Single-crystal Diffractometer Research Articles

Intermetallic compounds RE 2Ga2Mg (RE = Tb–Tm, Lu) with Mo2B2Fe-type structure

Abstract The rare earth intermetallic compounds RE 2Ga2Mg with RE = Tb–Tm and Lu were synthesized from the elements in sealed tantalum ampoules in a high-frequency furnace. These rare earth-rich phases crystallize with the tetragonal Mo2B2Fe-type structure, space group P4/mbm and Z = 2. The polycrystalline samples were characterized through their Guinier powder patterns. The structures of Er2Ga2.092(1)Mg0.908(1), Tm2Ga2.037(1)Mg0.963(1) and Lu2Ga2.176(1)Mg0.824(1) have been refined from single crystal X-ray diffractometer data. The refinements revealed small homogeneity ranges (small degrees of Mg/Ga mixing on the 2a sites). The magnesium atoms show square planar coordination by Ga2 dumbbells (282 pm Mg–Ga and 257 pm Ga–Ga in the lutetium compound). Geometrically one can describe the RE 2Ga2Mg phases as 1:1 intergrowth structures of CsCl and AlB2-related slabs of compositions REMg and REGa2. From DFT based calculations, charge transfer from the rare earth and magnesium atoms towards gallium can be illustrated in electron localization function ELF slice planes showing strong localization around gallium in the basal plane as well as along the tetragonal c axis signaling Ga–Ga pair interactions. The site-projected density of states DOS and COOP data further quantify this observation. Temperature dependent magnetic susceptibility measurements show Pauli paramagnetism for Sc2Ga2Mg and Lu2Ga2Mg with low room temperature susceptibility values of 2.1(1) × 10−4 and 1.1(1) × 10−4 emu mol−1, respectively. Ho2Ga2Mg, Er2Ga2Mg and Tm2Ga2Mg are Curie-Weiss paramagnets with stable trivalent rare earth ground states. Antiferromagnetic ordering was detected below the Néel temperatures of T N = 18.6(1) (RE = Ho), 11.9(1) (RE = Er) and 6.4(1) K (RE = Tm). The three compounds show metamagnetic transitions in their 3 K magnetization isotherms. Tm2Ga2Mg exhibits a square loop behavior with small hysteresis.

CRISTAL-ITE: a single-crystal X-ray diffractometer scale model for scientific dissemination

CRISTAL-ITE: a single-crystal X-ray diffractometer scale model for scientific dissemination

Development update of PIONEER, a single-crystal neutron diffractometer at the Second Target Station, ORNL

Development update of PIONEER, a single-crystal neutron diffractometer at the Second Target Station, ORNL

Quick and robust PDF data acquisition using a laboratory single-crystal X-ray diffractometer for study of polynuclear lanthanide complexes in solid form and in solution

Self-assembled polynuclear lanthanide hydroxo complexes are important objects in the reticular chemistry approach to the design of various functional materials. Revealing their structure in the solid state and understanding the molecular mechanism of self-assembly in solution require a universal and reliable structural method. Pair distribution function (PDF) analysis is a powerful technique which enables structural insight for a wide range of crystalline and amorphous materials on the nanoscale, but commonly measurements are performed at synchrotron X-ray sources or on specially designed laboratory diffractometers. In the present paper, a standard Bruker D8 QUEST single-crystal X-ray diffractometer equipped with a micro-focus Mo tube and CMOS Photon III detector was adapted to measure PDF data of high quality with Q max = 16.97 Å–1 for solid and liquid samples. An improved data collection strategy and the original data reduction software FormagiX enable calibration and azimuthal full-frame integration of 2D frames, delivering reliable PDFs up to 80 Å with instrumental parameters Q damp = 0.018 Å−1 and Q broad = 0.010 Å−1. The effectiveness of the developed approach was demonstrated with reference samples and real-case studies of tetranuclear lanthanide hydroxocarboxylates in solid form and in solution.

Intermediate ytterbium valence in YbRhSn2

Abstract The stannide YbRhSn2 has been synthesized. An arc-melted Rh25Sn48 precursor sample was reacted with ytterbium in a sealed tantalum ampoule in an induction furnace. The structure of YbRhSn2 was refined from single-crystal X-ray diffractometer data: MgCuAl2 type, Cmcm, a = 433.10(3), b = 1076.63(8), c = 739.36(5) pm, wR2 = 0.0676, 444 F 2 values and 16 variables. The rhodium and tin atoms form a three-dimensional [RhSn2] δ− polyanionic network with short Rh–Sn (271–273 pm) and Sn–Sn (301–324 pm) distances. The tin substructure is an orthorhombically distorted lonsdaleite network. YbRhSn2 shows paramagnetic behavior with a reduced magnetic moment of 2.2(1) µB per ytterbium atom, classifying it as an intermediate-valent compound.

Lu37Ru16.4In4 – coloring and vacancy formation in a new structure type closely related to a 8 × 8 × 8 bcc superstructure

Abstract The lutetium-rich intermetallic compound Lu37Ru16.4In4 was synthesized by induction melting of the elements in a sealed tantalum ampoule and subsequent annealing. The Lu37Ru16.4In4 structure was refined from single crystal X-ray diffractometer data: new type, I a 3 ‾ d $Ia\overline{3}d$ , a = 2756.21(11) pm, wR2 = 0.0579, 3056 F 2 values and 92 variables. The superstructure formation of Lu37Ru16.4In4 is discussed on the basis of a group–subgroup scheme starting from the bcc structure as the aristotype.

Ligand Modified and Light Switched On/Off Single-Chain Magnets of {Fe 2 Co} Coordination Polymers via Metal-to-Metal Charge Transfer

Ligand Modified and Light Switched On/Off Single-Chain Magnets of {Fe ₂ Co} Coordination Polymers via Metal-to-Metal Charge Transfer

EWALD: A macromolecular diffractometer for the second target station.

Revealing the positions of all the atoms in large macromolecules is powerful but only possible with neutron macromolecular crystallography (NMC). Neutrons provide a sensitive and gentle probe for the direct detection of protonation states at near-physiological temperatures and clean of artifacts caused by x rays or electrons. Currently, NMC use is restricted by the requirement for large crystal volumes even at state-of-the-art instruments such as the macromolecular neutron diffractometer at the Spallation Neutron Source. EWALD's design will break the crystal volume barrier and, thus, open the door for new types of experiments, the study of grand challenge systems, and the more routine use of NMC in biology. EWALD is a single crystal diffractometer capable of collecting data from macromolecular crystals on orders of magnitude smaller than what is currently feasible. The construction of EWALD at the Second Target Station will cause a revolution in NMC by enabling key discoveries in the biological, biomedical, and bioenergy sciences.

Diffraction methods in the characterization of new mineral species

Data from publications describing new minerals in the periods 2001–2005 and 2016–2020 have been analysed to evaluate the contributions of diffraction methods to the new mineral characterisations. The two periods were chosen to be on either side of a sudden increase in new mineral descriptions from ∼50 to 120 per year and coincidentally correspond to the changeover from the majority (60%) of the new descriptions using photographic film cameras to record the powder diffraction patterns of the minerals, to using modern diffractometers. During both periods, diffraction data obtained using laboratory-based single-crystal diffractometers accounted for almost three-quarters of the crystallographic studies. Modern diffractometers can now routinely be used to collect high-quality data on crystals down to a few μm in size, once the province of synchrotrons. Large facility-based diffraction centres like synchrotrons and scientific nuclear reactors account for less than 10% of the new mineral publications. The review focuses on diffraction methods for the characterisation of fine-grained minerals, with sub-μm sized crystals. Transmission electron microscopy/electron diffraction methods are important for these cases, with an exponential increase in 3D ED methods during the last 15 years and increased usage of electron back-scattered diffraction methods for micro-inclusion minerals, especially in meteorites.

Ordered CaCu5-type phases REPd2Zn3 (RE = Y, La–Nd, Sm, Gd–Dy)

Abstract The ternary intermetallic phases REPd2Zn3 (RE = Y, La–Nd, Sm, Gd–Dy) were synthesized from the elements by induction melting in sealed niobium ampoules followed by annealing. The CaCu5-type samples (space group P6/mmm) were characterized through Guinier powder patterns. The structures of YPd2Zn3 (a = 523.91(4), c = 430.88(3) pm, wR2 = 0.0570, 96 F 2 values, 9 variables) and NdPd2Zn3 (a = 535.08(7), c = 427.81(6) pm, wR2 = 0.0217, 123 F 2 values, 9 variables) were refined from single-crystal X-ray diffractometer data. The zinc atoms form Kagome layers in AA stacking which leave trigonal prismatic voids for the palladium and hexagonal prismatic voids for the rare earth atoms. The Zn–Zn distances within the Kagome network of YPd2Zn3 are 262 pm and the Pd–Zn distances in the Pd@Zn6 trigonal prisms are 263 pm.

The solid solutions TbCuIn1–x M x (M = Al, Ga)

Abstract The complete solid solutions TbCuIn1–x M x (M = Al, Ga) were studied by powder X-ray diffraction and scanning electron microscopy for samples equilibrated at T = 873 K. The influence of In substitution by Al or Ga, the solubility ranges and the changes of unit cell parameters have been determined: TbCuIn1.0–0Al0–1.0 (ZrNiAl type, space group P 6 ‾ 2 $\overline{6}2$ m, a = 0.7457(1)–0.7035(1), c = 0.3958(1)–0.4044(1) nm, V = 0.1906–0.1733 nm3); TbCuIn1–0.8Ga0–0.2 (ZrNiAl type, a = 0.74569(5)–0.73882(13), с = 0.39582(3)–0.39663(14) nm, V = 0.1906–0.1875 nm3); TbCuIn0.3–0Ga0.7–1.0 (KHg2 type, Imma, а = 0.43943(9)–0.43750(5), b = 0.70833(12)–0.70537(6), с = 0.74866(12)–0.74525(7) nm, V = 0.2330–0.2300 nm3). The crystal structure of TbCuIn0.42(1)Al0.58(1) was refined from single-crystal X-ray diffractometer data: ZrNiAl type, P 6 ‾ 2 $\overline{6}2$ m, a = 0.71633(6), c = 0.40785(3) nm, wR2 = 0.0379, 291 F 2 values and 16 variables. The basic crystal chemical features are discussed.

Scandium–copper–indides deriving from the ZrNiAl and MnCu2Al type structures

Abstract Phase analytical studies in the Sc–Cu–In system led to samples of the solid solutions ScCu1–x–y In1+x and ScCu2–x In which were studied by X-ray powder diffraction. At room temperature the compounds ScCu1–x–y In1+x crystallize with the ZrNiAl type, space group P 6 ‾ $\overline{6}$ 2m. Exemplarily, the structure of ScCu0.76In1.17 was refined from single crystal X-ray diffractometer data, revealing strong anisotropic displacements for the scandium atoms and a mixed occupied Cu/In site. Superstructure formation is observed at low temperatures. The ScCu0.78In1.14 and ScCu0.76In1.16 structures were refined from diffraction data recorded at 90 K. Both compounds adopt the HfRhSn type, space group P 6 ‾ $\overline{6}$ 2c, a klassengleiche subgroup of index 2; doubling of the subcell c axis. The Cu/In filled trigonal Sc6 prisms are strongly distorted in the superstructure, resulting from pairwise dislocation of the Cu/In atoms from ideal positions within an equidistant chain to shorter (311.0 pm) and longer (392.8 pm) Cu/In–Cu/In distances. Single crystal data of the Heusler phases ScCu1.95In and ScCu1.94In show small degrees of copper vacancies.

Crystallographic capture of caged diamondoids: Camphor and adamantanes’ guests‐encapsulation on specific recognition‐sites of host MOF

The research aimed at the detection of most stable caged diamondoids with varying functional groups, within host MOF by single crystal diffractometer, along with the observation of the trends, for recognition-sites, non-covalent interactions, encapsulation-efficiency, and occupancy of encapsulated diamondoids. The research adopted an optimized experiment and soaking strategy for guest-uptake by crystalline sponge method. Thus, the comparative structure revelation of an analogous-series of cage-compounds, with varying functionalities, in the same Zn-tpt MOF, was the core theme of this paper.In the method, dissolved diamondoids were soaked in the activated crystalline sponge, accredited to the shift of the crystallography study, to a non-crystalline state. MOF was acclimatized to match with the guests, to target the effective capture of diamondoids. Non-covalent capture of easily recognizable, cage-structured molecules was achieved, despite depraved crystal quality, due to strong guest-host interaction in the hydrophobic environment of crystalline sponge. Thus, by sorting the guest and host relation and optimizing the experimental conditions, guests were inserted into the designated MOF.

Study of a position-sensitive scintillator neutron detector prototype based on 6LiF/ZnS scintillator and silicon photomultiplier arrays readout

Due to the shortage of the 3He gas and its rapidly increasing price, scintillator detectors, the advantages of which are high spatial resolution and capability of detection in real time, become widely used in many neutron instruments. In this work, a position-sensitive neutron detector consisting of a 6LiF/ZnS scintillation screen and a silicon photomultiplier array linked to a capacitive network to detect the positions of incident neutrons, is constructed and tested. To evaluate the detector performance, a series of neutron beam experiments with the detector prototype were performed in the BL20 at the China Spallation Neutron Source. The spatial resolution was measured, and the energy-selective neutron imaging and Bragg edge measurements of a 316L stainless steel sample were performed. A sub-millimeter spatial resolution could be obtained for the detector prototype under study. The detector with such a high spatial resolution is promising for applications in neutron scattering experimental installations, especially for neutron single-crystal diffractometers.

RE 3Rh2Sn4 (RE = Y, Gd–Tm, Lu) – first stannides with Lu3Co2In4 type structure

Abstract The stannides RE 3Rh2Sn4 (RE = Y, Gd–Tm, Lu) were synthesized from the elements by arc-melting and subsequent annealing (1220 K for RE = Y, Gd–Tm and 1170 K for RE = Lu) in sealed silica ampoules for 11 days. X-ray powder diffraction studies confirm the hexagonal Lu3Co2In4 type structure, space group P 6 ‾ $P\overline{6}$ . The structure of Gd3Rh2Sn4 was refined from single crystal X-ray diffractometer data for a twinned crystal: a = 744.04(6), c = 409.23(4) pm, wR2 = 0.0288, 567 F 2 values and 21 variables. The RE 3Rh2Sn4 stannides derive from the well-known equiatomic stannides RERhSn (≍RE 3Rh3Sn3) by Rh/Sn ordering within the RE 6 trigonal prisms. The striking structural motif is the trigonal planar tin coordination of the Sn2 atoms with 288 pm Sn2–Sn1 distances. The Sn2 atoms carry substantially more negative charge than the Sn1 atoms. This is underlined by 119Sn isomer shifts of δ = 1.86(1) mm s−1 for Sn1 and δ = 2.26(1) mm s−1 for Sn2 detected in the Mössbauer spectrum of Lu3Rh2Sn4. From atoms in molecules (AIM) analysis of the charge density obtained with calculation based on density functional theory (DFT) for Y3Rh2Sn4, the charge transfer proceeds from yttrium towards more electronegative rhodium. Little departure from neutrality is observed for tin whose itinerant s-like states are little involved with the bonding. The site projected density of states (DOS) and the crystal orbital overlap population (COOP) plots further illustrate these observations and reveal major Y–Rh and Rh–Sn bonding, while Y–Sn bonding is weaker.

Crystal structure of Dy11Ge4.33In5.67 and Tm11Ge4In6 from X-ray single-crystal and powder data

Abstract Single crystals of Dy11Ge4.33In5.67 were grown from a sample of the starting composition Dy55Ge20In25 by arc-melting and subsequent annealing. Dy11Ge4.33In5.67 crystallizes with the Sm11Ge4In6-type structure, space group I4/mmm, which was refined from single-crystal X-ray diffractometer data: a = 11.4329(16), c = 16.168(3) Å, wR2 = 0.0341, 927 F 2 values and 42 refined parameters. The isotypic compound Tm11Ge4In6 was characterized by X-ray powder diffraction: a = 11.262(2), c = 15.979(3) Å, R Bragg = 3.53%. The Sm11Ge4In6-type structure is a coloring variant of the Ho11Ge10 type, realized through germanium-indium ordering. The p-element substructure has four crystallographically independent sites: isolated germanium atoms (Ge4− Zintl anions), In4 squares and In/Ge–In/Ge dumb-bells with pronounced Ge/In mixing.

CRISTAL-ITE: a single-crystal X-ray diffractometer scale model for scientific dissemination

This article presents the design and manufacture of an automated scale model of a four-circle single-crystal X-ray diffractometer that can be used for scientific dissemination. The purpose of this device is to reach out to the wider public and students to introduce them in an entertaining way to one of the laboratory apparatuses to which they do not usually have access, to talk to them about crystallography in the broadest sense, to develop concepts in various fields of science and technology, and to initiate interest and discussions. The main technical aspects of the project are described, with the expectation that such an approach could be useful to anyone involved in scientific dissemination and could be developed for other laboratory equipment and other disciplines. This kind of device can also be the subject of scientific and technological projects in close collaboration with educational institutions.

Crystal structure of the compound ScCo2Si2: single crystal investigation

For the first time, the complete single crystal structure study of the compound ScCo 2 Si 2 was performed. It belongs to the CeGa 2 Al 2 structure type, Pearson’s symbol tI 10,139, space group I 4/ mmm , lattice parameters a =3.7775(3) c =9.6208(11) Å. The compound was prepared by arc-melting of the initial elements with the purity of not less than 99.9 % under argon followed by annealing in silica tubes at 800 °C for 350 h. Single crystals for structural examination were selected under a microscope from the broken alloys obtained. X-ray diffraction data of one of the irregularly faceted single crystals obtained at a temperature of 300(2) K by means of single crystal X-ray diffractometer Bruker D8 Venture with monochromatized Mo K α-radiation. The structure is refined using the program SHELXL, version 2018/3 (full-matrix least-squares refinement with anisotropic atomic parameters), R 1 = 0,0247, wR 2 = 0,0614 for 57 unique reflections with I o > 2 σ(I o ) and 8 refined parameters. Coordinates of atoms are the following: 2Sc at 2 а 0 0 0; 4Co at 4 d 0 1/2 1/4; 4Si at 4 e 0 0 z , z =0.3776(2). Coordination numbers of Sc, Co and Si atoms are 20, 12 and 9, respectively. The interatomic distances, with the exception of Co–Si, are longer than the sum of the metal radii of the corresponding atoms. Co–Si distances (2.2525(9) Å) are smaller than the sum of the radii of these atoms (2.42 Å) and indicate a significant interaction between Co and Si in the structure. Currently known three scandium ternary compounds ScM 2 Si 2 (M=Co, Ni, Cu) are members of complete series of compounds RM 2 Si 2 (R=rare earths) isotypic with CeGa 2 Al 2 . Crystal chemical analysis of scandium intermetallic compounds of stoichiometric composition ScM 2 X 2 (M= d -element; X= p -element) was performed. Scandium occupies a special place among rare earths and shows crystal chemical affinity both with rare earths and Zr and Hf. Keywords : ternary silicides, rare earth elements, single crystal, crystal structure.

SDPD-SX: combining a single crystal X-ray diffraction setup with advanced powder data structure determination for use in early stage drug discovery

A method for routine molecular crystal structure determination on very small (typically <0.1 mg) amounts of crystalline material using powder X-ray diffraction data from a laboratory-based single-crystal diffractometer is reported.

Oxazolyl-Pyrimidines As Antibacterial And Antitubercular Agents: Synthesis, Biological Evaluation, in-silico ADMET And Molecular Docking Study

In search of novel biologically potent compounds, some new oxazolyl pyrimidines (7a-g) have been prepared in the current investigation. All new compounds were characterized using various spectroanalytical techniques such as FT-IR, NMR (1H & 13C), X-Ray single crystal diffractometer, elemental analysis, and mass spectral analysis. Further, the structure of one of the chalcone derivative 6b has been studied by X-Ray single crystal diffractometer. All new hybrids (7a-f) were screened in vitro for their antitubercular activity against M. tuberculosis H37Rv. All the newly prepared molecules exhibited good anti-mycobacterial activity. Amongst all compounds, 7d, 7e and 7f demonstrated the highest potency (MIC = 3.12 µg/mL). In addition, all the new derivatives were also screened for their in vitro antibacterial activity against three selected bacterial strains. New compounds have been docked for the CYP121 enzyme with favorable binding interactions. Further, in silico ADMET prediction and drug-like properties were also evaluated signifying that compounds are encouraging candidates for the design and development of new anti-TB agents with enriched activity and enhanced safety profile.