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At least 667 records · Page 37

Machine Learning an Ab-Initio Based Bond-Order Potential for Bismuthene

Bismuthene is a heavy 2D material whose strong spin–orbit coupling and recently observed single-element ferroelectricity have intensified interest in its structural, vibrational, and transport properties. Accurate modeling of these behaviors requires a short-range interatomic potential that can reproduce the underlying bonding physics at a fraction of the computational cost of first-principles methods. However, such a potential is currently unavailable. Here, in this work, we construct a Tersoff bond-order potential for β-bismuthene using a reinforcement-learning framework that integrates a continuous Monte Carlo Tree Search with a simplex-based local optimizer. The optimized parameter sets reproduce first-principles lattice constants, cohesive energy, the equation of state, elastic constants, and phonon dispersion. We validate the models by performing thermal-conductivity calculations and uniaxial fracture simulations our findings confirm the reliability of the resulting models across multiple thermomechanical regimes. Comparison of the three best solutions reveals how differences in pairwise interactions, angular terms, and bond-order behavior govern phonon features and mechanical responses. We demonstrate an interpretable and computationally efficient potential for bismuthene and demonstrate a general reinforcement-learning strategy for developing bond-order models in emerging 2D materials.

deformation↗

Mechanistic Exploration of Dodecanethiol-Treated Colloidal CsPbBr 3 Nanocrystals with Photoluminescence Quantum Yields Reaching Near 100%

Metal halide perovskite nanocrystals (NCs) are attractive materials for optoelectronics. However, further improvements in stability, reproducibility, and photoluminescence quantum yield (Φ PL ) are essential for enabling future applications. Inadequate surface passivation is a major cause of instability, irreproducibility, and less than unity Φ PL . Herein, we probe the influence of multiple ligand binding groups on the colloidal stability and Φ PL of CsPbBr 3 nanocrystals (NCs). Here, we find that post-synthetic treatment with dodecanethiol reproducibly yields highly stable NCs with near-unity Φ PL for a range of synthetic conditions and initial Φ PL of the as-synthesized NCs. A mechanistic investigation shows that thiol addition leads to thioether formation via the thiol–ene reaction with octadecene, oleic acid, and oleylamine. Both thiolates and thioethers are suspected to bind to undercoordinated Pb atoms on the NC surfaces, and this surface binding can be rapidly accelerated through exposure to blue or UV light. Furthermore, we show that metallic Pb nanoparticles appear in many batches of synthesized CsPbBr 3 NCs and that dodecanethiol addition eliminates these metallic Pb particles.

14 SOLAR ENERGY↗

Nanometer-Scale Correlations in Aqueous Salt Solutions

The intermediate-range (1–4 nm) correlation of cations, an- ions, and water in aqueous alkaline earth salt solutions is measured using synchrotron X-ray diffraction. We differentiate from the entire solution structure factor, S(Q), a separate region at low Q (<1 °A-1) containing local diffraction maxima (pre-peaks) that indicate nanometer-scale oscillatory behavior. These features are quantitatively reproduced with classical molecular dynamics simulations. At high concentrations, the pre-peaks emerge from correlations arising from existence of small quasi close-packed lattice- like structures comprised of cation hydration spheres. We also analyze the concentration dependence of the pre-peak and discuss the overall results in light of the rich literature dealing with intermediate-range correlations underlying universal phenomena in concentrated electrolytes. The authors were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is operated by Battelle for the U.S. Department of Energy under Contract No. DE-AC05-76RL01830. Computing resources were generously allocated by PNNL's Institutional Computing program. DOE Contract No. DEAC02- 06CH11357 supports operation of the Advanced Photon Source at Argonne National Laboratory.

Chemical physics, nucleation, Madelung potential↗

Internal Conversion between Bright (1 1 B $^+_u$) and Dark (21 A $^-_g$) States in s- trans -Butadiene and s- trans -Hexatriene

Internal conversion (IC) between the two lowest singlet excited states, 1 1 B$_u^+$ and 2 1 A$_g^–$, of s-trans-butadiene and s-trans-hexatriene is investigated using a series of single- and multi- reference wave function and density functional theory (DFT) methodologies. Three independent types of the equation-of-motion coupled-cluster (EOMCC) theory capable of providing an accurate and balanced description of one- as well as two-electron transitions, abbreviated as δ-CR-EOMCC(2,3), DIP-EOMCC(4h2p){N o }, and DEA-EOMCC(4p2h){N u } or DEA-EOMCC(3p1h,4p2h){N u }, consistently predict that the 1 1 B$_u^+$/2 1 A$_g^–$ crossing in both molecules occurs along the bond length alternation coordinate. However, the analogous 1 1 B$_u^+$ and 2 1 A$_g^–$ potentials obtained with some multireference approaches, such as CASSCF and MRCIS(D), as well as with the linear-response formulation of time-dependent DFT (TDDFT), do not cross. Hence, caution needs to be exercised when studying the low-lying singlet excited states of polyenes with conventional multiconfigurational methods and TDDFT. The multistate many-body perturbation theory methods, such as XMCQDPT 2 , do correctly reproduce the curve crossing. Among the simplest and least expensive computational methodologies, the DFT approaches that incorporate the contributions of doubly excited configurations, abbreviated as MRSF (mixed reference spin-flip) TDDFT and SSR( 4,4 ), accurately reproduce our best EOMCC results. This is highly promising for nonadiabatic molecular dynamics simulations in larger systems.

36 MATERIALS SCIENCE↗

Open-Source and FAIR Research Software for Proteomics

Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms, predictive models, and workflows, but the field faces challenges, including the increasing complexity of mass spectrometry data, limited reproducibility due to proprietary software, and difficulties integrating with other omics disciplines. Closed-source, platform-specific tools exacerbate these issues by restricting innovation, creating inefficiencies, and imposing hidden costs on the community. Open-source software (OSS), aligned with the FAIR Principles (Findable, Accessible, Interoperable, Reusable), offers a solution by promoting transparency, reproducibility, and community-driven development, which fosters collaboration and continuous improvement. In this manuscript, we explore the role of OSS in computational proteomics, its alignment with FAIR principles, and its potential to address challenges related to licensing, distribution, and standardization. Drawing on lessons from other omics fields, we present a vision for a future where OSS and FAIR principles underpin a transparent, accessible, and innovative proteomics community.

97 MATHEMATICS AND COMPUTING↗

Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards

Selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), is a data acquisition technique used in targeted analysis of molecules, including targeted proteomic studies. It exploits the unique capability of triple-quadrupole (QQQ) mass spectrometers to monitor the predefined precursor and fragment ion pairs of specific molecules of interest throughout a liquid chromatography (LC) elution profile. Compared to shotgun proteomics, targeted proteomics using SRM has high selectivity, high sensitivity, and a wide linear dynamic range,(1-3) which makes it especially useful in the accurate and reproducible quantification of low-abundance proteins in highly complex biological samples. SRM has been widely used in the fields of biomarker discovery,(4-7) analysis of protein post-translational modifications(8) and characterization of biological protein networks.(4,9) In the recent years, multiple technical advances have greatly improved the throughput of SRM analyses, allowing for the quantification of hundreds of peptides in a single analysis.(6,7,10) For example, a single 800-plex SRM assay (e.g., 400 unlabeled and heavy-labeled peptide pairs and 2400 transitions with retention time scheduling) using ultrahigh-performance liquid chromatography (UHPLC) has been developed to quantify proteins in plasma.(11) Advanced labeling techniques utilizing in vitro proteome-assisted MRM for protein absolute quantification (iMPAQT) demonstrated the capability of SRM in genome-wide protein quantification of over 18?000 human proteins.(12) Moreover, the scan speed of QQQ instrumentation has been greatly improved in recent releases of commercial instrumentation. The newly developed TSQ Altis (released in 2017) can scan more than 600 transitions per second, which is 6 times more than a traditional QQQ scan speed of 100 transitions per second. The breadth of measurement enabled by these technological improvements to QQQ mass spectrometry has increased the feasibility and popularity of large scale targeted proteomics studies,(13) a major application of which will be in clinical studies in which up to hundreds of protein candidates need to be quantified in hundreds of clinical specimens.(14) Quantitative accuracy is a primary motivating factor for utilizing a targeted proteomics protocol. The precise and reproducible absolute quantification produced by SRM assays is essential to many clinical and laboratory experiments.(15,16) Because the abundance of an endogenous peptide is calculated from the measurement of the spiked-in reference standard, it is essential to assess the data quality of these references.(17) In early applications of targeted proteomics, when instrument speed greatly limited the number of transitions that could be monitored, much of this quality assessment was done manually. However, recent improvements in instrument performance and experimental design have enabled a dramatic increase in the number of target peptides and associated SRM transitions, which makes manual quality assessment an untenable and laborious task. A variety of computational tools assist in SRM experiment design and data analysis. The first task in creating an SRM experiment is the choice of proteins and representative peptides to monitor. Achieving a reliable protein abundance requires appropriately choosing peptides that have a strong signal and are free from interferences in the biological matrix. Numerous computational tools exist to facilitate assay design by identifying peptides and refining SRM transitions.(18-21) To help share these assays and eliminate time spent designing the same transitions at multiple institutions, community portals have begun to host well-designed and vetted assays.(22-24) Analyzing the experimental data requires significant computational effort to align files across replicates and experimental conditions, pick peaks and produce quantitative values, normalize data and perform statistical tests, etc.(25-27)

Gibbons, Bryson C.↗

Automated “Cells-To-Peptides” Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes

Mass spectrometry-based quantitative proteomic analysis has proven valuable for clinical and biotechnology-related research and development. Improvements in sensitivity, resolution, and robustness of mass analyzers have also added value. However, manual sample preparation protocols are often a bottleneck for sample throughput and can lead to poor reproducibility, especially for applications where thousands of samples per month must be analyzed. To alleviate these issues, we developed a “cells-to-peptides” automated workflow for Gram-negative bacteria and fungi that includes cell lysis, protein precipitation, resuspension, quantification, normalization, and tryptic digestion. The workflow takes 2 h to process 96 samples from cell pellets to the initiation of the tryptic digestion step and can process 384 samples in parallel. We measured the efficiency of protein extraction from various amounts of cell biomass and optimized the process for standard liquid chromatography–mass spectrometry systems. The automated workflow was tested by preparing 96 Escherichia coli samples and quantifying over 600 peptides that resulted in a median coefficient of variation of 15.8%. Similar technical variance was observed for three other organisms as measured by highly multiplexed LC-MRM–MS acquisition methods. These results show that this automated sample preparation workflow provides robust, reproducible proteomic samples for high-throughput applications.

59 BASIC BIOLOGICAL SCIENCES↗

Physicochemical Gas–Solid Sorption Properties of Geologic Materials Using Inverse Gas Chromatography

The goal of this study was to determine the physicochemical properties of a variety of geologic materials using inverse gas chromatography (IGC) by varying probe gas selection, temperature, carrier gas flow rate, and humidity. This is accomplished by measuring the level of interaction between the materials of interest and known probe gases. Identifying a material’s physicochemical characteristics can help provide a better understanding of the transport of gaseous compounds in different geologic materials or between different geological layers under various conditions. Our research in this study focused on measuring the enthalpy (heat) of adsorption, Henry’s constant, and diffusion coefficients of a suite of geologic materials, including two soil types (sandy clay-loam and loam), quartz sand, salt, and bentonite clay, with various particle sizes. The reproducibility of IGC measurements for geologic materials, which are inherently heterogeneous, was also assessed in comparison to the reproducibility for more homogeneous synthetic materials. This involved determining the variability of physicochemical measurements obtained from different IGC approaches, instruments, and researchers. For the investigated IGC-determined parameters, the need for standardization became apparent, including the need for application-relevant reference materials. The inherent physical and chemical heterogeneities of soil and many geologic materials can make the prediction of sorption properties difficult. Characterizing the properties of individual organic and inorganic components can help elucidate the primary factors influencing sorption interactions in more complex mixtures. This research examined the capabilities and potential challenges of characterizing the gas sorption properties of geologic materials using IGC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantitative Encapsulation and Homogeneity Assessment of Sol–Gel Based Nuclear Explosive Debris Simulants

Nuclear explosive debris simulants are an important material in training and validating aspects of post-detonation nuclear forensic processes. Realistic simulants should replicate several aspects of nuclear explosive debris such as the size, shape, color, density, and chemical and radiological properties. Silica particles produced via sol-gel synthesis have recently been found to successfully reproduce many of these parameters including the controllable incorporation of radionuclide content. However, to be useful as a benchmarking material for validation and verification of laboratory methodologies, radionuclide content from batch-to-batch must be reproducible. Here, in this work, we explore the variance in radionuclide distribution incorporated into sol-gel benchmarking materials with respect to sample subdivision. Results will help inform the sample sizes required to minimize variance between samples.

36 - MATERIALS SCIENCE↗

Metal Halide Perovskites Demonstrate Radiation Hardness and Defect Healing in Vacuum

Herein, we subject formamidinium lead iodide films to oxygen-containing gases (flowing O 2 or free diffusion of lab atmosphere), inert gases (flowing He, Ar, or N 2 ), and vacuum. Our films are irradiated by Cu Ka X-rays and held at 75 °C while X-ray diffraction is recorded. Under all gas conditions, we observe a reproducible 1.1 ± 0.5 A 3 perovskite lattice contraction from an initial unit cell volume of 256.5 ± 0.8 A 3 concurrent with continuous perovskite loss and lead iodide growth. Oxygen-containing gases increase the reaction rates without materially altering perovskite structural changes. Under the same temperature and irradiation conditions in vacuo, a self-healing reaction is observed, exhibited by a reproducible (0.9 ± 0.3 A 3 ) lattice expansion and stabilization of the perovskite. Furthermore, interactions between the perovskite, defects, and minority phases are simulated by generalized gradient approximation Perdew-Burke-Ernzerhof (GGA-PBE) density functional theory. Lattice contraction indicates an increase in the concentration of Schottky defects-pairs of formamidinium and iodine vacancies. Under irradiation in every atmospheric condition, a solid solution of Schottky defects with a concentration of several percent diffuses and precipitates forming lead iodide and consuming the defects. In the presence of ionized gases, this framework is modified to include the continual loss of formamidinium and iodine ions from the perovskite forming Schottky defects.

14 SOLAR ENERGY↗

Remote Floating-Gate Field-Effect Transistor with 2-Dimensional Reduced Graphene Oxide Sensing Layer for Reliable Detection of SARS-CoV-2 Spike Proteins

Despite intensive research of nanomaterials-based field-effect transistors (FETs) as a rapid diagnostic tool, it remains to be seen for FET sensors to be used for clinical applications due to a lack of stability, reliability, reproducibility, and scalability for mass production. In this work, we propose a remote floating-gate (RFG) FET configuration to eliminate device-to-device variations of two-dimensional reduced graphene oxide (rGO) sensing surfaces and most of the instability at the solution interface. Also, critical mechanistic factors behind the electrochemical instability of rGO such as severe drift and hysteresis were identified through extensive studies on rGO–solution interfaces varied by rGO thickness, coverage, and reduction temperature. rGO surfaces in our RFGFET structure displayed a Nernstian response of 54 mV/pH (from pH 2 to 11) with a 90% yield (9 samples out of total 10), coefficient of variation (CV) < 3%, and a low drift rate of 2%, all of which were calculated from the absolute measurement values. As proof-of-concept, we demonstrated highly reliable, reproducible, and label-free detection of spike proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a saliva-relevant media with concentrations ranging from 500 fg/mL to 5 μg/mL, with an R 2 value of 0.984 and CV < 3%, and a guaranteed limit of detection at a few pg/mL. Taken together, this new platform may have an immense effect on positioning FET bioelectronics in a clinical setting for detecting SARS-CoV-2.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Integrated Strategies for Overcoming Resolution Limits in Electron Beam Lithography of Chemically Amplified Resists

Electron beam lithography (EBL) of chemically amplified resists (CARs) faces fundamental challenges, including stochastic electron scattering and acid diffusion, that limit resolution and reproducibility. Using SU-8 as a model CAR, this study systematically investigated complementary strategies to address these challenges, combining multipass exposure, proximity effect correction (PEC) with midrange correction factors, base quencher incorporation, and post-exposure bake (PEB) suppression. Monte Carlo simulations and calibrated PEC modeling revealed that extending the point spread function to include a midrange scattering component significantly improved critical dimension (CD) control across varying pattern densities, correcting deviations that conventional two-term PEC failed to capture. Multipass exposure, particularly 4-pass writing with a 25% offset, redistributed the dose to average stochastic beam and scattering fluctuations, reducing line-width roughness by more than 50% and yielding more uniform nanoscale features. Photoacid confinement was investigated by adding urea as a base quencher, which successfully reduced acid diffusion but introduced substantial sensitivity penalties without improving ultimate resolution or Z-factor performance, underscoring the trade-offs of chemical versus physical confinement. Suppressing PEB most directly minimized acid diffusion, resulting in improved Z-factors and reproducible 30 nm half-pitch dense line/space patterns. Overall, these results demonstrated that PEC with midrange correction, multipass strategies, quencher additives, and PEB-free processing addresses different aspects of the EBL process window and that their integration provides a comprehensive framework for managing stochastic scattering, diffusion, and chemical amplification effects. This framework advances dense nanoscale patterning in CARs and establishes guiding principles for optimizing resist design and process strategies in high-resolution EBL and potentially other advanced lithographies, such as extreme ultraviolet (EUV) lithography.

36 MATERIALS SCIENCE↗

Reaction Mechanism of Vapor-Phase Formic Acid Decomposition over Platinum Catalysts: DFT, Reaction Kinetics Experiments, and Microkinetic Modeling

A combination of periodic density functional theory (DFT, PW91-GGA) calculations, reaction kinetics experiments, and mean-field microkinetic modeling is used to derive insights on the reaction mechanism and determine the nature of the active site under reaction conditions for the vapor-phase decomposition of formic acid (FA, HCOOH) over Pt/C catalysts. Microkinetic models formulated using DFT energetics derived on the clean Pt(100) and Pt(111) required large parameter adjustments to reproduce the experimentally measured apparent activation energies and reaction orders. Further, these models predicted high surface coverage of adsorbed carbon monoxide (CO*), inconsistent with the environment of the active site in the DFT calculations on the clean surfaces. Consequently, we reperformed DFT calculations for the entire reaction network on partially CO*-covered (4/9 monolayer, ML) Pt(111) and Pt(100). The resultant microkinetic models, with thermochemistry and kinetics explicitly dependent on CO* coverage, were able to reproduce the experimentally determined activation energies and reaction orders, in addition to being self-consistent in CO* coverage. Our results suggest that Pt(100) is likely poisoned by CO* under typical reaction conditions and does not contribute significantly to the experimentally observed reactivity. Instead, we find that Pt(111) better represents the active site for FA decomposition reaction on Pt/C catalysts. The optimized model on 4/9 ML CO*-covered Pt(111) suggests that the reaction occurs via the carboxyl (COOH*) intermediate and that the spectator CO*-assisted pathways play a significant role under reaction conditions. Lastly, this study underscores the importance of spectator species on the energetics and the mechanism of a catalytic reaction and their key role in developing a model that better addresses the nature of the active site under realistic catalytic reaction conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tutorial on In Situ and Operando (Scanning) Transmission Electron Microscopy for Analysis of Nanoscale Structure–Property Relationships

In situ and operando (scanning) transmission electron microscopy [(S)TEM] is a powerful characterization technique that uses imaging, diffraction, and spectroscopy to gain nano-to-atomic scale insights into the structure–property relationships in materials. This technique is both customizable and complex because many factors impact the ability to collect structural, compositional, and bonding information from a sample during environmental exposure or under application of an external stimulus. In the past two decades, in situ and operando (S)TEM methods have diversified and grown to encompass additional capabilities, higher degrees of precision, dynamic tracking abilities, enhanced reproducibility, and improved analytical tools. Much of this growth has been shared through the community and within commercialized products that enable rapid adoption and training in this approach. This tutorial aims to serve as a guide for students, collaborators, and nonspecialists to learn the important factors that impact the success of in situ and operando (S)TEM experiments and assess the value of the results obtained. As this is not a step-by-step guide, readers are encouraged to seek out the many comprehensive resources available for gaining a deeper understanding of in situ and operando (S)TEM methods, property measurements, data acquisition, reproducibility, and data analytics.

(S)TEM↗

Interface and Thermophysical Properties of R 32 Refrigerant

Driven by the urgent demand for efficient cooling in microelectronics and advanced thermal management systems, difluoromethane (R32/CH 2 F 2 ) has emerged as a promising candidate owing to its favorable thermophysical properties, including high heat transfer efficiency and low viscosity. While bulk properties such as density, viscosity, and thermal conductivity have been widely studied, interfacial properties, including surface tension and interfacial thickness, remain comparatively underexplored, despite their importance in phase-transition dynamics. Here, we perform molecular dynamics (MD) simulations from 180 to 300 K using an optimized transferable force field for fluoropropenes with enhanced electrostatics to assess both bulk and interfacial behavior of R32. Simulations reproduced density within ±2.1%, viscosity within 3.05%, and thermal conductivity within 7.41% of NIST reference data. Heat capacities (C p and C v ) were predicted within 5%. For interfacial properties, surface tension trends were reproduced within 13.58% deviation, and the vapor–liquid coexistence curve closely matched reference data, yielding a critical temperature of 345.7 K (1.6% deviation) and a critical density of 0.397 g/cm 3 (6.4% deviation). Importantly, the vapor–liquid interface exhibited pronounced temperature-dependent broadening across the 180–290 K range. This behavior correlates with increasing molecular kinetic energy, reduction in intermolecular cohesive interactions, and a progressive loss of preferential dipole alignment, which collectively enhance thermal fluctuation amplitudes at elevated temperatures. These validated results provide predictive molecular-level insights, particularly for interfacial properties that remain less characterized. By reducing property prediction errors in key parameters such as critical temperature, this work provides reliable inputs for heat-exchanger and system models. Such correlations can support optimized component sizing, improved performance, and reduced refrigerant charge. Beyond R32, the methodology offers a transferable framework for blended and next-generation low-GWP refrigerants, contributing to sustainable thermal management aligned with the 2027 EU F-Gas regulation and 2030 Kigali Amendment.

Fluids↗

Surface-Enhanced Raman Scattering Optophysiology Nanofibers for the Detection of Heavy Metals in Single Breast Cancer Cells

Mercury(II) ions (Hg2+) and silver ions (Ag+) are two of the most hazardous pollutants causing serious damage to human health. Here, we constructed surface enhanced Raman scattering (SERS)-active nanofibers covered with 4-mercaptopyridine (4-Mpy)-modified gold nanoparticles (AuNPs) to detect Hg2+ and Ag+. Experimental evidence suggests that the observed spectral changes originate from the combined effect of (i) the coordination between the nitrogen on 4-Mpy and the metal ions and (ii) the 4-Mpy molecular orientation (from flatter to more perpendicular with respect to the metal surface). The relative intensity of a pair of characteristic Raman peaks (at ~428 and ~708 cm-1) was used to quantify the metal ion concentration, greatly increasing the reproducibility of the measurement compared to signal-on or signal-off detection based on a single SERS peak. The detection limit of this method for Hg2+ is lower than that for the Ag+ (5 nM vs 100 nM), which can be explained by the stronger interaction energy between Hg2+ and N compared to Ag+ and N, as demonstrated by density functional theory (DFT) calculations. The Hg2+ and Ag+ ions can be masked by adding ethylenediaminetetraacetate (EDTA) and Cl-, respectively, to the Hg2+ and Ag+ samples. The good sensitivity, high reproducibility and excellent selectivity of these nanosensors were also demonstrated. Furthermore, detection of Hg2+ in living breast cancer cells at the subcellular level is possible thanks to the nanometric size of the herein described SERS nanosensors, allowing high spatial resolution and minimal cell damage.

Zhao, Xingjuan↗

Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein

Hydrogen bonds are fundamental to biological systems and are regularly found in networks implicated in folding, molecular recognition, catalysis, and allostery. Given their ubiquity, we asked the fundamental questions of whether, and to what extent, hydrogen bonds within networks are structurally coupled. To address these questions, we turned to three protein systems, two variants of ketosteroid isomerase and one of photoactive yellow protein. We perturbed their hydrogen bond networks via a combination of site-directed mutagenesis and unnatural amino acid substitution, and we used 1 H NMR and high-resolution X-ray crystallography to determine the effects of these perturbations on the lengths of the two oxyanion hole hydrogen bonds that are donated to negatively charged transition state analogs. Perturbations that lengthened or shortened one of the oxyanion hole hydrogen bonds had the opposite effect on the other. The oxyanion hole hydrogen bonds were also affected by distal hydrogen bonds in the network, with smaller perturbations for more remote hydrogen bonds. Across 19 measurements in three systems, the length change in one oxyanion hole hydrogen bond was propagated to the other, by a factor of –0.30 ± 0.03. This common effect suggests that hydrogen bond coupling is minimally influenced by the remaining protein scaffold. The observed coupling is reproduced by molecular mechanics and quantum mechanics/molecular mechanics (QM/MM) calculations for changes to a proximal oxyanion hole hydrogen bond. However, effects from distal hydrogen bonds are reproduced only by QM/MM, suggesting the importance of polarization in hydrogen bond coupling. These results deepen our understanding of hydrogen bonds and their networks, providing strong evidence for long-range coupling and for the extent of this coupling. In conclusion, we provide a broadly predictive quantitative relationship that can be applied to and can be further tested in new systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Theoretical Study of C-H Bond Cleavage via Concerted Proton-Coupled Electron Transfer in Fluorenyl-Benzoates

Developing new strategies to activate and cleave C-H bonds is important for a broad range of applications. Recently a new approach for C-H bond activation using multi-site concerted proton-coupled electron transfer (PCET) involving intermolecular electron transfer to an oxidant coupled to intramolecular proton transfer was reported. For a series of oxidants reacting with 2-(9H-fluoren-9-yl)benzoate, experimental studies revealed an atypical Brønsted a, defined as the slope of the logarithm of the PCET rate constant versus the logarithm of the equilibrium constant or the scaled driving force. Herein this reaction is modeled with a vibronically nonadiabatic PCET theory. Hydrogen tunneling, thermal sampling of the proton donor-acceptor mode, solute and solvent reorganization, and contributions from excited vibronic states are found to play important roles. The calculations qualitatively reproduce the experimental observation of a Brønsted a significantly less than 0.5 and explain this shallow slope in terms of exoergic processes between pairs of electron-proton vibronic states. These fundamental mechanistic insights may guide the design of more effective strategies for C-H bond activation and cleavage.

Sayfutyarova, Elvira R.↗