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Crystal Structure Prediction (crystal + structure_prediction)
Selected AbstractsCrystal structure prediction of organic pigments: quinacridone as an exampleJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2007N. Panina The structures of the ,, , and , polymorphs of quinacridone (Pigment Violet 19) were predicted using Polymorph Predictor software in combination with X-ray powder diffraction patterns of limited quality. After generation and energy minimization of the possible structures, their powder patterns were compared with the experimental ones. On this basis, candidate structures for the polymorphs were chosen from the list of all structures. Rietveld refinement was used to validate the choice of structures. The predicted structure of the , polymorph is in accordance with the experimental structure published previously. Three possible structures for the , polymorph are proposed on the basis of X-ray powder patterns comparison. It is shown that the , structure in the Cambridge Structural Database is likely to be in error, and a new , structure is proposed. The present work demonstrates a method to obtain crystal structures of industrially important pigments when only a low-quality X-ray powder diffraction pattern is available. [source] Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2009Seonah Kim 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. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Crystal structure prediction for eniluracilJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 8 2001Mark Sacchetti Abstract State-of-the-art molecular modeling tools were used to predict the crystal structure of eniluracil, a compound for which it has not been possible to grow a single crystal. Two methods were used, one that incorporates molecular structure and powder X-ray diffraction data and another that employs molecular structure and lattice energy calculations into the search algorithm. Two structures were identified, one with P21/c and the other with P21 symmetry, both of which are consistent with the infrared and Raman spectra. A detailed analysis of the simulated and experimental powder X-ray diffraction patterns indicates that the P21/c structure is the best representation of the crystal structure. © 2001 Wiley-Liss, Inc. and the American Pharmaceutical Association J Pharm Sci 90:1049,1055, 2001 [source] Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2009Seonah Kim 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. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] The lines-of-force landscape of interactions between molecules in crystals; cohesive versus tolerant and `collateral damage' contactACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2010Angelo Gavezzotti A quantitative analysis of relative stabilities in organic crystal structures is possible by means of reliable calculations of interaction energies between pairs of molecules. Such calculations have been performed by the PIXEL method for 1108 non-ionic and 98 ionic organic crystals, yielding total energies and separate Coulombic polarization and dispersive contributions. A classification of molecule,molecule interactions emerges based on pair energy and its first derivative, the interaction force, which is estimated here explicitly along an approximate stretching path. When molecular separation is not at the minimum-energy value, as frequently happens, forces may be attractive or repulsive. This information provides a fine structural fingerprint and may be relevant to the mechanical properties of materials. The calculations show that the first coordination shell includes destabilizing contacts in ,,9% of crystal structures for compounds with highly polar chemical groups (e.g. CN, NO2, SO2). Calculations also show many pair contacts with weakly stabilizing (neutral) energies; such fine modulation is presumably what makes crystal structure prediction so difficult. Ionic organic salts or zwitterions, including small peptides, show a Madelung-mode pairing of opposite ions where the total lattice energy is stabilized from sums of strongly repulsive and strongly attractive interactions. No obvious relationships between atom,atom distances and interaction energies emerge, so analyses of crystal packing in terms of geometrical parameters alone should be conducted with due care. [source] Significant progress in predicting the crystal structures of small organic molecules , a report on the fourth blind testACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2009Graeme M. Day We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee. Three predictions were allowed for each system. The results demonstrate a dramatic improvement in rates of success over previous blind tests; in total, there were 13 successful predictions and, for each of the four targets, at least two groups correctly predicted the observed crystal structure. The successes include one participating group who correctly predicted all four crystal structures as their first ranked choice, albeit at a considerable computational expense. The results reflect important improvements in modelling methods and suggest that, at least for the small and fairly rigid types of molecules included in this blind test, such calculations can be constructively applied to help understand crystallization and polymorphism of organic molecules. [source] Blind crystal structure prediction of a novel second polymorph of 1-hydroxy-7-azabenzotriazoleACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2006Harriott Nowell The commercially available peptide coupling reagent 1-hydroxy-7-azabenzotriazole has been shown to crystallize in two polymorphic forms. The two polymorphs differ in their hydrogen-bonding motif, with form I having an (10) dimer motif and form II having a C(5) chain motif. The previously unreported form II was used as an informal blind test of computational crystal structure prediction for flexible molecules. The crystal structure of form II has been successfully predicted blind from lattice-energy minimization calculations following a series of searches using a large number of rigid conformers. The structure for form II was the third lowest in energy with form I found as the global minimum, with the energy calculated as the sum of the ab initio intramolecular energy penalty for conformational distortion and the intermolecular lattice energy which is calculated from a distributed multipole representation of the charge density. The predicted structure was sufficiently close to the experimental structure that it could be used as a starting model for crystal structure refinement. A subsequent limited polymorph screen failed to yield a third polymorphic form, but demonstrated that alcohol solvents are implicated in the formation of the form I dimer structure. [source] Ab initio crystal structure predictions for flexible hydrogen-bonded molecules.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2001Part III. Abstract In crystal structure predictions possible structures are usually ranked according to static energy. Here, this criterion has been replaced by the free energy at any temperature. The effects of harmonic lattice vibrations were found by standard lattice-dynamical calculations, including a rough estimate of the effects of thermal expansion. The procedure was tested on glycol and glycerol, for which accurate static energies had been obtained previously (Part II of this series). It was found that entropy and zero-point energy give the largest contribution to free energy differences between hypothetical crystal structures, adding up to about 3 kJ/mol for the structures with lowest energy. The temperature-dependent contribution to the energy and the effects of thermal expansion showed less variation among the structures. The overall accuracy in relative energies was estimated to be a few kJ/mol. The experimental crystal structure for glycol corresponded to the global free energy minimum, whereas for glycerol it ranked second at 1 kJ/mol. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 816,826, 2001 [source] Experimental and predicted crystal structures of Pigment Red 168 and other dihalogenated anthanthronesACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2010Martin U. Schmidt The crystal structures of 4,10-dibromo-anthanthrone (Pigment Red 168; 4,10-dibromo-dibenzo[def,mno]chrysene-6,12-dione), 4,10-dichloro- and 4,10-diiodo-anthanthrone have been determined by single-crystal X-ray analyses. The dibromo and diiodo derivatives crystallize in P21/c, Z = 2, the dichloro derivative in , Z = 1. The molecular structures are almost identical and the unit-cell parameters show some similarities for all three compounds, but the crystal structures are neither isotypic to another nor to the unsubstituted anthanthrone, which crystallizes in P21/c, Z = 8. In order to explain why the four anthanthrone derivatives have four different crystal structures, lattice-energy minimizations were performed using anisotropic atom,atom model potentials as well as using the semi-classical density sums (SCDS-Pixel) approach. The calculations showed the crystal structures of the dichloro and the diiodo derivatives to be the most stable ones for the corresponding compound; whereas for dibromo-anthanthrone the calculations suggest that the dichloro and diiodo structure types should be more stable than the experimentally observed structure. An experimental search for new polymorphs of dibromo-anthanthrone was carried out, but the experiments were hampered by the remarkable insolubility of the compound. A metastable nanocrystalline second polymorph of the dibromo derivative does exist, but it is not isostructural to the dichloro or diiodo compound. In order to determine the crystal structure of this phase, crystal structure predictions were performed in various space groups, using anisotropic atom,atom potentials. For all low-energy structures, X-ray powder patterns were calculated and compared with the experimental diagram, which consisted of a few broad lines only. It turned out that the crystallinity of this phase was not sufficient to determine which of the calculated structures corresponds to the actual structure of this nanocrystalline polymorph. [source] | ||||||||||