Structural and functional delineation of aerobactin biosynthesis in hypervirulent Klebsiella pneumoniae
Abstract not provided
Bailey, Daniel C.↗
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Composition and Structure of Oyster Adhesive Reveals Heterogeneous Materials Properties in a Biological Composite
Abstract not provided
Metzler, Rebecca A.↗
Structure and Potential–Dependent Selectivity in Redox–Metallopolymers: Electrochemically Mediated Multicomponent Metal Separations
Electro-responsive functional materials can play a critical role in selective metal recovery and recycling due to the need for molecular differentiation between transition metals in complex mixtures. Redox-active metallopolymers are a promising platform for electrochemical separations, offering versatile structural tuning and fast electron transfer. First, through a judicious selection of polymer structure between a main-chain metallopolymer (polyferrocenylsilane) and a pendant-group metallopolymer (polyvinylferrocene), charge-transfer interactions and binding strength toward competing metal ions are tuned, which as a result, dictate selectivity. For example, almost an order of magnitude increase in separation factor between chromate and meta-vanadate can be achieved, depending on polymer structure. Second, these metallopolymer electrodes exhibit potential-dependent selectivity that can even flip ion preference, based solely on electrical means—indicating a control parameter that is orthogonal to structural modifications. Finally, this work presents a framework for evaluating electrochemical separations in multicomponent ion mixtures and elucidates the underlying charge-transfer mechanisms resulting in molecular selectivity through a combination of spectroscopy and electronic structure calculations. Furthermore, the findings demonstrate the applicability of redox-metallopolymers in tailored electrochemical separations for environmental remediation, value-added metal recovery, waste recycling, and even mining processing.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Atomic Gradient Structure Alters Electronic Structure in 3D across the Bulk and Enhances Photoactivity
Abstract Understanding structure–function relationships enables the design of materials with tailored functionalities. The long‐standing challenge is to design materials with high active volume to improve efficiency. Tailored grain boundaries and lattice defects are traditionally used to tune the electronic structure near interfaces or defects to promote electron and hole separation. However, the active volume of point defect sites or interfaces in these traditional photocatalysts is extremely low. This study reports a structure with continuous atomic positional deformation across the bulk, altering the electronic structure in 3D and creating a significantly higher active volume. Such a structure in anatase is obtained and tuned by phase transformation during the heating process. Transmission electron microscopy and density functional theory results reveal that atomic deformations result in continuous band bending across the particles, facilitating electron–hole separation, inhibiting their recombination, and inducing dramatically enhanced photoactivity. These findings enable a different materials design paradigm that can potentially be harnessed for a broad range of applications.
Ren, Peng↗
Cation Adaptive Structures Based on Manganese Cyanide Prussian Blue Analogues: Application of Powder Diffraction Data to Solve Complex, Unprecedented Stoichiometries and New Structure Types
Abstract A Mn(II) salt and A + CN − under anaerobic conditions react to form 2‐D and 3‐D extended structured compounds of A m Mn II n (CN) m+2n stoichiometry. Here, the creation and characterization of this large family of compounds, for example AMn II 3 (CN) 7 , A 2 Mn II 3 (CN) 8 , A 2 Mn II 5 (CN) 12 , A 3 Mn II 5 (CN) 13 , and A 2 Mn II [Mn II (CN) 6 ], where A represents alkali and tetraalkylammonium cations, is reviewed. Cs 2 Mn II [Mn II (CN) 6 ] has the typical Prussian blue face centered cubic unit cell. However, the other alkali salts are monoclinic or rhombohedral. This is in accord with smaller alkali cation radii creating void space that is minimized by increasing the van der Waals stabilization energy by reducing ∠Mn−N≡C, which, strengthens the magnetic coupling and increases the magnetic ordering temperatures. This is attributed to the non‐rigidity of the framework structure due the significant ionic character associated with the high‐spin Mn II sites. For larger tetraalkylammonium cations, the high‐spin Mn sites lack sufficient electrostatic A + ⋅⋅⋅NC stabilization and form unexpected 4‐ and 5‐coordinated Mn sites within a flexible, extended framework around the cation; hence, the size, shape, and charge of the cation dictate the unprecedented stoichio‐metry and unpredictable cation adaptive structures. Antiferromagnetic coupling between adjacent Mn II sites leads to ferrimagnetic ordering, but in some cases antiferromagnetic coupling of ferrimagnetic layers are compensated and synthetic antiferromagnets are observed. The magnetic ordering temperatures for ferrimagnetic A 2 Mn II [Mn II (CN) 6 ] with both octahedral high‐ and low‐spin Mn II sites increase with decreasing ∠Mn−N≡C. The crystal structures for all of the extended structured materials were obtained by powder diffraction.
Chemistry↗
Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE b
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Smith, Kyle P.↗
Ultrasmall Mode Volumes in Plasmonic Cavities of Nanoparticle‐On‐Mirror Structures
The mode volume and Purcell factor are two important parameters to assess the performance of optical nanocavities. Achieving small mode volumes and high Purcell factors for nanocavity structures while simplifying their fabrication has been a major task to realize high‐performance and large‐scale photonic devices and systems. Different optical resonators based on nanoparticle‐on‐mirror (NPoM) structures are systematically analyzed, which are easy to fabricate and flexible to use. Direct comparison of these optical resonators is made through finite‐difference time‐domain (FDTD) simulations. The achievement of ultrasmall mode volumes below 10 −7 based on the NPoM structure through FDTD simulations is demonstrated by rationally selecting the structural parameters. Such NPoM structures provide a decent Purcell factor on the order of 10 7 , which can effectively enhance spontaneous emission and facilitate a number of photonic applications. The simulation results are confirmed by dark field scattering and second‐harmonic generation measurements. This work is scientifically important and offers practical guidelines for the design of optical resonators for state‐of‐the‐art optical and photonic devices.
Huang, Shengxi↗
Synthesis, Crystal and Electronic Structure of Layered AM Sb Compounds ( A = Rb, Cs; M = Zn, Cd): Synthesis, Crystal and Electronic Structure of Layered AM Sb Compounds ( A = Rb, Cs; M = Zn, Cd)
Synthesis, crystal structure, thermal stability, and electronic band structure of four new metal antimonides AMSb (A = Rb, Cs; M = Zn, Cd) are reported. CsZnSb and RbZnSb crystallize in the hexagonal ZrBeSi structure type, in a P6 3 /mmc space group (no. 194, Z = 2) and unit cell dimensions of a = 4.5588(2)/4.5466(4) Å and c = 11.9246(6)/11.0999(10) Å. CsCdSb and RbCdSb crystallize in the tetragonal PbFCl structure type in a P4/nmm space group (no. 129; Z = 2) and unit cell parameters of a = 4.8884(5)/4.8227(3) Å and c = 8.8897(9)/8.5492(7) Å. All four compounds are air- and water-sensitive and are shown through DSC measurements to decompose between 975 K and 1060 K. Analysis of the calculated electronic band structure shows that the Zn-containing antimonides are topologically trivial narrow bandgap semiconductors, whereas Cd-containing compounds exhibit a band inversion along Γ-Z direction.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ternary antimonide NaCd[subscript 4]Sb[subscript 3]: hydride synthesis, crystal structure and transp
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Courteau, Brittany↗
Process–structure–property relationships in bimodal machined microstructures using robust structure descriptors
Machining is a severe plastic deformation process that subjects materials to high rates of deformation and elevated temperatures. Dynamic recrystallization during severe plastic deformation drives grain refinement into the sub-micron range but the ductility and thermal stability of these structures is poor. In contrast, bimodal microstructures consisting of both fine and coarse grains have been shown to exhibit attractive strength and ductility properties at these temperatures. In this paper, we study the process–structure–property relationships for pure copper subject to a machining process where the cutting speeds are varied. Further, we investigate the role of thermal effects by varying the post-deformation cooling rates. Microstructures generated under these deformation conditions are quantified using angularly resolved chord length statistics. The derived metrics are found to be robust descriptors of the studied microstructures as they automatically capture complex features such as unimodal and bimodal distributions of grain structure, grain constituent length scales, and morphological anisotropy induced by shear deformation. The uniaxial equivalent yield strength of the generated structures are estimated using spherical nanoindentation and inverse modeling techniques. Lastly, we present a methodology for identifying the constrained property-process inverse mapping for machining using a Bayesian framework and the established forward process–structure–property mapping.
36 MATERIALS SCIENCE↗
Insights from the Structure of Mycobacterium tuberculosis Topoisomerase I with a Novel Protein Fold
The DNA topoisomerase I enzyme of Mycobacterium tuberculosis (MtTOP1) is essential for the viability of the organism and survival in a murine model. This topoisomerase is being pursued as a novel target for the discovery of new therapeutic agents for the treatment of drug-resistant tuberculosis. In this study, we succeeded in obtaining a structure of MtTOP1 by first predicting that the C-terminal region of MtTOP1 contains four repeated domains that do not involve the Zn-binding tetracysteine motifs seen in the C-terminal domains of Escherichia coli topoisomerase I. A construct (amino acids A2-T704), MtTOP1-704t, that includes the N-terminal domains (D1-D4) and the first predicted C-terminal domain (D5) of MtTOP1 was expressed and found to retain DNA cleavage-religation activity and catalyze single-stranded DNA catenation. MtTOP1-704t was crystallized, and a structure of 2.52 angstrom resolution limit was obtained. The structure of the MtTOP1 N-terminal domains has features that have not been observed in other previously available bacterial topoisomerase I crystal structures. The first C-terminal domain D5 forms a novel protein fold of a four-stranded antiparallel beta-sheet stabilized by a crossing-over alpha-helix. Since there is only one type IA topoisomerase present in Mycobacteriaceae and related Actinobacteria, this subfamily of type IA topoisomerase may be required for multiple functions in DNA replication, transcription, recombination, and repair. The unique structural features observed for MtTOP1 may allow these topoisomerase I enzymes to carry out physiological functions associated with topoisomerase III enzyme in other bacteria.
crystallization↗
First principles study of the structural, electronic, and optical properties of Sn 2+ -doped ZnO–P 2 O 5 glasses [First principles study of the structural, electronic and optical properties of Sn-doped ZnO-P2O5 glasses]
The atomic-structural, electronic, and optical properties of Sn-doped ZnO–P 2 O 5 glasses are examined using combined semi-empirical and density functional theory calculations. From model structures for two different ZnO–P 2 O 5 glass compositions, it is found that these glasses consist of nearly ideal tetrahedral PO 4 unit and largely distorted ZnO 4 and ZnO 5 units. The concentration of ZnO 5 units is calculated to increase and exceed that of ZnO 4 as the amount of ZnO in the glass is increased. Also, the concentration of terminal oxygen atoms shared by two Zn neighbors is largely increased for 70ZnO:30P 2 O 5 (70:30) glass compared to 60:40 glass, which can be rationalized by electrostatic bond strength calculations. Regarding medium-range order, calculations show that Q 1 and Q 2 structures (where Q n refers to structures containing n bridging oxygen atoms on PO 4 tetrahedra) are dominant for the 60:40 glass, while Q 0 and Q 1 prevail for the 70:30 glass, in good agreement with experimental observations. For the Sn-doped ZnO–P 2 O 5 glass, various Sn coordination geometries are found, with trigonal pyramidal SnO 3 and largely distorted pyramidal SnO 4 configurations being dominant and a small fraction of two-fold and five-fold coordinated Sn configurations also present. From combined cluster and glass model calculations, two-fold coordinated Sn are found to exhibit slightly smaller optical transition energy than three-fold and four-fold coordinated Sn. However, local variations in coordination structures throughout the glass likely result in a broad singlet transition (S 0 →S 1 ) around 5.4 eV for all the different Sn configurations. Finally, a triplet transition (S 0 →T 1 ) driven by spin-orbit coupling can occur around 4.5 – 4.8 eV, but the magnitude of this transition is predicted to be much smaller than the spin-allowed singlet transition.
36 MATERIALS SCIENCE↗
The structural response of gadolinium phosphate to pressure
Accurate elastic constants for gadolinium phosphate (GdPO{sub 4}) have been measured by single-crystal high-pressure diffraction methods. The bulk modulus of GdPO{sub 4} determined under hydrostatic conditions, 128.1(8) GPa (K′=5.8(2)), is markedly different from that obtained with GdPO{sub 4} under non-hydrostatic conditions (160(2) GPa), which indicates the importance of shear stresses on the elastic response of this phosphate. High pressure Raman and diffraction analysis indicate that the PO{sub 4} tetrahedra behave as rigid units in response to pressure and that contraction of the GdPO{sub 4} structure is facilitated by bending/twisting of the Gd–O–P links that result in increased distortion in the GdO{sub 9} polyhedra. - Graphical abstract: A high-pressure single crystal diffraction study of GdPO{sub 4} with the monazite structure is presented. The elastic behaviour of rare-earth phosphates are believed to be sensitive to shear forces. The bulk modulus of GdPO{sub 4} measured under hydrostatic conditions is 128.1(8) GPa. Compression of the structure is facilitated by bending/twisting of the Gd−O−P links that result in increased distortion in the GdO{sub 9} polyhedra. Display Omitted - Highlights: • The elastic responses of rare-earth phosphates are sensitive to shear forces. • The bulk modulus of GdPO{sub 4} measured under hydrostatic conditions is 128.1(8) GPa. • Twisting of the inter-polyhedral links allows compression of the GdPO{sub 4} structure. • Changes to the GdO{sub 9} polyhedra occur in response to pressure (<7.0 GPa).
36 MATERIALS SCIENCE↗
A family of rare earth uranium oxides, RE{sub 6}UO{sub 12-δ}, (RE = Rare Earth). Synthesis, structure and magnetic behavior
Highlights: • A series of rare earth urinates, RE{sub 6}UO{sub 12}, were synthesized using the solid state method. • The crystal structures of RE{sub 6}UO{sub 12} were refined using the Rietveld method. • Magnetic properties were measured and AF ordering was observed in RE = Gd, Tb, Dy. - Abstract: A series of rare earth uranates, RE{sub 6}UO{sub 12-δ} (RE = La, Nd, Sm – Dy, Er and Yb), were synthesized via the solid state method and their structures were determined using the Rietveld method. These compounds crystallize in the rhombohedral space group R-3H with the lattice parameters a = 10.47005(3) Å and c = 9.98034(3) Å for the La analogue. The temperature and field dependent magnetization are reported for each analogue. Antiferromagnetic ordering is observed for RE = Gd, Tb, and Dy with Néel temperatures of 2.1 K, 5.8 K, and 2.8 K, respectively. Magnetic measurements on the La{sub 6}UO{sub 12} analogue indicate the presence of some U{sup 5+}, and therefore, oxygen vacancies in the structure. The variability of the U valence is examined.
36 MATERIALS SCIENCE↗
Analysis of the structural, electronic, elastic and thermodynamic properties of CuAl2X4 (X = O, S) spinel structure
Highlights: • Fundamental properties of CuAl{sub 2}X{sub 4} (X = O, S) aluminate spinels have been investigated. • The pressure dependence of the elastic constants C{sub ij} can be successfully fit by a straight line. • CuAl{sub 2}X{sub 4} (X = O, S) compounds are mechanically stable at ambient conditions. • Temperature and pressure dependences of some macroscopic parameters are achieved. - Abstract: The structural, electronic, elastic and thermodynamic properties of oxo- and thio-spinels have been predicted based on the ultrasoft pseudo-potential scheme as implemented in the CASTEP code. The exchange-correlation potential was treated within the generalized gradient approximation (GGA-PBE). The calculated structural parameters such as lattice constants and internal parameters are in good agreement with the available experimental data. The ground state electronic band structure revealed that CuAl{sub 2}X{sub 4} (XO, S) spinels are direct band gap semiconductors with a transition along Γ-Γ symmetry points. The calculated values of elastic constants satisfy the Born criteria at ambient conditions and confirm that the spinel structures of CuAl{sub 2}O{sub 4} and CuAl{sub 2}S{sub 4} are mechanically stable. The thiospinel structure may have a phase transition under pressure, due to the negative value of C{sub 44}. The influence of temperature and pressure on macroscopic characteristics of CuAl{sub 2}O{sub 4} and CuAl{sub 2}S{sub 4} compounds was estimated using the quasi-harmonic Debye model.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
The Electronic Structure of the Metal Active Site Determines the Geometric Structure and Function of the Metalloregulator NikR
NikR is a nickel-responsive metalloregulator protein that controls the level of Ni 2+ ions in living cells. Previous studies have shown that NikR can bind a series of first-row transition metal ions but binds to DNA with high affinity only as a Ni 2+ complex. To understand this metal selectivity, S K-edge X-ray absorption spectroscopy of NikR bound to different metal ions was used to evaluate the different electronic structures. The experimental results are coupled with density functional theory calculations on relevant models. This study shows that both the Z eff of the metal ion and the donor nature of the ligands determine the electronic structure of the metal site. This impacts the geometric structure of the metal site and thus the conformation of the protein. Furthermore, this contribution of electronic structure to geometric structure can be extended to other metal selective metalloregulators.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Investigation of Structural Evolution of Li 1.1 V 3 O 8 by In Situ X-ray Diffraction and Density Functional Theory Calculations
Li 1.1 V 3 O 8 is a promising cathode material for Li-ion batteries, because of its high theoretical capacity (362 mAh g-1) and good rate performance. In this study, the structural evolution of Li 1.1 V 3 O 8 material during electrochemical dis(charge) processes was investigated using a combination of theoretical calculations and experimental data. Density functional theory (DFT) was used to predict the intermediate structures at various lithiation states, as well as the stability of major phases. In order to validate these predictions, in situ X-ray diffraction (XRD) data was collected operando, allowing for the phase transformations to be monitored under current load and eliminating the possibilities of structural relaxation processes and environmental oxidation. Rietveld refinement was performed to fit the diffraction data with the DFT-derived structures and to analyze the fractions of major phases as a function of dis(charge). The DFT calculations identified three stable states that were validated by the in situ XRD result: a Li-poor α-phase (Li1), a Li-rich α-phase (Li2.5), and a β-phase (Li4). The DFT-predicted particle shape based on the surface energy of the (100), (001), and (010) planes rationalized the preferential orientation of Li 1.1 V 3 O 8 particles along the [010] direction in the electrode. Furthermore, the onset and offset of the α → β transition, as well as the phase fractions of α and β determined via in situ XRD, related well with the DFT-derived relative stability of each phase. Thus, by integrating DFT calculations with experimental work, this work provides a thorough understanding of the structural transformations in Li 1.1 V 3 O 8 during electrochemical dis(charge).
25 ENERGY STORAGE↗