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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Quantum Simulations of Radiation Damage in a Molecular Polyethylene Analog

Abstract An atomic‐level understanding of radiation‐induced damage in simple polymers like polyethylene is essential for determining how these chemical changes can alter the physical and mechanical properties of important technological materials such as plastics. Ensembles of quantum simulations of radiation damage in a polyethylene analog are performed using the Density Functional Tight Binding method to help bind its radiolysis and subsequent degradation as a function of radiation dose. Chemical degradation products are categorized with a graph theory approach, and occurrence rates of unsaturated carbon bond formation, crosslinking, cycle formation, chain scission reactions, and out‐gassing products are computed. Statistical correlations between product pairs show significant correlations between chain scission reactions, unsaturated carbon bond formation, and out‐gassing products, though these correlations decrease with increasing atom recoil energy. The results present relatively simple chemical descriptors as possible indications of network rearrangements in the middle range of excitation energies. Ultimately, the work provides a computational framework for determining the coupling between nonequilibrium chemistry in polymers and potential changes to macro‐scale properties that can aid in the interpretation of future radiation damage experiments on plastic materials.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

Monatomic ions influence substrate permeation across bacterial microcompartment shells

Abstract Bacterial microcompartments (BMCs) are protein organelles consisting of an inner enzymatic core encased within a selectively permeable shell. BMC shells are modular, tractable architectures that can be repurposed with new interior enzymes for biomanufacturing purposes. The permeability of BMC shells is function-specific and regulated by biophysical properties of the shell subunits, especially its pores. We hypothesized that ions may interact with pore residues in a manner that influences the substrate permeation process. In vitro activity comparisons between native and broken BMCs demonstrated that increasing NaCl negatively affects permeation rates. Molecular dynamics simulations of the dominant shell protein (BMC-H) revealed that chloride ions preferentially occupy the positive pore, hindering substrate permeation, while sodium cations remain excluded. Overall, these results demonstrate that shell properties influence ion permeability and leverages the integration of experimental and computational techniques to improve our understanding of BMC shells towards their repurposing for biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

One Collision—Two Substituents: Gas–Phase Preparation of Xylenes under Single–Collision Conditions

The fundamental reaction pathways to the simplest dialkylsubstituted aromatics—xylenes (C 6 H 4 (CH 3 ) 2 )—in high-temperature combustion flames and in low-temperature extraterrestrial environments are still unknown, but critical to understand the chemistry and molecular mass growth processes in these extreme environments. Exploiting crossed molecular beam experiments augmented by state-of-the-art electronic structure and statistical calculations, this study uncovers a previously elusive, facile gas-phase synthesis of xylenes through an isomer-selective reaction of 1-propynyl (methylethynyl, CH 3 CC) with 2-methyl-1,3-butadiene (isoprene, C 5 H 8 ). The reaction dynamics are driven by a barrierless addition of the radical to the diene moiety of 2-methyl-1,3-butadiene followed by extensive isomerization (hydrogen shifts, cyclization) prior to unimolecular decomposition accompanied by aromatization via atomic hydrogen loss. This overall exoergic reaction affords a preparation of xylenes not only in high-temperature environments such as in combustion flames and around circumstellar envelopes of carbon-rich Asymptotic Giant Branch (AGB) stars, but also in low-temperature cold molecular clouds (10 K) and in hydrocarbon-rich atmospheres of planets and their moons such as Triton and Titan. Furthermore, our study established a hitherto unknown gas-phase route to xylenes and potentially more complex, disubstituted benzenes via a single collision event highlighting the significance of an alkyl-substituted ethynyl-mediated preparation of aromatic molecules in our Universe.

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

One Collision—Two Substituents: Gas–Phase Preparation of Xylenes under Single–Collision Conditions

The fundamental reaction pathways to the simplest dialkylsubstituted aromatics—xylenes (C 6 H 4 (CH 3 ) 2 )—in high-temperature combustion flames and in low-temperature extraterrestrial environments are still unknown, but critical to understand the chemistry and molecular mass growth processes in these extreme environments. Exploiting crossed molecular beam experiments augmented by state-of-the-art electronic structure and statistical calculations, this study uncovers a previously elusive, facile gas-phase synthesis of xylenes through an isomer-selective reaction of 1-propynyl (methylethynyl, CH 3 CC) with 2-methyl-1,3-butadiene (isoprene, C 5 H 8 ). The reaction dynamics are driven by a barrierless addition of the radical to the diene moiety of 2-methyl-1,3-butadiene followed by extensive isomerization (hydrogen shifts, cyclization) prior to unimolecular decomposition accompanied by aromatization via atomic hydrogen loss. This overall exoergic reaction affords a preparation of xylenes not only in high-temperature environments such as in combustion flames and around circumstellar envelopes of carbon-rich Asymptotic Giant Branch (AGB) stars, but also in low-temperature cold molecular clouds (10 K) and in hydrocarbon-rich atmospheres of planets and their moons such as Triton and Titan. Furthermore, our study established a hitherto unknown gas-phase route to xylenes and potentially more complex, disubstituted benzenes via a single collision event highlighting the significance of an alkyl-substituted ethynyl-mediated preparation of aromatic molecules in our Universe.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Self-Assembly of Flexible Linear–Semiflexible Bottlebrush–Flexible Linear Triblock Copolymers

Block copolymer (BCP) self-assembly is a fundamental process in which incompatible blocks spontaneously form organized microstructures with broad practical applications. Classical understanding is that the domain spacing is limited by the contour length of the polymer backbone. Here, using a combination of molecular design, chemical synthesis, small-/wide-angle X-ray scattering, transmission electron microscopy, and electron tomography, we discover that this molecular picture does not hold for architecturally semiflexible BCPs. For strongly segregated linear–semiflexible bottlebrush–linear triblock copolymers, the size of the bottlebrush domain can be twice the bottlebrush backbone contour length. The mechanism of such anomalous self-assembly is likely that the interfacial repulsion between the incompatible blocks is large enough to pull a part of the linear end blocks into the bottlebrush domain. This effectively increases the bottlebrush domain size. Moreover, the semiflexible bottlebrush widens the regime for the cylinder morphology that is associated with the volume fraction of the end blocks fC SFB ∈ (0.10, >0.41). This window is much wider than that for flexible linear BCPs, fC F ∈ (0.14, 0.35), and that predicted by the recent self-consistent field theory for linear-bottlebrush BCPs of the same chemistry and molecular architecture. Finally, our experimental findings reveal previously unrecognized mechanisms for the self-assembly of architecturally complex BCPs.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Multi-level Monte Carlo methods in chemical applications with Lennard-Jones potentials and other landscapes with isolated singularities

We describe and compare outcomes of various Multi-Level Monte Carlo (MLMC) method variants, motivated by the potential of improved computational efficiency over rejection based Monte Carlo, which scales poorly with problem dimension. With an eye toward its application to computational chemical physics, we test MLMC's ability to sample trajectories on two problems — a familiar double-well potential, with known stationary distributions, and a Lennard-Jones solid potential (a Galton Board). By sampling Brownian motion trajectories, we are able to compute expectations of observable averages. These multi-basin potential energy problems capture the essence of the challenges with using MLMC, namely, maintaining correspondence of sample paths as time-resolution is varied. Addressing this challenge properly can lead to MLMC significantly outperforming standard Monte Carlo path sampling. We describe the essence of this problem and suggest strategies that circumvent diverging multilevel sample paths for an important class of problems. In the tests we also compare the computational cost of several, “adaptive,” variants of MLMC. Our results demonstrate that MLMC overcomes the collision, time scale limitation of the more familiar Brownian path MC samplers, and our implementation provides tunable error thresholds, making MLMC a promising candidate for application to larger and more complex molecular systems.

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

Formation, chemical evolution and solidification of the dense liquid phase of calcium (bi)carbonate

Metal carbonates, which are ubiquitous in the near-surface mineral record, are a major product of biomineralizing organisms and serve as important targets for capturing anthropogenic CO 2 emissions. However, pathways of carbonate mineralization typically diverge from classical predictions due to the involvement of disordered precursors, such as the dense liquid phase (DLP), yet little is known about DLP formation or solidification processes. Using in situ methods we report that a highly hydrated bicarbonate DLP forms via liquid–liquid phase separation and transforms into hollow hydrated amorphous CaCO 3 particles. Acidic proteins and polymers extend DLP lifetimes while leaving the pathway and chemistry unchanged. Molecular simulations suggest that the DLP forms via direct condensation of solvated Ca 2+ •(HCO 3 – ) 2 complexes that react due to proximity effects in the confined DLP droplets. Furthermore, our findings provide insight into CaCO 3 nucleation that is mediated by liquid–liquid phase separation, advancing the ability to direct carbonate mineralization and elucidating an often-proposed complex pathway of biomineralization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Chain and Segmental Dynamics in Polymer–Nanoparticle Composites with High Nanoparticle Loading

Recent experimental and simulation studies have shown that polymer–nanoparticle (NP) composites (PNCs) with ultra-high NP loading (>50%) exhibit remarkable mechanical properties and dramatic increases in polymer glass-transition temperature, viscosity, and thermal stability compared to the bulk polymer. These deviations in macroscopic properties suggest a slowdown in both segmental and chain-scale polymer dynamics due to confinement. In this work, we examine the polymer conformations and dynamics in these PNCs using molecular dynamics simulations of both unentangled and entangled coarse-grained polymers in random-close-packed NP packings with varying polymer fill fractions. We find that the changes in the polymer dynamics depend on the number of NPs in contact with a polymer segment. Using the number of polymer–NP contacts and different polymer chain conformations as criteria for categorization, we further examine the polymer dynamics at multiple length scales to show the high level of dynamic heterogeneity in PNCs with ultra-high NP loading.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models

Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, natural population analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree–Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 Å of the central water) in the quantum chemical calculation converges the charges of the central water molecule. Furthermore, our final pragmatic quantum chemical charge-assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 Å.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Pathway toward Optical Cycling and Laser Cooling of Functionalized Arenes

Rapid and repeated photon cycling has enabled precision metrology and the development of quantum information systems using atoms and simple molecules. Extending optical cycling to structurally complex molecules would provide new capabilities in these areas, as well as in ultracold chemistry. Increased molecular complexity, however, makes realizing closed optical transitions more difficult. Building on already established strong optical cycling of diatomic, linear triatomic, and symmetric top molecules, recent work has pointed the way to cycling of larger molecules, including phenoxides. The paradigm for these systems is an optical cycling center bonded to a molecular ligand. Theory has suggested that cycling may be extended to even larger ligands, like naphthalene, pyrene, and coronene. For this paper, we study optical excitation and fluorescent vibrational branching of CaO-[illus. chemical structure], SrO-[illus. chemical structure], and CaO-[illus. chemical structure] and find only weak decay to excited vibrational states, indicating a promising path to full quantum control and laser cooling of large arene-based molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Machine learning overcomes human bias in the discovery of self-assembling peptides

Peptide materials have a wide array of functions, from tissue engineering and surface coatings to catalysis and sensing. Tuning the sequence of amino acids that comprise the peptide modulates peptide functionality, but a small increase in sequence length leads to a dramatic increase in the number of peptide candidates. Traditionally, peptide design is guided by human expertise and intuition and typically yields fewer than ten peptides per study, but these approaches are not easily scalable and are susceptible to human bias. Here, in this work, we introduce a machine learning workflow—AI-expert—that combines Monte Carlo tree search and random forest with molecular dynamics simulations to develop a fully autonomous computational search engine to discover peptide sequences with high potential for self-assembly. We demonstrate the efficacy of the AI-expert to efficiently search large spaces of tripeptides and pentapeptides. The predictability of AI-expert performs on par or better than our human experts and suggests several non-intuitive sequences with high self-assembly propensity, outlining its potential to overcome human bias and accelerate peptide discovery.

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

Nanocluster superstructures assembled via surface ligand switching at high temperature

Superstructures with nanoscale building blocks, when coupled with precise control of the constituent units, open opportunities in rationally designing and manufacturing desired functional materials. Yet, synthetic strategies for the large-scale production of superstructures are scarce. We report a scalable and generalized approach to synthesizing superstructures assembled from atomically precise Ce24O28(OH)8 and other rare-earth metal-oxide nanoclusters alongside a detailed description of the self-assembly mechanism. Combining operando small-angle X-ray scattering, ex situ molecular and structural characterizations, and molecular dynamics simulations indicates that a high-temperature ligand-switching mechanism, from oleate to benzoate, governs the formation of the nanocluster assembly. The chemical tuning of surface ligands controls superstructure disassembly and reassembly, and furthermore, enables the synthesis of multicomponent superstructures. Here, this synthetic approach, and the accurate mechanistic understanding, are promising for the preparation of superstructures for use in electronics, plasmonics, magnetics and catalysis.

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

Spatially Resolved Mapping of Three-Dimensional Molecular Orientations with ~2 nm Spatial Resolution through Tip-Enhanced Raman Scattering

We record local optical field images of silver nanocubes (75 nm) using tip-enhanced Raman (TER) spectral imaging. The images that we observe are consistent with several recent reports from our group, but here, we demonstrate sub-2 nm spatial resolution in local optical field nanoimaging under ambient laboratory conditions. This is achieved by scanning the substrate (nanocube on Si) relative to a 4-thiobenzonitrile (TBN)-functionalized Ag-coated TER probe. The spatial resolution that we obtain necessitates that only a few molecules govern the recorded optical response; molecular orientation becomes an important consideration in such measurements. We model the orientation through geometry optimization of a TBN molecule chemisorbed onto an Ag79 cluster (sphere with a ~1 nm diameter). Using the computed orientation of the cluster-bound molecule, we then model the optical response using formalism that accounts for the orientation of the molecule relative to vector components of the local optical fields. We find optimal agreement between experiment and theory. In effect, this work reveals the parallels between single-molecule Raman scattering and high-spatial-resolution TER spectroscopy, even when the images themselves cannot be used to visualize a single molecule in real space.

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

Artificial Transmembrane Channel Constructed from Shape-Persistent Covalent Organic Molecular Cages Capable of Ion and Small Molecule Transport

Shape-persistent arylene ethynylene molecular cages have been investigated as transmembrane channels for ions and small molecules. The molecular cages were obtained starting from tetrayne monomers through alkyne metathesis cyclooligomerization. We found these porphyrin-based rigid molecular cages can insert into the lipid bilayer and efficiently transport ions and small molecules (e.g., calcein). Our study reveals longer hydrophobic alkyl chains on the cage molecule promote the channeling efficiency, while shorter and/or more polar side chains impair such activity. Kinetic analysis shows linear correlation between the rate of proton transport and the concentration of the cage, suggesting the active species is likely a monomeric cage. We found that C70-encapsulated cages are nearly inactive for transmembrane ion transportation, indicating that ions are likely transported through the internal cavity of the cage. Discrete shape-persistent organic cages represent highly stable synthetic ion channels or pores, which could have interesting applications in biomimetic signaling and drug delivery.

alkyne metathesis↗
DOE OSTI2022

Dissolving salt is not equivalent to applying a pressure on water

Abstract Salt water is ubiquitous, playing crucial roles in geological and physiological processes. Despite centuries of investigations, whether or not water’s structure is drastically changed by dissolved ions is still debated. Based on density functional theory, we employ machine learning based molecular dynamics to model sodium chloride, potassium chloride, and sodium bromide solutions at different concentrations. The resulting reciprocal-space structure factors agree quantitatively with neutron diffraction data. Here we provide clear evidence that the ions in salt water do not distort the structure of water in the same way as neat water responds to elevated pressure. Rather, the computed structural changes are restricted to the ionic first solvation shells intruding into the hydrogen bond network, beyond which the oxygen radial-distribution function does not undergo major change relative to neat water. Our findings suggest that the widely cited pressure-like effect on the solvent in Hofmeister series ionic solutions should be carefully revisited.

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

Mode-specific pressure effects on the relaxation of an excited nitromethane molecule in an argon bath

The vibrational and rotational mode-specific relaxations of CH 3 NO 2 with 50 kcal/mol of initial internal energy in an argon bath is computed at 300 K at pressures of 10-400 atm. This work uses archived information from our previously published [J. Chem. Phys. 142, 014303 (2015)] molecular dynamics simulations and employs our previous published [J. Chem. Phys. 151, 034303 (2019)] method for projecting time-dependent Cartesian velocities onto normal mode eigenvectors. The computed relaxations cover three types of energies: vibrational, rotational, and Coriolis. In general, rotational and Coriolis relaxations in all modes are initially fast followed by an orders of magnitude slower relaxation. For all modes, that slower relaxation rate is approximately comparable to the vibrational relaxation rate. For all three types of energies, there are small-scale mode-to-mode variations. Of particular prominence is the exceptionally fast relaxation shared in common by the external rotation about the C-N axis, the internal hindered rotation of the CH 3 group relative to the NO 2 group, and the symmetric stretch of the CH 3 group.

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

Interplay of water and a supramolecular capsule for catalysis of reductive elimination reaction from gold

Abstract Supramolecular assemblies have gained tremendous attention due to their ability to catalyze reactions with the efficiencies of natural enzymes. Using ab initio molecular dynamics, we identify the origin of the catalysis by the supramolecular capsule Ga 4 L 6 12− on the reductive elimination reaction from gold complexes and assess their similarity to natural enzymes. By comparing the free energies of the reactants and transition states for the catalyzed and uncatalyzed reactions, we determine that an encapsulated water molecule generates electric fields that contributes the most to the reduction in the activation free energy. Although this is unlike the biomimetic scenario of catalysis through direct host-guest interactions, the electric fields from the nanocage also supports the transition state to complete the reductive elimination reaction with greater catalytic efficiency. However it is also shown that the nanocage poorly organizes the interfacial water, which in turn creates electric fields that misalign with the breaking bonds of the substrate, thus identifying new opportunities for catalytic design improvements in nanocage assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Electronic and structural properties of single-crystal Jahn–Teller active Co 1+x Mn 2–x O 4 thin films

Recent investigations on spinel CoMn 2 O 4 have shown its potential for applications in water splitting and fuel cell technologies as it exhibits strong catalytic behavior through oxygen reduction reactivity. To further understand this material, we report for the first time the synthesis of single-crystalline Co 1+x Mn 2-x O 4 thin films using molecular beam epitaxy. By varying sample composition, we establish links between cation stoichiometry and material properties using in-situ x-ray photoelectron spectroscopy, x-ray diffraction, scanning transmission electron microscopy, x-ray absorption spectroscopy, and spectroscopic ellipsometry. Our results indicate that excess Co ions occupy interstitial tetrahedral sites up to a certain stoichiometry, then are substitutional for octahedrally-coordinated Mn beyond this threshold. Here, we compare these results with density functional theory models of stoichiometric CoMn 2 O 4 to understand how the Jahn-Teller distortion and hybridization in Mn-O bonds impact the ability to hole dope the material with excess Co. The findings provide important insights into CoMn 2 O 4 and related spinel oxides for future application as inexpensive oxygen reduction reaction catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗