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Nanoscale electrochemical kinetics & dynamics: the challenges and opportunities of single-entity measurements
The stochastic nature of very fast single-entity events challenges current electrochemical methods and modern electronics, as illustrated using recent experiments from the authors’ laboratory.
A dynamic kinetic model captures cell-free metabolism for improved butanol production
Cell-free systems are useful tools for prototyping metabolic pathways and optimizing the production of various bioproducts. Mechanistically-based kinetic models are uniquely suited to analyze dynamic experimental data collected from cell-free systems and provide vital qualitative insight. However, to date, dynamic kinetic models have not been applied with rigorous biological constraints or trained on adequate experimental data to the degree that they would give high confidence in predictions and broadly demonstrate the potential for widespread use of such kinetic models. In this work, we construct a large-scale dynamic model of cell-free metabolism with the goal of understanding and optimizing butanol production in a cell-free system. Using a combination of parameterization methods, the resultant model captures experimental metabolite measurements across two experimental conditions for nine metabolites at timepoints between 0 and 24 hours. Here, we present analysis of the model predictions, provide recommendations for butanol optimization, and identify the aldehyde/alcohol dehydrogenase as the primary bottleneck in butanol production. Sensitivity analysis further reveals the extent to which various parameters are constrained, and our approach for probing valid parameter ranges can be applied to other modeling efforts.
Catalytic Dynamic Kinetic Resolutions in Tandem to Construct Two-Axis Terphenyl Atropisomers
The defined structure of molecules bearing multiple stereogenic axes is of increasing relevance to materials science, pharmaceuticals, and catalysis. However, catalytic enantioselective approaches to control multiple stereogenic axes remain synthetically challenging. Here, we report the catalytic synthesis of two-axis terphenyl atropisomers, with complementary strategies to both chlorinated and brominated variants, formed with high diastereo- and enantioselectivity. The chemistry proceeds through a sequence of two distinct dynamic kinetic resolutions: first, an atroposelective ring opening of Bringmann-type lactones produces a product with one established axis of chirality, and second, a stereoselective arene halogenation delivers the product with the second axis of chirality established. In order to achieve these results, a class of Brønsted basic guanidinylated peptides, which catalyze an efficient atroposelective chlorination, is reported for the first time. In addition, a complementary bromination is reported, which also establishes the second stereogenic axis. These bromo-terphenyls are accessible following the discovery that chiral anion phase transfer catalysis by C 2 -symmetric phosphoric acids allows catalyst control in the second stereochemistry-determining event. Accordingly, we established the fully catalyst-controlled stereodivergent synthesis of all possible chlorinated stereoisomers while also demonstrating diastereodivergence in the brominated variants, with significant levels of enantioselectivity in all cases.
ELECTRONIC STRUCTURE METHODS AND PROTOCOLS WITH APPLICATION TO DYNAMICS, KINETICS AND THERMOCHEMISTRY
Hydrocarbon combustion involves the reaction dynamics of a tremendous number of species beginning with many-component fuel mixtures and proceeding via a complex system of intermediates to form primary and secondary products. Combustion conditions corresponding to new advanced engines and/or alternative fuels rely increasingly on autoignition and low-temperature-combustion chemistry. In these regimes various transient radical species such as HO2, ROO·, ·QOOH, HCO, NO2, HOCO, and Criegee intermediates play important roles in determining the detailed as well as more general dynamics. A clear understanding and accurate representation of these processes is needed for effective modeling. Given the difficulties associated with making reliable experimental measurements of these systems, computation can play an important role in developing these energy technologies. Accurate calculations have their own challenges since even within the simplest dynamical approximations such as transition state theory, the rates depend exponentially on critical barrier heights and these may be sensitive to the level of quantum chemistry. Moreover, it is well-known that in many cases it is necessary to go beyond statistical theories and consider the dynamics. Quantum tunneling, resonances, radiative transitions, and non-adiabatic effects governed by spin-orbit or derivative coupling can be determining factors in those dynamics. Building upon progress made during a period of prior support through the DOE Early Career Program, this project combines developments in the areas of potential energy surface (PES) fitting and multistate multireference quantum chemistry to allow spectroscopically and dynamically/kinetically accurate investigations of key molecular systems (such as those mentioned above), many of which are radicals with strong multireference character and have the possibility of multiple electronic states contributing to the observed dynamics. An ongoing area of investigation is to develop general strategies for robustly convergent electronic structure theory for global multichannel reactive surfaces including diabatization of energy and other relevant surfaces such as dipole transition. Combining advances in ab initio methods with automated interpolative PES fitting allows the construction of high-quality PESs (incorporating thousands of high-level data) to be done rapidly through parallel processing on high-performance computing (HPC) clusters. In addition, new methods and approaches to electronic structure theory will be developed and tested through applications. This project will explore limitations in traditional multireference calculations (e.g., MRCI) such as those imposed by internal contraction, lack of high-order correlation treatment and poor scaling. Methods such as DMRG-based extended active-space CASSCF and various Quantum Monte Carlo (QMC) methods will be applied (including VMC/DMC and FCIQMC). Insight into the relative significance of different orbital spaces and the robustness of application of these approaches on leadership class computing architectures will be gained. Synergy with other components of this research program such as automated PES fitting and multireference quantum chemistry will be used to address challenges encountered by the standard approaches to computational thermochemistry (those being single-reference quantum chemistry and perturbative treatments of the anharmonic vibrational energy, which break down for some cases of electronic structure or floppy strongly coupled vibrational modes).
Influence of Nd(II) and Nd(III) Ions on the Speciation and Kinetic Dynamics of Radiolytic Transients in Molten LiCl-KCl Eutectic Salt Mixtures
In the pyrochemical reprocessing of used nuclear fuel, understanding the effects of ionizing radiation on the chemical behavior of fission products in molten chloride eutectic salt is crucial. Here, this study investigates the impact of radiation on the chemical and kinetic speciation of Nd ions in molten LiCl-KCl eutectic, which are challenging to separate due to their multivalent oxidation states and comproportionation reactions. Electron pulse radiolysis techniques were used to determine transient absorption spectra, chemical kinetics, and activation parameters for the reaction of Nd ions with the primary products of molten LiCl-KCl eutectic radiolysis: the solvated electron (e S - ) and dichlorine radical anion (Cl 2 •- ). Initially, Nd(III) reacted rapidly with e S - , forming Nd(II) with a second-order rate coefficient of k = (4.54 ± 0.07) × 10 10 M -1 s -1 at 673 K. The resulting Nd(II) ions then reacted slowly with Cl 2 •- , regenerating Nd(III) with an estimated rate of k = (1.72 ± 0.04) × 10 10 M -1 s -1 at 673 K. Additionally, the comproportionation reaction of Nd(III) and Nd(s) to form Nd(II) was monitored chemically and electrochemically. This work suggests that the comproportionation reaction of Nd(III) with Nd(s) to form Nd(II) is unstable in molten LiCl-KCl eutectic.
Far-from-equilibrium kinetic dynamics of λ ϕ 4 theory in an expanding universe
Not Available
Ion kinetic dynamics in strongly-shocked plasmas relevant to ICF
Implosions of thin-shell capsules produce strongly-shocked (M > 10), low-density (ρ ~1 mg/cc -1 ), high-temperature (T i ~keV) plasmas, comparable to those produced in the strongly-shocked DT-vapor in inertial confinement fusion (ICF) experiments. A series of thin-glass targets filled with mixtures of deuterium and Helium-3 gas ranging from 7% to 100% deuterium was imploded to investigate the impact of multi-species ion kinetic mechanisms in ICF-relevant plasmas over a wide range of Knudsen numbers (N K ≡ λ ii /R). Anomalous trends in nuclear yields and burn-averaged ion temperatures in implosions with N K > 0.5, which have been interpreted as signatures of ion species separation and ion thermal decoupling, are found not to be consistent with single-species ion kinetic effects alone. Experimentally inferred Knudsen numbers predict an opposite yield trend to those observed, confirming the dominance of multi-species physics in these experiments. In contrast, implosions with N K ~ 0.01 follow the expected yield trend, suggesting single-species kinetic effects are dominant. In conclusion, the impact of the observed kinetic physics mechanisms on the formation of the hotspot in ICF experiments is discussed.
Evidence for Dynamic Chemical Kinetics at Individual Molecular Ruthenium Catalysts
Not provided.
A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics
Kinetic Monte Carlo (KMC) simulations are used to study long-time dynamics of a wide variety of systems. Unfortunately, the conventional KMC algorithm is not scalable to larger systems, since its time scale is inversely proportional to the simulated system size. A promising approach to resolving this issue is the synchronous parallel KMC (SPKMC) algorithm, which makes the time scale size-independent. This paper introduces a formal derivation of the SPKMC algorithm based on local transition-state and time-dependent Hartree approximations, as well as its scalable parallel implementation based on a dual linked-list cell method. The resulting algorithm has achieved a weak-scaling parallel efficiency of 0.935 on 1024 Intel Xeon processors for simulating biological electron transfer dynamics in a 4.2 billion-heme system, as well as decent strong-scaling parallel efficiency. The parallel code has been used to simulate a lattice of cytochrome complexes on a bacterial-membrane nanowire, and it is broadly applicable to other problems such as computational synthesis of new materials.
The kinetics and dynamics of the coma of Halley's comet
This grant to the University of Michigan supported the efforts of Michael R. Combi to serve as a co-investigator in collaboration with a larger effort by the principal investigator, William Smyth of Atmospheric and Environmental Research, Inc. The overall objective of this project was to analyze in a self-consistent manner unique optical O((sup 1)D) and NH2 ultra-high resolution line profile data of excellent quality and other supporting lower-resolution spectral data for the coma of comet P/Halley by using highly developed and physically-based cometary coma models in order to determine and explain in terms of physical processes the actual dynamics and photochemical kinetics that occur in the coma. The justification for this work is that it provides a valuable and underlying physical base from which to interpret significantly different types of coma observations in a self-consistent manner and hence bring into agreement (or avoid) apparent inconsistencies that arise from non-physically based interpretations. The level of effort for the Michigan component amounted to less than three person-months over a planned period of three years. The period had been extended at no extra cost to four years because the Michigan grant and the AER contract did not have coincident time periods. An effort of somewhat larger scope was undertaken by the PI. The importance of the O((sup 1)D) profiles is that they provide a direct trace of the water distribution in comets. The line profile shape is produced by the convolution of the outflow velocity and thermal dispersion of the parent water molecules with the photokinetic ejection of the oxygen atoms upon photodissociation of the parent water molecules. Our understanding of the NH2 and its precursor ammonia are important for comet-to-comet composition variations as they relate to the cosmo-chemistry of the early solar nebula. Modeling of the distribution of NH2 is necessary in order to infer the ammonia production rates from NH2 observations.
Dynamic XRD: atomic-scale phase transformations and kinetics under dynamic compression
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Early stage growth of amorphous thin film: Average kinetics, nanoscale dynamics, and pressure dependence
We used the coherent grazing incidence small angle x-ray scattering technique to study the average kinetics and nanoscale dynamics during early-stage a-WSi 2 sputter deposition. The kinetic and dynamic properties are examined as a function of pressure, which is known to be a critical factor in determining final surface roughness. Surface growth kinetics and dynamics are characterized by time parameters extracted from the height-height structure factor and correlation functions. The roughness at a given length scale reaches a maximum before relaxing down to a steady state. The lateral length scale dependence and pressure dependence are then compared among the measured kinetics and dynamics time parameters. Surfaces grown at lower pressures are smoother, leading to longer correlation times. The time parameters to reach a dynamic steady state and a kinetic steady state show contrasting pressure dependence. A dynamic steady state is reached earlier than the kinetic steady state at high pressure. A more random deposition direction and lower kinetic energy at higher pressures can explain these phenomena, along with the hypothesis that larger nanoclusters form in vapor before arriving at the surface. Here, a continuum model is applied to simulate the overall behavior with mixed success.
Flame dynamics and kinetic coupling of ammonia and dimethyl-ether in non-premixed cool and warm flames at elevated pressure
Developing advanced low-temperature combustion engines with ammonia-biofuel blends requires a comprehensive understanding of low-temperature flame dynamics and kinetic interactions between ammonia and oxygenated fuels at elevated pressures. This work aims to study the dynamics and kinetics of non-premixed Dimethyl Ether (DME)/Ammonia (NH 3 ) cool and warm flames, and their reignition to hot flames. A counterflow burner is employed to establish DME/NH 3 cool/warm flames at pressures up to 5 atm. The extinction limits of cool flame and the reignition limits of warm flame to hot flame are measured by varying NH 3 concentrations and compared to simulations to quantitatively examine the effects on DME/NH 3 flames. It is found that NH 3 inhibits low-temperature DME oxidation and results in lower cool flame extinction limits. Warm flames in the presence of NH 3 are observed for the first time, revealing a non-monotonic effect of NH 3 addition: a small amount of NH 3 presence enhances warm flame chemistry and promotes reignition to hot flames, while a high NH 3 concentration weakens the warm flame. This trend is further explained by 0-D PSR kinetic simulations and 1-D S-curve flame dynamic calculations. Three flame transition regimes between cool flames (CF), warm flames (WF), and hot flames (HF) by different levels of NH 3 additions at a specific strain rate are identified, namely WFHF reignition, WF-CF transition, and WF extinction. Reaction sensitivity analyses of OH at low temperatures show that NH3 inhibits DME oxidation through OH consumption via H-abstraction and the kinetic couplings of RO 2 /NH 2 , RO 2 /NO x , R/NO x , and O 2 QOOH/NO x further suppress the low-temperature branching. At intermediate-temperatures, NH 2 /NO x /HO 2 coupling promotes warm flames via the pathway NH 2 → H 2 NO → HNO → NO by converting O 2 → HO 2 → OH. At even higher NH₃ concentrations, radical termination reactions of NH 2 + NO/NO 2 and excessive OH consumption via H-abstraction inhibit the flame. The insights into the kinetic coupling between NH 3 and low-temperature chemistry at elevated pressure and its impact on the dynamics of cool-warm-hot flame transitions will contribute to advancing combustion technologies with reduced emissions and improved energy-efficiency.
The kinetic and dynamic aspects of corrosion fatigue in a gaseous hydrogen environment.
The stable, subcritical crack growth stage of fracture under conditions of corrosion fatigue was studied experimentally in order to demonstrate the importance of the kinetic and dynamic aspects of environment-sensitive behavior. The cyclic loading of a titanium alloy in a low-pressure gaseous hydrogen environment is compared to that in a vacuum environment. The influence of the hydrogen environment on the rate of subcritical crack growth is discussed.
Classical trajectory studies of gas phase reaction dynamics and kinetics using ab initio potential energy surfaces
Strategies for constructing global potential energy surfaces from a limited number of accurate ab initio electronic energy calculations are discussed. Generally, these data are concentrated in small regions of configuration space (e.g., in the vicinity of saddle points and energy minima) and difficulties arise in generating a potential function that is globally well-behaved. Efficient computer codes for carrying out classical trajectory calculations on vector and parallel processors are also described. Illustrations are given from recent work on the following chemical systems: Ca + HF yields CaF + H, H + H + H2 yields H2 + H2, N + O2 yields NO + O and O + N2 yields NO + N. The dynamics and kinetics of metathesis, dissociation, recombination, energy transfer and complex formation processes will be discussed.
Gas Dynamics and Kinetics in the Cometary Coma: Theory and Observations
Our ability to describe the physical state of the expanding coma affects fundamental areas of cometary study both directly and indirectly. In order to convert measured abundances of gas species in the coma to gas production rates, models for the distribution and kinematics of gas species in the coma are required. Conversely, many different types of observations, together with laboratory data and theory, are still required to determine coma model attributes and parameters. Accurate relative and absolute gas production rates and their variations with time and from comet to comet are crucial to our basic understanding of the composition and structure of cometary nuclei and their place in the solar system. We review the gas dynamics and kinetics of cometary comae from both theoretical and observational perspectives, which are important for understanding the wide variety of physical conditions that are encountered.