xrdPlanner: exploring area detector geometries for powder diffraction and total scattering experiments.

xrdPlanner is a software package designed to aid in the planning and preparation of powder X-ray diffraction and total scattering beam times at synchrotron facilities. Many modern beamlines provide a flexible experimental setup and may have several different detectors available. In combination with a range of available X-ray energies, it often makes it difficult for the user to explore the available parameter space relevant for a given experiment prior to the scheduled beam time. xrdPlanner was developed to provide a fast and straightforward tool that allows users to visualize the accessible part of reciprocal space of their experiment at a given combination of photon energy and detector geometry. To plan and communicate the necessary geometry not only saves time but also helps the beamline staff to prepare and accommodate for an experiment. The program is tailored toward powder X-ray diffraction and total scattering experiments but may also be useful for other experiments that rely on an area detector and for which detector placement and achievable momentum-transfer range are important experimental parameters.

First-order antiferromagnetic transitions of SrMn2P2 and CaMn2P2 single crystals containing corrugated-honeycomb Mn sublattices.

SrMn2P2 and CaMn2P2 are insulators that adopt the trigonal CaAl2Si2-type structure containing corrugated Mn honeycomb layers. Magnetic susceptibility χ and heat capacity versus temperature T data reveal a weak first-order antiferromagnetic (AFM) transition at the Néel temperature [Formula: see text] K for SrMn2P2 and a strong first-order AFM transition at [Formula: see text] K for CaMn2P2 Both compounds exhibit isotropic and nearly T-independent [Formula: see text], suggesting magnetic structures in which nearest-neighbor moments are aligned at [Formula: see text] to each other. The 31P NMR measurements confirm the strong first-order transition in CaMn2P2 but show critical slowing down above [Formula: see text] for SrMn2P2, thus also evidencing second-order character. The 31P NMR measurements indicate that the AFM structure of CaMn2P2 is commensurate with the lattice whereas that of SrMn2P2 is incommensurate. These first-order AFM transitions are unique among the class of (Ca, Sr, Ba)Mn2 (P, As, Sb, Bi)2 compounds that otherwise exhibit second-order AFM transitions. This result challenges our understanding of the circumstances under which first-order AFM transitions occur.

Pair Distribution Function from Liquid Jet Nanoparticle Suspension using Femtosecond X-ray Pulses.

X-ray scattering data measured on femtosecond timescales at the SACLA X-ray Free Electron Laser (XFEL) facility on a suspension of HfO2 nanoparticles in a liquid jet were used for pair distribution function (PDF) analysis. Despite a non-optimal experimental setup resulting in a modest Qmax of ~8 Å-1 , a promising PDF was obtained. The main features were reproduced when comparing the XFEL PDF to a PDF obtained from data measured at the PETRA III synchrotron light source. Refining structural parameters such as unit cell dimension and particle size from the XFEL PDF provided reliable values. Although the reachable Qmax limited the obtainable information, the present results indicate that good quality PDFs can be obtained on femtosecond timescales if the experimental conditions are further optimized. The study therefore encourages a new direction in ultrafast structural science where structural features of amorphous and disordered systems can be studied.

Synchrotron X-ray Electron Density Analysis of Chemical Bonding in the Graphitic Carbon Nitride Precursor Melamine.

Melamine is a precursor and building block for graphitic carbon nitride (g-CN) materials, a group of layered materials showing great promise for catalytic applications. The synthetic pathway to g-CN includes a polycondensation reaction of melamine by evaporation of ammonia. Melamine molecules in the crystal organize into wave-like planes with an interlayer distance of 3.3 Šsimilar to that of g-CN. Here we present an extensive investigation of the experimental electron density of melamine obtained from modelling of synchrotron radiation X-ray single-crystal diffraction data measured at 25 K with special focus on the molecular geometry and intermolecular interactions. Both intra- and interlayer structures are dominated by hydrogen bonding and π-interactions. Theoretical gas-phase optimizations of the experimental molecular geometry show that bond lengths and angles for atoms in the same chemical environment (C-N bonds in the ring, amine groups) differ significantly more for the experimental geometry than for the gas-phase-optimized geometries, indicating that intermolecular interactions in the crystal affects the molecular geometry. In the experimental crystal geometry, one amine group has significantly more sp3 -like character than the others, hinting at a possible formation mechanism of g-CN. Topological analysis and energy frameworks show that the nitrogen atom in this amine group participates in weak intralayer hydrogen bonding. We hypothesize that melamine condenses to g-CN within the layers and that the unique amine group plays a key role in the condensation process.

Investigating Complex Magnetic Anisotropy in a Co(II) Molecular Compound: A Charge Density and Correlated Ab Initio Electronic Structure Study.

Understanding magnetic anisotropy and specifically how to tailor it is crucial in the search for high-temperature single-ion magnets. Herein, we investigate the magnetic anisotropy in a six-coordinated cobalt(II) compound that has a complex geometry and distinct triaxial magnetic anisotropy from the perspective of the electronic structure, using electronic spectra, ab initio calculations, and an experimental charge density, of which the latter two provides insight into the d-orbital splitting. The analysis showed that the d-orbital splitting satisfactorily predicted the complex triaxial magnetic anisotropy exhibited by the compound. Furthermore, a novel method to directly compare the ab initio results and the d-orbital populations obtained from the experimental charge density was developed, while a topological analysis of the density provided insights into the metal-ligand bonding. This work thus further establishes the validity of using d-orbitals for predicting magnetic anisotropy in transition metal compounds while also pointing out the need for a more frequent usage of the term triaxial anisotropy in the field of single-molecule magnetism.

Quantification of the Magnetic Anisotropy of a Single-Molecule Magnet from the Experimental Electron Density.

Reported here is an entirely new application of experimental electron density (EED) in the study of magnetic anisotropy of single-molecule magnets (SMMs). Among those SMMs based on one single transition metal, tetrahedral CoII-complexes are prominent, and their large zero-field splitting arises exclusively from coupling between the d x 2 - y 2 and dxy orbitals. Using very low temperature single-crystal synchrotron X-ray diffraction data, an accurate electron density (ED) was obtained for a prototypical SMM, and the experimental d-orbital populations were used to quantify the dxy-d x 2 - y 2 coupling, which simultaneously provides the composition of the ground-state Kramers doublet wave function. Based on this experimentally determined wave function, an energy barrier for magnetic relaxation in the range 193-268 cm-1 was calculated, and is in full accordance with the previously published value of 230 cm-1 obtained from near-infrared spectroscopy. These results provide the first clear and direct link between ED and molecular magnetic properties.

Chiral-at-Metal Phosphorescent Square-Planar Pt(II)-Complexes from an Achiral Organometallic Ligand.

The synthesis and characterization of a new kind of cis- and trans-cyclometalated square-planar platinum(II) complexes is reported. Uncharged organometallic compounds carrying one or two of the C∧N-donor ligand LCN were prepared. Due to the heterobidentate coordination of the achiral chelate ligand, the formed [PtLCNCl(SEt2)], cis- and trans-[PtLCN2] complexes are chiral with the metal serving as the stereo center. The enantiomers of complex trans-[PtLCN2] could be separated and their absolute configuration was determined by anomalous X-ray diffraction, in accordance with CD spectroscopic results and TD-DFT calculations. All compounds were fully characterized by NMR spectroscopy, mass spectrometry and X-ray structure determination. The photophysical properties of trans-[PtLCN2] have been investigated showing phosphorescence in solution and in the solid state with a moderate quantum yield. For the enantiomers, strong circular dichroism (CD) and circularly polarized luminescence (CPL) effects were observed, rendering this new structural motif suitable for application in chiroptical and luminescent materials.

Triggered exchange of anionic for neutral guests inside a cationic coordination cage.

Molecular encapsulation processes under the control of an external trigger play a major role in biological signal transduction processes and enzyme catalysis. Here, we present an artificial mimic of a controllable host system that forms via self-assembly from a simple bis-monodentate ligand and Pd(II) cations. The resulting interpenetrated double cage features three consecutive pockets which initially contain one tetrafluoroborate anion, each. Activation of this host system with two halide anions triggers a conformational change that renders the central pocket susceptible to the uptake of small neutral guest molecules. Thereby, the pentacationic cage expels the central anion and replaces it with a neutral molecule to give a hexacationic species. The cage structures prior and after the halide triggered binding of benzene were examined by X-ray crystallography, ESI MS, and NMR techniques. The kinetics and thermodynamics of the encapsulation of benzene, cyclohexane, and norbornadiene are compared.

Electron-induced conversion of silylones to six-membered cyclic silylenes.

A silicon atom in the zero oxidation state stabilized by two carbene ligands is known as siladicarbene (silylone). There are two pairs of electrons on the silicon atom in silylone. This was recently confirmed by both experimental and theoretical charge density investigations. The silylone is stable up to 195 °C in an inert atmosphere. However, a substoichiometric amount (33 mol%) of potassium metal triggers the activation of the unsaturated C:Si:C backbone, leading to a selective reaction with a tertiary C-H bond in an atom-economical approach to form a six-membered cyclic silylene with three-coordinate silicon atom. Cyclic voltammetry shows that this reaction proceeds via the formation of a silylone radical anion intermediate, which is further confirmed by EPR spectroscopy.

Synthesis and reactivity of a transient, terminal nitrido complex of rhodium.

Irradiation of rhodium(II) azido complex [Rh(N3){N(CHCHPtBu2)2}] allowed for the spectroscopic characterization of the first reported rhodium complex with a terminal nitrido ligand. DFT computations reveal that the unpaired electron of rhodium(IV) nitride complex [Rh(N){N(CHCHPtBu2)2}] is located in an antibonding Rh-N π* bond involving the nitrido moiety, thus resulting in predominant N-radical character, in turn providing a rationale for its transient nature and observed nitride coupling to dinitrogen.

Comparative study of conventional and synchrotron X-ray electron densities on molecular crystals.

Five different electron density datasets obtained from conventional and synchrotron single crystal X-ray diffraction experiments are compared. The general aim of the study is to investigate the quality of data for electron density analysis from current state-of-the-art conventional sources, and to see how the data perform in comparison with high-quality synchrotron data. A molecular crystal of melamine was selected as the test compound due to its ability to form excellent single crystals, the light atom content, and an advantageous suitability factor of 3.6 for electron density modeling. These features make melamine an optimal system for conventional X-ray diffractometers since the inherent advantages of synchrotron sources such as short wavelength and high intensity are less critical in this case. Data were obtained at 100 K from new in-house diffractometers Rigaku Synergy-S (Mo and Ag source, HyPix100 detector) and Stoe Stadivari (Mo source, EIGER2 1M CdTe detector), and an older Oxford Diffraction Supernova (Mo source, Atlas CCD detector). The synchrotron data were obtained at 25 K from BL02B1 beamline at SPring-8 in Japan (λ = 0.2480 Å, Pilatus3 X 1M CdTe detector). The five datasets were compared on general quality parameters such as resolution, ⟨I/σ⟩, redundancy and R factors, as well as the more model specific fractal dimension plot and residual density maps. Comparison of the extracted electron densities reveals that all datasets can provide reliable multipole models, which overall convey similar chemical information. However, the new laboratory X-ray diffractometers with advanced pixel detector technology clearly measure data with significantly less noise and much higher reliability giving densities of higher quality, compared to the older instrument. The synchrotron data have higher resolution and lower measurement temperature, and they allow for finer details to be modeled (e.g. hydrogen κ parameters).

Towards pump-probe single-crystal XFEL refinements for small-unit-cell systems.

Serial femtosecond crystallography for small-unit-cell systems has so far seen very limited application despite obvious scientific possibilities. This is because reliable data reduction has not been available for these challenging systems. In particular, important intensity corrections such as the partiality correction critically rely on accurate determination of the crystal orientation, which is complicated by the low number of diffraction spots for small-unit-cell crystals. A data reduction pipeline capable of fully automated handling of all steps of data reduction from spot harvesting to merged structure factors has been developed. The pipeline utilizes sparse indexing based on known unit-cell parameters, seed-skewness integration, intensity corrections including an overlap-based combined Ewald sphere width and partiality correction, and a dynamically adjusted post-refinement routine. Using the pipeline, data measured on the compound K4[Pt2(P2O5H2)4]·2H2O have been successfully reduced and used to solve the structure to an R1 factor of ∼9.1%. It is expected that the pipeline will open up the field of small-unit-cell serial femtosecond crystallography experiments and allow investigations into, for example, excited states and reaction intermediate chemistry.

Quantifying magnetic anisotropy using X-ray and neutron diffraction.

In this work, the magnetic anisotropy in two iso-structural distorted tetrahedral Co(II) complexes, CoX 2tmtu2 [X = Cl(1) and Br(2), tmtu = tetra-methyl-thio-urea] is investigated, using a combination of polarized neutron diffraction (PND), very low-temperature high-resolution synchrotron X-ray diffraction and CASSCF/NEVPT2 ab initio calculations. Here, it was found consistently among all methods that the compounds have an easy axis of magnetization pointing nearly along the bis-ector of the compression angle, with minute deviations between PND and theory. Importantly, this work represents the first derivation of the atomic susceptibility tensor based on powder PND for a single-molecule magnet and the comparison thereof with ab initio calculations and high-resolution X-ray diffraction. Theoretical ab initio ligand field theory (AILFT) analysis finds the d xy orbital to be stabilized relative to the d xz and d yz orbitals, thus providing the intuitive explanation for the presence of a negative zero-field splitting parameter, D, from coupling and thus mixing of d xy and . Experimental d-orbital populations support this interpretation, showing in addition that the metal-ligand covalency is larger for Br-ligated 2 than for Cl-ligated 1.

Accurate high-resolution single-crystal diffraction data from a Pilatus3†X CdTe detector.

Hybrid photon-counting detectors are widely established at third-generation synchrotron facilities and the specifications of the Pilatus3 X CdTe were quickly recognized as highly promising in charge-density investigations. This is mainly attributable to the detection efficiency in the high-energy X-ray regime, in combination with a dynamic range and noise level that should overcome the perpetual problem of detecting strong and weak data simultaneously. These benefits, however, come at the expense of a persistent problem for high diffracted beam flux, which is particularly problematic in single-crystal diffraction of materials with strong scattering power and sharp diffraction peaks. Here, an in-depth examination of data collected on an inorganic material, FeSb2, and an organic semiconductor, rubrene, revealed systematic differences in strong intensities for different incoming beam fluxes, and the implemented detector intensity corrections were found to be inadequate. Only significant beam attenuation for the collection of strong reflections was able to circumvent this systematic error. All data were collected on a bending-magnet beamline at a third-generation synchrotron radiation facility, so undulator and wiggler beamlines and fourth-generation synchrotrons will be even more prone to this error. On the other hand, the low background now allows for an accurate measurement of very weak intensities, and it is shown that it is possible to extract structure factors of exceptional quality using standard crystallographic software for data processing (SAINT-Plus, SADABS and SORTAV), although special attention has to be paid to the estimation of the background. This study resulted in electron-density models of substantially higher accuracy and precision compared with a previous investigation, thus for the first time fulfilling the promise of photon-counting detectors for very accurate structure factor measurements.

Comparison of different strategies for modelling hydrogen atoms in charge density analyses.

The quality of various approximation methods for modelling anisotropic displacement parameters (ADPs) for hydrogen atoms was investigated in a comparative study. A multipole refinement was performed against high-resolution single crystal X-ray data of 9-diphenylthiophosphoranylanthracene (SPAnH) and 9,10-bis-diphenylthiophosphoranylanthracene·toluene (SPAnPS). Hydrogen-atom parameters and structural properties derived from our collected neutron data sets were compared with those obtained from the SHADE-server, the software APD-Toolkit based on the invariom database, the results from Hirshfeld atom refinement conducted in the OLEX2 GUI (HARt), and the results of anisotropic hydrogen refinement within XD2016. Additionally, a free refinement of H-atom positions against X-ray data was performed with fixed ADPs from various methods. The resulting C-H bond distances were compared with distances from neutron diffraction experiments and the HARt results. Surprisingly, the refinement of anisotropic hydrogen displacement parameters against the X-ray data yielded the smallest deviations from the neutron values. However, the refinement of bond-directed quadrupole parameters turned out to be vital for the quality of the resulting ADPs. In both model structures, SHADE and, to a lesser extent, APD-Toolkit showed problems in dealing with atoms bonded to carbon atoms with refined Gram-Charlier parameters for anharmonic motion. The HARt method yields the most accurate C-H bond distances compared to neutron data results. Unconstrained refinement of hydrogen atom positions using ADPs derived from all other used approximation methods showed that even with well approximated hydrogen ADPs, the resulting distances were still significantly underestimated.

Validation of experimental charge-density refinement strategies: when do we overfit?

A cross-validation method is supplied to judge between various strategies in multipole refinement procedures. Its application enables straightforward detection of whether the refinement of additional parameters leads to an improvement in the model or an overfitting of the given data. For all tested data sets it was possible to prove that the multipole parameters of atoms in comparable chemical environments should be constrained to be identical. In an automated approach, this method additionally delivers parameter distributions of k different refinements. These distributions can be used for further error diagnostics, e.g. to detect erroneously defined parameters or incorrectly determined reflections. Visualization tools show the variation in the parameters. These different refinements also provide rough estimates for the standard deviation of topological parameters.

Comparison of silver and molybdenum microfocus X-ray sources for single-crystal structure determination.

The quality of diffraction data obtained using silver and molybdenum microsources has been compared for six model compounds with a wide range of absorption factors. The experiments were performed on two 30 W air-cooled Incoatec IµS microfocus sources with multilayer optics mounted on a Bruker D8 goniometer with a SMART APEX II CCD detector. All data were analysed, processed and refined using standard Bruker software. The results show that Ag Kα radiation can be beneficial when heavy elements are involved. A numerical absorption correction based on the positions and indices of the crystal faces is shown to be of limited use for the highly focused microsource beams, presumably because the assumption that the crystal is completely bathed in a (top-hat profile) beam of uniform intensity is no longer valid. Fortunately the empirical corrections implemented in SADABS, although originally intended as a correction for absorption, also correct rather well for the variations in the effective volume of the crystal irradiated. In three of the cases studied (two Ag and one Mo) the final SHELXL R1 against all data after application of empirical corrections implemented in SADABS was below 1%. Since such corrections are designed to optimize the agreement of the intensities of equivalent reflections with different paths through the crystal but the same Bragg 2θ angles, a further correction is required for the 2θ dependence of the absorption. For this, SADABS uses the transmission factor of a spherical crystal with a user-defined value of µr (where µ is the linear absorption coefficient and r is the effective radius of the crystal); the best results are obtained when r is biased towards the smallest crystal dimension. The results presented here suggest that the IUCr publication requirement that a numerical absorption correction must be applied for strongly absorbing crystals is in need of revision.

Narcissistic self-sorting vs. statistic ligand shuffling within a series of phenothiazine-based coordination cages.

Previously, we introduced a series of anion-binding interpenetrated double-cages based on phenothiazine and its mono- and di-S-oxygenated derivatives. Here, we complete the structural comparison of the three related assemblies by an X-ray single crystal analysis of the sulfone derivative. We further show that the three palladium cages coexist in solution upon post-assembly mixing due to the very slow ligand exchange whereas treatment of binary mixtures of the corresponding ligands with Pd(II) leads to the formation of mixed cages comprising a statistical ligand distribution. In contrast, mixtures of one of these ligands with a shorter ligand derivative lead to narcissistic self-assembly into a double-cage and a coexisting small monomeric cage, regardless of the order of mixing and Pd(II) addition.

Mixed valence η6-arene cobalt(I) and cobalt(II) compound.

The first carbonyl free mixed valence cobalt(I)/cobalt(II) compound [2{L2Co(I)(η(6)-C7H8)}](2+) [Co(II)2Cl6](2-) (1) [L = PhC(N(t)Bu)2SiCl] was obtained by the reaction of four equivalents of anhydrous CoCl2 with five equivalents of N-heterocyclic chlorosilylene L. In contrast, the reaction of L with CoBr2 yielded [L2CoBr2] (2). Compound 1 was formed by the cleavage of Co-Cl bonds, the reduction of Co(II) to Co(I) and by the coordination of a toluene molecule. The chlorosilylene (L) functions as a reducing agent as well as a neutral σ-donor ligand. The toluene molecule coordinates to the Co(I) atom in an η(6)-fashion.