Mads R. V. Jørgensen

Integration of neutron time-of-flight single-crystal Bragg peaks in reciprocal space

The intensity of single-crystal Bragg peaks obtained by mapping neutron time-of-flight event data into reciprocal space and integrating in various ways is compared. These methods include spherical integration with a fixed radius, ellipsoid fitting and integration of the peak intensity, and one-dimensional peak profile fitting. In comparison to intensities obtained by integrating in real detector histogram space, the data integrated in reciprocal space result in better agreement factors and more accurate atomic parameters. Furthermore, structure refinement using integrated intensities from one-dimensional profile fitting is demonstrated to be more accurate than simple peak-minus-background integration.

Quantitative analysis of intermolecular interactions in orthorhombic rubrene

A combination of single-crystal X-ray and neutron diffraction experiments are used to determine the electron density distribution in orthorhombic rubrene. The topology of electron density, NCI analysis and energetics of intermolecular interactions clearly demonstrate the presence of π⋯π stacking interactions in the crystalline state.

Contemporary X-ray electron-density studies using synchrotron radiation.

The use of synchrotron radiation for experimental electron-density determination during the last decade is reviewed. Possible future directions of this field are examined.

Atomic properties and chemical bonding in the pyrite and marcasite polymorphs of FeS2: a combined experimental and theoretical electron density study

The electron density distributions in both polymorphs of the promising photovoltaic material iron disulfide have been determined by multipole modelling against state-of-the-art synchrotron X-ray diffraction data collected at 10 K using minute single crystals with dimensions less than 10 μm. Charge density analysis of FeS2 pyrite and marcasite offers a unique opportunity to relate local atomic properties, such as 2-center chemical bonding, atomic charges and d-orbital populations, to polymorphism in extended crystal structures. In combination with results from periodic calculations on the compounds in the experimental geometries using WIEN2k, the study provides unambiguous answers to a number of unsolved issues regarding the nature of the bonding in FeS2. The Fe–S bonds exhibit all the virtues of polar covalent bonds, with only minor charge accumulation but significantly negative energy densities at the bond critical points. Compared to a non-interacting model, the density is found to be concentrated along the Fe–S interaction line in support of a partial covalent bonding description. The homopolar covalent S–S interaction is seemingly stronger in pyrite than in marcasite, determined not only from the shorter distance but also from all topological indicators. The study also clarifies that the atomic charges are significantly smaller than the estimation based on crystal-field theory of Fe2+, S−1. The experimentally derived Fe d-orbital populations are found to deviate from the commonly assumed full t2g set, empty eg set, and they fit exceptionally well with the theoretical individual atomic orbitals projected density of states showing a higher dxy participation in the valence band in marcasite compared with pyrite. Thus, the differences between the two polymorphic compounds are directly reflected in their valence density distributions and d-orbital populations.

Helium cryostat synchrotron charge densities determined using a large CCD detector – the upgraded beamline D3 at DESY

A 165 mm Mar CCD detector has been fitted on a large Huber four-circle diffractometer together with a helium cryostat at beamline D3 at Hasylab, DESY in Hamburg. This setup allows fast collection of accurate, short-wavelength, very low temperature X-ray diffraction data for charge-density analysis. As a test example, diffraction data have been collected in 10 h on a hydrogen-bonded network system with 15 unique atoms, and the electron density was modelled with the multipole formalism in an X–N procedure using matching-temperature neutron diffraction data collected at Institut Laue Langevin, Grenoble in France.

Redox‐Driven Migration of Copper Ions in the Cu‐CHA Zeolite as Shown by the In Situ PXRD/XANES Technique

Using quasi-simultaneous in situ PXRD and XANES, the direct correlation between the oxidation state of Cu ions in the commercially relevant deNOx NH3 -SCR zeolite catalyst Cu-CHA and the Cu ion migration in the zeolitic pores was revealed during catalytic activation experiments. A comparison with recent reports further reveals the high sensitivity of the redox-active centers concerning heating rates, temperature, and gas environment during catalytic activation. Previously, Cu+ was confirmed present only in the 6R. Results verify a novel 8R monovalent Cu site, an eventually large Cu+ presence upon heating to high temperatures in oxidative conditions, and demonstrate the unique potential in combining in situ PXRD and XANES techniques, with which both oxidation state and structural location of the redox-active centers in the zeolite framework could be tracked.

Analysis of the photomagnetic properties of cyano-bridged heterobimetallic complexes by X-ray diffraction.

Single crystal synchrotron X-ray diffraction measurements have been carried out on [Nd(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O (DMF = dimethyl-formamide), 1; [Y(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O, 2; [Ce(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O, 3; [Sm(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O, 4; [Tb(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O, 5; [Yb(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O, 6; and [Nd(DMF)(4)(H(2)O)(3)(μ-CN)Co(CN)(5)]·H(2)O, 7, at 15(2) K with and without UV illumination of the crystals. Significant changes in unit cell parameters are observed for all of the iron-containing complexes, while compound 7 shows no response to UV illumination. These results are consistent with previous results and are furthermore reproduced by powder synchrotron X-ray diffraction for compounds 1 and 7. Photoexcited crystal structures have been determined for 1-6 from refinements of two-conformer models, and excited state occupancies in the range 80-94% are found. Significant bond length changes are observed for the Fe-ligand bonds (up to 0.06 Å), the cyano bonds (up to 0.02 Å), and the lanthanide-ligand bonds (up to 0.1 Å). On the contrary, powder X-ray diffraction on the simple compound K(3)Fe(CN)(6), 8, upon UV illumination does not show any structural changes, suggesting that the photomagnetic effect requires the presence of both the transition metal and the lanthanide ion. Photomagnetic measurements show an increase in magnetization of the excited state of 1 of up to 3%, which is much diminished compared with previously published values of 45%. Furthermore, they show that the isostructural complex [La(DMF)(4)(H(2)O)(3)(μ-CN)Fe(CN)(5)]·H(2)O, 9, exhibits identical magnetic responses in the UV-induced excited crystal structure.

On the significance of Bragg reflections

Recently Henn & Meindl [Acta Cryst. (2010), A66, 676-684] examined the significance of Bragg diffraction data through the descriptor W = (I(1/2))/(σ(I)). In the Poisson limit for the intensity errors W equals unity, but any kind of data processing (background subtraction, integration, scaling, absorption correction, Lorentz and polarization correction etc.) introduces additional error as well as remaining systematic errors and thus the significance of processed Bragg diffraction data is expected to be below the Poisson limit (W(Bragg) < 1). Curiously, it was observed by Henn & Meindl for several data sets that W(Bragg) had values larger than one. In the present study this is shown to be an artefact due to the neglect of a data scale factor applied to the standard uncertainties, and corrected values of W(Bragg) applied to Bragg data on an absolute scale are presented, which are all smaller than unity. Furthermore, the error estimation models employed by two commonly used data-processing programs {SADABS (Bruker AXS Inc., Madison, Wisconsin, USA) and SORTAV [Blessing (1997). J. Appl. Cryst. 30, 421-426]} are examined. It is shown that the empirical error model in SADABS very significantly lowers the significance of the Bragg data and it also results in a very strange distributions of errors, as observed by Henn & Meindl. On the other hand, error estimation based on the variance of a population of abundant intensity data, as used in SORTAV, provides reasonable error estimates, which are only slightly less significant than the raw data. Given that modern area detectors make measurement of highly redundant data relatively straightforward, it is concluded that the latter is the best approach for processing of data.

Experimental and Theoretical Charge Densities of a Zinc-Containing Coordination Polymer, Zn(HCOO)2(H2O)2

We present a combined experimental and theoretical charge density study of the coordination polymer Zn(HCOO)(2)(H(2)O)(2), which serves as a nonmagnetic reference for the isostructural magnetic compounds containing 3d transition metals. The charge density has been modeled using the multipole formalism against a high-resolution single-crystal X-ray diffraction data set collected at 100 K. The theoretical model is based on periodic density functional theory calculations in the experimental geometry. To gauge the degree of systematic bias from the multipole model, the structure factors of the theoretical model were also projected into a multipole model and the two theoretical models are compared with the experimental results. All models, both experiment and theory, show that the Zn atom densities are highly spherical but show small accumulations of charge toward the negative ligands. The metal-ligand interactions are found to be primarily ionic, but there are subtle topological indications of covalent contributions to the bonds. The source function calculated at the bond critical points reveals a rather delocalized picture of the density in the bridging carboxylates, and this presumably reflects the exchange pathway in the magnetic analogues.

Pressure versus Temperature Effects on Intramolecular Electron Transfer in Mixed‐Valence Complexes

Mixed-valence trinuclear carboxylates, [M(3)O(O(2)CR)(6)L(3)] (M = metal, L = terminal ligand), have small differences in potential energy between the configurations M(II)M(III)M(III)⇔M(III)M(II)M(III)⇔M(III)M(III)M(II), which means that small external changes can have large structural effects, owing to the differences in coordination geometry between M(2+) and M(3+) sites (e.g., about 0.2 Å for Fe-O bond lengths). It is well-established that the electron transfer (ET) between the metal sites in these mixed-valence molecules is strongly dependent on temperature and on the specific crystal environment; however, herein, for the first time, we examine the effect of pressure on the electron transfer. Based on single-crystal X-ray diffraction data that were measured at 15, 90, 100, 110, 130, 160, and 298 K on three different crystals, we first unexpectedly found that our batch of Fe(3)O (O(2)CC(CH(3))(3))(6)(C(5)H(5)N)(3) (1) exhibited a different temperature dependence of the ET process than previous studies of compound 1 have shown. We observed a phase transition at around 130 K that was related to complete valence trapping and Hirshfeld surface analysis revealed that this phase transition was governed by a subtle competition between C-H⋅⋅⋅π and π⋅⋅⋅π intermolecular interactions. Subsequent high-pressure single-crystal X-ray diffraction at pressures of 0.15, 0.35, 0.45, 0.74, and 0.96 GPa revealed that it was not possible to trigger the phase transition (i.e., valence trapping) by a reduction of the unit-cell volume, owing to this external pressure. We conclude that modulation of the ET process requires anisotropic changes in the intermolecular interactions, which occur when various directional chemical bonds are affected differently by changes in temperature, but not by the application of pressure.