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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Uncovering the binding nature of thiocyanate in contact ion pairs with lithium ions

Ion pair formation is a fundamental molecular process that occurs in a wide variety of systems, including electrolytes, biological systems, and materials. In solution, the thiocyanate (SCN–) anion interacts with cations to form contact ion pairs (CIPs). Due to its ambidentate nature, thiocyanate can bind through either its sulfur or nitrogen atoms, depending on the solvent. This study focuses on the binding nature of thiocyanate with lithium ions as a function of the solvents using FTIR, 2D infrared spectroscopy (2DIR) spectroscopies, and theoretical calculations. The study reveals that the SCN– binding mode (S or N end) in CIPs can be identified through 2DIR spectroscopy but not by linear IR spectroscopy. Linear IR spectroscopy shows that the CN stretch frequencies are too close to one another to separate N- and S-bound CIPs. Moreover, the IR spectrum shows that the S–C stretch presents different frequencies for the salt in different solvents, but it is related to the anion speciation rather than to its binding mode. A similar trend is observed for the anion bend. 2DIR spectra show different dynamics for N-bound and S-bound thiocyanate. In particular, the frequency–frequency correlation function (FFCF) dynamics extracted from the 2DIR spectra have a single picosecond exponential decay for N-bound thiocyanate and a biexponential decay for S-bound thiocyanate, consistent with the binding mode of the anion. Lastly, it is also observed that the binding mode also affects the line shape parameters, probably due to the different molecular mechanisms of the FFCF for N- and S-bound CIPs.

25 ENERGY STORAGE↗
DOE OSTI2025

Characterizing the surface compositions of supported bimetallic PtSn clusters: Effects of cluster-support interactions and surface adsorbates

PtSn bimetallic clusters on TiO2(110) and highly oriented pyrolytic graphite (HOPG) surfaces have been characterized by scanning tunneling microscopy, low energy ion scattering (LEIS), Xray photoelectron spectroscopy, and temperature programmed desorption (TPD); density functional theory (DFT) calculations have also been performed to better understand adsorption of CO and D2 on the PtSn surfaces. On TiO2 at coverages of 2 ML of Pt and 2 ML of Sn, exclusively bimetallic clusters are formed for both orders of deposition because clusters of the first metal completely cover the surface such that all atoms of the second metal are incorporated into the existing clusters. In contrast, on HOPG, the high mobility and weak cluster-support interactions on HOPG result in much larger 2 ML monometallic clusters (~30 Å high) that do not completely cover the surface, and deposition of the second metal produces larger clusters as well as smaller ones. Despite the difference in cluster morphologies for the different orders of deposition and supports, the LEIS experiments demonstrate that in all cases, the PtSn clusters are rich in Sn at the surface, as expected based on the lower surface free energy for Sn compared to Pt. Furthermore, the +0.2 eV shift in the Sn(3d5/2) binding energy observed on all surfaces in the presence of Pt is consistent with PtSn alloy formation. Deposition of 2 ML of Sn on TiO2 produces two-dimensional clusters with oxidation of Sn and reduction of titania at the clustersupport interface, but addition of Pt to the Sn clusters causes Sn to diffuse away from this interface, leaving Sn in the metallic state. TPD experiments on 2 ML Pt/TiO2 with increasing coverages of Sn show that the number of adsorption sites for D2 sharply decreases to nearly zero at 0.5 ML, while CO adsorption decreases to zero only at much higher Sn coverages of 2 ML. DFT studies for Sn modified Pt surfaces and bulk structures demonstrate that for CO adsorption at low Sn coverages (<0.25 ML), the strong Pt-CO interactions induce diffusion of Pt to the cluster surface and the formation of a bulk Pt3Sn alloy, whereas D2 adsorption does not lead to interactions with the Pt surface that are strong enough to induce alloy formation. A single Sn adatom prevents D2 adsorption on four neighboring Pt atoms via site-blocking and the donation of electron density to Pt.

Li, Fangliang↗
DOE OSTI2020

Investigation of N2 adsorption on Fe3O4(001) using ambient pressure X-ray photoelectron spectroscopy and density functional theory

Reactions on iron oxide surfaces are prevalent in various chemical processes from heterogeneous catalysts to minerals. Nitrogen (N2) is known to dissociate on iron surfaces, a precursor for ammonia production in the Haber–Bosch process, where the dissociation of N2 is the limiting step in the reaction under equilibrium conditions. However, little is known about N2 adsorption on other iron-based materials, such as iron oxide surfaces that are ubiquitous in soils, steel pipelines, and other industrial materials. An atomistic description is reported for the binding of N2 on the Fe3O4(001) surface using first principles calculations with ambient pressure X-ray photoelectron spectroscopy. Two primary adsorption sites are experimentally identified from N2 dissociation on Fe3O4(001). The electronic signatures associated with the valence band region unambiguously show how the electronic structure of magnetite transforms near ambient pressures due to the binding of atomic nitrogen to different surface sites. Overall, the experimental and theoretical results of our study bridge the gap between ultra-high vacuum studies and reaction conditions to provide insight into other nitrogen-based chemistry on iron oxide surfaces that impact the agriculture and energy industries.

Degaga, Gemechis D. (ORCID:0000000205097118)↗
NASA NTRS1971

Deformed Brueckner-Hartree-Fock calculation for light nuclei

For the first time the Brueckner-Hartree-Fock (BHF) method was applied to nuclei whose intrinsic structure is nonspherical. One aim was to investigate whether the energy dependent reaction matrix calculated from a realistic nucleon-nucleon interaction leads to deformations similar to, or different from, those obtained from energy independent interactions in Hartree-Fock (HF) calculations. Reaction matrix elements were calculated as a function of starting energy for the Hamada-Johnston interaction, using a Pauli operator appropriate to O-16 and a shifted oscillator spectrum for virtual excited states. Binding energies, single-particle energies, radii, and shape deformations of the intrinsic state in unrenormalized as well as renormalized BHF are discussed and compared with previous HF studies. Results are presented for C-12, O-16, and Ne-20.

Braley, R. C.↗
DOE OSTI2025

Ultrafast Correlation Energy Estimator

A virtually no-cost method is proposed that can compute the correlation energies of general, covalently bonded, organic, and inorganic molecules (including conjugated π-electron systems) with a well-defined dominant Lewis structure at the accuracy of 99.5% of the near-exact values determined by the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] in the complete-basis-set (CBS) limit. This Correlation Energy Per Bond (CEPB) method assigns a partial correlation energy to each bond type (characterized by the identities of the two atoms forming the bond and its integer bond order) and to a lone pair, regardless of the bond length, bond angle, sp-hybridization, π-electron conjugation, ionicity, noncovalent interactions, etc. At its current stage, the method is mainly suitable for near-equilibrium geometries. The correlation energies per bond are determined by a fit to the CCSD(T)/CBS benchmarks. It can neither improve the equilibrium structures nor discern conformers or positional isomers, yet its accuracy for reaction energies rivals that of the second-order Møller–Plesset perturbation theory, which is far more expensive. Its promising performance underscores the possibility that surprisingly compact, chemically intuitive molecular fragments exist into which correlation energies can be partitioned, leading to various ultrafast correlation-energy estimators tailored to different purposes.

Binding energy↗
DOE OSTI2024

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↗
DOE OSTI2022

Large-scale application of free energy perturbation calculations for antibody design

Abstract Alchemical free energy perturbation (FEP) is a rigorous and powerful technique to calculate the free energy difference between distinct chemical systems. Here we report our implementation of automated large-scale FEP calculations, using the Amber software package, to facilitate antibody design and evaluation. In combination with Hamiltonian replica exchange, our FEP simulations aim to predict the effect of mutations on both the binding affinity and the structural stability. Importantly, we incorporate multiple strategies to faithfully estimate the statistical uncertainties in the FEP results. As a case study, we apply our protocols to systematically evaluate variants of the m396 antibody for their conformational stability and their binding affinity to the spike proteins of SARS-CoV-1 and SARS-CoV-2. By properly adjusting relevant parameters, the particle collapse problems in the FEP simulations are avoided. Furthermore, large statistical errors in a small fraction of the FEP calculations are effectively reduced by extending the sampling, such that acceptable statistical uncertainties are achieved for the vast majority of the cases with a modest total computational cost. Finally, our predicted conformational stability for the m396 variants is qualitatively consistent with the experimentally measured melting temperatures. Our work thus demonstrates the applicability of FEP in computational antibody design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Protein Adhesion on Semi-Fluorinated Polystyrene Surfaces in Static and Dynamic Measurements

Reducing protein adhesion is a critical strategy in fouling-resistant material innovation, with broad applications spanning biomedical and healthcare devices, biosensors, industrial and environmental systems, and other important technological domains. Here, in this study, we elucidated protein adhesion behavior on polystyrene-based thin films by neutron reflectometry (NR) and quartz crystal microbalance with dissipation (QCM-D), using both lysozyme and bovine serum albumin (BSA) as model proteins. To this end, semifluorinated polystyrene thin films with gradient wettability and surface energy were fabricated through dry processing using plasma oxidation and gas-phase deposition. Although it is believed that a fully fluorinated alkyl chain offers extremely low surface energy, thus rejecting foulants, and has been used in many fouling-resistant surface designs, enhanced protein–surface interactions were observed consistently in NR and QCM-D results, due to the combined effects of surface morphology and chemistry. On the contrary, depositing shorter fluorinated silane onto a hydrophilic PS surface contributed to a more homogeneous nanoscale fluorine coating, resulting in less initial protein adsorption and improved surface recovery. Comparative analysis of proteins with different sizes on the nanopatterned semifluorinated surface revealed the influence of molecular characteristics on surface interactions. Lysozyme, being smaller and more compact, showed faster adsorption kinetics and higher surface coverage but largely reversible binding, whereas BSA, with its larger and more flexible structure, formed broader and more stable interfacial layers. This study fills the gap in understanding protein adhesion within the range of hydrophobicity (water contact angle ∼90°), as current strategies often associate with extreme hydrophilic and superhydrophobic surfaces due to hydration or low-surface-energy rejection mechanisms, respectively. It also provides in-depth insights into current combinatorial fouling-resistant surface design.

Yuan, Yue [Oak Ridge National Laboratory (ORNL), O↗
DOE OSTI2020

A multiscale cohesive law for carbon fiber networks

Better predictive models of mechanical failure in low-weight heat shield composites would aid material certification for missions with aggressive atmospheric entry conditions. In this study, we develop such a model for the rapid engineering analysis of the failure limits of phenolic impregnated carbon ablator (PICA) - a leading heat shield material whose structural component is a carbon fiber network. We hypothesize inelastic deformation failure mechanisms and model their behavior using molecular dynamics simulations to calculate the binding energy. We then upscale this binding energy to the macroscale using a renormalization argument. The approach delivers insightful and reasonably accurate macroscale predictions that compare favorably to experiments. In application, the model is validated for a particular variety of PICA by comparison to experiment and would then be used to study design scenarios in different entry conditions.

36 MATERIALS SCIENCE↗
NASA NTRS2020

A Multiscale Cohesive Law for Carbon Fiber Networks

Better predictive models of mechanical failure in low-weight heat shield composites would aid material certification for missions with aggressive atmospheric entry conditions. Here, we develop such a model for the rapid engineering analysis of the failure limits of phenolic impregnated carbon ablator (PICA) - a leading heat shield material whose structural component is a carbon fiber network. We hypothesize inelastic deformation failure mechanisms and model their behavior using molecular dynamics simulations to calculate the binding energy. We then upscale this binding energy to the macroscale using a renormalization argument. The approach delivers insightful and reasonably accurate macroscale predictions that compare favorably to experiments. In application, the model is validated for a particular variety of PICA by comparison to experiment and would then be used to study design scenarios in different entry conditions.

W. SCHILL↗
DOE OSTI2025

Subsurface hydrogen, curvature, and strain: lessons from electro-reduction of benzaldehyde on nano-structured Pd catalysts

The unique ability of palladium (Pd) to absorb hydrogen and form a bulk hydride is vital for chemical transformations that involve hydrogenation reactions. Nano-structured Pd catalysts offer a promise of tuning these reaction rates by exploiting variations of reactant binding energies depending on the surface structure and morphological constraints that result in inhomogeneous strain. However, the interplay between the nano-structure of Pd and the ability of Pd to adsorb (and absorb) hydrogen as well as other reactive species needs to be better understood for a rational understanding of competitive chemical transformations at Pd surfaces. We consider the effects of the surface corrugation, strain, and subsurface Pd hydride on the reduction of benzaldehyde to benzyl alcohol in two qualitatively different samples – Pd nanoparticles and Pd gels formed by quasi-one-dimensional chains of these nanoparticles. Our electrochemical measurements and computational modelling suggest that surface concave sites, inherent to Pd gels, facilitate hydrogen transfer to the Pd subsurface region, thus weakening benzaldehyde binding to the surface. This effect is further modulated by the strain, depending on the local coordination environment on the corrugated surface. Furthermore, these findings demonstrate how structurally complex samples in the form of gels provide degrees of freedom for controlling the behavior of metal catalysts that are not available in isolated nanoparticles, which paves the way for new approaches in the design of catalytic materials and synthesis of metal hydrides.

Padavala, Sri Krishna Murthy [University of Minnes↗
DOE OSTI2023

The 2.4 Å structure of Zymomonas mobilis pyruvate kinase: Implications for stability and regulation

Human liver pyruvate kinase (hlPYK) catalyzes the final step in glycolysis, the formation of pyruvate (PYR) and ATP from phosphoenolpyruvate (PEP) and ADP. Fructose 1,6-bisphosphate (FBP), a pathway intermediate of glycolysis, serves as an allosteric activator of hlPYK. Zymomonas mobilis pyruvate kinase (ZmPYK) performs the final step of the Entner-Doudoroff pathway, which is similar to glycolysis in that energy is harvested from glucose and pyruvate is generated. The Entner-Doudoroff pathway does not have FBP as a pathway intermediate, and ZmPYK is not allosterically activated. In this work, we solved the 2.4 Å X-ray crystallographic structure of ZmPYK. The protein is dimeric in solution as determined by gel filtration chromatography, but crystallizes as a tetramer. The buried surface area of the ZmPYK tetramerization interface is significantly smaller than that of hlPYK, and yet tetramerization using the standard interfaces from higher organisms provides an accessible low energy crystallization pathway. Interestingly, the ZmPYK structure showed a phosphate ion in the analogous location to the 6-phosphate binding site of FBP in hlPYK. Circular Dichroism (CD) was used to measure melting temperatures of hlPYK and ZmPYK in the absence and presence of substrates and effectors. The only significant difference was an additional phase of small amplitude for the ZmPYK melting curves. We conclude that the phosphate ion plays neither a structural or allosteric role in ZmPYK under the conditions tested. In conclusion, we hypothesize that ZmPYK does not have sufficient protein stability for activity to be tuned by allosteric effectors as described for rheostat positions in the allosteric homologues.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Energetics and Structure of Ag–Water Clusters Formed in Mordenite

Zeolite-supported Ag 0 clusters have broad applications from catalysis to medicine, necessitating a mechanistic understanding of the formation of Ag 0 clusters in situ. Density functional theory (DFT) simulations have been performed on silver, water, and silver–water clusters in silica mordenite (Si-MOR), to identify the role of the confinement on the structure and energetics of Ag 0 cluster formation. The most favorable binding energy in the 12-membered ring (MR) pore of the Si-MOR is a 10–15-atom Ag 0 cluster. Computational pair distribution function (PDF) data indicates that the Ag 0 and Ag 0 –H 2 O clusters formed in vacuum versus in Si-MOR exhibit structural differences. Additionally, when the Ag 0 cluster is confined, the density decreases and the surface area increases, hypothesized to be due to the limiting geometry of the 12-MR main channel. An energetic drive toward formation of larger Ag 0 clusters was also identified, with hydrated silver atoms generating higher energy structures. In conclusion, this work identifies mechanistic and structural insight into the role of nanoconfinement on formation of Ag 0 clusters in mordenite.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Homo- and hetero-dimeric subunit interactions set affinity and efficacy in metabotropic glutamate receptors

Metabotropic glutamate receptors (mGluRs) are dimeric class C G-protein–coupled receptors that operate in glia and neurons. Glutamate affinity and efficacy vary greatly between the eight mGluRs. The molecular basis of this diversity is not understood. We used single-molecule fluorescence energy transfer to monitor the structural rearrangements of activation in the mGluR ligand binding domain (LBD). In saturating glutamate, group II homodimers fully occupy the activated LBD conformation (full efficacy) but homodimers of group III mGluRs do not. Strikingly, the reduced efficacy of Group III homodimers does not arise from differences in the glutamate binding pocket but, instead, from interactions within the extracellular dimerization interface that impede active state occupancy. By contrast, the functionally boosted mGluR II/III heterodimers lack these interface ‘brakes’ to activation and heterodimer asymmetry in the flexibility of a disulfide loop connecting LBDs greatly favors occupancy of the activated conformation. Our results suggest that dimerization interface interactions generate substantial functional diversity by differentially stabilizing the activated conformation. This diversity may optimize mGluR responsiveness for the distinct spatio-temporal profiles of synaptic versus extrasynaptic glutamate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Controlled mechanochemical coupling of anti-junctions in DNA origami arrays

Abstract Allostery is a hallmark of cellular function and important in every biological system. Still, we are only starting to mimic it in the laboratory. Here, we introduce an approach to study aspects of allostery in artificial systems. We use a DNA origami domino array structure which–upon binding of trigger DNA strands–undergoes a stepwise allosteric conformational change. Using two FRET probes placed at specific positions in the DNA origami, we zoom in into single steps of this reaction cascade. Most of the steps are strongly coupled temporally and occur simultaneously. Introduction of activation energy barriers between different intermediate states alters this coupling and induces a time delay. We then apply these approaches to release a cargo DNA strand at a predefined step in the reaction cascade to demonstrate the applicability of this concept in tunable cascades of mechanochemical coupling with both spatial and temporal control.

Science & Technology - Other Topics↗
NASA NTRS1984

Subbarrier absorption in a stationary superlattice

The calculation of the interband absorption coefficient was carried out in the classical case, when the frequency of light was assumed to bind two miniband subbarrier states of different bands. The influence of two dimensional Mott excitons on this absorption was studied and a comparison was made with the experiment. All of these considerations were done taking into account the photon wave vector (the phase spatial heterogeneity). The basic traits of the energy spectra of superlattice semiconductors, their kinetic and optical properties, and possible means of electromagnetic wave intensification were examined. By the density matrix method, a theory of electrical and electromagnetic properties of superlattices was suggested.

Arutyunyan, G. M.↗
DOE OSTI2023

Measuring the Exciton Binding Energy: Learning from a Decade of Measurements on Halide Perovskites and Transition Metal Dichalcogenides

The exciton binding energy ( E b ) is a key parameter that governs the physics of many optoelectronic devices. At their best, trustworthy and precise measurements of E b challenge theoreticians to refine models, are a driving force in advancing the understanding of a material system, and lead to efficient device design. At their worst, inaccurate E b measurements lead theoreticians astray, sow confusion within the research community, and hinder device improvements by leading to poor designs. Here, this review article seeks to highlight the pros and cons of different measurement techniques used to determine E b , namely, temperature‐dependent photoluminescence, resolving Rydberg states, electroabsorption, magnetoabsorption, scanning tunneling spectroscopy, and fitting the optical absorption. Due to numerous conflicting E b values reported for halide perovskites (HP) and transition metal dichalcogenides (TMDC) monolayers, an emphasis is placed on highlighting these measurements in an attempt to reconcile the variance between different measurement techniques. It is argued that the experiments with the clearest indicators are in agreement on the following values: ≈350–450 meV for TMDC monolayers between SiO 2 and vacuum, ≈150–200 meV for hBN‐encapsulated TMDC monolayers, ≈200–300 meV for common lead‐iodide 2D HPs, and ≈10 meV for methylammonium lead iodide.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Bridging the time scale in exascale computing of chemical systems (Final Technical Report)

This report summarizes the work carried out with support of the United States Department of Energy under Award DE-SC0019441. The theme of this project was to develop and apply methods that allowed for the acceleration of atomistic calculations, particularly in challenging areas such as multiphase systems, electrified interfaces, uncertainty estimation, and applications requiring chemical accuracy, which tend to be applications where simulation time is severely bottlenecked by the computational time requirements. Much of the focus was on the application of emerging machine-learning methodologies, although a wide range of methodologies were employed. This report has two major sections. The first focuses on the methodological advances themselves. Within this part, we report a number of major advances, a few examples of which are described here. We report the first machine-learning scheme for the acceleration of electronically grand-canonical calculations (that is, those applicable to electrochemistry). We report new methods of performing transfer learning, in which physics-based priors can be used to provide predictions, often with uncertainty estimates, of images well outside of training sets; we also offer ways to fine-tune these transfer-learning models. We provide a new systematic means to generate and apply minimal training data sets to very large (10,000’s of atoms) systems, with only small training sets appropriate for electronic structure. We developed new methodologies to integrate surface vibrations into surface adsorption calculations. We made advances to the applicability of diffusion Monte Carlo methods to allow (learned) force prediction, finite-size error correction, and force-free means of searching for transition states. We integrated machine-learned atomistic predictions into mechanism generation codes. Additionally, we released new software including AmpTorch, a modernized version of our original atomistic machine-learning code Amp. The second part of this report focuses on the scientific applications that accompanied, and were often enabled by, the methodological advances described earlier. A few examples follow, but full details are in the individual chapters of the report. For example, we developed a general theory of phonon-induced friction on molecular adsorbates. We showed fundamentally how solvent influences the adsorption and desorption process and how it differs from the processes typically involved at the solid–gas interface, making aqueous-phase and electrocatalysis different from traditional thermocatalysis. We examined how metal–insulator and magnetic transitions can be probed, and accelerated exciton dynamics via Frenkel Hamiltonian parameters. We showed that the nearsighted force-training approach, developed within this project, can predict both the stability and reactivity of large nanoparticles, and can also lead to insights on catalyst coverage on binding energies and entropies. These applied studies, which generally integrated with our method development, allowed us to push forward the theoretical understanding of several reaction classes.

08 HYDROGEN↗