Crystallographic Unit Cell Research Articles

Novel ternary cerium-rich intermetallic compound Ce 11 Ru 3.83 In 9 : Crystal structure and low-temperature physical properties

Abstract The formation of a novel intermetallic compound with high content of cerium, Ce 11 Ru 3.83 In 9 , was established in a systematic investigation of the Ce-Ru-In ternary system. The crystal structure of this phase was revealed by a single-crystal X-ray diffraction experiment to be of the Nd 11 Pd 4 In 9 -type: orthorhombic space group Cmmm , the lattice parameters a = 14.9523(10) A, b = 22.0133(15) A, c = 3.8240(2) A, Z = 2. By means of low-temperature magnetic susceptibility, magnetization, electrical resistivity and magnetoresistivity measurements, Ce 11 Ru 3.83 In 9 was found to exhibit localized magnetism due to trivalent Ce ions, with a ferromagnetic-like long-range ordering below 6.3 K. The likely nature of the magnetic structure is a ferrimagnetic arrangement of the cerium magnetic moments sited in the five independent sublattices in the crystallographic unit cell. The characteristic feature of Ce 11 Ru 3.83 In 9 , reported before also for the isostructural phases Ce 11 Ni 4 In 9 and Ce 11 Pd 4 In 9 , is strong crystalline electric field effect. The novel compound exhibits metallic conductivity with some contribution of spin-flip Kondo scattering.

Magnetic and magnetocaloric properties of polycrystalline La0.48Ca0.52MnO3 compound at low temperature: Influence of glassy magnetic state

We report the magnetic, magnetocaloric and electrical transport properties of polycrystalline bulk La0.48Ca0.52MnO3 compound. In addition to earlier reported properties viz. charge ordering and antiferromagnetic ordering, we address the presence of glassy magnetic phase at low temperature (T<40K) in this compound. Studies on magnetic and magnetocaloric properties reveal that, pronounced glassy behavior in this compound is due to presence of ferromagnetic clusters in the low-temperature region. In addition to that, analysis of low-temperature x-ray diffraction measurements indicate increasing crystallographic unit cell volume which is attributed to the enhancement of eg-electron bandwidth at low temperature.

Bulk growth of organic non-linear optical (NLO) L-arginine 4-nitrophenolate 4-nitrophenol dihydrate (LAPP) single crystals by Sankaranarayanan–Ramasamy (SR) method

Organic non-linear optical single crystals of L-arginine 4-nitrophenolate 4-nitrophenol dihydrate (LAPP) are grown by Sankaranarayanan–Ramasamy (SR) method and slow evaporation solution technique (SEST) with the sizes of about 45 mm length, 15 mm diameter and 6 × 5 × 5 mm3, respectively. The grown crystals were characterised by single crystal X-ray diffraction to determine the crystallographic unit cell parameter values. The etch pit density of SEST and SR method grown LAPP crystals have been calculated using chemical etching analysis. The mechanical and optical properties of the SEST and SR method grown LAPP crystals are studied using Vickers microhardness and UV–vis NIR measurement, respectively. Laser damage threshold analysis has been made on cut and polished SEST and SR method grown LAPP crystal of 5 mm thickness. Photoconductivity study of LAPP crystal grown by SEST and SR method reveals positive photoconductivity nature. The thermal properties of the grown crystal were carried out by thermogravimetric and differential thermal analysis. The second-harmonic generation efficiency of LAPP crystal was determined using powder Kurtz–Perry technique and it was found to be 2.3 times that of standard potassium dihydrogen phosphate material.

Thermal characterization of tetrabasic lead sulfate used in the lead acid battery technology

The thermal production of 4PbO·PbSO4 was comprehensively studied and characterized for two syntheses routes, i.e. either heating 3PbO·PbSO4·H2O, or a mixture of 4PbO:PbSO4, in air to about 700 °C. In the 3PbO·PbSO4·H2O approach, the formation of an intermediate amorphous phase occurred at around 210 °C with the loss of H2O from the hydrated structure. Formation of 4PbO·PbSO4 initiated at around 270 °C with predominantly 4PbO·PbSO4 and 13% residual PbO·PbSO4 existing at 700 °C. With the synthesis route of mixing a stoichiometric ratio of 4PbO with PbSO4, an intermediate phase of PbO·PbSO4 formed at around 300 °C, before the 4PbO·PbSO4 phase started to form at around 500 °C. Upon further heating, 4PbO·PbSO4 was the predominant phase with 8% of PbO·PbSO4 remaining. Both samples decomposed upon further heating to 850 °C. Powder neutron diffraction studies of the final 4PbO·PbSO4 products from the two different synthesis routes showed similar crystallographic unit cell lattice parameters with slight differences in the PbO:PbSO4 contents. This could possibly be linked to differences observed in the microscopic crystallite shapes from the two synthesis routes.

Computational Dehydration of Crystalline Hydrates Using Molecular Dynamics Simulations

Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach to the dehydration of ampicillin trihydrate. The crystallographic unit cell of the trihydrate is used to construct the simulation cell containing 216 ampicillin and 648 water molecules. This system is dehydrated by removing water molecules during a 2200 ps simulation, and depending on the computational dehydration rate, different dehydrated structures were observed. Removing all water molecules immediately and removing water relatively fast (10 water molecules/10 ps) resulted in an amorphous system, whereas relatively slow computational dehydration (3 water molecules/10 ps) resulted in a crystalline anhydrate. The structural changes could be followed in real time, and in addition, an intermediate amorphous phase was identified. The computationally identified dehydrated structure (anhydrate) was slightly different from the experimentally known anhydrate structure suggesting that the simulated computational structure could represent a kinetically trapped dehydration intermediate.

Thermodynamic Insight in the High-Pressure Behavior of UiO-66: Effect of Linker Defects and Linker Expansion.

In this Article, we present a molecular-level understanding of the experimentally observed loss of crystallinity in UiO-66-type metal–organic frameworks, including the pristine UiO-66 to -68 as well as defect-containing UiO-66 materials, under the influence of external pressure. This goal is achieved by constructing pressure-versus-volume profiles at finite temperatures using a thermodynamic approach relying on ab initio derived force fields. On the atomic level, the phenomenon is reflected in a sudden drop in the number of symmetry operators for the crystallographic unit cell because of the disordered displacement of the organic linkers with respect to the inorganic bricks. For the defect-containing samples, a reduced mechanical stability is observed, however, critically depending on the distribution of these defects throughout the material, hence demonstrating the importance of judiciously characterizing defects in these materials.

Phase‐field modelling of fracture in single crystal plasticity

AbstractWe propose a phase‐field model for ductile fracture in a single crystal within the kinematically linear regime, by combining the theory of single crystal plasticity as formulated in Gurtin et al. [1] and the phase‐field formulation for ductile fracture proposed by Ambati et al. [2]. The model introduces coupling between plasticity and fracture through the dependency of the socalled degradation function from a scalar global measure of the accumulated plastic strain on all slip systems. A viscous regularization is introduced both in the treatment of plasticity and in the phase‐field evolution equation. Testing of the model on two examples for face centred cubic single crystals indicates that fracture is predicted to initiate and develop in the regions of the maximum accumulated plastic strain, which is in agreement with phenomenological observations. A rotation of the crystallographic unit cell is shown to affect the test results in terms of failure pattern and corresponding global and local response. (© 2016 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

Liquid crystalline benzothiophenes. Part 3: 2,4- and 2,7-disubstituted benzothiophenes

ABSTRACTFive series of compounds based on 2,4- and 2,7-disubstituted benzothiophenes have been prepared and studied with respect to their mesomorphic properties. The molecular structure was modified by prolonging the molecular arms (varying the alkyl chain length) and orientation of the ester linkages. It was established that the transition temperatures and the type of the formed phases strictly depend on the ester orientation and only limited number of prepared compounds exhibited mesomorphic behaviour. Based on X-ray patterns, columnar phases were identified and found that they have centred crystallographic unit cell differing in the lattice parameters for homologous compounds. Although the bend angle of the studied materials is around 90° only, they exhibited formation of phases typical of the bent-shaped liquid crystals.

Glide reflection symmetry, Brillouin zone folding, and superconducting pairing for theP4/nmmspace group

Motivated by the studies of the superconducting pairing states in the iron-based superconductors, we analyze the effects of Brillouin zone folding procedure from a space group symmetry perspective for a general class of materials with the $P4/nmm$ space group. The Brillouin zone folding amounts to working with an effective one-Fe unit cell, instead of the crystallographic two-Fe unit cell. We show that the folding procedure can be justified by the validity of a glide reflection symmetry throughout the crystallographic Brillouin zone and by the existence of a minimal double degeneracy along the edges of the latter. We also demonstrate how the folding procedure fails when a local spin-orbit coupling is included although the latter does not break any of the space group symmetries of the bare Hamiltonian. In light of these general symmetry considerations, we further discuss the implications of the glide reflection symmetry for the superconducting pairing in an effective multi-orbital $t-J_{1}-J_{2}$ model. We find that the $P4/nmm$ space group symmetry allows only pairing states with even parity under the glide reflection and zero total momentum.

A New Tool for NMR Crystallography: Complete (13)C/(15)N Assignment of Organic Molecules at Natural Isotopic Abundance Using DNP-Enhanced Solid-State NMR.

NMR crystallography of organic molecules at natural isotopic abundance (NA) strongly relies on the comparison of assigned experimental and computed NMR chemical shifts. However, a broad applicability of this approach is often hampered by the still limited (1)H resolution and/or difficulties in assigning (13)C and (15)N resonances without the use of structure-based chemical shift calculations. As shown here, such difficulties can be overcome by (13)C-(13)C and for the first time (15)N-(13)C correlation experiments, recorded with the help of dynamic nuclear polarization. We present the complete de novo (13)C and (15)N resonance assignment at NA of a self-assembled 2'-deoxyguanosine derivative presenting two different molecules in the asymmetric crystallographic unit cell. This de novo assignment method is exclusively based on aforementioned correlation spectra and is an important addition to the NMR crystallography approach, rendering firstly (1)H assignment straightforward, and being secondly a prerequisite for distance measurements with solid-state NMR.

Common effect of chemical and external pressures on the magnetic properties ofRCoPO (R=La,Pr,Nd,Sm). II.

The direct correspondence between Co band ferromagnetism and structural parameters is investigated in the pnictide oxides $R$CoPO for different rare-earth ions ($R$ = La, Pr, Nd, Sm) by means of muon-spin spectroscopy and {\it ab-initio} calculations, complementing our results published previously [G. Prando {\it et al.}, {\it Phys. Rev. B} {\bf 87}, 064401 (2013)]. Both the transition temperature to the ferromagnetic phase $T_{_{\textrm{C}}}$ and the volume of the crystallographic unit cell $V$ are found to be conveniently tuned by the $R$ ionic radius and/or external pressure. A linear correlation between $T_{_{\textrm{C}}}$ and $V$ is reported and {\it ab-initio} calculations unambiguously demonstrate a full equivalence of chemical and external pressures. As such, $R$ ions are shown to be influencing the ferromagnetic phase only via the induced structural shrinkage without involving any active role from the electronic $f$ degrees of freedom, which are only giving a sizeable magnetic contribution at much lower temperatures.

3D-Printing Crystallographic Unit Cells for Learning Materials Science and Engineering

Introductory materials science and engineering courses universally include the study of crystal structure and unit cells, which are by their nature highly visual 3D concepts. Traditionally, such topics are explored with 2D drawings or perhaps a limited set of difficult-to-construct 3D models. The rise of 3D printing, coupled with the wealth of freely available crystallographic data online, offers an elegant solution to materials science visualization problems. Here, we report a concise and up-to-date method to easily and rapidly transform actual crystallography files to 3D models of diverse unit cells for use as instructional aids.

Systematic Enumeration of sp(3) Nanothreads.

Slow decompression of crystalline benzene in large-volume high-pressure cells has recently achieved synthesis of a novel one-dimensional allotrope of sp(3) carbon in which stacked columns of benzene molecules rehybridize into an ordered crystal of nanothreads. The progenitor benzene molecules function as six-valent one-dimensional superatoms with multiple binding sites. Here we enumerate their hexavalent bonding geometries, recognizing that the repeat unit of interatomic connectivity ("topological unit cell") need not coincide with the crystallographic unit cell, and identify the most energetically favorable cases. A topological unit cell of one or two benzene rings with at least two bonds interconnecting each adjacent pair of rings, accommodates 50 topologically distinct nanothreads, 15 of which are within 80 meV/carbon atom of the most stable member. Optimization of aperiodic helicity reveals the most stable structures to be chiral. We generalize Euler's rules for ring counting to cover this new form of very thin one-dimensional carbon, calculated their physical properties, and propose a naming convention that can be generalized to handle nanothreads formed from other progenitor molecules.

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement.

Structures of multisubunit macromolecular machines are primarily determined either by electron microscopy (EM) or by X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at a higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for the generation of atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the 'phase' information that is missing from an X-ray crystallography experiment; however, integration of EM and X-ray diffraction data has been technically challenging. Here we present a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over noncrystallographic symmetry. As the resolution gap between EM and X-ray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.

Changes in SOFC Cathode Crystallographic Structure Induced by Temperature, Potential and Oxygen Partial Pressure Studied Using in-Situ HT-XRD

Reversible changes in the lattice parameters of SOFC cathode were observed depending on the temperature (T), electrode potential (E) and oxygen partial pressure (p O2) applied. At fixed T and p O2, the cathode potential noticeably influences the unit cell volume, thus, the oxygen stoichiometry and concentration of vacancies. The stabilization time of the XRD peak was in minute scale similarly with the plateau time on chronoculonometric curves. Relaxation time of the changes in crystal dimensions are correlated with electrochemical measurement data. The electrode structure (porosity) has strong influence to the shift time of XRD peak. There was registered only slight influence of oxygen partial pressure and potential to the crystallographic parameters of LSM (La0.6Sr0.4MnO3 − δ). At the same time for LSC (La0.6Sr0.4CoO3 − δ) and GSC (Gd0.6Sr0.4CoO3 − δ) the crystallographic unit cell volume was a function of electrode polarization and oxygen partial pressure. There is no remarkable vacancy formation detectable with HT-XRD in LSM cathode lattice caused by electrode polarizations applied. Thermochemical crystallographic expansivity study of LSM, LSC and GSC cathodes with in situ HT-XRD method gives valuable experimental data about the crystallographic changes caused by changes in operating parameters like cell potential, temperature, and oxygen partial pressure in cathode compartment and therefore helps to understand thermomechanical and degradation behavior as a function of different conditions applied for SOFC cathode. Figure 1

Strongly anisotropic and complex magnetic behavior in EuRhGe3

Single crystals of EuRhGe3 were studied by means of magnetic susceptibility, magnetization, heat capacity, resistivity and magnetoresistance measurements, performed in wide ranges of temperature and magnetic field strength. The compound was characterized as a Curie–Weiss paramagnet, due to divalent Eu ions, that orders antiferromagnetically at TN = 11.3 K. In the ordered state, EuRhGe3 exhibits strong magnetic anisotropy. The magnetic moments are probably nearly confined within the ab plane of the tetragonal crystallographic unit cell, and the magnetic propagation vector is likely perpendicular to this plane. The bulk thermodynamic and transport data concordantly suggest that in zero magnetic field the magnetic structure of EuRhGe3 is incommensurate with the chemical one and bears an amplitude-modulated character. In external magnetic field applied within the easy magnetization plane, two other magnetic structures were detected, each of them having an antiferromagnetic nature.

Relationship between Torsion and Anisotropic Exchange Coupling in a Tb(III)-Radical-Based Single-Molecule Magnet.

The incorporation of paramagnetic ligands within rare-earth ion clusters exhibiting large magnetic anisotropy has provided significant advancement in the design of single-molecule magnets (SMMs) with large blocking temperatures. However, the exchange interaction in such systems is complex and difficult to probe by conventional magnetometry techniques, and little is known about the structural relationships. Inelastic neutron scattering and terahertz electron paramagnetic resonance measurements are used complimentarily to investigate the large exchange interaction between a rare earth-radical pair in a Tb(III)-based SMM complex. The origin of the exchange interaction is investigated for two molecular species in the crystallographic unit cell that exhibit different bonding structures between Tb(III) and a 2pyNO radical. A correlation between the Tb-O-N-C torsion angles and the magnitudes of exchange couplings is found. Interestingly, a large nondegeneracy within the ground-state doublet is present for the larger torsion angle species. It is essential to consider the balance of two channels of exchange coupling, 2p-4f hybridization and 2p-5d charge transfer, to explain this characteristic behavior. The former channel gives the antiferromagnetic interaction, and the latter gives the ferromagnetic one. When an effective Ĵ = (1)/2 Ising-type Hamiltonian is applied, the exchange couplings are evaluated to be antiferromagnetic J(z) = 9.89 meV (79.8 cm(-1)) for the low torsion angle (3.8°) species and J(z) = 7.39 meV (59.6 cm(-1)) for the larger torsion angle (15.8°) species. It is also found that a small percentage of the transverse exchange component must be included for the larger torsion angle to account for the observed nondegenerate ground state. The symmetry of the exchange couplings is discussed by considering the characters of d and f orbitals.

Structural analysis of zeolite beta through periodic ab initio simulations of XRD and [formula omitted] and [formula omitted] NMR spectra

For large systems containing hundreds of atoms in the unit cell, as usually is observed in the zeolitic materials, the use of periodic ab initio calculations is limited by the requirement of huge computation resources. In this work, by using the primitive unit cell of the zeolite beta crystal, which is 50% smaller than its conventional crystallographic unit cell, we are able to perform periodic ab initio calculations for this system. Contrary to cluster-type calculations, the correct chemical environment of the entire zeolite beta crystal is taken into account, allowing for an accurate determination of this XRD pattern and the NMR spectra of the 29Si and 17O nuclei. In particular, we present a complete characterization of the distribution of quadrupole coupling constants (Cq), asymmetry parameter (η), and isotropic chemical shifts for the δisoSi and the δisoO, which have not yet been investigated experimentally.

Mathematical aspects of molecular replacement. III. Properties of space groups preferred by proteins in the Protein Data Bank.

The main goal of molecular replacement in macromolecular crystallography is to find the appropriate rigid-body transformations that situate identical copies of model proteins in the crystallographic unit cell. The search for such transformations can be thought of as taking place in the coset space Γ\G where Γ is the Sohncke group of the macromolecular crystal and G is the continuous group of rigid-body motions in Euclidean space. This paper, the third in a series, is concerned with viewing nonsymmorphic Γ in a new way. These space groups, rather than symmorphic ones, are the most common ones for protein crystals. Moreover, their properties impact the structure of the space Γ\G. In particular, nonsymmorphic space groups contain both Bieberbach subgroups and symmorphic subgroups. A number of new theorems focusing on these subgroups are proven, and it is shown that these concepts are related to the preferences that proteins have for crystallizing in different space groups, as observed in the Protein Data Bank.

A fragmentation and reassembly method for ab initio phasing.

Ab initio phasing with de novo models has become a viable approach for structural solution from protein crystallographic diffraction data. This approach takes advantage of the known protein sequence information, predicts de novo models and uses them for structure determination by molecular replacement. However, even the current state-of-the-art de novo modelling method has a limit as to the accuracy of the model predicted, which is sometimes insufficient to be used as a template for successful molecular replacement. A fragment-assembly phasing method has been developed that starts from an ensemble of low-accuracy de novo models, disassembles them into fragments, places them independently in the crystallographic unit cell by molecular replacement and then reassembles them into a whole structure that can provide sufficient phase information to enable complete structure determination by automated model building. Tests on ten protein targets showed that the method could solve structures for eight of these targets, although the predicted de novo models cannot be used as templates for successful molecular replacement since the best model for each target is on average more than 4.0 Å away from the native structure. The method has extended the applicability of the ab initio phasing by de novo models approach. The method can be used to solve structures when the best de novo models are still of low accuracy.