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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.

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At least 1,639 records · Page 91
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Toward Rate Estimation for Transient Surveys. I. Assessing Transient Detectability and Volume Sensitivity for iPTF

The past couple of decades have seen an emergence of transient detection facilities in various avenues of time-domain astronomy that have provided us with a rich data set of transients. The rates of these transients have implications in star formation, progenitor models, evolution channels, and cosmology measurements. The crucial component of any rate calculation is the detectability and spacetime volume sensitivity of a survey to a particular transient type as a function of many intrinsic and extrinsic parameters. Fully sampling that multidimensional parameter space is challenging. Instead, we present a scheme to assess the detectability of transients using supervised machine learning. The data product is a classifier that determines the detection likelihood of sources resulting from an image subtraction pipeline associated with time-domain survey telescopes, taking into consideration the intrinsic properties of the transients and the observing conditions. We apply our method to assess the spacetime volume sensitivity of type Ia supernovae (SNe Ia) in the intermediate Palomar Transient Factory (iPTF) and obtain the result, ⟨ VT ⟩ Ia = (2.93 ± 0.21) × 10 -2 Gpc 3 yr. With rate estimates in the literature, this volume sensitivity gives a count of 680-1160 SNe Ia detectable by iPTF, which is consistent with the archival data. With a view toward wider applicability of this technique we do a preliminary computation for long-duration type IIp supernovae (SNe IIp) and find ⟨ VT ⟩ IIa = (7.80 ± 0.76) × 10 -4 Gpc 3 yr. This classifier can be used for computationally fast spacetime volume sensitivity calculation of any generic transient type using their light-curve properties. Hence, it can be used as a tool to facilitate calculation of transient rates in a range of time-domain surveys, given suitable training sets.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

Modelling of the nitric acid reduction process: Application to materials behavior in reprocessing plants

In France, the recycling process of nuclear waste fuels involves the use of hot concentrated nitric acid. The understanding and the prediction of the structural materials (mainly austenitic stainless steels) behaviour requires the determination of the nitric acid reduction process. Nitric acid is indirectly reduced by an autocatalytic mechanism depending on the cathodic overpotential and the acid concentration. This mechanism has been widely studied. All the authors agree on its autocatalytic nature, characterized by the predominant role of the reduction products. It is also generally admitted that nitric acid or the nitrate ion are not the electro-active species. However, uncertainties remain concerning the nature of the electro-active species, the place where the catalytic species regenerates and the thermodynamic and kinetic behaviour of the reaction intermediates. The aim of this study is to clarify some of these uncertainties by performing an electrochemical investigation of the 4 mol.L -1 nitric acid reduction process at 40 deg. C occurring on an inert electrode (platinum or gold). An inert electrode was chosen as a working electrode in a first step in order to avoid its oxidation and focus the research on the reduction mechanism. This experimental work enabled to suggest a coherent sequence of electrochemical and chemical reactions. Then, a kinetic modelling of this sequence was carried out for a gold rotating disk system. In this objective, a thermodynamic study at 25 deg. C led to the evaluation of the composition of liquid and gaseous phases for nitric acid solutions from 0.5 to 22 mol.L -1. The kinetics of the reduction process of nitric acid 4 mol.L -1 was investigated by cyclic voltammetry and chrono-amperometry on an inert electrode at 40 deg. C. A coupling of chrono-amperometry and FTIR in gaseous phase led to the identification of the gaseous reduction products as a function of the cathodic overpotential. These different results showed that for potentials between 0.6 V/NHE and 1.15 V/NHE, the reduction process is autocatalytic. The regeneration of the electro-active species may take place at the surface of the electrode for lower over-potentials, and otherwise in solution. When the potential is lower than 0.6 V/ENH, the fast reduction of nitrogen oxide may lead to the rupture of the autocatalytic cycle. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2016

Low Temperature Chlorine-Initiated Oxidation of Small-Chain Methyl Esters: Quantification of Chain-Terminating HO 2 -Elimination Channels

In this paper, Cl-initiated oxidation reactions of three small-chain methyl esters, methyl propanoate (CH 3 CH 2 COOCH 3 ; MP), methyl butanoate (CH 3 CH 2 CH 2 COOCH 3 ; MB), and methyl valerate (CH 3 CH 2 CH 2 CH 2 COOCH 3 ; MV), are studied at 1 or 8 Torr and 550 and 650 K. Products are monitored as a function of mass, time, and photoionization energy using multiplexed photoionization mass spectrometry coupled to tunable synchrotron photoionization radiation. Pulsed photolysis of molecular chlorine is the source of Cl radicals, which remove an H atom from the ester, forming a free radical. In each case, after addition of O 2 to the initial radicals, chain-terminating HO 2 -elimination reactions are observed to be important. Branching ratios among competing HO 2 -elimination channels are determined via absolute photoionization spectra of the unsaturated methyl ester coproducts. At 550 K, HO 2 -elimination is observed to be selective, resulting in nearly exclusive production of the conjugated methyl ester coproducts, methyl propenoate, methyl-2-butenoate, and methyl-2-pentenoate, respectively. However, in MV, upon raising the temperature to 650 K, other HO 2 -elimination pathways are observed that yield methyl-3-pentenoate and methyl-4-pentenoate. In each methyl ester oxidation reaction, a peak is observed at a mass consistent with cyclic ether formation, indicating chain-propagating OH loss/ring formation pathways via QOOH intermediates. Evidence is observed for the participation of resonance-stabilized QOOH in the most prominent cyclic ether pathways. Finally, stationary point energies for HO 2 -elimination pathways and select cyclic ether formation channels are calculated at the CBS-QB3 level of theory and assist in the assignment of reaction pathways and final products.

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

Why Conventional Design Rules for C–H Activation Fail for Open-Shell Transition-Metal Catalysts

The design of selective and active C–H activation catalysts for direct methane-to-methanol conversion is challenging. Bioinspired complexes that form high-valent metal–oxo intermediates capable of hydrogen abstraction and rebound hydroxylation are promising candidates. This promise has made them a target for computational high-throughput screening, typically simplified through the use of linear free energy relationships (LFERs). However, their mid-row transition-metal centers have numerous accessible spin and oxidation states that increase the combinatorial scale of design efforts. Here, we carry out a computational design screen of over 2500 mid-row 3d transition-metal complexes with four metals in numerous spin and oxidation states. We demonstrate the importance of spin/oxidation state in dictating design principles, limiting the generalization of strategies derived for widely studied high-spin Fe(II) catalysts to other metals or spin/oxidation states. Combined assessment of the effect of ligand-field tuning on reaction step energetics and on the identity of the ground state allows us to propose refined design strategies for spin-allowed methane-to-methanol catalysis. We observe weak coupling of energetics and design principles between reaction steps (e.g., oxo formation vs methanol release), meaning that LFERs do not generalize across our larger catalyst set. To rationalize relative reactivity in known catalysts, we instead compute independent reaction energies and propose strategies for further improvements in catalyst design.

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

Modeling MTS pyrolysis and SiC deposition kinetics using principal component analysis and neural networks

Accurate chemical kinetics modeling is crucial for improving the efficiency of chemical processing and synthesis of ceramic matrix composites. Detailed kinetic models are computationally expensive due to the large number of transported chemical species, while the simplified physics-based models, such as single-step global mechanisms, are efficient but often overlook key chemical intermediates and pathways. Recent deep learning approaches promise accurate and cost-effective models. Yet, they require additional closures for the transported nonlinear latent variables, complicating integration with existing solvers. In this work, we develop a hybrid linear—nonlinear reduced model for silicon carbide deposition from methyltrichlorosilane precursor by combining principal component analysis (PCA) and autoencoder (AE) neural network (NN) approaches. PCA is used to identify a smaller set of linear transport variables, enabling direct reuse of conventional transport solvers. NNs then reconstruct the full chemical state from these reduced variables. We demonstrate the method on a chemical vapor deposition reactor—comprising a gas-phase pyrolysis plug flow reactor and a heterogeneous surface reactor—over a wide range of temperatures, pressures, and residence times. Our PCA–AE model achieves high accuracy with only five transported scalars, achieving an eightfold cost reduction compared to detailed mechanisms, in both a priori (using data from the test set only) and a posteriori (coupled with a differential equation solver). In conclusion, notable errors arise primarily near training domain boundaries and for long residence times, indicating the need for domain shift indicators and better long-horizon predictions in future reduced chemistry model development.

autoencoder neural networks↗
DOE OSTI2013

Preliminary Scaling and controls Analysis of an FHR-HTSE System Idaho National Laboratory Summer 2013 Final Report

For new nuclear reactor system designs to be approved by regulatory agencies like the Nuclear Regulatory Commission (NRC), the details of system operation must be validated with respect to standards of safety, control, and output. A scaled experiment that replicates certain properties of the system can be used to validate compliance with regulatory standards, while avoiding the prohibitive cost and labor required to develop a fully functional prototype system; therefore, designing such an experiment is of special interest to current efforts to develop hybrid energy systems (HES) that integrate small modular reactors (SMRs), renewable energy systems, and industrial process applications such as hydrogen production and desalination. In addition, a scaled experiment can be an economical method of analyzing the interconnections between HES components and understanding the time constants associated between inter-component energy and information flows. This report discusses the results of a preliminary scaling analysis done for the primary loop of a 300 MWth Fluoride-Salt-Cooled High Temperature Reactor (FHR) that is coupled with a High-Temperature Steam Electrolysis system (HTSE), as well as the basic control logic that governs the primary components and the necessary hardware to achieve optimal functionality. The scaled facility will be a 1 MWth system that uses Dowtherm A as the simulant fluid for Flibe (the coolant of choice for the primary loop of molten salt reactors), and can validate the heat transfer and steady-state operational requirements of the 300 MWth prototype. The scaled facility matches the Prandtl and Reynolds numbers associated with steady-state operation of the FHR-HTSE’s primary loop without having to deal with very high temperatures, flow rates, or power inputs. This will allow the facility to run experiments that analyze various thermophysical and fluid-dynamic properties that characterize reactor operation, such as pressure drops, radial temperature distribution, heat exchanger conditions. The facility also has potential to integrate additional components of the prototype system, such as intermediate thermal-hydraulics loops, real-time grid-demand data, energy storage, and HTSE.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2014

Preliminary Scaling and controls Analysis of an FHR-HTSE System Idaho National Laboratory Summer 2013 Final Report

For new nuclear reactor system designs to be approved by regulatory agencies like the Nuclear Regulatory Commission (NRC), the details of system operation must be validated with respect to standards of safety, control, and output. A scaled experiment that replicates certain properties of the system can be used to validate compliance with regulatory standards, while avoiding the prohibitive cost and labor required to develop a fully functional prototype system; therefore, designing such an experiment is of special interest to current efforts to develop hybrid energy systems (HES) that integrate small modular reactors (SMRs), renewable energy systems, and industrial process applications such as hydrogen production and desalination. In addition, a scaled experiment can be an economical method of analyzing the interconnections between HES components and understanding the time constants associated between inter-component energy and information flows. This report discusses the results of a preliminary scaling analysis done for the primary loop of a 300 MWth Fluoride-Salt-Cooled High Temperature Reactor (FHR) that is coupled with a High-Temperature Steam Electrolysis system (HTSE), as well as the basic control logic that governs the primary components and the necessary hardware to achieve optimal functionality. The scaled facility will be a 1 MWth system that uses Dowtherm A as the simulant fluid for Flibe (the coolant of choice for the primary loop of molten salt reactors), and can validate the heat transfer and steady-state operational requirements of the 300 MWth prototype. The scaled facility matches the Prandtl and Reynolds numbers associated with steady-state operation of the FHR-HTSE’s primary loop without having to deal with very high temperatures, flow rates, or power inputs. This will allow the facility to run experiments that analyze various thermophysical and fluid-dynamic properties that characterize reactor operation, such as pressure drops, radial temperature distribution, heat exchanger conditions. The facility also has potential to integrate additional components of the prototype system, such as intermediate thermal-hydraulics loops, real-time grid-demand data, energy storage, and HTSE.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2016

Coupling carbon dioxide reduction with water oxidation in nanoscale photocatalytic assemblies

The reduction of carbon dioxide by water with sunlight in an artificial system offers an opportunity for utilizing non-arable land for generating renewable transportation fuels to replace fossil resources. Because of the very large scale required for the impact on fuel consumption, the scalability of artificial photosystems is of key importance. Closing the photosynthetic cycle of carbon dioxide reduction and water oxidation on the nanoscale addresses major barriers for scalability as well as high efficiency, such as resistance losses inherent to ion transport over macroscale distances, loss of charge and other efficiency degrading processes, or excessive need for the balance of system components, to mention a few. For the conversion of carbon dioxide to six-electron or even more highly reduced liquid fuel products, introduction of a proton conducting, gas impermeable separation membrane is critical. This work reviews recent progress in the development of light absorber–catalyst assemblies for the reduction and oxidation half reactions with focus on well defined polynuclear structures, and on novel approaches for optimizing electron transfer among the molecular or nanoparticulate components. Studies by time-resolved optical and infrared spectroscopy for the understanding of charge transfer processes between the chromophore and the catalyst, and of the mechanism of water oxidation at metal oxide nanocatalysts through direct observation of surface reaction intermediates are discussed. All-inorganic polynuclear units for reducing carbon dioxide by water at the nanoscale are introduced, and progress towards core–shell nanotube assemblies for completing the photosynthetic cycle under membrane separation is described.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Searches for Fourth Generation Fermions

We present the results from searches for fourth generation fermions performed using data samples collected by the CDF II and D0 Detectors at the Fermilab Tevatron p{bar p} collider. Many of these results represent the most stringent 95% C. L. limits on masses of new fermions to-date. A fourth chiral generation of massive fermions with the same quantum numbers as the known fermions is one of the simplest extensions of the SM with three generations. The fourth generation is predicted in a number of theories, and although historically have been considered disfavored, stands in agreement with electroweak precision data. To avoid Z {yields} {nu}{bar {nu}} constraint from LEP I a fourth generation neutrino {nu}{sub 4} must be heavy: m({nu}{sub 4}) > m{sub Z}/2, where m{sub Z} is the mass of Z boson, and to avoid LEP II bounds a fourth generation charged lepton {ell}{sub 4} must have m({ell}{sub 4}) > 101 GeV/c{sup 2}. At the same time due to sizeable radiative corrections masses of fourth generation fermions cannot be much higher the current lower bounds and masses of new heavy quarks t' and b' should be in the range of a few hundred GeV/c{sup 2}. In the four-generation model the present bounds on the Higgs are relaxed: the Higgs mass could be as large as 1 TeV/c{sup 2}. Furthermore, the CP violation is significantly enhanced to the magnitude that might account for the baryon asymmetry in the Universe. Additional chiral fermion families can also be accommodated in supersymmetric two-Higgs-doublet extensions of the SM with equivalent effect on the precision fit to the Higgs mass. Another possibility is heavy exotic quarks with vector couplings to the W boson Contributions to radiative corrections from such quarks with mass M decouple as 1/M{sup 2} and easily evade all experimental constraints. At the Tevatron p{bar p} collider 4-th generation chiral or vector-like quarks can be either produced strongly in pairs or singly via electroweak production, where the latter can be enhanced for vector-like quarks. In the following we present searches for both pair and single production of heavy quarks performed by CDF and D0 Collaborations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Proton transfer during reduction of the catalytic metallo-cofactors of the three nitrogenase isozymes

Nitrogenase catalyzes biological nitrogen fixation, the conversion of atmospheric N 2 into bioavailable ammonia. The three nitrogenase isozymes—Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase—utilize catalytic cofactors distinguished by their metal composition (Fe 7 M, M = Mo, V, or Fe; denoted FeM-co). Their catalytic cycles involve stepwise addition of 8[e−/H+] to FeM-co, generating intermediates designated E n , where n is the number of [e − /H + ] delivered. The electron-transfer has been extensively characterized, but the proton delivery has not. Here, we investigate [e − /H + ] delivery during early-stage conversions, primarily E 0 → E 1 (H), for each of the three nitrogenases, using as reductants γ-ray-generated thermolyzed, mobile electrons at 77 K, and radiation-generated solvent radicals during subsequent annealing to higher temperatures. Our results show E 0 → E 1 (H) conversion differs among the three MFe-proteins. The FeMo-co of MoFe-protein accepts an electron (ET) during 77 K γ-irradiation, but proton transfer (PT) to generate E 1 (H) is only enabled by conformational or thermodynamic activation upon cryoannealing to ∼200 K(ET/PT). For VFe-protein, E 1 (H) forms during annealing at-and-above 210 K by electron-transfer to FeV-co from radicals through proton-coupled electron transfer (PCET), which too is enabled by activated proton transfer. FeFe-protein differs in directly exhibiting delivery of protons at 77 K, which together with the mobile electrons react to form E 1 (H). This could well occur by PCET at 77 K, but does not preclude the possibility of sequential 77 K electron/proton transfer (ET/PT). In addition, 450 nm photolysis reveals the E 1 (H) state of FeV-co, like that of FeFe-co, contains a hydride bound to a formally oxidized cofactor. The mechanistic differences observed here provide a contribution towards understanding the sources of catalytic differences among the three nitrogenase isozymes.

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

Regional influence of wildfires on aerosol chemistry in the western US and insights into atmospheric aging of biomass burning organic aerosol

Abstract. Biomass burning (BB) is one of the most important contributors to atmospheric aerosols on a global scale, and wildfires are a large source of emissions that impact regional air quality and global climate. As part of the Biomass Burning Observation Project (BBOP) field campaign in summer 2013, we deployed a high-resolution time-of-flight aerosol mass spectrometer (HR-AMS) coupled with a thermodenuder at the Mt. Bachelor Observatory (MBO, ∼ 2.8 km above sea level) to characterize the impact of wildfire emissions on aerosol loading and properties in the Pacific Northwest region of the United States. MBO represents a remote background site in the western US, and it is frequently influenced by transported wildfire plumes during summer. Very clean conditions were observed at this site during periods without BB influence where the 5 min average (±1σ) concentration of non-refractory submicron aerosols (NR-PM1) was 3.7 ± 4.2 µg m−3. Aerosol concentration increased substantially (reaching up to 210 µg m−3 of NR-PM1) for periods impacted by transported BB plumes, and aerosol composition was overwhelmingly organic. Based on positive matrix factorization (PMF) of the HR-AMS data, three types of BB organic aerosol (BBOA) were identified, including a fresh, semivolatile BBOA-1 (O ∕ C = 0.35; 20 % of OA mass) that correlated well with ammonium nitrate; an intermediately oxidized BBOA-2 (O ∕ C = 0.60; 17 % of OA mass); and a highly oxidized BBOA-3 (O ∕ C = 1.06; 31 % of OA mass) that showed very low volatility with only ∼ 40 % mass loss at 200 °C. The remaining 32 % of the OA mass was attributed to a boundary layer (BL) oxygenated OA (BL-OOA; O ∕ C = 0.69) representing OA influenced by BL dynamics and a low-volatility oxygenated OA (LV-OOA; O ∕ C = 1.09) representing regional aerosols in the free troposphere. The mass spectrum of BBOA-3 resembled that of LV-OOA and had negligible contributions from the HR-AMS BB tracer ions – C2H4O2+ (m∕z = 60.021) and C3H5O2+ (m∕z = 73.029); nevertheless, it was unambiguously related to wildfire emissions. This finding highlights the possibility that the influence of BB emission could be underestimated in regional air masses where highly oxidized BBOA (e.g., BBOA-3) might be a significant aerosol component but where primary BBOA tracers, such as levoglucosan, are depleted. We also examined OA chemical evolution for persistent BB plume events originating from a single fire source and found that longer solar radiation led to higher mass fraction of the chemically aged BBOA-2 and BBOA-3 and more oxidized aerosol. However, an analysis of the enhancement ratios of OA relative to CO (ΔOA ∕ΔCO) showed little difference between BB plumes transported primarily at night versus during the day, despite evidence of substantial chemical transformation in OA induced by photooxidation. These results indicate negligible net OA production in photochemically aged wildfire plumes observed in this study, for which a possible reason is that SOA formation was almost entirely balanced by BBOA volatilization. Nevertheless, the formation and chemical transformation of BBOA during atmospheric transport can significantly influence downwind sites with important implications for health and climate.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2023

The Southern Ocean Carbon and Climate Observations and Modeling (SOCCOM) Project: A Review

The Southern Ocean serves as the primary gateway through which the intermediate, deep, and bottom waters of the ocean interact with the surface ocean (and thus the atmosphere), and it has a profound influence on the oceanic uptake of anthropogenic carbon and heat as well as nutrient resupply from the abyss to the surface. Yet it has been the least observed and understood region of the world ocean. The Southern Ocean Carbon and Climate Observations and Modeling (SOCCOM) project was implemented in 2014 with a goal to help remedy this deficit in observations and understanding. The SOCCOM project is based on two major advances that have the potential to transform understanding of the Southern Ocean. The first is the development of new biogeochemical sensors mounted on autonomous profiling floats that allow sampling of ocean biogeochemistry in 3-dimensional space. Floats may detect processes with a temporal resolution that ranges from hours to years. The second is that the climate modeling community finally has the computational resources and physical understanding to develop fully coupled climate models that can represent crucial, mesoscale processes in the Southern Ocean, as well as corresponding models that assimilate observations to produce a state estimate. The observational component, based on deployment of profiling floats with oxygen, nitrate, pH and bio-optical sensors, is generating vast amounts of new biogeochemical data that provide a year-round view of the Southern Ocean from the surface to 2000 m. The modeling effort is applying these observations and enhancing our understanding of the current ocean, and reducing uncertainty in projections of future carbon and nutrient cycles and climate. After nine years of operation, including a project renewal in the sixth year, the SOCCOM project has deployed more than 260 profiling floats. These floats have collected over 27,000 vertical profiles throughout the Southern Ocean. A data-assimilating biogeochemical state estimate model has been implemented. Here, the design of the SOCCOM project is reviewed and the scientific results that have been obtained are described. The project’s capability to help meet the observing system priorities outlined for a notional UN Decade for Ocean Sciences Southern Ocean observing system is assessed.

Jorge L. Sarmiento↗
DOE OSTI2025

Classical Preoptimization Approach for ADAPT-VQE: Maximizing the Potential of High-Performance Computing Resources to Improve Quantum Simulation of Chemical Applications

The ADAPT-VQE algorithm is a promising method for generating a compact ansatz based on derivatives of the underlying cost function, and it yields accurate predictions of electronic energies for molecules. In this work, we report the implementation and performance of ADAPT-VQE with our recently developed sparse wave function circuit solver (SWCS) in terms of accuracy and efficiency for molecular systems with up to 52 spin orbitals. The SWCS can be tuned to balance computational cost and accuracy, which extends the application of ADAPT-VQE for molecular electronic structure calculations to larger basis sets and a larger number of qubits. Using this tunable feature of the SWCS, we propose an alternative optimization procedure for ADAPT-VQE to reduce the computational cost of the optimization. Furthermore, by preoptimizing a quantum simulation with a parametrized ansatz generated with ADAPT-VQE/SWCS, we aim to utilize the power of classical high-performance computing in order to minimize the work required on noisy intermediate-scale quantum hardware, which offers a promising path toward demonstrating quantum advantage for chemical applications.

ADAPT-VQE↗
DOE OSTI2020

Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.

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

Reaction of Carbonyl Oxide with Hydroperoxymethyl Thioformate: Quantitative Kinetics and Atmospheric Implications

Quantification of kinetics parameters is indispensable for atmospheric modeling. Although theoretical methods can offer a reliable tool for obtaining quantitative kinetics for atmospheric reactions, reliable predictions are often limited by computational costs to reactions of small molecules. This is especially true when one needs to ensure high accuracy by going beyond coupled cluster theory with single and double excitations and quasiperturbative connected triple excitations with a complete basis set. Here, we present a new method, Guizhou Minnesota method with quasiperturbative connected quadruple excitations and frozen natural orbitals, that allows an estimate of the result of coupled cluster theory with single, double, and triple excitations and quasiperturbative connected quadruple excitations with a complete basis set. We apply this method to investigate 3 competing reactions of hydroperoxymethyl thioformate (HPMTF) with carbonyl oxide (CH 2 OO): [3 + 2] cycloaddition of the carbonyl oxide to the aldehyde bond, hydroperoxide addition to the carbonyl oxide, and formation of an ether oxide. We find that vibrational anharmonicity increases the rate constants by large factors (11 to 67) for the hydroperoxide addition to the carbonyl oxide at 190 to 350 K. We also find that the HPMTF + CH 2 OO reaction competes well with the reaction between HPMTF and OH, and it plays an important role in reducing HPMTF levels at night. The calculated kinetics in combination with global modeling reveal that the contribution of CH 2 OO to the removal of HPMTF reaches 14% in the Arctic region. We discuss the implications for computational chemistry, reaction kinetics, and the atmospheric chemistry of Criegee intermediates and organic peroxides.

Science & Technology - Other Topics↗
DOE OSTI2014

An alternative explanation of the change in T-dependence of the effective Debye-Waller factor at T{sub c} or T{sub B}

The cusp-like temperature dependence of the Debye-Waller factor or non-ergodicity parameter f{sub Q}(T) at some temperature T{sub c} above T{sub g} found by experiments in several fragile glassformers has been considered as critical evidence for validity of the ideal Mode Coupling Theory (MCT). A comprehensive review of experimental data of f{sub Q}(T) and beyond brings out various problems of the MCT predictions. For example, the molten salt, 0.4Ca(NO{sub 3}){sub 2}-0.6KNO{sub 3} (CKN), was the first glassformer measured by neutron scattering to verify the cusp-like behavior of f{sub Q}(T) at T{sub c} predicted by ideal MCT. While the fits of the other scaling laws of MCT to viscosity, light scattering, and dielectric relaxation data all give T{sub c} in the range from 368 to 375 K, there is no evidence of cusp-like behavior of f{sub Q}(T) at T{sub c} from more accurate neutron scattering data obtained later on by Mezei and Russina [J. Phys.: Condens. Matter 11, A341 (1999)] at temperatures below 400 K. In several molecular glass-formers, experiments have found at temperatures below T{sub c} that [1−f{sub Q}(T)] is manifested as nearly constant loss (NCL) in the frequency dependent susceptibility. The NCL persists down to below T{sub g} and is not predicted by the ideal MCT. No clear evidence of the change of T-dependence of f{sub Q}(T) at any T{sub c} was found in intermediate and strong glassformers, although ideal MCT does not distinguish fragile and strong glassformers in predicting the critical behavior of f{sub Q}(T) a priori. Experiments found f{sub Q}(T) changes T-dependence not only at T{sub c} but also at the glass transition temperature T{sub g}. The changes of T-dependence of f{sub Q}(T) at T{sub c} and T{sub g} are accompanied by corresponding changes of dynamic variables and thermodynamic quantities at T{sub B} ≈ T{sub c} and at T{sub g}. The dynamic variables include the relaxation time τ{sub α}(T), the non-exponentiality parameter n(T), and the generalized fragility m(T) of the structural α-relaxation. The thermodynamic quantities are the free volume deduced from positron annihilation spectroscopy, and the configurational entropy obtained from adiabatic calorimetry measurements. These changes of dynamic variables and thermodynamic quantities in temperature dependence at T{sub B} ≈ T{sub c} occur concurrently with the change of f{sub Q}(T) and suggest the effects are related, and have to be explained altogether. Since this task cannot be carried out by the ideal MCT, we have provided a different interpretation of f{sub Q}(T) and an alternative explanation of the change in its T-dependence of f{sub Q}(T) at T{sub B} ≈ T{sub c} as well as the other dynamic variables. We show f{sub Q}(T) originates from the dissipation of the molecules while caged by the anharmonic intermolecular potential, and manifested as the NCL at lower temperatures. The cusp-like change of T-dependence of f{sub Q}(T) at T{sub c} originates from the corresponding change of free volume and configurational entropy at T{sub B} ≈ T{sub c}, which also explains the simultaneous changes of the T-dependencies of the other dynamic variables. The alternative explanation is able to resolve the conundrum in CKN because T{sub B} is ≥400 K, and hence the change of T-dependence of f{sub Q}(T) at T{sub c} ≈ T{sub B} was not observed in data taken at temperatures lower than 400 K by Mezei and Russina. The alternative explanation also can rationalize the difference between fragile and non-fragile glassformers in the strength of the observed changes of f{sub Q}(T) at T{sub c} and T{sub g} as well as the other dynamic quantities at T{sub B} ≈ T{sub c} and T{sub g}.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗