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At least 451 records · Page 25

Stabilities of nitrogen containing heterocyclic radicals and geometrical influences on non-radiative processes in organic molecules

Stabilities of nitrogen containing heterocyclic radicals were studied to detect radicals of the type R-N-R, and to theoretically rationalize their electronic structure. The computation of simple potential energy surfaces for ground and excited states is discussed along with the photophysical properties of indolizine. Methods of calculation and problems associated with the calculations are presented. Results, tables, diagrams, discussions, and references are included.

Evleth, E. M.↗

Amorphous Carbon-Boron Nitride Nanotube Hybrids

A method for joining or repairing boron nitride nanotubes (BNNTs). In joining BNNTs, the nanotube structure is modified with amorphous carbon deposited by controlled electron beam irradiation to form well bonded hybrid a-C/BNNT structures. In repairing BNNTs, the damaged site of the nanotube structure is modified with amorphous carbon deposited by controlled electron beam irradiation to form well bonded hybrid a-C/BNNT structures at the damage site.

Kim, Jae Woo↗

Very high Mach number shocks - Theory

The theory and simulation of collisionless perpendicular supercritical shock structure is reviewed, with major emphasis on recent research results. The primary tool of investigation is the hybrid simulation method, in which the Newtonian orbits of a large number of ion macroparticles are followed numerically, and in which the electrons are treated as a charge neutralizing fluid. The principal results include the following: (1) electron resistivity is not required to explain the observed quasi-stationarity of the earth's bow shock, (2) the structure of the perpendicular shock at very high Mach numbers depends sensitively on the upstream value of beta (the ratio of the thermal to magnetic pressure) and electron resistivity, (3) two-dimensional turbulence will become increasingly important as the Mach number is increased, and (4) nonadiabatic bulk electron heating will result when a thermal electron cannot complete a gyrorbit while transiting the shock.

Quest, Kevin B.↗

Instrumentation and methods for efficient time-resolved X-ray crystallography of biomolecular systems with sub-10 ms time resolution

Time-resolved X-ray crystallography has great promise to illuminate structure–function relations and key steps of enzymatic reactions with atomic resolution. The dominant methods for chemically-initiated reactions require complex instrumentation at the X-ray beamline, significant effort to operate and maintain this instrumentation, and enormous numbers (∼10 5 –10 9 ) of crystals per time point. We describe instrumentation and methods that enable high-throughput time-resolved study of biomolecular systems using standard crystallography sample supports and mail-in X-ray data collection at standard high-throughput cryocrystallography synchrotron beamlines. The instrumentation allows rapid reaction initiation by mixing of crystals and substrate/ligand solution, rapid capture of structural states via thermal quenching with no pre-cooling perturbations, and yields time resolutions in the single-millisecond range, comparable to the best achieved by any non-photo-initiated method in both crystallography and cryo-electron microscopy. Our approach to reaction initiation has the advantages of simplicity, robustness, low cost, adaptability to diverse ligand solutions and small minimum volume requirements, making it well suited to routine laboratory use and to high-throughput screening. We report the detailed characterization of instrument performance, present structures of binding of N -acetylglucosamine to lysozyme at time points from 8 ms to 2 s determined using only one crystal per time point, and discuss additional improvements that will push time resolution toward 1 ms.

Indergaard, John A. (ORCID:000000022367699X)↗

Initial analysis of “stone” size Ryugu samples: current status

As a part of the initial analysis of the Ryugu samples, we perform a variety of analyses of millimeter-sized "stones". Our goals are to elucidate the entire formation process of C-type asteroid Ryugu from the viewpoint of petrology and mineralogy ande obtain necessary information by sample analysis, and then simulate the formation of Ryugu based on the evidencef obtained rom sample analysis. Eighteen stones (8 from Room A and 10 from Room C) were received from the ISAS curation facility on June 1, 2021, and brought into a fully nitrogen-displaced glove box at Tohoku University. At the same time, we also received the powder samples from Room A and Room C. To completely block the atmosphere from leaking into the container, all samples were put in the sample transport containers prepared by ISAS, transferred from the main chamber to the glovebox at ISAS, and then all containers were completely sealed in plastic bags with moisture and oxygen absorbers. No moisture or oxygen was detected when the bags were opened in the glove box at Tohoku University, so it was confirmed that there was no exposure to the atmosphere during transport. To date, a number of analyses have been carried out successfully and almost on schedule. The analysis started with the measurement of reflectance spectra, which are sensitive to atmospheric oxidation, hydroxylation, and adsorbed water. The visible, near-infrared, and mid-infrared reflectance spectra were measured while the samples were kept airtight. The spectra of powder samples and stone samples (as aggregates and as single stone) were successfully obtained. A major feature of the stone team's analysis is the use of synchrotron radiation facilities around the world. Since this analysis is non-destructive, stone samples whose reflectance spectra were measured were sent to KEK, SPring-8, ESRF (France), SOLEIL (France), DESY (Germany), and APS (USA). Using these synchrotron radiation facilities, high spatial resolution and sensitivity XRD, STXM, XANES, CT [1], IR-CT, FT-IR [2, 3], XRF, and Mössbauer analyses were performed. Most of the analyses were carried out under air-tight conditions on the stone samples and the particulates separated from the stone samples. These analyses allowed us to determine the three-dimensional distribution of minerals and elements, redox state, density and porosity of the stone samples. Furthermore, as a characteristic analysis of the stone team, light elemental analysis using negative Muon was performed at the MLF facility of J-PARC with an exceptionally long allocation of machine time. This is the only non-destructive method to measure the concentration of light elements in the whole (not the surface) of stone samples. Because the characteristic X-rays produced by muon irradiation are much higher in energy than the fluorescent X-rays produced by X-ray irradiation, there is little effect of self-absorption by the sample, and therefore, the concentration of light elements such as carbon, oxygen, and Na in the entire "stone" sample can be determined. Some stone samples are currently being measured for heat and strength physical properties in order to understand the physical properties of asteroid Ryugu. The data obtained from these measurements are useful for interpreting the remote-sensing data data taken from the surface layer of the asteroid Ryugu [4-7]. It is also important for understanding the behavior of the Ryugu material during impact events. The surfaces of many stone samples were observed by electron microscopy and other techniques, especially on natural “flat” surfaces formed on 5 stomes. As a result, characteristric mineral aggregates formed by the reactions with water and characteiristic impact features were observed on some of the samples. Based on the observations of surfaces and the synchrotron measurements of the whole stones, important objects such as characteristic structures and specific crystal aggregates for understanding the formation history of the asteroid were identified, and these parts were separated from the stone samples using an Xe beam (pFIB) and analyzed by various methods including transmission electron microscopy and synchrotron radiation analysis. Many stone samples, from which important objects have been separated, are embedded in epoxy resin and cut to produce many polished sections. Electron microscopy and spectroscopic measurements of the polished surfaces are being carried out to reveal the detailed mineralogical properties and elemental distribution inside the stone samples. In the fall, machine time for synchrotron radiation will begin, and we plan to analyze single crystals and characteristic objects separated from the stone samples.

Tomoki Nakamura↗

Accurate segmentation of localized corrosion in structural alloys via deep learning

This study presents a deep learning-based approach for the automated segmentation of corrosion damage in scanning electron microscopy (SEM) images. The proposed method enables rapid and accurate segmentation of corrosion features in these SEM images, making it highly suitable for real-time applications such as automated microscopy. Specifically, a dedicated corrosion segmentation database tailored for this task is constructed. The newly constructed dataset, alongside data from two public databases, are employed to jointly train a deep learning-based model modified with a texture refinement module. Compared to the same model without the texture refinement module, the refined model substantially enhances the efficacy and efficiency of corrosion segmentation. Furthermore, the methodology developed here is extendable to segmentation tasks for other materials with similar resolution, texture, and contrast characteristics, thereby paving the way for accelerated and automated analysis in corrosion science and beyond.

Artificial Intelligence↗

Visualization of Microbial Biomarkers by Scanning Electron Microscopy

We are developing tools to link the biochemical structure of selected biomarkers with putative biogenic structures observed in mineralized samples. The detection of evidence of life on Mars and other planets will rely on methods that can discriminate compounds formed exclusively by living organisms. While biogenic compounds, such as amino acids and nucleotides have been discovered in extraterrestrial sources, such as meteorites and comets, their formation can be explained by abiotic means. The formation of cellular structures, or more elaborate organic molecules, such as complex lipids, proteins or nucleic acids, however, is strongly correlated to the presence of even the most primitive life processes. Recent evidence lends support to the hypothesis that life may have once existed on Mars. Carbonate globules and ppm concentrations of polycyclic aromatic hydrocarbons (PAHs) have been described in ALH84001, a meteorite originating from Mars ejecta captured by Earth over 13,000 years ago. The localized high concentration of PAHs that follow an increasing gradient from the intact fusion crust towards the interior corresponds to microgram quantities of hydrocarbon. Even though ALH84001 and other similar meteorites have withstood the forces capable of ejecting rock through Mars' escape velocity, upon entering Earth's atmosphere, their core temperatures are likely not to have been raised significantly, as evidenced by the survival of remanent magnetic signatures. Ideal biomarkers of ancient or modern biological life would include molecules that are (or were) pervasive and highly resistant to degradation. Also, requisite methods of detection should be simple, extremely sensitive and broadly inclusive (NASA SP-530). Lipopolysaccharide (LPS), peptidoglycan or pseudopeptidoglycan and beta-glucan are microbial cell wall components which together cover the entire microbial spectrum of eubacteria, archea and fungi. They are all remarkably resistant to thermal degradation. Fortunately, many antimicrobial defense systems of higher organisms require sensitive detection to combat microbial pathogens. We employ here the primitive immune system of the evolutionarily ancient horseshoe crab, Limulus polyphemus. This species relies on multi-enzyme signal amplification detection of cell wall molecules and they can be applied to the development of useful detectors of life. An extension of this work includes the visualization of microbial signatures by labeling LAL components with chromogenic or electron dense markers. The protein Limulus Anti-LPS Factor (LALF) has an extremely high affinity for LPS. By coupling LALF binding with colloidal gold labels we demonstrate a correlation of the structures visible by electron microscopy with biochemical evidence of microbial cell wall materials. Pure silica particles were mixed with cultures of E. coli (10(exp 6) cfu/mL). Samples were washed sequentially with buffered saline, LALF, antibody to LALF and finally colloidal gold-labeled Protein A. Negative controls were not exposed to E. coli but received identical treatment otherwise. Samples were coated with carbon and imaged on a JEOL JSM-840 scanning electron microscope with LaB6 source in the back scatter mode with the JEOL annular back scatter detector. 20 nm-scale black spots in this contrast-reversed image originate from electrons back-scattered by gold atoms. Negative controls did not give any signal. Future work will expand application of this technique to soil simulants and mineralized rock samples.

Wainwright, Norman R.↗

Soft X-Ray Tomography Has Evolved into a Powerful Tool for Revealing Cell Structures

Over the past three decades, soft X-ray tomography (SXT) has rapidly evolved from a proof-of-concept microscopy method into a high-throughput quantitative imaging modality. This advancement enables researchers to address central questions in cell biology. Despite its relatively short developmental period compared to light and electron microscopy, SXT has emerged as a powerful imaging technology. It enables measuring chemical changes in cellular organelles, analyzing three-dimensional structures of whole cells and creating digital cellular models to study cell motility. We discuss the unique nature of SXT to visualize cells without fixation or labeling, enabling quantitative analyses of organelle chemical composition. We explore SXT microscopes available worldwide, SXT segmentation software, and the diverse cell types studied using this technique. We conclude with emerging directions in SXT imaging, including a brief discussion of recent discoveries that are highly influential and likely to become integral to cell biology textbooks.

Weinhardt, Venera↗

Instrumentation for Studies of Electron Emission and Charging From Insulators

Making measurements of electron emission properties of insulators is difficult since insulators can charge either negatively or positively under charge particle bombardment. In addition, high incident energies or high fluences can result in modification of a material s conductivity, bulk and surface charge profile, structural makeup through bond breaking and defect creation, and emission properties. We discuss here some of the charging difficulties associated with making insulator-yield measurements and review the methods used in previous studies of electron emission from insulators. We present work undertaken by our group to make consistent and accurate measurements of the electron/ion yield properties for numerous thin-film and thick insulator materials using innovative instrumentation and techniques. We also summarize some of the necessary instrumentation developed for this purpose including fast response, low-noise, high-sensitivity ammeters; signal isolation and interface to standard computer data acquisition apparatus using opto-isolation, sample-and-hold, and boxcar integration techniques; computer control, automation and timing using Labview software; a multiple sample carousel; a pulsed, compact, low-energy, charge neutralization electron flood gun; and pulsed visible and UV light neutralization sources. This work is supported through funding from the NASA Space Environments and Effects Program and the NASA Graduate Research Fellowship Program.

Thomson, C. D.↗

Hydride and Seek: Comparing Crystallographic Hydride Placement Techniques with an Open-Shell Cobalt Complex

Locating hydrides is crucial in organometallic chemistry but difficult to do accurately using X-ray diffraction. Electron diffraction has been proposed as a way to overcome this problem but has not been systematically compared to neutron diffraction and to quantum crystallography (Hirshfeld atom refinement, HAR) to test this hypothesis. Here, we present a comparative analysis of methods for a terminal cobalt hydride complex by comparing a single-crystal neutron diffraction reference structure to results from single-crystal X-ray diffraction with and without Hirshfeld atom refinement (HAR, NoSpherA2), density functional theory (DFT), and electron diffraction (3D-ED/MicroED) refined under kinematical and dynamical formalisms. Conventional X-ray diffraction gives lower precision than neutron diffraction as expected. Despite expected improvements, HAR gives systematic deviation from the neutron benchmark. Interestingly, optimized DFT equilibrium geometries are closer to the neutron value than the value from HAR. On the other hand, electron diffraction with a high-quality data set coupled with dynamical refinement localizes the hydride in difference maps and gives excellent agreement with the neutron data. Dynamical refinement is crucial, as kinematical refinement does not allow assignment of a hydride peak. This cross-modal comparison defines the conditions under which 3D-ED/MicroED delivers high-precision metal–hydride distances for this open-shell cobalt hydride.

anions↗

Three-dimensional hard X-ray ptychographic reflectometry imaging on extended mesoscopic surface structures

Many nanodevices and quantum devices, with their sizes often spanning from millimeters down to sub-nanometer, have intricate low-dimensional, non-uniform, or hierarchical structures on surfaces and interfaces. Since their functionalities are dependent on these structures, high-resolution surface-sensitive characterization becomes imperative to gain a comprehensive understanding of the function–structure relationship. We thus developed hard x-ray ptychographic reflectometry imaging, a new technique that merges the high-resolution two-dimensional imaging capabilities of hard x-ray ptychography for extended objects, with the high-resolution depth profiling capabilities of x-ray reflectivity for layered structures. The synergy of these two methods fully leverages both amplitude and phase information from ptychography reconstruction to not only reveal surface topography and localized structures, such as shapes and electron densities, but also yields statistical details, such as interfacial roughness that is not readily accessible through coherent imaging solely. The hard x-ray ptychographic reflectometry imaging is well-suited for three-dimensional imaging of mesoscopic samples, particularly those comprising planar or layered nanostructures on opaque supports, and could also offer a high-resolution surface metrology and defect analysis on semiconductor devices, such as integrated nanocircuits and lithographic photomasks for microchip fabrications.

47 OTHER INSTRUMENTATION↗

Ion and electron temperatures in the SUMMA mirror device by emission spectroscopy

Ion and electron temperatures, and ion drift were measured in a superconducting magnetic mirror apparatus by observing the Doppler-broadened charge-exchange component of the 667.8 and 587.6 nanometer He lines in He plasma, and the H sub alpha and H sub beta lines in H2 plasma. The second moment of the line profiles was used as the parameter for determining ion temperature. Corrections for magnetic splitting, fine structure, monochromator slit function, and variation in charge-exchange cross section with energy are included. Electron temperatures were measured by the line ratio method for the corona model, and correlations of ion and electron temperatures with plasma parameters are presented.

Patch, R. W.↗

Structure and properties of solid surfaces

Difficulties in experimental studies of crystalline surfaces are related to the fact that surface atoms have an intrinsic tendency to react with their environment. A second problem is connected with the effective thickness of surfaces, which ranges from one to several atom layers. The phenomenology of surface interactions with gases are considered, taking into account physical adsorption, chemisorption, and the oxidation of surfaces. Studies of the surface structure are discussed, giving attention to field emission microscopy, field-ion microscopy, electron diffraction techniques, Auger spectroscopy, scanning electron microscopy, electron probe microanalysis, ion microprobe methods, and low-energy backscattering spectroscopy. Investigations of semiconductor surfaces are also described.

Gatos, H. C.↗

Calculation of electrostatic fields in periodic structures of complex shape

A universal algorithm is presented for calculating electrostatic fields in an infinite periodic structure consisting of electrodes of arbitrary shape which are located in mirror-symmetrical manner along the axis of electron-beam propagation. The method is based on the theory of R-functions, and the differential operators which are derived on the basis of the functions. Numerical results are presented and the accuracy of the results is examined.

Kravchenko, V. F.↗

Removing Basis Set Incompleteness Error in Finite-Temperature Electronic Structure Calculations: Two-Electron Systems

We investigate the basis-set-size dependence for quantities related to interacting electrons in the canonical ensemble. Calculations are performed using exact diagonalization (finite temperature full configuration interaction method) on two-electron model systems–the uniform electron gas (UEG) and the helium atom. Our data reproduce previous observations of a competition for how the internal energy converges between the ground-state correlation energy and the high-temperature kinetic energy. We explore how this can be related to component parts of the internal energy including kinetic, exchange, and correlation energies and show there is surprising nuance in how this can be broken down into mostly monotonically converging quantities. We also show that separation of the free energy into a free energy with/without correlation allows for monotonic convergence with basis set size due to the variational principle. We find that the free energy convergence matches the previously observed convergence properties of the internal energy. We discuss the free energy divergence that happens when converging a finite basis analytical hydrogen atom to the complete basis set limit and compare this to the energies of a helium atom in a large periodic box. Reducing the box size, we saw convergence trends for the helium atom that were similar to the UEG.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Charge-induced atomic strain as a predictor of structural phase transformation in rare-earth intermetallics

We present a descriptor based on charge-induced atomic strain in crystalline lattices for predicting structural phase transformations in rare-earth intermetallic compounds containing lanthanides and transition metals. The charge-induced local atomic strain was obtained from structural optimization of experimentally known crystalline phases using state of the art density-functional theory methods. The predictive power of the descriptor was evaluated on 𝑅⁢𝐸 2 ⁢In (𝑅𝐸 = rare earth) compounds, a class known for diverse phase transformations. We show that incorporating quantum-mechanical effects—such as local charge distribution, bonding, symmetry, and electronic structure—enhances the robustness of the descriptor. To gain further insight, we analyzed phononic and electronic behavior in Y 2 ⁢In and demonstrated that experimental phase transformations are captured only when atomic strain effects are included. The descriptor was further used to predict structural phase changes in (Y⁢b 1–𝑥 ⁢E⁢r 𝑥 ) 2 ⁢In and G⁡d 2 ⁡(I⁢n 1–𝑥⁢ A⁢l 𝑥 ), with predictions confirmed by x-ray powder diffraction. Here, while the current study is focused on lanthanide-based intermetallics, the underlying principles of the descriptor suggest potential applicability to other closely related classes of rare-earth intermetallics.

Density functional theory↗

Quantitative x-ray scattering of free molecules

Advances in x-ray free electron lasers have made ultrafast scattering a powerful method for investigating molecular reaction kinetics and dynamics. Accurate measurement of the ground-state, static scattering signals of the reacting molecules is pivotal for these pump-probe x-ray scattering experiments as they are the cornerstone for interpreting the observed structural dynamics. Here, this article presents a data calibration procedure, designed for gas-phase x-ray scattering experiments conducted at the Linac Coherent Light Source x-ray Free-Electron Laser at SLAC National Accelerator Laboratory, that makes it possible to derive a quantitative dependence of the scattering signal on the scattering vector. A self-calibration algorithm that optimizes the detector position without reference to a computed pattern is introduced. Angle-of-scattering corrections that account for several small experimental non-idealities are reported. Their implementation leads to near quantitative agreement with theoretical scattering patterns calculated with ab-initio methods as illustrated for two x-ray photon energies and several molecular test systems.

74 ATOMIC AND MOLECULAR PHYSICS↗

From Oxo to Oxyl to Biradical: Systematic Multireference Calculations of Methane Activation at MOF Nodes

Methane C–H activation at transition-metal sites often involves electronic structures that challenge conventional single-reference electronic structure descriptions. Although Kohn–Sham density functional theory (DFT) is widely used to study catalytic trends, its reliability for reactions involving strongly correlated species remains uncertain. Here we present a systematic multireference investigation of methane activation at metal–organic framework (MOF) node catalysts across the 3d transition-metal series. We introduce an automated workflow for active space selection to enable consistent application of multireference methods, including multiconfiguration pair-density functional theory and n-electron valence state perturbation theory, to these catalytic systems. These calculations show substantial static correlation in the C–H activation reaction step and predict activation barriers that differ from DFT by 30–70 kJ mol–1, with DFT often qualitatively disagreeing in barrier height trends across transition metals. Analysis of multireference wave functions shows that reactivity is governed by the electronic structure of the M–O moiety along a continuum from metal–oxo to oxyl radical and O biradical character. Increased oxygen-centered spin density and weakened M–O bonding are identified as descriptors of catalytic activity which correlate with lower activation barriers.

Wardzala, Jacob↗