: 23503809 DOI: 10.1039/c3cp41095a] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A protocol for the ab initio crystal structure determination of powdered solids at natural isotopic abundance by combining solid-state NMR spectroscopy, crystal structure prediction, and DFT chemical shift calculations was evaluated to determine the crystal structures of four small drug molecules: cocaine, flutamide, flufenamic acid, and theophylline. For cocaine, flutamide and flufenamic acid, we find that the assigned (1)H isotropic chemical shifts provide sufficient discrimination to determine the correct structures from a set of predicted structures using the root-mean-square deviation (rmsd) between experimentally determined and calculated chemical shifts. In most cases unassigned shifts could not be used to determine the structures. This method requires no prior knowledge of the crystal structure, and was used to determine the correct crystal structure to within an atomic rmsd of less than 0.12 Å with respect to the known reference structure. For theophylline, the NMR spectra are too simple to allow for unambiguous structure selection.
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Affiliation(s)
- Maria Baias
- Université de Lyon, (CNRS/ENS-Lyon/UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
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Kusukawa T, Niwa G, Sasaki T, Oosawa R, Himeno W, Kato M. Observation of a Hydrogen-Bonded 3D Structure of Crystalline Glycerol. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20120300] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Takahiro Kusukawa
- Department of Chemistry and Materials Technology, Graduate School of Engineering, Kyoto Institute of Technology
| | - Genki Niwa
- Kyoto Prefectural Momoyama Senior High School
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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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Kazantsev AV, Karamertzanis PG, Adjiman CS, Pantelides CC. Efficient Handling of Molecular Flexibility in Lattice Energy Minimization of Organic Crystals. J Chem Theory Comput 2011; 7:1998-2016. [DOI: 10.1021/ct100597e] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. V. Kazantsev
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - P. G. Karamertzanis
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - C. S. Adjiman
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - C. C. Pantelides
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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van de Streek J, Neumann MA. Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2010; 66:544-58. [PMID: 20841921 PMCID: PMC2940256 DOI: 10.1107/s0108768110031873] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 08/09/2010] [Indexed: 12/01/2022]
Abstract
The accuracy of a dispersion-corrected density functional theory method is validated against 241 experimental organic crystal structures from Acta Cryst. Section E. This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.
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Affiliation(s)
- Jacco van de Streek
- Avant-garde Materials Simulation, Merzhauser Str. 177, D-79100 Freiburg im Breisgau, Germany.
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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: 196] [Impact Index Per Article: 14.0] [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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Kim S, Orendt AM, Ferraro MB, Facelli JC. Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field. J Comput Chem 2009; 30:1973-85. [PMID: 19130496 DOI: 10.1002/jcc.21189] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential.
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Affiliation(s)
- Seonah Kim
- Center for High Performance Computing, University of Utah, 155 South 1452 East Room 405, Salt Lake City, Utah 84112-0190, USA
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25
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Schön JC, Jansen M. Determination, prediction, and understanding of structures, using the energy landscapes of chemical systems – Part II. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zkri.216.7.361.20362] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
In the past decade, new theoretical approaches have been developed to determine, predict and understand the struc-ture of chemical compounds. The central element of these methods has been the investigation of the energy landscape of chemical systems. Applications range from extended crystalline and amorphous compounds over clusters and molecular crystals to proteins. In this review, we are going to give an introduction to energy landscapes and methods for their investigation, together with a number of examples. These include structure prediction of extended and mo-lecular crystals, structure prediction and folding of proteins, structure analysis of zeolites, and structure determination of crystals from powder diffraction data.
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Mitchell-Koch KR, Matzger AJ. Evaluating Computational Predictions of the Relative Stabilities of Polymorphic Pharmaceuticals. J Pharm Sci 2008; 97:2121-9. [PMID: 17828731 DOI: 10.1002/jps.21127] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The ability of computational methods to describe the relative energies of polymorphic pharmaceuticals is investigated for a diverse array of compounds. The initial molecular geometries were taken from crystal structures, and energy differences between polymorphic pairs were calculated with various geometry optimization methods. Results using molecular mechanics were compared to experimental calorimetric data and periodic density functional theory (DFT) calculations. The best agreement with experimental heats of transition was shown with energies calculated from geometry optimizations using the Compass force field. Calculations that optimized atomic positions with the Compass force field gave correct energy rankings for all 11 polymorphic pairs studied, with an average deviation of 0.61 kcal/mol from experimental results. These findings suggest that computational methods are poised to predict enthalpy differences between polymorphic forms with levels of accuracy that are quite acceptable when proper approaches are employed.
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Affiliation(s)
- Katie R Mitchell-Koch
- Department of Chemistry, Macromolecular Science and Engineering Program, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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29
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Modelling Intermolecular Forces for Organic Crystal Structure Prediction. STRUCTURE AND BONDING 2005. [DOI: 10.1007/b135616] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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30
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Mellot-Draznieks C, Férey G. Assembling molecular species into 3D frameworks: Computational design and structure solution of hybrid materials. PROG SOLID STATE CH 2005. [DOI: 10.1016/j.progsolidstchem.2005.11.047] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Copley RCB, Deprez LS, Lewis TC, Price SL. Computational prediction and X-ray determination of the crystal structures of 3-oxauracil and 5-hydroxyuracil—an informal blind test. CrystEngComm 2005. [DOI: 10.1039/b504756k] [Citation(s) in RCA: 9] [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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Datta S, Grant DJW. Crystal structures of drugs: advances in determination, prediction and engineering. Nat Rev Drug Discov 2004; 3:42-57. [PMID: 14708020 DOI: 10.1038/nrd1280] [Citation(s) in RCA: 292] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sharmistha Datta
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, Minnesota 55455-0343, USA
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Karamertzanis PG, Pantelides CC. Ab initio crystal structure prediction?I. Rigid molecules. J Comput Chem 2004; 26:304-24. [PMID: 15622548 DOI: 10.1002/jcc.20165] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A new methodology for the prediction of molecular crystal structures using only the atomic connectivity of the molecule under consideration is presented. The approach is based on the global minimization of the lattice enthalpy of the crystal. The modeling of the electrostatic interactions is accomplished through a set of distributed charges that are optimally and automatically selected and positioned based on results of quantum mechanical calculations. A four-step global optimization algorithm is used for the identification of the local minima of the lattice enthalpy surface. A parallelized implementation of the algorithm permits a much more extensive search of the solution space than has hitherto been possible, allowing the identification of crystal structures in less frequently occurring space groups and with more than one molecule in the asymmetric unit. The algorithm has been applied successfully to the prediction of the crystal structures of 3-aza-bicyclo(3.3.1)nonane-2,4-dione (P2(1)/a, Z' = 1), allopurinol (P2(1)/c, Z' = 1), 1,3,4,6,7,9-hexa-azacycl(3.3.3)azine (Pbca, Z' = 2), and triethylenediamine (P6(3)/m, Z' = 1). In all cases, the experimentally known structure is among the most stable predicted structures, but not necessarily the global minimum.
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Affiliation(s)
- Panagiotis G Karamertzanis
- Centre for Process Systems Engineering, Department of Chemical Engineering and Chemical Technology, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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Van Eijck BP. Crystal structure predictions using five space groups with two independent molecules. The case of small organic acids. J Comput Chem 2002; 23:456-62. [PMID: 11908081 DOI: 10.1002/jcc.10042] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Crystal structure generations with two independent molecules have been performed for a series of carboxylic acids, using a slightly modified version of the OPLS force field. It was found that in this way the experimental structures with one independent molecule were produced as special cases, except for the molecules with four or more internal degrees of freedom. This work shows that a search with two independent molecules in only five space groups, although costly in computer power, can automatically also find structures with one independent molecule in many supergroups. Considering the observed abundances of structural classes, such a search should cover more than 95% of the possible homomolecular crystal structures.
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Affiliation(s)
- Bouke P Van Eijck
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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Xu Z, Lee S, Lobkovsky EB, Kiang YH. Structure rationalization and topology prediction of two-distinct-component organic crystals: the role of volume fraction and interface topology. J Am Chem Soc 2002; 124:121-35. [PMID: 11772069 DOI: 10.1021/ja0115518] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We consider here small-length-scale crystal structures with two clearly different molecular components (e.g., hydrophobic and hydrophilic). Using a perspective developed by studies on large-length-scale block copolymers and liquid crystals, we focus on the crystalline interface between the two components. We examine four types of two-component crystals: aromatic ammonium carboxylates, aromatic oligo(ethylene oxides), cyclohexylammonium carboxylates, and ether-thioether compounds. Of the 111 crystal structures found in the Cambridge Structure Database (CSD), 108 adopt one of the five generic topologies found in diblock copolymers: spheres, columns, perforated layers, layers, and bicontinuous structures. As in diblock copolymers, a key factor controlling the interfacial topology is shown to be the volume ratio of the two components. When the volume fraction of one component is less than 30% of the whole, more than five-sixths of the examined crystal structures are of columnar or spherical type. For volume fractions between 40 and 50% more than three-quarters are of lamellar or bicontinuous type. We use this model to predict the topologies of small-length-scale two-component crystals. We predict the crystal topolgies of six new crystal structures: three are predicted to be columnar, and the other three, lamellar or bicontinuous. The crystal structures of these systems were then determined by single-crystal X-ray methods. Five of the structures form in topologies consistent with the predictions: three in columns and two in layers. The remaining one forms as a perforated layer instead of the predicted columnar structure. Such predictive accuracy is consistent with the statistics of the CSD investigation.
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Affiliation(s)
- Zhengtao Xu
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853-1301, USA
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van Eijck BP, Mooij WTM, Kroon J. Crystal Structure Prediction for Six Monosaccharides Revisited. J Phys Chem B 2001. [DOI: 10.1021/jp012366j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bouke P. van Eijck
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Accelrys Ltd., 230/250 The Quorum, Barnwell Road, Cambridge CB5 8RE, England
| | - Wijnand T. M. Mooij
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Accelrys Ltd., 230/250 The Quorum, Barnwell Road, Cambridge CB5 8RE, England
| | - Jan Kroon
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Accelrys Ltd., 230/250 The Quorum, Barnwell Road, Cambridge CB5 8RE, England
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Beyer T, Lewis T, Price SL. Which organic crystal structures are predictable by lattice energy minimisation? CrystEngComm 2001. [DOI: 10.1039/b108135g] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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van Eijck BP. Ab initio crystal structure predictions for flexible hydrogen-bonded molecules. Part III. Effect of lattice vibrations. J Comput Chem 2001. [DOI: 10.1002/jcc.1047] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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39
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van Eijck BP, Mooij WTM, Kroon J. Ab initio crystal structure predictions for flexible hydrogen-bonded molecules. Part II. Accurate energy minimization. J Comput Chem 2001. [DOI: 10.1002/jcc.1046] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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