Influence of Selective Carbon 1s Excitation on Auger–Meitner Decay in the ESCA Molecule
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
SEARCH · Search NASA
Results for “Chemical binding”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Atomic-Scale Interface for Pt Nanoparticles on SrTiO 3 (001)
The interfacial structure formed by Pt nanoparticles grown epitaxially on a SrTiO 3 (001) surface by pulsed laser deposition was studied by X-ray standing-wave (XSW) excited core-level photoelectron emission. The XSW-generated 3D atomic map of the Pt and interfacial oxygens for the oxidized Pt/SrTiO 3 interface differs significantly from that of the as-deposited interface. After oxidation, the Pt atoms shifted upward and their atomic occupation at fcc-like sites evolved as the oxidation temperature increased. Interfacial oxygen atoms were differentiated from bulk O atoms by the chemical shift in the binding energy of their 1s electrons. After oxidation, the interfacial oxygen atoms rearranged to form a TiO 2 bilayer at the interface. Furthermore, these results provide a more complete description of the strong metal–support interaction process at the interface.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Coverage Self-Consistent Microkinetic Model for Vapor-Phase Formic Acid Decomposition over Pd/C Catalysts
An iterative approach utilizing density functional theory (DFT, PW91-GGA)-informed mean-field microkinetic models and reaction kinetics experiments is used to determine the reaction mechanism and the active site for formic acid (HCOOH, FA) decomposition over a Pd/C catalyst. Models parametrized using DFT energetics on clean Pd(100) and Pd(111) required large corrections to the DFT energetics for capturing our experimental data. Further, both Pd(111) and Pd(100) models predicted a high coverage of adsorbed CO (CO*), inconsistent with the assumption of a clean surface at which the rate parameters for these models were calculated. To better represent the active site under reaction conditions and explicitly account for the presence of CO*, subsequent microkinetic models were formulated using DFT energetics that were calculated on partially (5/9 ML) CO*-covered Pd (111) and (100) facets. Upon parameter adjustment, the resultant 5/9 ML CO*-covered Pd(100) model, although consistent in terms of CO* coverage, was unable to capture the dehydration path measured in the experiments and was, therefore, deemed not to offer an accurate representation of the active site for FA decomposition over Pd/C. In contrast, a partially CO*-covered Pd(111) model was better at representing the catalytic active site, as in addition to being consistent in terms of CO* coverages, it required small adjustments of the DFT parameters to accurately capture the experimental data set (both dehydrogenation and dehydration). Our results suggest that the reaction occurs via the spectroscopically elusive carboxyl (COOH*) intermediate and that spectator CO*-assisted decomposition pathways play an important role under typical experimental conditions. In addition, our study highlights the importance of striving for coverage self-consistent microkinetic models and for including spectator-assisted mechanisms in order to develop an improved picture of the active site under reaction conditions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Computational and Experimental Approaches to Controlling Bacterial Microcompartment Assembly
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Impact of Vertex Functionalization on Flexibility of Porous Organic Cages
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Dynamics of pectic homogalacturonan in cellular morphogenesis and adhesion, wall integrity sensing and plant development
Homogalacturonan (HG) is the most abundant pectin subtype in plant cell walls. Although it is a linear homopolymer, its modification states allow for complex molecular encoding. HG metabolism affects its structure, chemical properties, mobility and binding capacity, allowing it to interact dynamically with other polymers during wall assembly and remodelling and to facilitate anisotropic cell growth, cell adhesion and separation, and organ morphogenesis. HGs have also recently been found to function as signalling molecules that transmit information about wall integrity to the cell. Here we highlight recent advances in our understanding of the dual functions of HG as a dynamic structural component of the cell wall and an initiator of intrinsic and environmental signalling. Here, we also predict how HG might interconnect the cell wall, plasma membrane and intracellular components with transcriptional networks to regulate plant growth and development.
59 BASIC BIOLOGICAL SCIENCES↗
Demystifying the Stern layer at a metal–electrolyte interface: Local dielectric constant, specific ion adsorption, and partial charge transfer
Electric double layer (EDL) represents one of the most basic concepts in electrochemistry and is pertinent to diverse engineering applications ranging from electrocatalysis to energy storage. Whereas phenomenological and coarse-grained models have been long established to describe ionic distributions in the diffuse layer, a faithful prediction of the physicochemical properties of the electrode–electrolyte interface from a molecular perspective remains a daunting challenge. In this work, we investigate the charging behavior of an Ag (111) electrode in NaF aqueous solutions leveraging experimental results and theoretical calculations based on the classical density functional theory for ion distributions in the diffuse layer and on the joint density functional theory (JDFT) for the electronic structure. When the Ag electrode is applied with a negative voltage, the surface charge density can be reasonably described by assuming a neutral Stern layer with the dielectric constant dependent on the local electric field as predicted by the Kirkwood equation. However, the specific adsorption of F− ions must be considered when the electrode is positively charged and the fluoride adsorption can be attributed to both physical and chemical interactions. Qualitatively, F− binding and partial charge transfer are supported by JDFT calculations, which predict an increased binding energy as the voltage increases. Our findings shed insight on the molecular characteristics of the Stern layer and the charge behavior of adsorbed species not specified by conventional EDL models.
Wang, Xuepeng (ORCID:0000000285704546)↗
Sensitivity measurements for a 250 MHz quartz shear-horizontal surface acoustic wave biosensor under liquid viscous loading
Surface acoustic wave (SAW) devices have been used in biochemical assays due to their high sensitivity. The device sensitivity is a function of changes in the density and viscosity of the liquid. Here, we studied the effect of fluid viscosity using a 250 MHz quartz shear-horizontal (SH)-SAW biosensor by monitoring different concentrations of binary aqueous/glycerol solutions. In this study, the sensitivity of the biosensor was determined by fitting the data to models derived from perturbation theory. Measurements in water were used as the reference. For a 0% to 50% glycerol solution, an 87°–204° separation in the phase shift was observed. The slope of the plot of the phase shift vs (ηρ)0.5 was used to indicate the sensor’s sensitivity. The sensitivity for our 250 MHz quartz SH-SAW sensors was calculated to be 3.7×10−3m2sKg. The corresponding mass sensitivity was determined to be 9.25 × 105m2Kg. The limit of detection was calculated to be 36 picograms (pg), while the limit of quantification or LOQ was calculated to be 109 pg. Traditionally, liquid phase measurements have been challenging for SAW devices because liquids dampen the vibrating sensors severely. This problem has been largely solved using a transverse (shear) wave instead of the more popular longitudinal or Rayleigh waves. Liquid measurements are now possible using transverse waves, also known as shear waves, because transverse waves are only minimally attenuated by liquids. Shear-horizontal SAW sensors (SH-SAW) show great promise as label-free biosensors because of their ability to handle liquid samples. However, the viscosity of the liquid still induces loading effects and can be measured when the liquid is loaded onto the SH-SAW propagating surface (delay line). When the liquid above the delay line is perturbed by physical or chemical changes, such as binding to a receptor, it alters the propagating acoustic wave. The SH-SAW device can measure these changes in liquid properties as a change in the wave’s phase compared to the original wave. The device’s phase shift was recorded as a function of the changes in the density and viscosity of the binary glycerol solution and used to determine the sensitivity in the linear dynamic range of responses.
Materials Science↗
Structural basis for heme-dependent NCoR binding to the transcriptional repressor REV-ERBβ
Heme is the endogenous ligand for the constitutively repressive REV-ERB nuclear receptors, REV-ERBα (NR1D1) and REV-ERBβ (NR1D2), but how heme regulates REV-ERB activity remains unclear. Cellular studies indicate that heme is required for the REV-ERBs to bind the corepressor NCoR and repress transcription. However, fluorescence-based biochemical assays suggest that heme displaces NCoR; here, we show that this is due to a heme-dependent artifact. Using ITC and NMR spectroscopy, we show that heme binding remodels the thermodynamic interaction profile of NCoR receptor interaction domain (RID) binding to REV-ERBβ ligand-binding domain (LBD). We solved two crystal structures of REV-ERBβ LBD cobound to heme and NCoR peptides, revealing the heme-dependent NCoR binding mode. ITC and chemical cross-linking mass spectrometry reveals a 2:1 LBD:RID stoichiometry, consistent with cellular studies showing that NCoR-dependent repression of REV-ERB transcription occurs on dimeric DNA response elements. Our findings should facilitate renewed progress toward understanding heme-dependent REV-ERB activity.
59 BASIC BIOLOGICAL SCIENCES↗
Using data-science approaches to unravel insights for enhanced transport of lithium ions in single-ion conducting polymer electrolyte
Solid polymer electrolytes have yet to achieve the an ionic conductivity > 1 mS/cm at room temperature for realistic applications. This target implies the need to reduce the effective energy barriers of ion transport in polymer electrolytes to around 20 kJ/mol. In this work, we combine information extracted from existing experimental results with theoretical calculations to provide insights into ion transport in single-ion conductors (SICs) with a focus on lithium ion SICs. Through the analysis of temperature-dependent ionic conductivity data obtained from the literature, we evaluate different methods of extracting energy barriers for lithium transport. The traditional Arrhenius fit to the temperature-dependent ionic conductivity data indicates that the Meyer-Neldel rule holds for SICs. However, the values of the fitting parameters remain unphysical. Our modified approach based on recent work (Macromolecules, 56, 15, 6051(2023)), which incorporates a fixed pre-exponential factor, reveals that the energy barriers exhibit temperature dependence over a wide range of temperatures. Using this approach, we identify a series of anions leading to the energy barriers less than 30 kJ/mol, which include trifluoromethane sulfonimide (TFSI), fluoromethane sulfonimide (FSI), and boron-based organic anions. In our efforts to design the next generation of anions, which can exhibit the energy barriers less than 20 kJ/mol, we focused on boron-containing SICs, and performed density functional theory (DFT) based calculations to connect the chemical structures via the binding energy of cation (lithium)-anion pairs with the experimentally derived effective energy barriers for ion transport. Not only have we identified a correlation between the binding energy and the energy barriers, but we also propose a strategy to design new boron-based anions by using the correlation. This combined approach involving experiments and theoretical calculations is capable of facilitating the identification of promising new anions, which can exhibit ionic conductivity $> 1$ mS/cm near room temperature, thereby expediting the development of novel superionic single-ion conducting polymer electrolytes. The published datasets include all the temperature-dependent ionic conductivity collected from the literature with literature DOIs, DFT calculated binding energies, and python scripts to analyze data, construct statistical models, and generate plots.
36 MATERIALS SCIENCE↗
Filtration membranes
A membrane assembly is provided. The membrane assembly includes a non-metallic, porous substrate. A graphene oxide membrane is formed over the non-metallic, porous substrate. A chemical linker interface covalently binds the graphene oxide membrane to the non-metallic, porous substrate.
Hibbs, Michael↗
Cyclic Peptides for Lanthanide Binding
Lanthanide ions are difficult to separate from one another due to their similar chemical properties. The discovery of lanthanide-binding peptides and proteins in nature has led to an increased interest in the possibility of utilizing the strong binding of peptides to lanthanide ions for their separations; as such, there has been an effort to identify or design peptides with improved lanthanide binding and selectivity toward particular lanthanide ions. Here, in this study, we designed and characterized lanthanide-binding cyclic peptides (LBCPs) with molecular dynamics simulations, electronic structure calculations, and emission spectroscopy. Luminescent decay measurements were done to determine the number of water molecules coordinated to the Eu 3+ ion in Eu-LBCP complexes and compare to the predicted number of water molecules by computation to assess the lanthanide-binding affinity of LBCPs. Measured stability constants show binding of the LBCPs to the Eu 3+ ion with stronger than micromolar affinity. We were able to identify multiple peptides that selectively bind to middle lanthanides. We describe the structural basis of the lanthanide-binding selectivity trend with strongest binding to the middle lanthanides, followed by the heavier lanthanides, and finally to the lighter ions.
ions↗
Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors
Optimization of binding affinities for ligands to their target protein is a primary objective in rational drug discovery. Herein, we report on a collaborative study that evaluates various compounds designed to bind to the SET and MYND domain-containing protein 3 (SMYD3). SMYD3 is a histone methyltransferase and plays an important role in transcriptional regulation in cell proliferation, cell cycle, and human carcinogenesis. Experimental measurements using the scintillation proximity assay show that the distributions of binding free energies from a large number of independent measurements exhibit non-normal properties. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to predict the binding free energies and to provide a detailed chemical insight into the nature of ligand-protein binding. Our results show that the 1-trajectory ESMACS protocol works well for the set of ligands studied here. Although one unexplained outlier exists, we obtain excellent statistical ranking across the set of compounds from the ESMACS protocol and good agreement between calculations and experiments for the relative binding free energies from the TIES protocol. ESMACS and TIES are again found to be powerful protocols for the accurate comparison of the binding free energies.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Magnetically Induced Binary Ferrocene with Oxidized Iron
Ferrocene is perhaps the most popular and well-studied organometallic molecule, but our understanding of its structure and electronic properties has not changed for more than 70 years. In particular, all previous attempts of chemically oxidizing pure ferrocene by binding directly to the iron center have been unsuccessful, and no significant change in structure or magnetism has been reported. Here, using a metal organic framework host material, we were able to fundamentally change the electronic and magnetic structure of ferrocene to take on a never-before observed physically stretched/bent high-spin Fe(II) state, which readily accepts O 2 from air, chemically oxidizing the iron from Fe(II) to Fe(III). We also show that the binding of oxygen is reversible through temperature swing experiments. Our analysis is based on combining Mößbauer spectroscopy, extended X-ray absorption fine structure, in situ infrared, SQUID, thermal gravimetric analysis, and energy dispersive X-ray fluorescence spectroscopy measurements with ab initio modeling.
36 MATERIALS SCIENCE↗
Electrostatically Enhanced Buried Interface Binding of Self‐Assembled Monolayers for Efficient And Stable Inverted Perovskite Solar Cells
Inverted p‐i‐n structure perovskite solar cells (PSCs) have outperformed traditional n‐i‐p PSCs in recent years. A key advancement is the use of self‐assembled monolayers (SAMs) as hole transport layers. One class of widely used SAMs is carbazole‐based phosphonic acids. However, it is found that these SAMs lack strong binding with transparent conducting oxides (TCO) and perovskite. The weak binding strength results in suboptimal interfacial adhesion of the buried interface, which limits the device's stability. Here, interfacial binding is enhanced by increasing the dipole moment that creates a strong interfacial electric field that enhances electrostatic interactions at the TCO/perovskite interface, while incorporating tailored functional groups in SAMs to improve chemical anchoring to TCO and binding to perovskite. Specifically, the donor‐acceptor SAM molecule 4‐(7‐(4‐(bis(4‐methoxyphenyl)amino)‐2,5‐difluorophenyl)benzo[c][1,2,5]thiadiazol‐4‐yl)benzoic acid (PAFTB) is employed, which features an enhanced dipole moment along with electron‐donating and electron‐withdrawing functional groups to optimize interfacial interactions. Compared to extensively used [2‐(9H‐carbazol‐9‐yl)ethyl]phosphonic acid (2PACz), PAFTB enhances total interfacial adhesion by 2.8 times, thereby improving the thermal stability of the layer. Using this approach, PSCs are demonstrated with a certified quasi‐steady‐state power conversion efficiency of 24.9% and maintain 80% of the initial efficiency after 900 h of maximum power point tracking at 85 °C.
Interfacial adhesion↗
Exploring the Effects of Node Topology, Connectivity, and Metal Identity on the Binding of Nerve Agents and Their Hydrolysis Products in Metal–Organic Frameworks
Recent studies have shown that metal–organic frameworks (MOFs) built from hexanuclear M(IV) oxide cluster nodes are effective catalysts for nerve agent hydrolysis, where the properties of the active sites on the nodes can strongly influence the reaction energetics. The connectivity and metal identity of these M6 nodes can be easily tuned, offering extensive opportunities for computational screening to predict promising new materials. Thus, we used density functional theory (DFT) to examine the effects of node topology, connectivity, and metal identity on the binding energies of multiple nerve agents and their corresponding hydrolysis products. By computing an optimization metric based on the relative binding strengths of key hydrolysis reaction species (water, agent, and bidentate-bound products), we predicted optimal M6 nodes for hydrolyzing specific nerve agent and simulant molecules, where our results are in qualitative agreement with observed experimental trends. This analysis highlighted the notion that no single metal or node topology is optimal for all possible organophosphates, suggesting that MOFs should be selected based on the agent of interest. Using the large amount of data generated from our DFT calculations, we then derived quantitative structure–activity relationship (QSAR) models to help explain the complex trends observed in the binding energies. Through linear regression, we identified the most important descriptors for describing the binding of nerve agents and their hydrolysis products to M6 nodes. These results suggested that both molecular and node properties, including both structural and chemical features, collectively contribute to the binding energetics. By performing a thorough statistical analysis, we showed that our QSAR models are capable of making quantitatively accurate binding energy predictions for nerve agents and their hydrolysis products in a wide variety of M(IV)-MOFs. In conclusion, the insights gained herein can be used to guide future experiments for the synthesis of MOFs with enhanced catalytic activity for organophosphate hydrolysis.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Computational Workflow for Accelerated Molecular Design Using Quantum Chemical Simulations and Deep Learning Models
Efficient methods for searching the chemical space of molecular compounds are needed to automate and accelerate the design of new functional molecules such as pharmaceuticals. Given the high cost in both resources and time for experimental efforts, computational approaches play a key role in guiding the selection of promising molecules for further investigation. Here, we construct a workflow to accelerate design by combining approximate quantum chemical methods [i.e. density-functional tight-binding (DFTB)], a graph convolutional neural network (GCNN) surrogate model for chemical property prediction, and a masked language model (MLM) for molecule generation. Property data from the DFTB calculations are used to train the surrogate model; the surrogate model is used to score candidates generated by the MLM. The surrogate reduces computation time by orders of magnitude compared to the DFTB calculations, enabling an increased search of chemical space. Furthermore, the MLM generates a diverse set of chemical modifications based on pre-training from a large compound library. We utilize the workflow to search for near-infrared photoactive molecules by minimizing the predicted HOMO-LUMO gap as the target property. Our results show that the workflow can generate optimized molecules outside of the original training set, which suggests that iterations of the workflow could be useful for searching vast chemical spaces in a wide range of design problems.
Blanchard, Andrew↗
Desorption characteristics of selenium and tellurium thin films
The temperature-dependent desorption behavior of selenium and tellurium is investigated using a heated quartz crystal microbalance. Prior to heating the quartz crystal microbalance, selenium and tellurium films with varying thickness were deposited using thermal effusion cells in a molecular beam epitaxy system for subsequent determination of temperature-dependent mass loss of the deposited films. The desorption rate for tellurium was found to exhibit one sharp peak around 190°C, indicating the loss of the entire film irrespective of film thickness within a temperature window of 20°C, which was completely evaporated at 200°C. Similar experiments for selenium revealed that the thermal desorption took place via a two-stage process with a smaller portion of the material desorbing within an even narrower temperature window of 5°C at a much lower peak temperature of 65°C, while most selenium desorbed within a temperature range of 10°C around 90°C. This two-stage behavior indicated the presence of at least two chemically distinct selenium species or binding states. The direct and quantitative determination of the chalcogen desorption process provides important insights into the kinetics of chalcogenide-based film growth and is in addition of applied benefit to the research community in the area of Se/Te capping and decapping of air sensitive materials as it provides temperature ranges and rates at which full desorption is achieved. Our work furthermore points toward the need for a more detailed understanding of the chemical composition state of atomic and molecular beams supplied from thermal evaporation sources during growth.
36 MATERIALS SCIENCE↗