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In situ structural study of manganese and iron oxide promoted rhodium catalysts for oxygenate synthesis
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Impact of Structural Defects and Hydronium Ion Concentration on the Stability of Zeolite BEA in Aqueous Phase
The presence of fluoride anions in the synthesis gel leads to zeolite BEA with high hydrothermal stability. This longer lifetime is caused by a lower concentration of internal silanol defects that are sites of the initial framework hydrolysis eventually destroying the lattice structure. The lifetime of these zeolites was the higher the lower the concentration of framework bridging hydroxyl groups that form hydronium ions was. While lattice hydrolysis was initiated at defect sites in all cases, the role of defects became less important as the concentration of hydronium ions increased. At higher concentration of hydrated hydronium ions, the presence of water associated with the hydrated hydronium ions limits the useful lifetime of zeolite catalysts in water. For such materials, the selective hydrophobization of the external surface extends the lifetime. Acknowledgments: S.P. and M.A.D. acknowledge support by the Materials Synthesis and Simulation Across Scales (MS3 Initiative) conducted under Laboratory Directed Research & Development Program at PNNL. H.S. and H.W. were supported by the Chemical Transformation Initiative (CTI) conducted under Laboratory Directed Research & Development Program at PNNL. J.A.L. was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.
The Fe-heme structure of met-indoleamine 2,3-dioxygenase-2 determined by X-ray absorption fine structure
Highlights: • IDO2 is a newly discovered tryptophan metabolising enzyme with a role in immunity. • IDO2’s active site contains a heme moiety for tryptophan binding and catabolism. • EXAFS/XANES analysis provides the first data of an IDO2 Fe-heme environment. • IDO2 Fe-heme exists as a low spin bis(His) form at 10 K; mixed spin-state at RT. - Abstract: Multiple-scattering (MS) analysis of EXAFS data on met-indoleamine 2,3-dioxygenase-2 (IDO2) and analysis of XANES have provided the first direct structural information about the axial donor ligands of the iron center for this recently discovered protein. At 10 K, it exists in a low-spin bis(His) form with Fe–N{sub p}(av) = 1.97 Å, the Fe–N{sub Im} bond lengths of 2.11 Å and 2.05 Å, which is in equilibrium with a high-spin form at room temperature. The bond distances in the low-spin form are consistent with other low-spin hemeproteins, as is the XANES spectrum, which is closer to that of the low-spin met-Lb than that of the high-spin met-Mb. The potential physiological role of this spin equilibrium is discussed.
Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase
Here, the functional efficacy of colocalized, linked protein domains is dependent on linker flexibility and system compaction. However, the detailed characterization of these properties in aqueous solution presents an enduring challenge. Here, we employ a novel, to our knowledge, combination of complementary techniques, including small-angle neutron scattering, neutron spin-echo spectroscopy, and all-atom molecular dynamics and coarse-grained simulation, to identify and characterize in detail the structure and dynamics of a compact form of mercuric ion reductase (MerA), an enzyme central to bacterial mercury resistance. MerA possesses metallochaperone-like N-terminal domains (NmerA) tethered to its catalytic core domain by linkers. The NmerA domains are found to interact principally through electrostatic interactions with the core, leashed by the linkers so as to subdiffuse on the surface over an area close to the core C-terminal Hg(II)-binding cysteines. How this compact, dynamical arrangement may facilitate delivery of Hg(II) from NmerA to the core domain is discussed.
A Consistent Spatially Adaptive Smoothed Particle Hydrodynamics Method for fluid-structure interactions
A new consistent, spatially adaptive, smoothed particle hydrodynamics (SPH) method for Fluid-Structure Interactions (FSI) is presented. The method combines several attributes that have not been simultaneously satisfied by other SPH methods. Specifically, it is second-order convergent; it allows for resolutions spatially adapted with moving (translating and rotating) boundaries of arbitrary geometries; and, it accelerates the FSI solution as the adaptive approach leads to fewer degrees of freedom without sacrificing accuracy. The key ingredients in the method are a consistent discretization of differential operators, a posteriori error estimator/distance-based criterion of adaptivity, and a particle-shifting technique. The method is applied in simulating six different flows or FSI problems. The new method's convergence, accuracy, and efficiency attributes are assessed by comparing the results it produces with analytical, finite element, and consistent SPH uniform high-resolution solutions as well as experimental data.
In situ characterization of silver nanoparticle synthesis in maltodextrin supramolecular structures
In this study, the use of maltodextrin supramolecular structures (MD SMS) as a reducing agent and colloidal stabilizing agent for the synthesis of Ag nanoparticles (Ag NPs) identified three key points. First, the maltodextrin (MD) solutions are effective in the formation of well-dispersed Ag NPs utilizing alkaline solution conditions, with the resulting Ag NPs ranging in size from 5 to 50 nm diameter. Second, in situ characterization by Raman spectroscopy and small angle X-ray scattering (SAXS) are consistent with initial nucleation of Ag NPs within the MD SMS up to a critical size of ca. 1 nm, followed by a transition to more rapid growth by aggregation and fusion between MD SMS, similar to micelle aggregation reactions. Third, the stabilization of larger Ag NPs by adsorbed MD SMS is similar to hemi-micelle stabilization, and monomodal size distributions are proposed to relate to integer surface coverage of the Ag NPs. Conditions were identified for preparing Ag NPs with monomodal distributions centered at 30–35 nm Ag NPs.
An analysis of the structure of an n-dodecane spray flame using TPDF modelling
With a view to understanding ignition and combustion behaviours in diesel engines, this study investigates several aspects of ignition and combustion of an n-dodecane spray in a high pressure, high temperature chamber, known as Spray A, using data resulting from modelling using the transported probability density function (TPDF) method. The model has been validated comprehensively with good to excellent agreement in our previous work against all available experimental data including for mixture-fraction and velocity fields in non-reacting cases, and flame lift-off length and ignition delay in reacting cases. This good agreement encourages further investigation of the numerical model results to help understand the structure of this flame, which serves to complement the experimental information that is available, which is very limited due to the difficult experimental conditions in which this flame exists. For example, quantitative experimental measurements of local mixture-fraction, temperature, velocity gradients, etc. are not yet possible in reacting cases. Analysis of the model results shows that two-stage ignition is found to occur across the ambient temperature conditions considered: the first stage is rapidly initiated on the lean side where temperatures are high and sequentially moves to richer, cooler conditions. The first stage is extremely resilient to turbulence, occurring in a region of very low Damkohler number. The second stage of ignition occurs first in rich mixtures in a region behind the head of the fuel jet where mixture gradients are low, and appears to be influenced strongly by turbulence. Relative to a homogeneous reactor, it is delayed on the lean side but advanced on the rich side, suggesting entrainment and mixing from the early igniting lean regions into richer mixtures is an important moderator of the ignition process. The second-stage ignition front propagates at very high velocities initially, suggesting it is a sequential ignition moving according to gradients of ignition delay and/or residence time. The flame stabilises however on the lean side in a region of much lower velocity, where turbulent velocity fluctuations are sufficiently high such that turbulent transport influences the propagation. It stabilises in a region of low Damkohler number which implies that a competition of chemistry versus micro-mixing might also be involved in stabilisation. The stabilisation mechanism is investigated by an analysis of the transport budgets, showing the flame is stabilised by autoignition but moderated by turbulent diffusion. Further analysis of the flame index supports this stabilisation mechanism, and demonstrates the simultaneous existence of non-premixed and premixed combustion modes in the same flame. Analysis of the flow fields also reveals that local entrainment and dilatation are important flow features near the flame base. (C) 2015 The Combustion Institute. Published by Elsevier Inc. All rights reserved.
The X-ray crystal structure of Shewanella oneidensis OmcA reveals new insight at the microbe-mineral interface
The x-ray crystal structure of Shewanella oneidensis OmcA, an extracellular decaheme cytochrome involved in mineral reduction, was solved to a resolution of 2.7 Å. The four OmcA molecules in the asymmetric unit were arranged so the distance between heme-5 on adjacent OmcA monomers was less than 1 nm, indicative of a transient OmcA dimer capable of intermolecular electron transfer. A previously identified hematite binding motif was identified near heme 10, forming a hydroxylated surface that would bring a heme-10 electron egress site to ~ 1 nm of mineral surface.
Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection
Protein glycosylation, an important and complex post-translational modification (PTM), is involved in various biological processes including the receptor-ligand and cell-cell interaction, and plays a crucial role in many biological functions. However, little is known about the glycan structures of important biological complex samples, and the conventional glycan enrichment strategy (i.e., size-exclusion column [SEC] separation,) prior to nuclear magnetic resonance (NMR) detection is time-consuming and tedious. In this study, we employed SEC, Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC), and ZIC-HILIC coupled with dialysis strategies to enrich the glycopeptides from the pronase E digests of RNase B, followed by NMR analysis of the glycoconjugate. Our results suggest that the ZIC-HILIC enrichment coupled with dialysis is the most efficient, which was thus applied to the analysis of biological complex sample, the pronase E digest of the secreted proteins from the fungi Aspergillus niger. The NMR spectra revealed that the secreted proteins from A. niger contain both N-linked glycans with a high-mannose core and O-linked glycans bearing mannose and glucose with 1->3 and 1->6 linkages. In all, our study provides compelling evidence that ZIC-HILIC separation coupled to dialysis is superior to the commonly used SEC separation to prepare glycopeptides for the downstream NMR analysis, which could greatly facilitate the future NMR-based glycoproteomics research.
Transient heat and mass transfer analysis in a porous ceria structure of a novel solar redox reactor
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Structural and magnetic properties of morphotropic phase boundary involved Tb1−xGdxFe2 compounds
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Local structure of NiPd solid solution alloys and its response to ion irradiation
Abstract not provided
Structural disorder, phase stability and compressibility of refractory body-centered cubic solid-solution alloys
Abstract not provided
High-pressure vapor-phase hydrodeoxygenation of lignin-derived oxygenates to hydrocarbons by a PtMo bimetallic catalyst: Product selectivity, reaction pathway, and structural characterization
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A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein
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Analysis of the rotational structure in the high-resolution infrared spectra of trans-hexatriene-2-d1 and -3-d1
Not Available