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Results for “formation kinetics”

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DOE OSTI2024

Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms

Abstract Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant unusually preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employ static and dynamic structural methods and observe that, compared to R132H, the R132Q active site adopts a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling reveals a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Guided Ion Beam and Quantum Chemical Investigation of the Thermochemistry of Thorium Dioxide Cations: Thermodynamic Evidence for Participation of f Orbitals in Bonding

Kinetic energy dependent reactions of ThO + with O 2 are studied using a guided ion beam tandem mass spectrometer. The formation of ThO 2 + in the reaction of ThO + with O 2 is observed to be slightly endothermic and also exhibits two obvious features in the cross section. These kinetic energy dependent cross sections were modeled to determine a 0 K bond dissociation energy of D 0 (OTh + - O) = 4.94 ± 0.06 eV. This value is slightly larger but within experimental uncertainty of less precise previously reported experimental values. The higher energy feature in the ThO 2 + cross section was also analyzed and suggests formation of an excited state of the product ion lying 3.1 ± 0.2 eV above the ground state. Additionally, the thermochemistry of ThO 2 + was explored by quantum chemical calculations, including a full Feller-Peterson-Dixon (FPD) composite approach with correlation contributions up to CCSDT(Q) and four-component spin-orbit corrections, as well as more approximate CCSD(T) calculations including semiempirical estimates of spin-orbit energy contributions. The FPD approach predicts D 0 (OTh + -O) = 4.87 ± 0.04 eV, in good agreement with the experimental value. Analogous FPD results for ThO+, ThO, and ThO 2 are also presented, including ionization energies for both ThO and ThO 2 . The ThO 2 + bond energy is larger than those of its transition metal congeners, TiO 2 + and ZrO 2 + , which can be attributed partially to an actinide contraction, but also to contributions from the participation of f orbitals on thorium that are unavailable to the transition metal systems.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Additive friction stir deposition of SS316: Effect of process parameters on microstructure evolution

Solid state nature of additive friction stir deposition (AFSD) additive manufacturing process is very advantageous in terms of defect formation and microstructural refinement in the material. Current study presents the process optimization, microstructural evolution and kinetics of recrystallization for AFSD deposited low stacking fault energy material - SS316. As deposited microstructure shows equiaxed ultra fine grains with an average grain size of ~5.0 ± 0.5 μm. Shear deformation at high temperature during processing leads to the operation of restoration mechanisms. Observation of necklace type microstructure in the as deposited SS316 is attributed to discontinuous dynamic recrystallization during processing. Recrystallization kinetics of the AFSD SS316 is characterized using Johnson-Mehl-Avarami-Kolmogorov (JMAK) model. Deformation – thermal cycling during AFSD process resulted in inconsistent recrystallization kinetics. Variation in strain, strain rate and temperature during processing with processing parameters result in varying microstructure and tool wear. Further, high strength-ductility combination and sustained work hardening in as deposited SS316 appear to arise from transformation and twinning during deformation, leading to the formation of hierarchical twins and martensitic phase after deformation.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Chemistry of Sugar Formation in the Gas Phase: Following the Activated Aldehyde

Sugars are produced by living organisms, and are required building blocks for life as we know it, which raises the foundational question of how sugars formed in a prebiotic environment. The abiotic formose reaction produces sugars from formaldehyde, but our understanding of its initiation step remains murky, with chemists invoking the concept of an “activated aldehyde” to seed this reaction. Singlet hydroxycarbenes, high-energy isomers of aldehydes, were recently reported to facilitate sugar formation under cold, nonaqueous conditions relevant to interstellar environments. Here, we generate singlet methylhydroxycarbene ( 1 CH 3 –C̈–OH) from the photodissociation of pyruvic acid and experimentally measure its gas-phase reaction with d 4 -acetaldehyde using multiplexed photoionization mass spectrometry. The C 4 H 4 D 4 O 2 isomer d 4 -acetoin is the sole product, which we kinetically link to the reactant CH 3 –C̈–OH, and attribute to a carbonyl-ene formation mechanism. We see no evidence of 3-hydroxybutanal, the C–H insertion product expected in carbene chemistry. Using automated exploration we calculate stationary points on the potential energy surface and report master equation rate coefficients from T = 20–600 K, providing quantitative kinetics of this fast reaction for use in chemical models. The prereactive complex in this reaction is stabilized by both hydrogen bonding and electrophilic carbene C═O interactions. These effects create a short-range dynamical bottleneck for the reaction besides the long- and midrange barrierless bottlenecks. Combined with recent reports of 1 HC̈OH production from methanol photodissociation and pyruvic acid production in cold irradiated ices, this work provides evidence that singlet hydroxycarbene + aldehyde chemistry is a feasible path to prebiotic sugar formation.

aldehydes↗

NASA NTRS1991

The formation of molecules in protostellar winds

The production and destruction processes for molecules in very fast protostellar winds are analyzed and modeled with a one-dimensional chemical kinetics code. Radial density and temperature distributions suggested by protostellar theory are explored as are a range of mass-loss rates. The efficiency of in situ formation of heavy molecules is found to be high if the wind temperature falls sufficiently rapidly, as indicated by theory. The degree of molecular conversion is a strong function of the mass-loss rate and of density gradients associated with the acceleration and collimation of the wind. Even in cases where essentially all of the heavy atoms are processed into molecules, a significant fraction of atomic hydrogen remains so that hghly molecular, protostellar winds are able to emit the 21-cm line. Although CO has a substantial abundance in most models relevant to very young protostars, high abundances of other molecules such as SiO and H2O signify more complete association characteristic of winds containing regions of very high density. Although the models apply only to regions close to the protostar, they are in qualitative accord with recent observations at much larger distances of both atomic and molecular emission from extremely high-velocity flow.

Glassgold, A. E.↗

DOE OSTI2021

Formation of a single quasicrystal upon collision of multiple grains

Abstract Quasicrystals exhibit long-range order but lack translational symmetry. When grown as single crystals, they possess distinctive and unusual properties owing to the absence of grain boundaries. Unfortunately, conventional methods such as bulk crystal growth or thin film deposition only allow us to synthesize either polycrystalline quasicrystals or quasicrystals that are at most a few centimeters in size. Here, we reveal through real-time and 3D imaging the formation of a single decagonal quasicrystal arising from a hard collision between multiple growing quasicrystals in an Al-Co-Ni liquid. Through corresponding molecular dynamics simulations, we examine the underlying kinetics of quasicrystal coalescence and investigate the effects of initial misorientation between the growing quasicrystalline grains on the formation of grain boundaries. At small misorientation, coalescence occurs following rigid rotation that is facilitated by phasons. Our joint experimental-computational discovery paves the way toward fabrication of single, large-scale quasicrystals for novel applications.

36 MATERIALS SCIENCE↗

DOE OSTI2020

In situ laser reflectivity to monitor and control the nucleation and growth of atomically thin 2D materials*

The growth of atomically thin two-dimensional (2D) layered and other quantum materials is typically performed without in situ monitoring or control. Here, a simple laser reflectivity approach is demonstrated to provide in situ control over sub-monolayer thickness and growth kinetics during pulsed laser deposition (PLD) of MoSe 2 layers. First, the general technique is presented with emphasis on designing the maximum sensitivity of the optical contrast through consideration of Fresnel's equations with proper choice of layer thickness, substrate, and laser monitoring wavelength, incidence angle, and laser polarization. Then the 632.8 nm optical reflectivity of MoSe 2 layers on SiO 2 /Si substrates was predicted and compared with in situ monitoring of MoSe 2 growth by PLD under actual growth conditions using a probe HeNe laser beam. The measurements showed high sensitivity and excellent agreement with MoSe 2 surface coverages calculated from atomic resolution STEM analysis of 2D layers deposited in arrested growth experiments. Finally, growth kinetics revealed by these measurements showed sigmoidal nucleation and growth stages in the formation of the 2D MoSe 2 layers that are described by a simple model, indicating the promise of the laser reflectivity technique for in situ monitoring and control of 2D materials deposition.

2D materials↗

DOE OSTI2022

Multiple Roles of Alkanethiolate‐Ligands in Direct Formation of H 2 O 2 over Pd Nanoparticles

Abstract Coadsorbed organic species including thiolates can promote direct synthesis of hydrogen peroxide from H 2 and O 2 over Pd particles. Here, density functional theory based kinetic modeling, augmented with activity measurements and vibrational spectroscopy are used to provide atomistic understanding of direct H 2 O 2 formation over alkylthiolate(RS) Pd. We find that the RS species are oxidized during reaction conditions yielding RSO 2 as the effective ligand. The RSO 2 ligand shows superior ability for proton transfer to the intermediate surface species OOH, which accelerates the formation of H 2 O 2 . The ligands promote the selectivity also by blocking sites for unselective water formation and by modifying the electronic structure of Pd. The work rationalizes observations of enhanced selectivity of direct H 2 O 2 formation over ligand‐funtionalized Pd nanoparticles and shows that engineering of organic surface modifiers can be used to promote desired hydrogen transfer routes.

Chen, Lin↗

DOE OSTI2022

Multiple Roles of Alkanethiolate‐Ligands in Direct Formation of H 2 O 2 over Pd Nanoparticles

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1973

Laboratory simulation of graphite formation in stellar envelopes

A technique has been developed which permits laboratory simulation of graphite condensation in the envelopes of cool, late sequence stars. Processes in the stellar envelope were simulated by allowing hydrogen-carbon mixtures of typical circumstellar composition and temperature to expand freely into vacuum, cooling and supersaturating the vapor. Expansion products were determined mass spectrometrically through the use of molecular beam techniques. The results of laboratory expansions were scaled to those occurring near M and N stars by comparing the number of collisional events in each case. Kinetic considerations indicate that the important rate process in rarefied envelopes will be C2 formation; consequently scaling by termolecular collisions was employed. Results of this study imply that envelope expansions near M giants contribute at most .01 of the observed interstellar grain density. In the case of pulsating N stars, on the other hand, the results are not inconsistent with previous predictions of essentially complete carbon condensation.

Dorfeld, W. G.↗

DOE OSTI2025

Neutron generation dynamics inside a MA-class dense plasma focus Z-pinch

Dense plasma focii (DPFs) are appealing as energy efficient sources of short pulses of ions, neutrons, and x rays. The output of these sources is expected to scale with input current (I4), but has been shown to drop at the MA level [S. K. H. Auluck, “On the failure of neutron yield scaling in the dense plasma focus,” Phys. Plasmas 30, 080701 (2023)]. New results on the MegaJOuLe Neutron Imaging Radiography DPF showed neutron yield production in agreement with the input current scaling beyond the previously observed drop. This work provides insight into the pinch formation on a DPF and reports on the two different mechanisms leading to neutron generation inside a DPF using a combination of kinetic simulations and experimental data. A combination of particle-in-cell (PIC) and 1D shock theory results are used to describe the pinch formation and disassembly and the corresponding thermonuclear and beam-target mechanisms. The temporal evolution of the pinch column predicted by the PIC simulations shows qualitative agreement with the experimental data from plasma photon emission as well as temporal neutron pulse shapes. In MJ-class DPFs, both thermonuclear and beam-target mechanisms can occur over the course of the implosion and contribute to the total neutron production. Hence the neutron source size of a DPF will change throughout the implosion. Experimental neutron radiographs show the increase in source size as the pinch breaks apart, in agreement with simulation's prediction.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1995

Faster rates with less catalyst in template-directed reactions

We have recently shown that the polycytidylic acid-directed polymerization of guanosine 5'-monophosphate 2-methylimidazolide (2-MeImpG) is amenable to kinetic study and that rate determinations as a function of 2-MeImpG concentration can reveal much mechanistic detail (Kanavarioti et al. 1993). Here we report kinetic data which show that, once the reaction has been initiated by the formation of dimers, the elongation of dimers to form longer oligomers is accelerated by decreasing polycytidylate (poly(C)) concentration from 0.05 to 0.002 M. This result is consistent with the previously proposed mechanism. The increase in the observed pseudo-first order rate constant for formation of the trimer, k3', and the corresponding constant for formation of oligomers longer than the trimer, ki' (ki' is independent of oligomer length for i > or = 4), with decreasing template concentration for a given monomer concentration is attributed to an increase in template occupancy as template concentration is reduced.

NASA Discipline Exobiology↗

DOE OSTI2021

Role of surface diffusion in formation of unique reactivity for graphite oxidation: Time-resolved measurements in a pulsed diffusion reactor

Quantification of oxidation kinetics is essential to develop graphitic materials for diverse applications: from refractories found in gas-cooled nuclear reactors to catalysts needed for chemical manufacturing. In this work, using well-defined highly oriented pyrolytic graphite, low-pressure isotopic transient experiments combined with controlled annealing periods, we resolve the role of surface diffusion and quantify oxidation kinetics with nanomole-precision. We observe an unexpected increase in reactivity following annealing which is explained by the role of surface diffusion increasing the probability for trapping mobile oxygen at more reactive edge sites. Here, the locus of adsorption and spillover to the basal plane is distinct from the trapping location creating a more active oxygen species. Isotopic products reflect the population dynamics of oxygen added at the edge and surface diffusion that relocates basal plane oxygen to more reactive edge sites. Since this process proceeds in parallel with direct oxidation reactions, it is not likely to be observed using steady-state or conventional ‘bulk’ characterization techniques. Our unique time-resolved non-equilibrium measurement in a well-defined transport regime, enables observation of three distinct behaviors: short-term deactivation due to the balance of rates in oxygen supply/product formation, reactivity increases due to surface diffusion and longer-term reactivity increase with oxygen accumulation.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Bulk and surface diffusion of neodymium in alpha-uranium: Ab initio calculations and kinetic Monte Carlo simulations

A fundamental understanding of lanthanide transport in metallic fuels is critical for high fidelity modeling of the fuel-cladding chemical interaction (FCCI) phenomenon, which can lead to the formation of brittle intermetallic compounds and premature failure of the cladding. Here we report a combined ab initio density functional theory (DFT) and kinetic Monte Carlo (KMC) study of the bulk diffusivity of Nd in α-U, fully taking into account the effect of radiation enhanced diffusion. In this work, the vacancy mechanism is considered to be the dominant mechanism for the bulk diffusion of Nd since a Nd interstitial is found to be intrinsically unstable in α-U. The surface diffusivity of a Nd adatom on α-U (001) surface has been further predicted using KMC simulations parameterized by DFT calculations. The present study suggests that Nd transport via the surface diffusion mechanism can be many orders of magnitude faster than bulk diffusion. Furthermore, the results from the present lower length scale study can be used to inform mesoscale phase-field simulations to determine the effective diffusion coefficient of Nd through α-U with a porous microstructure.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Unimolecular and bimolecular formic acid decomposition routes on dispersed Cu nanoparticles

The elementary steps and site requirements in formic acid (HCOOH) dehydrogenation on Cu surfaces remain of keen interest because formate species act as intermediates or spectators in methanol synthesis and water–gas shift reactions. Steady-state and transient kinetic data, isotopic effects, infrared spectra during catalytic and stoichiometric reactions, and theoretical treatments based on density functional theory (DFT) provide evidence for bimolecular reactions, in which saturated bidentate formate (*HCOO*) adlayers, present at 0.25 ML (0.25 *HCOO* per surface Cu atom), react with undissociated species (HCOOH$^\square$) bound at interstices within formate adlayers ($^\square$) to form H-bonded bimolecular HCOOH$^\square$-*HCOO* adducts. The co-existence of vicinal HCOOH$^\square$ and *HCOO* moieties is evident from antisymmetric infrared bands for *HCOO* that become stronger as a result of their H-bonding that perturbs the induced dipole moment of *HCOO* upon vibration, consistent with DFT-derived vibrational frequencies and intensities for such perturbed species. The *HCOO* moiety in this complex undergoes C-H activation via a transition state that is preferentially stabilized through H-bonding with the vicinal HCOOH$^\square$ relative to its *HCOO* precursor. DFT-derived HCOOH dehydrogenation activation barriers and those determined from the evolution of CO 2 from pre-adsorbed *HCOO* species are about 10 kJ mol -1 smaller in the presence of gaseous HCOOH reactants (because of HCOOH$^\square$-*HCOO* interactions) than those for the unimolecular decomposition of bound *HCOO* species. Such bimolecular routes are consistent with measured effects of HCOOH, H 2 , and CO pressures and of H/D isotopic substitution on dehydrogenation turnover rates and represent the predominant channel for the formation of CO 2 and H 2 during catalytic HCOOH dehydrogenation on Cu nanoparticles. A saturated *HCOO* adlayer that retains binding interstices and the presence of HCOOH(g) enable a sequence of elementary steps unavailable for *HCOO* species, thus circumventing unassisted unimolecular routes that exhibit higher activation barriers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

PAH formation from jet stirred reactor pyrolysis of gasoline surrogates

Soot particles and their precursor polycyclic aromatic hydrocarbon (PAH) species, formed during combustion, are responsible for particulate emissions in gasoline direct injection (GDI) engines. To better understand the effects of fuel composition on formation of soot in GDI engines, the pyrolysis of several gasoline surrogates was studied in a jet-stirred reactor across a broad temperature range at atmospheric pressure and 1 s residence time. Fuel and intermediate species, including aromatics up to naphthalene, were measured using gas chromatography (GC). PAH concentrations from pyrolysis of surrogate fuels were compared to gain insight into the effects of fuel composition on PAH formation. In addition, synergistic effects were observed in pyrolysis experiments of binary blends. A detailed kinetic model, recently developed at Lawrence Livermore National Laboratory (LLNL), successfully captured the effects of blending and the concentration of major PAHs. Major reaction pathways are discussed, as well as the role of important intermediate species, such as acetylene, and resonantly stabilized radicals such as allyl, propargyl, cyclopentadienyl, and benzyl in the formation of PAH.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Abbreviated Technical Report: Experimentally Interrogating Detonation Chemistry on Sub-Nanosecond to Nanosecond Timescales

Direct experimental measurement of chemical reactions during high explosive detonation remains challenging. Theory and modeling have long preceded experiment in the fundamental physical and chemical kinetic properties of detonation, and experimentation at the relevant timescales are needed to both validate models and provide fundamental understanding of detonation. In this LDRD-ER project, two approaches, x-ray diffraction and core-level x-ray Raman, were developed and used to further experimental capabilities to address this gap. We further developed dynamic x-ray diffraction to directly detect nanodiamond formation during detonation, providing experimental data towards resolving longstanding controversy in the scientific literature, and although the full kinetics have not yet been fully mapped, diamond diffraction appears on the same timescales as detonation soot formation. In the second research thrust, we have developed core-level x-ray Raman for use with high explosives. This technique provides information analogous to x-ray absorption spectroscopy and electron energy loss spectroscopy, but uses inelastic scattering of hard x-rays that can interrogate chemistry around light elements much deeper into the material. The low cross section and requisite high solid angle collection have hindered its use for ultra-fast spectroscopy. We developed and tested a high-q spectrometer which will substantially increase cross section and signal-to-noise, showing this method will also not dramatically alter, compared to x-ray absorption, the most discriminating spectral features of C, N, and O from various high explosives and expected detonation products. We have also used x-ray Raman combined with OCEAN electronic structure calculations to explore dynamic photodegradation mechanisms in PETN and CL-20 explosives. This provides a pathway towards implementing capability to dynamically explore chemistry at an x-ray free electron laser.

36 MATERIALS SCIENCE↗

NASA NTRS2021

Particle Acceleration by Dense Impulsive Structures Moving in Ambient Magnetospheric Plasma. 3-D Hybrid Kinetic Modeling and MMS Observations

High resolution observations of dense plasma impulsive structures moving through an ambient background magnetospheric flows were captured by the Magnetospheric Multiscale mission. The observations show particle heating and acceleration, shock-like wave formation, and whistler wave excitation inside the interface between the dense impulsive plasma structures and the ambient plasma. A multiscale hybrid kinetic simulation provides an explanation of the observed wave-particle interactions with the assumption that the dense plasma structures may be represented by plasma clouds which are formed at the magnetopause layer due to reconnection processes. Plain Language Summary: Dense, impulsive plasma structures moving through a background plasma were captured by the NASA Magnetospheric Multiscale mission. The observations show that the dense structures can generate strong perturbations in the electromagnetic field and shock-like waves. Interactions between these electromagnetic waves and the particles results in particle acceleration. 3-D hybrid kinetic modeling (particle description for ions and fluid description for electrons) was used to investigate the plasma physics of the observed structures. It was assumed that the plasma clouds were formed by magnetic field reconnection inside the magnetopause, which is the interface between the solar wind particles and the cold low-density magnetospheric plasma. The work helps us understand the plasma environment at the interface between the Earth and solar wind, near planetary moons, within astrophysical explosions, and possibly at the interface between the solar wind and local interstellar medium.

A. S. Lipatov↗