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At least 919 records · Page 51

Enzymatic Nitrogen Insertion into Unactivated C–H Bonds

Selective functionalization of aliphatic C–H bonds, ubiquitous in molecular structures, could allow ready access to diverse chemical products. While enzymatic oxygenation of C–H bonds is well established, the analogous enzymatic nitrogen functionalization is still unknown; nature is reliant on pre-oxidized compounds for nitrogen incorporation. Likewise, synthetic methods for selective nitrogen derivatization of unbiased C–H bonds remain elusive. In this work, new-to-nature heme-containing nitrene transferases were used as starting points for the directed evolution of enzymes to selectively aminate and amidate unactivated C(sp3)–H sites. The desymmetrization of methyl- and ethylcyclohexane with divergent site selectivity is offered as demonstration. The evolved enzymes in these lineages are highly promiscuous and show activity towards a wide array of substrates, providing a foundation for further evolution of nitrene transferase function. Computational studies and kinetic isotope effects (KIEs) are consistent with a stepwise radical pathway involving an irreversible, enantiodetermining hydrogen atom transfer (HAT), followed by a lower-barrier diastereoselectivity determining radical rebound step. In-enzyme molecular dynamics (MD) simulations reveal a predominantly hydrophobic pocket with favorable dispersion interactions with the substrate. Here, by offering a direct path from saturated precursors, these enzymes present a new biochemical logic for accessing nitrogen-containing compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Proton-Coupled Electron Transfer in a Ruthenium(II) Bipyrimidine Complex in Its Ground and Excited Electronic States

In this work, proton-coupled electron transfer (PCET) was studied for the ground and excited electronic states of a [Ru(terpy)(bpm)(OH 2 )(PF 6 ) 2 ] complex, Ru-bpm. Cyclic voltammetry measurements show that the Ru(II)-aqua moiety undergoes PCET to form a Ru(IV)-oxo moiety in the anodic region, while the bpm ligand undergoes PCET to form bpmH 2 in the cathodic region. The photophysical behavior of Ru-bpm was studied using steady-state and femtosecond transient UV–vis absorption spectroscopy, coupled with density functional theory (DFT) calculations. The lowest-lying excited state of Ru-bpm is described as a (Ru → bpm) metal-to-ligand charge-transfer (MLCT) state, while the metal-centered (MC) excited state was found computationally to be close in energy to the lowest-energy bright MLCT state (MC state was 0.16 eV above the MLCT state). The excited-state kinetics of Ru-bpm were found via transient absorption spectroscopy to be short-lived and were fit well to a biexponential function with lifetimes $τ_1$ = 4 ps and $τ_2$ = 65 ps in aqueous solution. Kinetic isotope effects of 1.75 ($τ_1$) and 1.61 ($τ_2$) were observed for both decay components, indicating that the solvent plays an important role in the excited-state dynamics of Ru-bpm. Based on the pH-dependent studies and the results from prior studies of similar Ru-complexes, we hypothesize that the 3 MLCT state forms an excited-state hydrogen-bond adduct with the solvent molecules and that this process occurs with a 4 ps lifetime. The formation of such a hydrogen-bond complex is consistent with the electronic density accumulation at the peripheral N atoms of the bpm moiety in the 3 MLCT state. The hydrogen-bonded state 3 MLCT decays to the ground state with a 65 ps lifetime. Such a short lifetime is likely associated with the efficient vibrational energy transfer from the 3 MLCT state to the solvent.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deciphering Reaction Mechanisms of Molecular Proton Reduction Catalysts with Cyclic Voltammetry: Kinetic vs Thermodynamic Control

The kinetics and thermodynamics of elementary reaction steps involved in the catalytic reduction of protons to hydrogen define the reaction landscape for catalysis. The mechanisms can differ in the order of the elementary proton transfer, electron transfer, and bond-forming steps and can be further differentiated by the sites at which protons and electrons localize. Access to fully elucidated mechanistic, kinetic, and thermochemical details of molecular catalysts is crucial to facilitate the development of new catalysts that operate with optimal efficiency, selectivity, and durability. The mechanism by which a catalyst operates, as well as the kinetics and thermodynamics associated with the individual steps, can often be accessed through electroanalytical studies. Here, this Account details the application of cyclic voltammetry to interrogate reaction mechanisms and quantify the kinetics and thermodynamics of elementary reaction steps for a series of molecular catalysts that mediate electrochemical proton reduction. I distinguish the limiting scenarios wherein a catalyst operates under kinetic control vs thermodynamic control, with a focus on detecting how cyclic voltammetry features shift with proton source strength and concentration, as well as scan rate. For systems that operate under kinetic control, catalytic currents are observed at, or slightly positive toward, the formal potential for the redox process that triggers catalysis. Under thermodynamic control, catalytic responses shift as a function of the proton source pKa and effective pH of the solution. After drawing this distinction, we introduce the appropriate voltammetry experiments and accompanying analytical expressions for extracting key metrics from the data. To illustrate analytical strategies to quantify elementary reaction steps of catalysts operating under kinetic control, I describe our studies of proton reduction catalysts Co(dmgBF 2 ) 2 (CH 3 CN) 2 (dmgBF 2 = difluoroboryl-dimethylglyoxime) and [Ni(P 2 Ph N 2 Ph ) 2 ] 2+ (P 2 Ph N 2 Ph = 1,5-phenyl-3,7-phenyl-1,5-diaza-3,7-diphosphacyclooctane). Here, peak shift analysis, foot-of-the-wave analysis, and plateau current analysis are applied to data sets wherein voltammetric response are recorded as a function of catalyst concentration, proton source concentration, proton source strength, and scan rate to quantify rate constants for elementary proton transfer and bond-forming steps in a catalytic cycle. Further, the case study of [Ni(P 2 Ph N 2 Ph ) 2 ] 2+ illustrates how complementary spectroscopic methods can bolster the mechanistic assignment. Collectively, these two studies showcase how detailed mechanistic studies inform on rate-limiting elementary steps in catalysis and other key processes underpinning catalysis. Second, I present analytical strategies to interrogate catalysts operating under thermodynamic control, centered on the case study of [Ni II (P 2 Ph N 2 Bn ) 2 ] 2+ (P 2 Ph N 2 Bn = 1,5-dibenzyl-3,7-diphenyl-1,5-diaza-3,7-diphosphacyclooctane). Here, the application of nonaqueous Pourbaix theory to extract thermodynamic information is introduced, and the construction of a coupled Pourbaix diagram is detailed. This study identifies ligand-based protonation as the key process that places catalysis under thermodynamic control and influences the reaction mechanism. Together, the work detailed in this Account showcases the utility of electroanalytical methods to disentangle complex reaction mechanisms and extract key thermochemical and kinetic parameters for elementary steps of catalysis. Through detailed presentation of the key analytical expressions that underpin these analyses, this Account seeks to facilitate the adoption of cyclic voltammetry by the community to fully extract kinetic, thermochemical, and mechanistic information on electrochemical small-molecule activation.

catalysts↗

Breaking the Linear Scaling Relations for the Oxygen Reduction Reaction with a Dual‐Atom Catalyst Composed of a MnFe‐Porphyrrole Aerogel

Bimetallic catalysts offer enhanced catalytic performance through synergistic interactions between the two metals, allowing them to break the linear scaling relations and reach high electrocatalytic activity. This study presents bimetallic aerogel-based catalyst synthesized as a covalent, three-dimensional framework containing neighboring iron and manganese sites. The aerogel structure provides a high surface area and porosity, facilitating an ultra-high active site density and efficient mass transport. The MnFe porphyrrole's unique structure is obtained by alternately linking Mn-porphyrin and Fe-corrole complexes. It exhibited outstanding performance with an onset potential of 0.99 V RHE . Comparative studies with a free-base Fe porphyrrole catalyst (E onset 0.97 V RHE ) revealed that while Mn incorporation led to only a slight improvement in half-cell performance, it resulted in significantly enhanced performance in anion exchange membrane fuel cell. The MnFe catalyst achieved an OCV of 0.97 V and a peak power density of 0.27 W cm −2 , outperforming the free-base Fe counterpart. Using density functional theory calculations, we show that the higher ORR activity of MnFe-porphyrrole is due to charge transfer between Mn and Fe atoms, which is absent in the reference free-base Fe-porphyrrole. These findings underscore the advantages of bimetallic catalysts in improving ORR activity and fuel cell efficiency by leveraging synergistic effects.

Aerogel↗

Physics-guided neural networks with engineering domain knowledge for hybrid process modeling

As neural networks are more frequently used to solve problems in science and engineering, the methods used to incorporate scientific knowledge into these networks are becoming increasingly complex. Here, this work breaks down these complicated techniques into a set of basic strategies which can easily be applied to diverse situations. Several novel neural networks are built using the categories laid out in this work. These networks are tested on simulated data from a continuous stirred tank reactor (CSTR) model to evaluate the advantages provided by each network. The three points demonstrated in this work are: (1) architectural hybrid models can speed up convergence and reduce the amount of data necessary to train a model; (2) adding a physics-guided loss function can improve model generalization and make models more physically consistent; (3) using physics-guided initialization and transfer learning improves accuracy and speeds up convergence, but can harm generalizability if used incorrectly.

42 ENGINEERING↗

Well-Tunable, 3D-printable, and Fast Autonomous Self-Healing Elastomers

Self-healing elastomers provide extended longevity of functional materials, due to their unique adaptability and durability. However, a major scientific challenge remains in developing materials with a rapid healing process combined with decent mechanical properties, that can be prepared by a relatively simple synthesis approach. Herein, we report a versatile design approach on self-healing elastomers by incorporating two different hydrogen bonding containing monomers, i.e., 2-[[(butylamino)carbonyl]oxy]ethyl acrylate (BCOE) and 2-ureido-4[1H]pyrimidinone (UPy) functionalized ethyl methacrylate. Poly(BCOE-r-UPy)s are synthesized by reversible addition-fragmentation chain-transfer (RAFT) polymerization, and controlling the ratio of two monomers enables well-tunable mechanical properties with tensile strength ranging from 0.04 to 6.3 MPa and tensile strain up to 3,000 %. The characteristic dissociation energy is calculated from a temperature dependence of terminal relaxation followed by subtracting the segmental relaxation. The rapid autonomous self-healing is achieved when the molar composition of Poly(BCOE-r-UPy) is tailored to BCOE/UPy = 99/1. The self-healing process is monitored in situ by a helium-ion microscope, and its macroscopic study using tensile tests indicates that Poly(BCOE-r-UPy1) with 1 % molar ratio of UPy recovers 70 % of its original toughness at ambient temperature within 10 mins. 3D printing of Poly(BCOE-r-UPy) affords a self-healable 3D structure, demonstrating the adaptability of Poly(BCOE-r-UPy) for on-demand fabrication. The simplicity of synthesis, well-tunable mechanical properties, unique self-healability, and 3D printing capability of Poly(BCOE-r-UPy)s indicate their potential for a range of applications.

36 MATERIALS SCIENCE↗

Flow over an espresso cup: inferring 3-D velocity and pressure fields from tomographic background oriented Schlieren via physics-informed neural networks

Tomographic background oriented Schlieren (Tomo-BOS) imaging measures density or temperature fields in three dimensions using multiple camera BOS projections, and is particularly useful for instantaneous flow visualizations of complex fluid dynamics problems. We propose a new method based on physics-informed neural networks (PINNs) to infer the full continuous three-dimensional (3-D) velocity and pressure fields from snapshots of 3-D temperature fields obtained by Tomo-BOS imaging. The PINNs seamlessly integrate the underlying physics of the observed fluid flow and the visualization data, hence enabling the inference of latent quantities using limited experimental data. In this hidden fluid mechanics paradigm, we train the neural network by minimizing a loss function composed of a data mismatch term and residual terms associated with the coupled Navier–Stokes and heat transfer equations. We first quantify the accuracy of the proposed method based on a two-dimensional synthetic data set for buoyancy-driven flow, and subsequently apply it to the Tomo-BOS data set, where we are able to infer the instantaneous velocity and pressure fields of the flow over an espresso cup based only on the temperature field provided by the Tomo-BOS imaging. Moreover, we conduct an independent PIV experiment to validate the PINN inference for the unsteady velocity field at a centre plane. To explain the observed flow physics, we also perform systematic PINN simulations at different Reynolds and Richardson numbers and quantify the variations in velocity and pressure fields. Furthermore, the results in this paper indicate that the proposed deep learning technique can become a promising direction in experimental fluid mechanics.

97 MATHEMATICS AND COMPUTING↗

Red-Colored Circularly Polarized Luminescence from a Benzo-Fused BODIPY-BINOL Complex

Red emission with sharp bandwidth and high quantum yield are desired characteristics for organic chromophores in optoelectronic, spintronic, and biomedical applications. Here, we observe circularly polarized luminescence (CPL) with these characteristics from a benzo-fused BODIPY-BINOL complex (1). Using time-resolved optical spectroscopy, electrochemistry, and density functional theory calculations, we showed that the emissive excited state of 1 does not have a charge-transfer character, unlike the regular BODIPY counterpart (2). In conclusion, the rigidity and the lack of charge-transfer character make this class of molecules an appealing platform for CPL-active molecules in the red spectral region with ample room for improvement in the dissymmetry factor and brightness.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Radiation-Induced Interfacial Hydroxyl Transformation on Boehmite and Gibbsite Basal Surfaces

Understanding the radiolytic reactivity of aluminum oxyhydroxide phases widely present in stored nuclear wastes is essential to develop reliable processing approaches. Recent experiments using vibrational sum frequency generation (VSFG), a surface sensitive technique, have shown that rehydration of γ-irradiated boehmite (010) and gibbsite (001) surfaces does not recover the initial hydroxyl density prior to irradiation. In this study, using density functional theory and nudged elastic band calculations, we examine dehydration and rehydration of these surfaces and attendant proton transfer mechanisms. While dehydration of both surfaces is predicted to be energetically unfavorable, rehydration of boehmite (010) is favorable after overcoming an energy barrier of 0.52 eV that relates to the orientation of surface hydroxyls controlling the hydrogen bonding network of adsorbed water. In the case of gibbsite (001), for which the experimental results suggest that rehydration mainly involves the reformation of interlayer hydroxyls, we found that a two-proton transfer mechanism is more likely than a one-proton transfer mechanism, and that it prevents the reorientation of interlayer hydroxyls into intralayer hydroxyls consistent with experimental VSFG findings. A detailed analysis of the effect of surface hydrogen vacancy on the strength of hydrogen bond interactions was performed, which indicates that H 2 and H 2 O are the energetically most favorable product species to form from radiation-induced surface H and/or OH defects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Excited State Intramolecular Proton Transfer with Nuclear-Electronic Orbital Ehrenfest Dynamics

The recent development of the Ehrenfest dynamics approach in the nuclear-electronic orbital (NEO) framework provides a promising way to simulate coupled nuclear-electronic dynamics. Our previous study showed that the NEO-Ehrenfest approach with a semi- classical traveling proton basis method yields accurate predictions of molecular vibrational frequencies. In this work, we provide a more thorough analysis of the semiclassical traveling proton basis method to elucidate its validity and convergence behavior. We also conduct NEO-Ehrenfest dynamics simulations to study an excited state intramolecular proton transfer process. These simulations reveal that nuclear quantum effects influence the predictions of proton transfer reaction rates and kinetic isotope effects due to the intrinsic delocalized nature of the quantum nuclear wave function. This work illustrates the importance of nuclear quantum effects in coupled nuclear-electronic dynamical processes and shows that the NEO-Ehrenfest approach can be a powerful tool to provide insights and predictions for these processes.

Zhao, Luning↗

On the Relationship Between Shallow Cumulus Cloud Field Properties and Surface Solar Irradiance

Abstract Shallow cumulus clouds exhibit highly three‐dimensional (3‐D) spatial structure leading to complex variability in the surface solar irradiance (SSI) beneath. This variability is captured by the typically bimodal shape of the SSI probability density function (PDF). Using large eddy simulation to generate well‐resolved cloud fields and Monte Carlo 3‐D radiative transfer to reproduce realistic associated SSI PDFs, we seek direct relationships between the cloud field properties and the SSI PDF shape. Applying both random forest and artificial neural network algorithms, we find variations in the two modes of the SSI PDF are well predicted by just a handful of cloud field properties. The two algorithms utilize cloud properties similarly, with indistinguishable performance despite their different architectures. These results offer a marked improvement in realism relative to one‐dimensional radiative transfer while bypassing computationally expensive 3‐D radiative transfer, with immediate application to renewable energy assessments, and potential for several other geophysical applications.

58 GEOSCIENCES↗

Complexions at the iron-magnetite interface

Synthesizing distinct phases and controlling crystalline defects are key concepts in materials design. These approaches are often decoupled, with the former grounded in equilibrium thermodynamics and the latter in nonequilibrium kinetics. By unifying them through defect phase diagrams, we can apply phase equilibrium models to thermodynamically evaluate defects—including dislocations, grain boundaries, and phase boundaries—establishing a theoretical framework linking material imperfections to properties. Using scanning transmission electron microscopy (STEM) with differential phase contrast (DPC) imaging, we achieve the simultaneous imaging of heavy Fe and light O atoms, precisely mapping the atomic structure and chemical composition at the iron-magnetite (Fe/Fe 3 O 4 ) interface. We identify a well-ordered two-layer interface-stabilized phase state (referred to as complexion) at the Fe[001]/Fe 3 O 4 [001] interface. Using density-functional theory (DFT), we explain the observed complexion and map out various interface-stabilized phases as a function of the O chemical potential. The formation of complexions increases interface adhesion by 20% and alters charge transfer between adjacent materials, impacting transport properties. Our findings highlight the potential of tunable defect-stabilized phase states as a degree of freedom in materials design, enabling optimized corrosion protection, catalysis, and redox-driven phase transitions, with applications in materials sustainability, efficient energy conversion, and green steel production.

36 MATERIALS SCIENCE↗

Colistin resistance plasmids dually enhance bacterial virulence and antibiotic resistance via surface polysaccharide biosynthesis

Plasmids carrying the mobilized colistin-resistance gene mcr-1 are prevalent among multidrug-resistant Gram-negative pathogens, yet their broad impact on bacterial physiology and virulence remains unclear. Here, we demonstrate that acquisition of an mcr-1 plasmid concurrently increases antimicrobial resistance and pathogenicity in Escherichia coli. On the same plasmid, the XRE-family transcriptional regulator EcaR cooperates with MCR-1 to activate the wec operon, driving biosynthesis of two surface polysaccharides: enterobacterial common antigen (ECA) and a high-molecular-weight O-chain. Expression of these surface polysaccharides increases bile resistance and virulence in a murine model and further elevates colistin resistance. MCR-1 enhances transcription of upstream genes in the wec operon, whereas EcaR directly activates an internal promoter (PwecE) to induce downstream gene expression. Thus, both components are required for surface polysaccharide expression, and deletion of either abolishes the phenotype. Genomic analysis of publicly available mcr plasmids reveals widespread co-occurrence of mcr-1 and ecaR on IncI2 and IncX4 plasmids, indicating their functional complementarity. These findings uncover a mechanism by which resistance plasmids remodel the bacterial surface, linking horizontal gene transfer to coordinated regulation of antimicrobial resistance and virulence.

Antimicrobial resistance↗

The Mycobacterium tuberculosis mycothiol S -transferase is divalent metal-dependent for mycothiol binding and transfer

Mycothiol S-transferase (MST) (encoded by the rv0443 gene) was previously identified as the enzyme responsible for the transfer of Mycothiol (MSH) to xenobiotic acceptors in Mycobacterium tuberculosis (M.tb) during xenobiotic stress. To further characterize the functionality of MST in vitro and the possible roles in vivo, X-ray crystallographic, metal-dependent enzyme kinetics, thermal denaturation studies, and antibiotic MIC determination in rv0433 knockout strain were performed. The binding of MSH and Zn 2+ increases the melting temperature by 12.9 °C as a consequence of the cooperative stabilization of MST by both MSH and metal. The co-crystal structure of MST in complex with MSH and Zn 2+ to 1.45 Å resolution supports the specific utilization of MSH as a substrate as well as affording insights into the structural requirements of MSH binding and the metal-assisted catalytic mechanism of MST. Further, contrary to the well-defined role of MSH in mycobacterial xenobiotic responses and the ability of MST to bind MSH, cell-based studies with an M.tb rv0443 knockout strain failed to provide evidence for a role of MST in processing of rifampicin or isoniazid. These studies suggest the necessity of a new direction to identify acceptors of the enzyme and better define the biological role of MST in mycobacteria.

59 BASIC BIOLOGICAL SCIENCES↗

Size-dependent errors in real-time electron density propagation

Real-time (RT) electron density propagation with time-dependent density functional theory (TDDFT) or Hartree–Fock (TDHF) is one of the most popular methods to model the charge transfer in molecules and materials. However, both RT-TDHF and RT-TDDFT within the adiabatic approximation are known to produce inaccurate evolution of the electron density away from the ground state in model systems, leading to large errors in charge transfer and erroneous shifting of peaks in absorption spectra. Given the poor performance of these methods with small model systems and the widespread use of the methods with larger molecular and material systems, here we bridge the gap in our understanding of these methods and examine the size-dependence of errors in RT density propagation. We analyze the performance of RT density propagation for systems of increasing size during the application of a continuous resonant field to induce Rabi-like oscillations, during charge-transfer dynamics, and for peak shifting in simulated absorption spectra. We find that the errors in the electron dynamics are indeed size dependent for these phenomena, with the largest system producing the results most aligned with those expected from linear response theory. The results suggest that although the RT-TDHF and RT-TDDFT methods may produce severe errors for model systems, the errors in charge transfer and resonantly driven electron dynamics may be much less significant for more realistic, large-scale molecules and materials.

Chemistry↗

Evaluating the gradients of localized diabatic state energies and couplings at minimum cost

We calculate the gradients of Boys diabatic state energies and couplings when the electronic vector space is generated by configuration interaction singles. Our approach follows the Lagrangian approach of Paz and Glover (rather than direct differentiation of the adiabatic-to-diabatic approaches that have been published previously). The result is that we achieve a dramatic increase in savings over previous approaches, and the present approach should be immediately useful to scientists focused on electronic relaxation, especially chemists studying electron transfer who wish to go beyond the Condon approximation. Here, a future extension to time-dependent density functional theory in the Tamm–Dancoff approximation is clear.

Chemical physics↗

Quantitative surface studies of moiré intercalated Pb structures under Gr/SiC

Quantitative growth studies using surface diffraction and scanning tunneling microscopy are carried out to determine the intercalation conditions for Pb under Gr/SiC, with initial phase a mixture of buffer-layer and single-layer graphene. Intercalation is a kinetically complex, multistage process with intercalated Pb moving between different subsurface locations with annealing, eventually to the location of higher stability. The transfer is determined by monitoring the difference of a given spot intensity from its clean value, as a function of growth parameters. In addition, a broad, low-intensity (10×10) gr moiré phase is observed exclusively originating from intercalated Pb. Well-defined growth conditions are identified for the moiré spot to be observed reversibly. The (10×10) gr phase follows changes of the Pb(10) spot during growth and annealing experiments, instead of changes of the other Gr/SiC spots indicating preferred nucleation of Pb islands on the (10×10) gr domains. These structural results are discussed in connection to different models proposed for the (10×10) gr supercell and the subsurface Pb coverage. In conclusion, mass transport of subsurface Pb is unusually high, possibly because of the very high compression of the intercalated Pb, when compared to metallic Pb(111).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Electronic Excitation Response of DNA to High-Energy Proton Radiation in Water

The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer therapies. In particular, the dependence of different types of DNA damage on high-energy protons represents a significant knowledge void. Here, in this work, we employ first-principles real-time time-dependent density functional theory simulation, using a massively parallel supercomputer, to unravel the quantum-mechanical details of the energy transfer from high-energy protons to DNA in water. The calculations reveal that protons deposit significantly more energy onto the DNA sugar-phosphate side chains than onto the nucleobases, and greater energy transfer is expected onto the DNA side chains than onto water. As a result of this electronic stopping process, highly energetic holes are generated on the DNA side chains as a source of oxidative damage.

74 ATOMIC AND MOLECULAR PHYSICS↗