Hans-Beat Bürgi

Definitive Molecular Level Characterization of Defects in UiO‐66 Crystals

The identification and characterization of defects, on the molecular level, in metal-organic frameworks (MOFs) remain a challenge. With the extensive use of single-crystal X-ray diffraction (SXRD), the missing linker defects in the zirconium-based MOF UiO-66, Zr6 O4 (OH)4 (C8 H4 O4 )6 , have been identified as water molecules coordinated directly to the zirconium centers. Charge balancing is achieved by hydroxide anions, which are hydrogen bonded within the pores of the framework. Furthermore, the precise nature of the defects and their concentration can be manipulated by altering the starting materials, synthesis conditions, and post-synthetic modifications.

Hirshfeld atom refinement

The new automated iterative Hirshfeld atom refinement method is explained and validated through comparison of structural models of Gly–l-Ala obtained from synchrotron X-ray and neutron diffraction data at 12, 50, 150 and 295 K. Structural parameters involving hydrogen atoms are determined with comparable precision from both experiments and agree mostly to within two combined standard uncertainties.

Low-energy contamination of Mo microsource X-ray radiation: analysis and solution of the problem

In recent years, microsource sealed tubes in combination with multilayer optics have been adopted in many crystallography laboratories for very low power X-ray generation, monochromatization and high-brilliance microfocusing. All these factors allow high-performance experiments on a laboratory scale. However, a fundamental defect of this technology has been discovered, namely a significant contamination of the characteristic radiation by low-energy photons. Some simple experiments are reported, showing that the contamination can significantly reduce the accuracy of the measured intensities, especially when Mo Kα radiation is used. A simple and economic solution to the problem is proposed: an aluminium filter approximately 100 µm thick, which efficiently removes the low-energy contaminant photons.

Molecular dynamics simulations of structure and dynamics of organic molecular crystals

A set of model compounds covering a range of polarity and flexibility have been simulated using GAFF, CHARMM22, OPLS and MM3 force fields to examine how well classical molecular dynamics simulations can reproduce structural and dynamic aspects of organic molecular crystals. Molecular structure, crystal structure and thermal motion, including molecular reorientations and internal rotations, found from the simulations have been compared between force fields and with experimental data. The MM3 force field does not perform well in condensed phase simulations, while GAFF, CHARMM and OPLS perform very similarly. Generally molecular and crystal structure are reproduced well, with a few exceptions. The atomic displacement parameters (ADPs) are mostly underestimated in the simulations with a relative error of up to 70%. Examples of molecular reorientation and internal rotation, observed in the simulations, include in-plane reorientations of benzene, methyl rotations in alanine, decane, isopropylcyclohexane, pyramidal inversion of nitrogen in amino group and rotation of the whole group around the C-N bond. Frequencies of such dynamic processes were calculated, as well as thermodynamic properties for reorientations in benzene and alanine. We conclude that MD simulations can be used for qualitative analysis, while quantitative results should be taken with caution. It is important to compare the outcomes from simulations with as many experimental quantities as available before using them to study or quantify crystal properties not available from experiment.

Analyzing diffuse scattering with supercomputers

Two new approaches to quantitatively analyze diffuse diffraction intensities from faulted layer stacking are reported. The parameters of a probability-based growth model are determined with two iterative global optimization methods: a genetic algorithm (GA) and particle swarm optimization (PSO). The results are compared with those from a third global optimization method, a differential evolution (DE) algorithm [Storn & Price (1997). J. Global Optim. 11, 341–359]. The algorithm efficiencies in the early and late stages of iteration are compared. The accuracy of the optimized parameters improves with increasing size of the simulated crystal volume. The wall clock time for computing quite large crystal volumes can be kept within reasonable limits by the parallel calculation of many crystals (clones) generated for each model parameter set on a super- or grid computer. The faulted layer stacking in single crystals of trigonal three-pointed-star-shaped tris(bicylco[2.1.1]hexeno)benzene molecules serves as an example for the numerical computations. Based on numerical values of seven model parameters (reference parameters), nearly noise-free reference intensities of 14 diffuse streaks were simulated from 1280 clones, each consisting of 96 000 layers (reference crystal). The parameters derived from the reference intensities with GA, PSO and DE were compared with the original reference parameters as a function of the simulated total crystal volume. The statistical distribution of structural motifs in the simulated crystals is in good agreement with that in the reference crystal. The results found with the growth model for layer stacking disorder are applicable to other disorder types and modeling techniques, Monte Carlo in particular.

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.

4,4'-Dinitro-2,2'-bipyridine

The title compound, C 10 H 6 N 4 O 4 , has crystallographic C i symmetry and is almost planar. Analysis of its crystal packing reveals molecular tapes formed by C-H...O hydrogen bonds.

TiGePt – a study of Friedel differences

The X-ray single-crystal diffraction intensities of the intermetallic compound TiGePt were analysed. These showed beyond doubt that the crystal structure is non-centrosymmetric. The analysis revolves around the resonant-scattering contribution to differences in intensity between Friedel opposites hkl and \bar h\bar k\bar l. The following techniques were used: R(merge) factors on the average (A) and difference (D) of Friedel opposites; statistical estimates of the resonant-scattering contribution to Friedel opposites; plots of 2A(obs) against 2A(model) and of D(obs) against D(model); the antisymmetric D-Patterson function. Moreover it was possible to show that a non-standard atomic model was unnecessary to describe TiGePt. Two data sets are compared. That measured with Ag Kα radiation at 295 K to a resolution of 1.25 Å(-1) is less conclusive than the one measured with Mo Kα radiation at 100 K to the lower resolution of 0.93 Å(-1). This result is probably due to the fact that the resonant scattering of Pt is larger for Mo Kα than for AgKα radiation.

Comments on `Hydrogen bonds in crystalline D -alanine: diffraction and spectroscopic evidence for differences between enantiomers'

The recent claim of structural differences between alanine enantiomers in the solid state is critically discussed.

Impact of Disordered Guest–Framework Interactions on the Crystallography of Metal–Organic Frameworks

It is a general and common practice to carry out single-crystal X-ray diffraction experiments at cryogenic temperatures in order to obtain high-resolution data. In this report, we show that this practice is not always applicable to metal-organic frameworks (MOFs), especially when these structures are highly porous. Specifically, two new MOFs are reported here, MOF-1004 and MOF-1005, for which the collection of the diffraction data at lower temperature (100 K) did not give data of sufficient quality to allow structure solution. However, collection of data at higher temperature (290 K) gave atomic-resolution data for MOF-1004 and MOF-1005, allowing for structure solution. We find that this inverse behavior, contrary to normal practice, is also true for some well-established MOFs (MOF-177 and UiO-67). Close examination of the X-ray diffraction data obtained for all four of these MOFs at various temperatures led us to conclude that disordered guest-framework interactions play a profound role in introducing disorder at low temperature, and the diminishing strength of these interactions at high temperatures reduces the disorder and gives high-resolution diffraction data. We believe our finding here is more widely applicable to other highly porous MOFs and crystals containing highly disordered molecules.