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  1. Free, publicly-accessible full text available September 19, 2024
  2. Abstract

    Hemoproteins have recently emerged as promising biocatalysts for new-to-nature carbene transfer reactions. However, mechanistic understanding of the interplay between productive and unproductive pathways in these processes is limited. Using spectroscopic, structural, and computational methods, we investigate the mechanism of a myoglobin-catalyzed cyclopropanation reaction with diazoketones. These studies shed light on the nature and kinetics of key catalytic steps in this reaction, including the formation of an early heme-bound diazo complex intermediate, the rate-determining nature of carbene formation, and the cyclopropanation mechanism. Our analyses further reveal the existence of a complex mechanistic manifold for this reaction that includes a competing pathway resulting in the formation of an N-bound carbene adduct of the heme cofactor, which was isolated and characterized by X-ray crystallography, UV-Vis, and Mössbauer spectroscopy. This species can regenerate the active biocatalyst, constituting a non-productive, yet non-destructive detour from the main catalytic cycle. These findings offer a valuable framework for both mechanistic analysis and design of hemoprotein-catalyzed carbene transfer reactions.

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  3. Understanding the relationship among elemental compositions, nanolamellar microstructures, and mechanical properties enables the rational design of high-entropy alloys (HEAs). Here, we construct nanolamellar AlxCoCuFeNi HEAs with alternating high– and low–Al concentration layers and explore their mechanical properties using a combination of molecular dynamic simulation and density functional theory calculation. Our results show that the HEAs with nanolamellar structures exhibit ideal plastic behavior during uniaxial tensile loading, a feature not observed in homogeneous HEAs. This remarkable ideal plasticity is attributed to the unique deformation mechanisms of phase transformation coupled with dislocation nucleation and propagation in the high–Al concentration layers and the confinement and slip-blocking effect of the low–Al concentration layers. Unexpectedly, this ideal plasticity is fully reversible upon unloading, leading to a remarkable shape memory effect. Our work highlights the importance of nanolamellar structures in controlling the mechanical and functional properties of HEAs and presents a fascinating route for the design of HEAs for both functional and structural applications.

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    Free, publicly-accessible full text available October 13, 2024
  4. Free, publicly-accessible full text available August 11, 2024
  5. Free, publicly-accessible full text available June 1, 2024
  6. Abstract

    A photochemical model of photosynthetic electron transport (PET) is needed to integrate photophysics, photochemistry, and biochemistry to determine redox conditions of electron carriers and enzymes for plant stress assessment and mechanistically link sun‐induced chlorophyll fluorescence to carbon assimilation for remotely sensing photosynthesis. Towards this goal, we derived photochemical equations governing the states and redox reactions of complexes and electron carriers along the PET chain. These equations allow the redox conditions of the mobile plastoquinone pool and the cytochrome b6f complex (Cyt) to be inferred with typical fluorometry. The equations agreed well with fluorometry measurements from diverse C3/C4species across environments in the relationship between the PET rate and fraction of open photosystem II reaction centres. We found the oxidation of plastoquinol by Cyt is the bottleneck of PET, and genetically improving the oxidation of plastoquinol by Cyt may enhance the efficiency of PET and photosynthesis across species. Redox reactions and photochemical and biochemical interactions are highly redundant in their complex controls of PET. Although individual reaction rate constants cannot be resolved, they appear in parameter groups which can be collectively inferred with fluorometry measurements for broad applications. The new photochemical model developed enables advances in different fronts of photosynthesis research.

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    Free, publicly-accessible full text available May 1, 2024
  7. Abstract

    Hydrologically mediated hot moments (HM‐HMs) of transient anomalous diffusion (TAD) denote abrupt shifts in hydraulic conditions that can profoundly influence the dynamics of anomalous diffusion for pollutants within heterogeneous aquifers. How to efficiently model these complex dynamics remains a significant challenge. To bridge this knowledge gap, we propose an innovative model termed “the impulsive, tempered fractional advection‐dispersion equation” (IT‐fADE) to simulate HM‐HMs of TAD. The model is approximated using an L1‐based finite difference solver with unconditional stability and an efficient convergence rate. Application results demonstrate that the IT‐fADE model and its solver successfully capture TAD induced by hydrologically trigged hot phenomena (including hot moments and hot spots) across three distinct aquifers: (a) transient sub‐diffusion arising from sudden shifts in hydraulic gradient within a regional‐scale alluvial aquifer, (b) transient sub‐ or super‐diffusion due to convergent or push‐pull tracer experiments within a local‐scale fractured aquifer, and (c) transient sub‐diffusion likely attributed to multiple‐conduit flow within an intermediate‐scale karst aquifer. The impulsive terms and fractional differential operator integrated into the IT‐fADE aptly capture the ephemeral nature and evolving memory of HM‐HMs of TAD by incorporating multiple stress periods into the model. The sequential HM‐HM model also characterizes breakthrough curves of pollutants as they encounter hydrologically mediated, parallel hot spots. Furthermore, we delve into discussions concerning model parameters, extensions, and comparisons, as well as impulse signals and the propagation of memory within the context of employing IT‐fADE to capture hot phenomena of TAD in aquatic systems.

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  8. Free, publicly-accessible full text available March 1, 2024
  9. Abstract

    Engineered heme proteins were developed to possess numerous excellent biocatalytic nitrenoid C−H functionalizations. Computational approaches such as density functional theory (DFT), hybrid quantum mechanics/molecular mechanics (QM/MM), and molecular dynamics (MD) calculations were employed to help understand some important mechanistic aspects of these heme nitrene transfer reactions. This review summarizes advances of computational reaction pathway results of these biocatalytic intramolecular and intermolecular C−H aminations/amidations, focusing on mechanistic origins of reactivity, regioselectivity, enantioselectivity, diastereoselectivity as well as effects of substrate substituent, axial ligand, metal center, and protein environment. Some important common and distinctive mechanistic features of these reactions were also described with brief outlook of future development.

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