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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Functional analysis of Pogostemon cablin farnesyl pyrophosphate synthase gene and its binding transcription factor PcWRKY44 in regulating biosynthesis of patchouli alcohol

Farnesyl pyrophosphate synthase (FPPS) plays an important role in the synthesis of plant secondary metabolites, but its function and molecular regulation mechanism remain unclear in Pogostemon cablin . In this study, the full-length cDNA of the FPP synthase gene from P. cablin ( PcFPPS ) was cloned and characterized. The expressions of PcFPPS are different among different tissues (highly in P. cablin flowers). Subcellular localization analysis in protoplasts indicated that PcFPPS was located in the cytoplasm. PcFPPS functionally complemented the lethal FPPS deletion mutation in yeast CC25. Transient overexpression of PcFPPS in P. cablin leaves accelerated terpene biosynthesis, with an ~47% increase in patchouli alcohol. Heterologous overexpression of PcFPPS in tobacco plants was achieved, and it was found that the FPP enzyme activity was significantly up-regulated in transgenic tobacco by ELISA analysis. In addition, more terpenoid metabolites, including stigmasterol, phytol, and neophytadiene were detected compared with control by GC-MS analysis. Furthermore, with dual-LUC assay and yeast one-hybrid screening, we found 220 bp promoter of PcFPPS can be bound by the nuclear-localized transcription factor PcWRKY44. Overexpression of PcWRKY44 in P. cablin upregulated the expression levels of PcFPPS and patchoulol synthase gene ( PcPTS ), and then promote the biosynthesis of patchouli alcohol. Taken together, these results strongly suggest the PcFPPS and its binding transcription factor PcWRKY44 play an essential role in regulating the biosynthesis of patchouli alcohol.

Wang, Xiaobing↗
DOE OSTI2026

Finite-element-based simulations of electrodes for CO 2 cascade reduction reactions

The multielectron reduction of CO 2 to liquid fuels could be a path to scalable energy storage, but reaching this goal requires major advances in catalysis and systems engineering. Cascade catalysis, which couples sequential reactions without isolating intermediates, has emerged as a promising route to enhance selectivity and efficiency in CO 2 reduction (CO 2 R). In this review, we examine how finite-element-based simulations of continuum model [finite element method (FEM)] approaches are being used to analyze and guide CO 2 R cascade systems. We first outline the fundamentals of cascade catalysis and recent advances in catalytic materials (metallic, molecular, and hybrid architectures). We then focus on FEM developments at the electrode and device scales, emphasizing how these models capture transport phenomena, local microenvironments, and geometry-dependent effects. To clarify design principles, we present case studies of cascade electrodes organized in systems without and with integrated semiconductors. We further emphasize the integration of FEM with multiscale frameworks (density functional theory, molecular dynamics, kinetic Monte Carlo) and its role in bridging atomic-level insights with device-level performance. Finally, we identify current limitations and future prospects, including improved boundary conditions, coupling with operando experiments, and machine learning-accelerated model development. Together, these insights provide design principles for next-generation CO 2 R cascade systems for efficient solar fuel production.

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

Distinguishing Electron and Hole Dynamics in Functionalized CdSe/CdS Core/Shell Quantum Dots Using Complementary Ultrafast Spectroscopies and Kinetic Modeling

The evolution of excitation energy and photogenerated charges in semiconductor quantum dots (QDs) functionalized with molecular acceptors can be probed on ultrafast time scales using techniques such as transient absorption (TA) spectroscopy. However, historical interpretations that the 1S(e)-1S 3/2 (h) transition in Cd-chalcogenide QDs is fully attributable to electrons may be misleading, and multiexponential models used to fit TA kinetics do not correspond directly to specific photophysical processes. Here, we present visible-wavelength and mid-IR TA and time-resolved photoluminescence measurements to inform a comprehensive kinetic model of the photoexcited CdSe/CdS core/shell QDs functionalized with passivating oleic acid (OA), hole-accepting ferrocene, or electron-accepting naphthalene bisimide (NBI). We show that ~30% of the 1S signal and 72% of the IR signal can originate from holes in well-passivated core/shell QDs. We also demonstrate evidence of electron trapping in OA-capped core/shell QDs, with additional electron transfer and hole trapping in the QDs functionalized with NBI. Electron (hole) trapping and detrapping occur in 450 ± 100 ps (430 ± 70 ps) and 340 ± 100 ps (1.1 ± 0.4 ns) respectively, while the time constant for electron transfer to NBI is ~1.8 ns. The comprehensive picture of photophysical processes provided by the complementary ultrafast techniques and kinetic modeling can accelerate both the fundamental science and application development of nanostructured and molecular systems.

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

Monte Carlo simulation to study the effect of molecular spin state on the spatio-temporal evolution of equilibrium magnetic properties of magnetic tunnel junction based molecular spintronics devices

With a variable spin state, paramagnetic molecules can affect the impact of magnetic exchange coupling strength between two ferromagnetic electrodes. Our magnetic tunnel junction based molecular spintronics devices (MTJMSD) were successful in connecting paramagnetic single molecular magnet (SMM) between two ferromagnetic electrodes. Isolated SMM exhibited a wide range of spin states. However, it was extremely challenging to identify the SMM spin state when connected to the ferromagnetic electrodes. Our prior experimental and Monte Carlo Simulations (MCS) studies showed that paramagnetic molecules produced unprecedented strong antiferromagnetic coupling between two ferromagnets at room temperature. The overall antiferromagnetic coupling occurred when a paramagnetic SMM made antiferromagnetic coupling to the first electrode and ferromagnetic coupling to the second ferromagnetic electrode. This paper studies the impact of variable molecular spin states of the SMMs, producing strong antiferromagnetic coupling between the ferromagnetic electrodes of MTJMSD. The MTJMSD used in this study was represented by an 11 x 50 x 50 Ising model, with 11 being the thickness of the MTJMSD and 5 x 10 x 50 being each electrode’s size. We employed a continuous MCS algorithm to investigate SMM’s spin state’s impact as a function of molecular exchange coupling strength and thermal energy.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Multifunctional textured graphene-based coatings on elastomeric gloves for chemical protection

Nanotechnology offers a variety of new tools for the design of next-generation personal protective equipment (PPE). One example is the use of two-dimensional materials as coatings that enhance the performance and ergonomics of elastomeric gloves designed to protect users from hazardous chemicals. Desirable features in such coatings may include molecular barrier function, liquid droplet repellency, stretchability for compatibility with the elastomer, breathability, and an ultrathin profile that preserves the user's manual dexterity and tactile sensation. The present work explores the potential of engineered graphene-based films with out-of-plane texturing as a novel platform to meet these multifold requirements. Graphene-based films in different formulations were fabricated from water-borne inks by vacuum filtration and solution casting methods on glove-derived nitrile rubber substrates. The various coatings were then subjected to tests of molecular permeation by model volatile organic compounds, droplet contact angle, breathability, and mechanical stability during stretching and solvent immersion. The films dramatically improve the barrier properties of glove-derived nitrile. The out-of-plane graphene texturing imparts stretchability through microscale folding/unfolding, while also enhancing droplet repellency in some cases through a lotus-like roughening effect. The combined results suggest that engineered textured graphene-based films are a promising platform for creating multifunctional coatings for a next generation of chemically protective gloves and other elastomer-based PPE.

36 MATERIALS SCIENCE↗
NASA NTRS2021

Predicting the Functional State of Protein Kinases Using Interpretable Graph Neural Networks

Kinases are a family of proteins that function as molecular switches, regulating several essential cellular activities such as cell proliferation. Dysfunctional kinases are implicated in several types of cancers and hence they are actively pursued as drug targets. Given the vast number of complex kinase structures that are available in the protein data bank (PDB), there is a necessity to develop methodologies that can identify structurally important moieties of the kinases in an automated fashion, for such techniques can be instrumental in identifying novel drug targets. In this work, we develop a graph neural network (GNN) based deep learning framework for classifying the functionally active and inactive states of a large set of eukaryotic protein kinases, making use of their 3D structure from the PDB. We show that GNN based machine learning models can classify protein states with an accuracy greater than 97%. We further use the GNN models to automatically identify regions of the kinases that are important for its function. For this purpose, Gradient-weighted Class Activation Mapping (Grad-CAM) was implemented on the protein graphs. Remarkably, Grad-CAM consistently identifies the highly conserved DFG motif as the most important part of the protein across the entire kinome, without any prior input. Other regions of the hydrophobic core such as the HRD motif were also identified by the interpretable GNN framework, consistent with the literature. We discuss the significance of each of these regions in detail.

Ashwin Ravichandran↗
NASA NTRS2008

Large-Scale Structure of the Molecular Gas in Taurus Revealed by High Spatial Dynamic Range Spectral Line Mapping

Viewgraph topics include: optical image of Taurus; dust extinction in IR has provided a new tool for probing cloud morphology; observations of the gas can contribute critical information on gas temperature, gas column density and distribution, mass, and kinematics; the Taurus molecular cloud complex; average spectra in each mask region; mas 2 data; dealing with mask 1 data; behavior of mask 1 pixels; distribution of CO column densities; conversion to H2 column density; variable CO/H2 ratio with values much less than 10(exp -4) at low N indicated by UV results; histogram of N(H2) distribution; H2 column density distribution in Taurus; cumulative distribution of mass and area; lower CO fractional abundance in mask 0 and 1 regions greatly increases mass determined in the analysis; masses determined with variable X(CO) and including diffuse regions agrees well with the found from L(CO); distribution of young stars as a function of molecular column density; star formation efficiency; star formation rate and gas depletion; and enlarged images of some of the regions with numerous young stars. Additional slides examine the origin of the Taurus molecular cloud, evolution from HI gas, kinematics as a clue to its origin, and its relationship to star formation.

molecular clouds↗
DOE OSTI2023

Interaction energy and isosteric heat of adsorption between hydrogen and magnesium diboride

Hydrogen storage materials form a crucial research topic for future energy utilization employing hydrogen and among those of interest magnesium diboride (MgB 2 ) has shown its prevalence. In this study, a first-principles analytical adsorption model of one hydrogen molecule in the vicinity of various magnesium diboride crystal surfaces was developed in order to obtain surface thermodynamic properties as a function of molecular and lattice properties. Henry's law constant (K H ) and isosteric heat of adsorption (ΔH ads ) indicators of the affinity between a gaseous molecule and a solid surface are thus calculated. The results in this paper not only address questions pertaining to the first stage of hydrogen storage processes but also advance the understanding of physisorption thermodynamics of a neutral molecule (H 2 ) coming in contact with a layered metallic-like surface (MgB 2 ). Although the model is built from a framework of classical calculations, quantum effects are incorporated as the fractional charge of the ions on the free surfaces, which is essential for the calculation of analytic thermodynamic values that approximate calculations from other methods. To benchmark our theoretical models, periodic density functional calculations were performed to determine the interactions between H 2 and different MgB 2 surfaces from first-principles. By considering both the top and sublayers of MgB 2 in calculating interaction energy, we have analytically and computationally calculated the interaction energies of H 2 molecules and MgB 2 's terminated planes, and witnessed the strong dependence of interaction energies on surface charges. We have also observed a dipole flipping phenomenon which explains the discontinuity seen in the interaction energy graph of Mg(0001). Both analytical and computational results showed heat of adsorption at zero coverage varying at a very low range (<7 kJ mol -1 ).

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

Selective Enhancement of Spectroscopic Features by Quantum Optimal Control

Tailored light can be used to steer atomic motions into selected quantum pathways. In optimal control theory (OCT), the target is usually expressed in terms of the molecular wave function, a quantity that is not directly observable in experiment. In this study, we present simulations using OCT that optimize the spectroscopic signal itself. By shaping the optical pump, the x-ray stimulated Raman signal, which occurs solely during the passage through conical intersections, is temporally controlled and amplified by up to 2 orders of magnitude. This enhancement can be crucial in order to bring small coherence-based signatures above the detectable threshold. Our approach is applicable to any signal that depends on the expectation value of a positive definite operator.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Probing Heterogeneous Charge Distributions at the α-Al 2 O 3 (0001)/H 2 O Interface

Unlike metal or semiconductor electrodes, the surface charge resulting from the protonation or deprotonation of insulating mineral oxides is highly localized and heterogeneous in nature. In this work the Stark active C≡N stretch of potassium thiocyanate is used as a molecular probe of the heterogeneity of the interfacial electrostatic potential at the α-Al 2 O 3 (0001)/H 2 O interface. Vibrational sum frequency generation (vSFG) measurements performed in the OH stretching region suggest that thiocyanate species organize interfacial water similarly to halide ions. Changes in the electrostatic potential are then tracked via Stark shifts of the vibrational frequency of the thiocyanate stretch. Our vSFG measurements show that we can simultaneously measure the vSFG response of SCN – ions experiencing charged and neutral surface sites. We assign local potentials of +308 and -154 mV to positively and negatively charged aluminol groups that are present at pH = 4 and pH = 10, respectively. Thiocyanate anions at positively charged surface sites and negatively charged surface sites and those participating in contact ion pairing adopt similar orientations and are oppositely oriented relative to thiocyanate ions near neutral surface sites. All four species followed Langmuir adsorption isotherms. Density functional theory–molecular dynamics (DFT-MD) simulations of SCN – near the neutral α-Al 2 O 3 (0001)/H 2 O interface show that the vSFG response in the C≡N stretch region originates from a SCN–H–O–Al complex, suggesting the surface site specificity of these experiments. To our knowledge this is the first spectroscopic measurement of local potentials associated with a heterogeneously charged surface. The ability to probe the evolution of local charges in situ could provide vital insight into many industrial, electrochemical, and geochemically relevant interfaces.

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

Investigating the Role of Silver Oxidation State on the Thermodynamic Interactions between Xenon and Silver-Functionalized Zeolites

The molecular level understanding of the strong adsorption of Xe to silver-modified zeolites remains elusive. Here, we probe the effect of silver oxidation state on the thermodynamics of Xe sorption in silver-functionalized zeolites by measuring the enthalpies of adsorption after various treatments using inverse gas chromatography (IGC). The enthalpy of adsorption was measured for silver-functionalized chabazites (AgCHA) before and after hydrogen reduction and subsequent reoxidation. The sorption enthalpy (ΔH) for AgCHA was 35.2 kJ/mol, which decreased to 25.8 kJ/mol with hydrogen reduction. After reoxidation (O 2 -AgCHA), 95% of the binding strength was restored. Hydrogen reduction of the base chabazite (CHA) did not influence Xe adsorption. Henry’s law constant for Xe adsorption increased in the order AgCHA > O 2 -AgCHA > H 2 -AgCHA > CHA. A decrease in enthalpy and Henry’s constant with silver reduction and increase with reoxidation suggest that ionic silver is playing a role in Xe binding. The effect of reduction and reoxidation on the zeolite microstructure was analyzed using surface area analysis, powder X-ray diffraction (p-XRD), scanning electron microscopy/energy-dispersive X-ray spectroscopy (SEM/EDS), and X-ray photoelectron spectroscopy (XPS). Finally, these results lay the groundwork for better material design of strong noble gas adsorbents.

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

A structural underpinning of the lower critical solution temperature (LCST) behavior behind temperature-switchable liquids

In this work, we use state-of-the-art X-ray scattering and molecular dynamics to analyze amine-water mixtures that show the unusual lower critical solution temperature (LCST) behavior. The goal is to provide direct experimental evidence for the entropy-lowering molecular cluster formation hypothesized as necessary for LCST behavior. Differential wide-angle X-ray scattering and pair distribution analysis and small-angle X-ray scattering measurements were combined with molecular modeling and liquid-liquid equilibrium measurements, revealing direct experimental evidence for the hypothesis. However, the response of the amine phase to accommodating water is even more subtle than the simple hypothesis suggests, with the formation of robust nanoscale reverse micelles. The techniques developed in this paper can be expected to yield insights in the use of temperature-switchable liquids in solvent extraction and other separations, and the stabilization of organelles in living cells that do not have physical membranes but do require compositional gradients to operate.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Many-body effects in the X-ray absorption spectra of liquid water

Significance In X-ray absorption spectroscopy, an electron–hole excitation probes the local atomic environment. The interpretation of the spectra requires challenging theoretical calculations, particularly in a system like liquid water, where quantum many-body effects and molecular disorder play an important role. Recent advances in theory and simulation make possible new calculations that are in good agreement with experiment, without recourse to commonly adopted approximations. Based on these calculations, the three features observed in the experimental spectra are unambiguously attributed to excitonic effects with different characteristic correlation lengths, which are distinctively affected by perturbations of the underlying H-bond structure induced by temperature changes and/or by isotopic substitution. The emerging picture of the water structure is fully consistent with the conventional tetrahedral model.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Electric-Field-Driven Localization of Molecular Nanowires in Wafer-Scale Nanogap Electrodes

As integrated circuits continue to scale toward the atomic limit, bottom-up processes, such as epitaxial growth, have come to feature prominently in their fabrication. At the same time, chemistry has developed highly tunable molecular semiconductors that can perform the functions of ultimately scaled circuit components. Hybrid techniques that integrate programmable structures comprising molecular components into devices however are sorely lacking. Here we demonstrate a wafer-scale process that directs the localization of a conductive polymer, M w = 20 kg mol –1 polyaniline, from dilute solutions into 50 nm vertical nanogap device architectures using electric-field-driven self-assembly. The resulting metal–polymer–metal junctions were characterized by electron microscopy, Raman spectroscopy and transport measurements demonstrating that our technique is highly selective, assembling conductive polymers only in electrically activated nanogaps. Our results represent a step toward scalable hybrid nanoelectronics that seamlessly integrate established lithographic top-down fabrication with bottom-up synthesized molecular functional circuit components.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Aqueous Photoelectrochemical CO 2 Reduction to CO and Methanol over a Silicon Photocathode Functionalized with a Cobalt Phthalocyanine Molecular Catalyst

Abstract We report a precious‐metal‐free molecular catalyst‐based photocathode that is active for aqueous CO 2 reduction to CO and methanol. The photoelectrode is composed of cobalt phthalocyanine molecules anchored on graphene oxide which is integrated via a (3‐aminopropyl)triethoxysilane linker to p‐type silicon protected by a thin film of titanium dioxide. The photocathode reduces CO 2 to CO with high selectivity at potentials as mild as 0 V versus the reversible hydrogen electrode (vs RHE). Methanol production is observed at an onset potential of −0.36 V vs RHE, and reaches a peak turnover frequency of 0.18 s −1 . To date, this is the only molecular catalyst‐based photoelectrode that is active for the six‐electron reduction of CO 2 to methanol. This work puts forth a strategy for interfacing molecular catalysts to p‐type semiconductors and demonstrates state‐of‐the‐art performance for photoelectrochemical CO 2 reduction to CO and methanol.

Shang, Bo↗
DOE OSTI2022

Aqueous Photoelectrochemical CO 2 Reduction to CO and Methanol over a Silicon Photocathode Functionalized with a Cobalt Phthalocyanine Molecular Catalyst

We report a precious-metal-free molecular catalyst-based photocathode that is active for aqueous CO 2 reduction to CO and methanol. The photoelectrode is composed of cobalt phthalocyanine molecules anchored on graphene oxide which is integrated via a (3-aminopropyl)triethoxysilane linker to p-type silicon protected by a thin film of titanium dioxide. The photocathode reduces CO 2 to CO with high selectivity at potentials as mild as 0 V versus the reversible hydrogen electrode (vs RHE). Methanol production is observed at an onset potential of –0.36 V vs RHE, and reaches a peak turnover frequency of 0.18 s –1 . To date, this is the only molecular catalyst-based photoelectrode that is active for the six-electron reduction of CO 2 to methanol. Furthermore, this work puts forth a strategy for interfacing molecular catalysts to p-type semiconductors and demonstrates state-of-the-art performance for photoelectrochemical CO 2 reduction to CO and methanol.

14 SOLAR ENERGY↗