The Crystal Structure of Trimethyl Borate by Neutron and X‐ray Powder Diffraction

The crystal structure of one of the simplest organoboron compounds, trimethyl borate does not appear to have been determined hitherto. The compound is of interest for the study of π‐donor ligands and their interaction with the π‐acceptor behavior of trigonal boron and the consequences of such interactions on molecular structure. We used powder neutron (with isotopically labeled material) and X‐ray diffraction to determine the crystal structure of trimethyl borate at 15 K and 200 K (neutron) and 200 K (X‐ray). The material is hexagonal (Z = 2) with a = b = 6.950(8) Å and c = 6.501(3) Å at 15 K. The unit cell volume is 272.00(1) ų. The space group is P6₃/m (SG 176) at 15 K and 200 K. This is the first crystal structure solved on the Neutron Powder Diffractometer (NPDF) at the Lujan Center.     

Aspherical‐Atom Modeling of Coordination Compounds by Single‐Crystal X‐ray Diffraction Allows the Correct Metal Atom To Be Identified

Single‐crystal X‐ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid‐state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical‐atom least‐squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld‐atom refinement (Acta Crystallogr. Sect. A­ 2008 , 64, 383–393; IUCrJ. 2014 , 1,61–79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B­ 2013 , 69, 91–104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear‐coordinate 3d metal complexes, for which the wrong element is found if standard independent‐atom model scattering factors are relied upon, are studied, and it is shown that only aspherical‐atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed.     

Stable Anilinyl Radicals Coordinated to Nickel: X‐ray Crystal Structure and Characterization

Two anilinosalen and a mixed phenol‐anilinosalen ligands involving sterically hindered anilines moieties were synthesized. Their nickel(II) complexes 1 , 2 , and 3 were prepared and characterized. They could be readily one‐electron oxidized (E_1/2=?0.30, ?0.26 and 0.10 V vs. Fc⁺/Fc, respectively) into anilinyl radicals species [ 1]⁺ , [ 2]⁺ , and [ 3]⁺ , respectively. The radical complexes are extremely stable and were isolated as single crystals. X‐ray crystallographic structures reveal that the changes in bond length resulting from oxidation do not exceed 0.02 Å within the ligand framework in the symmetrical [ 1]⁺ and [ 2]⁺ . No quinoid bond pattern was present. In contrast, larger structural rearrangements were evidenced for the unsymmetrical [ 3]⁺ , with shortening of one C_ortho? C_meta bond. Radical species [ 1]⁺ and [ 2]⁺ exhibit a strong absorption band at around 6000 cm^?1 (class III mixed valence compounds). This band is significantly less intense than [ 3]⁺ , consistent with a rather localized anilinyl radical character, and thus a classification of this species as class II mixed‐valence compound. Magnetic and electronic properties, as well as structural parameters, have been computed by DFT methods.     

The Crystal Structure of InGaO3(ZnO)4: A Single Crystal X‐ray and Electron Diffraction Study

The crystal structure of the mixed oxide InGaO₃(ZnO)₄ has been determined from electron diffraction and single‐crystal X‐ray diffraction data. The compound crystallises in a hexagonal space group (P6₃/mmc; No. 194), deduced from convergent beam electron diffraction (CBED). Single crystals of InGaO₃(ZnO)₄ were grown from a K₂MoO₄ flux in sealed platinum tubes. Single crystal structure refinement from XRD data [a = 3.2850(2) Å; c = 32.906(3) Å; Z = 2; 4232 data, R₁ = 0.0685] reveals a compound with oxygen anions forming a closest‐packed arrangement. Within this packing In³⁺ cations occupy octahedral interstices, forming layers of edge sharing octahedra. In between these layers are regions with composition [Zn₄GaO₅]⁺ forming a wurtzite type of structure. Inversions of the ZnO₄ tetrahedra occurs (i) at the InO₆ octahedral layer and (ii) halfway in the wurtzite type region, where the inversion boundary is built by Ga³⁺ in trigonal bipyramidal coordination with a long Ga–O_apical distance of 2.19(1) Å. The site occupation of Zn²⁺ and Ga³⁺, respectively, was confirmed by bond valence sum calculations. The compounds described here have the same structural charactistics as other known members with general formula ARO₃(ZnO)_m with m = integer.     

Variable‐Temperature Powder X‐ray Diffraction of Aromatic Carboxylic Acid and Carboxamide Cocrystals

The effect of temperature on the cocrystallization of benzoic acid (BA), pentafluorobenzoic acid (FBA), benzamide (BAm), and pentafluorobenzamide (FBAm) is examined in the solid state. BA and FBA formed a 1:1 complex 1 at ambient temperature by grinding with a mortar and pestle. Grinding FBA and BAm together resulted in partial conversion into the 1:1 adduct 2 at 28 °C and complete transformation into the product cocrystal at 78 °C. Further heating (80–100 °C) and then cooling to room temperature gave a different powder pattern from that of 2 . BAm and FBAm hardly reacted at ambient temperature, but they afforded the 1:1 cocrystal 3 by melt cocrystallization at 110–115 °C. Both BA+FBAm ( 4 ) and BA+BAm ( 5 ) reacted to give new crystalline phases upon heating, but the structures of these products could not be determined owing to a lack of diffraction‐quality single crystals. The stronger COOH and CONH₂ hydrogen‐bonding groups of FBA and FBAm yielded the equimolar cocrystal 6 at room temperature, and heating of these solids to 90–100 °C gave a new crystalline phase. The X‐ray crystal structures of 1 , 2 , 3 , and 6 are sustained by the acid–acid/amide–amide homosynthons or acid–amide heterosynthon, with additional stabilization from phenyl–perfluorophenyl stacking in 1 and 3 . The temperature required for complete transformation into the cocrystal was monitored by in situ variable‐temperature powder X‐ray diffraction (VT‐PXRD), and formation of the cocrystal was confirmed by matching the experimental peak profile with the simulated diffraction pattern. The reactivity of H‐bonding groups and the temperature for cocrystallization are in good agreement with the donor and acceptor strengths of the COOH and CONH₂ groups. It was necessary to determine the exact temperature range for quantitative cocrystallization in each case because excessive heating caused undesirable phase transitions.     

X‐ray Excited Optical Fluorescence and Diffraction Imaging of Reactivity and Crystallinity in a Zeolite Crystal: Crystallography and Molecular Spectroscopy in One

Structure–activity relationships in heterogeneous catalysis are challenging to be measured on a single‐particle level. For the first time, one X‐ray beam is used to determine the crystallographic structure and reactivity of a single zeolite crystal. The method generates μm‐resolved X‐ray diffraction (μ‐XRD) and X‐ray excited optical fluorescence (μ‐XEOF) maps of the crystallinity and Brønsted reactivity of a zeolite crystal previously reacted with a styrene probe molecule. The local gradients in chemical reactivity (derived from μ‐XEOF) were correlated with local crystallinity and framework Al content, determined by μ‐XRD. Two distinctly different types of fluorescent species formed selectively, depending on the local zeolite crystallinity. The results illustrate the potential of this approach to resolve the crystallographic structure of a porous material and its reactivity in one experiment via X‐ray induced fluorescence of organic molecules formed at the reactive centers.     

Revealing the Dynamic Structure of Complex Solid Catalysts Using Modulated Excitation X‐ray Diffraction

X‐ray diffraction (XRD) is typically silent towards information on low loadings of precious metals on solid catalysts because of their finely dispersed nature. When combined with a concentration modulation approach, time‐resolved high‐energy XRD is able to provide the detailed redox dynamics of palladium nanoparticles with a diameter of 2 nm in 2 wt % Pd/CZ (CZ=ceria–zirconia), which is a difficult sample for extended X‐ray absorption fine structure (EXAFS) measurements because of the cerium component. The temporal evolution of the Pd(111) and Ce(111) reflections together with surface information from synchronous diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) measurements reveals that Ce maintains Pd oxidized in the CO pulse, whereas reduction is detected at the beginning of the O₂ pulse. Oxygen is likely transferred from Pd to Ce³⁺ before the onset of Pd re‐oxidation. In this context, adsorbed carbonates appear to be the rate‐limiting species for re‐oxidation.     

Direct In Situ Investigation of Milling Reactions Using Combined X‐ray Diffraction and Raman Spectroscopy

The combination of two analytical methods including time‐resolved in situ X‐ray diffraction (XRD) and Raman spectroscopy provides a new opportunity for a detailed analysis of the key mechanisms of milling reactions. To prove the general applicability of our setup, we investigated the mechanochemical synthesis of four archetypical model compounds, ranging from 3D frameworks through layered structures to organic molecular compounds. The reaction mechanism for each model compound could be elucidated. The results clearly show the unique advantage of the combination of XRD and Raman spectroscopy because of the different information content and dynamic range of both individual methods. The specific combination allows to study milling processes comprehensively on the level of the molecular and crystalline structures and thus obtaining reliable data for mechanistic studies.     

A Constrained Disorder Refinement: “Reinvestigation of “Single‐Crystal X‐ray Structure of 1,3‐Dimethylcyclobutadiene” by M. Shatruk and I. V. Alabugin”

Shatruk and Alabugin propose an alternative structural model for the observed electron density that we have attributed to the photochemical formation of 1,3‐dimethylcyclobutadiene in a protective solid crystalline matrix. The main criticism from Shatruk and Alabugin concerns the modeling of the disorder in the calixarene cavity and in particular the neglect of a residual electron density close to the O1 atom. We published (Chem. Eur. J. 2011 , 17, 10021) our opinion concerning this “ignored peak” in the Supporting Information of the paper. The current response to the Correspondence demonstrates that Shatruk and Alabugin have over‐modeled our data by assigning a small electron density peak, which is hardly more than the density corresponding to a hydrogen atom, to an under‐occupied oxygen site, using inappropriate refinement contraints.     

Dehydration of raffinose pentahydrate: structures of raffinose 5‐, 4.433‐, 4.289‐ and 4.127‐hydrate at 93 K

Raffinose [or O‐α‐D‐galactopyranosyl‐(1→6)‐α‐D‐glucopyranosyl‐(1→2)‐β‐D‐fructofuranoside] pentahydrate, C₁₈H₃₂O₁₆·5H₂O, (I), and three lower hydrates, namely the 4.433‐, (II), 4.289‐, (III), and 4.127‐hydrated, (IV), forms, obtained in the course of the dehydration of (I), have been studied. The unit cells in the space group P2₁2₁2₁ are of similar dimensions for all the crystals. The conformation of the raffinose molecules remains almost the same across the four crystal structures. The raffinose molecules are linked into a three‐dimensional hydrogen‐bonded network involving all the –OH groups, the ring and glycosidic O atoms, and the water molecules. Six water sites were identified in the structures of (II), (III) and (IV), of which W1, W4 and W6 (W = water) are partially occupied with their populations coupled. W1, W4 and one of the –OH groups of the galactose ring form an infinite hydrogen‐bonding chain around a 2₁ axis parallel to the a axis (denoted chain A), and W6 and the same –OH group form a similar chain (chain A′) disordered with chain A. The occupancy ratio of chain A to chain A′ for N‐hydrates (N is a hydration number between 4 and 5) is (N− 4):(5 −N). The transformation of chain A to chain A′ as part of the dehydration process has little effect on the rest of the structure. Thus, the dehydration proceeds without significant impact on the crystal structure.     

Heavy‐Atom Labeled Transmembrane β‐Peptides: Synthesis,CD‐Spectroscopy,and X‐ray Diffraction Studies in Model Lipid Multilayer

Transmembrane β‐peptides are promising candidates for the design of well‐controlled membrane anchors in lipid membranes. Here, we present the synthesis of transmembrane β‐peptides with and without tryptophan anchors, as well as a novel iodine‐labeled d ‐β³‐amino acid. By using one or more of the heavy‐atom labeled amino acids as markers, the orientation of the helical peptide was inferred based on the electron‐density profile determined by X‐ray reflectivity. The β‐peptides were synthesized through manual Fmoc‐based solid‐phase peptide synthesis (SPPS) and reconstituted in unilamellar vesicles forming a right‐handed 3₁₄‐helix secondary structure, as shown by circular dichroism spectroscopy. We then integrated the β‐peptide into solid‐supported membrane stacks and carried out X‐ray reflectivity and grazing incidence small‐angle X‐ray scattering to determine the β‐peptide orientation and its effect on the membrane bilayers. These β‐peptides adopt a well‐ordered transmembrane motif in the solid‐supported model membrane, maintaining the basic structure of the original bilayer with some distinct alterations. Notably, the helical tilt angle, which accommodates the positive hydrophobic mismatch, induces a tilt of the acyl chains. The tilted chains, in turn, lead to a membrane thinning effect.     

Substituent effects in trans‐p,p′‐disubstituted azobenzenes: X‐ray structures at 100 K and DFT‐calculated structures

The crystal and molecular structures of two para‐substituted azobenzenes with π‐electron‐donating –NEt₂ and π‐electron‐withdrawing –COOEt groups are reported, along with the effects of the substituents on the aromaticity of the benzene ring. The deformation of the aromatic ring around the –NEt₂ group in N,N,N′,N′‐tetraethyl‐4,4′‐(diazenediyl)dianiline, C₂₀H₂₈N₄, (I), may be caused by steric hindrance and the π‐electron‐donating effects of the amine group. In this structure, one of the amine N atoms demonstrates clear sp²‐hybridization and the other is slightly shifted from the plane of the surrounding atoms. The molecule of the second azobenzene, diethyl 4,4′‐(diazenediyl)dibenzoate, C₁₈H₁₈N₂O₄, (II), lies on a crystallographic inversion centre. Its geometry is normal and comparable with homologous compounds. Density functional theory (DFT) calculations were performed to analyse the changes in the geometry of the studied compounds in the crystalline state and for the isolated molecules. The most significant changes are observed in the values of the N=N—C—C torsion angles, which for the isolated molecules are close to 0.0°. The HOMA (harmonic oscillator model of aromaticity) index, calculated for the benzene ring, demonstrates a slight decrease of the aromaticity in (I) and no substantial changes in (II).     

Advances in Synchrotron Radiation‐based X‐ray Absorption Spectroscopy to Characterize the Fine Atomic Structure of Single‐atom Nanozymes

Single‐atom nanozymes (SAzymes) with high atomic utilization, excellent catalytic activities, and selectivity have recently attracted significant interest. Usually, they contain only isolated metal atoms embedded in host matrices. However, traditional measuring instruments are extremely difficult to obtain their useful structural information due to ultra‐low metal loading, amorphous structure, coordination with light‐weight surface atoms and/or co‐existing of other metal elements. Synchrotron radiation‐based X‐ray absorption fine structure spectroscopy (XAFS) has demonstrated its usefulness for this type of catalyst. In this mini‐review, we have summarized the recent progress using XAFS to characterize the fine atomic structure of these nanozymes. The synthetic strategies of SAzymes, the principle of XAFS, delicate structural information by XAFS, and the applications of SAzymes have been presented. Furthermore, the outlook and challenges in this active research field have also been discussed. We expect that the help of XAFS can offer a wealth of opportunities to design and develop more efficient SAzymes and apply them to various fields.     

Crystal Structure Refinement of M(NCNH)2 (M = Fe,Co) Based on Combined Neutron and X‐ray Diffraction Data

The crystal structures of Fe(NCNH)₂ and Co(NCNH)₂, isotypical with Ni(NCNH)₂, have been refined by means of combined X‐ray and neutron powder diffraction data (SPODI, FRM II). The lattice parameters are a = 6.6655(7), b = 8.7923(8), c = 3.3304(3) Å for Fe(NCNH)₂ and a = 6.5696(2), b = 8.8058(2), c = 3.2622(1) Å for Co(NCNH)₂ in the orthorhombic system Pnmm (no. 58). The positions of the hydrogen atoms have been clearly resolved.     

Rationalising the Geometric Variation between the A and B Monomers in the 1.9 Å Crystal Structure of Photosystem II

Density functional theory calculations are reported on a set of models of the water‐oxidising complex (WOC) of photosystem II (PSII), exploring structural features revealed in the most recent (1.9 Å resolution) X‐ray crystallographic studies of PSII. Crucially, we find that the variation in the Mn–Mn distances seen between the A and B monomers of this crystal structure can be entirely accounted for, in the low oxidation state (LOS) paradigm, by consideration of the interplay between two hydrogen‐bonding interactions involving proximate amino acid residues with the oxo bridges of the WOC, that is, His337 with O3 (which leads to a general elongation in the Mn–Mn distances between Mn1, Mn2 and Mn3) and Arg357 with O2 (which results in a specific elongation of the Mn2?Mn3 distance).     

Crystal structure of a high‐pressure phase of magnesium chloride hexahydrate determined by in‐situ X‐ray and neutron diffraction methods

A high‐pressure phase of magnesium chloride hexahydrate (MgCl₂·6H₂O‐II) and its deuterated counterpart (MgCl₂·6D₂O‐II) have been identified for the first time by in‐situ single‐crystal X‐ray and powder neutron diffraction. The crystal structure was analyzed by the Rietveld method for the neutron diffraction pattern based on the initial structure determined by single‐crystal X‐ray diffraction. This high‐pressure phase has a similar framework to that in the known ambient‐pressure phase, but exhibits some structural changes with symmetry reduction caused by a subtle modification in the hydrogen‐bond network around the Mg(H₂O)₆ octahedra. These structural features reflect the strain in the high‐pressure phases of MgCl₂ hydrates.