Jacco van de Streek

Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures

The program Mercury, developed by the Cambridge Crystallographic Data Centre, is designed primarily as a crystal structure visualization tool. A new module of functionality has been produced, called the Materials Module, which allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns. This new module also includes the ability to perform packing similarity calculations between structures containing the same compound. In addition to the Materials Module, a range of further enhancements to Mercury has been added in this latest release, including void visualization and links to ConQuest, Mogul and IsoStar.

Mercury: visualization and analysis of crystal structures

Since its original release, the popular crystal structure visualization program Mercury has undergone continuous further development. Comparisons between crystal structures are facilitated by the ability to display multiple structures simultaneously and to overlay them. Improvements have been made to many aspects of the visual display, including the addition of depth cueing, and highly customizable lighting and background effects. Textual and numeric data associated with structures can be shown in tables or spreadsheets, the latter opening up new ways of interacting with the visual display. Atomic displacement ellipsoids, calculated powder diffraction patterns and predicted morphologies can now be shown. Some limited molecular-editing capabilities have been added. The object-oriented nature of the C++ libraries underlying Mercury makes it easy to re-use the code in other applications, and this has facilitated three-dimensional visualization in several other programs produced by the Cambridge Crystallographic Data Centre.

DASH : a program for crystal structure determination from powder diffraction data

DASH is a user-friendly graphical-user-interface-driven computer program for solving crystal structures from X-ray powder diffraction data, optimized for molecular structures. Algorithms for multiple peak fitting, unit-cell indexing and space-group determination are included as part of the program. Molecular models can be read in a number of formats and automatically converted to Z-matrices in which flexible torsion angles are automatically identified. Simulated annealing is used to search for the global minimum in the space that describes the agreement between observed and calculated structure factors. The simulated annealing process is very fast, which in part is due to the use of correlated integrated intensities rather than the full powder pattern. Automatic minimization of the structures obtained by simulated annealing and automatic overlay of solutions assist in assessing the reproducibility of the best solution, and therefore in determining the likelihood that the global minimum has been obtained.

Significant progress in predicting the crystal structures of small organic molecules – a report on the fourth blind test

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.

Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test

The results of the fifth blind test of crystal structure prediction, which show important success with more challenging large and flexible molecules, are presented and discussed.

Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations

The accuracy of a dispersion-corrected density functional theory method is validated against 241 experimental organic crystal structures from Acta Cryst. Section E.

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

The accuracy of 215 experimental organic crystal structures from powder diffraction data is validated against a dispersion-corrected density functional theory method.

Searching the Cambridge Structural Database for the `best' representative of each unique polymorph

A computer program has been written that removes suspicious crystal structures from the Cambridge Structural Database and clusters the remaining crystal structures as polymorphs or redeterminations. For every set of redeterminations, one crystal structure is selected to be the best representative of that polymorph. The results, 243 355 well determined crystal structures grouped by unique polymorph, are presented and analysed.

Ligand flexibility and framework rearrangement in a new family of porous metal–organic frameworks

Ligand flexibility permits framework rearrangement upon evacuation and gas uptake in a new family of porous MOFs.

The Thermodynamically Stable Form of Solid Barbituric Acid: The Enol Tautomer

Barbituric acid, which has been known since 1863, is drawn in textbooks always as the keto tautomeric form 1 (Scheme 1). Indeed, this is the most stable form in the gas phase and in solution. Also in the solid state, the keto tautomer is observed in the metastable phase I, the commercial phase II, and a high-temperature phase III, as well as in its dihydrates. In contrast, we now observe that the recently discovered tautomeric polymorph IV consists of molecules in the enol form 2, and that this polymorph is actually the thermodynamically stable phase at ambient conditions. The preference for the enol form in the solid state is explained by the formation of an additional strong hydrogen bond in the crystal, leading to a more favorable lattice energy. Polymorph IV is obtained from phase II by grinding or milling. Solid-state NMR (SSNMR), IR, and Raman experiments revealed this to be a tautomeric polymorph, which does not consist of the keto tautomer 1, but of one of the enol forms. The spectroscopic data suggested the trienol tautomer, but other enol tautomers could not be ruled out. All attempts to obtain single crystals of phase IV by recrystallization failed, and dehydration of the dihydrate yielded only phase II. The grinding or milling processes resulted in powders of poor crystallinity. However, it was possible to index the laboratory X-ray powder data and to solve the crystal structure by simulated annealing, while refinement was carried out by the Rietveld method from synchrotron data (Figure 1). The bond lengths in the OCN framework revealed phase IV to consist of molecules in the enol form 2. Scheme 1. Barbituric acid in the keto (1) and enol (2) tautomeric forms.