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At least 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Comparative Genomic Analyses of Cellulolytic Machinery Reveal Two Nutritional Strategies of Marine Labyrinthulomycetes Protists

Labyrinthulomycetes are a group of ubiquitous and diverse unicellular Stramenopiles and have long been known for their vital role in ocean carbon cycling. However, their ecological function from the perspective of organic matter degradation remains poorly understood. This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains, namely, Botryochytrium sp. strain S-28 and Oblongichytrium sp. strain S-429, and provides molecular analysis of their ecological functions using comparative genomics and a biochemical assay. Our results suggest that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems because of the significant differences in gene function among different genera. Certain strains could degrade wheat bran independently by secreting cellulase. The key glycoside hydrolase families (GH1, GH5, and GH9) related to cellulase and the functional domains of carbohydrate-active enzymes (CAZymes) were more enriched in their genomes. This group can actively participate in marine biochemical cycles as decomposers. In contrast, other strains that could not produce cellulase may thrive as “leftover scavengers” and act as a source of nutrients to the higher-trophic-level plankton. In addition, our findings emphasize the dual roles of endoglucanase, acting as both exo- and endoglucanases, in the process of cellulose degradation. Using genomic, biochemical, and phylogenetic analyses, our study provides a broader insight into the nutritional patterns and ecological functions of Labyrinthulomycetes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Isolation of a Terminal Cobalt Nitride in a Metal–Organic Framework

Transition metal nitrides are reactive intermediates in biological and industrial processes. Chemists have synthesized molecular model complexes of such reactive species to understand their function and electronic requirements for new applications. However, molecular chemistry can suffer from intra- and intermolecular decomposition pathways, which preclude further discovery of unknown reactive species. Metal-organic frameworks offer an opportunity for creating long-lived forms of such species with the vacuum of the pore suppressing degradation while simultaneously enabling substrate access for controlled reactivity studies. Here, in this study, we report the characterization of an elusive terminal cobalt nitride species generated through photolysis or thermolysis of a site-isolated cobalt azide within the evacuated metal-organic framework CoN 3 -MFU-4l. The first crystal structure of such a species is presented, with vibrational, X-ray absorption, and electron paramagnetic resonance spectroscopies providing further direct evidence for its formation while elucidating its electronic structure. The system additionally enables subsequent reactivity studies with selected substrates, revealing a unique ambiphilic behavior for a metal nitride species.

Börgel, Jonas [University of California, Berkeley,↗
DOE OSTI2025

Renormalization of states and quasiparticles in many-body downfolding

We explore the principles of many-body Hamiltonian complexity reduction via downfolding on an effective low-dimensional representation. We show that the renormalization factor provides a unique measure of the quality of the compression as it directly represents the projection between the approximate stationary state of the many-body Hamiltonian and the full many-body wavefunction. Hence, the renormalization factor is a measure of fidelity between the effective (reduced-rank) description and the full many-body treatment for arbitrary (i.e., ground and excited) states. When the entire problem is mapped on a system of interacting quasiparticles [Romanova et al., npj Comput. Mater. 9, 126 (2023)], the effective Hamiltonians can faithfully reproduce the physics only when a clear energy scale separation exists between the subsystems and their environment. We also demonstrate that it is necessary to include quasiparticle renormalization at distinct energy scales, capturing the distinct interaction between subsystems and their surrounding environments. Numerical results from simple, exactly solvable models highlight the limitations and strengths of this approach, particularly for ground and low-lying excited states. This work lays the groundwork for applying dynamical downfolding techniques to problems concerned with (quantum) interfaces.

Green-functions technique↗
NASA NTRS2009

Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.

Hinkley, J.A.↗
DOE OSTI2023

Higher-order SPOP assembly reveals a basis for cancer mutant dysregulation

The speckle-type POZ protein (SPOP) functions in the Cullin3-RING ubiquitin ligase (CRL3) as a receptor for the recognition of substrates involved in cell growth, survival, and signaling. SPOP mutations have been attributed to the development of many types of cancers, including prostate and endometrial cancers. Prostate cancer mutations localize in the substrate-binding site of the substrate recognition (MATH) domain and reduce or prevent binding. However, most endometrial cancer mutations are dispersed in seemingly inconspicuous solvent-exposed regions of SPOP, offering no clear basis for their cancer-causing and peculiar gain-of-function properties. Herein, we present the first structure of SPOP in its oligomeric form, uncovering several new interfaces important for SPOP self-assembly and normal function. Given that many previously unaccounted-for cancer mutations are localized in these newly identified interfaces, we uncover molecular mechanisms underlying dysregulation of SPOP function, with effects ranging from gross structural changes to enhanced self-association, and heightened stability and activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Uncovering the Functional Role of Coherent Phonons during the Photoinduced Phase Transition in a Molecular Crystal

The atomic motions that make up phonons and molecular vibrations in molecular crystals influence their photophysical and electronic properties, including polaron formation, carrier mobility, and phase transitions. Discriminating between spectator and driving motions is a significant challenge hindering optimization. Unlocking this information and developing fine-tuned controls over actively participating phonon modes would not only lead to a stronger understanding of photochemistry but also provide a significant new tool in controlling solid state chemistry. We present a strategy using rationally designed double pulses to unveil the unique function of specific excited state phonon modes. Using ultrafast spectroscopy, we identified 50 and 90 cm –1 phonons involved in modulating the photoinduced spin-Peierls melting of potassium tetracyanoquinodimethane crystals. Here, we show that the 50 cm –1 phonon specifically corresponds to the coherent nuclear wavepacket involved in the charge transfer component of the overall spin-Peierls phase melting process, while the 90 cm –1 phonon facilitates the phase transition component.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Cyclopropenylidenes as Strong Carbene Anchoring Groups on Au Surfaces

The creation of stable molecular monolayers on metallic surfaces is a fundamental challenge of surface chemistry. N-Heterocyclic carbenes (NHCs) were recently shown to form self-assembled monolayers that are significantly more stable than the traditional thiols on Au system. In this study, we theoretically and experimentally demonstrate that the smallest cyclic carbene, cyclopropenylidene, binds even more strongly than NHCs to Au surfaces without altering the surface structure. We deposit bis(diisopropylamino)cyclopropenylidene (BAC) on Au(111) using the molecular adduct BAC–CO 2 as a precursor and determine the structure, geometry, and behavior of the surface-bound molecules through high-resolution X-ray photoelectron spectroscopy, atomic force microscopy, and scanning tunneling microscopy. Our experiments are supported by density functional theory calculations of the molecular binding energy of BAC on Au(111) and its electronic structure. Our work is the first demonstration of surface modification with a stable carbene other than NHC; more broadly, it drives further exploration of various carbenes on metal surfaces.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

First Principles Determination of the Potential-of-Zero-Charge in an Alumina-Coated Aluminum/Water Interface Model for Corrosion Applications

The surfaces of most metals immersed in aqueous electrolytes have a several-nanometer-thick oxide/hydroxide surface layer. This gives rise to the existence of both metal|oxide and oxide|liquid electrotlyte interfaces, and makes it challenging to correlate atomic length-scale structures with electrochemical properties such the potential-of-zero-charge (PZC). The PZC has been shown to be correlated the onset potential for pitting corrosion. Here, we conduct large-scale Density Functional Theory and ab initio molecular dynamics to calculate the PZC of a Al(111)| γ -Al 2 O 3 (110)| water double-interface model within the context of aluminum corrosion. By partitioning the multiple interfaces involved into binary components with additive contributions to the overall work function and voltage, we predict the PZC to be -1.53 V vs SHE for this model. Furthermore, we calculate the orbital energy levels of defects like oxygen vacancies in the oxide, which are critical parameters in theories associated with pitting corrosion. We predict that the Fermi level at the PZC lies above the impurity defect levels of the oxygen vacancies, which are therefore uncharged at the PZC. From the PZC estimate, we predict the voltage needed to create oxygen vacancies with net positive charges within a flatband approximation.

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

Deconstructing the Local Intermolecular Ordering and Dynamics of Liquid Chloroform and Bromoform

Local intermolecular structure and dynamics of the polar molecular liquids chloroform and bromoform are studied by molecular dynamics simulation. Structural distribution functions, including 1- and 2-D pair correlations and dipole contour plots allow direct comparison and show agreement with recent analyses of diffraction experiments. Studies of the haloforms’ reorientational dynamics and longevity of structural features resulting from intermolecular interaction extend previous work toward deeper understanding of the factors controlling these features. Analyses of ensemble average structures and dynamical properties isolate mass, electrostatics, and steric packing as driving forces or contributing factors for the observed ordering and dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1991

The formation of molecules in protostellar winds

The production and destruction processes for molecules in very fast protostellar winds are analyzed and modeled with a one-dimensional chemical kinetics code. Radial density and temperature distributions suggested by protostellar theory are explored as are a range of mass-loss rates. The efficiency of in situ formation of heavy molecules is found to be high if the wind temperature falls sufficiently rapidly, as indicated by theory. The degree of molecular conversion is a strong function of the mass-loss rate and of density gradients associated with the acceleration and collimation of the wind. Even in cases where essentially all of the heavy atoms are processed into molecules, a significant fraction of atomic hydrogen remains so that hghly molecular, protostellar winds are able to emit the 21-cm line. Although CO has a substantial abundance in most models relevant to very young protostars, high abundances of other molecules such as SiO and H2O signify more complete association characteristic of winds containing regions of very high density. Although the models apply only to regions close to the protostar, they are in qualitative accord with recent observations at much larger distances of both atomic and molecular emission from extremely high-velocity flow.

Glassgold, A. E.↗
NASA NTRS2017

Comparison of Two Bioinformatics Tools Used to Characterize the Microbial Diversity and Predictive Functional Attributes of Microbial Mats from Lake Obersee, Antarctica

In this study, using NextGen sequencing of the collective 16S rRNA genes obtained from two sets of samples collected from Lake Obersee, Antarctica, we compared and contrasted two bioinformatics tools, PICRUSt and Tax4Fun. We then developed an R script to assess the taxonomic and predictive functional profiles of the microbial communities within the samples. Taxa such as Pseudoxanthomonas, Planctomycetaceae, Cyanobacteria Subsection III, Nitrosomonadaceae, Leptothrix, and Rhodobacter were exclusively identified by Tax4Fun that uses SILVA database; whereas PICRUSt that uses Greengenes database uniquely identified Pirellulaceae, Gemmatimonadetes A1-B1, Pseudanabaena, Salinibacterium and Sinibacteraceae. Predictive functional profiling of the microbial communities using Tax4Fun and PICRUSt separately revealed common metabolic capabilities, while also showing specific functional IDs not shared between the two approaches. Combining these functional predictions using a customized R script revealed a more inclusive metabolic profile, such as hydrolases, oxidoreductases, transferases; enzymes involved in carbohydrate and amino acid metabolisms; and membrane transport proteins known for nutrient uptake from the surrounding environment. Our results present the first molecular-phylogenetic characterization and predictive functional profiles of the microbial mat communities in Lake Obersee, while demonstrating the efficacy of combining both the taxonomic assignment information and functional IDs using the R script created in this study for a more streamlined evaluation of predictive functional profiles of microbial communities.

Hyunmin Koo↗
DOE OSTI2025

Molecular Level Understanding of Polyethylene Terephthalate (PET) Depolymerization in Base/Alcohol Hybrid Systems

Polyethylene terephthalate (PET) depolymerization in base/alcohol hybrid systems represents a promising low-energy approach for chemically recycling PET waste into valuable monomers. This study investigates the mechanistic pathways of PET depolymerization in NaOH/alcohol solutions, emphasizing the competing roles of hydroxide and alkoxide species. Utilizing a combination of experimental techniques, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations, we explore how factors such as base concentration, alcohol chain length, and pKa values of alcohols influence PET depolymerization efficiency and pathways. Our findings indicate that alkoxide ions (RO⁻) exhibit notably higher reactivity than hydroxide ions (HO⁻), favoring an alcoholysis pathway in the base/alcohol hybrid system. Experimental results across a series of C1 to C5 alcohols show that longer-chain alcohols, particularly 1-butanol, achieve higher PET conversion, although this does not align solely with simple nucleophilicity trends of alkoxides. While DFT calculations reveal comparable activation energies for various alkoxides in PET depolymerization, MD simulations underscore the significant role of alcohol chain length, with longer-chain alcohols forming more stable or frequent interactions with PET. Additionally, the alkoxide concentration, influenced by the alcohol’s pK a , directly impacts PET conversion. These suggest that PET depolymerization is governed by a balance between alkoxide concentration and alkoxide-PET interactions, rather than activation energies or nucleophilicity alone. From a practical perspective, incorporating long-chain alcohols as cosolvents may enhance process efficiency but increases raw material costs by approximately 30%. However, long-chain alcohols present a safer and more sustainable alternative to hazardous cosolvents such as dichloromethane. This work offers a molecular-level understanding of PET depolymerization in base/alcohol systems and provides insights into optimizing these systems for more efficient and sustainable PET recycling processes.

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

Freestanding epitaxial SrTiO 3 nanomembranes via remote epitaxy using hybrid molecular beam epitaxy

The epitaxial growth of functional oxides using a substrate with a graphene layer is a highly desirable method for improving structural quality and obtaining freestanding epitaxial nanomembranes for scientific study, applications, and economical reuse of substrates. However, the aggressive oxidizing conditions typically used in growing epitaxial oxides can damage graphene. Here, we demonstrate the successful use of hybrid molecular beam epitaxy for SrTiO 3 growth that does not require an independent oxygen source, thus avoiding graphene damage. This approach produces epitaxial films with self-regulating cation stoichiometry. Furthermore, the film (46-nm-thick SrTiO 3 ) can be exfoliated and transferred to foreign substrates. These results open the door to future studies of previously unattainable freestanding oxide nanomembranes grown in an adsorption-controlled manner by hybrid molecular beam epitaxy. This approach has potentially important implications for the commercial application of perovskite oxides in flexible electronics and as a dielectric in van der Waals thin-film electronics.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Tuning dispersity of linear polymers and polymeric brushes grown from nanoparticles by atom transfer radical polymerization

Molecular weight distribution imposes considerable influence on the properties of polymers, making it an important parameter, impacting morphology and structural behavior of polymeric materials. Atom transfer radical polymerization (ATRP) has established itself as a powerful tool to prepare polymers with predetermined molecular weight, preserved chain-end functionality, and low dispersity. More recently, ATRP has also been shown to provide a means to deliberately broaden molecular weight distributions, and, via retaining living chain-ends, to enable the formation of block copolymers with designed block dispersity, featuring new microstructures and potentially attractive properties. Here, similar methodologies have been developed to facilitate tuning of the dispersity of polymeric brushes grown from nanoparticles thus resulting in hybrid materials with enhanced fracture toughness and high inorganic content. Recent advances have given access to brush architectures comprised of uni- and bimodal block copolymers with unique morphologies along with interesting mechanical, thermal, and optical properties.

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

Modeling dark- and light-induced crystal structures and single-crystal optical absorption spectra of ruthenium-based complexes that undergo SO 2 -linkage photoisomerization

A family of coordination complexes of the type [Ru(SO 2 )(NH 3 ) 4 X] m+ Y n – (m, n = 1 or 2) exhibit optical switching capabilities in their single-crystal states. This striking effect is caused by the light-induced formation of SO 2 -linkage photoisomers, which are metastable if kept at suitably cool temperatures. We modeled the dark- and light-induced states of these large crystalline complexes via plane-wave (PW)- and molecular-orbital (MO)-based density functional theory (DFT) and time-dependent DFT in order to calculate their structural and optical properties; the calculated results are compared with experimental data. We show that the PW-DFT-based periodic models replicate the structural properties of these complexes more effectively than the MO-DFT-based molecular-fragment models, observing only small deviations in key bond lengths relative to the experimentally derived crystal structures. The periodic models were also found to more effectively simulate trends seen in experimental optical absorption spectra, with optical absorbance and coverage of the visible region increasing with the formation of the photoinduced geometries. The contribution of the metastable photoisomeric species more heavily focuses on the lower-energy end of the spectra. Spectra generated from the molecular-fragment models are limited by the geometry of the fragment used and the number of excited-state roots considered in those calculations. In general, periodic models outperform the molecular-fragment models owing to their ability to better appreciate the periodic phenomena that are present in these crystalline materials as opposed to MO approaches, which are finite methods. We thus demonstrate that PW-DFT-based periodic models should be considered as a more than viable method for simulating the optical and electronic properties of these single-crystal optical switches.

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

Tuning the Functionalities of Porous Liquids for Emergent Gas-Capture Properties

Type 3 Porous Liquids (PLs) are a class of materials with the potential to revolutionize gas capture, storage, and utilization. These PLs are formed by suspending sorbent nanoparticles (e.g., metal−organic frameworks) in sterically excluded solvents, creating permanent porosity for gas capture in a processable, low-viscosity phase. Herein, a computational study revealed sorbent surface functionalization strategies to enhance CO 2 sorption, and the molecular structural signatures underpinning the enhancements in gas uptake. PLs composed of a ZIF-8 surface functionalized with 3-amino-1,2,4-triazole (Atz) in glyceryl triacetate were targeted for emergent CO 2 capture, exceeding that of the unfunctionalized ZIF-8 PL. ZIF-8 was surface functionalized with Atz at various surface coverage fractions (f), and classical molecular dynamics simulations predicted an increase in CO 2 sorption capacity with increasing f, up to f = 0.75. Additionally, detailed structural analyses revealed that solvent orientational order, derived from the solvent triplet-angle distribution, can identify the gas-capture potential of a PL without requiring computationally expensive direct modeling of the CO 2 sorption. Combined with experimental validation, initial computational screening of PL compositions promises to accelerate the discovery of PL compositions for novel gas separation materials platforms.

gas capture↗
DOE OSTI2021

Dipole Moment Calculations Using Multiconfiguration Pair-Density Functional Theory and Hybrid Multiconfiguration Pair-Density Functional Theory

The dipole moment is the molecular property that most directly indicates molecular polarity. The accuracy of computed dipole moments depends strongly on the quality of the calculated electron density, and the breakdown of single-reference methods for strongly correlated systems can lead to poor predictions of the dipole moments in those cases. Here, we derive the analytical expression for obtaining the electric dipole moment by multiconfiguration pair density functional theory (MCPDFT), and we assess the accuracy of MC-PDFT for predicting dipole moments at equilibrium and nonequilibrium geometries. We show that MC-PDFT dipole moment curves have reasonable behavior even for stretched geometries, and they significantly improve upon the CASSCF results by capturing more electron correlation. Herein, the analysis of a dataset consisting of 18 first-row transition metal diatomics and 6 main-group polyatomic molecules with multireference character suggests that MC-PDFT and its hybrid extension (HMC-PDFT) perform comparably to CASPT2 and MRCISD+Q methods and have a mean unsigned deviation of 0.2–0.3 D with respect to the best available dipole moment reference values. We explored the dependence of the predicted dipole moments upon the choice of the on-top density functional and active space, and we recommend the tPBE and hybrid tPBE0 on-top choices for the functionals combined with the moderate correlated participating orbital scheme for selecting the active space. With these choices, the mean unsigned deviations (in debyes) of the calculated equilibrium dipole moments from the best estimates are 0.77 for CASSCF, 0.29 for MC-PDFT, 0.24 for HMCPDFT, 0.28 for CASPT2, and 0.25 for MRCISD+Q. These results are encouraging because the computational cost of MC-PDFT or HMC-PDFT is largely reduced compared to the CASPT2 and MRCISD+Q methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗