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At least 73 records · Page 4

Toward a Unified Kinetic Model of Nitrogenase Catalysis

The microbial enzyme nitrogenase catalyzes the MgATP-dependent reduction of N 2 to 2NH 3 , a transformation central to the global nitrogen cycle. While the canonical Thorneley−Lowe (TL) kinetic model has long served as a mechanistic framework, it does not incorporate several recent insights. Here, we present an updated kinetic model for Monitrogenase that incorporates these new findings. A significant insight is that electron transfer (ET) from the reduced Fe protein to the FeMo-cofactor is gated by MgATP-dependent conformational transitions and can be described as a probabilistic event that is dependent on the ligand bound to the active-site metallocofactor. The updated kinetic model quantitatively reproduces steady-state product formation rates across a broad range of experimental conditions, yielding revised estimates for key rate constants. It is demonstrated that under N 2 turnover, the probability of productive ET to the active site decreases by ∼60%, resulting in a significant fraction of Fe protein cycles that are unproductive for electron delivery. This mechanistic feature explains the observed rate limitation in N 2 reduction and implies a revised minimum energetic cost of approximately 25 MgATP per N 2 reduced. Integrating these new features into the revised kinetic model provides a more complete and usable foundation for understanding nitrogenase catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Temperature dependence of the self-reaction of CH3O2 radicals

The rate constants for the reaction CH3O2 + CH3O2 yields products (1) were measured in the temperature range from 248 to 417 K, taking into consideration pressures in the range from 60 to 700 torr of N2. The experimental investigation was carried out in a Pyrex flash photolysis system employing ultraviolet absorption detection. Methylperoxy radicals (CH3O2) were produced by the photolysis of Cl2-CH4-O2 mixtures. Rate constants were measured by observing the second-order disappearance of CH3O2 radicals. Plots of 1/(CH3O2 optical density) vs. time were observed to be linear over a concentration change of a factor of 10-50. Results of the kinetic runs at each temperature are summarized in a table, and an Arrhenius plot of the data is shown in a graph.

Sander, S. P.↗

Kinetics and mechanism of the disproportionation of BrO radicals

In the reported investigation, measurements were conducted of the rate constant for the reaction BrO + BrO yields products (1), taking into account the temperature range from 223 to 338 K and the pressure range from 50 to 475 torr of He. The flash photolysis-ultraviolet absorption technique was employed in the experiments. Two independent approaches were used to determine the relative rates of the two reaction branches, BrO + BrO yields BrOO + Br (1a), and BrO + BrO yields Br2 + O2 (1b), one dependent and the other independent of the BrO absorption cross section with the results being in excellent agreement. The rate constant, k(1), was found to be independent of pressure.

Sander, S. P.↗

Dynamics of Product Branching from Radical Intermediates in Elementary Combustion Reactions (Final Technical Report)

While the total rate constant for many elementary reactions is well-characterized, understanding the product branching in complex reactions presents a formidable challenge. To gain an incisive probe of such reactions, our experiments investigate the dynamics of the product channels that arise from transient radical intermediates along the bimolecular reaction coordinates. Our recent published work uses the methodology developed in my group in the last fifteen years, using both imaging and scattering apparatuses. The experiments generate a particular isomeric form of an unstable radical intermediate along a bimolecular reaction coordinate and study the branching between the ensuing product channels of the energized radical as a function of its internal rotational and vibrational energy under collision-less conditions. The experiments use a combination of: 1) measurement of product velocity and angular distributions in a crossed laser-molecular beam apparatus, with electron bombardment detection in my lab in Chicago or 2) with tunable vacuum ultraviolet photoionization detection at Taiwan's National Synchrotron Radiation Research Center (NSRRC), and 3) velocity map imaging using state-selective REMPI and single photon VUV ionization of radical intermediates and reaction products. We also employ tunable VUV photoionization detection in our imaging apparatus, using difference frequency four-wave mixing to produce photoionization light tunable from 8 to 10.8 eV. This year of support funded our work to photolytically generate the radical intermediate important in the OH + propene reaction when OH adds to an end carbon. Our other major result this past year was on the photoionization detection of vinoxy radicals. Our experiments at the NSRRC definitively show that vinoxy dissociatively ionizes to both CH 3 + and HCO + , and establishes the absolute partial photoionization cross section of vinoxy to CH 3 + at 10.5 and 11.44 eV. This should allow experimentalists detecting vinoxy radicals produced in bimolecular reactions such as OH + propene to get good branching fractions to that product channel. Finally we initiated studies of the photodissociation of 1-bromo-2-chloroethane and 1,1-bromochloroethane at 193 nm at the NSRRC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Pre-steady-state kinetics of nanocrystal:molybdenum nitrogenase biohybrids reveals hole-scavenging efficiency is critical to N 2 reduction

Molybdenum (Mo) nitrogenase is a two-component enzyme complex that catalyzes the reduction of dinitrogen to ammonia and protons to hydrogen gas. We have shown that electrons for dinitrogen reduction can be delivered photochemically to the catalytic MoFe protein component by cadmium sulfide (CdS) nanocrystals. In this study, we used electron paramagnetic resonance spectroscopy to measure the transient populations of catalytic intermediates. We fit the populations with a pre-steady-state kinetic model, which allowed us to distinguish between productive and non-productive reaction pathways and extract the rate constants for the reaction. Our results demonstrated that the rate of catalytic electron delivery into MoFe protein increased with the concentration of the sacrificial electron donor. This enabled electron delivery to exceed the rate of hydride protonation, a relaxation pathway that competes with N 2 binding. Thus, managing the balance between electron transfer and hole transfer reactions is required to achieve a kinetic regime that favors N 2 reduction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Reaction Rates of Amidogen and Ammonia with Nitrous Oxide: Implications for Combustion Mechanisms

Pulsed laser photolysis experiments with laser-induced fluorescence detection of NH 2 set an upper limit to the rate constant for reaction with N 2 O of k < 1 × 10 −15 cm 3 molecule −1 s −1 at 513 K. Computations were based on geometries and anharmonic frequency analysis (B2PLYP-D3/cc-pVTZ) followed by coupled cluster calculations extrapolated to the infinite basis set limit, with corrections for core−valence electron correlation, scalar relativistic effects, and correlation up to CCSDT(Q). Species that showed multireference character were quantified with MRCI(7,7)+Q/cc-pVTZ theory. Rate constants were obtained for the dominant product channel H 2 NN + NO, along with HN 3 + OH, H 2 NO + N 2 , NNH + HNO, ON(NH) 2 and HNNH + NO. The last channel is slow even at 2500 K, contrary to an early empirical estimate and confirming recent suggestions. Modeling of literature experiments on oxidation of NH 3 by N 2 O shows that all channels are too slow to make a significant impact on the loss of N 2 O in ammonia flames. Similarly, the direct NH 3 + N 2 O reaction is found to be negligibly slow.

Ammonia↗

PoolDilutionR : An R package for easy optimization of isotope pool dilution calculations

Abstract Isotopic pool dilution is a powerful approach to quantify gross biogeochemical transformation rates, but remains seldom used despite its potential. To facilitate broader implementation of pool dilution methods, we present a user‐friendly R package that optimizes gross production and consumption rates (and optionally fractionation constants as well) based on standard pool dilution time series data. This package features extensive documentation and example analyses, and is easily integrated into analytical pipelines. With this open‐source tool, the biogeochemistry community will be able to readily apply isotope pool dilution to a wide range of processes.

59 BASIC BIOLOGICAL SCIENCES↗

Kinetic Model of Photochemical Nitrogen Reduction [SWR-25-97]

The code in this repository was used to model the kinetics of photochemical nitrogen reduction. Each directory represents a manuscript. The directory titled Dahl_CRPS_2025 contains the code used to fit the kinetic models presented in the manuscript titled, "Pre-steady-state kinetics of nanocrystal:molybdenum nitrogenase biohybrids reveals hole-scavenging efficiency is critical to achieving N2 reduction" by Peter J. Dahl, Lauren M. Pellows, Zhi-Yong Yang, Lance C. Seefeldt, John W. Peters, Gordana Dukovic, David W. Mulder, and Paul W. King. Molybdenum (Mo) nitrogenase is a two-component enzyme complex that catalyzes the reduction of dinitrogen to ammonia and protons to hydrogen gas. We have shown that electrons for dinitrogen reduction can be delivered photochemically to the catalytic MoFe protein component by CdS nanocrystals. In this study, we used electron paramagnetic resonance spectroscopy to measure the transient populations of catalytic intermediates. We fit the populations with a pre-steady-state kinetic model which allowed us to distinguish between productive and non-productive reaction pathways and extract the rate constants for the reaction. Our results demonstrated that the rate of catalytic electron delivery into MoFe protein increased with the concentration of sacrificial electron donor. This enabled electron delivery to exceed the rate of hydride protonation, a relaxation pathway which competes with N2 binding. Thus, managing the balance between electron transfer and hole transfer reactions is required to achieve a kinetic regime that favors N2 reduction.

Dahl, Peter [National Renewable Energy Laboratory ↗

Soil Incubation, Methane Pool Dilution, Edgewater, MD, USA, July 2022 v1.0.1

Isotopic pool dilution is a powerful approach to quantify gross biogeochemical transformation rates, but remains seldom used despite its potential. To facilitate broader implementation of pool dilution methods, we developed a user-friendly R package that optimizes gross production and consumption rates (and optionally fractionation constants as well) based on standard pool dilution time series data. This data package is the soil methane pool dilution data and code for building and using this software, including source code (R) and raw data (.csv). This package features extensive documentation and example analyses, and is easily integrated into analytical pipelines as R software is free and open source. Operation of this package requires R version 2.10 or newer, and we recommend its use in conjunction with packages testthat (3.0.0), knitr, rmarkdown, ggploto2, tibble, and tidyr.

54 ENVIRONMENTAL SCIENCES↗

Quantitative photoexcitation and fluorescence studies of C2H2 in vacuum ultraviolet

Synchrotron radiation light source measurements were conducted in the 105-155 nm region to obtain the photoabsorption and fluorescence cross sections of C2H2, and the quantum yield for producing the C2H-asterisk fluorescence from C2H2's photodissociation was measured in the 106-136.5 nm region. The products of the radiative lifetime quenching rate constant increase with excitation wavelengths. The data obtained on lifetimes, quenchings, and fluorescence spectra point to an upper state of the C2H-asterisk fluorescence that is well bound, while the lower state is a repulsive or weak-bound state.

Suto, M.↗

Determination of Comet Halley gas emission characteristics from mass loading of the solar wind

The velocity profile of the solar wind during Giotto's approach to Comet Halley is fitted with the mass loading produced by a simple model of the neutral particle distribution. The model is used to calculate the implanted ion flux at Giotto for any given time and position along the spacecraft trajectory. Comparing the added flux with Giotto's solar wind proton data from the inbound leg outside the bow shock, the ratio of the total mass-loaded ion flux to the solar wind flux at the spacecraft is computed. Hence, using equations given by Galeev et al. (1985) values of the solar wind velocity, u-infinity, far upstream from the comet are inferred. Imposing the condition that u-infinity should be as nearly as possible constant in time, values of gas production rate and the ratio between radial expansion velocity and ionization rate required to fit the model to data are derived. The values obtained are consistent with those derived by more direct methods.

Huddleston, D. E.↗

Measurement and analysis of grain boundary grooving by volume diffusion

Experimental measurements of isothermal grain boundary grooving by volume diffusion are carried out for Sn bicrystals in the Sn-Pb system near the eutectic temperature. The dimensions of the groove increase with a temporal exponent of 1/3, and measurement of the associated rate constant allows the determination of the product of the liquid diffusion coefficient D and the capillarity length Gamma associated with the interfacial free energy of the crystal-melt interface. The small-slope theory of Mullins is generalized to the entire range of dihedral angles by using a boundary integral formulation of the associated free boundary problem, and excellent agreement with experimental groove shapes is obtained. By using the diffusivity measured by Jordon and Hunt, the present measured values of Gamma are found to agree to within 5 percent with the values obtained from experiments by Gunduz and Hunt on grain boundary grooving in a temperature gradient.

Hardy, S. C.↗

Seasonal variability of light availability and utilization in the Sargasso Sea

A 2 year time series of optical, biogeochemical, and physical parameters, taken near the island of Bermuda, is used to evaluate the sources of temporal variability in light avaliability and utilization in the Sargasso Sea. Integrated assessments of light availability are made by examining the depth of constant percent incident photosynthetically available radiation (% PAR) isolumes. To first order, changes in the depth %PAR isolumes were caused by physical processes: deep convection mixing in the winter which led to the spring bloom and concurrent shallowing of %PAR depths and the occurrence of anomalous thermohaline water masses during the summer and fall seasons. Spectral light availability variations are assessed using determinations of diffuse attenuation coefficient spectra which illustrates a significant seasonal cycle in colored detrital particulate and/or dissolved materials that is unrelated to changes in chlorophyll pigment concentrations. Temporal variations in the photosynthetic light utilization index Psi are used to assess vertically intergrated light utilization variations. Values of Psi are highly variable and show no apparent seasonal pattern which indicates that Psi is not simply a 'biogeochemical constant.' Determinations of in situ primary production rates and daily mean PAR fluxes are used to diagnose the relative role of light limitation in determining vertically integrated rates of primary production integral PP. The mean depth of the light-saturated zone (the vertical region where the daily mean PAR flux was greater than or equal to the saturation irradiance) is only approximately 40 m, although more than one half of interal PP occurred within this zone. Production model results illustrate that accurate predictions of integral PP are dependent upon rates of light-saturated production rather than upon indices of light limitation. It seems unlikely that significant improvements in simple primary production models will come from the partitioning of the Earth's seas into biogeochemical provinces.

Siegel, David A.↗

Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

Computed potential energy surfaces are often required for computation of such observables as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method with the Dunning correlation consistent basis sets to obtain accurate energetics, gives useful results for a number of chemically important systems. Applications to complex reactions leading to NO and soot formation in hydrocarbon combustion are discussed.

Walch, Stephen P.↗

Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions

Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. For some dynamics methods, global potential energy surfaces are required. In this case, it is necessary to obtain the energy at a complete sampling of all the possible arrangements of the nuclei, which are energetically accessible, and then a fitting function must be obtained to interpolate between the computed points. In other cases, characterization of the stationary points and the reaction pathway connecting them is sufficient. These properties may be readily obtained using analytical derivative methods. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives usefull results for a number of chemically important systems. The talk will focus on a number of applications including global potential energy surfaces, H + O2, H + N2, O(3p) + H2, and reaction pathways for complex reactions, including reactions leading to NO and soot formation in hydrocarbon combustion.

Walch, Stephen P.↗

Minimum Energy Pathways for Chemical Reactions

Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives useful results for a number of chemically important systems. The talk will focus on a number of applications to reactions leading to NOx and soot formation in hydrocarbon combustion.

Walch, S. P.↗

Kinetic Re-Evaluation of Fuel Neutralization by AKGA

Baseline characterization testing previously identified alpha-ketoglutaric acid (AKGA) cis a potential alternative to the current standard hydrazine (HZ) family fuel neutralization techniques in use at Kennedy Space Center (KSC). Thus far, the reagent shows promise for use in hardware decontamination operations and as a drop-in replacement for the scrubber liquor currently used in KSC four tower vapor scrubbers. Implementation of AKGA could improve process safety and reduce or eliminate generation of hydrazine-Iaden waste streams. This paper focuses on evaluation of the kinetics of these decontamination reactions in solution. Pseudo first order reaction rate constants with respect to the pyridazine products (6-oxo-4,5-dihydro-1H-pyridazine-3-carboxylic acid, (PCA) and 1-methyl-6-oxo-4,5-dihydro-pyridazine-3-carboxylic acid (mPCA)) in the presence of excess AKGA were determined by monitoring product formation using a ultra-violet visible absorption spectroscopy method. The results are presented here in comparison to previous data obtained by monitoring reactant depletion by gas chromatography with nitrogen phosphorus detector (GC-NPD).

Oropeza Cristina↗

Applicability of the Delplot method for the determination of catalytic reaction sequences: Hydrodeoxygenation of $\gamma$-valerolactone on Ni 2 P/MCM-41

Contact-time measurements based on sites are used to investigate the reaction sequence of the hydrodeoxygenation of γ-valerolactone (GVL) on Ni 2 P/MCM-41. Here the study is carried out at 300 °C and 0.5 MPa with site times of 0.29–6.1 s. A reaction network is proposed in which pentanoic acid and 2-methyltetrahydrofuran (2-MTHF) are formed in parallel initially and pentanal, butane and pentane are formed subsequently. A first-rank Delplot analysis (selectivity) gives a good fit, but higher-rank Delplots do not. The lack of applicability is explained by the magnitude of the rate constants, in which the rate constant for one of the later steps (the consumption of pentanal) is substantially larger than those for the preceding steps. For this reason, pentanal demonstrated the characteristics of a primary product and consequently affected the discrimination of higher rank products. A simulation of a model sequence with assumed rate constants confirms the reason why the Delplot method does not work for this reaction. Since the rate constants cannot be determined a priori to be of close magnitude, the Delplot method cannot be generally used to ascertain reaction sequences.

42 ENGINEERING↗