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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Direct Observation of Twin van der Waals Molecular Chains

The van der Waals (vdW) assemblies are the most common structures of materials. However, directly mapping intermolecular electron clouds of a vdW assembly has never been obtained, even though the intramolecular electron clouds were visualized by atomic-resolution techniques. In this report, we unprecedently mapped the intermolecular electron cloud of the assembles of ethanol molecules via ethyl groups with noncontact atomic force microscopy at 5 K, leading to the first visualization of vdW molecular chains, in which ethanol molecules assemble into twin vdW molecular chains in a reverse parallel configuration on Ag(111) plane. Furthermore, spontaneous order-disorder transitions in the chain were dynamically observed, suggesting its unusual properties different from 2D vdW materials. In conclusion, these findings provide an "eye" to see the atomic world of vdW materials.

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

Impact of environmental oxygen on nanoparticle formation and agglomeration in aluminum laser ablation plumes

Here, the role of ambient oxygen gas (O 2 ) on molecular and nanoparticle formation and agglomeration was studied in laser ablation plumes. As a lab-scale surrogate to a high explosion detonation event, nanosecond laser ablation of an aluminum alloy (AA6061) target was performed in atmospheric pressure conditions. Optical emission spectroscopy and two mass spectrometry techniques were used to monitor the early to late stages of plasma generation to track the evolution of atoms, molecules, clusters, nanoparticles, and agglomerates. The experiments were performed under atmospheric pressure air, atmospheric pressure nitrogen, and 20% and 5% O 2 (balance N 2 ), the latter specifically with in situ mass spectrometry. Electron microscopy was performed ex situ to identify crystal structure and elemental distributions in individual nanoparticles. We find that the presence of ≈20% O 2 leads to strong AlO emission, whereas in a flowing N 2 environment (with trace O 2 ), AlN and strong, unreacted Al emissions are present. In situ mass spectrometry reveals that as O 2 availability increases, Al oxide cluster size increases. Nanoparticle agglomerates formed in air are found to be larger than those formed under N 2 gas. High-resolution transmission electron microscopy demonstrates that Al 2 O 3 and AlN nanoparticle agglomerates are formed in both environments; indicating that the presence of trace O 2 can lead to Al 2 O 3 nanoparticle formation. The present results highlight that the availability of O 2 in the ambient gas significantly impacts spectral signatures, cluster size, and nanoparticle agglomeration behavior. These results are relevant to understanding debris formation in an explosion event, and interpreting data from forensic investigations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Non-resonant Raman optical activity from phase-space electronic structure theory

In order to model experimental non-resonant Raman optical activity, chemists must compute a host of second-order response tensors (e.g., the electric-dipole–magnetic-dipole polarizability) and their nuclear derivatives along a set of vibrational modes. While these response functions are almost always computed within a Born–Oppenheimer (BO) framework, here we provide a natural interpretation of the electric-dipole–magnetic-dipole polarizability within phase space electronic structure theory, a beyond-BO model whereby the electronic structure depends on nuclear momentum (P) in addition to nuclear position (R). By coupling to nuclear momentum, phase space electronic structure theory is able to capture the asymmetric response of the electronic properties to an external field, in so far as for a vibrating (non-stationary) molecule, $\frac{∂μ}{∂B}$≠$\frac{∂m}{∂F}$, where μ and m are the electrical linear and magnetic dipoles, and F and B are electric and magnetic fields. As an example, for a prototypical methyloxirane molecule, we show that phase space electronic structure theory is able to deliver a reasonably good match with experimental results in a manner that is formally invariant to gauge origin G 0 —provided that one uses a complete basis or, alternatively, gauge invariant atomic orbitals.

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

DFT-Based Calculation of Dissolution Activation Energy and Kinetics of Ni–Cr Alloys

A density functional theory investigation of the process of dissolution of Ni and Cr adatoms from model Ni–Cr(111) alloy surfaces is presented, both in vacuum and with explicit water molecules. The goal is to understand how the electronic structures solved using DFT can provide insights as to changes in valence, energy and coordination of the adatoms in the process of dissolving from the alloy surface. It is found that nearby Cr solute atoms increase the dissolution activation energy of Ni. Cr adatoms have a similar dissolution activation energy as Ni adatoms, except for one particular surface configuration that has a much smaller dissolution activation energy, which might promote selective dissolution of Cr in Ni–Cr alloys. To interpret the first-principles modeling results for the potential energy trajectory along the dissolution reaction coordinate, we provide a thermodynamic breakdown of the various terms that contribute to the dissolution activation and total reaction energy. The role of addition of Cr is explored on the dissolution kinetics of a Ni–Cr alloys of varying composition by constructing a model for the corrosion current density with DFT-based activation energies. Lastly, dissolution resistance index is proposed as a quantifiable descriptor of the dissolution resistance of corrosion resistant alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Building Atomic and Plasmonic Devices via Electron Beams: from Desired Structures to Desired Properties

The evolution of the aberration correction in Scanning Transmission Electron Microscopy (STEM) has enabled multiple advances including high-resolution structural imaging, pm-level position detection of atomic columns, and ~3-5 mV resolution electron energy loss spectroscopy of the chemical and physical functionalities. These developments have further enabled the precise manipulation of the atomic structure of materials, including removal and formation of atomic planes in 3D materials, controlled atomic motion, and even direct atomic assembly of homo- and heteroatomic artificial molecules. Here, we will discuss several recent advances in STEM-EELS automated experiments as applied to quantum and nanoplasmonic systems.

42 ENGINEERING↗
DOE OSTI2023

Multielectron Bond Cleavage Processes Enabled by Redox-Responsive Phosphinimide Ligands

The activation of small molecules via multielectron redox processes offers promise in mediating difficult transformations related to energy conversion processes. While molecular systems that engage in one- and two-electron redox processes are widespread, those that participate in the direct transfer of four or more electrons to small molecules are very rare. To that end, we report a mononuclear Cr II complex competent for the 4-electron reduction of dioxygen (O 2 ) and nitrosoarenes. These systems additionally engage in facile two-electron group transfer reactivity, including O atom excision and nitrene transfer. Structural, spectroscopic, and computational studies support bond activation processes that intimately occur at a mononuclear chromium(phosphinimide) center and highlight the unusual structural responsiveness of the phosphinimides in stabilizing a range of metal redox states.

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

General Design Rules for Bimetallic Platinum(II) Complexes

A series of platinum(II) bimetallic complexes were studied to investigate the effects of ligands on both the geometric and electronic structure. Modulating the Pt-Pt distance through the bridging ligand architecture was found to dictate the nature of the lowest energy electronic transitions, localized in one-half of the molecule or delocalized across the entire molecule. By reducing the separation between the platinum atoms, the lowest energy electronic transitions will be dominated by the metal-metal-to-ligand charge transfer transition. Conversely, by increasing the distance between the platinum atoms, the lowest electronic transition will be largely localized metal-to-ligand charge transfer or ligand centered in nature. Additionally, the cyclometalating ligands were observed to have a noticeable stabilizing effect on the triplet excited states as the conjugation increased, arising from geometric reorientation and increased electron delocalization of the ligands. Furthermore, such stabilization of the triplet state energy has been shown to alter the excited state potential energy landscape as well as the excited state trajectory.

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

Hybrid Quantum-Classical Neural Network for Calculating Ground State Energies of Molecules

We present a hybrid quantum-classical neural network that can be trained to perform electronic structure calculation and generate potential energy curves of simple molecules. The method is based on the combination of parameterized quantum circuits and measurements. With unsupervised training, the neural network can generate electronic potential energy curves based on training at certain bond lengths. To demonstrate the power of the proposed new method, we present the results of using the quantum-classical hybrid neural network to calculate ground state potential energy curves of simple molecules such as H 2 , LiH, and BeH 2 . The results are very accurate and the approach could potentially be used to generate complex molecular potential energy surfaces.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Significant charge transport effects due to subtle molecular changes in nitroxide radical single crystals

Radical-containing materials have received renewed interest due to their charge-conducting properties. However, most work focuses on macromolecules, while less attention has been paid to radical-containing small molecules. Here, we quantify the electrical conductivity in two organic radical single crystals and demonstrate that a subtle change in atomic connectivity drastically alters the macroscopic electronic properties of the materials. One radical crystal has an electrical conductivity of 3S m –1 , which is the among the highest values for nonconjugated radical conductors over a 1 μm scale. However, the other radical crystal has a 1,000-fold lower conductivity, despite their extremely similar molecular structures. The temperature-dependent conductivity follows the variable range hopping mechanism for both radical crystals, and the difference in effective charge mobility is the reason for the conductivity difference. These results present a clear picture of the design rules and charge transport mechanism for radical-based small-molecule materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. Additionally, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. Finally, the capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Advancing density functional tight-binding method for large organic molecules through equivariant neural networks

Semi-empirical quantum-mechanical (QM) methods have become valuable tools for studying complex (bio)molecular systems due to their balance between computational efficiency and accuracy. A key aspect of these methods is their parameterization, which not only governs the reliability of the results but also provides an opportunity to enhance their overall performance. In our previous work [J. Phys. Chem. Lett., 2021, 11, 16], we advanced the third-order semi-empirical density functional tight-binding (DFTB3) method for computing multiple properties of small molecules by developing the machine learning (ML) potential NN rep to bridge the gap between DFTB3 electronic components and those of the hybrid DFT-PBE0 functional. To overcome the limitations of NN rep , we introduce the EquiDTB framework, which leverages physics-inspired equivariant neural networks (NN) to parameterize scalable and transferable many-body Δ TB potentials, replacing the standard pairwise DFTB repulsive potential. This advancement extends the applicability of our ML-corrected DFTB approach to larger molecules and non-covalent systems (including only C, N, O, and H atoms), going beyond the chemical space represented in the training QM datasets. The enhanced performance of EquiDTB over the standard TB methods is demonstrated by the accurate computation of the atomic forces of S66x8 molecular dimers, as well as their interaction energies. Moreover, EquiDTB can be effectively employed to explore the potential energy surfaces of large and flexible drug-like molecules—for example, to determine the minimum energy path between isomers, analyze structural transitions during dynamical simulations, compute vibrational modes, and investigate energetic rankings. The performance for single molecules slightly decreases when the DFTB electronic energy is reduced to first-order but remains superior to standard TB methods. Our work thus demonstrates that an optimal integration of an equivariant NN with QM datasets can advance the DFTB method while maintaining high efficiency, paving the way for reliable (bio)molecular simulations.

Medrano Sandonas, Leonardo [Technische Universität↗
DOE OSTI2025

Effect of tert -Butyl Substitution on the Interactions of Cobalt Phthalocyanine with a Carbon Monoxide-Functionalized Tip

Supported cobalt phthalocyanines (CoPc) are promising catalysts for CO 2 reduction, a critical process for mitigating greenhouse gas emissions. Enhancing the catalytic performance of CoPc involves modifying the interaction between the cobalt center and intermediate species. This study focuses on the effects of tert-butyl substitution on CoPc using (tert-butyl) 4 CoPc, where the substitution can both directly alter the molecule’s intramolecular electronic structure and indirectly alter it by the bulky group weakening the interaction with the support. Toward this end, we investigated the structural and chemical properties of (tert-butyl) 4 CoPc on a Ag(111) surface at the single-molecule level using three-dimensional atomic force microscopy (AFM) with a CO-terminated tip and discussed them in comparison with data for unmodified CoPc and amino-substituted CoPc. Notably, distance-dependent force measurements revealed anomalies in the tert-butyl groups’ force curves, attributed to their rotational flexibility. The tert-butyl (t-butyl) groups were also observed to increase the attraction of the central Co atom to CO, but this effect was attributed largely to enhanced interactions of the back of the tip with the peripheral t-butyl groups. In conclusion, while this longer-range interaction would not be expected to impact the interaction of small molecules with the catalytic center, the results reveal the ability of AFM to characterize longer range environmental interactions that can enhance adsorption and subsequent reactions of larger molecules, as well as the role side chains that offer configurational adaptability may play in these interactions.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

The Crucial Role of Sb 2 F 10 in the Chemical Synthesis of F 2

The purely chemical synthesis of fluorine is a spectacular reaction which for more than a century had been believed to be impossible. In 1986, it was finally experimentally achieved, but since then this important reaction has not been further studied and its detailed mechanism had been a mystery. The known thermal stability of MnF 4 casts serious doubts on the originally proposed hypothesis that MnF 4 is thermodynamically unstable and decomposes spontaneously to a lower manganese fluoride and F 2 . This apparent discrepancy has now been resolved experimentally and by electronic structure calculations. It is shown that the reductive elimination of F 2 requires a large excess of SbF 5 and occurs in the last reaction step when in the intermediate [SbF 6 ][MnF 2 ][Sb 2 F 11 ] the addition of one more SbF 5 molecule to the [SbF 6 ] - anion generates a second tridentate [Sb 2 F 11 ] - anion. The two tridentate [Sb 2 F 11 ] - anions then provide six fluorine bridges to the Mn atom thereby facilitating the reductive elimination of the two fluorine ligands as F 2 .

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

Atomic-Scale Dynamic Interaction of H 2 O Molecules with Cu Surface

Atomic-scale interaction of water vapor with metal surfaces beyond surface adsorption under technologically relevant conditions remains mostly unexplored. Using aberration-corrected environmental transmission electron microscopy, we reveal the dynamic surface activation of Cu by H 2 O at elevated temperature and pressure. In this study, we find a structural transition from flat to corrugated surface for the Cu(011) under low water-vapor pressure. Increasing the water-vapor pressure leads to the surface reaction of Cu with dissociated H 2 O, resulting in the formation of a metastable “bilayer” Cu-O-H phase. Corroborated by density functional theory and ab initio molecular dynamics calculations, the cooperative O and OH interaction with Cu is responsible for the formation and subsurface propagation of this phase.

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

Site-specific interrogation of an ionic chiral fragment during photolysis using an X-ray free-electron laser

Abstract Short-wavelength free-electron lasers with their ultrashort pulses at high intensities have originated new approaches for tracking molecular dynamics from the vista of specific sites. X-ray pump X-ray probe schemes even allow to address individual atomic constituents with a ‘trigger’-event that preludes the subsequent molecular dynamics while being able to selectively probe the evolving structure with a time-delayed second X-ray pulse. Here, we use a linearly polarized X-ray photon to trigger the photolysis of a prototypical chiral molecule, namely trifluoromethyloxirane (C 3 H 3 F 3 O), at the fluorine K-edge at around 700 eV. The created fluorine-containing fragments are then probed by a second, circularly polarized X-ray pulse of higher photon energy in order to investigate the chemically shifted inner-shell electrons of the ionic mother-fragment for their stereochemical sensitivity. We experimentally demonstrate and theoretically support how two-color X-ray pump X-ray probe experiments with polarization control enable XFELs as tools for chiral recognition.

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

Probing atom dynamics of excited Co-Mo-S nanocrystals in 3D

Advances in electron microscopy have enabled visualizations of the three-dimensional (3D) atom arrangements in nano-scale objects. The observations are, however, prone to electron-beam-induced object alterations, so tracking of single atoms in space and time becomes key to unravel inherent structures and properties. Here, we introduce an analytical approach to quantitatively account for atom dynamics in 3D atomic-resolution imaging. The approach is showcased for a Co-Mo-S nanocrystal by analysis of time-resolved in-line holograms achieving ~1.5 Å resolution in 3D. The analysis reveals a decay of phase image contrast towards the nanocrystal edges and meta-stable edge motifs with crystallographic dependence. These findings are explained by beam-stimulated vibrations that exceed Debye-Waller factors and cause chemical transformations at catalytically relevant edges. This ability to simultaneously probe atom vibrations and displacements enables a recovery of the pristine Co-Mo-S structure and establishes, in turn, a foundation to understand heterogeneous chemical functionality of nanostructures, surfaces and molecules.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Quantum Molecular Charge-Transfer Model for Multistep Auger–Meitner Decay Cascade Dynamics

The fragmentation of molecular cations following inner-shell decay processes in molecules containing heavy elements underpins the X-ray damage effects observed in X-ray scattering measurements of biological and chemical materials, as well as in medical applications involving Auger electron-emitting radionuclides. Traditionally, these processes are modeled using simulations that describe the electronic structure at an atomic level, thereby omitting molecular bonding effects. This work addresses the gap by introducing a novel approach that couples Auger–Meitner decay to nuclear dynamics across multiple decay steps, by developing a decay spawning dynamics algorithm and applying it to potential energy surfaces characterized with ab initio molecular dynamics simulations. We showcase the approach on a model decay cascade following K-shell ionization of IBr and subsequent Kβ fluorescence decay. We examine two competing channels that undergo two decay steps, resulting in ion pairs with a total 3+ charge state. This approach provides a continuous description of the electron transfer dynamics occurring during the multistep decay cascade and molecular fragmentation, revealing the combined inner-shell decay and charge transfer time scale to be approximately 75 fs. In conclusion, our computed kinetic energies of ion fragments show good agreement with experimental data.

Ab initio molecular dynamics↗
DOE OSTI2021

OrbNet Denali: A machine learning potential for biological and organic chemistry with semi-empirical cost and DFT accuracy

We present OrbNet Denali, a machine learning model for an electronic structure that is designed as a drop-in replacement for groundstate density functional theory (DFT) energy calculations. The model is a message-passing graph neural network that uses symmetryadapted atomic orbital features from a low-cost quantum calculation to predict the energy of a molecule. OrbNet Denali is trained on a vast dataset of 2.3 × 10 6 DFT calculations on molecules and geometries. This dataset covers the most common elements in biochemistry and organic chemistry (H, Li, B, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Br, and I) and charged molecules. OrbNet Denali is demonstrated on several well-established benchmark datasets, and we find that it provides accuracy that is on par with modern DFT methods while offering a speedup of up to three orders of magnitude. For the GMTKN55 benchmark set, OrbNet Denali achieves WTMAD-1 and WTMAD-2 scores of 7.19 and 9.84, on par with modern DFT functionals. For several GMTKN55 subsets, which contain chemical problems that are not present in the training set, OrbNet Denali produces a mean absolute error comparable to those of DFT methods. For the Hutchison conformer benchmark set, OrbNet Denali has a median correlation coefficient of R 2 = 0.90 compared to the reference DLPNO-CCSD(T) calculation and R 2 = 0.97 compared to the method used to generate the training data (ωB97X-D3/def2- TZVP), exceeding the performance of any other method with a similar cost. Similarly, the model reaches chemical accuracy for noncovalent interactions in the S66x10 dataset. For torsional profiles, OrbNet Denali reproduces the torsion profiles of ωB97X-D3/def2-TZVP with an average mean absolute error of 0.12 kcal/mol for the potential energy surfaces of the diverse fragments in the TorsionNet500 dataset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗