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At least 109 records · Page 6

A Comparison of Electronic Structure Methods for Predicting the Hydrogenation Energies of Candidate Molecules for Hydrogen Storage

The development of novel energy materials and fuels is required to expand current available energy sources. Aiming to reach this goal, there is growing interest in using molecular hydrogen as an energy carrier due to its abundance and high energy density. Liquid organic hydrogen carriers (LOHCs) are a promising route to the large-scale storage and transport of hydrogen for use in the energy economy. The search for thermodynamically viable LOHC molecules for real world use has led to a set of constraints on the dehydrogenation enthalpy and the minimum gravimetric hydrogen capacity. These constraints allow one to formulate the search for an ideal LOHC candidate molecule as an optimization problem well suited to the strengths of machine learning and artificial intelligence computational approaches. A critical barrier to a large-scale, high-throughput screening of LOHC candidate molecules is the lack of reliable training data. Computational electronic structure methods including density functional theory, coupled cluster approximations, and diffusion Monte Carlo can be used to provide training data where experimental data are either unreliable or do not exist. In this work, we use these methods to calculate the dehydrogenation energies and enthalpies of candidate LOHC molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spin-informed universal graph neural networks for simulating magnetic ordering

The screening and discovery of magnetic materials are hindered by the computational cost of first-principles density-functional theory (DFT) calculations required to find the ground state magnetic ordering. Although universal machine-learning interatomic potentials (uMLIPs), also known as atomistic foundation models, offer high-fidelity models of many atomistic systems with significant speedup, they currently lack the inputs required for predicting magnetic ordering. In this work, we present a data-efficient, spin-informed graph neural network framework that incorporates spin degrees of freedom as inputs and preserves physical symmetries, extending the functionality of uMLIPs to simulate magnetic orderings. This framework speeds up DFT calculations through better initial guesses for magnetic moments, determines the ground-state ordering of bulk materials and even generalizes to magnetic ordering in surfaces. Furthermore, we implement a closed-loop anomaly detection approach that effectively addresses the classic "chicken-and-egg" problem of creating a high-quality dataset while developing a uMLIP, unearthing anomalies in large benchmark datasets and boosting model accuracy.

Xu, Wenbin↗

Aqueous Carbon Capture Using Guanidinium-Functionalized Hollow Fiber Sorbent Contactors

As part of the growing suite of technologies aimed at combatting rising temperatures, negative emissions technologies have become a powerful tool in the global effort to minimize the consequences of human-induced climate change. Among these, carbon removal from aqueous sources, which contain much higher carbon concentrations than the atmosphere, remains largely unexplored. Indeed, developing robust and efficient carbon capture materials for usage in complex aqueous environments remains a significant challenge. Here, we explore the potential of functionalizing polyvinylidene fluoride (PVDF) hollow fiber contactors grafted with a guanidinium-derived polymer sorbent for carbon removal from aqueous sources, including saline waters. Computational screening against amine-based analogs is utilized to identify guanidinium as a promising motif for bicarbonate (HCO 3 – ) ions binding. To leverage this finding, synthesis of a guanidinium polymer and subsequent covalent grafting onto PVDF hollow fibers is employed to structured polymer–sorbent–grafted hollow fiber contactors. Our prototype achieves an initial HCO 3 – removal of 34% with an increase to 98% after four cycles. The functionalized fibers demonstrate aqueous stability over 13 adsorption/desorption cycles in model NaHCO 3 solutions where regeneration is facilitated by a mild pH swing. Importantly, the system maintains selective performance in the presence of competitive chloride ions over multiple cycles; carbon removal remained above 10% even at high (10:1) NaCl/NaHCO 3 ratios. These findings demonstrate the feasibility of sorbent-based aqueous carbon removal and highlight its potential as a promising approach for negative emissions.

carbon capture↗

Screening of transition metals for PFAS adsorption: A comparative DFT investigation

Transition metals are promising candidates for catalytic destruction of per- and polyfluoroalkyl substances (PFAS). This study employed density functional theory (DFT) calculations to systematically investigate the adsorption of PFAS, which is a critical step in the catalytic process, onto a group of transition metals, namely Cu, Pd, Pt, and Rh. The investigation considered the influence of different PFAS characteristics, including chain length, functional group (i.e., sulfonic vs. carboxylic), and protonation state (i.e., protonated, anionic, and deprotonated radical) on the adsorption mechanism. Overall, the findings indicated that the adsorption of PFAS on transition metals exhibited thermodynamically favorable energetics, with Rh showing the most favorable adsorption for PFAS. However, the adsorption strength was significantly dependent on the protonation state of PFAS. Cu was the highest electron donor, while Pt was the highest electron acceptor. Results were compared to experimental studies in the literature for qualitative validation.

Adsorption↗

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES↗

Extending Orbital-Optimized Density Functional Theory to L-Edge XPS and Beyond: Spin–Orbit Coupling via Nonorthogonal Quasi-Degenerate Perturbation Theory

Quantum mechanical calculations of core electron binding energies (CEBEs) are relevant to interpreting X-ray photoelectron spectroscopy (XPS). Orbital-optimized density functional theory (OO-DFT) accurately predicts K-edge CEBEs but is challenged by the presence of significant spin–orbit coupling (SOC) at L- and higher edges involving inner-shell orbitals with nonzero angular momentum. Here, to extend OO-DFT to L-edges and higher, our method utilizes scalar-relativistic, spin-restricted open-shell OO-DFT to construct a minimal, quasi-degenerate basis of core-hole states corresponding to a chosen inner-shell (e.g., ionizing all six possible 2p spin orbitals). Nonorthogonal configuration interaction (NOCI) is then used to obtain the matrix elements of the full Hamiltonian including SOC in this quasi-degenerate model space of determinants. Using a screened 1-electron SOC operator parametrized with the Dirac-Coulomb-Breit (DCB) Hamiltonian results in doublet splitting (DS) values for third row elements that are nearly in quantitative agreement with experiment. The resulting NOCI eigenvalues are shifted by the average of the (scalar) OO-DFT CEBEs to yield CEBEs (split by SOC) corrected for dynamic correlation. Comparing calculations on gas phase molecules with experimental results establishes that NO-QDPT with the SCAN functional (NO-QDPT/SCAN), using the DCB screened 1-electron SOC operator is accurate to about 0.2 eV for L-edge CEBEs of molecules containing third row atoms. However, this NO-QDPT approach becomes less accurate for fourth-row elements starting in the middle of the 3d transition metal series, with errors increasing as atomic number increases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nitroarene Photoactivation Promotes Oxidative Deconstruction of Olefinic Polymers

Photoactivation of nitroarenes has been recently reported to induce the transformation of alkenyl bonds into carbonyl functionalities. Capitalizing on this unique photochemical mechanism, this study explores the use of nitroarenes to achieve oxidative cleavage of olefinic polymers under visible light irradiation. The degradation of various olefinic polymers, including commercially available polybutadiene, polynorbornene, both linear and cyclic poly(phenylacetylene), as well as backbone-modified polyacrylates with alkenyl functionality was investigated. To elucidate the efficacy of this methodology, a series of nitroarene derivatives bearing variable substituents were screened for their degradative efficiency on polybutadiene. Varying nitroarene stoichiometry, reaction temperature, and pos-treaction workup conditions were investigated to optimize degradation conditions. Furthermore, the results demonstrated that photoexcited nitroarenes enable efficient oxidative degradation of olefinic polymers in a safe and sustainable manner, providing a novel strategy for mild macromolecular deconstruction.

Bond cleavage↗

Computational Advances in Ionic Liquid Applications for Green Chemistry: A Critical Review of Lignin Processing and Machine Learning Approaches

The valorization and dissolution of lignin using ionic liquids (ILs) is critical for developing sustainable biorefineries and a circular bioeconomy. This review aims to critically assess the current state of computational and machine learning methods for understanding and optimizing IL-based lignin dissolution and valorization processes reported since 2022. The paper examines various computational approaches, from quantum chemistry to machine learning, highlighting their strengths, limitations, and recent advances in predicting and optimizing lignin-IL interactions. Key themes include the challenges in accurately modeling lignin’s complex structure, the development of efficient screening methodologies for ionic liquids to enhance lignin dissolution and valorization processes, and the integration of machine learning with quantum calculations. These computational advances will drive progress in IL-based lignin valorization by providing deeper molecular-level insights and facilitating the rapid screening of novel IL-lignin systems.

09 BIOMASS FUELS↗

Machine Learning-Driven Solvent Screening for Biobased 2,3-Butanediol Extraction

Biobased 2,3-butanediol (2,3-BDO) is a valuable biomass-derived chemical due to its versatility in being transformed into a wide variety of products. However, the separation and purification of 2,3-BDO from fermentation broth remain a significant challenge owing to its high boiling point and hydrophilic nature. Herein, we developed a machine learning (ML)-based screening workflow that uses molecular calculations as training data and requires only a small number of experimental measurements for validation to identify alternative solvent candidates for the liquid–liquid extraction (LLE) of 2,3-BDO from aqueous solution. In particular, 130 density functional theory (DFT) calculations with the implicit solvation method not only built a correlation between the computational partition coefficient and the experimental distribution coefficient of 2,3-BDO but also parameterized an Extra-Trees ML model to screen the distribution coefficient for a wider range of 6717 organic solvents. The experimental measurements of only 24 solvents were needed to validate the computational results. A list of 50 prioritized solvents was proposed for 2,3-BDO LLE, and seven additional experimental measurements were conducted to further verify our selected solvents. The impact of the extraction temperature and solvent-to-feed ratio was also investigated for selected solvents in experiments. Furthermore, this work suggested alternative solvents for 2,3-BDO LLE and proposed a versatile workflow that requires fewer experiments and can be applied to a broader range of LLE studies.

Extraction↗

An Innovative High Throughput Genome Releaser for Rapid and Efficient PCR Screening

High-throughput PCR screening is vital in synthetic biology and metabolic engineering as it allows researchers to rapidly analyze and detect numerous targeted genetic mutation in the genome. Current challenges for high-throughput PCR screening in synthetic biology include efficiently preparing genomic DNA, optimizing protocols for diverse sample types, managing contamination risks, and effectively analyzing the large volumes of data generated while ensuring consistent and accurate results. In this study, we present the development of a High Throughput Genome Releaser (HTGR), an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed based on a squash method for rapid, cost-effective, and efficient DNA release, optimized for subsequent PCR reactions. After experimenting with various synthetic materials, we selected a plastic that closely replicates the smooth surface and compression properties of microscope slides, ensuring reliable performance. We engineered a device featuring a 96-Well Plate and a shear applicator, operable both manually and automatically, and compatible with standard liquid-handling robot platform. This compatibility enhances ease of use in high-throughput PCR workflows. Additionally, we developed software to support its automatic functions. Our results demonstrated that the specially engineered 96-Well Plate and HTGR can effectively squash fungal spores , which release enough genome DNA for PCR screening. The genome releaser facilitates the preparation of PCR-amplifiable genomic DNA substrate from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells, which could significantly advance biomanufacturing processes.

Yuan, Guoliang [BATTELLE (PACIFIC NW LAB)]↗

Physical signatures of fermion-coupled axion dark matter

In the presence of axion dark matter, fermion spins experience an “axion wind” torque and an “axioelectric” force. We investigate new experimental probes of these effects and find that magnetized analogs of multilayer dielectric haloscopes can explore orders of magnitude of new parameter space for the axion-electron coupling. We also revisit the calculation of axion absorption into in-medium excitations, showing that axioelectric absorption is screened in spin-polarized targets, and axion wind absorption can be characterized in terms of a magnetic energy loss function. Finally, our detailed theoretical treatment allows us to critically examine recent claims in the literature. We find that axioelectric corrections to electronic energy levels are smaller than previously estimated and that the purported electron electric dipole moment due to a constant axion field is entirely spurious.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

From Obsolete to Optimal (ATR Demineralized Water System)

My project was migrating a Human-Machine Interface (HMI) and Programmable Logic Controller (PLC) program from legacy software to a modern platform, enhancing operational efficiency and eliminating unsupported, obsolete equipment. Initially, I used a migration tool to transfer the programs to the new software, then manually updated variables to align with the new PLC. I optimized the PLC code by leveraging new scaling features in the I/O cards, removing over 45 obsolete rungs, and enhancing clarity with functional tag aliases. Next, I modernized the HMI's visuals with an updated color scheme and 3D buttons. I developed multiple interface versions iteratively refining them based on operator feedback. I also designed and created a dedicated "Rounds" screen incorporating insights from a previous intern’s project to streamline daily rounds. To improve clarity, consistency, and efficiency I redesigned the entire interface. Adding visual indicators to enhance operational awareness: red is used for values outside normal specifications, green for normal operating modes, yellow for manual mode, and grey for offline units. Additionally, I added a dynamic visual representation of tank levels, creating PLC logic to show the level in inches as well as inches and feet. I then incorporated a navigation sidebar to facilitate efficient screen transitions. Risk of human error was mitigated by defining narrow input ranges for tank level shutoff and password protecting setpoint changes. I also fixed issues with datatypes that caused inaccuracies in the original code. Overall, this comprehensive upgrade significantly enhanced the HMI's functionality, user experience, and operational reliability.

47 - OTHER INSTRUMENTATION↗

Computational Design of Interlayers for Thermally Stable Compositionally Graded Coatings on Nickel Alloys

To extend the service life of Ni-based superalloys, refractory metal coatings are often used. However, direct bonding between metals with dissimilar crystal structure promotes brittle intermetallic phase formation. This work presents a computational thermodynamic framework for high throughput design of functionally graded interlayers to suppress deleterious phases that may form at the interlayer. The Thermo-Calc software package was used to screen candidate metallic interlayer elements based on stability of solid-solution phases. Vanadium was identified as a promising interlayer due to its consistent suppression of intermetallic phases. Temperature-dependent phase diagram mapping between 600 and 1000 °C guided selection of a compositional pathway that significantly reduced intermetallic formation compared to directly joining the Ni-based and Nb refractory alloys. Time–temperature–transformation analysis was performed to assess whether equilibrium-predicted phases are kinetically accessible along regions of the graded path where non-solid-solution phases are not fully suppressed. The methodology was further applied to additional Ni-based alloy and coating systems, illustrating its transferability as an approach for rapid computational design of graded interlayers in dissimilar high-temperature materials.

36 MATERIALS SCIENCE↗

Sac1 links phosphoinositide turnover to cryptococcal virulence

Cryptococcus neoformans is an environmentally acquired fungal pathogen that causes over 140,000 deaths per year. Cryptococcal infection occurs when infectious particles are deposited into the lung, where they encounter host phagocytic cells. C. neoformans may be engulfed by these phagocytes, an important step of infection that leads to outcomes ranging from termination of infection to cryptococcal dissemination. To study this critical process, we screened approximately 4,700 cryptococcal gene deletion mutants for altered uptake, using primary mouse and human phagocytic cells. Among the hits of these two screens, we identified 93 mutants with perturbed uptake in both systems, as well as others with differences in uptake by only one cell type. We further screened the hits for changes in thickness of the capsule, a protective polysaccharide layer around the cell which is an important cryptococcal virulence factor. The combination of our three screens yielded 45 mutants, including one lacking the phosphatidylinositol-4-phosphate phosphatase Sac1. In this work, we implicate Sac1 in both host cell uptake and capsule production. We found that sac1 mutants exhibit lipid trafficking defects, reductions in secretory system function, and changes in capsule size and composition. Many of these changes occur specifically in tissue culture media, highlighting the role of Sac1 phosphatase activity in responding to the stress of host-like conditions. Overall, these findings show how genome-scale screening can identify cellular factors that contribute to our understanding of cryptococcal biology and demonstrate the role of Sac1 in determining fungal virulence.

59 BASIC BIOLOGICAL SCIENCES↗

Descriptors for Cu facets for CO2 reduction reaction activity

Computation screening is crucial for designing efficient electrochemical catalysts for carbon dioxide (CO2R) reduction to valuable hydrocarbons and oxygenates. Herein, leveraging density functional theory calculations of the CO adsorption energy ΔE_CO on seventeen Cu terminations, we discover a strong linear correlation between ΔE_CO and the recently experimentally measured CO2R electrochemical currents (ACS Catal. 2022, 12, 11, 6578–6588). Examining the ab initio thermodynamics of the early critical intermediates CO*, COH*, and CHO*, we find that CO* → CHO* is the thermodynamically preferred step, and notably shows a volcano trend with the experimental currents where the maximum CO2R current corresponds to the moderate CHO* formation energy. Importantly, we show that increasing the step and kink density of the Cu termination not only enhances CO adsorption strength but also modulates the CO* → CHO* pathway, as respectively exemplified in the (941) and (741) facets. We also explain why (741) is exceptional with high CO2R activity as measured experimentally due to its relatively low activity toward the hydrogen evolution reaction compared with the other Cu surfaces. Beyond the general CO adsorption energy that only shows a linear trend with CO2R activity, we show that the reaction CO* → CHO* free energy is a descriptor that displays a volcano relationship with the overall CO2R activity on Cu facets.

machine learning↗

Liquid state theory of the structure of model polymerized ionic liquids

We employ polymer integral equation theory to study a simplified model of semiflexible polymerized ionic liquids (PolyILs) that interact via hard core repulsions and short range screened Coulomb interactions. The multi-scale structure in real and Fourier space of PolyILs (ions chosen to mimic Li, Na, K, Br, PF 6 , and TFSI) are determined as a function of melt density, Coulomb interaction strength, and ion size. Comparisons with a homopolymer melt, a neutral polymer–solvent-like athermal mixture, and an atomic ionic liquid are carried out to elucidate the distinct manner that ions mediate changes of polymer packing, the role of excluded volume effects, and the influence of chain connectivity, respectively. The effect of Coulomb strength depends in a rich manner on ion size and density, reflecting the interplay of steric packing, ion adsorption, and charge layering. Ion-mediated bridging of monomers is found, which intensifies for larger ions. Intermediate range charge layering correlations are characterized by a many-body screening length that grows with PolyIL density, cooling, and Coulomb strength, in disagreement with Debye–Hückel theory, but in accord with experiments. Qualitative differences in the collective structure, including an ion-size-dependent bifurcation of the polymer structure factor peak and pair correlation function, are predicted. The monomer cage order parameter increases significantly, but its collective ion counterpart decreases, as ions become smaller. Such behaviors allow one to categorize PolyILs into two broad classes of small and large ions. Furthermore, dynamical implications of the predicted structural results are qualitatively discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure and Synthesizability of Iron–Sulfur Metal–Organic Frameworks

Sulfur-based metal–organic frameworks (MOFs) and coordination polymers (CPs) are an emerging class of hybrid materials that have received growing attention due to their magnetic, conductive, and catalytic properties with potential applications in electrocatalysis and energy storage. In this work, we report a high-throughput virtual screening protocol to predict the synthesizability of candidate metal–sulfur MOFs/CPs by computing the thermodynamically stable structures resulting from a particular combination of metal cluster, linker, cation, and synthetic conditions. Free energies are computed by using all-atom classical mechanical thermodynamic integration. Low-free-energy structures are refined using ab initio density functional theory, and pair distribution functions and powder X-ray diffraction patterns are calculated to complement and guide experimental structure determination. We validate the computational approach by retrospective predictions of the stable structure produced by experimental syntheses, and a subsequent screen predicts Fe 4 S 4 -BDT–TPP as a new thermodynamically stable one-dimensional (1D) CP comprising a redox-active Fe 4 S 4 cluster, a 1,4-benzenedithiolate (BDT) linker, and a tetraphenylphosphonium (TPP) countercation. Furthermore, this material is experimentally synthesized, and the 1D chain structure of the crystal is confirmed using microcrystal electron diffraction. The computational screening pipeline is generically transferable to neutral and ionic MOFs/CPs comprising arbitrary metal clusters, linkers, cations, and synthetic conditions, and we make it freely available as an open source tool to guide and accelerate the discovery and engineering of novel porous materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Elucidating the Impact of Cis – Trans Organic Structure Directing Agent Isomer Ratios on the Aluminum Distribution Within SSZ-39

Despite their widespread use, the mechanisms governing the synthesis of zeolite catalysts are still poorly understood. A notable example of this problem is the uncertainty surrounding the influence of synthesis conditions on the placement of Al atoms in the zeolite framework which determines the active sites available for catalytic species. In this work, the role of the cis to trans isomer ratio of the OSDA N,N-dimethyl-3-5-dimethylpiperidinium on the energetics of 26 distinct Al pair distributions in SSZ-39 is examined both in the presence and absence of Na using density functional theory calculations. The initial orientation of the OSDA was found to have a significant impact on the final energies present, necessitating the screening of a large number of initial orientations with force field calculations and single point DFT calculations. Ground state energies were found to vary significantly with the ratio of cis to trans OSDAs with a Boltzmann distribution revealing the most likely Al pair distributions shift from sharing the same 8 membered rings to sharing the same double six membered rings to having no shared subunits as one increases the amount of cis OSDA present within the framework. The presence of Na was found to favor Al pair distributions where both Als occupied the same 6-membered ring. When an implicit solvent model was used to evaluate ground state energies the ideal Na sites shifted from 6-membered rings to empty SSZ-39 cages while OSDA positions and orientations remained largely the same. To provide insight on how kinetic factors may influence Al distributions, formation energies we calculated for connected double six membered rings. Further, these formation energies revealed a preference for Al pairs to occupy the same 4-membered ring which indicates kinetic and thermodynamic control may lead to different Al distributions in SSZ-39.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗