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High valent metal-oxo intermediates are versatile oxidants known to facilitate both oxygen atom transfer (OAT) and hydrogen atom transfer (HAT) reactions in nature.
We report a Kohn–Sham density functional theory calculation of a system with more than 200 000 atoms and 800 000 electrons using a real-space high-order finite-difference method to investigate the electronic structure of large spherical silicon nanoclusters. Our system of choice was a 20 nm large spherical nanocluster with 202 617 silicon atoms and 13 836 hydrogen atoms used to passivate the dangling surface bonds. To speed up the convergence of the eigenspace, we utilized Chebyshev-filtered subspace iteration, and for sparse matrix–vector multiplications, we used blockwise Hilbert space-filling curves, implemented in the PARSEC code. For this calculation, we also replaced our orthonormalization + Rayleigh–Ritz step with a generalized eigenvalue problem step. We utilized all of the 8192 nodes (458 752 processors) on the Frontera machine at the Texas Advanced Computing Center. We achieved two Chebyshev-filtered subspace iterations, yielding a good approximation of the electronic density of states. Our work pushes the limits on the capabilities of the current electronic structure solvers to nearly 106 electrons and demonstrates the potential of the real-space approach to efficiently parallelize large calculations on modern high-performance computing platforms.
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Two new extremely high precision measurements of the proton rms charge radius performed in 2010-2013 with muonic hydrogen atom demonstrated up to six standard deviations smaller values than the accepted average from all previous experiments performed with different methods (scattering and atomic spectroscopy) on ordinary hydrogen. This discrepancy triggered the well-known ?proton radius puzzle? in hadronic physics. To address this puzzle, the PRad collaboration in spring of 2016 performed a novel magnetic-spectrometer-free ep-scattering experiment in Hall B at Jefferson Lab accumulating high statistics and a rich experimental data set. The specifics of the PRad experiment and the final physics results, including the extracted proton radius, as well as, the current status of the puzzle will be presented and discussed in this talk.
This work investigates the effects of argon ions, hydrogen atoms, and hydrogen ions on the diamond (100) surface using classical molecular dynamics simulations. The purpose of this investigation was to asses plasma processing techniques for applications in quantum device manufacturing. The simulations suggest that combining argon ion smoothing with selective, near threshold energy H removal of amorphous C could be an effective strategy for diamond surface engineering, leading to more reliable and sensitive diamond color center devices. Results were found to differ significantly with interatomic potential, and an analysis of these differences was also carried out. Included in this repository are LAMMPS source files, input scripts, and plotting scripts required to reproduce the data. Also included are the output data required to make all the plots included in the associated publication.
Here, the adsorption of atomic H and H 2 on copper mono- and submonolayers supported on hexagonal WC(0001) surfaces has been investigated using density functional theory with the Perdew–Burke–Ernzerhof exchange correlation functional and D2 van der Waals corrections. Results evidence the impact of the termination of the carbide substrate on fundamental properties of Cu adatoms, and, hence, on the stability of molecular and atomic hydrogen, defining copper's catalytic activity for hydrogen evolution reaction. Using H adsorption energy as a descriptor, catalytic activity of Cu adlayers for hydrogen evolution reaction was estimated using traditional volcano curves and a curve, obtained at low hydrogen coverage. Obtained results evidence that copper adlayers supported on the WC may present a viable low-cost alternative to noble metal-based catalysts, with improved catalytic activity compared to that of copper. This, potentially, can be a useful basis for designing and developing novel functional materials with predetermined catalytic properties.
Stereocontrol is of critical importance in organic synthesis. In this study, we demonstrate how heterogeneous electrochemical hydrogenation enables diastereocontrol simply by tuning electrochemical hydrogenation mechanisms without altering the adsorption conformation of a reactant on the electrode. We use 4-hydroxy-1-tetralone (4-OH-tetralone) as a model reactant, where diastereomers can be produced during the hydrogenation of the carbonyl group. In traditional thermocatalytic hydrogenation, H 2 first dissociates on the catalyst surface to form surface-adsorbed hydrogen (H*), and therefore, H* is always added to the organic reactant from the catalyst side via hydrogen atom transfer (HAT). Thus, in order to flip the diastereoselectivity, the adsorbed reactant itself must be physically flipped. In contrast, electrochemical hydrogenation can occur either via HAT, where H is added from the electrode surface, or via proton-coupled electron transfer (PCET), where H is added from the solution side of the adsorbed reactant. Thus, without changing the adsorption conformation of the reactant, opposite diastereomers can be obtained by switching the hydrogenation mechanism (HAT vs PCET). In this work, using a combination of experimental and computational studies, we demonstrate two examples of flipping diastereoselectivity by different electrochemical hydrogenation mechanisms. In the first case, we achieve opposite diastereoselectivities using metals that adopt different hydrogenation mechanisms (HAT vs PCET). In the second case, we flip the diastereoselectivity by varying the applied potential, which switches one hydrogenation mechanism to the other on the same metal electrode. In each case, our results offer an atomic-level understanding of the preferred hydrogenation mechanism that enables the corresponding diastereoselectivity.
The Polarized Atomic Hydrogen Gas Jet Target polarimeter (HJET) is operated at the Relativistic Heavy Ion Collider (RHIC) since 2004 to measure the absolute polarization of each colliding proton beam. Polarimeter detectors and data acquisition were upgraded in 2015 to increase the solid angle, energy range, and to improve the energy and time resolution. These upgrades along with an improved beam intensity and polarization allowed us to greatly reduce the statistical and systematic errors for the proton polarization measurements in RHIC Runs 15 (E beam = 100 GeV) and 17 (255 GeV). For a typical 8 hour RHIC store, the measured proton beam average polarization was about P beam ~ 55 ± 2.0 stat ± 0.3 syst %. The elastic pp analyzing power, AN(t)~0.04, was determined with a precision of about |δA N (t)|~0.0002 in the momentum transfer squared range 0.001<-t<0.020 GeV 2 . In this paper we present a detailed systematic error analysis of the polarization measurements at HJET. Perspectives of using the HJET based absolute polarimeters in the future Electron Ion Collider (EIC) will be also discussed.
Auranofin, initially developed as a treatment for rheumatoid arthritis, is currently under extensive investigation as a potential drug for various conditions, including cancer, bacterial infections, and parasitic infections. The compound is a known inhibitor of thioredoxin reductase (TXNRD1) and related selenoproteins. Although preliminary studies on the auranofin crystal polymorphism exist, and a low-quality crystal structure has been reported, a comprehensive crystallographic characterization remains unexplored. Utilizing X-ray crystallography techniques, we conducted detailed structural analysis of auranofin and compared our findings with related organogold compounds. Implementation of Hirshfeld atom refinement (HAR) enabled a more accurate hydrogen atom positioning in the structure. The crystal packing reveals a layered arrangement stabilised by numerous weak hydrogen bonds and dispersive interactions. Notably, our attempts to reproduce the previously reported polymorphic form of auranofin, purportedly more water-soluble, were unsuccessful despite following published protocols. To our knowledge, this is the first study describing a “disappearing polymorph” phenomenon of any pharmaceutically relevant transition metal coordination compound. Our findings may have significant implications for medicinal chemistry and pharmacology of coordination complexes, suggesting the need for systematic revision of historical crystallographic data in this field.
We have used a combination of pico-to-nano temporal/spatial scale computational physics and chemistry modeling of plasma–material interfaces in the tokamak fusion plasma edges to unravel the evolving characteristics, not readily accessible by empirical means, of lithium-, oxygen-, and hydrogen-containing materials of plasma-facing components under irradiation by hydrogen and its isotopes. In the present calculation, amorphous lithium compound surfaces containing oxygen, Li 2 O, and LiOH were irradiated by 1-100 eV particles at incident angles on the surface ranging from perpendicular to almost grazing angles. Consequential surface processes, reflection, retention, and sputtering were studied at “the same footing” and compared to earlier results from amorphous Li and LiH surfaces. In conclusion, the critical role of charging dynamics of lithium, oxygen, and hydrogen atoms in the surface chemistry during hydrogen-fuel irradiation was found to drive the kinetics and dynamics of these surfaces in unexpected ways that ultimately could have profound effects on fusion plasma confinement behavior and surface erosion.
Direct Reduction of Iron ore using hydrogen (H-DRI) is a promising pathway towards efficient steelmaking and accurate predictive models are a necessity for scale-up and optimization of this technology. However, accurate models of this process remain limited because existing models oversimplify grain-scale phenomena, such as nonlinearity inside grain, self-sufficient porosity, surface reactions, and the role of plasma species. These phenomena are important for flash steelmaking and plasma-assisted H-DRI processes. To address this need, we present a phenomenological model for simulating H-DRI at the scale of a single micron-sized grain of the iron ore. We call this the Transient Reactive Grain Model (TRGM). TRGM incorporates key physical process: gas species transport, a chemical kinetics of material conversion, nanopore structural evolution and, adsorption-desorption surface kinetics at the reactive nanopore surface. The important contribution of this work is that the model provides a dependence on different reductant species, specifically hydrogen atoms versus molecules, so that role of hydrogen plasma reduction can be clarified compared to the use of pure hydrogen gas reduction. TRGM predictions agree well with experimental data for both molecular H2 reduction of Fe2O3 and plasma hydrogen reduction of Fe3O4. Results reveal species concentration gradients with a diffuse reaction zone, and enhanced hydrogen diffusion at the grain outer surface due to evolving porosity. These findings challenge common assumptions in existing models, including sharp reaction fronts, quasi-steady diffusion and kinetics, and the neglect of surface chemistry. As a generalized grain-scale model for H-DRI processes, TRGM has practical applications in flash steelmaking and in-flight reduction using both molecular and plasma hydrogen.
NO x concentrations in some geographic regions are harmful to human health. Gas filters to trap NO x and other toxic chemicals contain metal oxides, including MoO 3 and CuO. These materials are also being investigated for NO x gas sensors. In a step to understand the fundamental adsorption mechanism in sensors and the effect on binding site availability in gas filters, ambient-pressure X-ray photoelectron spectroscopy (APXPS) was used to study the interaction of NO 2 with polycrystalline MoO 3 and CuO surfaces under pressures up to 0.01 Torr (14 parts per million volume (ppmv)). Density functional theory-based computational modeling was performed to reveal the mechanisms of NO 2 interactions with the MoO 3 (010) and CuO(111) surfaces to aid interpretation of the experimental results. With pressure dependence, NO 2 interacts with reduced Mo 5+ atoms generated by oxygen vacancies and abstracts hydrogen atoms from hydroxyl groups on MoO 3 without accumulating N-containing species on the surface; vacancy-induced electronic states in the band gap are also removed, hinting toward an increase in the resistivity of the material. N-containing species begin accumulating on the CuO surface at atmospherically relevant pressures of 140 ppbv. NO 2 only decomposes at oxygen vacancy sites of CuO. The nitrogen species leave the CuO surface upon evacuation, highlighting the importance of in situ surface characterization when studying gas sensing and adsorption mechanisms. Finally, these results imply that NO 2 removes hydroxyl and O vac binding sties on these materials when used in gas filtration and sensing applications. Furthermore, the results show the key role of O vac sites in the gas sensing mechanism of MoO 3 and highlight the potential of APXPS for further studies of gas sensors.
Electrocatalytic nitrogen reduction (eNRR) offers a green pathway for the production of NH 3 from N 2 and H 2 O under ambient conditions. Transition metal oxynitrides (TMO x N y ) are among the most promising catalysts but face challenges in achieving a high yield and faradaic efficiency (FE). This work develops a hybrid WO x N y /WO 3 catalyst with a unique heterogeneous interfacial complexion (HIC) structure. This design enables in situ generation and delivery of highly active hydrogen atoms (H*) in acidic electrolytes, promoting nitrogen hydrogenation and the formation of nitrogen vacancies (Nv) on the WO x N y surface. This significantly enhances the selectivity of eNRR for NH 3 synthesis while suppressing the hydrogen evolution reaction (HER). A simple two-step fabrication process─microwave hydrothermal growth followed by plasma-assisted surface nitridation─was developed to fabricate the designed catalyst electrode, achieving an NH 3 yield of 3.2 × 10 –10 mol·cm –2 ·s –1 with 40.1% FE, outperforming most TMN/TMO x N y electrocatalysts. Multiple control experiments confirm that the eNRR follows an HIC-enhanced Mars–van Krevelen (MvK) mechanism.
The tricyclic polycyclic aromatic hydrocarbons (PAHs) 3H-cyclopenta[a]naphthalene (C 13 H 10 ), 1H-cyclopenta[b]naphthalene (C 13 H 10 ) and 1H-cyclopenta[a]naphthalene (C 13 H 10 ) along with their indene-based bicyclic isomers (E)-5-(but-1-en-3-yn-1-yl)-1H-indene, (E)-6-(but-1-en-3-yn-1-yl)-1H-indene, 5-(but-3-ene-1-yn-1-yl)-1H-in-dene, and 6-(but-3-ene-1-yn-1-yl)-1H-indene were formed via a “directed synthesis” in a high-temperature chemical micro reactor at the temperature of 1300 ± 10 K through the reactions of the 5- and 6-indenyl radicals (C 9 H 7 ˙) with vinylacetylene (C 4 H 4 ). The isomer distributions were probed utilizing tunable vacuum ultraviolet light by recording the photoionization efficiency curves at mass-to-charge of m/z = 166 (C 13 H 10 ) and 167 ( 13 CC 12 H 10 ) of the products in a supersonic molecular beam. Here, the underlying reaction mechanisms involve the initial formation of van-der-Waals complexes followed by addition of the 5- and 6-indenyl radicals to vinylacetylene via submerged barriers, followed by isomerization (hydrogen shifts, ring closures), and termination via atomic hydrogen elimination accompanied by aromatization. All the barriers involved in the formation of 3H-cyclopenta[a]naphthalene, 1H-cyclopenta[b]naphthalene and 1H-cyclopenta[a]naphthalene are submerged with respect to the reactants indicating that the mechanisms are in fact barrierless, potentially forming PAHs via the hydrogen abstraction – vinylacetylene addition (HAVA) pathway in the cold molecular clouds such as Taurus Molecular Cloud-1 (TMC-1) at temperatures as low as 10 K.
Development of supported single-site catalysts using small metal sulfide complexes could significantly help in the development of cost-effective catalytic materials to drive selective hydrogenation and hydrogenolysis. The goal of this study is to contribute to the development of metal sulfide catalysts by calculating the thermodynamics of a catalytic cyclic involving a metal organic framework functionalized by insertion of metal sulfide. Anchored metal sulfide complexes can potentially be designed with ligands with distinctly different electronic and catalytic properties for specific catalytic applications. Here we examine the hydrogenation of ethylene as a model. We use density functional theory to investigate molybdenum–sulfur complexes as active catalysts anchored on the metal–organic framework UiO-66 as a stable support. Our calculations show that the anchored complexes with more than two sulfur ligands are unfavorable for ethylene adsorption, so we study complexes with one or two sulfur ligands. Hydrogenation of the unsaturated carbon double bond requires the transfer of two hydrogen atoms, which can occur via heterolytic activation of hydrogen to form a Mo-hydride and a protonated sulfur – either by hydride transfer followed by proton transfer or via proton transfer followed by hydride transfer, and we find that both mechanisms proceed via two-state reactivity involving two spin states along the reaction path. Of the two catalysts studied in gas the phase, the MoS single-sulfur–ligand complex with lower oxidation states produces thermodynamically more favorable intermediates along the pathway for the first hydrogen transfer for both the hydride-first mechanism and the proton-first mechanism. As a result, the quantum mechanical calculations provide experimentally inaccessible partial atomic charges and geometries of the various intermediates encountered along the steps of the reaction mechanisms.
We study the excitation of the hydrogen atom by bichromatic circularly polarized laser pulses using numerical solutions of the time-dependent Schrödinger equation. The results are in agreement with the selection rules for multiphoton processes in such fields, namely, excited states are populated in which orbital angular momentum and magnetic quantum numbers are either both odd or both even, independent of the relative helicity, peak intensity, and pulse duration of the pulses. For co-rotating pulses the results show that excitation predominantly proceeds to states with magnetic quantum number of the same helicity as the laser pulses. Besides pathways via direct photon absorption from the ground state our results indicate that a transfer of population among the Rydberg states occurs via Λ-type transitions. In the case of counter-rotating pulses the largest excitation probability is found for Rydberg states that differ in magnetic quantum number by Δm=±3. This pattern allows us to estimate how many photons from each of the two bichromatic fields have been absorbed. Finally, we confirm that a population in Rydberg states beyond a maximum orbital angular quantum number is unlikely.
Diamond is a promising material for multiple applications in quantum information processing and sensing as well as applications in microelectronics. However, diamond devices can be limited by surface defects that compromise charge stability and spin coherence, among others. Improved strategies in plasma etching of diamond could play an important role in minimizing or eliminating these defects. In this work, we explore plasma-assisted atomic scale etching of diamond using argon ions (Ar + ), hydrogen ions (H + ) and hydrogen atoms (H). We employ classical molecular dynamics (MD) simulations and test several interatomic potentials based on the Reactive Empirical Bond Order (REBO) form with comparisons to a variety of published experimental results. We performed MD simulations of low-energy hydrogen ($\leqslant$50 eV) and argon ( $\leqslant$200 eV) ion bombardment of diamond surfaces. Ar + bombardment can be used to locally smooth initially rough diamond surfaces via the formation of an amorphous C layer, the thickness of which increases with argon ion energy. Subsequent exposure with hydrogen ions (or fast neutrals) will selectively etch this amorphous C layer, leaving the underlying diamond layer mostly intact if the H energy is maintained below about 10 eV. The simulations suggest that combining Ar + smoothing with selective, near threshold energy H removal of amorphous C can be an effective strategy for diamond surface engineering, leading to more reliable and sensitive diamond color center devices.
Nickel photocatalysis has recently become vital to organic synthesis, but how the Ni (II) X 2 L pre-catalyst (X = Cl, Br; L = bidentate ligand) becomes activated to Ni (I) XL has remained puzzling and is typically addressed on a case-by-case basis. Here, we reveal a general mechanism where light induces photolysis of the Ni (II) -X bond, either via direct excitation or triplet energy transfer. Photolysis produces Ni (I) XL and a halogen radical, X*. Subsequent hydrogen atom abstraction, often from the solvent, produces a C(sp 3 ) radical, R*, that recombines with Ni (I) to form organonickel(II) complexes, Ni (II) XRL. Rather than acting as a loss pathway, Ni (II) XRL behaves as a light-activated reservoir of Ni (I) via photolysis of the Ni (II) -C bond. These results explain the role of the solvent in protecting the catalyst from off-cycle dimerization, demonstrate that two photons are often required to drive the reaction, and show how tuning the ligand can control the concentration of active Ni (I) species.