Search NASA⌕ Search

SEARCH · Search NASA

Results for “Abstract”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A Thioether-Ligated Cupric Superoxide Model with Hydrogen Atom Abstraction Reactivity

The central role of cupric superoxide intermediates proposed in hormone and neurotransmitter biosynthesis by noncoupled binuclear copper monooxygenases like dopamine-β-monooxygenase has drawn significant attention to the unusual methionine ligation of the Cu M (“Cu B ”) active site characteristic of this class of enzymes. The copper–sulfur interaction has proven critical for turnover, raising still-unresolved questions concerning Nature’s selection of an oxidizable Met residue to facilitate C–H oxygenation. We describe herein a model for Cu M , [( TMG N 3 S)Cu I ] + ([1] + ), and its O 2 -bound analog [( TMG N 3 S)Cu II (O 2 •– )] + ([1·O 2 ] + ). The latter is the first reported cupric superoxide with an experimentally proven Cu–S bond which also possesses demonstrated hydrogen atom abstraction (HAA) reactivity. Introduction of O2 to a precooled solution of the cuprous precursor [1]B(C 6 F 5 ) 4 (-135 °C, 2-methyltetrahydrofuran (2-MeTHF)) reversibly forms [1·O 2 ]B(C 6 F 5 ) 4 (UV/vis spectroscopy: λ max 442, 642, 742 nm). Resonance Raman studies (413 nm) using 16 O 2 [ 18 O 2 ] corroborated the identity of [1·O 2 ] + by revealing Cu–O (446 [425] cm –1 ) and O–O (1105 [1042] cm –1 ) stretches, and extended X-ray absorption fine structure (EXAFS) spectroscopy showed a Cu–S interatomic distance of 2.55 Å. HAA reactivity between [1·O 2 ] + and TEMPO–H proceeds rapidly (1.28 × 10 –1 M –1 s –1 , -135 °C, 2-MeTHF) with a primary kinetic isotope effect of kH/kD = 5.4. Comparisons of the O 2 -binding behavior and redox activity of [1] + vs [2] + , the latter a close analog of [1]+ but with all N atom ligation (i.e., N 3 S vs N 4 ), are presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications

Lack of standardization in biofoundries limits the scalability and efficiency of synthetic biology research. Here, we propose an abstraction hierarchy that organizes biofoundry activities into four interoperable levels: Project, Service/Capability, Workflow, and Unit Operation, effectively streamlining the Design‑Build‑Test‑Learn (DBTL) cycle. This framework enables more modular, flexible, and automated experimental workflows. It improves communication between researchers and systems, supports reproducibility, and facilitates better integration of software tools and artificial intelligence. Our approach lays the foundation for a globally interoperable biofoundry network, advancing collaborative synthetic biology and accelerating innovation in response to scientific and societal challenges.

Kim, Haseong↗
DOE OSTI2018

H-Abstraction reactions by OH, HO 2 , O, O 2 and benzyl radical addition to O 2 and their implications for kinetic modelling of toluene oxidation

Here, alkylated aromatics constitute a significant fraction of the components commonly found in commercial fuels. Toluene is typically considered as a reference fuel. Together with n-heptane and iso-octane, it allows for realistic emulations of the behavior of real fuels by the means of surrogate mixture formulations. Moreover, it is a key precursor for the formation of poly-aromatic hydrocarbons, which are of relevance to understanding soot growth and oxidation mechanisms. In this study the POLIMI kinetic model is first updated based on the literature and on recent kinetic modelling studies of toluene pyrolysis and oxidation. Then, important reaction pathways are investigated by means of high-level theoretical methods, thereby advancing the present knowledge on toluene oxidation. H-Abstraction reactions by OH, HO 2 , O and O 2 , and the reactivity on the multi well benzyl-oxygen (C 6 H 5 CH 2 + O 2 ) potential energy surface (PES) were investigated using electronic structure calculations, transition state theory in its conventional, variational, and variable reaction coordinate forms (VRC-TST), and master equation calculations. Exploration of the effect on POLIMI model performance of literature rate constants and of the present calculations provides valuable guidelines for implementation of the new rate parameters in existing toluene kinetic models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Imaging H abstraction dynamics in crossed molecular beams: O( 3 P) + propanol isomers

The crossed beam reaction dynamics of ground state O( 3 P) atoms with propanol isomers (1-propanol and 2-propanol) have been studied for the first time using the velocity map imaging technique. The hydroxypropyl radical products, generated from H-abstraction of the secondary and tertiary C–H groups of propanol isomers, were detected via single photon ionization at 157 nm under single collision conditions with collision energies of 8 and 10 kcal mol –1 . Direct rebound dynamics were suggested by the angular distributions, which show overall sideways-backward scattering but more pronounced backward scattering for both isomer reactions under all collision energies studied here. All the translational energy distributions peak at low energy, on average 20–40% of the total available energy. This indicates high internal excitation in the products that is treated by various models of energy release. As a result, we infer that most of the total available energy is partitioned into rotational excitation due to the long-rang dipole–dipole interaction between the dipolar OH and hydroxypropyl radicals.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Energetics and kinetics of various cyano radical hydrogen abstractions

The cyano radical (CN) is an abundant, open-shell molecule found in a variety of environments, including the atmosphere, the interstellar medium and combustion processes. In these environments, it often reacts with small, closed-shell molecules via hydrogen abstraction. Both carbon and nitrogen atoms of the cyano radical are reactive sites, however the carbon is more reactive with reaction barrier heights generally between 2–15 kcal mol -1 lower than those of the analogous nitrogen. The CN + HX → HCN/HNC + X, with X = H, CH 3 , NH 2 , OH, F, SiH 3 , PH 2 , SH, Cl, C 2 H, CN reactions have been studied at a high-level of theory, including CCSD(T)-F12a. Finally, kinetics were obtained over the 100–1000 K temperature range, showing excellent agreement with those rate constants that have been determined experimentally.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The highly exothermic hydrogen abstraction reaction H 2 Te + OH → H 2 O + TeH: comparison with analogous reactions for H 2 Se and H 2 S

The “gold standard” CCSD(T) method is adopted along with the correlation consistent basis sets up to aug-cc-pV5Z-PP to study the mechanism of the hydrogen abstraction reaction H 2 Te + OH. Here, the predicted geometries and vibrational frequencies for reactants and products are in good agreement with the available experimental results. With the ZPVE corrections, the transition state in the favorable pathway of this reaction energetically lies 1.2 kcal mol -1 below the reactants, which is lower than the analogous relative energies for the H 2 Se + OH reaction (-0.7 kcal mol -1 ), the H 2 S + OH reaction (+0.8 kcal mol -1 ) and the H 2 O + OH reaction (+9.0 kcal mol -1 ). Accordingly, the exothermic reaction energies for these related reactions are predicted to be 47.8 (H 2 Te), 37.7 (H 2 Se), 27.1 (H 2 S), and 0.0 (H 2 O) kcal mol -1 , respectively. Geometrically, the low-lying reactant complexes for H 2 Te + OH and H 2 Se + OH are two-center three-electron hemibonded structures, whereas those for H 2 S + OH and H 2 O + OH are hydrogen-bonded. With ZPVE and spin–orbit coupling corrections, the relative energies for the reactant complex, transition state, product complex, and the products for the H 2 Te + OH reaction are estimated to be -13.1, -1.0, -52.0, and -52.6 kcal mol -1 , respectively. Finally, twenty-eight DFT functionals have been tested systematically to assess their ability in describing the potential energy surface of the H 2 Te + OH reaction. The best of these functionals for the corresponding energetics are -9.9, -1.4, -46.4, and -45.4 kcal mol -1 (MPWB1K), or -13.1, -2.4, -57.1, and -54.6 kcal mol -1 (M06-2X), respectively.

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

Master equation study of hydrogen abstraction from HCHO by OH via a chemically activated intermediate

The abstraction reaction of hydrogen from formaldehyde by OH radical plays an important role in formaldehyde oxidation. The reaction involves a bimolecular association to form a chemically activated hydrogen-bonded reaction complex followed by a unimolecular reaction of the complex to generate the products. The reaction rate is usually considered to be pressure-independent by assuming equilibrium between the reactants and the complex. However, our nonequilibrium calculations based on the chemically significant eigenmode of the master equation, carried out with our recently developed TUMME program, indicate that the reaction complex makes the rate constant dependent on pressure at low temperatures (T < 200 K). The calculations include anharmonicity, variational effects, and multi-dimensional tunneling. We find that the reaction rate constant reaches a low-pressure limit at pressures below 10 Torr over the whole investigated temperature range (20–1800 K), which explains why the available low-temperature experiments, which are for pressures below 2 Torr, did not observe the pressure dependence. A new extension of the TUMME master-equation program is used to explore the time evolutions of the concentrations of the OH radical and the complex under pseudo-first-order conditions. The time-dependent evolution of the concentrations of the complex at a low temperature provide direct evidence for the stabilization of the reaction complex at high pressures, and it shows the negligible role of the stabilized reaction complex at low pressures. Finally, the picture that emerges is qualitatively consistent with our previous study of the reaction of methanol with OH in that the tunneling in the unimolecular step from the complex to the products affects the phenomenological reaction rate constants differently at high and low pressures and leads to a significant pressure effect.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

The hydrogen abstraction reaction O({sup 3}P) + CH{sub 4}: A new analytical potential energy surface based on fit to ab initio calculations

Based exclusively on high-level ab initio calculations, a new full-dimensional analytical potential energy surface (PES-2014) for the gas-phase reaction of hydrogen abstraction from methane by an oxygen atom is developed. The ab initio information employed in the fit includes properties (equilibrium geometries, relative energies, and vibrational frequencies) of the reactants, products, saddle point, points on the reaction path, and points on the reaction swath, taking especial caution respecting the location and characterization of the intermediate complexes in the entrance and exit channels. By comparing with the reference results we show that the resulting PES-2014 reproduces reasonably well the whole set of ab initio data used in the fitting, obtained at the CCSD(T) = FULL/aug-cc-pVQZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical surface we perform an extensive dynamics study using quasi-classical trajectory calculations, comparing the results with recent experimental and theoretical data. The excitation function increases with energy (concave-up) reproducing experimental and theoretical information, although our values are somewhat larger. The OH rotovibrational distribution is cold in agreement with experiment. Finally, our results reproduce experimental backward scattering distribution, associated to a rebound mechanism. These results lend confidence to the accuracy of the new surface, which substantially improves the results obtained with our previous surface (PES-2000) for the same system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Dynamics of H{sub 2} Eley-Rideal abstraction from W(110): Sensitivity to the representation of the molecule-surface potential

Dynamics of the Eley-Rideal (ER) abstraction of H{sub 2} from W(110) is analyzed by means of quasi-classical trajectory calculations. Simulations are based on two different molecule-surface potential energy surfaces (PES) constructed from Density Functional Theory results. One PES is obtained by fitting, using a Flexible Periodic London-Eyring-Polanyi-Sato (FPLEPS) functional form, and the other by interpolation through the corrugation reducing procedure (CRP). Then, the present study allows us to elucidate the ER dynamics sensitivity on the PES representation. Despite some sizable discrepancies between both H+H/W(110) PESs, the obtained projectile-energy dependence of the total ER cross sections are qualitatively very similar ensuring that the main physical ingredients are captured in both PES models. The obtained distributions of the final energy among the different molecular degrees of freedom barely depend on the PES model, being most likely determined by the reaction exothermicity. Therefore, a reasonably good agreement with the measured final vibrational state distribution is observed in spite of the pressure and material gaps between theoretical and experimental conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

A reactant-coordinate-based wave packet method for full-dimensional state-to-state quantum dynamics of tetra-atomic reactions: Application to both the abstraction and exchange channels in the H + H 2 O reaction

Here, an efficient and accurate wave packet method is proposed for the calculation of the state-to-state S -matrix elements in bimolecular reactions involving four atoms. This approach propagates an initial state specific wave packet in reactant Jacobi coordinates. The projection in product channels is carried out on projection planes, which have one less degree of freedom, by transforming both the time-dependent wave packet and final product states into a set of intermediate coordinates. This reactant-coordinate-based method is more efficient than product-coordinate-based methods because it typically requires a smaller number of basis functions or grid points and allows the determination of S -matrix elements for multiple product channels from a single propagation. This method is demonstrated in calculating the ( J tot = 0) state-to-state S -matrix elements for both the abstraction and exchange channels of the H + H 2 O reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Full-dimensional global potential energy surfaces describing abstraction and exchange for the H + H{sub 2}S reaction

For the H + H{sub 2}S system, ∼34 000 data points are sampled over a large configuration space including both abstraction and exchange channels, and calculated at the level of explicitly correlated unrestricted coupled cluster method with singles, doubles, and perturbative triples excitations with the augmented correlation-consistent polarized triple zeta basis set (UCCSD(T)-F12a/aug-cc-pVTZ). The data set was fit using the newly proposed permutation invariant polynomial-neural network (PIP-NN) method with three different vectors as the input: two redundant sets of PIPs, one with the maximum order four (PES-I) and one with the maximum order three (PES-II), and nine non-redundant PIPs (PES-III). All these PESs show small fitting errors and essentially the same performance in representing the title system. Various kinetics and dynamical properties are calculated using the tunneling corrected transition state theory and quasi-classical trajectory, and compared with available experimental results. At a collision energy of 10 kcal/mol, both the H{sub 2} and SH products are found to be internally cold, with ∼20% of H{sub 2} at its first vibrational excited state, while SH is essentially a spectator. The angular distributions of the products are mainly in backward with considerable contributions from sideway direction. In addition, analytical partial derivatives of any PIP-NN PES with respect to the coordinates of atoms are derived by making use of the monomial symmetrization algorithm [Z. Xie and J. M. Bowman, J. Chem. Theory Comput. 6, 26–34 (2010)]. It can not only accelerate the evaluation of the derivatives, but also improve the energy convergence significantly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Introducing Weirs: An Abstraction for Next Generation Streaming Workflows

In HPC applications, it is widely understood that in situ systems will play a significant role in next generation systems. The rate that next-generation leadership machines will be able to generate data will exceed the bandwidths of the planned I/O systems, leading to a need for in situ processing of the resulting data to reduce it. There have been a number of techniques proposed for in situ workflow systems; we are concerned here specifically with the needs of publish/subscribe or streaming-based approaches, which allow the in situ system to be composed of completely separate executables running concurrently on the hardware. In this paper we introduce an abstract known as a Weir. A weir is a useful mechanism to control state in a point to point streaming workflow in the absence of a third party publish subscribe system.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

Toward Abstracting the Communication Intent in Applications to Improve Portability and Productivity

Programming with communication libraries such as the Message Passing Interface (MPI) obscures the high-level intent of the communication in an application and makes static communication analysis difficult to do. Compilers are unaware of communication libraries' specifics, leading to the exclusion of communication patterns from any automated analysis and optimizations. To overcome this, communication patterns can be expressed at higher-levels of abstraction and incrementally added to existing MPI applications. In this paper, we propose the use of directives to clearly express the communication intent of an application in a way that is not specific to a given communication library. Our communication directives allow programmers to express communication among processes in a portable way, giving hints to the compiler on regions of computations that can be overlapped with communication and relaxing communication constraints on the ordering, completion and synchronization of the communication imposed by specific libraries such as MPI. The directives can then be translated by the compiler into message passing calls that efficiently implement the intended pattern and be targeted to multiple communication libraries. Thus far, we have used the directives to express point-to-point communication patterns in C, C++ and Fortran applications, and have translated them to MPI and SHMEM.

Mintz, Tiffany M.↗
DOE OSTI2014

Compiler verification meets cross-language linking via data abstraction

Many real programs are written in multiple different programming languages, and supporting this pattern creates challenges for formal compiler verification. We describe our Coq verification of a compiler for a high-level language, such that the compiler correctness theorem allows us to derive partial-correctness Hoare-logic theorems for programs built by linking the assembly code output by our compiler and assembly code produced by other means. Our compiler supports such tricky features as storable cross-language function pointers, without giving up the usual benefits of being able to verify different compiler phases (including, in our case, two classic optimizations) independently. Here, the key technical innovation is a mixed operational and axiomatic semantics for the source language, with a built-in notion of abstract data types, such that compiled code interfaces with other languages only through axiomatically specified methods that mutate encapsulated private data, represented in whatever formats are most natural for those languages.

97 MATHEMATICS AND COMPUTING↗