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At least 235 records · Page 13

Nonvariational ADAPT algorithm for quantum simulations

We explore a nonvariational quantum state preparation approach combined with the ADAPT operator selection strategy in the application of preparing the ground state of a desired target Hamiltonian. In this algorithm, energy gradient measurements determine both the operators and the gate parameters in the quantum circuit construction. We compare this nonvariational algorithm with ADAPT-VQE and with feedback-based quantum algorithms in terms of the rate of energy reduction, the circuit depth, and the measurement cost in molecular simulation. We find that, despite using deeper circuits, this new algorithm reaches chemical accuracy at a similar measurement cost to ADAPT-VQE. Since it does not rely on a classical optimization subroutine, it may provide robustness against circuit parameter errors due to imperfect control or gate synthesis.

Tang'S, Ho Lun [Virginia Polytechnic Inst. and Sta↗

Carbon mineralization pathways in interfacial adsorbed water nanofilms

Carbon mineralization in humidified carbon dioxide offers a promising route to mitigate anthropogenic emissions in a world stressed by water security. Despite its technological importance, our understanding of carbonation in water-poor environments lags, as traditional dissolution-precipitation pathways struggle to explain the adsorbed water nanofilm-mediated reactivity. Here, we utilize in operando X-ray diffraction (XRD) and advanced molecular simulations to investigate nanoconfined reactions driving forsterite carbonation, the magnesium-rich olivine. By examining magnesium ion dissolution and transport in atomistic simulations of the forsterite-water-carbon dioxide interface and comparing these with the in operando XRD activation energies, we identify both processes as rate-limiting at saturation. Our simulations reveal a mechanistic view of interfacial carbonation, where dissolution and precipitation are mediated by anomalous quasi two-dimensional diffusion. The transport process involves intermittent diffusive hopping in the desorbed state, separated by crawling events that are spatially short but temporally long. This understanding transcends carbon mineralization, with implications for understanding the transport of contaminants in geosystems, the design of multifunctional materials, water desalination, and molecular recognition systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

KBKit: A Python Toolkit for Kirkwood–Buff Theory from Molecular Dynamics

Thermodynamic properties of liquid mixtures govern processes that range from drug delivery to energy storage, yet extracting these properties from molecular simulations remains challenging. Kirkwood–Buff (KB) theory offers a rigorous route by linking microscopic pair distribution functions to macroscopic free energies, but practical use of the theory has been hindered by two obstacles: (i) the long simulations needed to obtain well-converged Kirkwood-Buff integrals (KBIs) and (ii) the specialized corrections required to translate finite-size data to the thermodynamic limit. $\texttt{KBKit}$ is an open-source Python package that removes these barriers. It automatically computes KBIs and derived thermodynamic quantities from GROMACS input files, applies state-of-the-art finite-size corrections, and provides built-in diagnostic tools to quantify statistical uncertainty. Written with modern software-engineering practices—continuous integration, extensive unit testing, and thorough documentation—$\texttt{KBKit}$ is both reliable and easy to extend. By condensing complex KBI analysis into a few intuitive commands, $\texttt{KBKit}$ enables researchers to incorporate KB theory into routine simulation workflows and accelerate the discovery of solution-phase thermodynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Elucidating molecular level interfacial interactions between a de novo protein and nucleated calcite with solid-state NMR

Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic–inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. Here, to understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31–calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ∼2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31–calcite interactions. While this work provides the first experimental confirmation that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31–calcite interface has advanced our fundamental understanding of the atomic interactions at the organic–inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.

Close, Emily G. S. [Pacific Northwest National Lab↗

DataSet for Elucidating molecular level interfacial interactions between a de novo protein and nucleated calcite with solid-state NMR

Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic-inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. To understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31-calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ~2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31-calcite interactions. These studies provide the first experimental evidence to confirm that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template. However, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31-calcite interface has advanced our fundamental understanding of the atomic interactions at the organic-inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.

Saccuzzo Close, Emily Grace [Pacific Northwest Nat↗

Field-driven ion pairing dynamics in concentrated electrolytes

Here, we investigate ion pairing dynamics in electrolytes driven far from equilibrium using molecular simulations and nonequilibrium rate theory. Focusing on 0.5M LiPF 6 in water and acetonitrile under uniform electric fields, we compute transition path theory observables, including reactive fluxes and mean first-passage times of ion pairing. Moreover, we introduce a dynamical proxy of free-ion population, where its field-induced change is strongly correlated with the nonlinear enhancement of conductivity, yielding an increase of 40% at 50 mV/Å in acetonitrile, compared to that of less than 10% in aqueous electrolytes. Further kinetic analysis elucidates that Onsager’s classical theory substantially overestimates field-induced enhancement of ion pair dissociation in molecular electrolytes. This discrepancy arises from solvent-mediated dynamical pathways and field-induced dielectric decrement that suppress ion pair dissociation within explicit solvents, highlighting that a faithful description of molecular details is essential. Our results provide a molecular interpretation of nonlinear electrolyte transport beyond continuum theories and establish a general framework for quantifying nonequilibrium reaction kinetics in condensed phase systems.

Moon, Seokjin [University of California, Berkeley,↗

Chromatin structures from integrated AI and polymer physics model

The physical organization of the genome in three-dimensional space regulates many biological processes, including gene expression and cell differentiation. Three-dimensional characterization of genome structure is critical to understanding these biological processes. Direct experimental measurements of genome structure are challenging; computational models of chromatin structure are therefore necessary. We develop an approach that combines a particle-based chromatin polymer model, molecular simulation, and machine learning to efficiently and accurately estimate chromatin structure fromindirectmeasures of genome structure. More specifically, we introduce a new approach where the interaction parameters of the polymer model are extracted from experimental Hi-C data using a graph neural network (GNN). We train the GNN on simulated data from the underlying polymer model, avoiding the need for large quantities of experimental data. The resulting approach accurately estimates chromatin structures across all chromosomes and across several experimental cell lines despite being trained almost exclusively on simulated data. The proposed approach can be viewed as a general framework for combining physical modeling with machine learning, and it could be extended to integrate additional biological data modalities. Ultimately, we achieve accurate and high-throughput estimations of chromatin structure from Hi-C data, which will be necessary as experimental methodologies, such as single-cell Hi-C, improve.

Biochemistry & Molecular Biology↗

Multifunctional Catalysts for the Tandem Reactions of Oxygenates

Industrially-relevant catalytic reactions rarely consist of a simple sequence of elementary steps. Moreover, kinetic coupling of multiple reactions on a catalyst surface is highly desired for process intensification and improved energy efficiency for large scale chemical transformations. The shifting landscape of hydrocarbon chemical feedstocks in the US also motivates research on the selective conversion of more complex molecules. One desirable type of catalytic reaction is the reduction of carboxylic acids that are produced from biomass feedstocks to their corresponding alcohols. The proposed research explores the fundamental importance of hydrogen spillover on a multifunctional catalyst for carboxylic acid reduction with H 2 composed of metal particles coupled to metal oxide particles. Recent work has demonstrated the excellent performance of supported tungsten oxide clusters for carboxylic acid reduction, but only after they are promoted with a late transition metal such as palladium. Elucidating the active state of the catalyst and the associated reaction mechanism for acid reduction on that active state are the overall goals of the proposed project and successful completion will enable future design of efficient multifunctional catalysts. The critically important role of the metal promoter is hypothesized to be its ability to dissociate H2 and spillover atomic H to the support. Although hydrogen spillover is a well-recognized phenomenon in catalysis, its role in both catalyst activation and catalytic turnover are still unresolved. The study combined materials synthesis, characterization, reactivity testing, and molecular simulations, to explore the effect of hydrogen chemical potential on the formation of the active catalytic sites and on the steady state catalytic reduction of carboxylic acid. Varying the hydrogen chemical potential through modification of the gas conditions, support composition, and metal loading to modulated the structure and catalytic performance of the reducible metal oxide. Dual function catalysts containing supported Pd and WO x species co-located on a non-reducible carrier (silica) and a reducible carrier (titania) were synthesized and characterized by electron microscopy, temperature-programmed reduction, and chemisorption. Spectroscopic methods such as X-ray absorption and UV-vis were also used to evaluate the catalysts, which were used in the reduction of propionic acid to aldehyde and alcohol. Quantum chemical calculations, including ab initio phase diagrams provided molecular insights into the H spillover phenomenon.

09 BIOMASS FUELS↗

Quantification of the REE 3+ aqua ions and chloride species in aqueous fluids by in situ Raman spectroscopy using perturbations of the water band

Acidic NaCl-rich aqueous fluids play a crucial role in forming hydrothermal rare earth elements (REE) mineral deposits. Aqueous REE mobility is mostly controlled by the stabilities of REE 3+ and REE chloride species. Our current knowledge of REE speciation is based on solubility data, thermodynamic models and in situ spectroscopic measurements, sometimes coupled with molecular simulations. Here, in this study, we investigate Nd and Yb speciation in pH2 Cl-bearing solutions at 25 °C and 0.1 MPa with variable Cl/REE ratios using Raman Spectroscopy in solutions with 0.1 to 0.6 mol/kg NdCl 3 or YbCl 3 and 0.2 to 3.2 mol/kg NaCl. Due to the challenges in resolving the REE-Cl band, we developed a new method using the water vibrational mode and multivariate curve resolution (MCR) analysis. The Raman spectra for the vibrational band of water (2700 to 3900 cm –1 ) were collected at 25 °C and fitted by three Gaussian sub-peaks, then quantified using MCR analysis to de-convolute the water band into bulk H 2 O and the perturbations caused by of Cl – , REE 3+ , and REE chloride species. REE speciation based on the perturbations of the water band indicates that REE 3+ aqua ions dominate acidic solutions at 25 °C, but up to ~20 mol% YbCl 2+ forms at high YbCl 3 concentrations. The new method is promising for quantifying in situ speciation of the REE 3+ aqua ions and REE chloride species in aqueous fluids while providing information on the hydration of ions. This method improves our molecular level understanding of REE aqueous species stability and their role in REE mobilization during fluid-rock interaction.

58 GEOSCIENCES↗

Protein–Protein Complex Stability Controls Substrate Scope in a β‐Ketoacyl‐ACP Reductase Specific for Medium Chains

Assembly-line enzymes carry out multistep synthesis of important metabolites by using acyl carrier proteins (ACPs) to shuttle intermediates along defined sequences of active sites. Despite longstanding interest in reprogramming these systems for metabolic engineering and biosynthetic chemistry, the mechanisms underlying their reaction order remain poorly understood and difficult to control. In this work, we describe a β-ketoacyl-ACP reductase from Pseudomonas putida (PpFabG4) with an unusual selectivity for medium chains and use it to explore the molecular basis of substrate specificity in enzymes that pull intermediates from fatty acid synthesis, a common route to specialized products. X-ray crystallography shows no obvious barriers to short-chain binding. Molecular simulations and supporting mutational analyses indicate that substrate preference arises instead from a weak enzyme–ACP interaction that is stabilized by medium acyl chains but not by short chains. Indeed, mutations that strengthen this interaction for PpFabG4 or weaken it for EcFabG, an Escherichia coli β-ketoacyl-ACP reductase with a broad substrate specificity, can enhance or reduce activity on short-chain substrates by over 100-fold. Our findings show how the stability of enzyme-ACP interactions can control substrate scope in promiscuous enzymes and guide the exchange of intermediates between (and within) assembly-line systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sub-5 Ångstrom Porosity Tuning in Calixarene-Derived Porous Liquids via Supramolecular Complexation Construction

Sub-Ångstrom-level porosity engineering, which is appealing in gas separations, has been demonstrated in solid carbon, polymer, and framework materials but rarely achieved in the liquid phase. In this work, a gas molecular sieving effect in the liquid phase at sub-5 Ångstrom scale is created via sophisticated porosity tuning in calixarene-derived porous liquids (PLs). Type II PLs are constructed via supramolecular complexation between the sodium salts of calixarene derivatives and crown ether solvents. The chemical structure variation and assembly behavior of the porous host upon PL construction are monitored by spectroscopy-, X-ray-, and neutron-scattering techniques. The presence of permanent porosity in calixarene-derived PLs is verified by pressure swing gas uptake, altered CO 2 physisorption behavior, and molecular simulations. Sub-5 Ångstrom porosity tuning within the PL phase is achieved by introducing bulky substituted groups on the benzene ring of the calixarene host, which then greatly affects the dynamic motion and transport behavior of CO 2 molecules and the Xe uptake performance. Further, the approach being demonstrated in this work represents a promising pathway to tune and leverage the porosity effect for enhanced gas uptake capacity and selectivity in liquid sorbents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Novel Zwitterionic Polyurethane-in-Salt Electrolytes with High Ion Conductivity, Elasticity, and Adhesion for High-Performance Solid-State Lithium Metal Batteries

This study presents a novel polymer-in-salt (PIS) zwitterionic polyurethane-based solid polymer electrolyte (zPU-SPE) that offers high ionic conductivity, strong interaction with electrodes, and excellent mechanical and electrochemical stabilities, making it promising for high-performance all solid-state lithium batteries (ASSLBs). The zPU-SPE exhibits remarkable lithium-ion (Li+) conductivity (3.7 × 10⁻⁴ S cm−1 at 25 °C), enabled by exceptionally high salt loading of up to 90 wt.% (12.6 molar ratio of Li salt to polymer unit) without phase separation. It addresses the limitations of conventional SPEs by combining high ionic conductivity with a Li+ transference number of 0.44, achieved through the incorporation of zwitterionic groups that enhance ion dissociation and transport. The high surface energy (338.4 J m−2) and elasticity ensure excellent adhesion to Li anodes, reducing interfacial resistance and ensuring uniform Li+ flux. When tested in Li||zPU||LiFePO₄ and Li||zPU||S/C cells, the zPU-SPE demonstrated remarkable cycling stability, retaining 76% capacity after 2000 cycles with the LiFePO4 cathode, and achieving 84% capacity retention after 300 cycles with the S/C cathode. Molecular simulations and a range of experimental characterizations confirm the superior structural organization of the zPU matrix, contributing to its outstanding electrochemical performance. The findings strongly suggest that zPU-SPE is a promising candidate for next-generation ASSLBs.

Wang, Kun↗

Computational screening of fly ash zeolite sorbents for boric acid removal

In the United States, many impoundments at coal-fired power plants contain elevated contaminants like arsenic, boron, barium, and selenium. Zeolites synthesized from fly ash show promise as sorbents for these contaminants. However, optimizing sorption capacity is challenging due to numerous possible topologies, silicon to aluminum (Si/Al) ratios, and cation types. In this study, molecular simulations are used to design cationic zeolites for boric acid adsorption. Force field models based on quantum mechanical calculations (PBE + D2) for Na-, Ca-, Mn-, and Fe-exchanged chabazite and LTA are presented. The new D2FF force fields reproduce DFT energies with about half the error of UFF. Zeolite performance depends on Si/Al ratio and cation type, with low Si/Al ratio chabazite (CHA) and phillipsite (PHI) zeolite frameworks exchanged with Ca 2+ or Na + /Ca 2+ mixtures showing the highest adsorption. In conclusion, these findings suggest tailored fly ash-derived zeolites could provide effective boron removal from leachate ponds.

CCR impoundment↗

Sub‐5 Ångstrom Porosity Tuning in Calixarene‐Derived Porous Liquids via Supramolecular Complexation Construction

Abstract Sub‐Ångstrom‐level porosity engineering, which is appealing in gas separations, has been demonstrated in solid carbon, polymer, and framework materials but rarely achieved in the liquid phase. In this work, a gas molecular sieving effect in the liquid phase at sub‐5 Ångstrom scale is created via sophisticated porosity tuning in calixarene‐derived porous liquids (PLs). Type II PLs are constructed via supramolecular complexation between the sodium salts of calixarene derivatives and crown ether solvents. The chemical structure variation and assembly behavior of the porous host upon PL construction are monitored by spectroscopy‐, X‐ray‐, and neutron‐scattering techniques. The presence of permanent porosity in calixarene‐derived PLs is verified by pressure swing gas uptake, altered CO 2 physisorption behavior, and molecular simulations. Sub‐5 Ångstrom porosity tuning within the PL phase is achieved by introducing bulky substituted groups on the benzene ring of the calixarene host, which then greatly affects the dynamic motion and transport behavior of CO 2 molecules and the Xe uptake performance. The approach being demonstrated in this work represents a promising pathway to tune and leverage the porosity effect for enhanced gas uptake capacity and selectivity in liquid sorbents.

Li, Errui [Department of Chemistry University of T↗

Nonadditive CO 2 Uptake of Type II Porous Liquids Based on Imine Cages

Type II porous liquids can potentially exploit the fluidity of liquids and sorption properties of porous sorbents, yet CO 2 uptake in porous liquids is still poorly understood. Molecular simulations and experiments are used to examine CO 2 uptake by a prototypical porous liquid composed of porous organic cages (CC13) in 2′-hydroxyacetophenone (2′-HAP). The simulations are in reasonable agreement with experimental measurements of CO 2 solubility and provide unambiguous information on the partitioning of CO 2 within microenvironments in the liquid. Analysis of CO 2 dynamics is performed using these simulations, including assessing the self-diffusivity of CO 2 in both the neat solvent and porous liquid. This offers insights into the kinetics of CO 2 uptake and transport in type II porous liquids based on imine cages. Experiments with type II porous liquids formed by dissolving CC13 in three different size-excluded solvents show nonadditive CO 2 absorption relative to predictions based on ideal volume additivity. This nonadditive absorption behavior is also observed in simulations. Nonadditive CO 2 uptake is also demonstrated in type II porous liquids based on another imine-based porous cage, CC19.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of Galactic Irradiation on Thermal and Electronic Transport in Tungsten

The impact of irradiation on the thermal and electronic properties of materials is a persistent puzzle, particularly defect formation at the atomic and nanoscales. This work examines the nanoscale effects of low-energy irradiation on tungsten (W), focusing on defect-induced modifications to thermal and electronic transport. Using the site-projected thermal conductivity (SPTC) method [A. Gautam et al. PSS-RRL, 2400306, 2024], bulk and twin-grain boundary W with vacancy defects based on the Norgett–Robinson–Torrens displacements per atom model is analyzed. SPTC provides a detailed prediction of postcascade spatial thermal conductivity distribution. Electronic conductivity activity is estimated using the “N 2 method” [K. Nepal et al. Carbon, 119711, 2025] to explore the consequences of vacancies and grain boundaries, highlighting the defect-dependent nature of charge transport behavior. These findings offer high-resolution insights into irradiation-driven transport phenomena, with implications for space-exposed materials and nanoscale thermal/electronic management.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Broad range material-to-system screening of metal–organic frameworks for hydrogen storage using machine learning

Hydrogen is pivotal in the transition to sustainable energy systems, playing major roles in power generation and industrial applications. Metal–organic frameworks (MOFs) have emerged as promising mediums for efficient hydrogen storage. However, identifying potential candidates for deployment is challenging due to the vast number of currently available synthesized MOFs. This study integrates molecular simulations, machine learning, and techno-economic analysis to evaluate the performance of MOFs across broad operation conditions for hydrogen storage applications. While previous screenings of MOF databases have predominantly emphasized high hydrogen capacities under cryogenic conditions, this study reveals that optimal temperatures and pressures for cost minimization depend on the raw price of the MOF. Specifically, when MOFs are priced at $15/kg, among the 9720 MOFs tested, 9692 MOFs achieve the lowest cost at temperatures between 170 K and 250 K and a pressure of 150 bar. Under these optimal conditions, 362 MOFs deliver a lower levelized cost of storage than 350 bar compressed gas hydrogen storage. Furthermore, this study reveals key material properties that result in low system cost, such as high surface areas (>3000 m2/g), large void fractions (>0.78), and large pore volumes (>1.1 cm3/g).

Hydrogen storage↗

Membrane-based solvent extraction for the recovery of rare earths from phosphate mining process streams

This study reports on the capture of rare earth elements (REEs) from phosphate industry process streams, including phosphoric acid (PA) sludge and phosphogypsum (PG), using a membrane solvent extraction (MSX) process. While MSX has been proven effective for a relatively concentrated feed, its effectiveness for dilute REEs solutions remains unexplored. Investigated PA-sludge and PG particles contain total REEs concentrations of ∼1100 and ∼320 ppm, respectively. Acid leaching, implemented to dissolve the REEs, significantly dilutes the REEs concentration to ∼210 ppm for PA-sludge leachate and ∼60 ppm for PG leachate. These low concentrations, compounded by the higher levels of non-REE ions and radioactive species, uranium (U) and thorium (Th), poses challenges to the MSX process. Here, we demonstrated that N,N,N′,N′-tetraoctyl-diglycolamide (TODGA) selectively binds REEs from a >3 M nitric-acid leachate while effectively rejecting U and Th. Concentrations of light REEs in strip solution were doubled compared to the feed, while heavy REEs were preferentially extracted. Furthermore, >99% purity gypsum, free of U and Th, was precipitated during the acid leaching process, aiding separation by removing significant amounts of non-REEs species (e.g., calcium) prior to the MSX process. Molecular simulations support the experimental data, suggesting preferential separation of heavy over light REEs. Based on these results, a cost-effective integrated process including pretreatment, acid leaching, MSX, and wastewater treatment is proposed for the co-recovery of REEs, phosphoric acid, gypsum, and U. This study shows MSX as a technically and economically feasible process for the recovery of REEs from low-concentration process streams, offering advantages over conventional solvent extraction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗