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All sources NASA NTRS DOE OSTI

DOE OSTI2021

Zero-Valent Palladium Single-Atoms Catalysts Confined in Black Phosphorus for Efficient Semi-Hydrogenation

Single-atom catalysts (SACs) represent a new frontier in heterogeneous catalysis due to their remarkable catalytic properties and maximized atomic utilization. However, single atoms often bond to the support with polarized electron density and thus exhibit a high valence state, limiting their catalytic scopes in many chemical transformations. In this study, it is demonstrated that 2D black phosphorus (BP) acts as giant phosphorus (P) ligand to confine a high density of single atoms (e.g., Pd 1 , Pt 1 ) via atomic layer deposition. Unlike other 2D materials, BP with relatively low electronegativity and buckled structure favors the strong confinement of robust zero-valent palladium SACs in the vacancy site. Metallic Pd 1 /BP SAC shows a highly selective semi-hydrogenation of phenylacetylene toward styrene, distinct from metallic Pd nanoparticles that facilitate the formation of fully hydrogenated products. Density functional theory calculations reveal that Pd atom forms covalent-like bonding with adjacent P atoms, wherein H atoms tend to adsorb, aiding the dissociative adsorption of H 2 . Zero-valent Pd in the confined space favors a larger energy gain for the synthesis of partially hydrogenated product over the fully hydrogenated one. This work provides a new route toward the synthesis of zero-valent SACs on BP for organic transformations.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Diamond under extremes

Diamond is, by virtue of the covalent bonding between atoms and the very strong carbon to carbon bonds, the hardest natural material. It has been a fascinating material since its discovery, first as a decorative gem and more recently, for its numerous industrial uses because of its extreme hardness, elastic modulus, and optical transparency. In recent years, it has become a preferred ablator for laser shock experiments, and this has led to its choice as the capsule material for fusion experiments at the National Ignition Facility. Further, this review covers both experimental and computational (including machine learning) advancements in research on diamond subjected extreme conditions of temperature and pressure. The synergy between shock and ramp loading experiments and atomic level simulations is proving to be powerful in advancing our understanding of diamond under extremes.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Linear Combination of Atomic Dipoles to Calculate the Bond and Molecular Dipole Moments of Molecules and Molecular Liquids

Here we report a linear combination of atomic dipole (LCAD) method for calculating the bond dipole moments of molecules. We show that the LCAD method reproduces the known molecular dipole moments of small to large molecules with a small error with respect to experimental and benchmark ab initio calculations, and molecular dipole distributions of bulk water that agree with maximally localized Wannier functions. The bond dipole moments derived from LCAD are also chemically interpretable in terms of the trend in bond ionicity in going from neutral to charged molecules. Moreover, the LCAD method accurately captures the influence of electric fields, supported by the correct trend in the change of the dipole moment under a uniform external electric field. The better grounding of bond dipole calculations indicates that it should also serve as a useful approach to bond dipole-field models used in catalysis or to reconstruct the small dipole of a H-terminated graphene flake.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Intramolecular hydrogen bonding analysis

The quasi-atomic orbital (QUAO) bonding analysis is used to study intramolecular hydrogen bonding (IMHB) in salicylic acid and an intermediate that is crucial to the synthesis of aspirin. The bonding analysis rigorously explores IMHB through directly accessing information that is intrinsic to the molecular wave function, thereby bypassing the need for intrinsically biased methods. The variables that affect the strength of IMHB are determined using kinetic bond orders, QUAO populations, and QUAO hybridizations. Important properties include both the interatomic distance between hydrogen and oxygen participating in the IMHB and the hybridization on the oxygen. The bonding analysis further shows that each intramolecular hydrogen bond is a four-electron three-center bond. Here, the bonding analysis is used to understand how aromatic reactivity changes due to the effect of functional groups on the aromatic ring.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

The Debye-Waller factor of disordered solids: The case for amorphous silicon

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (α-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in α-Si networks. It has been observed that the MSDs associated with tetrahedrally bonded Si atoms are considerably lower than their dangling-bond counterparts—originating from isolated and vacancy-induced clustered defects—and those on the surface of microvoids, leading to an asymmetric non-Gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in α-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of α-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of α-Si at low temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Ab initio studies of the impact of the Debye-Waller factor on the structural and dynamical properties of amorphous semiconductors: The case of a-Si

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (a-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in a-Si networks. It has been observed that the MSDs associated with tetrahedrally-bonded Si atoms are considerably lower than their dangling-bond counterparts – originating from isolated and vacancy-induced clustered defects – and those on the surface of microvoids, leading to an asymmetric non-gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in a-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of a-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of a-Si at low temperatures.

36 MATERIALS SCIENCE↗

DOE OSTI2025

The overlapping fragment approach for non-orthogonal configuration interaction with fragments

The non-orthogonal configuration interaction with fragments (NOCI-F) approach is extended opening the possibility to study intramolecular processes and materials with covalent or ionic lattices. So far, NOCI-F has been applied to study intermolecular energy and electron transfer employing ensembles of fragments that do not have atoms or bonds in common. The here presented approach divides the target system into two overlapping fragments that share one or more atoms and/or one or more bonds. After the construction of a collection of (multiconfigurational) fragment wave functions in a state specific optimization procedure, the fragment wave functions are combined to form many-electron basis functions for the non-orthogonal configuration interaction of the whole system. The orbitals in the overlapping fragment are defined by a corresponding orbital transformation of the fragment orbitals through a singular value decomposition. The overlapping fragments approach is first illustrated for a model system and then used to highlight some possible applications of NOCI with overlapping fragments. In conclusion, the results of excited state diffusion in transition metal oxide, intramolecular singlet fission and magnetic interactions in organic biradicals and ionic compounds are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Efficient and interpretable graph network representation for angle-dependent properties applied to optical spectroscopy

Abstract Graph neural networks are attractive for learning properties of atomic structures thanks to their intuitive graph encoding of atoms and bonds. However, conventional encoding does not include angular information, which is critical for describing atomic arrangements in disordered systems. In this work, we extend the recently proposed ALIGNN (Atomistic Line Graph Neural Network) encoding, which incorporates bond angles, to also include dihedral angles (ALIGNN-d). This simple extension leads to a memory-efficient graph representation that captures the complete geometry of atomic structures. ALIGNN-d is applied to predict the infrared optical response of dynamically disordered Cu(II) aqua complexes, leveraging the intrinsic interpretability to elucidate the relative contributions of individual structural components. Bond and dihedral angles are found to be critical contributors to the fine structure of the absorption response, with distortions that represent transitions between more common geometries exhibiting the strongest absorption intensity. Future directions for further development of ALIGNN-d are discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Developing Reaction Chemistry Models from Reactive Molecular Dynamics: TATB

Reactive Molecular Dynamic (RMD) are used to simulate the cook-off chemistry of TATB at a variety of fixed density and fixed temperature conditions. The chemical transformations are monitored using a Coordination Geometry Analysis (CGA) approach which tracks which atom types are bonded to each specific atom. This particularly identifies oxidation state changes that occur during the transformations. Correlations between these different chemical changes are identified using a Non-negative Matrix Factorization (NMF) approach. These identify reduced order chemistry models for the TATB system which contains six components whose concentration profiles are a function of both the temperature and density/pressure. The time histories of these transformations appear to show exponential growth/decay properties that could be fit with Arrhenius rates. These components should form the basis of deflagration rate models for these materials which could then be used in mesoscale simulations to analyze accidental initiation, shock-to-detonation and detonation propagation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Mapping 1D Confined Electromagnetic Edge States in 2D Monolayer Semiconducting MoS 2 Using 4D-STEM

Here, four-dimensional (4D) scanning transmission electron microscopy is used to study the electric fields at the edges of 2D semiconducting monolayer MoS2. Sub-nanometer 1D features in the 2D electric field maps are observed at the outermost region along zigzag edges and also along nanowire MoS-terminated MoS 2 edges. Atomic-scale oscillations are detected in the magnitude of the 1D electromagnetic edge state, with spatial variations that depend on the specific periodic edge reconstructions. Electric field reconstructions, along with integrated differential phase contrast reconstructions, reveal the presence of low Z number atoms terminating many of the uniform edges, which are difficult to detect by annular dark field scanning transmission electron microscopy due to its limited dynamic range. Density functional theory calculations support the formation of periodic 1D edge states and also show that enhancement of the electric field magnitude can occur for some edge terminations. The experimentally observed electric fields at the edges are attributed to the absence of an opposing electric field from a nearest neighbor atom when the electron beam propagates through the 2D monolayer and interacts. These results show the potential of 4D-STEM to map the atomic scale structure and fluctuations of electric fields around edge atoms with different bonding states than bulk atoms in 2D materials, beyond conventional imaging.

2D materials↗

NASA NTRS1974

Preparation of thick molybdenum targets

Thick natural molybdenum deposits on nickel plated copper substrates were prepared by thermal decomposition of molybdenum hexacarbonyl vapors on a heated surface in an inert gas atmosphere. The molybdenum metal atoms are firmly bonded to the substrate atoms, thus providing an excellent thermal contact across the junction. Molybdenum targets thus prepared should be useful for internal bombardment in a cyclotron where thermal energy inputs can exceed 10 kW.

Singh, J. J.↗

NASA NTRSDate not supplied

REACTER 2.0: Quantum-Informed Reaction Constraints and Automated Interaction Typing

REACTER is a heuristic method for modeling chemical reactions in classical molecular dynamics simulations, implemented in LAMMPS as fix bond/react. The authors recently extended LAMMPS to support alphanumeric labels for atom types, bond types etc., which enables the pre- and post-reaction templates required by the REACTER protocol to be portable between different simulations and greatly simplifies the task of creating simulation-ready reaction templates. To further increase the generality of reaction templates, support for wildcard characters within atom types has been added, along with the automatic assignment of interaction types for new bonds, angles, etc. based on the involved atom types. In some cases, this feature can express a class of reactions with one pair of reaction templates, where previously dozens may have been required. Advanced reaction constraints have also been added, including an Arrhenius constraint to enforce an effective activation energy, a root-mean-square-deviation option for complex geometrical constraints, as well as a custom constraint that leverages LAMMPS’ powerful built-in variable framework. Other new features include variable support for various inputs (e.g., to allow reaction rates or cutoffs to be dependent on overall conversion), on-the-fly update of molecule IDs, and the ability to create new atoms positioned with respect to the reaction site. The new features are applied to modeling polymeric, thermosetting and composite materials, and advanced applications of the new reaction constraints are demonstrated. For example, REACTER is shown to accurately reproduce mechanically-induced bond breaking, as characterized by third-order DFT-based tight-binding (DFTB3) simulations, via a constraint on the total potential energy of the involved atoms.

polymer simulations↗

DOE OSTI2021

Single Atom Catalysts: A Review of Characterization Methods

Abstract Single atom catalysts (SACs) harbor a potential to exceed nanoparticle catalysts in terms of activity, stability and selectivity in a growing number of chemical reactions. Although their investigation is attracting significant attention, important fundamental questions focusing on key physicochemical properties of SACs (e. g., structure – property relationships, structural dynamics, reaction‐driven restructuring) remain unanswered. A main challenge for research in the field is how to reliably characterize the environments of single atoms in the presence of complicating factors such as low weight loadings, strong metal‐support interactions, and atomic and multiscale heterogeneity of bonding in the single atom sites. This review addresses this challenge – identifying catalytically relevant features of physicochemical properties of single atoms (charge state, electronic structure, atomic configuration, bonding interactions with a support) and surveying advanced tools/methods for characterizing them. The review places a strong emphasis on multimodal methods exploiting X‐ray absorption, emission and photoelectron spectroscopies, and provides several examples from the authors’ research that demonstrate their use as powerful tools for SAC characterization.

Kottwitz, Matthew↗

DOE OSTI2025

Atomic-scale insights into topotactic transformations in an extra-large-pore zeolite using time-resolved 3D electron diffraction

Understanding the atomic-scale structural dynamics of phase transformations is crucial for developing materials and tailoring their properties. However, many materials are obtained as polycrystalline powders with large unit cells and/or complex structures, making it challenging to investigate detailed structural changes using conventional X-ray diffraction techniques. Here we employ time-resolved three-dimensional electron diffraction to reveal the topotactic reactions and transformations that convert the extra-large-pore silicate zeolite ECNU-45 into ECNU-46. ECNU-45 features three-dimensional interconnecting 24 × 10 × 10-ring channels, while ECNU-46 consists of one-dimensional 24-ring channels connected to 10-ring pockets. ECNU-45 and ECNU-46 are both examples of pure silicate zeolites with pore openings larger than 22-ring. Our findings indicate changes at six distinct tetrahedral silicon sites, involving atom displacement, addition and removal of framework atoms through bond breakage and formation. This work presents the synthesis of zeolites and also provides atomic-level insights into the dynamic processes of topotactic reactions. Our results have implications for advancing materials engineering and understanding complex solid-state reactions at an atomic scale.

Inorganic chemistry↗

DOE OSTI2023

Chlorination of Hydrogenated Silicon Nanosheets Revealed by Solid-State Nuclear Magnetic Resonance Spectroscopy

We report two-dimensional silicon nanosheets (Si-NS) synthesized by topotactic deintercalation of CaSi 2 are hypothesized to consist of buckled layers of sp 3 -hybridized silicon atoms that are bonded to three other framework Si atoms and a terminal atom or functional group such as H, Cl, or OH. Here, we apply 1 H{ 35 Cl} and 29 Si{ 35 Cl} Resonance-Echo Saturation-Pulse DOuble-Resonance (RESPDOR) solid-state NMR experiments to directly confirm the presence of chlorinated Si atoms within Si-NS. Plotting the 1 H{ 35 Cl} RESPDOR dephasing as a function of the 35 Cl saturation pulse offset reveals that the 35 Cl quadrupolar coupling constant (C Q ) is 38 MHz, consistent with Cl atoms that are covalently bonded to silicon. Modeling the 1 H{ 35 Cl} RESPDOR dephasing curve shows that the Si–Si interlayer spacing is approximately 6 Å. Plane-wave density functional theory (DFT) calculations show that the direct band gap transition of the Si-NS decreases with increasing chlorination and hydroxylation, suggesting that the band gap of Si-NS can be tuned by modifying the terminal atoms or functional groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1986

The importance of atomic and molecular correlation on the bonding in transition metal compounds

The determination of accurate spectroscopic parameters for molecular systems containing transition metal atoms is shown to require extensive data sets and a high level correlation treatment, and techniques and their limitations are considered. Extensive results reported on the transition metal atoms, hydrides, oxides, and dimers makes possible the design of a calculation to correctly describe the mixing of different atomic asymptotes, and to give a correct balance between molecular bonding and exchange interactions. Examples considered include the dipole moment of the 2Delta state of NiH, which can help determine the mixture of 3d(8)4s(2) and 3d(9)4s(1) in the NiH wavefunction, and the bonding in CrO, where an equivalent description of the relative energies associated with the Cr 3d-3d atomic exchange and the Cr-O bond is important.

Bauschlicher, Charles W., Jr.↗

DOE OSTI2023

Signatures of the Bromine Atom and Open-Shell Spin Coupling in the X-ray Spectrum of the Bromobenzene Cation

Tabletop X-ray spectroscopy measurements at the carbon K-edge complemented by ab initio calculations are used to investigate the influence of the bromine atom on the carbon core–valence transitions in the bromobenzene cation (BrBz + ). The electronic ground state of the cation is prepared by resonance-enhanced two-photon ionization of neutral bromobenzene (BrBz) and probed by X-rays produced by high-harmonic generation (HHG). Replacing one of the hydrogen atoms in benzene with a bromine atom shifts the transition from the 1s C* orbital of the carbon atom (C*) bonded to bromine by ~1 eV to higher energy in the X-ray spectrum compared to the other carbon atoms (C). Moreover, in BrBz + , the X-ray spectrum is dominated by two relatively intense transitions, 1s C →π* and 1s C* →σ*(C*–Br), where the second transition is enhanced relative to the neutral BrBz. In addition, a doublet peak shape for these two transitions is observed in the experiment. The 1s C →π* doublet peak shape arises due to the spin coupling of the unpaired electron in the partially vacant π orbital (from ionization) with the two other unpaired electrons resulting from the transition from the 1s C core orbital to the fully vacant π* orbitals. Here, the 1s C* →σ* doublet peak shape results from several transitions involving σ* and vibrational C*–Br mode activations following the UV ionization, which demonstrates the impact of the C*–Br bond length on the core–valence transition as well as on the relaxation geometry of BrBz + .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Inherent Anharmonicity of Harmonic Solids

Atomic vibrations, in the form of phonons, are foundational in describing the thermal behavior of materials. The possible frequencies of phonons in materials are governed by the complex bonding between atoms, which is physically represented by a spring-mass model that can account for interactions (spring forces) between the atoms (masses). The lowest-order, harmonic , approximation only considers linear forces between atoms and is thought incapable of explaining phenomena like thermal expansion and thermal conductivity, which are attributed to nonlinear, anharmonic , interactions. Here, we show that the kinetic energy of atoms in a solid produces a pressure much like the kinetic energy of atoms in a gas does. This vibrational or phonon pressure naturally increases with temperature, as it does in a gas and therefore results in a thermal expansion. Because thermal expansion thermodynamically defines a Grüneisen parameter γ , which is a typical metric of anharmonicity, we show that even a harmonic solid will necessarily have some anharmonicity. A consequence of this phonon pressure model is a harmonic estimation of the Grüneisen parameter as γ ≈ 3 / 2 3 − 4 x 2 / 1 + 2 x 2 , where x = v t / v l is the ratio of the transverse and longitudinal speeds of sound. We demonstrate the immediate utility of this model by developing a high-throughput harmonic estimate of lattice thermal conductivity that is comparable to other state-of-the-art estimations. By linking harmonic and anharmonic properties explicitly, this study provokes new ideas about the fundamental nature of anharmonicity, while also providing a basis for new material engineering design metrics.

42 ENGINEERING↗