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Electronic structure and optical properties of CdS{sub x}Se{sub 1−x} solid solution nanostructures from X-ray absorption near edge structure, X-ray excited optical luminescence, and density functional theory investigations
The electronic structure and optical properties of a series of iso-electronic and iso-structural CdS{sub x}Se{sub 1−x} solid solution nanostructures have been investigated using X-ray absorption near edge structure, extended X-ray absorption fine structure, and X-ray excited optical luminescence at various absorption edges of Cd, S, and Se. It is found that the system exhibits compositions, with variable local structure in-between that of CdS and CdSe accompanied by tunable optical band gap between that of CdS and CdSe. Theoretical calculation using density functional theory has been carried out to elucidate the observations. It is also found that luminescence induced by X-ray excitation shows new optical channels not observed previously with laser excitation. The implications of these observations are discussed.
Local structure and structural rigidity of the green phosphor β-SiAlON:Eu{sup 2+}
Eu{sup 2+} inserted in β-Si{sub 3−x}Al{sub x}O{sub x}N{sub 4−x} is a material that shows exceptional promise as a green-emitting phosphor. Synchrotron X-ray and neutron scattering, in conjunction with first-principles calculations and Eu L{sub 3} X-ray absorption measurements, yield a consistent picture of the composition, and the favorable position for Eu{sup 2+} substitution in the crystal structure. The Debye temperature Θ{sub D}, which is a proxy for structural rigidity relating to effectiveness as a phosphor, is very high for the starting β-Si{sub 3}N{sub 4} framework and is determined to decrease only slightly for the small amounts of Al{sup 3+} and O{sup 2−} co-substitution that are required for charge balance associated with Eu{sup 2+} insertion.
Structure of Nanocrystalline Ti 3 C 2 MXene Using Atomic Pair Distribution Function
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Structured photocathodes for improved high-energy x-ray efficiency in streak cameras
Abstract not provided
Structural insights into the recognition of Nucleoside Reverse Transcriptase Inhibitors (NRTIs) by HIV‐1 reverse transcriptase: First crystal structures with RT and the active triphosphate forms of lamivudine and emtricitabine
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The structure of CO{sub 2} hydrate between 0.7 and 1.0 GPa
A deuterated sample of CO{sub 2} structure I (sI) clathrate hydrate (CO{sub 2}·8.3 D{sub 2}O) has been formed and neutron diffraction experiments up to 1.0 GPa at 240 K were performed. The sI CO{sub 2} hydrate transformed at 0.7 GPa into the high pressure phase that had been observed previously by Hirai et al. [J. Phys. Chem. 133, 124511 (2010)] and Bollengier et al. [Geochim. Cosmochim. Acta 119, 322 (2013)], but which had not been structurally identified. The current neutron diffraction data were successfully fitted to a filled ice structure with CO{sub 2} molecules filling the water channels. This CO{sub 2}+water system has also been investigated using classical molecular dynamics and density functional ab initio methods to provide additional characterization of the high pressure structure. Both models indicate the water network adapts a MH-III “like” filled ice structure with considerable disorder of the orientations of the CO{sub 2} molecule. Furthermore, the disorder appears to be a direct result of the level of proton disorder in the water network. In contrast to the conclusions of Bollengier et al., our neutron diffraction data show that the filled ice phase can be recovered to ambient pressure (0.1 MPa) at 96 K, and recrystallization to sI hydrate occurs upon subsequent heating to 150 K, possibly by first forming low density amorphous ice. Unlike other clathrate hydrate systems, which transform from the sI or sII structure to the hexagonal structure (sH) then to the filled ice structure, CO{sub 2} hydrate transforms directly from the sI form to the filled ice structure.
Characterizing the nano-structure and defect structure of nano-scaled non-ferrous structural alloys
The presence and interaction of nanotwins, geometrically necessary dislocations, and grain boundaries play a key role in the mechanical properties of nanostructured crystalline materials. Therefore, it is vital to determine the orientation, width and distance of nanotwins, the angle and axis of grain boundary misorientations as well as the type and the distributions of dislocations in an automatic and statistically meaningful fashion in a relatively large area. In this paper, such details are provided using a transmission electron microscope-based orientation microscopy technique called ASTAR™/precession electron diffraction. The remarkable spatial resolution of this technique (~ 2 nm) enables highly detailed characterization of nanotwins, grain boundaries and the configuration of dislocations. This orientation microscopy technique provides the raw data required for the determination of these parameters. The procedures to post-process the ASTAR™/PED datasets in order to obtain the important (and currently largely hidden) details of nanotwins as well as quantifications of dislocation density distributions are described in this study. - Highlights: • EBSD cannot characterize defects such as dislocations, grain boundaries and nanotwins in severely deformed metals. • TEM based orientation microscopy technique called ASTAR™/PED was used to resolve the problem. • Locations and orientations of nanotwins, dislocation density distribution and grain boundary characters can be resolved. • This work provides the bases for further studies on the interactions between dislocations, grain boundaries and nanotwins. • The computation part is explained sufficiently which helps the readers to post process their own data.
Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies
Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum – Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among those, Mdm12, Mmm1 and Mdm34 each contain an SMP domain functioning as a lipid transfer module. We previously showed that the SMP domains of Mdm12 and Mmm1 form a hetero-tetramer. Here we describe our strategy to diversify the number of Mdm12/Mmm1 complexes suited for structural studies. We use sequence analysis of orthologues combined to protein engineering of disordered regions to guide the design of protein constructs and expand the repertoire of Mdm12/Mmm1 complexes more likely to crystallize. Using this combinatorial approach we report crystals of Mdm12/Mmm1 ERMES complexes currently diffracting to 4.5 Å resolution and a new structure of Mdm12 solved at 4.1 Å resolution. Our structure reveals a monomeric form of Mdm12 with a conformationally dynamic N-terminal β-strand; it differs from a previously reported homodimeric structure where the N-terminal β strands where swapped to promote dimerization. Based on our electron microscopy data, we propose a refined pseudo-atomic model of the Mdm12/Mmm1 complex that agrees with our crystallographic and small-angle X-ray scattering (SAXS) solution data. - Highlights: • We solved a 4.1 Å resolution crystal structure of Mdm12, the soluble subunit of ERMES. • The two Mdm12 apo monomers differ in the conformation of their N-terminal β-strands. • We reconstituted and crystallized two distinct Mdm12/Mmm1 complexes. • SAXS analysis of the complexes agrees with our previous electron microscopy data. • The structure suggests a head-to-tail association in the Mdm12/Mmm1 complex.
Structural and electronic modification of photovoltaic SnS by alloying
Emergence of a terawatt scalable photovoltaic (PV) thin film technology is currently impeded by the limited supply of relatively rare elements like In or Te, which has spurred active research in recent years on earth-abundant PV materials. Instead of searching for alternative PV materials, we approach the problem here by structural modification through alloying of a known PV material, namely, tin sulfide. Although SnS is a strong visible light absorber that is naturally p-doped, its indirect band gap reduces the open circuit voltage of SnS-based solar cells. The anisotropic crystal structure results in undesirable anisotropic transport properties. Based on the observation that the isoelectronic sulfides MgS, CaS, and SrS assume the rock-salt structure, we use ab initio calculations to explore the structure and electronic properties of metastable Sn{sub 1−x}(II){sub x}S (II = Mg, Ca, Sr) alloys, finding that the isotropic rock-salt phase is stabilized above x = 0.2–0.3, and predicting direct band gaps in the range of interest for PV applications, i.e., 0.6–1.5 eV for Ca and Sr alloying. We subsequently synthesized such Sn{sub 1−x}(Ca){sub x}S films by pulsed laser deposition, confirmed the cubic rock-salt structure, and observed optical band gaps between 1.1 and 1.3 eV. These results highlight the potential of structural modification by alloying as a route to widen the otherwise limited materials base for promising earth-abundant materials.
Oxygen trapped by rare earth tetrahedral clusters in Nd{sub 4}FeOS{sub 6}: Crystal structure, electronic structure, and magnetic properties
Single crystals of Nd{sub 4}FeOS{sub 6} were grown from an Fe–S eutectic solution. Single crystal X-ray diffraction analysis revealed a Nd{sub 4}MnOSe{sub 6}-type structure (P6{sub 3}mc, a=9.2693(1) Å, c=6.6650(1)Å, V=495.94(1) Å{sup 3}, Z=2), featuring parallel chains of face-sharing [FeS{sub 6×1/2}]{sup 4−} trigonal antiprisms and interlinked [Nd{sub 4}OS{sub 3}]{sup 4+} cubane-like clusters. Oxygen atoms were found to be trapped by Nd{sub 4} clusters in the [Nd{sub 4}OS{sub 3}]{sup 4{sub +}} chains. Structural differences among Nd{sub 4}MnOSe{sub 6}-type Nd{sub 4}FeOS{sub 6} and the related La{sub 3}CuSiS{sub 7}− and Pr{sub 8}CoGa{sub 3}-type structures have been described. Magnetic susceptibility measurements on Nd{sub 4}FeOS{sub 6} suggested the dominance of antiferromagnetic interactions at low temperature, but no magnetic ordering down to 2 K was observed. Spin-polarized electronic structure calculations revealed magnetic frustration with dominant antiferromagnetic interactions. - Graphical abstract: Trapping of oxygen in Nd{sub 4} tetrahedral clusters results in the formation of the Nd{sub 4}MnOSe{sub 6}-type Nd{sub 4}FeOS{sub 6}, in contrast to the La{sub 3}CuSiS{sub 7}-type oxygen-free Nd{sub 4}FeS{sub 7} and related Pr{sub 8}CoGa{sub 3}-type structures. Complex magnetic frustration inhibits magnetic ordering at low temperature. - Highlights: • Single crystals of Nd{sub 4}FeOS{sub 6} were grown using self-flux method. • Oxygen was found trapped by Nd{sub 4} tetrahedral clusters. • Comparison with two closely related structural types were discussed. • Magnetic measurements revealed antiferromagnetic (AFM) interaction. • VASP calculations confirmed strong magnetic frustration in AFM model.
The structure of water around the compressibility minimum
Here we present diffraction data that yield the oxygen-oxygen pair distribution function, g{sub OO}(r) over the range 254.2–365.9 K. The running O-O coordination number, which represents the integral of the pair distribution function as a function of radial distance, is found to exhibit an isosbestic point at 3.30(5) Å. The probability of finding an oxygen atom surrounding another oxygen at this distance is therefore shown to be independent of temperature and corresponds to an O-O coordination number of 4.3(2). Moreover, the experimental data also show a continuous transition associated with the second peak position in g{sub OO}(r) concomitant with the compressibility minimum at 319 K.
Structure-Guided, Single-Point Modifications in the Phosphinic Dipeptide Structure Yield Highly Potent and Selective Inhibitors of Neutral Aminopeptidases
Seven crystal structures of alanyl aminopeptidase from Neisseria meningitides (the etiological agent of meningitis, NmAPN) complexed with organophosphorus compounds were resolved to determine the optimal inhibitor-enzyme interactions. The enantiomeric phosphonic acid analogs of Leu and hPhe, which correspond to the P1 amino acid residues of well-processed substrates, were used to assess the impact of the absolute configuration and the stereospecific hydrogen bond network formed between the aminophosphonate polar head and the active site residues on the binding affinity. For the hPhe analog, an imperfect stereochemical complementarity could be overcome by incorporating an appropriate P1 side chain. The constitution of P1'-extended structures was rationally designed and the lead, phosphinic dipeptide hPhePψ[CH2]Phe, was modified in a single position. Introducing a heteroatom/heteroatom-based fragment to either the P1 or P1' residue required new synthetic pathways. The compounds in the refined structure were low nanomolar and subnanomolar inhibitors of N. meningitides, porcine and human APNs, and the reference leucine aminopeptidase (LAP). The unnatural phosphinic dipeptide analogs exhibited a high affinity for monozinc APNs associated with a reasonable selectivity versus dizinc LAP. Another set of crystal structures containing the NmAPN dipeptide ligand were used to verify and to confirm the predicted binding modes; furthermore, novel contacts, which were promising for inhibitor development, were identified, including a π-π stacking interaction between a pyridine ring and Tyr372.
Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures
The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A , which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.
On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin
Details of five very high-resolution accurate structures of bovine trypsin are compared in the context of the reproducibility of models obtained from crystals grown under identical conditions. Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C{sup α} and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5 Å and more than one third were conserved within 0.1 Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from different crystals. However, several features of residues or ligands located in flexible parts of the macromolecule may vary significantly, such as side-chain orientations and the occupancies of certain fragments.