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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.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Electronic coarse-graining of long conjugated molecules: Case study of non-fullerene acceptors

By considering only one electronic state per molecule, charge transport models of molecular solids neglect intramolecular charge transfer. This approximation excludes materials with quasi-degenerate spatially separated frontier orbitals, such as non-fullerene acceptors (NFAs) and symmetric thermally activated delayed fluorescence emitters. By analyzing the electronic structure of room-temperature molecular conformers of a prototypical NFA, ITIC-4F, we conclude that the electron is localized on one of the two acceptor blocks with the mean intramolecular transfer integral of 120 meV, which is comparable with intermolecular couplings. Therefore, the minimal basis for acceptor–donor–acceptor (A–D–A) molecules consists of two molecular orbitals localized on the acceptor blocks. This basis is robust even with respect to geometry distortions in an amorphous solid, in contrast to the basis of two lowest unoccupied canonical molecular orbitals withstanding only thermal fluctuations in a crystal. The charge carrier mobility can be underestimated by a factor of two when using single site approximation for A–D–A molecules in their typical crystalline packings.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Molecular dynamics study of hydrogen Cottrell atmosphere in aluminum: Influence of solute-solute interactions in the dislocation core

Cottrell atmospheres form when solute atoms segregate to dislocations, and is one of the most basic processes by which solutes alter mechanical properties of materials. In the case of hydrogen, Cottrell atmospheres are believed to contribute to hydrogen embrittlement. Here, in this study, we use direct molecular dynamics simulations to study the formation of hydrogen Cottrell atmospheres around edge dislocations in aluminum. Using coarse-graining techniques, we resolve the temporal and spatial evolution of the hydrogen concentration field. By comparing our results with theories of Cottrell atmosphere formation and thermodynamics, we show that a repulsive, concentration-dependent H-H interaction reduces the peak atmosphere concentration at the dislocation core. Furthermore, this interaction differs significantly from the H-H interaction that is experienced in the bulk away from a dislocation.

Aluminum↗
DOE OSTI2023

Ab initio quantum dynamics of plasmonic charge carriers

Surface plasmons respond strongly to electric fields and generate energetic (hot) charge carriers that can be used in optoelectronic devices. However, utilization of hot carriers has to outcompete fast carrier relaxation in metals. Often, the reported efficiencies of nanoscale devices based on plasmon excitations are low and the mechanisms of device operation remain inconsistent within the field. Further developments hinge on fundamental understanding of the nature and kinetics of plasmon decay processes. In this work, we provide an overview of time domain ab initio modeling of hot carrier dynamics, demonstrating that atomistic details of the surface structure of plasmonic materials, and their chemical interaction with semiconducting and molecular charge acceptors and substrates, play key roles in governing the dynamics pathways. Considered case studies represent various dynamics channels and illustrate solar energy and optoelectronic applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Time-Resolved X-ray Emission Spectroscopy and Synthetic High-Spin Model Complexes Resolve Ambiguities in Excited-State Assignments of Transition-Metal Chromophores: A Case Study of Fe-Amido Complexes

To fully harness the potential of abundant metal coordination complex photosensitizers, a detailed understanding of the molecular properties that dictate and control the electronic excited-state population dynamics initiated by light absorption is critical. In the absence of detectable luminescence, optical transient absorption (TA) spectroscopy is the most widely employed method for interpreting electron redistribution in such excited states, particularly for those with a charge-transfer character. The assignment of excited-state TA spectral features often relies on spectroelectrochemical measurements, where the transient absorption spectrum generated by a metal-to-ligand charge-transfer (MLCT) electronic excited state, for instance, can be approximated using steady-state spectra generated by electrochemical ligand reduction and metal oxidation and accounting for the loss of absorptions by the electronic ground state. However, the reliability of this approach can be clouded when multiple electronic configurations have similar optical signatures. Using a case study of Fe(II) complexes supported by benzannulated diarylamido ligands, we highlight an example of such an ambiguity and show how time-resolved X-ray emission spectroscopy (XES) measurements can reliably assign excited states from the perspective of the metal, particularly in conjunction with accurate synthetic models of ligand-field electronic excited states, leading to a reinterpretation of the long-lived excited state as a ligand-field metal-centered quintet state. Furthermore, a detailed analysis of the XES data on the long-lived excited state is presented, along with a discussion of the ultrafast dynamics following the photoexcitation of low-spin Fe(II)-N amido complexes using a high-spin ground-state analogue as a spectral model for the 5 T 2 excited state.

14 SOLAR ENERGY↗
DOE OSTI2020

Electro-reduction of organics on metal cathodes: A multiscale-modeling study of benzaldehyde on Au (111)

Here, we present a multiscale modeling study on the electro-reduction of benzaldehyde (BZY) on Au(111) under realistic electrochemical conditions. To model the electrochemical cell, we adopt a capacitor model in which complex solvents are confined between a Au cathode and a carbon anode. Classical molecular dynamics simulations reveal that electrode charge density and the presence of alcohol show strong effects on the density, adsorption geometry and dynamics of benzaldehyde on the Au electrode. Under charging conditions, the surface concentration of benzaldehyde on the Au electrode decreases, while the content of other species increases. Finally, we proposed a scheme that correlates the electric current running through the Au/solvent interface with the applied bias. This study provides a molecular level understanding of how solvent composition, in this case water/alcohol content, controls the activity of electrocatalytic hydrogenation

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

Substrate Channeling via a Transient Protein-Protein Complex: The case of D-Glyceraldehyde-3-Phosphate Dehydrogenase and L-Lactate Dehydrogenase

Molecular dynamics studies showed that LDH and GAPDH tetramers can form a complex which can breakdown when the enzymes are saturated with NADH molecules. The interaction sites are conserved between LDH isozymes from heart and muscle cells, and between GAPDH molecules from rabbit and yeast cells. Positive electric fields between the NAD(H) binding sites showed that NAD(H) channeling within LDH-GAPDH complex can be an extension of NAD(H) channeling between the adjacent subunits within LDH and GAPDH tetramers. Analytical ultracentrifugation and enzyme kinetics studies indicated that LDH and GAPDH molecules can form a transient channeling complex. The transient complex can support the channeled and the diffusive paths in parallel, the relative contribution from each path depends on the off-rates for (GAPDH-NADH)-LDH complex and GAPDH-NADH complex. Negative cooperativity in NADH binding to different subunits in GAPDH tetramers can provide allosteric regulation of NADH channeling from GAPDH to LDH.

INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMI↗
DOE OSTI2021

Genome-wide discovery of G-quadruplexes in barley

G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5' untranslated region (5' UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Molecular dynamics and continuum analyses of the electrokinetic zeta potential in nanostructured slit channels

This work presents a theoretical and numerical study of electrokinetic flow and the zeta potential for the case of slit channels with nanoscale surface features of dimensions comparable to the Debye length, by employing molecular dynamics simulations and continuum-level analyses. Additionally, a simple analytical model for considering the average effect of such surface features producing nanoscale roughness is proposed by employing matched asymptotic solutions for the charge density and fluid flow field, and matching conditions that satisfy electroneutrality and the Onsager reciprocal relation between the electroosmotic flow rate and streaming current. The proposed analytical model quantitatively accounts for results from molecular dynamics simulations that consider the presence of ion solvation shells and surface hydration layers. Our analysis indicates that a simultaneous knowledge of the electroosmotic and pressure-driven flow rate or streaming current can be instrumental to unambiguously determine the zeta potential in the presence of nanoscale surface features.

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

Inferring colloidal interaction from scattering by machine learning

A machine learning solution for the potential inversion problem in elastic scattering is outlined. The inversion scheme consists of two major components, a generative network featuring a variational autoencoder which extracts the targeted static two-point correlation functions from experimentally measured scattering cross sections, and a Gaussian process framework which probabilistically infers the relevant structural parameters from the inverted correlation functions. Via a case study of charged colloidal suspensions, the feasibility of this approach for quantitative study of molecular interaction is critically benchmarked and its merit over existing deterministic approaches, in terms of numerical accuracy and computationally efficiency, is demonstrated.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Investigation of fracture in porous materials: a phase-field fracture study informed by ReaxFF

Microscopic features (e.g, pore shapes, sizes, and distribution) in porous material substantially affect the overall mechanical properties such as stiffness and strength. In turn, these material properties determine the macroscopic behaviors of fracture in the porous material. In certain cases, macroscopic properties can be derived from the porous skeleton and void ratio (i.e., porosity), but in many other cases, such derivation is a challenging task. This paper presents a numerical investigation of microporosity and micropore shapes effect on the macrofracture behavior in porous amorphous silica. For this study, we extend the recently-proposed combined molecular dynamic (MD) and phase-field (PF) fracture modeling approach by including different pore shapes in the atomistic domain. In the MD simulations, we adopt ReaxFF to evaluate the material properties, where four different micropore cases are considered. Based on the material properties derived from MD simulations, the macrofracture propagation of porous media is studied using hybrid PF simulation. In the characterization of the pore structure, the concept of pore ligament is proposed to relate the pore shape and the critical energy release rate. Two classical fracture problems were used to evaluate the effect of pore shape on the macrofracture behavior. The results of the case study show that although the micropore shapes change the macrofracture behaviors, these effects vary with the geometry and loading conditions of macroscopic boundary value problems. Furthermore, the case study also shows that the influence of micropore structure can be captured at the macroscopic level through the material properties derived from the MD simulations.

42 ENGINEERING↗
DOE OSTI2021

From Molecules to Solids: A vdW-DF-C09 Case Study of the Mercury Dihalides

The mercury dihalides show a remarkable diversity in the structural preferences in their minimum energy structure types, spanning molecular to strongly bound ionic solids. A challenge in the development of density functional methods for extended systems is to arrive at strategies that serve equally well such a broad range of bonding modes or structural preferences. The chemical bonding and the stabilities of mercury dihalides and the general utility and reliability of the van der Waals density functional with C09 exchange (vdW-DF-C09) in predicting or describing the energetics and structural preferences in these metal dihalides is examined. Here, we show that, in contrast with the uncorrected generalized gradient approximation of the Perdew-Burke-Erzenhoff (PBE) exchange-correlation functional, qualitative and quantitative patterns in the bonding of the mercury dihalide solids are well reproduced with vdW-DF-C09 for the full series of HgX 2 systems for X = F, Cl, Br, and I. The possible existence of a low-temperature cotunnite polymorph for HgF 2 and PbF 2 is posited.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗
DOE OSTI2023

Solution Structure and Hydration Forces between Mica and Hydrophilic Versus Hydrophobic Surfaces

Solid-liquid interfaces are central to a range of interesting phenomena including catalysis, heterogeneous nucleation, water desalination, and biomolecular assembly. While three-dimensional Fast Force Mapping (3D FFM) has emerged as a technique for resolving interfacial solution structure at the molecular scale, key challenges for data interpretation persist, most notably regarding the influence of the probe on the measured structure. Using the mica-water system as a case study, we investigate the effect of hydrophilic and hydrophobic probes on interfacial solution structure measured by 3D FFM. Data from hydrophilic silicon-based probes are in good agreement with molecular dynamics simulations, wherein the innermost water molecules adsorb preferentially at the surface ditrigonal cavity sites followed by two subsequent hydration layers. In contrast, the hydrophobic carbon-based probes detect vertical oscillatory features, but do not show lateral patterning that matches the underlying mica lattice. At high ionic strength, up to six of these oscillatory features are observed extending 2 nm into the solution phase with an average spacing of 0.29 ± (0.04) nm. Further, we also determine that the repulsive hydration force between mica and the hydrophilic probe depends on the nature and concentration of ions in solution. Specifically, solutions with stronger ion-water and ion-ion interactions increase the interfacial viscosity, which results in a stronger repulsive hydration force as the probe approaches the surface. Based on these observations, we present a scheme for controlling the outcomes of particle attachment and aggregation by varying the solution conditions to tune the hydration force.

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

Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids

Premise Recent advances in generating large‐scale phylogenies enable broad‐scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results. Methods We used a supermatrix for rosids and one well‐sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR). Results We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa. Conclusions We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Finite-element-based simulations of electrodes for CO 2 cascade reduction reactions

The multielectron reduction of CO 2 to liquid fuels could be a path to scalable energy storage, but reaching this goal requires major advances in catalysis and systems engineering. Cascade catalysis, which couples sequential reactions without isolating intermediates, has emerged as a promising route to enhance selectivity and efficiency in CO 2 reduction (CO 2 R). In this review, we examine how finite-element-based simulations of continuum model [finite element method (FEM)] approaches are being used to analyze and guide CO 2 R cascade systems. We first outline the fundamentals of cascade catalysis and recent advances in catalytic materials (metallic, molecular, and hybrid architectures). We then focus on FEM developments at the electrode and device scales, emphasizing how these models capture transport phenomena, local microenvironments, and geometry-dependent effects. To clarify design principles, we present case studies of cascade electrodes organized in systems without and with integrated semiconductors. We further emphasize the integration of FEM with multiscale frameworks (density functional theory, molecular dynamics, kinetic Monte Carlo) and its role in bridging atomic-level insights with device-level performance. Finally, we identify current limitations and future prospects, including improved boundary conditions, coupling with operando experiments, and machine learning-accelerated model development. Together, these insights provide design principles for next-generation CO 2 R cascade systems for efficient solar fuel production.

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

When do hydrocarbons dewet metal surfaces? The case of coronene on Cu(111)

Here, we have used scanning tunneling microscopy and density functional theory calculations to study molecular layers of coronene on Cu(111). The structure and stability of these layers is determined by the balance between coronene-substrate and coronene-coronene interactions. Here, we characterize this balance by measuring the maximum coverage before coronene dewets the substrate to form three-dimensional islands. We find that coronene molecules lie parallel to the substrate at the maximum coverage, in contrast to previous observations of tilted coronene on metal surfaces. We attribute this previously reported tilt to a metastability caused by an activation barrier to nucleate three-dimensional islands.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Analysis of multi-electron, multi-step homogeneous catalysis by rotating disc electrode voltammetry: theory, application, and obstacles

Rotating disc electrode (RDE) voltammetry has been widely adopted for the study of heterogenized molecular electrocatalysts for multi-step fuel-forming reactions but this tool has never been comprehensively applied to their homogeneous analogues. Here, the utility and limitations of RDE techniques for mechanistic and kinetic analysis of homogeneous molecular catalysts that mediate multi-electron, multi-substrate redox transformations are explored. Using the ECEC' reaction mechanism as a case study, two theoretical models are derived based on the Nernst diffusion layer model and the Hale transformation. Current–potential curves generated by these computational strategies are compared under a variety of limiting conditions to identify conditions under which the more minimalist Nernst Diffusion Layer approach can be applied. Based on this theoretical treatment, strategies for extracting kinetic information from the plateau current and the foot of the catalytic wave are derived. RDEV is applied to a cobaloxime hydrogen evolution reaction (HER) catalyst under non-aqueous conditions in order to experimentally validate this theoretical framework and explore the feasibility of RDE as a tool for studying homogeneous catalysts. Importantly, analysis of the foot-of-the-wave via this theoretical framework provides rate constants for elementary reaction steps that agree with those extracted from stationary voltammetric methods, supporting the application of RDE to study homogeneous fuel-forming catalysts. Lastly, obstacles encountered during the kinetic analysis of cobaloxime, along with the voltammetric signatures used to diagnose this reactivity, are discussed with the goal of guiding groups working to improve RDE set-ups and help researchers avoid misinterpretation of RDE data.

08 HYDROGEN↗
DOE OSTI2025

Interfacial Cation Arrangement Controls Electrocatalytic Kinetics in CO 2 Reduction

The identity of electrolyte cations is known to strongly influence electrocatalytic activity, but the relationship between their interfacial arrangement and observed performance remains poorly understood. Organic cations, with their molecular tunability, provide a powerful platform for systematically probing these effects. Here, we leverage phosphonium-based geminal dications to control interfacial cation arrangement and identify the variables that most strongly influence catalytic rates. As a case study, we examine CO 2 reduction to CO over polycrystalline silver electrodes in dry aprotic acetonitrile. Through a combination of rotating disk electrode measurements, electrochemical impedance spectroscopy, and molecular dynamics simulations, we decouple the effects of cation–electrode distance and interfacial cation density on catalytic rates. We find that smaller, more densely packed cations induce stronger interfacial electric fields, which lower the activation barrier for CO 2 adsorption and increase reaction rates. Using geminal phosphonium dications [C n (P mmm ) 2 ][ClO 4 ] 2 , we demonstrate that both the vertical and lateral positioning of organic cations within the electrical double layer independently affect reactivity. These results demonstrate that electrolyte cation identity primarily influences catalytic kinetics by determining how efficiently charge can be arranged at electrochemical interfaces. Altogether, our findings support an electrostatic view of cation effects in catalysis and provide design principles for next-generation electrolytes.

Cations↗