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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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Singlet Fission Driven by Anisotropic Vibronic Coupling in Single-Crystalline Pentacene

Vibronic coupling is believed to play an important role in siglet fission, wherein a photoexcited singlet exciton is converted into two triplet excitons. In the present study, we examine the role of vibronic coupling in singlet fission using polarized transient absorption microscopy and ab initio simulations on single-crystalline pentacene. It was found that singlet fission in pentacene is greatly facilitated by the vibrational coherence of a 35.0 cm(-1) phonon, where anisotropic coherence persists extensively for a few picoseconds. This coherence-preserving phonon that drives the anisotropic singlet fission is made possible by a unique cross-axial charge-transfer intermediate state. In the same fashion, this phonon was also found to predominantly drive the quantum decohence of a correlated triplet pair to form a decoupled triplet dimer. Moreover, our transient kinetic experimental data illustrates notable directional anisotropicity of the singlet fission rate in single-crystalline pentacene.

Deng, Gang-Hua↗
DOE OSTI2019

Spontaneous Formation of 1D Pattern in Monolayer VSe 2 with Dispersive Adsorption of Pt Atoms for HER Catalysis

Creation of functional patterns in two-dimensional (2D) materials provides opportunities to extend their potential for applications. Transition-metal dichalcogenides (TMDCs) are suitable 2D materials for pattern generation because of properties including alterable polymorphic phases, easy chalcogen-vacancy formation, metal-atom insertion, and alloying. Such patterning can be used for selective functionalization. Here we report the spontaneous formation of long-range, well-ordered 1D patterns in monolayer vanadium diselenide (VSe 2 ) by a single annealing stage during growth. Atomic-resolution images in real space combined with density-functional-theory (DFT) calculations reveal the 1D features of patterned VSe 2 . Further experimental characterization of the intermediate states in the growth process confirm the spontaneous formation of the 1D pattern by annealing-induced Se-deficient linear defects. The 1D pattern can be reversibly transformed to homogenous VSe 2 monolayer by reintroducing Se atoms. Moreover, additional experiments demonstrate that a dispersive deposition of Pt atoms along the 1D structures of patterned VSe 2 is achieved, while DFT calculations find that their catalytic activity for hydrogen evolution reaction (HER) is as good as that of Pt surfaces. Further, the formation of long-range, well-ordered 1D patterns not only demonstrates an effective way of dimension modulation in 2D materials but also enriches the potential of intrinsically patterned 2D materials for promising catalytic activities.

Chemical structure↗
DOE OSTI2019

Enhanced Activity of Heterogeneous Pd(II) Catalysts on Acid-Functionalized Metal–Organic Frameworks

Single-site heterogeneous catalysts (SSHCs) play important roles in fundamental science and technology, owing to the molecular level control of structure–support interactions that is possible in these systems. Recently, SSHCs supported by acidic oxides have attracted particular interest because catalytically active metal centers can be formed at the surface sites. Here, we incorporated a palladium SSHC in phosphated and sulfated metal–organic frameworks (MOFs), hafnium-based MOF-808 (Hf-MOF-808-PO 4 and Hf-MOF-808-SO 4 ). The structural and electronic properties of the Pd(II) sites coordinated to the acidic sites in these MOFs were investigated through X-ray photoelectron spectroscopy, vibrational spectroscopy, X-ray crystallographic techniques, catalytic studies, and quantum mechanical electronic structure calculations employing density functional theory. We demonstrated that the presence of node-bound acidic functional groups stabilizes the Pd(II) site in these MOFs, resulting in enhanced catalytic activities (compared to in the nonacid functionalized Hf-MOF-808) in the oxidative Heck reaction where Pd(II) is the active species. The density functional calculations support the interpretation that the acid functionalization of the MOF node can stabilize the Pd(0) intermediate state during the catalytic reactions, thereby suppressing Pd(0) aggregation leading to catalyst deactivation. Furthermore, these findings offer insights and methodology for the catalytic investigation of SSHCs in MOFs.

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

Kinetic Isotope Effects: Interpretation and Prediction Using Degrees of Rate Control

Kinetic isotope effects (KIEs) have been used for decades in catalysis research as a tool for clarifying reaction mechanisms. Significant primary kinetic isotope effects have usually been interpreted as being a result of isotope substitution at a site of bond breaking (or forming) in the rate-determining step in the reaction mechanism. However, quantitative analysis of the magnitude of the KIE in complex multistep reaction mechanisms is seldom reported. We prove here that the logarithm of the rate ratio for two isotopes is the weighted average over all species in the mechanism of their standard-state free energy difference between the two isotopes, divided by RT. The weighting factor is the degree of rate control (DRC) for that species (e.g., transition state, intermediate, reactant) when the rate is measured separately for each isotope. It is instead the degree of selectivity ratio control (DSRC) when the KIE is measured as the product selectivity in a parallel competition between two isotopes within the same reactant molecule. Since only a few species have non-zero DRCs (or DSRCs) for most reactions, only these few contribute to this weighted average and the KIE. We show that this provides a simple way to interpret and quantitatively predict kinetic isotope effects that is powerful in the insights it provides, allowing one to evaluate directly which species contribute most to the KIE. By applying it to H/D KIEs in several example mechanisms, we further show that the traditional way of interpreting KIEs that focuses only on the rate-determining step can easily lead to misunderstanding of KIE and the reaction mechanism. Finally, this highlights the importance to consider the effect of isotope substitution on the energies of all species with large DRCs (i.e, those whose energies are kinetically relevant). This method also offers opportunities for quantitative validation of mechanism-based microkinetic models.

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

Interfacial Reactivity and Speciation Emerging from Na-Montmorillonite Interactions with Water and Formic Acid at 200 °C: Insights from Reactive Molecular Dynamics Simulations, Infrared Spectroscopy, and X-ray Scattering Measurements

Reactive organic fluid - mineral interactions at elevated temperatures contribute to the evolution of planetary matter. One of the less studied but important transformations in this regard involves the reactions of formic acid with naturally occurring clays such as sodium montmorillonite. To advance a mechanistic understanding of these interactions, we use ReaxFF reactive molecular dynamics simulations in conjunction with infrared (IR) spectroscopy and X-ray scattering experiments to investigate the speciation behavior of water-formic acid mixtures on sodium montmorillonite interfaces at 473 K and 1 atm. Using a newly developed reactive forcefield, we show that the experimental IR spectra of unreacted and reacted mixture can be accurately reproduced by ReaxFF/MD. We further benchmark the simulation predictions of sodium carbonate and bicarbonate formation in the clay interlayers using Small and Wide-Angle X-ray Scattering measurements. Subsequently, leveraging the benchmarked forcefield, we interrogate the pathway of speciation reactions with emphasis on carbonate, formate, and hydroxide groups elucidating the energetics, transition states, intermediates, and preferred products. Further, we also delineate the differences in reactivities and catalytic effects of clay edges, facets, and interlayers owing to their local chemical environments, which have far reaching consequences in their speciation behavior. The experimental and simulation approaches described in this study and the transferable forcefields can be applied translationally to advance the science of clay-fluid interactions for several applications including subsurface fluid storage and recovery and clay-pollutant dynamics.

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

Pentavalent Uranium Enriched Mineral Surface under Electrochemically Controlled Reducing Environments

Redox reactions of uranium (U) in aqueous environments have important impacts on the mobility and isotopic fractionation of U in the geosphere. Pentavalent U as the cationic uranyl ion, UO 2 +, is rarely observed in naturally occurring samples because of its limited lifetime, but it may be an important intermediate state controlling the redox kinetics between hexavalent and tetravalent U. Increasing evidence has indicated that U(V) can be stabilized under laboratory conditions. Here, we showed that U(V) is the dominant species on the magnetite (Fe 3 O 4 ) surface under reducing conditions controlled by electrochemical methods. Cyclic voltammetry reveals coupled redox peaks corresponding to the U(VI)O 2 2+ /U(V)O 2+ one-electron redox reaction. Magnetite electrodes polarized at a series of potentials to reduce U(VI)O 2 2+ were characterized by X-ray photoelectron spectroscopy (XPS), X-ray absorption spectroscopy (XAS), and Auger electron mapping. Overall, the results showed that up to twice the amount of U(V) to U(VI) was present on the magnetite surface. U(V) adopted a typical uranyl-type structure, and the U coverage on the magnetite surface increased with decreasing potentials. The formation of mixed-valence U(V)/U(VI) species on the surface of magnetite may hinder the U(V) disproportionation reaction, thereby eliminating the presence of tetravalent U. These results show that U(V) can exist over short time scales as the dominant U species on mineral surfaces under selected reducing conditions by the controlled polarization of a mineral electrode.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2010

Fluoride Inhibition of Enolase: Crystal Structure and Thermodynamics

Enolase is a dimeric metal-activated metalloenzyme which uses two magnesium ions per subunit: the strongly bound conformational ion and the catalytic ion that binds to the enzyme-substrate complex inducing catalysis. The crystal structure of the human neuronal enolase-Mg{sub 2}F{sub 2}P{sub i} complex (enolase fluoride/phosphate inhibitory complex, EFPIC) determined at 1.36 {angstrom} resolution shows that the combination of anions effectively mimics an intermediate state in catalysis. The phosphate ion binds in the same site as the phosphate group of the substrate/product, 2-phospho-d-glycerate/phosphoenolpyruvate, and induces binding of the catalytic Mg{sup 2+} ion. One fluoride ion bridges the structural and catalytic magnesium ions while the other interacts with the structural magnesium ion and the ammonio groups of Lys 342 and Lys 393. These fluoride ion positions correspond closely to the positions of the oxygen atoms of the substrate's carboxylate moiety. To relate structural changes resulting from fluoride, phosphate, and magnesium ions binding to those that are induced by phosphate and magnesium ions alone, we also determined the structure of the human neuronal enolase-Mg{sub 2}Pi complex (enolase phosphate inhibitory complex, EPIC) at 1.92 {angstrom} resolution. It shows the closed conformation in one subunit and a mixture of open and semiclosed conformations in the other. The EPFIC dimer is essentially symmetric while the EPIC dimer is asymmetric. Isothermal titration calorimetry data confirmed binding of four fluoride ions per dimer and yielded K{sub b} values of 7.5 x 10{sup 5} {+-} 1.3 x 10{sup 5}, 1.2 x 10{sup 5} {+-} 0.2 x 10{sup 5}, 8.6 x 10{sup 4} {+-} 1.6 x 10{sup 4}, and 1.6 x 10{sup 4} {+-} 0.7 x 10{sup 4} M{sup -1}. The different binding constants indicate negative cooperativity between the subunits; the asymmetry of EPIC supports such an interpretation.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Accurate rates of the complex mechanisms for growth and dissolu-tion of minerals using a combination of rare event theories

Mineral growth and dissolution are often treated as occurring via a single, reversible process that governs the rate of reaction. We show that multiple, distinct intermediate states can occur during both growth and dissolution. Specifically, we have used metadynamics, a method to efficiently explore the free energy landscape of a system, coupled to umbrella sampling and reactive flux calculations, to examine the mechanism and rates of attachment and detachment of a barium ion onto a stepped, barite (BaSO4) surface. The activation energies calculated for the rate limiting reactions, which are different for attachment and detachment, precisely match those measured experimentally during both growth and dissolution. These results can potentially explain anomalous, non-steady state mineral reaction rates observed experimentally, and will enable the design of more efficient growth inhibitors and facilitate an understanding of the effect of impurities.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Single-Molecule Detection of the Encounter and Productive Electron Transfer Complexes of a Photosynthetic Reaction Center

Small, diffusible redox proteins play an essential role in electron transfer (ET) in respiration and photosynthesis, sustaining life on Earth by shuttling electrons between membrane-bound complexes via finely tuned and reversible interactions. Ensemble kinetic studies show transient ET complexes form in two distinct stages: an “encounter” complex largely mediated by electrostatic interactions, which subsequently, through subtle reorganization of the binding interface, forms a “productive” ET complex stabilized by additional hydrophobic interactions around the redox-active cofactors. Here, using single-molecule force spectroscopy (SMFS) we dissected the transient ET complexes formed between the photosynthetic reaction center-light harvesting complex 1 (RC-LH1) of Rhodobacter sphaeroides and its native electron donor cytochrome c 2 (cyt c 2 ). Importantly, SMFS resolves the distribution of interaction forces into low (~150 pN) and high (~330 pN) components, with the former more susceptible to salt concentration and to alteration of key charged residues on the RC. Thus, the low force component is suggested to reflect the contribution of electrostatic interactions in forming the initial encounter complex, whereas the high force component reflects the additional stabilization provided by hydrophobic interactions to the productive ET complex. Employing molecular dynamics simulations, we resolve five intermediate states that comprise the encounter, productive ET and leaving complexes, predicting a weak interaction between cyt c 2 and the LH1 ring near the RC-L subunit that could lie along the exit path for oxidized cyt c 2 . The multimodal nature of the interactions of ET complexes captured here may have wider implications for ET in all domains of life.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Tuning the Conformations of an M4L4 Cage and Their Impact on Catalysis

Enzymes catalyze chemical reactions with remarkable rate enhancements and selectivity. Supramolecular catalysis seeks to understand and emulate these outcomes, leveraging noncovalent interactions, electric fields, and controlled active site microenvironments to enhance catalysis in an enzyme-like fashion. The effects of conformational dynamics on supramolecular catalysts and assemblies are, however, relatively unexplored, despite their crucial role in enzyme rate enhancement. Here, we elucidate the conformational landscape of a model M4L4 supramolecular host through a rational approach: stabilizing a high-energy conformer through distal ligand modification and a transient intermediate state through symmetry-matched guest encapsulation, as well as tuning the conformer distribution through same-charge metal exchange at the host vertices. Each of these structural modifications induces a substantial shift in the host's conformational landscape, offering insights into the rational design of conformationally dynamic cages and enzymes. Although the thermodynamic properties of the dynamic Ga4L412- cage can be influenced by temperature, solvent, and guest binding, we find that conformational change occurs on a time scale that renders it rate-limiting in a model catalytic reaction, precluding rate enhancement through conformational selection. This concept is illustrated by locking the catalytically inactive conformer to a high-energy conformer that is catalytically competent. These findings demonstrate that precise modulation of the conformational landscape of supramolecular hosts provides an effective strategy for controlling their catalytic activity and binding.

Catalysis↗
DOE OSTI2014

Tribute to A. W. Castleman, Jr.

It is with great pleasure that we join our many colleagues who contributed to this special issue of The Journal of Physical Chemistry A in dedicating it in honor of Professor A. W. “Will” Castleman, Jr. Will is a pioneer in the field of cluster science, and the far-reaching impact of his career is demonstrated by the broad range of topics covered in this issue. This diversity validates Will’s teaching that “fundamental research in cluster science allows you to explore any problem you want”. This ability to extend to other research areas comes because, as Will has shown both rigorously and elegantly, clusters are an intermediate state of matter that bridge the gap between molecular and bulk levels.

Johnson, Grant E.↗
DOE OSTI2016

Giant phonon anomaly associated with superconducting fluctuations in the pseudogap phase of cuprates

The pseudogap in underdoped cuprates leads to significant changes in the electronic structure, and was later found to be accompanied by anomalous fluctuations of superconductivity and certain lattice phonons. Here we propose that the Fermi surface breakup due to the pseudogap, leads to a breakup of the pairing order into two weakly coupled sub-band amplitudes, and a concomitant low energy Leggett mode due to phase fluctuations between them. This increases the temperature range of superconducting fluctuations containing an overdamped Leggett mode. In this range inter-sub-band phonons show strong damping due to resonant scattering into an intermediate state with a pair of overdamped Leggett modes. In the ordered state, the Leggett mode develops a finite energy, changing the anomalous phonon damping into an anomaly in the dispersion. Finally, this proposal explains the intrinsic connection between the anomalous pseudogap phase, enhanced superconducting fluctuations and giant anomalies in the phonon spectra.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Uncleaved prefusion-optimized gp140 trimers derived from analysis of HIV-1 envelope metastability

The trimeric HIV-1 envelope glycoprotein (Env) is critical for host immune recognition and neutralization. Despite advances in trimer design, the roots of Env trimer metastability remain elusive. Here we investigate the contribution of two Env regions to metastability. First, we computationally redesign a largely disordered bend in heptad region 1 (HR1) of SOSIP trimers that connects the long, central HR1 helix to the fusion peptide, substantially improving the yield of soluble, well-folded trimers. Structural and antigenic analyses of two distinct HR1 redesigns confirm that redesigned Env closely mimics the native, prefusion trimer with a more stable gp41. Next, we replace the cleavage site between gp120 and gp41 with various linkers in the context of an HR1 redesign. Electron microscopy reveals a potential fusion intermediate state for uncleaved trimers containing short but not long linkers. Together, these results outline a general approach for stabilization of Env trimers from diverse HIV-1 strains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Atomically engineering activation sites onto metallic 1T-MoS 2 catalysts for enhanced electrochemical hydrogen evolution

Engineering catalytic sites at the atomic level provides an opportunity to understand the catalyst’s active sites, which is vital to the development of improved catalysts. Here we show a reliable and tunable polyoxometalate template-based synthetic strategy to atomically engineer metal doping sites onto metallic 1T-MoS 2 , using Anderson-type polyoxometalates as precursors. Benefiting from engineering nickel and oxygen atoms, the optimized electrocatalyst shows great enhancement in the hydrogen evolution reaction with a positive onset potential of ~ 0 V and a low overpotential of –46 mV in alkaline electrolyte, comparable to platinum-based catalysts. First-principles calculations reveal co-doping nickel and oxygen into 1T-MoS 2 assists the process of water dissociation and hydrogen generation from their intermediate states. This research will expand on the ability to improve the activities of various catalysts by precisely engineering atomic activation sites to achieve significant electronic modulations and improve atomic utilization efficiencies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Protein and RNA dynamical fingerprinting

Protein structural vibrations impact biology by steering the structure to functional intermediate states; enhancing tunneling events; and optimizing energy transfer. Strong water absorption and a broad continuous vibrational density of states have prevented optical identification of these vibrations. Recently spectroscopic signatures that change with functional state were measured using anisotropic terahertz microscopy. The technique however has complex sample positioning requirements and long measurement times, limiting access for the biomolecular community. Here we demonstrate that a simplified system increases spectroscopic structure to dynamically fingerprint biomacromolecules with a factor of 6 reduction in data acquisition time. Using this technique, polarization varying anisotropy terahertz microscopy, we show sensitivity to inhibitor binding and unique vibrational spectra for several proteins and an RNA G-quadruplex. The technique’s sensitivity to anisotropic absorbance and birefringence provides rapid assessment of macromolecular dynamics that impact biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Membrane translocation process revealed by in situ structures of type II secretion system secretins

The GspD secretin is the outer membrane channel of the bacterial type II secretion system (T2SS) which secrets diverse toxins that cause severe diseases such as diarrhea and cholera. GspD needs to translocate from the inner to the outer membrane to exert its function, and this process is an essential step for T2SS to assemble. Here, we investigate two types of secretins discovered so far in Escherichia coli , GspD α , and GspD β . By electron cryotomography subtomogram averaging, we determine in situ structures of key intermediate states of GspD α and GspD β in the translocation process, with resolution ranging from 9 Å to 19 Å. In our results, GspD α and GspD β present entirely different membrane interaction patterns and ways of transitioning the peptidoglycan layer. From this, we hypothesize two distinct models for the membrane translocation of GspD α and GspD β , providing a comprehensive perspective on the inner to outer membrane biogenesis of T2SS secretins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Controlled mechanochemical coupling of anti-junctions in DNA origami arrays

Abstract Allostery is a hallmark of cellular function and important in every biological system. Still, we are only starting to mimic it in the laboratory. Here, we introduce an approach to study aspects of allostery in artificial systems. We use a DNA origami domino array structure which–upon binding of trigger DNA strands–undergoes a stepwise allosteric conformational change. Using two FRET probes placed at specific positions in the DNA origami, we zoom in into single steps of this reaction cascade. Most of the steps are strongly coupled temporally and occur simultaneously. Introduction of activation energy barriers between different intermediate states alters this coupling and induces a time delay. We then apply these approaches to release a cargo DNA strand at a predefined step in the reaction cascade to demonstrate the applicability of this concept in tunable cascades of mechanochemical coupling with both spatial and temporal control.

Science & Technology - Other Topics↗
DOE OSTI2019

Ab initio investigation of the cyclodehydrogenation process for polyanthrylene transformation to graphene nanoribbons

Graphene nanoribbons (GNRs) can be synthesized from molecular precursors with atomic precision. A prominent case is the 7-atom-wide armchair GNR made from 10,10'-dibromo-9,9'-bianthryl (DBBA) precursors on metal substrates through dehalogenation/polymerization followed by cyclodehydrogenation. We investigate the key aspects of the cyclodehydrogenation process by evaluating the energy profiles of various reaction pathways using density functional theory and the nudged elastic band method. The metal substrate plays a critical catalytic role by providing stronger adsorption for products and facilitating H desorption. For polyanthrylene on an extra layer of GNR on Au, the underlying GNR insulates it from the Au substrate and increases the reaction barriers, rendering the polyanthrylene “quasi-freestanding”. However, positive charge injection can induce localized cyclodehydrogenation. We find that this is due to the stabilization of an intermediate state through an arenium ion mechanism and favorable orbital symmetries. These results provide mechanistic insight into the effects of the metal substrate and charge injection on cyclodehydrogenation during GNR synthesis and offer guidance for the design and growth of new graphitic structures.

36 MATERIALS SCIENCE↗