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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A massive open cluster hiding in full sight

ABSTRACT Obscuration and confusion conspire to limit our knowledge of the inner Milky Way. Even at moderate distances, the identification of stellar systems becomes compounded by the extremely high density of background sources. Here, we provide a very revealing example of these complications by unveiling a large, massive, young cluster in the Sagittarius arm that has escaped detection until now despite containing more than 30 stars brighter than G = 13. By combining Gaia DR2 astrometry, Gaia and 2MASS photometry, and optical spectroscopy, we find that the new cluster, which we name Valparaiso 1, located at $\sim 2.3\,$ kpc, is about 75 Ma old and includes a large complement of evolved stars, among which we highlight the 4 d classical Cepheid CM Sct and an M-type giant that probably represents the first detection of an asymptotic giant branch star in a Galactic young open cluster. Although strong differential reddening renders accurate parameter determination unfeasible with the current data set, direct comparison to clusters of similar age suggests that Valparaiso 1 was born as one of the most massive clusters in the solar neighbourhood, with an initial mass close to $10^{4}\, \mathrm{M}_{\odot }$.

Negueruela, I.↗
DOE OSTI2025

Formation of U(VI) peroxide nanoclusters from cascade reactions with a persulfate radical initiator

Radiolysis of water in high radiation fields generates a variety of reactive oxygen species that influence the chemical behavior and complexation of hexavalent uranium. This study investigates the behavior of interaction of a uranyl cation (UO 2 2+ (VI)) with a series of free radicals that are formed in situ via activation of the free radical initiator persulphate (S 2 O 8 2− ), which releases both SO 4 ˙ − and ˙OH species in the solution. Electron Paramagnetic Resonance (EPR) and Raman spectroscopy were used to evaluate the presence of the hydroperoxyl radical (HO 2 ˙) and superoxide radicals (O 2 ˙ − ) that are formed within the solution through radical cascade reactions. In addition, a uranyl peroxide cluster solid (NaU 24 ) was crystallized and characterized using single crystal X-ray diffraction (SCXRD), vibrational spectroscopy, and EPR spectroscopy. The presence of the hydroperoxyl radical (HO 2 ˙) and superoxide radicals (O 2 ˙ − ) was also observed in the solid-state compound, but spectroscopic evidence suggests that it was associated with the Na + network and not the cluster itself. Density functional theory (DFT) calculations were also utilized to further confirm the radical species produced and determine the potential stabilization of radicals detected within the cluster and lattice.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Photodissociation and Infrared Spectroscopy of U + (CO 2 ) n , UO + (CO 2 ) n , and UO 2+ (CO 2 ) n Cation-Molecular Complexes

Laser vaporization of uranium in a pulsed supersonic expansion of carbon dioxide is used to produce complexes of the form U + (CO 2 ) n , UO + (CO 2 ) n , and UO 2+ (CO 2 ) n . These ions are selected in a reflectron time-offlight mass spectrometer and studied with visible laser photodissociation and tunable infrared laser photodissociation spectroscopy in the region of the CO 2 antisymmetric stretch. The dissociation patterns and spectroscopy of these ions indicate that CO 2 ligands are intact molecules. Although reaction products that form oxide-carbonyl or oxalate species are predicted to be stable, there is no direct evidence in the frequency range studied for the formation of these species. There is no clear indication for the coordination numbers for singly charged uranium and its oxide complexes with CO 2 . However, there is strong support in the vibrational patterns for an eight-coordinate complex of the doubly charged UO 2+ species, i.e., UO 2+ (CO 2 ) 8 .

Cluster chemistry↗
DOE OSTI2020

Flash Formation of I-Rich Clusters during Multistage Halide Segregation Studied in MAPbI 1.5 Br 1.5

Wide band gap mixed halide perovskites such as MAPb(I 1–x Br x ) 3 sparked great research interest because of their outstanding optoelectronic properties, ease of fabrication, and band gap tunability. Their application thus far is however limited by light-induced halide segregation in which microscopic clusters with a high iodide content are formed and act as recombination centers. The key mechanism(s) underlying this halide segregation process are still debated. Here, we present a study on the photoluminescence evolution in MAPb(I 1.5 Br 1.5 ) perovskites with varying microstructures under constant illumination at room temperature and at elevated temperature. Our findings reveal a more complicated picture of the segregation mechanism occurring in three stages instead of two as commonly reported. The process starts with a flash formation of I-rich domains. Following is a rapid blue shift before the gradual and typically observed red shift occurs. The evolution of the three stages is fully reversible in the dark and is also present at elevated temperatures (50 °C). We explain the existence of multiple stages during light-induced halide segregation by natural compositional fluctuations of the halides and the formation of halide clusters with a dynamically changing distribution in I–Br content. The variation in the I–Br ratio depends on the grain size and film heterogeneity. Overall, these findings add further details in the quest of unraveling the underlying segregation mechanism(s), which need to be identified to stabilize halides in wide band gap perovskites.

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

Towards accurate prediction of configurational disorder properties in materials using graph neural networks

Abstract The prediction of configurational disorder properties, such as configurational entropy and order-disorder phase transition temperature, of compound materials relies on efficient and accurate evaluations of configurational energies. Previous cluster expansion methods are not applicable to configurationally-complex material systems, including those with atomic distortions and long-range orders. In this work, we propose to leverage the versatile expressive capabilities of graph neural networks (GNNs) for efficient evaluations of configurational energies and present a workflow combining attention-based GNNs and Monte Carlo simulations to calculate the disorder properties. Using the dataset of face-centered tetragonal gold copper without and with local atomic distortions as an example, we demonstrate that the proposed data-driven framework enables the prediction of phase transition temperatures close to experimental values. We also elucidate that the variance of the energy deviations among configurations controls the prediction accuracy of disorder properties and can be used as the target loss function when training and selecting the GNN models. The work serves as a fundamental step toward a data-driven paradigm for the accelerated design of configurationally-complex functional material systems.

Chemistry↗
DOE OSTI2021

Boron nitride nanotube precursor formation during high-temperature synthesis: kinetic and thermodynamic modelling

In this work, we performed integrated modelling of the chemical pathways of formation for boron nitride nanotube (BNNT) precursors during high-temperature synthesis in a B/N 2 mixture. Integrated modelling includes quantum chemistry, Quantum–classical molecular dynamics, thermodynamic modelling, and kinetic approaches. We demonstrate that BN compounds are formed via the interaction of molecular nitrogen with small boron clusters, rather than through interactions with less reactive liquid boron. (This process can also be described as N 2 molecule fixation.) Liquid boron evaporates to produce these boron clusters (B m with m ≤ 5), which are subsequently converted into B m N n chains. The production of such chains is crucial to the growth of BNNTs because these chains form the building blocks of bigger and longer BN chains and rings, which are in turn the building blocks of fullborenes and BNNTs. Additionally, kinetic modelling revealed that B 4 N 4 and B 5 N 4 species in particular play a major role in the N 2 molecule fixation process. Furthermore, the formation of these species via reactions with B 4 and B 5 clusters is not adequately described under the assumption of thermodynamic equilibrium, as is demonstrated in our kinetic modelling. Thus, the accumulation of both B 4 N 4 and B 5 N 4 depends on the background gas pressure and the gas cooling rate. Long BN chains and rings, which are precursors of the fullborene and BNNT growth, form via self-assembly of components B 4 N 4 and B 5 N 4 . Our modelling results—particularly the increased densities of B 4 N 4 and B 5 N 4 species at higher gas pressures—explain the experimentally observed effect of gas pressure on the yield of high-quality BNNTs. The catalytic role of hydrogen was also studied; it is shown that HBNH molecules can be the main precursor of BNNT synthesis in the presence of hydrogen.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Bridging Aromatic/Antiaromatic Units: Recent Advances in Aromaticity and Antiaromaticity in Main-group and Transition-Metal Clusters from Bonding and Magnetic Analyses

Synthetic exploration and theoretical characterization of metal clusters are actively developing branches of modern inorganic chemistry. Advances in these areas constantly expand the rich structural diversity of viable species, allowing a detailed study of the fundamental characteristics of bench-stable compounds. In this minireview, we summarize recent achievements in synthesis and computational analyses of main-group and heterometallic clusters containing multiple aromatic/antiaromatic units. These systems range from bare clusters to ligand-decorated aggregates, providing a fundamental understanding of the aromaticity and antiaromaticity concepts in species exhibiting unprecedented shapes and composition. The review gives a comprehensive summary of bonding and magnetic response properties of such systems deciphered from the Adaptive Natural Density Partitioning (AdNDP) approach and induced magnetic field analyses.

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

ThC 2 @C 82 versus Th@C 84 : unexpected formation of triangular thorium carbide cluster inside fullerenes

Synthesis of the first thorium-containing clusterfullerenes, ThC 2 @C s (6)–C 82 and ThC 2 @C 2 (5)–C 82 , is reported. These two novel actinide fullerene compounds were characterized by mass spectrometry, single-crystal X-ray diffraction crystallography, UV–vis–NIR spectroscopy, and theoretical calculations. Crystallographic studies reveal that the encapsulated ThC 2 clusters in both C s (6)–C 82 and C 2 (5)–C 82 feature a novel bonding structure with one thorium metal center connected by a C≡C unit, forming an isosceles triangular configuration, which has not been hitherto observed for endohedral fullerenes or for solid phase thorium carbides. Electronic structure calculations assign a formal electronic structure of [Th 4+ (C 2 ) 2- ] 2+ @[C 82 ] 2- , with pronounced donation bonding from (C 2 ) 2- to Th 4+ , secondary backbonding from the fullerene to thorium and Th–C double bond character in both compounds. This work presents a new family of endohedral fullerenes, MC 2 @C 2n-2 , being unexpected isomers of MC 2n , and provides broader understanding of thorium bonding.

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

Solvothermal Synthesis of [Cr 7 S 8 (en) 8 Cl 2 ]Cl 3 ⋅ 2H 2 O with Magnetically Frustrated [Cr 7 S 8 ] 5+ Double‐Cubes**

Abstract A novel transition metal chalcohalide [Cr 7 S 8 (en) 8 Cl 2 ]Cl 3 ⋅ 2H 2 O, with [Cr 7 S 8 ] 5+ dicubane cationic clusters, has been synthesized by a low temperature solvothermal method, using dimethyl sulfoxide (DMSO) and ethylenediamine ( en ) solvents. Ethylenediamine ligand exhibits bi‐ and monodentate coordination modes; in the latter case ethylenediamine coordinates to Cr atoms of adjacent clusters, giving rise to a 2D polymeric structure. Although magnetic susceptibility shows no magnetic ordering down to 1.8 K, a highly negative Weiss constant, θ =−224(2) K, obtained from Curie‐Weiss fit of inverse susceptibility, suggests strong antiferromagnetic (AFM) interactions between S =3/2 Cr(III) centers. Due to the complexity of the system with (2 S +1) 7 =16384 microstates from seven Cr 3+ centers, a simplified model with only two exchange constants was used for simulations. Density‐functional theory (DFT) calculations yielded the two exchange constants to be J 1 =−21.4 cm −1 and J 2 =−30.2 cm −1 , confirming competing AFM coupling between the shared Cr 3+ center and the peripheral Cr 3+ ions of the dicubane cluster. The best simulation of the experimental data was obtained with J 1 =−20.0 cm −1 and J 2 =−21.0 cm −1 , in agreement with the slightly stronger AFM exchange within the triangles of the peripheral Cr 3+ ions as compared to the AFM exchange between the central and peripheral Cr 3+ ions. This compound is proposed as a synthon towards magnetically frustrated systems assembled by linking dicubane transition metal‐chalcogenide clusters into polymeric networks.

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

Resilience of the Aurivillius structure upon La and Cr doping in a Bi 5 Ti 3 FeO 15 multiferroic

Here, combining the experimental techniques of high-resolution X-ray diffraction, magnetometry, specific heat measurement, and X-ray photoelectron, Raman and dielectric spectroscopy techniques, we have studied the influence of La and Cr doping on the crystal structure and magnetism of the room temperature Aurivillius multiferroic Bi 5 Ti 3 FeO 15 by investigating the physical properties of (Bi 4 La)Ti 3 FeO 15 and Bi 5 Ti 3 (Fe 0.5 Cr 0.5 )O 15 . The parent (Bi 5 Ti 3 FeO 15 ) and the doped ((Bi 4 La)Ti 3 FeO 15 and Bi 5 Ti 3 (Fe 0.5 Cr 0.5 )O 15 ) compounds crystallize in the A2 1 am space group, which is confirmed through our analysis of high-resolution synchrotron X-ray diffraction data obtained on phase-pure polycrystalline powders. We determined the oxidation states of the metal atoms in the studied compounds as Fe 3+ , Ti 4+ , Cr 3+ , and La 3+ through the analysis of X-ray photoelectron spectroscopy data. The magnetic susceptibilities of the three compounds are marked by the absence of a long-range ordered ground state, but dominated by superparamagnetic clusters with dominant antiferromagnetic interactions. This signature of short-range magnetism is also seen in specific heat as a low temperature enhancement which is suppressed upon the application of external magnetic fields up to 8 T. Our dielectric spectroscopy experiments showed that the three studied compounds display similar features in the dielectric constant measured as a function of frequency. However, upon doping La at the Bi site, the width of the ferroelectric hysteresis loop increases for (Bi 4 La)Ti 3 FeO 15 compared to that of the parent compound Bi 5 Ti 3 FeO 15 , and with Cr doping, Bi 5 Ti 3 (Fe 0.5 Cr 0.5 )O 15 becomes a leaky dielectric. The resilience of the Aurivillius crystal structure towards doping of La at the Bi site and Cr at the Fe site is clearly seen in the bulk properties of magnetic susceptibility, specific heat and the average crystal structure. The relevance of changes in the local structure is evident from our Raman spectroscopy and X-ray pair distribution function studies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Chapter 7 - CRISPR-Based Tools for Microbial Cell Factories

The development of microbial chassis for the production of a variety of biochemicals and biofuels is a growing area of research. How to efficiently manipulate genetic information to achieve optimal production of these compounds is a key area of focus in the field. In recent years, clustered regularly interspaced palindromic repeats (CRISPR) and its associated proteins (Cas) have become a popular strategy for gene editing and regulation in many organisms due to its versatility and efficacy. Here, we describe methods developed utilizing CRISPR-Cas systems for engineering microbial cell factories (e.g., bacteria and yeast) at the single gene to genome scale for mutagenesis and transcriptional regulation of target genes. Finally, we provide a perspective on the challenges and opportunities for the applications of advanced CRISPR-Cas-based tools for engineering microbial cell factories.

BIOMASS FUELS↗
DOE OSTI2020

Bimetallics in a Nutshell: Complexes Supported by Chelating Naphthyridine-Based Ligands

Bimetallic motifs are a structural feature common to some of the most effective and synthetically useful catalysts known, including in the active sites of many metalloenzymes and on the surfaces of industrially relevant heterogeneous materials. However, the complexity of these systems often hampers detailed studies of their fundamental properties. To glean valuable mechanistic insight into how these catalysts function, this research group has prepared a family of dinucleating 1,8-naphthyridine ligands that bind two first-row transition metals in close proximity, originally designed to help mimic the proposed active site of metal oxide surfaces. Of the various bimetallic combinations examined, dicopper(I) is particularly versatile, as neutral bridging ligands adopt a variety of different binding modes depending on the configuration of frontier orbitals available to interact with the Cu centers. Organodicopper complexes are readily accessible, either through the traditional route of salt metathesis or via the activation of tetraarylborate anions through aryl group abstraction by a dicopper(I) unit. The resulting bridging aryl complexes engage in C-H bond activations, notably with terminal alkynes to afford bridging alkynyl species. In this work, the μ-hydrocarbyl complexes are surprisingly tolerant of water and elevated temperatures. This stability was leveraged to isolate a species that typically represents a fleeting intermediate in Cu-catalyzed azide-alkyne coupling (CuAAC); reaction of a bridging alkynyl complex with an organic azide afforded the first example of a well-defined, symmetrically bridged dicopper triazolide. This complex was shown to be an intermediate during CuAAC, providing support for a proposed bimetallic mechanism. These platforms are not limited to formally low oxidation states; chemical oxidation of the hydrocarbyl complexes cleanly results in formation of mixed valence Cu I Cu II complexes with varying degrees of distortion in both the bridging moiety and the dicopper core. Higher oxidation states, e.g. , dicopper(II), are easily accessed via oxidation of a dicopper(I) compound with air to give a Cu II 2 (μ-OH) 2 complex. Reduction of this compound with silanes resulted in the unexpected formation of pentametallic copper(I) dihydride clusters or trimetallic monohydride complexes, depending on the nature of the silane. Finally, development of an unsymmetrical naphthyridine ligand with mixed donor side-arms enables selective synthesis of an isostructural series of six heterobimetallic complexes, demonstrating the power of ligand design in the preparation of heterometallic assemblies.

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

Main and Satellite Features in the Ni 2p XPS of NiO

The origin and assignment of the complex main and satellite XPS features of the cations in ionic compounds has been the subject of extensive theoretical studies using different methods. There is agreement that within a molecular orbital model one needs to take into account different types of configurations. Specifically, those where a core electron is removed but no other configuration changes are made and those where in addition to ionization there are also shake or charge transfer changes to the ionic configuration. However, there are strong disagreements about the assignment of XPS features to these configurations. The present work is directed toward resolving the origin of main and satellite features for the Ni 2p XPS of NiO based on ab initio molecular orbital wavefunctions for a cluster model of NiO. A major problem in earlier ab initio XPS studies of ionic compounds has been the use of a common set of orbitals that was not able to properly describe all the ionic configurations that contribute to the full XPS spectra. This is resolved in the present work by using orbitals that are optimized for averages of the occupations of the different configurations that contribute to the XPS. The approach of using State Averaged orbitals is validated through comparisons between different averages and through use of higher order excitations in the wavefunctions for the ionic states. It represents a major extension of our earlier work on the main and satellite features of the Fe 2p XPS of Fe 2 O 3 and proves the reliability and the generality of the assignments of the character and origin of the different features of the XPS obtained with orbitals optimized for State Averages. These molecular orbital methods permit the characterization of the ionic states in terms of the importance of shake excitations and of the coupling of ionization of 2p 1/2 and 2p 3/2 spin-orbit split sub shells. Further, the work lays the foundation for definitive assignments of the character of main and satellite XPS features and points to their origin in the electronic structure of the material.

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

Ab initio study and assignment of electronic states in molecular RaCl

Radium compounds have attracted recently considerable attention due to both development of experimental techniques for high-precision laser spectroscopy of molecules with short-lived nuclei and amenability of certain radium compounds for direct cooling with lasers. Currently, radium monofluoride (RaF) is one of the most studied molecules among the radium compounds, both theoretically and recently also experimentally. Complementary studies of further diatomic radium derivatives are highly desired to assess the influence of chemical substitution on diverse molecular parameters, especially on those connected with laser cooling, such as vibronic transition probabilities, and those related to violations of fundamental symmetries. Here in this article high-precision ab initio studies of electronic and vibronic levels of diatomic radium monochloride (RaCl) are presented. Recently developed approaches for treating electronic correlation with Fock-space coupled cluster methods are applied for this purpose. Theoretical results are compared to an early experimental investigation by Lagerqvist and used to partially reassign the experimentally observed transitions and molecular electronic levels of RaCl. Effective constants of $\mathscr{P}$-odd hyperfine interaction W a and $\mathscr{P, T}$-odd scalar-pseudoscalar nucleus-electron interaction Ws in the ground electronic state of RaCl are estimated within the framework of a quasirelativistic Zeroth-Order Regular Approximation approach and compared to parameters in RaF and RaOH.

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

Transfer Learning Meets Embedded Correlated Wavefunction Theory for Chemically Accurate Molecular Simulations: Application to Calcium Carbonate Ion Pairing

Achieving chemical accuracy for molecular simulations remains a central challenge in computational chemistry. Here, we present an embedded correlated wavefunction transfer learning (ECW-TL) framework for accurately simulating molecular dynamics in the condensed phase. ECW-TL incorporates high-level electron exchange and correlation effects in ECW theory while preserving the training and computational efficiency of machine-learned interatomic potentials. We demonstrate the framework on Ca 2+ –CO 3 2– ion pairing in aqueous solution, a key process underlying CO 2 mineralization in seawater. As proof of principle, we first show that fine-tuning a DFT-revPBE-D3(BJ) baseline model with embedded-DFT-SCAN data reproduces the DFT-SCAN free-energy surface within 1 kcal/mol across all solvation states. Extending the framework to embedded MP2 and localized natural-orbital CCSD(T) further refines the free-energy profile, revealing the crucial role of exact electron exchange and correlation in determining ion-pair stability and structure. The computed ion-pair association free energy is in quantitative agreement with experimental measurements, further validating the accuracy of the ECW-TL framework. ECW-TL thus provides a general, data-efficient route for transferring CW accuracy to efficient simulations of complex aqueous and interfacial chemical processes.

cluster chemistry↗
DOE OSTI2024

Prediction of photodynamics of 200 nm excited cyclobutanone with linear response electronic structure and ab initio multiple spawning

Simulations of photochemical reaction dynamics have been a challenge to the theoretical chemistry community for some time. In an effort to determine the predictive character of current approaches, we predict the results of an upcoming ultrafast diffraction experiment on the photodynamics of cyclobutanone after excitation to the lowest lying Rydberg state (S 2 ). A picosecond of nonadiabatic dynamics is described with ab initio multiple spawning. Herein we use both time dependent density functional theory (TDDFT) and equation-of-motion coupled cluster singles and doubles (EOM-CCSD) theory for the underlying electronic structure theory. We find that the lifetime of the S 2 state is more than a picosecond (with both TDDFT and EOM-CCSD). The predicted ultrafast electron diffraction spectrum exhibits numerous structural features, but weak time dependence over the course of the simulations.

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

Detecting Cage Crossing and Filling Clusters of Magnesium and Carbon Atoms in Zeolite SSZ-13 with Atom Probe Tomography

The conversion of methanol to valuable hydrocarbon molecules is of great commercial interest, as the process serves as a sustainable alternative for the production of, for instance, the base chemicals for plastics. The reaction is catalyzed by zeolite materials. By the introduction of magnesium as a cationic metal, the properties of the zeolite, and thereby the catalytic performance, are changed. With atom probe tomography (APT), nanoscale relations within zeolite materials can be revealed: i.e., crucial information for a fundamental mechanistic understanding. We show that magnesium forms clusters within the cages of zeolite SSZ-13, while the framework elements are homogeneously distributed. These clusters of just a few nanometers were analyzed and visualized in 3-D. Magnesium atoms seem to initially be directed to the aluminum sites, after which they aggregate and fill one or two cages in the zeolite SSZ-13 structure. The presence of magnesium in zeolite SSZ-13 increases the lifetime as well as the propylene selectivity. By using operando UV–vis spectroscopy and X-ray diffraction techniques, we are able to show that these findings are related to the suppression of aromatic intermediate products, while maintaining the formation of polyaromatic compounds. Further nanoscale analysis of the spent catalysts showed indications of magnesium redistribution after catalysis. Unlike zeolite H-SSZ-13, for which only a homogeneous distribution of carbon was found, carbon can be either homogeneously or heterogeneously distributed within zeolite Mg-SSZ-13 crystals as the magnesium decreases the coking rate. Carbon clusters were isolated, visualized, and analyzed and were assumed to be polyaromatic compounds. Small one-cage-filling polyaromatic compounds were identified; furthermore, large-cage-crossing aromatic molecules were found by isolating large coke clusters, demonstrating the unique coking mechanism in zeolite SSZ-13. Short-length-scale evidence for the formation of polyaromatic compounds at acid sites is discovered, as clear nanoscale relations between aluminum and carbon atoms exist.

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

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

In this work, we present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.

60 APPLIED LIFE SCIENCES↗