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Crystal structure and orientation, and solubility effects on adhesion and sliding friction of four metal single crystals in vacuum
A crystal structure of alpha poly-p-xylylene is proposed with the help of data of oriented crystals grown during polymerization. The unit cell is monoclinic with the parameters a = 8.57 A, b = 10.62 A, c = 6.54 A (chain axis), and beta = 101.3 deg. Four repeating units per cell lead to a calculated density of 1.185 g/cu cm and a packing density of 0.71. The probable space group is P2 sub 1/m.
Abstract Noncentrosymmetric ternary and quaternary chalcogenides are studied as promising nonlinear optical (NLO) materials in the mid‐infrared region. Here, we report the synthesis of a new material BaCu 2 SiS 4 in the A II B I 2 M IV Q 4 family ( A =divalent metal; B =monovalent metal; M =tetrel, Q =chalcogen), and discuss its crystal structure, thermal stability, optical behavior, and electronic structure. BaCu 2 SiS 4 crystallizes in the noncentrosymmetric chiral space group P 3 2 21 with lattice parameters a =6.1440(3) Å, c =15.3542(8) Å, V =501.95(6) Å 3 , Z =3. The structure features helical channels formed by corner‐sharing [CuS 4 ] and [SiS 4 ] tetrahedral units. Synthesis was carried out in a molten salt flux, as opposed to a traditional solid‐state route from elements, to minimize the formation of a competing ternary phase, Ba 2 SiS 4 . BaCu 2 SiS 4 is a semiconductor with an experimentally‐determined direct bandgap of ~2.2 eV. The material exhibits second harmonic generation (SHG) activity, confirming the noncentrosymmetric nature of the structure. Analysis of reported A II B I 2 M IV Q 4 crystal structures pointed out a correlation among potential structure types and the radii of the constituent elements. Total energy calculations were carried out to explore the relative stability of several reported crystal structures in this family of compounds.
The crystal structure of indacaterol hydrogen maleate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Indacaterol hydrogen maleate crystallizes in space groupP-1 (#24) witha= 8.86616(9),b= 9.75866(21),c= 16.67848(36) Å,α= 102.6301(10), β = 94.1736(6),γ= 113.2644(2)°,V= 1273.095(7) Å 3 , andZ= 2 at 295 K. The crystal structure consists of layers of cations and anions parallel to theab-plane. Traditional N–H⋯O and O–H⋯O hydrogen bonds link the cations and anions into chains along thea-axis. There is a strong intramolecular charge-assisted O–H⋯O hydrogen bond in the non-planar hydrogen maleate anion. There are also two C–H⋯O hydrogen bonds between the anion and cation. The cation makes a strong N–H⋯O hydrogen bond to the anion, but also acts as a hydrogen bond donor to an aromatic C in another cation. The amino group makes bifurcated N–H⋯O hydrogen bonds, one intramolecular and the other intermolecular. The hydroxyl group acts as a donor to another cation. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).
Abstract Mason‐Pfizer monkey virus protease (PR) was crystallized in complex with two pepstatin‐based inhibitors in P 1 space group. In both crystal structures, the extended flap loops that lock the inhibitor/substrate over the active site, are visible in the electron density either completely or with only small gaps, providing the first observation of the conformation of the flap loops in dimeric complex form of this retropepsin. The H‐bond network in the active site (with D26N mutation) differs from that reported for the P 2 1 crystal structures and is similar to a rarely occurring system in HIV‐1 PR.
In Gram-negative bacteria, lipopolysaccharide (LPS) is an essential component of the asymmetric outer membrane (OM). LptE is an OM lipoprotein that forms a complex with the β-barrel OM protein, LptD. Incorporation of LPS into the OM outer leaflet is essential for bacterial viability, and mediated by the LptD/E complex. The genome of Campylobacter jejuni, a major foodborne pathogen, contains over 20 putative lipoproteins including Cj1090c. Here, we report the crystal structure of Cj1090c at 2.4 Å resolution, revealing structural evidence for LptE in C. jejuni. The analysis of this crystal structure, along with the genomic context, allows us to propose the C. jejuni LPS transport system for the first time, and also permits for discussion of the features of the LptD/E complex of C. jejuni.
Crystal structure of ammonium tricyanomethide determined by X-ray diffraction
The biologically active derivative of vitamin B1; thiamin pyrophosphate; is used as cofactor by many enzymes that perform a wide range of catalytic functions in the pathways of energy production. In alpha2beta2-heterotetrameric human pyruvate dehydrogenase, the first catalytic component enzyme of human pyruvate dehydrogenase complex, this cofactor is used to cleave the C(sup alpha)-C(=0) bond of pyruvate followed by reductive acetyl transfer to lipoyl-dihydrolipoamide acetyltransferase, the second catalytic component of the complex. The dynamic nonequivalence of two, otherwise chemically equivalent, catalytic sites have puzzled researchers from earlier functional studies of this enzyme. In order to gain insight into the mechanism of action of this enzyme, we determined the crystal structure of the holoform of human pyruvate dehydrogenase at 1.958, resolution. We propose a kinetic model for the flip-flop action of this enzyme through the concerted approx. 2A, shuttle-like motion of the heterodimers. The similarity of thiamin pyrophosphate binding in human pyruvate dehydrogenase and other functionally related enzymes suggests this newly defined mechanism of shuttle-like motion of domains to be common for the family of thiamin pyrophosphate-dependent enzymes.
The local crystal structure of Y 3 NbO 7 was probed using neutron total scattering. Five different structural models were fit to the experimental pair distribution function of this material up to 15 Å. Fits of defect fluorite (Fm$\overline{3}$m), pyrochlore (Fd$\overline{3}$m), and orthorhombic C weberite models (C222 1 ) were attempted based on prior structural investigations of Y 3 NbO 7 and related fluorite-based materials. Orthorhombic P weberite (P222 1 ) and monoclinic weberite models (P112 1 ) were derived via symmetry reduction of the orthorhombic C weberite structure. All models except monoclinic weberite failed to reproduce the experimental pair distribution function. Misfits were clearly visible for peaks arising from atom pairs within the first coordination shell (defect fluorite and pyrochlore) and beyond (orthorhombic C and P weberite). By contrast, monoclinic weberite (γ ≈ 91.8°) provided an excellent fit, with no major misfits observed. This unit cell features distorted YO 8 dodecahedra, YO 7 monocapped octahedra, and NbO 6 octahedra as building blocks. Comparison between the topologies of the cationic and anionic substructures in monoclinic weberite and its parent orthorhombic C structure revealed displacements of the metal atoms along the [100] direction and a less compact spatial distribution of oxygen atoms along the a axis. In conclusion, the monoclinic weberite model presented herein may serve as a starting point to revisit structural modeling of fluorite-based materials with challenging local structures.
Magnesium silicate crystal structure, discussing transformations under high pressure, crystallochemistry and implications for physics of earth mantle
Mechanical properties of metals at low temperatures as function of crystal structure
Genome maintenance is an essential process in all cells. In prokaryotes, the RadD protein is important for survival under conditions that include DNA-damaging radiation. Precisely how RadD participates in genome maintenance remains unclear. Here we present a high-resolution X-ray crystal structure of ADP-bound Escherichia coli RadD, revealing a zinc-ribbon element that was not modelled in a previous RadD crystal structure. Insights into the mode of nucleotide binding and additional structure refinement afforded by the new RadD model will help to drive investigations into the activity of RadD as a genome stability and repair factor.
Correlated oxides, such as BiMnO 3 and LaMnO 3 , show a complex interplay of electronic correlations and crystal structure exhibiting multiple first-order phase transitions, some without a clear order parameter. The quantitative theoretical description of this temperature-dependent electronic-structural interplay in the vicinity of a Mott transition is still a challenge. Here we address this issue by simultaneously considering both structural and electronic degrees of freedom, within a self-consistent density functional theory with embedded dynamical mean field theory. Our results show the existence of novel electronic states characterized by the coexistence of insulating, semimetallic, and metallic orbitals. This state is in agreement with resonant x-ray scattering. Here we also show that electronic entropy plays a decisive role in both electronic and structural phase transitions. By self-consistent determination of both the electronic state and the corresponding crystal structure, we show that the temperature evolution of these phases can be quantitatively explained from first principles, thus demonstrating the predictive power of the theoretical method for both the structural and the electronic properties.
The crystal structure of two different samples of pyrope garnet, ideally Mg 3 Al 2 Si 3 O 12 , from South Africa was refined using the Rietveld method, space group Ia3¯d, and monochromatic synchrotron high-resolution powder X-ray diffraction (HRPXRD) data. Sample 1 from Wesselton Mine is a single cubic phase and is optically isotropic. Electron-probe microanalysis (EPMA) provided an average composition {Mg 2.30 Fe 2+ 0.26 Ca 0.42 Mn 2+ 0.02 } Σ3 [Al 1.53 Fe 3+ 0.06 Cr 3+ 0.40 Ti 4+ 0.01 Fe 2+ 0.01 ] Σ2 Si 3 O 12 , which contains a significant amount of Cr cations. The unit-cell parameter (Å) and bond distances (Å) are a = 11.56197(1) Å, average = 2.2985, Al-O = 1.9101(4), and Si-O = 1.6343(3) Å. Sample 2 from De Beers Diamond Mine has an average composition {Mg 2.33 Fe 2+ 0.33 Ca 0.33 Mn 2+ 0.01 } Σ3 [Al 1.73 Fe 3+ 0.12 Cr 3+ 0.06 Ti 4+ 0.05 Fe 2+ 0.05 ] Σ2 Si 3 O 12 and is a fine-scale intergrowth of two cubic phases. The weight percentage, unit-cell parameter (Å), and bond distances (Å) for phase 2a are 62.2(1)%, a = 11.56185(1) Å, average = 2.3006, Al-O = 1.9080(4), Si-O = 1.6334(4) Å. The corresponding values for phase 2b are 37.8(1)%, a = 11.53896(1) Å, average = 2.2954, Al-O = 1.9020(6), Si-O = 1.6334(6) Å. The two cubic phases in sample 2 cause the crystal to be optically anisotropic because of strain induce birefringence. The unit-cell parameter and bond distances for sample 1 are similar to those in phase 2a.
Binary III-N nitride semiconductors with wurtzite crystal structure such as GaN and AlN have been long used in many practical applications ranging from optoelectronics to telecommunication. The structurally related ZnGeN2 or ZnSnN2 derived from the parent binary compounds by cation mutation (elemental substitution) have recently attracted attention, but such ternary nitride materials are mostly limited to II-IV-N2 compositions. This paper demonstrates synthesis and characterization of zinc niobium nitride (Zn2NbN3) – a previously unreported II2-V-N3 ternary nitride semiconductor. The Zn2NbN3 thin films are synthesized using a one-step adsorption-controlled growth, and a two-step deposition/annealing method that suppresses the loss of Zn and N. Measurements indicate that this sputtered Zn2NbN3 crystalizes in cation-disordered wurtzite-derived structure, in contrast to chemically related rocksalt-derived Mg2NbN3 compound, also synthesized here for comparison using the two-step method. The estimated wurtzite lattice parameter ratio of Zn2NbN3 is 1.55, and the optical absorption onset is at 2.1 eV. Both of these values are lower compared to published Zn2NbN3 computational values of c/a = 1.62 and Eg = 3.5 - 3.6 eV. Additional theoretical calculations indicate that this difference is due to cation disorder in experimental samples, suggesting a way to tune the structural parameters and the resulting properties of heterovalent ternary nitride materials. Overall, this work expands the wurtzite family of nitride semiconductors to include Zn2NbN3, and suggests that related II2-V-N3 and other ternary nitrides should be possible to synthesize.
Single-component polymeric materials open up a great potential for self-assembly into mesoscale complex crystal structures that are known as Frank-Kasper (FK) phases. Predicting the packing structures of the soft-matter spheres, however, remains a challenge even when the molecular design is precisely known. Here, we investigate the role of the molecules' enthalpic interaction in determining the low-symmetry crystal structures. To this end, we synthesize architecturally asymmetric dendrons by varying their apex functionalities and examine the packing structures of the second-generation (G2) dendritic wedges. Our work shows that weakening the hydrogen bonding of the dendron apex makes the particles softer and smaller, and leads to the formation of various FK structures at lower temperatures, including the new observation of a FK C14 phase in the cone-shaped dendron systems. As a consequence of the free energy balance between the particle's interfacial tension and the chain's stretching, various packing structures are mainly tuned by designing the hydrogen bonding interaction.
Epidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of the Arabidopsis thaliana SPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.
This work details the synthesis and the crystal structures of the quaternary Zintl phases Na2CaCdSb2, Na2SrCdSb2 and Na2EuCdSb2. They are isostructural and their noncentrosymmetric structure is with the space group Pmc21 (Pearson code oP12). All structural work is carried out via single-crystal X-ray diffraction methods. The structure features [CdSb2]4– layers of corner-shared CdSb4 tetrahedra, which are stacked along the b-crystallographic axis and are separated by cations. The results from the structure refinements suggest that in addition to full cation ordering, which is typical for this structure, there also exists a possibility for an accommodation of a small degree of cation disorder.