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The calculated transition state structure of 1-iodobutane reacting with DABCO is shown. The kinetic rates of this reaction in several organic solvents and temperatures have been measured along with those of iodomethane reacting with DABCO.
Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5′-phosphate (PLP) dependent enzyme that catalyzes a chemical transformation essential for the one-carbon (1C) metabolism. SHMT reversibly converts L-Ser into Gly and transfers a 1C unit to tetrahydrofolate (THF) to give 5,10-methylene-THF (5,10-MTHF). 5,10-MTHF, a 1C-unit donor, plays a crucial role in the downstream biomolecular syntheses required for the cell homeostasis and proliferation. SHMT is a prominent target for the drug discovery to battle bacterial and parasitic infections, and to treat various types of cancer. SHMT-catalyzed chemistry is governed by the general acid-base catalysis. Knowledge of the catalytic mechanism can aid drug design but can only be achieved when the atomic details of each reaction step are mapped, including accurate determination of hydrogen atom positions. Here we utilized the inactive E53Q mutant of Thermus thermophilus ( Tth ) SHMT to directly determine protonation states with room-temperature neutron crystallography and to capture a reactive intermediate containing the PLP-L-Ser external aldimine and THF in the enzyme active site. We observed protonation of the Schiff base nitrogen (N SB ) in the PLP internal aldimine but no change in the protonation states of other ionizable PLP groups and active site residues compared to wild-type Tth SHMT. X-ray structural analysis of the ternary intermediate complex E53Q-Ser-THF that eluded previous structural characterization shows the strategic positioning of the E53Q side chain in close proximity to the external aldimine and THF and reinforces the proposed role for E53 as the driver of proton transfer events along the reaction pathway.
We demonstrate a novel approach to the generation of femtosecond electron bunch trains via laser-driven wakefield acceleration. We use two independent high-intensity laser pulses, a drive, and an injector, each creating their own plasma wakes. The interaction of the laser pulses and their wakes results in a periodic injection of free electrons in the drive plasma wake via several mechanisms, including ponderomotive drift, wake-wake interference, and pre-acceleration of electrons directly by strong laser fields. Electron trains were generated with up to four quasi-monoenergetic bunches, each separated in time by a plasma period. In conclusion, the time profile of the generated trains is deduced from an analysis of beam loading and confirmed using 2D particle-in-cell simulations
Vacancy and self-interstitial atomic diffusion coefficients in concentrated solid solution alloys can have a non-monotonic concentration dependence. Here, the kinetics of monovacancies and $\langle$100$\rangle$ dumbbell interstitials in Ni–Fe alloys are assessed using lattice kinetic Monte Carlo (kMC). The non-monotonicity is associated with superbasins, which impels using accelerated kMC methods. Detailed implementation prescriptions for first passage time analysis kMC (FPTA-kMC), mean rate method kMC (MRM-kMC), and accelerated superbasin kMC (AS-kMC) are given. The accelerated methods are benchmarked in the context of diffusion coefficient calculations. The benchmarks indicate that MRM-kMC underestimates diffusion coefficients, while AS-kMC overestimates them. In this application, MRM-kMC and AS-kMC are computationally more efficient than the more accurate FPTA-kMC. Our calculations indicate that composition dependence of migration energies is at the origin of the vacancy’s non-monotonic behavior. In contrast, the difference between formation energies of Ni–Ni, Ni–Fe, and Fe–Fe dumbbell interstitials is at the origin of their non-monotonic diffusion behavior. Additionally, the migration barrier crossover composition—based on the situation where Ni or Fe atom jumps have lower energy barrier than the other one—is introduced. KMC simulations indicate that the interplay between composition dependent crossover of migration energy and geometrical site percolation explains the non-monotonic concentration-dependence of atomic diffusion coefficients.
We present a photoconductive terahertz detector that employs a plasmonic nanocavity to offer high-sensitivity and broadband operation when used in a terahertz time-domain spectroscopy system even at very low optical pump power levels. By employing a plasmonic nanocavity, all of the photocarriers are generated within a 100 nm distance from the photoconductor contact electrodes, enabling a short transport time for almost all of the photogenerated carriers. As a result, the photoconductive detector maintains high quantum efficiency and ultrafast operation simultaneously, enabling high-sensitivity and broadband operation at very low optical pump power levels. We utilize a photoconductive detector based on a plasmonic nanocavity optimized for operation at a 770 nm optical wavelength in a terahertz time-domain spectroscopy system and demonstrate a 100 dB signal-to-noise ratio and a 0.1–6 THz noise-equivalent bandwidth at a record-low average optical pump power of 0.1 mW, compared to the state-of-the-art photoconductive terahertz detectors. The extremely low optical power budget of the demonstrated photoconductive detector makes this detector attractive for multi-pixel terahertz imaging systems.
Photon upconversion, particularly via triplet-triplet annihilation (TTA), could prove beneficial in expanding the efficiencies and overall impacts of optoelectronic devices across a multitude of technologies. The recent development of bulk metal halide perovskites as triplet sensitizers is one potential step toward the industrialization of upconversion-enabled devices. In this work, we investigate the impact of varying additions of bromide into a lead iodide perovskite thin film on the TTA upconversion process in the annihilator molecule rubrene. We find an interplay between the bromide content and the overall device efficiency. In particular, a higher bromide content results in higher internal upconversion efficiencies, enabled by more efficient charge extraction at the interface, likely due to a more favorable band alignment. However, the external upconversion efficiency decreases, as the absorption cross section in the near infrared is reduced. The highest upconversion performance is found in our study for a bromide content of 5%. This result can be traced back to a high absorption cross section in the near infrared and higher photoluminescence quantum yield in comparison to the iodide-only perovskite, as well as an increased driving force for charge transfer.
Oxygen vacancies in Hf x Zr (1-x) O 2 (HZO) both contribute to stabilization of the ferroelectric orthorhombic phase and promote leakage pathways that limit the endurance of devices based on the material. Here, for this reason, the defect states of oxygen vacancies were investigated using photoemission electron microscopy (PEEM) and photoluminescence spectroscopy (PL), as their concentration was varied via ex situ laser exposure. Following a controlled oxygen vacancy reduction via visible (2.54 eV) laser dosing of HZO, deep-ultraviolet (DUV, 5.82 eV) PEEM was used to spatially probe the resulting mid-gap defect states and work function. Work function was found to increase monotonically with the laser-induced reduction in oxygen vacancy concentration culminating in a total increase near 70 meV. The change implies a Fermi level shift toward the valence band as the total available electron-filled charge states are reduced with the removal of oxygen vacancies. A reduction in charge states is corroborated by the observed lessening of both photoemission and photoluminescence intensities after laser dosing. The deduced position of the Fermi level is within a band of near-conduction band defect states produced by oxygen vacancies that are linked to endurance limiting leakage currents. Together, these results directly identify the primary role of oxygen vacancies on the defect states in HZO while demonstrating that laser exposure can be used for their modification.
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Elongating RNA polymerase II (Pol II) can be paused or arrested by a variety of obstacles. These obstacles include DNA lesions, DNA-binding proteins, and small molecules. Hairpin pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA in a sequence-specific manner and induce strong transcriptional arrest. Remarkably, this Py-Im–induced Pol II transcriptional arrest is persistent and cannot be rescued by transcription factor TFIIS. In contrast, TFIIS can effectively rescue the transcriptional arrest induced by a nucleosome barrier. The structural basis of Py-Im–induced transcriptional arrest and why TFIIS cannot rescue this arrest remain elusive. Here we determined the X-ray crystal structures of four distinct Pol II elongation complexes (Pol II ECs) in complex with hairpin Py-Im polyamides as well as of the hairpin Py-Im polyamides–dsDNA complex. We observed that the Py-Im oligomer directly interacts with RNA Pol II residues, introduces compression of the downstream DNA duplex, prevents Pol II forward translocation, and induces Pol II backtracking. These results, together with biochemical studies, provide structural insight into the molecular mechanism by which Py-Im blocks transcription. Our structural study reveals why TFIIS fails to promote Pol II bypass of Py-Im–induced transcriptional arrest.
The siderophore biosynthetic enzyme A (SidA) ornithine hydroxylase from Aspergillus fumigatus is a fungal disease drug target involved in the production of hydroxamate-containing siderophores, which are used by the pathogen to sequester iron. SidA is an N -monooxygenase that catalyzes the NADPH-dependent hydroxylation of l -ornithine through a multistep oxidative mechanism, utilizing a C4a-hydroperoxyflavin intermediate. Here we present four new crystal structures of SidA in various redox and ligation states, including the first structure of oxidized SidA without NADP(H) or l -ornithine bound (resting state). The resting state structure reveals a new out active site conformation characterized by large rotations of the FAD isoalloxazine around the C1–'C2' and N10–C1' bonds, coupled to a 10-Å movement of the Tyr-loop. Additional structures show that either flavin reduction or the binding of NADP(H) is sufficient to drive the FAD to the in conformation. The structures also reveal protein conformational changes associated with the binding of NADP(H) and l -ornithine. Some of these residues were probed using site-directed mutagenesis. Docking was used to explore the active site of the out conformation. These calculations identified two potential ligand-binding sites. Altogether, our results provide new information about conformational dynamics in flavin-dependent monooxygenases. Overall, understanding the different active site conformations that appear during the catalytic cycle may allow fine-tuning of inhibitor discovery efforts.
Comparative modelling of ion temperature gradient (ITG)/trapped electron mode (TEM) turbulence in negative (NT) and positive (PT) triangularity plasma shapes was done using the nonlinear global full-f gyrokinetic particle code JOREK-GK in the realistic X-point tokamak geometry including the Scrape Off Layer (SOL) for TCV and DIII-D parameters. A comparison of JOREK-GK code with the gyrokinetic codes GS2 and GENE was done using NT/PT triangularity TCV L-modes parameters showing good agreement between codes in linear growth rates and clear beneficial effect of NT as compared to PT. Global non-linear modelling of the ITG/TEM saturated turbulence for realistic DIII-D NT pulses was done and compared with numerically constructed PT equilibrium with the same plasma profiles. Existence of longer correlation length of density fluctuations in PT compared to NT was demonstrated. Stronger and more sheared zonal flows are generated via Reynolds stress in NT compared to PT. These factors are stabilizing for TEM/ITG turbulence in NT and lead to smaller heat fluxes and heat conductivities in NT compared to PT configuration. Weak dependence of plasma confinement on collisionality and plasma rotation was found in modelling of DIII-D NT shots similar to the experiment. The confinement scaling with normalized ion gyro-radius ρ* was estimated both for NT and PT. Bohm-like scaling was obtained in both configurations, however with better confinement for NT compared to PT which could be favourable factor for reactor size machines.
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Abstract A series of MD and DFT simulations were performed to investigate hydrogen self-clustering and retention in tungsten. Using a newly develop machine learned interatomic potential, spontaneous formation of hydrogen platelets was observed after implanting low-energy hydrogen into tungsten at high fluxes and temperatures. The platelets formed along low miller index orientations and neighboring tetrahedral and octahedral sites and could grow to over 50 atoms in size. High temperatures above 600 K and high hydrogen concentrations were needed to observe significant platelet formation. A critical platelet size of six hydrogen atoms was needed for long term stability. Platelets smaller than this were found to be thermally unstable within a few nanoseconds. To verify these observations, characteristic platelets from the MD simulations were simulated using large-scale DFT. DFT corroborated the MD results in that large platelets were also found to be dynamically stable for five or more hydrogen atoms. The LDOS from the DFT simulated platelets indicated that hydrogen atoms, particularly at the periphery of the platelet, were found to be at least as stable as hydrogen atoms in bulk tungsten. In addition, electrons were found to be localized around hydrogen atoms in the platelet itself and that hydrogen atoms up to 4.2 Å away within the platelet were found to share charge suggesting that the hydrogen atoms are interacting across longer distances than previously suggested. These results reveal a self-clustering mechanisms for hydrogen within tungsten in the absence of radiation induced or microstructural defects that could be a precursor to blistering and potentially explain the experimentally observed high hydrogen retention particularly in the near surface region.
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