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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Cryo-EM structure determination of small therapeutic protein targets at 3 Å-resolution using a rigid imaging scaffold

Cryoelectron microscopy (Cryo-EM) has enabled structural determination of proteins larger than about 50 kDa, including many intractable by any other method, but it has largely failed for smaller proteins. Here, we obtain structures of small proteins by binding them to a rigid molecular scaffold based on a designed protein cage, revealing atomic details at resolutions reaching 2.9 Å. We apply this system to the key cancer signaling protein KRAS (19 kDa in size), obtaining four structures of oncogenic mutational variants by cryo-EM. Importantly, a structure for the key G12C mutant bound to an inhibitor drug (AMG510) reveals significant conformational differences compared to prior data in the crystalline state. The findings highlight the promise of cryo-EM scaffolds for advancing the design of drug molecules against small therapeutic protein targets in cancer and other human diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Liquid–Vapor Phase Equilibrium in Molten Aluminum Chloride (AlCl 3 ) Enabled by Machine Learning Interatomic Potentials

Molten salts are promising candidates in numerous clean energy applications, where knowledge of thermophysical properties and vapor pressure across their operating temperature ranges is critical for safe operations. Due to challenges in evaluating these properties using experimental methods, fast and scalable molecular simulations are essential to complement the experimental data. In this study, we developed machine learning interatomic potentials (MLIP) to study the AlCl 3 molten salt across varied thermodynamic conditions (T = 473–613 K and P = 2.7–23.4 bar), which allowed us to predict temperature-surface tension correlations and liquid–vapor phase diagram from direct simulations of two-phase coexistence in this molten salt. Two MLIP architectures, a Kernel-based potential and neural network interatomic potential (NNIP), were considered to benchmark their performance for AlCl 3 molten salt using experimental structure and density values. The NNIP potential employed in two-phase equilibrium simulations yields the critical temperature and critical density of AlCl 3 that are within 10 K (∼3%) and 0.03 g/cm 3 (∼7%) of the reported experimental values. An accurate correlation between temperature and viscosities is obtained as well. In doing so, we report that the inclusion of low-density configurations in their training is critical to more accurately represent the AlCl 3 system across a wide phase-space. The MLIP trained using PBE-D3 functional in the ab initio molecular dynamics (AIMD) simulations (120 atoms) also showed close agreement with experimentally determined molten salt structure comprising Al 2 Cl 6 dimers, as validated using Raman spectra and neutron structure factor. Furthermore, the PBE-D3 as well as its trained MLIP showed better liquid density and temperature correlation for AlCl 3 system when compared to several other density functionals explored in this work. Overall, the demonstrated approach to predict temperature correlations for liquid and vapor densities in this study can be employed to screen nuclear reactors-relevant compositions, helping to mitigate safety concerns.

Ab initio molecular dynamics↗
DOE OSTI2020

The Generality of the GUGA MRCI Approach in COLUMBUS for Treating Complex Quantum Chemistry

The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying out all of these calculations effectively is the availability of an efficient parallel code for the CI step. Configuration spaces of several billion in size now can be treated quite routinely on standard parallel computer clusters. Emerging developments in COLUMBUS, including the all configuration mean energy multiconfiguration self-consistent field method and the graphically contracted function method, promise to allow practically unlimited configuration space dimensions. Spin density based on the GUGA approach, analytic spin-orbit energy gradients, possibilities for local electron correlation MR calculations, development of general interfaces for nonadiabatic dynamics, and MRCI linear vibronic coupling models conclude this overview.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

The relation between lignin sequence and its 3D structure

Background: Lignin, the second most abundant biopolymer on earth, plays a major structural role in plants, conferring mechanical strength and regulating water conduction. Understanding the three-dimensional structure of lignin is important for fundamental reasons as well as engineering plants towards lignin valorization. Lignin lacks a specific primary sequence, making its average chemical composition the focus of most recent studies. However, it remains unclear whether the 3D structure of lignin molecules depends on their sequence. Methods: In this work, we performed all-atom molecular dynamics simulation of three S/G-lignin molecules with the same average composition but different sequence. Results: A detailed statistical analysis of the radius of gyration and relative shape anisotropy reveals that the lignin sequence has no statistically significant effect on the global three-dimensional structure. We found however, that homopolymers of C-lignin with the same molecular weight have smaller radii of gyration than S/G-lignin. We attribute this to lower hydroxyl content of C-lignin, which makes it more compact and rigid. Conclusions: The 3D structure of lignin is influenced by the overall content of monomeric units and interunit linkages and not by its precise primary sequence. General Significance: Lignin is assumed to not have a well-defined primary structure. The results presented here demonstrate there are no significant differences in the global 3D structure of lignin molecules with the same average composition but different primary sequence.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1975

Friction differences between aliphatic and aromatic structures in lubrication of titanium

Sliding friction experiments were conducted with a titanium (0001) single crystal surface with various adsorbed aliphatic and aromatic compounds containing the same number of carbon atoms. An Auger emission spectroscopy analysis was used to monitor the presence of the organic lubricating compounds. Results of the investigation indicate that hexane and benzene give the same friction coefficients over a range of loads. At light loads the friction decreased with an increase in the halogen atom size where the halogens chlorine, bromine, and iodine are incorporated into the benzene molecular structure. The aliphatic compounds chlorohexane and bromohexane exhibited lower friction coefficients than the aromatic structures chlorobenzene and bromobenzene.

Buckley, D. H.↗
DOE OSTI2024

Recent Advances in X-ray Absorption Near Edge Structure (XANES) Simulation for Catalysis: Theories and Applications

X-ray absorption spectroscopy (XAS) is a powerful spectroscopic technique for characterizing catalytic active sites. In particular, X-ray Absorption Near Edge Structure (XANES) provides insights into the oxidation state and local coordination environment of the absorbing atom, shedding light on the catalytic structure. Computational XANES simulations provide one-on-one correspondence between the molecular structure and their corresponding spectra, making them an effective approach for interpreting experimental XANES features. This work outlines various theories used to simulate XANES spectra and highlights recent advancements in computational XANES applications for homogeneous, heterogeneous, and single-atom catalysts focusing on identifying the active site structures, the site heterogeneity, and the dynamic evolution of catalysts.

Xu, Jiayi↗
DOE OSTI2022

Improving the Accuracy of Atomistic Simulations of the Electrochemical Interface

Atomistic simulation of the electrochemical double layer is an ambitious undertaking, requiring quantum mechanical description of electrons, phase space sampling of liquid electrolytes, and equilibration of electrolytes over nanosecond time scales. All models of electrochemistry make different trade-offs in the approximation of electrons and atomic configurations, from the extremes of classical molecular dynamics of a complete interface with point-charge atoms to correlated electronic structure methods of a single electrode configuration with no dynamics or electrolyte. Here, we review the spectrum of simulation techniques suitable for electrochemistry, focusing on the key approximations and accuracy considerations for each technique. Additionally, we discuss promising approaches, such as enhanced sampling techniques for atomic configurations and computationally efficient beyond density functional theory (DFT) electronic methods, that will push electrochemical simulations beyond the present frontier.

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

Structural water in amorphous carbonate minerals: ab initio molecular dynamics simulations of X-ray pair distribution experiments

Water is known to play a controlling role in directing mineralization pathways and stabilizing metastable amorphous intermediates in hydrous carbonate mineral MCO 3 ·nH 2 O systems, where M 2+ is a divalent metal cation. Despite this recognition, the nature of the controls on crystallization is poorly understood, largely owing to the difficulty in characterizing the dynamically disordered structures of amorphous intermediates at the atomic scale. Here, we present a series of atomistic models, derived from ab initio molecular dynamics simulation, across a range of experimentally relevant cations (M = Ca, Mg, Sr) and hydration levels (0 ≤ n ≤ 2). Theoretical simulations of the dependence of the X-ray pair distribution function on the hydration level n show good agreement with available experimental data and thus provide further evidence for a lack of significant nanoscale structure in amorphous carbonates. Upon dehydration, the metal coordination number does not change significantly, but the relative extent of water dissociation increases, indicating that a thermodynamic driving force exists for water dissociation to accompany dehydration. Mg strongly favors monodentate conformation of carbonate ligands and shows a marked preference to exchange monodentate carbonate O for water O upon hydration, whereas Ca and Sr exchange mono- and bidentate carbonate ligands with comparable frequency. Finally, water forms an extensive hydrogen bond network among both water and carbonate groups that exhibits frequent proton transfers for all three cations considered suggesting that proton mobility is likely predominantly due to water dissociation and proton transfer reactions rather than molecular water diffusion.

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

Dynamic and weak electric double layers in ultrathin nanopores

The unique properties of aqueous electrolytes in ultrathin nanopores have drawn a great deal of attention in a variety of applications, such as power generation, water desalination, and disease diagnosis. Inside the nanopore, at the interface, properties of ions differ from those predicted by the classical ionic layering models (e.g., Gouy–Chapman electric double layer) when the thickness of the nanopore approaches the size of a single atom (e.g., nanopores in a single-layer graphene membrane). Here, using extensive molecular dynamics simulations, the structure and dynamics of aqueous ions inside nanopores are studied for different thicknesses, diameters, and surface charge densities of carbon-based nanopores [ultrathin graphene and finite-thickness carbon nanotubes (CNTs)]. The ion concentration and diffusion coefficient in ultrathin nanopores show no indication of the formation of a Stern layer (an immobile counter-ionic layer) as the counter-ions and nanopore atoms are weakly correlated in time compared to the strong correlation observed in thick nanopores. The weak correlation observed in ultrathin nanopores is indicative of a weak adsorption of counter-ions onto the surface compared to that of thick pores. The vanishing counter-ion adsorption (ion–wall correlation) in ultrathin nanopores leads to several orders of magnitude shorter ionic residence times (picoseconds) compared to the residence times in thick CNTs (seconds). The results of this study will help better understand the structure and dynamics of aqueous ions in ultrathin nanopores.

2D materials↗
DOE OSTI2023

X-ray induced Coulomb explosion imaging of transient excited-state structural rearrangements in CS2

Abstract Structural imaging of transient excited-state species is a key goal of molecular physics, promising to unveil rich information about the dynamics underpinning photochemical transformations. However, separating the electronic and nuclear contributions to the spectroscopic observables is challenging, and typically requires the application of high-level theory. Here, we employ site-selective ionisation via ultrashort soft X-ray pulses and time-resolved Coulomb explosion imaging to interrogate structural dynamics of the ultraviolet photochemistry of carbon disulfide. This prototypical system exhibits the complex motifs of polyatomic photochemistry, including strong non-adiabatic couplings, vibrational mode couplings, and intersystem crossing. Immediately following photoexcitation, we observe Coulomb explosion signatures of highly bent and stretched excited-state geometries involved in the photodissociation. Aided by a model to interpret such changes, we build a comprehensive picture of the photoinduced nuclear dynamics that follows initial bending and stretching motions, as the reaction proceeds towards photodissociation.

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

Uncovering metallic glasses hidden vacancy-like motifs using machine learning

Vacancies are a ubiquitous type of defect in crystalline materials that can affect their properties and behavior, including atomic diffusivity, deformation processes, thermal conductivity, and electrical conductivity. While well-defined in crystals, it is challenging to identify such topological footprints in the amorphous structure of metallic glasses (MGs). Here, we uncover an unforeseen vacancy-like structural motif named Q7, which refers to an atomic Voronoi polyhedron with seven quadrangular faces, by investigating MG local atomic configurations with the help of machine learning. The Q7 motif exhibits characteristics similar to crystalline vacancies and plays a significant role in short-range structural disorder in MGs. The atoms at the center of the Q7 motif display larger local entropy, atomic volume, and local tension. Additionally, its concentration follows an Arrhenius-like relationship with temperature, accurately indicating the glass transition temperature, and is strongly correlated with the yield and failure of MGs during mechanical deformation. The discovery of the Q7 motif provides new insights into understanding the intricate relationship between local disorder and structural relaxation in MGs, offering a remarkable ability to predict their thermal and mechanical behavior. This potentially paves the way for enhancements in the design and manufacturing processes of MGs and other amorphous materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Toward Full Configuration Interaction for Transition-Metal Complexes

In this work, an efficacious approximation to full configuration interaction (FCI) is adapted to calculate singlet-triplet gaps for transition-metal complexes. This strategy, incremental FCI (iFCI), uses a many-body expansion to systematically add correlation to a simple reference wave function and therefore achieves greatly reduced computational costs compared to FCI. iFCI through the 3-body expansion is demonstrated on four model transition-metal complexes involving the metals Zn, V, and Cu. Screening techniques to increase the computational efficiency of iFCI are proposed and tested, showing reduction in the number of 3-body terms by more than 90% with controlled errors. The largest complex treated by iFCI has 142 valence electrons, all of which are correlated among the full set of 444 active orbitals. Computed spin gaps approach experimental results for the four complexes, though room for improvement remains.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Neat, Simple, and Wrong: Debunking Electrostatic Fallacies Regarding Noncovalent Interactions

Multipole moments such as charge, dipole, and quadrupole are often invoked to rationalize intermolecular phenomena, but a low-order multipole expansion is rarely a valid description of electrostatics at the length scales that characterize nonbonded interactions. This is illustrated by examining several common misunderstandings rooted in erroneous electrostatic arguments. First, the notion that steric repulsion originates in Coulomb interactions is easily disproved by dissecting the interaction potential for Ar2. Second, the Hunter-Sanders model of π–π interactions, which is based on quadrupolar electrostatics, is shown to have no basis in accurate calculations. Third, curved “buckybowls” exhibit unusually large dipole moments, but these are ancillary to the forces that control their intermolecular interactions, as illustrated by two examples involving corannulene. Finally, the assumption that interactions between water and small anions are dictated by the dipole moment of H 2 O is shown to be false in the case of binary halide–water complexes. Furthermore, these examples present a compelling case that electrostatic explanations based on low-order multipole moments are very often counterfactual for nonbonded interactions at close range and should not be taken seriously in the absence of additional justification.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Investigating phase transitions from local crystallographic analysis based on statistical learning of atomic environments in 2D MoS 2 -ReS 2

Traditionally, phase transitions are explored using a combination of macroscopic functional characterization and scattering techniques, providing insight into the average properties and symmetries of the lattice but local atomic level mechanisms during phase transitions generally remain unknown. Here, we explore the mechanisms of a phase transition between the trigonal prismatic and distorted octahedral phases of layered chalcogenides in the 2D MoS 2 - ReS 2 system from the observations of local degrees of freedom, namely atomic positions by Scanning Transmission Electron Microscopy (STEM). We employ local crystallographic analysis based on statistical learning of atomic environments to build a picture of the transition from the atomic level up and determine local and global variables controlling the local symmetry breaking. In particular, we argue that the dependence of the average symmetry breaking distortion amplitude on global and local concentration can be used to separate local chemical as well as global electronic effects on transition. This approach allows exploring atomic mechanisms beyond the traditional macroscopic descriptions, utilizing the imaging of compositional fluctuations in solids to explore phase transitions over a range of realized and observed local stoichiometries and atomic configurations.

25 ENERGY STORAGE↗
DOE OSTI2023

Evaluation of the excitation spectra with diffusion Monte Carlo on an auxiliary bosonic ground state

We aim to improve upon the variational Monte Carlo (VMC) approach for excitations replacing the Jastrow factor by an auxiliary bosonic (AB) ground state and multiplying it by a fermionic component factor. The instantaneous change in imaginary time of an arbitrary excitation in the original interacting fermionic system is obtained by measuring observables via the ground-state distribution of walkers of an AB system that is subject to an auxiliary effective potential. The effective potential is used to (i) drive the AB system’s ground-state configuration space toward the configuration space of the excitations of the original fermionic system and (ii) subtract from a diffusion Monte Carlo (DMC) calculation contributions that can be included in conventional approximations, such as mean-field and configuration interaction (CI) methods. In this novel approach, the AB ground state is treated statistically in DMC, whereas the fermionic component of the original system is expanded in a basis. The excitation energies of the fermionic eigenstates are obtained by sampling a fermion–boson coupling term on the AB ground state. We show that this approach can take advantage of and correct for approximate eigenstates obtained via mean-field calculations or truncated interactions. We demonstrate that the AB ground-state factor incorporates the correlations missed by standard Jastrow factors, further reducing basis truncation errors. Relevant parts of the theory have been tested in soluble model systems and exhibit excellent agreement with exact analytical data and CI and VMC approaches. In particular, for limited basis set expansions and sufficient statistics, AB approaches outperform CI and VMC in terms of basis size for the same systems. The implementation of this method in current codes, despite being demanding, will be facilitated by reusing procedures already developed for calculating ground-state properties with DMC and excitations with VMC.

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

Analytic gradients for compressed multistate pair-density functional theory

Photochemical reactions often involve states that are closely coupled due to near degeneracies, for example by proximity to conical intersections. Therefore, a multistate method is used to accurately describe these states; for example, ordinary perturbation theory is replaced by quasidegenerate perturbation theory. Multiconfiguration pair-density functional theory (MC-PDFT) provides an efficient way to approximate the full dynamical correlation energy of strongly correlated systems, and we recently proposed compressed multistate pair-density functional theory (CMS-PDFT) to treat closely coupled states. In the present paper, we report the implementation of analytic gradients for CMS-PDFT in both OpenMolcas and PySCF, and here we illustrate the use of these gradients by applying the method to the excited states of formaldehyde and phenol.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Dynamic Observation of Dendritic Quasicrystal Growth upon Laser-Induced Solid-State Transformation

In this paper, we report the laser-induced solid-state transformation between a periodic “approximant” and quasicrystal in the Al-Cr system during rapid quenching. Dynamic transmission electron microscopy allows us to capture in situ the dendritic growth of the metastable quasicrystals. The formation of dendrites during solid-state transformation is a rare phenomenon, which we attribute to the structural similarity between the two intermetallics. Through ab initio molecular dynamics simulations, we identify the dominant structural motif to be a 13-atom icosahedral cluster transcending the phases of matter.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Colossal Density-Driven Resistance Response in the Negative Charge Transfer Insulator MnS 2

A reversible density driven insulator to metal to insulator transition in high-spin MnS 2 is experimentally observed, leading with a colossal electrical resistance drop of $10^8$ Omega by 12 GPa. Density functional theory simulations reveal the metallization to be unexpectedly driven by previously unoccupied $S_{2}^{-2}$ $\sigma^{*}_{3p}$ antibonding states crossing the Fermi level. This is a unique variant of the charge transfer insulator to metal transition for negative charge transfer insulators having anions with an unsaturated valence. By 36 GPa the emergence of the low-spin insulating arsenopyrite ($P2_1/c$) is confirmed, and the bulk metallicity is broken with the system returning to an insulative electronic state.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗