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Novel Cooperative Interactions and Structural Ordering in H[subscript 2]S-H[subscript 2]
Hydrogen sulfide (H{sub 2}S) and hydrogen (H{sub 2}) crystallize into a 'guest-host' structure at 3.5 GPa and, at the initial formation pressure, the rotationally disordered component molecules exhibit weak van der Waals-type interactions. With increasing pressure, hydrogen bonding develops and strengthens between neighboring H{sub 2}S molecules, reflected in a pronounced drop in S-H vibrational stretching frequency and also observed in first-principles calculations. At 17 GPa, an ordering process occurs where H{sub 2}S molecules orient themselves to maximize hydrogen bonding and H{sub 2} molecules simultaneously occupy a chemically distinct lattice site. Intermolecular forces in the H{sub 2}S+H{sub 2} system may be tuned with pressure from the weak hydrogen-bonding limit to the ordered hydrogen-bonding regime, resulting in a novel clathrate structure stabilized by cooperative interactions.
Structure of a bacterial RNA polymerase holoenzyme open promoter complex
Abstract not provided
Structural study of biotic and abiotic poorly-crystalline manganese oxides using atomic pair distribution function analysis
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Effect of vacancies on the structure and properties of Ga[subscript 2](Se[subscript 0.33]Te[subscript 0.67])[subscript 3]
Abstract not provided
Cluster-mining: an approach for determining core structures of metallic nanoparticles from atomic pair distribution function data
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Enzyme Design From the Bottom Up: An Active Nickel Electrocatalyst with a Structured Peptide Outer Coordination Sphere
Functional, peptide-containing metal complexes with a well-defined peptide structure have the potential to enhance molecular catalysts via an enzyme-like outer coordination sphere. Here, we report the synthesis and characterization of an active, peptide-based metal complex built upon the well characterized hydrogen production catalyst, Ni(PPh2NPh)2. The incorporated peptide maintains its B-hairpin structure when appended to the metal core, and the electrocatalytic activity of the peptide-based metal complex (~100,000 s-1) is fully retained. The combination of an active molecular catalyst with a structured peptide outer coordination sphere provides a scaffold that permits the incorporation of features of an enzyme-like outer-coordination sphere necessary to create molecular electrocatalysts with en-hanced functionality.
The three-dimensional structure of NeoB: An aminotransferase involved in the biosynthesis of neomycin: Structure of NeoB
Abstract not provided
The Structural Transition Behavior of CdSe/ZnS Core/shell Quantum Dots under High Pressure
The structural phase transition of CdSe/ZnS core/shell quantum dots (QDs) has been studied by in situ angle-dispersive X-ray diffraction under high pressure up to 53.6?GPa. The CdSe core transforms from wurtzite to rock-salt structure near 6.3?GPa and then to Cmcm or distorted Cmcm structure probably occurs at 45.1?GPa which has not been observed in CdSe nanomaterials before. The critical pressure from wurtzite to rock-salt and the bulk modulus of rock-salt phase are much higher than those for bulky and uncapped nanoparticle CdSe. The released sample can be kept in rock-salt phase for a certain time, verified by photoluminescence (PL) spectra, quite different from the reversible transition for pure CdSe. A reasonable interpretation of the experimental phenomena is given by comparing the bulk modulus of the core and shell and studying the stress sate of the core after decompression. Our study suggests that capping a hard shell is an effective approach to quench the high pressure phase of nanomaterial with a reversible phase transition.
Analysis of the solution structure of Thermosynechococcus elongatus photosystem I in n-dodecyl-β-d-maltoside using small-angle neutron scattering and molecular dynamics simulation
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Efficacy of acetate-amended biostimulation for uranium sequestration: Combined analysis of sediment/groundwater geochemistry and bacterial community structure
Systematic flow-through column experiments were conducted using sediments and ground water collected from different subsurface localities at the U.S. Department of Energy's Integrated Field Research Challenge site in Rifle, Colorado. The principal purpose of this study is to gain a better understanding of the interactive effects of groundwater geochemistry, sediment mineralogy, and indigenous bacterial community structures on the efficacy of uranium removal from the groundwater with/without acetate amendment. Overall, we find that the subtle variations in the sediments' mineralogy, particle size, redox conditions, as well as contents of metal(loid) co-contaminants showed a pronounced effect on the associated bacterial population and composition, which mainly determines the system's performance with respect to uranium removal. Positive relationship was identified between the abundance of dissimilatory sulfate-reduction genes (i.e., drsA), markers of sulfatereducing bacteria, and the sediments' propensity to sequester aqueous uranium. In contrast, no obvious connections were observed between the abundance of common iron-reducing bacteria, e.g., Geobacter spp., and the sediments' ability to sequester uranium. In the sediments with low bacterial biomass and the absence of sulfate-reducing conditions, abiotic adsorption onto mineral surfaces such as phyllosilicates likely played a relatively major role in the attenuation of aqueous uranium; however, in these scenarios, acetate amendment induced detectable rebounds in the effluent uranium concentrations. The results of this study suggest that reductive immobilization of uranium can be achieved under predominantly sulfate-reducing conditions, and provide insight into the integrated roles of various biogeochemical components in long-term uranium sequestration.
Mass spectrometry footprinting reveals the structural rearrangements of cyanobacterial orange carotenoid protein upon light activation
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Spatially adaptive stochastic methods for fluid–structure interactions subject to thermal fluctuations in domains with complex geometries
We develop stochastic mixed finite element methods for spatially adaptive simulations of fluid–structure interactions when subject to thermal fluctuations. To account for thermal fluctuations, we introduce a discrete fluctuation–dissipation balance condition to develop compatible stochastic driving fields for our discretization. We perform analysis that shows our condition is sufficient to ensure results consistent with statistical mechanics. We show the Gibbs–Boltzmann distribution is invariant under the stochastic dynamics of the semi-discretization. To generate efficiently the required stochastic driving fields, we develop a Gibbs sampler based on iterative methods and multigrid to generate fields with O(N) computational complexity. Our stochastic methods provide an alternative to uniform discretizations on periodic domains that rely on Fast Fourier Transforms. To demonstrate in practice our stochastic computational methods, we investigate within channel geometries having internal obstacles and no-slip walls how the mobility/diffusivity of particles depends on location. Our methods extend the applicability of fluctuating hydrodynamic approaches by allowing for spatially adaptive resolution of the mechanics and for domains that have complex geometries relevant in many applications.
Pressure-induced volume collapse and structural phase transitions in SrRuO{sub 3}
We report on the low temperature (6 K) structural properties of SrRuO{sub 3} under quasi-hydrostatic pressure studied by synchrotron X-ray powder diffraction in a diamond anvil cell. First principle calculations predict a first-order perovskite (Pv) to post-perovskite (pPv) phase transition at ∼40 GPa accompanied by a 1.9% volume collapse. Our results rule out the occurrence of a pPv phase to 54 GPa. Instead, we find a Pv to monoclinic to triclinic sequence of phase transitions. The monoclinic to triclinic phase transition at ∼38 GPa is accompanied by a 3.5% volume collapse. X-ray absorption spectroscopy indicates that this volume collapse is not accompanied by a change in Ru valence state. Our results should help guide improvements to theoretical treatments of this and other correlated d-electron systems based on density functional theory. - Graphical abstract: Unit cell volume as a function of pressure (T=6 K). Black squares and red circles correspond to Ne and He pressure media, respectively. Blue dashed lines are fit to the data before the volume collapse using a second-order Birch–Murnaghan equation of state excluding (lower curve) and including (upper curve) neutron diffraction data for the low temperature, ambient pressure volume. Dashed lines denote structural phase boundaries. Display Omitted - Highlights: • Crystal structure of SrRuO3 was studied under high pressure up to 54 GPa. • Pv to monoclinic to triclinic sequence of phase transitions was observed. • Transition to triclinic phase at ∼38 GPa is accompanied by a 3.5% volume collapse. • Volume collapse in SrRuO3 is not driven by a change in Ru valence state. • Pv-to-pPv phase transition predicted by DFT at 40 Gpa is not observed up to 54 GPa.
Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-Monophosphate
Cyclic nucleotide phosphodiesterases (PDEs) decompose second messengers cAMP and cGMP that play critical roles in many physiological processes. PDE1 of Saccharomyces cerevisiae has been subcloned and expressed in Escherichia coli . Recombinant yPDE1 has a K M of 110 μM and a k cat of 16.9 s⁻¹ for cAMP and a K M of 105 μM and a k cat of 11.8 s₅⁻¹ for cGMP. Thus, the specificity constant (k cat /K M cAMP )/(k cat /K M cGMP ) of 1.4 indicates a dual specificity of yPDE1 for hydrolysis of both cAMP and cGMP. The crystal structures of unliganded yPDE1 and its complex with GMP at 1.31 Å resolution reveal a new structural folding that is different from those of human PDEs but is partially similar to that of some other metalloenzymes such as metallo-β-lactamase. In spite of their different structures and divalent metals, yPDE1 and human PDEs may share a common mechanism for hydrolysis of cAMP and cGMP.
Structural analysis of Notch-regulating Rumi reveals basis for pathogenic mutations
Abstract not provided