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At least 1,297 records · Page 72
All sourcesNASA NTRSDOE OSTI
NASA NTRS1999

Both necrosis and apoptosis contribute to HIV-1-induced killing of CD4 cells

BACKGROUND: Data currently available on HIV-1-induced cytopathology is unclear regarding the mechanism of cell killing. OBJECTIVE: To clarify the extent to which apoptosis or necrosis is involved in HIV-1-induced cell death in view of conflicting existing data. METHODS: T lymphoblastoid cells or peripheral blood mononuclear cells were infected by various strains of HIV-1 and the numbers of apoptotic or necrotic cells were quantified at various times after infection using video-image analysis techniques; the results were compared with the amount of fragmented DNA using a quantitative method. Measurement of mitochondrial transmembrane potential (deltapsi(m)) and intracellular calcium concentrations [Ca2+]i was performed with fluorescent probes and fluorescence concentration analysis (FCA). RESULTS: Although lymphoblastoid and monocytoid cells acutely infected by HIV-1 had increased levels of fragmented DNA, a marker of apoptotic cell death, few (<12%) had condensed chromatin and fragmented nuclei, the morphological features of apoptosis. The predominant alterations in acutely infected cells were distended endoplasmic reticulum and abnormal mitochondria; these ultrastructural changes are consistent with necrosis, although some infected cells simultaneously displayed features of both necrosis and apoptosis. Viability of cells persistently infected by HIV-1 was only minimally reduced from that of uninfected cells. This reduction was accounted for by an increased propensity of the persistently infected cells to die by apoptosis. Alterations in [Ca2+]i and deltapsi(m) occurred in both acutely and persistently infected cells. CONCLUSION: Both necrosis and apoptosis contribute to HIV-1-induced killing of CD4 cells.

Non-NASA Center↗
DOE OSTI2025

Meso-scale modeling of UO2 nuclear fuel to high burnup

To improve the economics of light water reactors for commercial nuclear energy generation, utility operators are seeking to obtain regulatory approval to run UO2 fuel to higher levels of burnup. One potential impediment to obtaining this approval is the phenomenon of fuel fragmentation, relocation, and dispersal (FFRD). FFRD can result when fuel experiences a rapid temperature transient, such as that occurring during a Loss Of Coolant Accident (LOCA). FFRD has historically been most associated with the rim region in UO2 fuel pellets, where the phenomenon of fragmentation is also referred to as pulverization due to the small size of the fragments. More recent evidence suggests that the so-called “dark zone” (due to its appearance in micrographs) that can be observed in the mid-radial regions of high burnup fuel is also susceptible to FFRD. Although empirical fuel performance models have been developed that can adequately predict pulverization in the rim region under typical LWR conditions, a scientific understanding of what underlies fuel restructuring and subsequent FFRD is lacking even in the rim region, and no models are currently available for the behavior the dark zone. To address these challenges, the U.S. Department of Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program has employed a multi-scale modeling approach to improve scientific understanding and develop new fuel performance models. In this talk, I will focus on meso-scale efforts, which form a crucial link between atomic-scale and engineering-scale models. Phase-field modeling combined with cluster dynamics is used to predict the restructuring process in the rim region. Phase-field fracture modeling, informed by atomistic simulations, is used to predict the onset of pulverization in the rim region. Combining these techniques together allows the extent of rim pulverization to be predicted. The formation and evolution of the dark zone has also been simulated with the phase-field method, using an improved approach to vacancy source term parameterization. The work shows the important impact of microstructure on fuel performance.

fracture↗
DOE OSTI2023

Are Phosphatidic Acids Ubiquitous in Mammalian Tissues or Overemphasized in Mass Spectrometry Imaging Applications?

Abstract Mass spectrometry imaging (MSI) is an invaluable tool for the spatial visualization of molecules in vivo. However, the question of whether observed annotations are endogenous or artificial (i. e., from in‐source fragmentation) is critical and has been largely unexplored in multimodal MSI. In matrix‐assisted laser desorption/ionization (MALDI)‐MSI datasets from researchers worldwide, PAs were found to represent up to 18 % of annotations in rat brain. Rat brain was additionally imaged here using nanospray desorption electrospray ionization (nano‐DESI), a softer ionization strategy. No PAs observed with MALDI were present in the nano‐DESI dataset. Further investigation strongly indicated lipid fragmentation to PAs for MALDI‐MSI, but not with nano‐DESI‐MSI. We finally extend this observation to the MALDI‐MSI analyses of human tissues, showing that PA annotations comprised up to 16 % of annotations. Therefore, this study shows that MSI annotations should be carefully interrogated, as in‐source fragmentation or modification of lipids may contribute substantially to false annotations and incorrect biological interpretations.

Vandergrift, Gregory W.↗
DOE OSTI2022

Position-specific carbon isotope analysis of serine by gas chromatography/Orbitrap mass spectrometry, and an application to plant metabolism

Position-specific 13 C/ 12 C ratios within amino acids remain largely unexplored in environmental samples due to methodological limitations. We hypothesized that natural-abundance isotope patterns in serine may serve as a proxy for plant metabolic fluxes including photorespiration. Here we describe an Orbitrap method optimized for the position-specific carbon isotope analysis of serine to test our hypothesis and discuss the generalizability of this method to other amino acids. Position-specific carbon isotope ratios of serine were measured using a Thermo Scientific™ Q Exactive™ GC Orbitrap™. Amino acids were hydrolyzed from Arabidopsis biomass, purified from potential matrix interferences, and derivatized alongside standards. Derivatized serine (N,O-bis(trifluoroacetyl)methyl ester) was isolated using gas chromatography, trapped in a reservoir, and purged into the electron ionization source over tens of minutes, producing fragment ions containing different combinations of atoms from the serine-derivative molecule. The 13 C/ 12 C ratios of fragments with monoisotopic masses of 110.0217, 138.0166, and 165.0037 Da were monitored in the mass analyzer and used to calculate position-specific δ 13 C values relative to a working standard. This methodology constrains position-specific δ 13 C values for nanomole amounts of serine isolated from chemically complex mixtures. The δ 13 C values of fragment ions of serine were characterized with ≤1‰ precisions, leading to propagated standard errors of 0.7–5‰ for each carbon position. Position-specific δ 13 C values differed by up to ca 28 ± 5‰ between serine molecules hydrolyzed from plants grown under contrasting pCO 2 , selected to promote different fluxes through photosynthesis and photorespiration. The method was validated using pure serine standards characterized offline. Here this study presents the first Orbitrap-based measurements of natural-abundance, position-specific carbon isotope variation in an amino acid isolated from a biological matrix. We present a method for the precise characterization of isotope ratios in serine and propose applications probing metabolism in plants. We discuss the potential for extending these approaches to other amino acids, paving the way for novel applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Next-to-next-to-leading power corrections to unpolarized Semi-Inclusive Deep Inelastic Scattering

Semi-Inclusive Deep Inelastic Scattering (SIDIS) is a key tool for exploring the three-dimensional structure of the nucleon through Transverse Momentum Dependent parton distributions and fragmentation functions. While leading-power contributions to the SIDIS cross-section are well established, next-to-leading power (NLP) corrections of order 1/Q and next-to-next-to-leading power (NNLP) corrections of order 1/Q 2 to the hadronic tensor have only recently begun to be systematically investigated. These corrections are essential for reliable phenomenology and interpretation of modern high-precision data. In recent papers by one of the authors, NNLP corrections to the Drell-Yan process were derived using the rapidity factorization formalism. In the present work, we extend this approach to SIDIS and obtain analytic expressions for the unpolarized structure functions. We derive NNLP corrections that include convolutions of unpolarized distributions, f 1 , with unpolarized fragmentation functions, D 1 , and Boer-Mulders functions, ${h}_1^{\perp }$, with Collins fragmentation functions, ${H}_1^{\perp }$. We compare our results with previous formulations, provide numerical studies, confront our predictions with HERMES and COMPASS measurements, and present predictions for future experiments at Jefferson Lab and the Electron-Ion Collider.

deep inelastic scattering↗
DOE OSTI2021

Mafic explosive volcanism at Llaima Volcano: 3D x-ray microtomography reconstruction of pyroclasts to constrain shallow conduit processes

Abstract Mafic volcanic activity is dominated by effusive to mildly explosive eruptions. Plinian and ignimbrite-forming mafic eruptions, while rare, are also possible; however, the conditions that promote such explosivity are still being explored. Eruption style is determined by the ability of gas to escape as magma ascends, which tends to be easier in low-viscosity, mafic magmas. If magma permeability is sufficiently high to reduce bubble overpressure during ascent, volatiles may escape from the magma, inhibiting violent explosive activity. In contrast, if the permeability is sufficiently low to retain the gas phase within the magma during ascent, bubble overpressure may drive magma fragmentation. Rapid ascent may induce disequilibrium crystallization, increasing viscosity and affecting the bubble network with consequences for permeability, and hence, explosivity. To explore the conditions that promote strongly explosive mafic volcanism, we combine microlite textural analyses with synchrotron x-ray computed microtomography of 10 pyroclasts from the 12.6 ka mafic Curacautín Ignimbrite (Llaima Volcano, Chile). We quantify microlite crystal size distributions (CSD), microlite number densities, porosity, bubble interconnectivity, bubble number density, and geometrical properties of the porous media to investigate the role of magma degassing processes at mafic explosive eruptions. We use an analytical technique to estimate permeability and tortuosity by combing the Kozeny-Carman relationship, tortuosity factor, and pyroclast vesicle textures. The groundmass of our samples is composed of up to 44% plagioclase microlites, > 85% of which are < 10 µm in length. In addition, we identify two populations of vesicles in our samples: (1) a convoluted interconnected vesicle network produced by extensive coalescence of smaller vesicles (> 99% of pore volume), and (2) a population of very small and completely isolated vesicles (< 1% of porosity). Computed permeability ranges from 3.0 × 10 −13 to 6.3 × 10 −12 m 2 , which are lower than the similarly explosive mafic eruptions of Tarawera (1886; New Zealand) and Etna (112 BC; Italy). The combination of our CSDs, microlite number densities, and 3D vesicle textures evidence rapid ascent that induced high disequilibrium conditions, promoting rapid syn-eruptive crystallization of microlites within the shallow conduit. We interpret that microlite crystallization increased viscosity while simultaneously forcing bubbles to deform as they grew together, resulting in the permeable by highly tortuous network of vesicles. Using the bubble number densities for the isolated vesicles (0.1-3 −3 × 10 4 bubbles per mm 3 ), we obtain a minimum average decompression rate of 1.4 MPa/s. Despite the textural evidence that the Curacautín magma reached the percolation threshold, we propose that rapid ascent suppressed outgassing and increased bubble overpressures, leading to explosive fragmentation. Further, using the porosity and permeability of our samples, we estimated that a bubble overpressure > 5 MPa could have been sufficient to fragment the Curacautín magma. Other mafic explosive eruptions report similar disequilibrium conditions induced by rapid ascent rate, implying that syn-eruptive disequilibrium conditions may control the explosivity of mafic eruptions more generally.

Valdivia, Pedro↗
DOE OSTI2020

Intramolecular 13 C isotope distributions of butane from natural gases

A single-step method allowing the measurement of 13 C intramolecular distribution of butane isomers (n- and i-butane) from natural gas samples was developed. The method builds up on the one that has been developed for propane, using on-line pyrolysis followed by isotope analysis of the pyrolytic fragments. The isotopic filiation between n-butane and its pyrolytic fragments was elucidated using samples spiked with 13 C on terminal positions. The isotopic filiation for i-butane could not be shown experimentally due to the lack of commercially available enriched i-butane. We thus used a recent model named Reaction Mechanism Generator (RMG) to assess the origin of the fragments arising from i-butane pyrolysis. Butanes from natural gas samples from the Carnarvon Basin (Australia) and the Arkoma Basin (USA) were analyzed. The results are consistent with a model for thermogenic natural gas generation and suggest that combined intramolecular isotope composition of propane and n-butane can be related to the gas maturity. In addition, the method allows the detection and shed light on the mechanism of n-butane and i-butane biodegradation in natural gas reservoirs.

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

Losses of CO and CO 2 upon collision-activated dissociation of substituted 2-methoxyphenoxides after methyl radical loss

Some deprotonated, substituted 2-methoxyphenols fragment by methyl radical loss followed by competing losses of CO and CO 2 upon collisional activation in linear quadrupole ion trap mass spectrometers. These reactions were examined experimentally and computationally in order to determine their mechanisms. For deprotonated vanillin, the CO loss was found to involve ring contraction, with the highest free energy barrier of 58.0 kcal mol -1 (for the syn rotamer; here, syn refers to the relationship between the aldehyde oxygen atom and the oxygen atom of the methoxy group) for the entire process. The atoms lost in this fragmentation are the oxygen atom that was bound to the first eliminated methyl group and the aromatic carbon atom bound to this oxygen. Examination of carbon-13 labeled vanillin supports these assignments. Examination of several model compounds revealed that this reaction requires the presence of an electron-withdrawing substituent in the para-position relative to the phenol moiety. In contrast, the CO 2 loss from deprotonated vanillin occurs via ring opening followed by re-cyclization and then ring contraction, leading to the loss of CO 2 in a process wherein the highest free energy barrier is 84.5 kcal mol -1 (for the syn isomer). The atoms lost in this fragmentation are the carbon and oxygen atoms from the phenoxide group and the oxygen atom that was bound to the first eliminated methyl group, which is supported by examination of carbon-13 labeled vanillin. Despite the higher total free energy requirement, the CO 2 loss is competitive with CO loss, possibly due to favorable entropy and low activation energy (free energy barrier of 48.9 kcal mol -1 ) for the first reaction step (the analogous value for CO loss is 58.0 kcal mol -1 ). The extent of CO 2 loss is strongly affected by substituents – it either is not observed or is very slow for the other compounds studied here. For example, it is substantially less favorable than CO loss (highest free energy barrier 60.9 kcal mol -1 ) for deprotonated acetovanillone for which the first reaction step for CO 2 loss has a substantially greater free energy barrier (60.6 kcal mol-1) than for vanillin.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

High-burnup fuel stress analysis prior to and during a LOCA transient

High-burnup fuel fragmentation and pulverization have been experimentally observed during simulated loss-of-coolant accident (LOCA) transient testing of high-burnup (>62 GWd/tU) nuclear fuel. The cause of this phenomenon is generally accepted to be the formation of stresses arising from the off-normal conditions. However, the primary mechanism(s) contributing to the stress formation is/are still being debated. Leading hypotheses suggest that the concurrence of fission gas bubbles and high burnup structure on the pellet periphery (i.e., the rim) leave the fuel susceptible to pulverization. Other hypotheses suggest that pulverization is artificially inflated during externally heated tests that do not reproduce prototypic fuel stresses and radial temperature profiles as the fuel transitions from full-power nuclear heating to decay heating. This work performs finite element analyses of fuel pellet temperatures and macroscopic stresses prior to and during a LOCA transient to identify (1) operating conditions that may exacerbate the fuel pellet stress state, (2) differences in predicted stresses with nuclear vs. furnace heating, and (3) how fuel cracking impacts the subsequent stress state in the pellet fragments. Analyses predict that macroscopic transient fuel stresses resulting from constrained thermal expansion will remain below the fracture stress of fresh UO 2 once the fragment size reaches ~4 mm or less. Calculated fuel stresses from simulated LOCA tests performed with representative nuclear vs. electrical heating rates are shown to be equal within 5% and essentially unchanged for all times after the first 27 seconds of the transients. Because the fuel stresses do not change once the temperature profile becomes uniform, macroscopic transient stresses would be no different than those following a normal shutdown. Because pulverization of high burnup fuel does not occur prior to a LOCA test, pulverization of high burnup UO 2 cannot be initiated by differential thermal stresses.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Stopping Force Analysis of 235 U Elemental Fission Product Yields for $E_n$ = 0.11–92.4 MeV

We report most evaluated elemental fission product yield distributions are not experimentally measured. Instead, the majority of evaluated distributions are based on analytic expressions of the Zp-model for relevant cumulative yields. Here we report independent elemental fission product yield distributions of a 235 U target for incident neutron energies ranging from 0.11 MeV through 92.4 MeV. Atomic numbers are calculated by an approach that combines a 2E analysis with a stopping force analysis method, developed within this paper. These analyses are applied to more than 6.1 × 10 6 fission fragment ionization tracks captured within the NIFFTE (Neutron Induced Fission Fragment Tracking Experiment) collaboration fission time projection chamber (fissionTPC). A 3-Z resolution was obtained with the fissionTPC spatial and energy resolutions. Tabulated results are presented for the atomic yield and experimentally derived Zp values as a function of pre-neutron-emission fragment masses for the complete range of incident neutron energies. The stopping-force-derived Zp values tend to support the unchanged charge distribution theory within uncertainty.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Development and demonstration of a methodology to evaluate high burnup fuel susceptibility to pulverization under a loss of coolant transient

For economic reasons, the US nuclear industry is renewing efforts to build a technical basis to extend rod average burnup limits above the current regulatory burnup limit of 62 GWd/MTU. The primary driver is to increase pressurized water reactor cycle lengths to 24 months, reducing the number of fresh fuel assemblies and core design constraints, thereby making core energy utilization more efficient. However, fuel pellet fragmentation and pulverization, termed high burnup fuel fragmentation (HBFF), has been observed in the high burnup (>90 GWd/MTU) Halden loss-of-coolant-accident (LOCA) integral test series. The issue gained attention when fuel fragmentation and pulverization were also observed closer to the current US regulatory limit during the US Nuclear Regulatory Commission (NRC) sponsored out-of-core integral test at Studsvik Nuclear in early 2011. This led to NRC concerns with potential changes to fuel and core designs relative to fuel pellet pulverization. In a letter to the NRC Commissioners, the staff specifically identified a need to “…define the boundary of safe operation for key fuel design and operating parameters,” stating that “the staff is challenged to evaluate the acceptability of future fuel design advancements and fuel utilization changes.” As such, it can be concluded that HBFF and potential dispersal into the reactor coolant system introduces additional complications in light-water reactor (LWR) fuel safety evaluations. However, it is not clear how much fuel will be susceptible to HBFF; nor has there been a methodology developed to evaluate fuel susceptibility to HBFF. To that end, this paper proposes an analysis methodology to assess fuel susceptibility to HBFF during LOCA scenarios. The work presented here uses the BISON fuel performance code to evaluate a representative pressurized water reactor fuel rod exposed to a rod average burnup of 75 GWd/MTU. Sensitivity studies investigated the impact of the peak cladding temperature, transient fission gas released, and pre-transient fission gas release on cladding ballooning and burst timing. Subsequently, a methodology to assess fuel susceptibility to HBFF will be developed based on experimental data published in the open literature. The methodology will then be demonstrated by calculating the mass of fuel susceptibility to HBFF. The BISON results conclude that increasing peak cladding temperature drastically decreased time to failure, and decreased balloon size both of which have been confirmed experimentally. Additionally, the effect of pre-transient and transient fission gas release affected cladding balloon size and burst timing. Finally, fuel susceptibility to HBFF significantly decreased as a function of peak cladding temperature.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Impact of LWR assembly structural features on cladding burst behavior under LOCA conditions

This provides an initial scoping study on clad balloon and burst behavior for burnup extension of reactor fuel. The associated issues with burnup extension are fuel fragmentation, relocation, and dispersal in the event of cladding failure. The general finding of this work is that the structural features, spacer grids and mixing vanes, locally suppress cladding deformation but have little impact on the overall clad performance during loss-of-coolant accidents. The work detailed in a previous report by Capps et al. focused on core optimization via neutronics, thermal hydraulics and thermomechanical analysis for burnups beyond 62 GWD/tU and enrichments above 5%. Uncertainty of fuel fragmentation relocation and dispersal in high-burnup rods during accident conditions was also investigated. The dispersal aspect of fuel fragmentation depends on cladding rupture. Thus, assessing uncertainties in the rupture behavior is helpful in estimating the dispersal of high-burnup fuel. This study builds on the previous work by assessing the impact of assembly structural features on cladding balloon and burst behavior in a full-length fuel rod. In this work, the BISON fuel performance code was used to generate 2D radial and height meshes containing structural features commonly used in nuclear fuel assemblies. First, meshes were generated with spacer grids. Results were then compared to the cladding burst temperature and balloon strain results from the previous work. A mesh sensitivity study was performed to ensure that mixing vanes and spacer grid effects were appropriately considered, resulting in a more refined mesh than the previous study. The balloon deformation and burst times of the cladding were compared to the original case. Consideration was also given to the effect of rod initial pressure. In conclusion, 3D quarter rod simulations were also performed and found good agreement with the 2D simulations in clad deformation and reasonable agreement in burst times.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Controlling the Interface between Salts, Solvates, Co-crystals, and Ionic Liquids with Non-stoichiometric Protic Azolium Azolates [Plus Supporting Information]

In this work, a non-stoichiometric approach to control the solid-state behavior of protic ionic liquids (PILs) was demonstrated by direct mixing of 4,5-dicyanoimidazole (HDCNim) with either 1-ethylimidazole (C 2 im) or 1-butylimidazole (C 4 im) in different mole fractions. Isolation and characterization of three crystalline materials (all having melting points < 100 °C, thus fitting the PIL definition) revealed three different but closely related systems. The structure of [HC 2 im][DCNim] consists of a confused proton system, which is so named for the fast proton exchange between basic and acidic fragments and the formation of hydrogen-bonded anionic oligomers. The compound [HC 2 im][DCNim]·HDCNim consists of an oligomeric delocalized anion (a confused proton located between two azole fragments, in which one acts as a neutral moiety while the other as an ionic fragment, DCNim-H-DCNim) and [HC 4 im][DCNim]·HDCNim can be classified as a salt co-crystal. We believe that these observations will allow a deeper understanding of the behavior of “confused protons” and provide additional strategies for controlling the properties of important classes of materials such as active pharmaceutical ingredients.

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

Forces from Stochastic Density Functional Theory under Nonorthogonal Atom-Centered Basis Sets

We develop a formalism for calculating forces on the nuclei within the linear-scaling stochastic density functional theory (sDFT) in a nonorthogonal atom-centered basis set representation (Fabian et al. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2019, 9, e1412, 10.1002/wcms.1412) and apply it to the Tryptophan Zipper 2 (Trp-zip2) peptide solvated in water. We use an embedded-fragment approach to reduce the statistical errors (fluctuation and systematic bias), where the entire peptide is the main fragment and the remaining 425 water molecules are grouped into small fragments. We analyze the magnitude of the statistical errors in the forces and find that the systematic bias is of the order of 0.065 eV/Å (~1.2 × 10 -3 E h / a 0 ) when 120 stochastic orbitals are used, independently of system size. This magnitude of bias is sufficiently small to ensure that the bond lengths estimated by stochastic DFT (within a Langevin molecular dynamics simulation) will deviate by less than 1% from those predicted by a deterministic calculation.

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

Revisiting Artifacts of Kohn–Sham Density Functionals for Biosimulation

We revisit the problem of unphysical charge density delocalization/fractionalization induced by the self-interaction error of common approximate Kohn–Sham (KS) density functional theory functionals on simulation of small to medium-sized proteins in a vacuum. Aside from producing unphysical electron densities and total energies, the vanishing of the HOMO–LUMO gap associated with the unphysical charge delocalization leads to an unphysical low-energy spectrum and catastrophic failure of most popular solvers for the KS self-consistent field (SCF) problem. We apply a robust quasi-Newton SCF solver to obtain solutions for some of these difficult cases. The anatomy of the charge delocalization is revealed by the natural deformation orbitals obtained from the density matrix difference between the Hartree–Fock and KS solutions; the charge delocalization not only can occur between charged fragments (such as in zwitterionic polypeptides) but also involves neutral fragments. The vanishing-gap phenomenon and troublesome SCF convergence are both attributed to the unphysical KS Fock operator eigenspectra of molecular fragments (e.g., amino acids or their side chains). Analysis of amino acid pairs suggests that the unphysical charge delocalization can be partially ameliorated by the use of some range-separated hybrid functionals but not by semilocal or standard hybrid functionals. Last, we demonstrate that solutions without the unphysical charge delocalization can be located even for semilocal KS functionals highly prone to such defects, but such solutions have non-Aufbau character and are unstable with respect to mixing of the non-overlapping “frontier” orbitals. Caution should be exercised when unexpectedly small (or vanishing) HOMO–LUMO gaps and atypical SCF convergence patterns (e.g., oscillatory) are observed in KS DFT simulations in any context (bio or otherwise).

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

Quantum Molecular Charge-Transfer Model for Multistep Auger–Meitner Decay Cascade Dynamics

The fragmentation of molecular cations following inner-shell decay processes in molecules containing heavy elements underpins the X-ray damage effects observed in X-ray scattering measurements of biological and chemical materials, as well as in medical applications involving Auger electron-emitting radionuclides. Traditionally, these processes are modeled using simulations that describe the electronic structure at an atomic level, thereby omitting molecular bonding effects. This work addresses the gap by introducing a novel approach that couples Auger–Meitner decay to nuclear dynamics across multiple decay steps, by developing a decay spawning dynamics algorithm and applying it to potential energy surfaces characterized with ab initio molecular dynamics simulations. We showcase the approach on a model decay cascade following K-shell ionization of IBr and subsequent Kβ fluorescence decay. We examine two competing channels that undergo two decay steps, resulting in ion pairs with a total 3+ charge state. This approach provides a continuous description of the electron transfer dynamics occurring during the multistep decay cascade and molecular fragmentation, revealing the combined inner-shell decay and charge transfer time scale to be approximately 75 fs. In conclusion, our computed kinetic energies of ion fragments show good agreement with experimental data.

Ab initio molecular dynamics↗
DOE OSTI2021

Sub-picosecond Production of Solute Radical Cations in Tetrahydrofuran after Radiolysis

Ultrafast hole transfer from solvent radical cations produced by radiolysis with ~10 ps, 9 MeV electron pulses to solutes was investigated in tetrahydrofuran (THF). Because of rapid fragmentation of initially produced THF +• , solute radical cations are not expected and have not previously been reported. Using 9,9-Dihexyl-2,7-dibromofluorene (Br 2 F) at 5 to 1000 mM, Br 2 F +• was observed with radiation chemical yields up to G = 2.23 / 100 eV absorbed. While more than half of this was the result of direct solute ionization, the results highlight the importance of capture of holes from THF +• prior to solvation and fragmentation. The observed data show a time-resolution limited (15 ps) rise in transient absorption of Br 2 F +• , identical in form to reports of pre-solvated or dry electron capture in water and a few organic liquids, including THF. The results were thus interpreted with a similar formalism, finding C 37 = 1.7 M, the concentration at which 37% of holes escape capture. The yield of solvent hole capture can be accounted for by the formation of solvent holes adjacent to solute molecules reacting faster than they can fragment, however mechanisms such as delocalized holes or rapid hopping may play a role. Finally, low temperature results find over two times more capture, supporting the speculation that if THF +• was longer lived, the yield of capture in under 15 ps would have been at least 2x larger at 1 M Br 2 F, possibly capturing nearly all available holes from the solvent.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Two-Dimensional Projected-Momentum Covariance Mapping for Coulomb Explosion Imaging

We introduce projected-momentum covariance mapping, an extension of recoil-frame covariance mapping for 2D ion imaging studies. By considering the two-dimensional projection of the ion momenta as recorded by the detector, one opens the door to a complex suite of analysis tools adapted from three-dimensional momentum imaging studies. This includes the use of different frames of reference to unravel the dynamics of fragmentation and the application of fragment momentum constraints to isolate specific fragmentation channels. The technique is demonstrated on data from a two-dimensional ion imaging study of the Coulomb explosion of the cis and trans isomers of 1,2-dichloroethene, following strong-field ionization by an intense near-infrared femtosecond laser pulse. Classical simulations are used to guide the interpretation of projected-momentum covariance maps. The results offer a detailed insight into the distinct Coulomb explosion dynamics for this pair of isomers and lay the groundwork for future time-resolved studies of photoisomerization dynamics in this molecular system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗