Polymorphism of 7-dimethylaminocyclopenta[c]coumarin: packing analysis and generation of trial crystal structures

1996 ◽  
Vol 52 (1) ◽  
pp. 201-208 ◽  
Author(s):  
A. Gavezzotti
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
Acta Cryst ◽  
Structure Generation ◽  
Space Groups ◽  
Energy Hypersurface ◽  
Packing Analysis ◽  
Potential Energy Hypersurface

The crystal structures of two polymorphs of the title compound [Pbca and Pna21; Jasinski & Woudenberg (1995). Acta Cryst. C51, 107–109] were analysed. Packing energies and indices were compared. Molecules in the two forms show a slight conformational difference; both conformers were packed in some of the most frequent space groups for organic molecules (P21, P21/c, P212121 and Pna21) using a computer program for crystal structure generation and prediction (PROMET3). The results of such calculations are used to provide tentative explanations for the preference of the two conformers for centrosymmetric and non-centrosymmetric space groups. Several comments on general problems encountered in crystal structure prediction are also presented, concerning in particular the multi-minima structure of the potential energy hypersurface.

scholarly journals Crystal structures of two furazidin polymorphs revealed by a joint effort of crystal structure prediction and NMR crystallography

2020 ◽  
Vol 76 (3) ◽  
pp. 322-335 ◽  
Author(s):  
Marta K. Dudek ◽  
Piotr Paluch ◽  
Edyta Pindelska
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Determination ◽  
Structure Prediction ◽  
Structural Features ◽  
Crystal Structure Determination ◽  
Crystal Structure Prediction ◽  
Crystal Forms ◽  
Space Groups ◽  
Nmr Crystallography

This work presents the crystal structure determination of two elusive polymorphs of furazidin, an antibacterial agent, employing a combination of crystal structure prediction (CSP) calculations and an NMR crystallography approach. Two previously uncharacterized neat crystal forms, one of which has two symmetry-independent molecules (form I), whereas the other one is a Z′ = 1 polymorph (form II), crystallize in P21/c and P 1 space groups, respectively, and both are built by different conformers, displaying different intermolecular interactions. It is demonstrated that the usage of either CSP or NMR crystallography alone is insufficient to successfully elucidate the above-mentioned crystal structures, especially in the case of the Z′ = 2 polymorph. In addition, cases of serendipitous agreement in terms of 1H or 13C NMR data obtained for the CSP-generated crystal structures different from the ones observed in the laboratory (false-positive matches) are analyzed and described. While for the majority of analyzed crystal structures the obtained agreement with the NMR experiment is indicative of some structural features in common with the experimental structure, the mentioned serendipity observed in exceptional cases points to the necessity of caution when using an NMR crystallography approach in crystal structure determination.

scholarly journals Exploration and Optimization in Crystal Structure Prediction: Combining Basin Hopping with Quasi-Random Sampling

2020 ◽  
Author(s):  
Shiyue Yang ◽  
Graeme Day
Keyword(s):  
Crystal Structure ◽  
Random Sampling ◽  
Structure Prediction ◽  
Molecular Crystals ◽  
Optimization Procedure ◽  
Low Energy ◽  
Random Structure ◽  
Crystal Structure Prediction ◽  
Structure Generation ◽  
Basin Hopping

We describe the implementation of a Monte Carlo basin hopping global optimization procedure for the prediction of molecular crystal structure. The basin hopping method is combined with quasi-random structure generation in a hybrid method for crystal structure prediction, QR-BH, which combines the low-discrepancy sampling provided by quasi-random sequences with basin hopping's efficiency at locating low energy structures. Through tests on a set of single-component molecular crystals and co-crystals, we demonstrate that QR-BH provides faster location of low energy structures than pure quasi-random sampling, while maintaining the efficient location of higher energy structures that are important for identifying important polymorphs.

scholarly journals First-year experience with fully automated crystal structure prediction

2014 ◽  
Vol 70 (a1) ◽  
pp. C1618-C1618
Author(s):  
Marcus Neumann ◽  
Bernd Doser
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Density Functional ◽  
Method Development ◽  
Force Fields ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Structure Generation ◽  
Statistical Correlations ◽  
Pharmaceutical Molecules

With improving hardware and software performance, usability has become one of the main obstacles to a more widespread use of Crystal Structure Prediction (CSP) with the GRACE program. In terms of method development, important milestones had already been passed by the time of the 5th blind test [1] in 2010, including the parameterization of dispersion-corrected Density Functional Theory (DFT-D) [2], the generation of tailor-made force fields from ab-initio reference data [3], a Monte-Carlo parallel tempering crystal structure generation engine and a DFT-d reranking procedure exploiting statistical correlations. These components have now been incorporated in automated data flow processes that remove the burden of scores of expert decisions from the user. Summarizing the results of CSP studies performed with the new Force Field Factory and CSP Factory modules throughout a year, the current performance of CSP is critically assessed and further method development needs are pinpointed. Studied compounds include 20 small molecules with competing hydrogen bonds motifs, 4 mono-hydrates of non-ionic molecules and the hydrates and chloride salts of several amino acids. The ability to handle flexible pharmaceutical molecules is demonstrated by a validation study on aripiprazole with one and two molecules per asymmetric unit. Salient features of the energy landscapes of other pharmaceutical molecules are discussed. Statistics are presented for the accuracy of tailor-made force fields, and the energy ranking performance of several DFT-d flavors is compared.

scholarly journals Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

2017 ◽  
Vol 8 (7) ◽  
pp. 4926-4940 ◽  
Author(s):  
Alexander G. Shtukenberg ◽  
Qiang Zhu ◽  
Damien J. Carter ◽  
Leslie Vogt ◽  
Johannes Hoja ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Structure Prediction ◽  
Prediction Method ◽  
Crystal Structure Prediction ◽  
Free Energies ◽  
Structure Prediction Method

Crystal structures of four new coumarin polymorphs were solved by crystal structure prediction method and their lattice and free energies were calculated by advanced techniques.

Molecular packing groups and ab initio crystal-structure prediction

1999 ◽  
Vol 55 (4) ◽  
pp. 621-627 ◽  
Author(s):  
Daquan Gao ◽  
Donald E. Williams
Keyword(s):  
Crystal Structure ◽  
Ab Initio ◽  
Energy Minimization ◽  
Structure Prediction ◽  
Group Symmetry ◽  
Crystal Structure Prediction ◽  
Asymmetric Unit ◽  
Efficient Procedure ◽  
Space Groups ◽  
Independent Molecules

Ab initio crystal structure prediction can proceed by minimization of the packing energy of Z independent molecules per cell, or alternatively by energy minimization taking one molecule as independent and Z-1 molecules as related by assumed space-group symmetry. In the former method, a large number of positional variables must be considered. In the latter method, a large number of space groups must be considered. An alternative, more efficient, procedure is proposed, where it is recognized that values of Z and the number of molecules in the asymmetric unit, Z′, impose restrictions on possible space groups. Examples of application of this method to crystal structure prediction are given.

scholarly journals Exploration and Optimization in Crystal Structure Prediction: Combining Basin Hopping with Quasi-Random Sampling

2020 ◽  
Author(s):  
Shiyue Yang ◽  
Graeme Day
Keyword(s):  
Crystal Structure ◽  
Random Sampling ◽  
Structure Prediction ◽  
Molecular Crystals ◽  
Optimization Procedure ◽  
Low Energy ◽  
Random Structure ◽  
Crystal Structure Prediction ◽  
Structure Generation ◽  
Basin Hopping

We describe the implementation of a Monte Carlo basin hopping global optimization procedure for the prediction of molecular crystal structure. The basin hopping method is combined with quasi-random structure generation in a hybrid method for crystal structure prediction, QR-BH, which combines the low-discrepancy sampling provided by quasi-random sequences with basin hopping's efficiency at locating low energy structures. Through tests on a set of single-component molecular crystals and co-crystals, we demonstrate that QR-BH provides faster location of low energy structures than pure quasi-random sampling, while maintaining the efficient location of higher energy structures that are important for identifying important polymorphs.

scholarly journals Nicotinamide: Seven New Polymorphic Structures Revealed by Melt Crystallization and Crystal Structure Prediction

2020 ◽  
Author(s):  
Xizhen Li ◽  
Xiao Ou ◽  
Bingquan Wang ◽  
Haowei Rong ◽  
Bing Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
Melt Crystallization ◽  
Efficient Tool ◽  
Single Crystal Structures ◽  
Solution Crystallization

<p>Here, we reported nicotinamide (NIC), a long-known vitamin, was revealed in fact to be a highly polymorphic compound with nine solved single-crystal structures by performing melt crystallization. A CSP calculation successfully identified all six Z’ = 1 and 2 experimental structures. Melt crystallization has turned out to be an efficient tool for exploring polymorphic landscape, especially in regions inaccessbile by solution crystallization.</p>

COMPACK: a program for identifying crystal structure similarity using distances

2005 ◽  
Vol 38 (1) ◽  
pp. 228-231 ◽  
Author(s):  
James Alexander Chisholm ◽  
Sam Motherwell
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Structural Features ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Interatomic Distances ◽  
Structure Similarity ◽  
Measure Of Similarity ◽  
Orientation Of Molecules

A method is presented for comparing crystal structures to identify similarity in molecular packing environments. The relative position and orientation of molecules is captured using interatomic distances, which provide a representation of structure that avoids the use of space-group and cell information. The method can be used to determine whether two crystal structures are the same to within specified tolerances and can also provide a measure of similarity for structures that do not match exactly, but have structural features in common. Example applications are presented that include the identification of an experimentally observed crystal structure from a list of predicted structures and the process of clustering a list of predicted structures to remove duplicates. Examples are also presented to demonstrate partial matching. Such searches were performed to analyse the results of the third blind test for crystal structure prediction, to identify the frequency of occurrence of a characteristic layer and a characteristic hydrogen-bonded chain.

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