In-house time-resolved photocrystallography on the millisecond timescale using a gated X-ray hybrid pixel area detector.

With the remarkable progress of accelerator-based X-ray sources in terms of intensity and brightness, the investigation of structural dynamics from time-resolved X-ray diffraction methods is becoming widespread in chemistry, biochemistry and materials science applications. Diffraction patterns can now be measured down to the femtosecond time-scale using X-ray free electron lasers or table-top laser plasma X-ray sources. On the other hand, the recent developments in photon counting X-ray area detectors offer new opportunities for time-resolved crystallography. Taking advantage of the fast read-out, the internal stacking of recorded images, and the gating possibilities (electronic shutter) of the XPAD hybrid pixel detector, we implemented a laboratory X-ray diffractometer for time-resolved single-crystal X-ray diffraction after pulsed laser excitation, combined with transient optical absorption measurement. The experimental method and instrumental setup are described in detail, and validated using the photoinduced nitrosyl linkage isomerism of sodium nitroprusside, Na2[Fe(CN)5NO]·2H2O, as proof of principle. Light-induced Bragg intensity relative variations ΔI(hkl)/I(hkl) of the order of 1%, due to the photoswitching of the NO ligand, could be detected with a 6 ms acquisition window. The capabilities of such a laboratory time-resolved experiment are critically evaluated.

Crystal structures of increasingly large molecules: meeting the challenges with CRYSTALS software.

BACKGROUND: The size and complexity of molecules being studied by single crystal diffraction is growing year by year, resulting in an increase in the difficulties encountered during structure determination. From the crystallisation itself and sample handling, to structure solution and refinement, specific problems due to larger molecules are discussed. RESULTS: During refinement, several methods are available to deal with the problems encountered with large structures within the software Crystals. Hydrogens atoms can neither be found easily nor refined freely, but restraints can be applied automatically. Special scattering factors can be used to model complex disorder. Finally chemical information can be included in the form of restraints in order to help the determination of a good model. Multicollinearity problems are more likely in the refinement of large structures; to some extent more precise and accurate algorithms can help. Also, if the global minimum is less well defined, faster refinement enables more cycles to be carried out, a necessity for good convergence. The efficiency of the algorithms in Crystals have been increased to help address these issues. CONCLUSIONS: Thus, crystal structures are getting larger and their complexity is increasing. Recent developments in precision and speed during the least squares in Crystals is helping the structural scientist to deal with larger structures more efficiently.

XPAD X-ray hybrid pixel detector for charge density quality diffracted intensities on laboratory equipment.

The new generation of X-ray detectors, the hybrid pixel area detectors or `pixel detectors', is based on direct detection and single-photon counting processes. A large linearity range, high dynamic and extremely low noise leading to an unprecedented high signal-to-noise ratio, fast readout time (high frame rates) and an electronic shutter are among their intrinsic characteristics which render them very attractive. First used on synchrotron beamlines, these detectors are also promising in the laboratory, in particular for pump-probe or quasi-static experiments and accurate electron density measurements, as explained in this paper. An original laboratory diffractometer made from a Nonius Mach3 goniometer equipped with an Incoatec Mo microsource and an XPAD pixel area detector has been developed at the CRM2 laboratory. Mo Kα accurate charge density quality data up to 1.21 Å(-1) resolution have been collected on a sodium nitroprusside crystal using this home-made diffractometer. Data quality for charge density analysis based on multipolar modelling are discussed in this paper. Deformation electron densities are compared to those already published (based on data collected with CCD APEXII and CAD4 diffractometers).

Linear transformations of variance/covariance matrices.

Many applications in crystallography require the use of linear transformations on parameters and their standard uncertainties. While the transformation of the parameters is textbook knowledge, the transformation of the standard uncertainties is more complicated and needs the full variance/covariance matrix. For the transformation of second-rank tensors it is suggested that the 3 × 3 matrix is re-written into a 9 × 1 vector. The transformation of the corresponding variance/covariance matrix is then straightforward and easily implemented into computer software. This method is applied in the transformation of anisotropic displacement parameters, the calculation of equivalent isotropic displacement parameters, the comparison of refinements in different space-group settings and the calculation of standard uncertainties of eigenvalues.

Temperature-dependent analysis of thermal motion, disorder and structures of tris(ethylenediamine)zinc(II) sulfate and tris(ethylenediamine)copper(II) sulfate.

The crystal structures of the title compounds have been determined in the temperature range 140-290 K for the zinc complex, and 190-270 K for the copper complex. The two structures are isostructural in the trigonal space group P31c with the sulfate anion severely disordered on a site with 32 (D(3)) symmetry. This sulfate disorder leads to a disordered three-dimensional hydrogen-bond network, with the N-H atoms acting as donors and the sulfate O atoms as acceptors. The displacement parameters of the N and C atoms in both compounds contain disorder contributions in the out-of-ligand plane direction owing to ring puckering and/or disorder in hydrogen bonding. In the Zn compound the vibrational amplitudes in the bond directions are closely similar. Their differences show no significant deviations from rigid-bond behaviour. In the Cu compound, a (presumably) dynamic Jahn-Teller effect is identified from a temperature-independent contribution to the displacement ellipsoids of the N atom along the N-Cu bond. These conclusions derive from analyses of the atomic displacement parameters with the Hirshfeld test, with rigid-body models at different temperatures, and with a normal coordinate analysis. This analysis considers the atomic displacement parameters (ADPs) from all different temperatures simultaneously and provides a detailed description of both the thermal motion and the disorder in the cation. The Jahn-Teller radii of the Cu compound derived on the basis of the ADP analysis and from the bond distances in the statically distorted low-temperature phase [Lutz (2010). Acta Cryst. C66, m330-m335] are found to be the same.

The effect of pressure on the crystal structure of [Gd(PhCOO)3(DMF)]n to 3.7 GPa and the transition to a second phase at 5.0 GPa.

The effect of pressure on the crystal structure of the coordination polymer [Gd(PhCOO)(3)(DMF)](n) has been studied to 5.0 GPa. At ambient pressure the structure is tetragonal (space group P4(2)/n) with the polymers extending along the c-direction of the unit cell; successive Gd atoms are alternately bridged by four benzoates and by two benzoates; the coordination spheres of the metal atoms are completed by DMF ligands. This results in two different Gd...Gd repeats, measuring 3.8953(3) and 5.3062(3) A, respectively. The polymer chains interact with each other via dispersion interactions, including a number of CH...pi contacts to phenyl rings in which the H...ring-centroid distances are 3.19 to 3.28 A. Up to 3.7 GPa the crystal remains in a compressed form of its ambient-pressure phase. The a-axis shortens by 7.7%, and the c-axis by 2.9%, the difference reflecting the greater ease of compression along the crystallographic directions mediated by weak intermolecular interactions. At ambient pressure the Gd-O distances span 2.290(2)-2.559(2) A, with an average of 2.39(3) A. At 3.7 GPa the corresponding parameters are 2.259(3) to 2.509(4) and 2.36(3) A. The Gd...Gd distances shortened by 0.0467(4) and 0.1851(4) A, and the CH...pi distances span the range 2.76-2.90 A. During compression a number of H...H contacts develop, the shortest measuring 1.84 A at 3.7 GPa. On increasing the pressure to 5.0 GPa a phase transition occurred in which the shortest H...H contact is relieved by conversion of an edge-to-edge phenyl-phenyl contact into a pi...pi stacking interaction. The new phase is also tetragonal, space group P4, the inversion symmetry present in phase-I being lost in phase-II. The phase transition allows more efficient packing of ligands, and while the a-axis decreases in length the c-axis increases. This leads to Gd...Gd distances of 3.8373(4) and 5.3694(4) A, the latter being longer than at ambient pressure. Gd-O distances at 5.0 GPa span the range 2.265(5) to 2.516(5) A, with a mean of 2.36(2) A.

Pressure-induced Jahn-Teller switching in a Mn12 nanomagnet.

Pressure-induced switching of a fast-relaxing single-molecule magnet to a slow-relaxing isomer is observed for the first time by using a combination of high pressure single-crystal X-ray diffraction and high pressure magnetic measurements.

catena-Poly[[bis-(ethyl-enediamine)copper(II)]-µ-sulfato].

In the title compound, [Cu(SO(4))(C(2)H(8)N(2))(2)](n), the Cu, S and two O atoms lie on a mirror plane. The Cu atom is in a distorted octa-hedral environment and the ethyl-enediamine ligand is in a gauche conformation. The sulfate dianion is bridging, forming a one-dimensional chain. A two-dimensional net parallel to (001) is generated by N-H⋯O hydrogen bonding between the chains.