Influence of nanovoids on α–α′ phase separation in FeCrAl oxide dispersion strengthened alloy
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Capdevila, C.↗
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CDB-AP: An application for coincidence Doppler broadening spectroscopy analysis
Coincidence Doppler Broadening (CDB) Positron Annihilation Spectroscopy (PAS) is a material analysis technique that can be used to non-destructively measure characteristics of structural defects in samples. Analyzing and comparing large datasets obtained using this technique, however, can be complicated and time intensive. The Coincidence Doppler Broadening Analysis Program (CDB-AP) is a graphical user interface that facilitates rapid analysis of many data files while using transparent processes. It is already used in three laboratories at Idaho National Laboratory and can be used in laboratories worldwide.
36 MATERIALS SCIENCE↗
Mitochondrial-targeted aryl hydrocarbon receptor and the impact of 2,3,7,8-tetrachlorodibenzo-p-dioxin on cellular respiration and the mitochondrial proteome
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor within the Per-Arnt-Sim (PAS) domain superfamily. Exposure to the most potent AHR ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), is associated with various pathological effects including metabolic syndrome. While research over the last several years has demonstrated a role for oxidative stress and metabolic dysfunction in AHR-dependent TCDD-induced toxicity, the role of the mitochondria in this process has not been fully explored. Our previous research suggested that a portion of the cellular pool of AHR could be found in the mitochondria (mitoAHR). Using a protease protection assay with digitonin extraction, we have now shown that this mitoAHR is localized to the inter-membrane space (IMS) of the organelle. TCDD exposure induced a degradation of mitoAHR similar to that of cytosolic AHR. Furthermore, siRNA-mediated knockdown revealed that translocase of outer-mitochondrial membrane 20 (TOMM20) was involved in the import of AHR into the mitochondria. In addition, TCDD altered cellular respiration in an AHR-dependent manner to maintain respiratory efficiency as measured by oxygen consumption rate (OCR). Stable isotope labeling by amino acids in cell culture (SILAC) identified a battery of proteins within the mitochondrial proteome influenced by TCDD in an AHR-dependent manner. Among these, 17 proteins with fold changes ≥ 2 are associated with various metabolic pathways, suggesting a role of mitochondrial retrograde signaling in TCDD-mediated pathologies. Collectively, these studies suggest that mitoAHR is localized to the IMS and AHR-dependent TCDD-induced toxicity, including metabolic dysfunction, wasting syndrome, and hepatic steatosis, involves mitochondrial dysfunction. - Highlights: • The mitoAHR is localized in the mitochondrial intermembrane space. • TOMM20 participates in mitoAHR translocation. • AHR contributes to the maintenance of respiratory control ratio following TCDD exposure. • TCDD-induced AHR-dependent changes in the mitochondrial proteome are identified.
60 APPLIED LIFE SCIENCES↗
Control of Peptide Amphiphile Supramolecular Nanostructures by Isosteric Replacements
Supramolecular nanostructures with tunable properties can have applications in medicine, pharmacy, and biotechnology. In this work, we show that the self-assembly behavior of peptide amphiphiles (PAs) can be effectively tuned by replacing the carboxylic acids exposed to the aqueous media with isosteres, functionalities that share key physical or chemical properties with another chemical group. Transmission electron microscopy, atomic force microscopy, and small-angle X-ray scattering studies indicated that the nanostructure’s morphologies are responsive to the ionization states of the side chains, which are related to their pK a values. Circular dichroism studies revealed the effect of the isosteres on the internal arrangement of the nanostructures. The interactions between diverse surfaces and the nanostructures and the effect of salt concentration and temperature were assessed to further understand the properties of these self-assembled systems. These results indicate that isosteric replacements allow the pH control of supramolecular morphology by manipulating the pK a of the charged groups located on the nanostructure’s surface. Theoretical studies were performed to understand the morphological transitions that the nanostructures underwent in response to pH changes, suggesting that the transitions result from alterations in the Coulomb forces between PA molecules. Furthermore, this work provides a strategy for designing biomaterials that can maintain or change behaviors based on the pH differences found within cells and tissues.
36 MATERIALS SCIENCE↗
Capturing Correlation Effects in Positron Binding to Atoms and Molecules
A major challenge in contemporary electronic structure theory involves the development of methods to describe in a balanced manner the contribution of correlation effects to energy differences. This challenge can be even greater for multicomponent systems containing more than one type of quantum particle. In the present work, we describe a flexible code for carrying out self-consistent field and configuration interaction (CI) calculations on multicomponent systems and use it to generate trial wave functions for use in diffusion Monte Carlo (DMC) calculations of the positron affinity of Be, Be 2 , Be 4 , Mg, CS 2 , and benzene. The resulting positron affinities (PAs) are in good agreement with the best values from the literature.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Modeling Interactions within and between Peptide Amphiphile Supramolecular Filaments
Many peptides are able to self-assemble into one-dimensional (1D) nanostructures, such as cylindrical fibers or ribbons of variable widths, but the relationship between the morphology of 1D objects and their molecular structure is not well understood. Here, we use coarse-grained molecular dynamics (CG-MD) simulations to study the nanostructures formed by self-assembly of different peptide amphiphiles (PAs). The results show that ribbons are hierarchical superstructures formed by laterally assembled cylindrical fibers. Simulations starting from bilayer structures demonstrate the formation of filaments, whereas other simulations starting from filaments indicate varying degrees of interaction among them depending on chemical structure. These interactions are verified by observations using atomic force microscopy of the various systems. The interfilament interactions are predicted to be strongest in supramolecular assemblies that display hydrophilic groups on their surfaces, while those with hydrophobic ones are predicted to interact more weakly as confirmed by viscosity measurements. The simulations also suggest that peptide amphiphiles with hydrophobic termini bend to reduce their interfacial energy with water, which may explain why these systems do not collapse into superstructures of bundled filaments. The simulations suggest that future experiments will need to address mechanistic questions about the self-assembly of these systems into hierarchical structures, namely, the preformation of interactive filaments vs equilibration of large assemblies into superstructures.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Enhancing Cooperativity in Bifunctional Acid–Pd Catalysts with Carboxylic Acid-Functionalized Organic Monolayers
Here, cooperative catalysts containing a combination of noble metal hydrogenation sites and Bronsted acid sites are critical for many reactions, including the deoxygenation (DO) of biomass-derived oxygenates in the upgrading of pyrolysis oil. One route toward the design of cooperative catalysts is to tether two different catalytically active functions so that they are in close proximity while avoiding undesirable interactions that can block active sites. Here, we deposited carboxylic acid (CA)-functionalized organophosphonate monolayers onto Al 2 O 3 -supported Pd nanoparticle catalysts to prepare bifunctional catalysts containing both Bronsted acid and metal sites. Modification with phosphonic acids (PAs) improved activity and selectivity for gas-phase DO reactions, but the degree of improvement was highly sensitive to both the presence and positioning of the CA group, suggesting a significant contribution from both the PA and CA sites. Short spacer lengths of 1-2 methylene groups between the phosphonate head and CA tail were found to yield the best DO rates and selectivities, whereas longer chains performed similarly to self-assembled monolayers having alkyl tails. Results from a combination of density functional theory and Fourier transform infrared spectroscopy suggested that the enhanced catalyst performance on the optimally positioned CAs was due to the generation of strong acid sites on the Al 2 O 3 support adjacent to the metal. Furthermore, the high activity of these sites was found to result from a hydrogen-bonded cyclic structure involving cooperativity between the phosphonate head group and CA tail function. More broadly, these results indicate that functional groups tethered to supports via organic ligands can influence catalytic chemistry on metal nanoparticles.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular Insight into the β-Sheet Twist and Related Morphology of Self-Assembled Peptide Amphiphile Ribbons
Self-assembly of high-aspect-ratio filaments containing β-sheets has attracted much attention due to potential use in bioengineering and biomedicine. However, precisely predicting the assembled morphologies remains a grand challenge because of insufficient understanding of the self-assembly process. We employed an atomistic model to study the self-assembly of peptide amphiphiles (PAs) containing valine–glutamic acid (VE) dimeric repeats. By changing of the sequence length, the assembly morphology changes from flat ribbon to left-handed twisted ribbon, implying a relationship between β-sheet twist and strength of interstrand hydrogen bonds. The calculations are used to quantify this relationship including both magnitude and sign of the ribbon twist angle. Interestingly, a change in chirality is observed when we introduce the RGD epitope into the C-terminal of VE repeats, suggesting arginine and glycine’s role in suppressing right-handed β-sheet formation. Furthermore, this study provides insight into the relationship between β-sheet twist and self-assembled nanostructures including a possible design rule for PA self-assembly.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Organic Modifiers Promote Furfuryl Alcohol Ring Hydrogenation via Surface Hydrogen-Bonding Interactions
Interactions between surface adsorbed species can affect catalyst reactivity, and thus, the ability to tune these interactions is of considerable importance. Deposition of organic modifiers provides one method of intentionally introducing controllable surface interactions onto catalyst surfaces. In this study, Pd/Al2O 3 catalysts were modified with either thiol or phosphonic acid (PA) ligands and tested in the hydrogenation of furanic species. The thiol modifiers were found to inhibit ring hydrogenation (RH) activity, with the degree of inhibition trending with the thiol surface coverage. This suggests that thiols do not strongly interact with the reactants and simply serve to block active sites on the Pd surface. PAs, on the other hand, were found to enhance RH when furfuryl alcohol (FA) was used as the reactant. Density functional theory calculations suggested that this enhancement was due to hydrogen-bonding interactions between FA-derived surface intermediates and PA modifiers. Here, installation of hydrogen-bonding groups on the Pd surface served to preferentially stabilize RH product states. Furthermore, the promotional effect on the RH of FA was observed to be greater when a higher-coverage PA was used, providing a rate more than twice that of the unmodified Pd/Al2O 3 . The results of this work suggest that organic ligands can be designed to impart tunable surface interactions on heterogeneous catalysts, providing an additional method of controlling catalytic performance.
09 BIOMASS FUELS↗
High Temperature Polymer Electrolyte Membrane Fuel Cells with High Phosphoric Acid Retention
Phosphoric acid loss poses immense hurdles for the durability of high-temperature polymer electrolyte membrane fuel cells (HT-PEMFCs). Here we report quaternary ammonium-biphosphate ion-pair HT-PEMFCs that do not lose phosphoric acids under normal and accelerated stress conditions. Additionally, our energetics study explains the acid loss behavior of the conventional phosphoric acid-polybenzimidazole (PA-PBI) system by two mechanisms. If PA loss occurs via acid evaporation, the acid loss is constant over time. On the other hand, when water activity in the PA-PBI system is high, exponential decay of PA loss occurs via the water replacement mechanism. Combined 31 P NMR and computational studies show that the proposed ion-pair system has six times higher interaction energy, which allows for containing all PAs in the membrane electrode assemblies under a broad range of operating conditions. In addition, polar interactions between the phosphonic acid ionomer and phosphoric acid explain acid retention in the electrodes of the ion-pair HT-PEMFCs.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structure and mechanism of the essential two-component signal-transduction system WalKR in Staphylococcus aureus
Most low GC Gram-positive bacteria possess an essential walKR two-component system (TCS) for signal transduction involved in regulating cell wall homoeostasis. Despite the well-established intracellular regulatory mechanism, the role of this TCS in extracellular signal recognition and factors that modulate the activity of this TCS remain largely unknown. Here we identify the extracellular receptor of the kinase ‘WalK’ (erWalK) as a key hub for bridging extracellular signal input and intracellular kinase activity modulation in Staphylococcus aureus . Characterization of the crystal structure of erWalK revealed a canonical Per-Arnt-Sim (PAS) domain for signal sensing. Single amino-acid mutation of potential signal-transduction residues resulted in severely impaired function of WalKR. A small molecule derived from structure-based virtual screening against erWalK is capable of selectively activating the walKR TCS. Lastly, the molecular level characterization of erWalK will not only facilitate exploration of natural signal(s) but also provide a template for rational design of erWalK inhibitors.
59 BASIC BIOLOGICAL SCIENCES↗
Mapping in situ the assembly and dynamics in aqueous supramolecular polymers
Supramolecular polymers, bonded through directional non-covalent interactions, closely mimic dynamic behaviors of biological nanofibers. However, the complexity of assembly pathways makes it highly challenging to unravel the nature of supramolecular dynamics in aqueous environments. Here we introduce a precise combinatorial titration methodology to probe in situ the assembly of peptide amphiphiles (PAs). This approach reveals a binary assembly mechanism governed by equilibrium between spheroidal micelles and β-sheet polymers. Weakening hydrogen bonding shifts the equilibrium towards micelles and decreases the internal structural order of filamentous polymers, promoting supramolecular dynamics. Extending this methodology to two-component copolymerization systems, we find a surprising tendency to form blocky nanostructures with reduced internal phase separation as the mismatch in peptide sequence decreases. Interestingly, while well-mixed copolymers acquire different dynamics, mismatched ones retain the characteristic supramolecular motion of their homopolymer counterparts. These critical insights into supramolecular dynamics offer strategies to tailor the dynamic functions of supramolecular nanomaterials.
Molecular self-assembly↗
A multimodal approach to revisiting oxidation defects in Cr 2 O 3
The oxidation of chromium in air at 700 °C was investigated with a focus on point defect behavior and transport during oxide layer growth. A comprehensive set of characterization techniques targeted characteristics of chromium oxide microstructure and chemical composition analysis. TEM showed that the oxide was thicker with longer oxidation times and that, for the thicker oxides, voids formed at the metal/oxide interface. PAS revealed that the longer the oxidation time, there was an overall reduction in vacancy-type defects, though chromium monovacancies were not found in either case. EIS found that the longer oxidized material was more electrochemically stable and that, while all oxides displayed p-type character, the thicker oxide had an overall lower charge carrier density. Together, the results suggest anion oxygen interstitials and chromium vacancy cluster complexes drive transport in an oxidizing environment at this temperature, providing invaluable insight into the mechanisms that regulate corrosion.
36 MATERIALS SCIENCE↗
Photosensing and Thermosensing by Phytochrome B Require Both Proximal and Distal Allosteric Features within the Dimeric Photoreceptor
Phytochromes (Phys) encompass a diverse collection of bilin-containing photoreceptors that help plants and microorganisms perceive light through photointerconversion between red light (Pr) and far-red light (Pfr)-absorbing states. In addition, Pfr reverts thermally back to Pr via a highly enthalpic process that enables temperature sensation in plants and possibly other organisms. Through domain analysis of the Arabidopsis PhyB isoform assembled recombinantly, coupled with measurements of solution size, photoconversion, and thermal reversion, we identified both proximal and distal features that influence all three metrics. Included are the downstream C-terminal histidine kinase-related domain known to promote dimerization and a conserved patch just upstream of an N-terminal Period/Arnt/Sim (PAS) domain, which upon removal dramatically accelerates thermal reversion. We also discovered that the nature of the bilin strongly influences Pfr stability. Whereas incorporation of the native bilin phytochromobilin into PhyB confers robust Pfr → Pr thermal reversion, that assembled with the cyanobacterial version phycocyanobilin, often used for optogenetics, has a dramatically stabilized Pfr state. Taken together, we conclude that Pfr acquisition and stability are impacted by a collection of opposing allosteric features that inhibit or promote photoconversion and reversion of Pfr back to Pr, thus allowing Phys to dynamically measure light, temperature, and possibly time.
59 BASIC BIOLOGICAL SCIENCES↗
Comprehensive characterization of the structure of Zr-based metallic glasses
Structure of metallic glasses fascinates as the generic amorphous structural template for ubiquitous systems. Its specification necessitates determination of the complete hierarchical structure, starting from short-range-order (SRO) → medium-range-order (MRO) → bulk structure and free volume (FV) distribution. This link has largely remained elusive since previous investigations adopted one-technique-at-a-time approach, focusing on limited aspects of any one domain. Reconstruction of structure from experimental data inversion is non-unique for many of these techniques. As a result, complete and precise structural understanding of glass has not emerged yet. In this work, we demonstrate the first experimental pathway for reconstruction of the integrated structure, for and glasses. Our strategy engages diverse (×7) multi-scale techniques [XAFS, 3D-APT, ABED/NBED, FEM, XRD, PAS, FHREM] on the same glass. This strategy complemented mutual limitations of techniques and corroborated common parameters to generate complete, self-consistent and precise parameters. Further, MRO domain size and inter-void separation were correlated to identify the presence of FV at MRO boundaries. This enabled the first experimental reconstruction of hierarchical subset: SRO → MRO → FV → bulk structure. The first ever image of intermediate region between MRO domains emerged from this link. We clarify that determination of all subsets is not our objective; the essence and novelty of this work lies in directing the pathway towards finite solution, in the most logical and unambiguous way.
36 MATERIALS SCIENCE↗
Proton affinities of pertechnetate (TcO 4 - ) and perrhenate (ReO 4 - )
The anions pertechnetate, TcO 4 - , and perrhenate, ReO 4 - , exhibit very similar chemical and physical properties. Revealing and understanding disparities between them enhances fundamental understanding of both. Electrospray ionization generated the gas-phase proton bound dimer (TcO 4 - )(H + )(ReO 4 - ). Collision induced dissociation of the dimer yielded predominantly HTcO 4 - and ReO 4 - , which according to Cooks’ kinetic method indicates that the proton affinity (PA) of TcO 4 - is greater than that of Re O 4 - . Density functional theory computations agree with the experimental observation, providing PA[TcO 4 - ] = 300.1 kcal mol -1 and PA[ReO 4 - ] = 297.2 kcal mol -1 . Attempts to rationalize these relative PAs based on elementary molecular parameters such as atomic charges indicate that the entirety of bond formation and concomitant bond disruption needs to be considered to understand the energies associated with such protonation processes. Although in both the gas and solution phases, TcO 4 - is a stronger base than ReO 4 - , it is noted that the significance of even such qualitative accordance is tempered by the very different natures of the underlying phenomena.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Determinants for proton location and electron coupled proton transfer in hydrogen bonded pentafluorophenol-anion clusters
This work aims to reveal the determinant factors for proton locations and electron coupled proton transfer (ECPT) in biologically relevant hydrogen bonded systems. Pentafluorophenol-anion clusters [C6F5O-•H+•A-]- are chosen to model active sites of biological functions, with the anion A- being systematically varied to ensure the proton affinities (PAs) of the anions well cover the referenced PA of C6F5O- from being appreciably smaller, similar, and to significantly larger. Negative ion photoelectron spectroscopy of these clusters provides spectroscopic evidence showing that proton location in the anionic state is largely following the PA prediction, while ECPT is observed only for the clusters with the anion possessing the electron binding energy (EBE) significantly larger than that of the referenced C6F5O-. Theoretical calculations suggest these clusters are stabilized by forming single strong hydrogen bond between donor and acceptor, and the associated charge and MO analyses fully support the experimental observations. The current holistic cluster model study indicates that PA is the right determinant that can be used to predict the proton location and describe hydrogen bonding structures, while both PA and EBE of anionic groups play important roles in facilitating ECPT process. This work was supported by U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Science, Geosciences, and Biosciences (X.-B.W.), and performed using EMSL, a national scientific user facility sponsored by DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory, which is operated by Battelle Memorial Institute for the DOE. Part of this work was supported by the National Natural Science Foundation of China (No-11604046 for JZ; No. 11727810 for ZRS), as well as “Chenguang Program” by Shanghai Education Development Foundation, Shanghai Municipal Education Commission (No. 16CG38) and Natural Science Foundation of Shanghai (No. 16ZR1448100) (JZ).
Zhang, Jian↗
Thermal evolution of defects in undoped zinc oxide grown by pulsed laser deposition
Undoped ZnO films are grown by pulsed laser deposition on c-plane sapphire with different oxygen pressures. Thermal evolutions of defects in the ZnO films are studied by secondary ion mass spectroscopy (SIMS), Raman spectroscopy, and positron annihilation spectroscopy (PAS), and with the electrical properties characterized by the room temperature Hall measurement. Oxygen deficient defect related Raman lines 560 cm{sup −1} and 584 cm{sup −1} are identified and their origins are discussed. Thermal annealing induces extensive Zn out-diffusion at the ZnO/sapphire interface and leaves out Zn-vacancy in the ZnO film. Two types of Zn-vacancy related defects with different microstructures are identified in the films. One of them dominates in the samples grown without oxygen. Annealing the sample grown without oxygen or growing the samples in oxygen would favor the Zn-vacancy with another microstructure, and this Zn-vacancy defect persists after 1100 °C annealing.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗