Difference Fourier Map Research Articles

Gowerite, Ca[B5O8(OH)][B(OH)3]·3H2O: Revisiting the crystal structure and exploring its formation context

Abstract Investigations into the crystal structure of gowerite are limited, and a comprehensive understanding of the H positions is lacking. Hence, in this study, we synthesized single crystals of gowerite under hydrothermal conditions and obtained reliable single-crystal X-ray diffraction data to determine the H positions, thereby facilitating elucidation of the structural characteristics and formation environment of gowerite. The crystal structure of synthetic gowerite, Ca[B5O8(OH)][B(OH)3]·3H2O, is monoclinic with unit-cell parameters: a = 12.872(4), b = 16.326(4), c = 6.5634(18) Å, and β = 121.319(3)°, and volume V = 1178.3(6) Å3. The crystal symmetry corresponds to the space group P21/a; the unit cell contains four formula units (Z = 4). The structure is refined via full-matrix least-squares on F2 to a final R1 index of 4.13% for 1730 unique observed [Fo ≥ 4σ(Fo)] reflections, measured with MoKα radiation. The locations of the H atoms are identified on the difference Fourier maps and refined considering constraints on O-H distances together with interatomic distances between the H atoms. The crystal structure is characterized by a curved, corrugated, two-dimensional sheet in the a-c plane, composed of double three-membered borate rings and Ca atoms coordinated to six O atoms from the double three-membered rings. The Ca atom is further coordinated to a H2O molecule, and an isolated B(OH)3 triangle is oriented approximately perpendicular to the sheets. Hydrogen-bonding interactions solely govern the linkages between the sheets. Consequently, three H2O groups are accommodated in the spaces between the sheets. An important feature of gowerite is that within the triangle geometry, the B-O bond length between the B atom and the hydroxyl group cannot be clearly distinguished from that between the B and O atoms. Ab initio quantum chemical calculations reveal that the molecular orbitals are spatially well spread over the three-membered borate ring, indicating that the B atoms are connected to the O atoms through covalent bonding. During the secondary mineralization process, the structural units of the fundamental building blocks (FBBs) are released from parent borate minerals, such as colemanite, priceite, and hydroboracite, by mineral weathering and inherited by the FBBs in gowerite. In addressing gaps in the existing literature, this study provides further information on the crystal structure and structural characteristics of gowerite, shedding light on its possible formation environment and growth conditions.

Variable stoichiometry and a salt-cocrystal intermediate in multicomponent systems of flucytosine: structural elucidation and their impact on stability.

New cocrystals and a salt-cocrystal intermediate system involving the antifungal drug flucytosine (FCY) and various coformers including caffeic acid (CAF), 2-chloro-4-nitrobenzoic acid (CNB), hydroquinone (HQN), resorcinol (RES) and catechol (CAL), are reported. The crystal structures of the prepared multicomponent systems were determined through SC-XRD analysis and characterized by different solid-state techniques. All FCY multicomponent systems crystallize in anhydrous form with different stoichiometric ratios. The cocrystals FCY-HQN, FCY-RES and FCY-CAL crystallize in 2:0.5, 2:0.5 and 3:2 stoichiometric ratios respectively. In contrast, FCY-CAF and FCY-CNB crystallize in a 1:1 stoichiometric ratio. The FCY-CAF cocrystal is formed via an acid-pyrimidine heterosynthon. Due to the partial proton transfer from the acid group of CNB to FCY, a three-point homosynthon is observed between two FCY molecules and the molecules interact via an N-H...O hydrogen bond between FCY and CNB. In FCY phenolic cocrystals, a single-point O-H...O hydrogen bond is observed. The formation of cocrystals and salt-cocrystal intermediate was further confirmed by difference Fourier map analysis and bond angle differences. Except for FCY-CAL, all the multicomponent systems were reproduced in the bulk scale for further characterization. A detailed Crystal Structural Database search was carried out on the multicomponent systems of FCY with acid coformers and we evaluated the formation of cocrystals/salt based on the ΔpKa values, the difference in the bond distances and bond angles. Additionally, the prepared multicomponent systems exhibited hydration stability for one month under accelerated conditions [40 (2)°C and relative humidity 90-95 (5)%].

Ray-tracing analytical absorption correction for X-ray crystallography based on tomographic reconstructions.

Processing of single-crystal X-ray diffraction data from area detectors can be separated into two steps. First, raw intensities are obtained by integration of the diffraction images, and then data correction and reduction are performed to determine structure-factor amplitudes and their uncertainties. The second step considers the diffraction geometry, sample illumination, decay, absorption and other effects. While absorption is only a minor effect in standard macromolecular crystallography (MX), it can become the largest source of uncertainty for experiments performed at long wavelengths. Current software packages for MX typically employ empirical models to correct for the effects of absorption, with the corrections determined through the procedure of minimizing the differences in intensities between symmetry-equivalent reflections; these models are well suited to capturing smoothly varying experimental effects. However, for very long wavelengths, empirical methods become an unreliable approach to model strong absorption effects with high fidelity. This problem is particularly acute when data multiplicity is low. This paper presents an analytical absorption correction strategy (implemented in new software AnACor) based on a volumetric model of the sample derived from X-ray tomography. Individual path lengths through the different sample materials for all reflections are determined by a ray-tracing method. Several approaches for absorption corrections (spherical harmonics correction, analytical absorption correction and a combination of the two) are compared for two samples, the membrane protein OmpK36 GD, measured at a wavelength of λ = 3.54 Å, and chlorite dismutase, measured at λ = 4.13 Å. Data set statistics, the peak heights in the anomalous difference Fourier maps and the success of experimental phasing are used to compare the results from the different absorption correction approaches. The strategies using the new analytical absorption correction are shown to be superior to the standard spherical harmonics corrections. While the improvements are modest in the 3.54 Å data, the analytical absorption correction outperforms spherical harmonics in the longer-wavelength data (λ = 4.13 Å), which is also reflected in the reduced amount of data being required for successful experimental phasing.

Lithium‐Filled Skutterudites by Intercalation at Ambient‐Temperature

AbstractThe incorporation of lithium as a filler species in Co1‐2xFexNixSb3 skutterudites was accomplished by intercalation at 60 °C, using n‐BuLi as a reducing agent. Solid state 7Li NMR and ICP‐MS analysis confirm the presence of lithium in the product phases and provide an estimate of the lithium content. The maximum uptake of lithium increases as cobalt is progressively substituted by an equimolar mixture of iron and nickel. Difference Fourier maps, calculated during Rietveld structure refinement using powder neutron diffraction data, locate the lithium cations at the 2a (0,0,0) sites within the cavities of the skutterudite framework. The intercalation of lithium results in reductions in thermal conductivity of up to 47 %, indicative of phonon glass electron crystal (PGEC) type behaviour. Charge transfer from lithium to the framework that accompanies intercalation results in a substantial decrease in electrical resistivity in lithiated phases and a more metal‐like temperature dependence. The increased carrier concentration also decreases the Seebeck coefficient, with the consequence that modest increases in the figure of merit occur, despite the reduced thermal conductivity.

Accurate structure models and absolute configuration determination using dynamical effects in continuous-rotation 3D electron diffraction data

Continuous-rotation 3D electron diffraction methods are increasingly popular for the structure analysis of very small organic molecular crystals and crystalline inorganic materials. Dynamical diffraction effects cause non-linear deviations from kinematical intensities that present issues in structure analysis. Here, a method for structure analysis of continuous-rotation 3D electron diffraction data is presented that takes multiple scattering effects into account. Dynamical and kinematical refinements of 12 compounds—ranging from small organic compounds to metal–organic frameworks to inorganic materials—are compared, for which the new approach yields significantly improved models in terms of accuracy and reliability with up to fourfold reduction of the noise level in difference Fourier maps. The intrinsic sensitivity of dynamical diffraction to the absolute structure is also used to assign the handedness of 58 crystals of 9 different chiral compounds, showing that 3D electron diffraction is a reliable tool for the routine determination of absolute structures.

SnSe:Kx intermetallic thermoelectric polycrystals prepared by arc-melting

Neutron powder diffraction and thermoelectric characterization of SnSe:Kx intermetallic alloys are presented. Nanostructured ingots were prepared by arc-melting elemental tin and selenium along with potassium hydride. Up to x = 0.1 of K can be incorporated into SnSe. Rietveld refinement of the diffractograms locates potassium on the Sn site in the high-temperature Cmcm structure. However, in the low-temperature Pnma structure, K cannot be localized by difference Fourier maps, indicating the incorporation of K in a disordered form in the interlayer space. STEM-EELS indicates the incorporation of K into the SnSe grains. The resistivity upon K-doping at intermediate temperatures decreases by 1–2 orders of magnitude, but at high temperature is higher than the undoped SnSe. The Seebeck coefficient of K-doped SnSe remains p-type and almost temperature independent (400 μV/K for x = 0.1). The ultralow thermal conductivity of undoped SnSe decreases further upon K-doping to below 0.3 W/m K.

An Inorganic–Organic Hybrid Polymer Cocatalyst for Photoelectrochemical Water Oxidation with Dual Functions of Accelerating Kinetics and Improving Charge Transfer

Oxygen evolution cocatalysts (OECs) play important roles in improving the efficiency of photocatalysts in solar water splitting. Inorganic–organic hybrid polymers (IOHPs), which have good electroly...

Positive/Negative Phototropism: Controllable Molecular Actuators with Different Bending Behavior

Herein, a series of molecular actuators based on the crystals of (E)-2-(4-fluorostyryl)benzo[d]oxazole (BOAF4), (E)-2-(2,4-difluorostyryl)benzo[d]oxazole (BOAF24), (E)-2-(4-fluorostyryl)benzo[d]thi...

The Order–Disorder (OD) Polytypism of [Cu2ZnTeO4]2+[SO4·H2O]2−

Abstract[Cu2ZnTeO4]2+[SO4·H2O]2− crystallizes as a category IV order‒disorder (OD) structure with two kinds of nonpolar layers with the formal composition [Cu2ZnTeO4]2+ and [SO4·H2O]2−, respectively. Reflection symmetry that is only valid for the [Cu2ZnTeO4]2+ layers leads to two ways of placing the [SO4·H2O]2− layers. Two of the polytypes are of a maximum degree of order (MDO1: P21/m and MDO2: Pnma). The crystal under investigation is mostly of the MDO2 polytype. Remaining positive electron density peaks in the difference Fourier maps indicate fragments of the MDO1 polytype.

Syntheses and crystal structures of a new pyrazine dicarboxamide ligand, N 2,N 3-bis-(quinolin-8-yl)pyrazine-2,3-dicarboxamide, and of a copper perchlorate binuclear complex.

The title pyrazine dicarboxamide ligand, N 2,N 3-bis-(quinolin-8-yl)pyrazine-2,3-dicarboxamide (H2L1), C24H16N6O2, has a twisted conformation with the outer quinoline groups being inclined to the central pyrazine ring by 9.00 (6) and 78.67 (5)°, and by 79.94 (4)° to each other. In the crystal, molecules are linked by C-H⋯O hydrogen bonds, forming layers parallel to the (10) plane, which are in turn linked by offset π-π inter-actions [inter-centroid distances 3.4779 (9) and 3.6526 (8) Å], forming a supra-molecular three-dimensional structure. Reaction of the ligand H2L1 with Cu(ClO4)2 in aceto-nitrile leads to the formation of the binuclear complex, [μ-(3-{hy-droxy[(quinolin-8-yl)imino]-meth-yl}pyrazin-2-yl)[(quinolin-8-yl)imino]-methano-lato]bis-[diaceto-nitrile-copper(II)] tris-(per-chlor-ate) aceto-nitrile disolvate, [Cu2(C24H15N6O2)(CH3CN)4](ClO4)3·2CH3CN or [Cu2(HL1-)(CH3CN)4](ClO4)3·2CH3CN (I). In the cation of complex I, the ligand coordinates to the copper(II) atoms in a bis-tridentate fashion. A resonance-assisted O-H⋯O hydrogen bond is present in the ligand; the position of this H atom was located in a difference-Fourier map. Both copper(II) atoms are fivefold coordinate, being ligated by three N atoms of the ligand and by the N atoms of two aceto-nitrile mol-ecules. The first copper atom has a perfect square-pyramidal geometry while the second copper atom has a distorted shape. In the crystal, the cation and perchlorate anions are linked by a number of C-H⋯O hydrogen bonds, forming a supra-molecular three-dimensional structure.

Manganese behavior in hydroxyapatite crystals revealed by X-ray difference Fourier maps

The use of magnetic nanoparticles in association with scaffolds is considered an important way to transform typical passive scaffolds into active scaffolds. Manganese can develop magnetic properties in hydroxyapatites, as can iron, copper, cobalt and samarium, but lacks the high toxicity of these latter compounds. Because the magnetic properties exhibited by transition metal-containing hydroxyapatite are entirely dependent on site occupation and on the formation of magnetic oxides under heating, it is extremely important to understand how manganese behaves when inserted into hydroxyapatite. In this paper, we demonstrated by using X-ray difference Fourier maps that the insertion of Mn into the hydroxyapatite structure induces several perturbations in its hexagonal channels, with a preference for occupying Ca(2) sites, particularly when the hydroxyapatite lattice is poorly ordered and has CO32− inserted at PO43− sites. When CO32− is released at high temperature and the structure is better ordered, Ca(1) sites become more susceptible to occupation by Mn atoms, while the occupation of PO43− sites by MnO43− is reduced. However, with increasing time and calcination temperature, Mn atoms tend to be released from the hydroxyapatite structure in the form of Mn3O4 nanoparticles through the hydroxyl channels, occupying Ca(2) sites in the final stage of the segregation pathway. These findings are fundamental to the development of new strategies to synthesize active hydroxyapatite-based scaffolds under remote control by a magnetic field.

Exploring new hydrated delta type vanadium oxides for lithium intercalation.

Three hydrated double layered vanadium oxides, namely Na0.35V2O5·0.8(H2O), K0.36(H3O)0.15V2O5 and (NH4)0.37V2O5·0.15(H2O), were obtained by using mild hydrothermal conditions. Their delta type structural frameworks were solved by high-resolution synchrotron X-ray powder diffraction and the interlayer spacings were interpreted from difference Fourier maps. The inter-slab distances are modulated by the water content and the special arrangements of the alkali and ammonium cations. The XPS measurements denote mixed valence systems with high contents of V4+ ions up to 40%. The monitoring of the V4+ EPR signal over time suggests a reduction of the electronic delocalization on account of the partial oxidation to V5+. The electrochemical performance of the active phases is strongly conditioned by the vacuum-drying process of the electrodes, showing better capacity retention when vacuum is not applied. In situ X-ray diffraction shows a structural mechanism of contraction/expansion of the bilayers upon lithium insertion/extraction where the alkali ions behave as structural stabilizers. Galvanostatic cycling at very low current density implies migration of the alkali "pillars" triggering the collapse of the structure.

Structural analysis of biological targets by host:guest crystal lattice engineering

To overcome the laborious identification of crystallisation conditions for protein X-ray crystallography, we developed a method where the examined protein is immobilised as a guest molecule in a universal host lattice. We applied crystal engineering to create a generic crystalline host lattice under reproducible, predefined conditions and analysed the structures of target guest molecules of different size, namely two 15-mer peptides and green fluorescent protein (sfGFP). A fusion protein with an N-terminal endo-α-N-acetylgalactosaminidase (EngBF) domain and a C-terminal designed ankyrin repeat protein (DARPin) domain establishes the crystal lattice. The target is recruited into the host lattice, always in the same crystal form, through binding to the DARPin. The target structures can be determined rapidly from difference Fourier maps, whose quality depends on the size of the target and the orientation of the DARPin.

Aluminum dual doping and oxygen transport pathway in novel Sr11Mo4−xAlxO23 oxide-ion solid electrolytes

Three new electrolytes of composition Sr11Mo4-xAlxO23-δ (x = 0.5, 1.0 and 1.5) were synthesized by wet-chemistry procedures (citrate method) as polycrystalline samples. They were crystallographically studied from synchrotron and neutron diffraction techniques. They derive from the Sr11Mo4O23 complex perovskite, which can be rewritten as Sr1.75□0.25SrMoO5.75, highlighting the relationship with double perovskites A2B′B″O6. From these analyses via Rietveld refinement, a dual doping was found from synchrotron data, where the aluminum is equally allocated at both Sr (B′) and Mo (B″) sites. A detailed analysis of the neutron data from Difference Fourier Maps (DFM) unveiled the oxygen delocalization around the Mo site. From the refined crystal structures at room and high temperatures, a Bond Valence Sum Map (BVSM) analysis was useful to find the oxygen pathway in the crystal structure, and the minimum density to allow connections among oxygen atoms. The structural characterization was complemented with thermogravimetric and thermodilatometric analysis. The ionic conductivity was measured from electrochemical impedance spectroscopy (EIS) in wet and dry air and nitrogen atmospheres.

Solving the structure of Lgl2, a difficult blind test of unsupervised structure determination

In the companion paper by Ufimtsev and Levitt [Ufimtsev IS, Levitt M (2019) Proc Natl Acad Sci USA, 10.1073/pnas.1821512116], we presented a method for unsupervised solution of protein crystal structures and demonstrated its utility by solving several test cases of known structure in the 2.9- to 3.45-Å resolution range. Here we apply this method to solve the crystal structure of a 966-amino acid construct of human lethal giant larvae protein (Lgl2) that resisted years of structure determination efforts, at 3.2-Å resolution. The structure was determined starting with a molecular replacement (MR) model identified by unsupervised refinement of a pool of 50 candidate MR models. This initial model had 2.8-Å RMSD from the solution. The solved structure was validated by comparison with a model subsequently derived from an alternative crystal form diffracting to higher resolution. This model could phase an anomalous difference Fourier map from an Hg derivative, and a single-wavelength anomalous dispersion phased density map made from these sites aligned with the refined structure.

Dynamic Disorder Restriction of Methylammonium (MA) Groups in Chloride-Doped MAPbBr3 Hybrid Perovskites: A Neutron Powder Diffraction Study.

The hybrid methylammonium (MA) lead halide MAPbX3 perovskites present an appealing optoelectronic behavior with applications in high-efficiency solar cells. The orientation of the organic MA units may play an important role in the properties, given the degrees of freedom for internal motion of MA groups within the PbX6 network. The present neutron powder diffraction study reveals the dynamic features of the MA units in the hybrid perovskite series MAPb(Br1-x Clx )3 , with x=0, 0.33, 0.5, 0.67, and 1. From difference Fourier maps, the H and C/N positions were located within the PbX6 lattice; the refinement of the crystal structures unveiled the MA conformations. Three different orientations were found to exist as a function of the chlorine content (x) and, therefore, of the cubic unit-cell size. These conformations are stabilized by H-bond interactions with the halide ions, and were found to agree with those reported from theoretical calculations.

On the role of isotopic composition in crystal structure, thermal and charge-transport characteristics of dodecaborides LuNB12 with the Jahn-Teller instability

Crystal structures, thermal and charge-transport (resistivity and Seebeck coefficient) characteristics of dodecaborides LuNB12 are studied to determine the role of boron isotopic composition N = 10, 11, natural. Small distortions of the fcc lattice are observed and attributed to cooperative Jahn-Teller effect in the boron sublattice. The Einstein and Debye temperatures, respectively for Lu and B atoms, are determined based on equivalent atomic displacement parameters (ADPs) refined as a part of structure model. Additionally, ADP values are separated into temperature dependent and independent components, arising from (i) thermal and (ii) zero temperature vibrations, together with (iii) static shifts of few atoms from lattice sites. Atomic disordering is most expressed in LunatB12 as follows from its ADP values and the Schottky anomalies in heat capacity. The largest static ADP components of LunatB12 are surprisingly combined with the lower resistivity and thermopower as compared to isotopically pure crystals. One may suppose the static shifts (defects) are centers of pinning facilitating formation of additional conductive channels (dynamic charge stripes), which reveal themselves on difference Fourier maps of electron density.

Crystal Structure of the Protonated Germanide Cluster [HGe9]3−

A single crystal X-ray diffraction study of the new compound [Rb([2.2.2]crypt)]2[Rb([18]crown−6)][HGe9]·4NH3 revealed the presence of the first protonated nine-atom germanide cluster [HGe9]3−. It forms from Rb4Ge9 in liquid ammonia, so that [Ge9]4− can be considered as the base and [HGe9]3− its formally conjugated acid. The H atom is attached to a germanium vertex atom of the basal square plane, as it is known for [RGe9]3− (R = C5H9, Mes, etc.) or [HE9]3− (E = Si, Sn). In addition, the proton could be located unambiguously in the Fourier difference map. [HGe9]3− also represents a nido cluster species with 22 cluster-bonding electrons, which can be considered the most stable structure for nine-atom cluster species for all group 14 elements.

Locating Si atoms in Si-doped boron carbide: A route to understand amorphization mitigation mechanism

The well-documented formation of amorphous bands in boron carbide (B4C) under contact loading has been identified in the literature as one of the possible mechanisms for its catastrophic failure. To mitigate amorphization, Si-doping was suggested by an earlier computational work, which was further substantiated by an experimental study. However, there have been discrepancies between theoretical and experimental studies, about Si replacing atom/s in B12 icosahedra or the C-B-C chain. Dense single phase Si-doped boron carbide was produced through a conventional scalable route. A powder mixture of SiB6, B4C, and amorphous boron was reactively sintered, yielding a dense single phase Si-doped boron carbide material. A combined analysis of Rietveld refinement on XRD pattern coupled with electron density difference Fourier maps and DFT simulations were performed in order to investigate the location of Si atoms in the boron carbide lattice. Si atoms occupy an interstitial position, between the icosahedra and the chain. These Si atoms are bonded to the chain end C atoms, which result in a kinked chain. Additionally, these Si atoms are also bonded to the neighboring equatorial B atom of the icosahedra, which is already bonded to the C atom of the chain, forming a bridge like structure. Owing to this bonding, Si is anticipated to stabilize the icosahedra through electron donation, which is expected to help in mitigating stress-induced amorphization. Possible supercell structures are suggested along with the most plausible structure for Si-doped boron carbide.

Silicon Containing Nine Atom Clusters from Liquid Ammonia Solution: Crystal Structures of the First Protonated Clusters [HSi9]3– and [H2{Si/Ge}9]2–

Experiments in liquid ammonia, originally aiming at reactions between Si containing Zintl clusters and transition metal complexes, lead to crystallization of several solvates of nine‐atomic cluster compounds. Starting with the solid Zintl compounds K12Si17, K6Rb6Si17, Rb12Si17, or K12Si8Ge9, the following compounds were crystallized: K4Si9·9 NH3 (1), K4[Si5.6Ge3.4]·9NH3 (2), K0.8Rb3.2Si9·5NH3 (3), K5Si9(OH)·8NH3 (4), K6.5Si9[H0.5N3(Si(NH2)2)3]·4.5NH3 (5), and (Rb[2.2.2]crypt)3Si9·NH3 (6). Most intriguingly, the structural characterization of [K(18‐crown‐6)]3[HSi9]·2NH3·2thf (7) and [K(18‐crown‐6)]2[H2Si4.9Ge4.1]·py (8), succeeded after dilution with tetrahydrofurane and exchange of NH3 by pyridine respectively. The different crystallization products cover bare [E9]4–, purely from Si as well as from mixed Si9–xGex composition, and partially oxidized [Si9]3– clusters, whereas compounds 7 and 8 contain the first protonated nine‐atomic Si clusters, [HSi9]3– and [H2Si4.9Ge4.1]2–. The hydrogen atoms of the protonated clusters in 7 and 8 could be located from difference Fourier maps. Besides an unharmed [Si9]4– cluster compound 5 consists of a cyclotrisilazane ring which arises from an ammonolysis reaction of one of the Si components in the solution.