Capecitabine from X-ray powder synchrotron data

Direct-space solution in theEXPOpackage: the combination of the HBB–BC algorithm with GRASP

The hybrid big bang–big crunch algorithm is a combination of a global optimization algorithm inspired by one of the theories of the evolution of the universe, named the big bang and big crunch theory, and the simulated annealing method. The procedure was implemented in the latest version of the programEXPOand applied to crystal-structure solution from powder diffraction data. Several aspects of the hybrid big bang–big crunch algorithm can be further optimized with the aim of obtaining good quality solutions in a shorter computation time. In the present study, the hybrid big bang–big crunch procedure has been combined with the greedy randomized adaptive search procedure (GRASP) and some steps of the algorithm have been improved. The new approach, implemented in theEXPOpackage, has been successfully tested on numerous known crystal structures.

Multinuclear NMR Measurements and DFT Calculations for Capecitabine Tautomeric Form Assignment in a Solution

The molecular structure of capecitabine (a widely applied prodrug of 5-fluorouracil) was studied by multinuclear NMR measurements and DFT quantum mechanical calculations. One or two tautomeric forms in a solution were detected depending on the solvent used. In the organic solvents, a mixture of two forms of capecitabine was observed: carbamate and imine tautomers. In the aqueous solution, only the carbamate form was found. The methylation of capecitabine yields mainly two products in different proportions: N³-methylcapecitabine and N⁷-methylcapecitabine. The protonation of capecitabine in organic solvents with perchloric acid occurs at the N3 nitrogen atom. DFT calculations strongly support the results coming from the analysis of the NMR spectra.

Erratum: Capecitabine from X-ray powder synchrotron data. Corrigendum

Erratum to Acta Cryst. (2009), E65, o1325–o1326.

In the paper by Rohlicek et al. [Acta Cryst. (2009), E65, o1325–o1326], one H atom was placed incorrectly.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

The hybrid big bang–big crunch method for solving crystal structure from powder diffraction data

The big bang–big crunch method is a global optimization approach developed upon the analogy of one of the cosmological theories of the evolution of the universe. It has been suitably combined with a simulated annealing algorithm and used for solving crystal structure from powder diffraction data in direct space. When compared with the traditional simulated annealing method, it provides a significant advance: good solutions are attained in a shorter time. The new method has been implemented in theEXPOpackage. Its successful application is demonstrated with examples of already known structures.