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At least 307 records · Page 17

From bulk to surface: Structure and dynamics of amorphous alumina from deep potential molecular dynamics

Understanding the atomic-scale structure and dynamics of amorphous oxide surfaces is essential for interpreting their chemical reactivity, mechanical stability, and interfacial behavior, yet direct experimental characterization remains challenging. We employ Deep Potential (DP) molecular dynamics to generate large-scale, ab initio -quality models of amorphous Al 2 O 3 bulk glasses and melt-quenched free surfaces, enabling a quantitative analysis of both structure and relaxation dynamics with statistical confidence inaccessible to direct ab initio simulation. The trained DP model reproduces experimental liquid and glass structure, captures the cooling-rate dependence of the bulk glass transition, and corrects systematic biases in the polyhedral populations predicted by widely used classical force fields. At the free surface, mass density recovers to bulk values over ~10 Å, while local coordination requires a slightly wider subsurface region to fully converge. The outermost layer is oxygen-enriched, exhibits altered polyhedral connectivity with contracted Al–O bonds, and hosts a broad population of under-coordinated motifs (notably AlO 3 and OAl 2 ) whose abundances are governed by glass stability. These under-coordinated surface motifs exhibit distinct vibrational signatures and occur as locally paired Lewis acid and Brønsted base sites consistent with bond-valence compensation, yet remain spatially dispersed rather than aggregating into extended clusters. Despite this pronounced structural heterogeneity, surface relaxation and the glass-transition temperature remain comparable to their bulk counterparts, suggesting that the disordered surface is kinetically stable once formed. Together, these results establish a molecular-level picture of amorphous alumina surfaces and demonstrate the capability of machine-learned potentials to resolve structure–property relationships in disordered oxide interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spatiotemporal Formation and Growth Kinetics of Polyelectrolyte Complex Micelles with Millisecond Resolution

We have directly observed the in situ self-assembly kinetics of polyelectrolyte complex (PEC) micelles by synchrotron time-resolved small-angle X-ray scattering, equipped with a stopped-flow device that provides millisecond temporal resolution. A synthesized neutral-charged diblock polycation and homopolyanion that we have previously investigated as a model charge-matched, core-shell micelle system were selected for this work. The initial micellization of the oppositely charged polyelectrolytes was completed within the dead time of mixing of 100 ms, followed by micelle growth and equilibration up to several seconds. By combining the structural evolution of the radius of gyration (R-g) with complementary molecular dynamics simulations, we show how the self-assemblies evolve incrementally in size over time through a two-step kinetic process: first, oppositely charged polyelectrolyte chains pair to form nascent aggregates that immediately assemble into spherical micelles, and second, these PEC micelles grow into larger micellar entities. Furthermore, this work has determined one possible kinetic pathway for the initial formation of PEC micelles, which provides useful physical insights for increasing fundamental understanding self-assembly dynamics, driven by polyelectrolyte complexation that occurs on ultrafast time scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Charge regulation effects on colloidal mixture nanoparticles

Changes in pH within a system containing dissociable sites affect the protonation and deprotonation of these groups, thereby influencing their physical properties. In response, the system modifies their surface charge, affecting electrostatic interactions, aggregation, stability, and structural behavior. Although the pH can be tuned in experiments, it is difficult to model this phenomenon using simulations or theoretical approaches. Here, we perform hybrid Monte Carlo-molecular dynamics simulations to model charge regulation effects in an equimolar colloidal charged system. We compare charge regulation effects with those of a system in which the charges of colloidal nanoparticles are not dissociable. The comparison between the two cases modifies the phase diagram, and it changes the volume fraction where a percolation network of nanoparticles is found. Charge regulation is found to destroy network formation, as the charge in the nanoparticles is modified because of the cooperativity dependency of the degree of charge dissociation sites among the nanoparticles favoring cluster formation. Furthermore, our work suggests that the ionic and/or electronic conductivity in functionalized nanoparticles can be modified by changing pH values. It also guides the experimental design of oppositely charged nanoparticles as inks for 3D printing processes.

Classical statistical mechanics↗

Origins of the protein synthesis cycle

Largely derived from experiments in molecular evolution, a theory of protein synthesis cycles has been constructed. The sequence begins with ordered thermal proteins resulting from the self-sequencing of mixed amino acids. Ordered thermal proteins then aggregate to cell-like structures. When they contained proteinoids sufficiently rich in lysine, the structures were able to synthesize offspring peptides. Since lysine-rich proteinoid (LRP) also catalyzes the polymerization of nucleoside triphosphate to polynucleotides, the same microspheres containing LRP could have synthesized both original cellular proteins and cellular nucleic acids. The LRP within protocells would have provided proximity advantageous for the origin and evolution of the genetic code.

Fox, S. W.↗

Perturbation of nanoplastics on biomembranes: molecular insights from neutron scattering

Plastic waste is now pervasive in the environment, breaking down into microplastics and nanoplastics under many environmental conditions. These particles have been found in various ecosystems and even in human tissues, raising significant environmental and health concerns. In this study, we investigated the interaction of polystyrene nanoplastics, with and without surface modifications, on biomembrane structures using contrast-matching small-angle neutron scattering and neutron spin echo spectroscopy. The neutron contrast matching enabled the selective study of biomembranes in the presence of nanoplastics. Two model membranes were employed: a simple zwitterionic bilayer (i.e., dimyristoylphosphatidylcholine [DMPC]) and an Escherichia coli lipid extract as a bacterial membrane model. The results show profound membrane disruptions, including possible thinning, vesicle fragmentation, lipid monolayer formation, and inter-vesicle aggregation, with the more severe effects observed in DMPC membranes. Notably, E. coli membranes exhibited greater resilience, suggesting that natural membranes with diverse lipid compositions may reduce susceptibility to perturbation by extracellular nanoplastics. Here, these findings highlight potential risks posed by environmental nanoplastic particles to biological membranes, with insights into molecular-level interactions and the environmental toxicity of nanoplastics. This work provides a foundation for future studies into nanoplastic–biomembrane interactions and their broader implications for health and environment using neutrons.

Qian, Shuo [Oak Ridge National Laboratory (ORNL), ↗

Elucidating the formation mechanisms of zeolites using data-driven modelling and in-situ characterization

Zeolites are the main solid catalysts used by the chemical industry. The use of zeolites in separations and as shape selective catalysts requires control of the width and connectivity of their pores. 235 distinct zeolite frameworks have been synthesized to date, of over 2 million that have been proposed. Recent work indicates that the limitation is in large part kinetic: new synthetic pathways are required to access new zeolites. Organic cations are used to direct the synthesis towards specific zeolites. However, the molecular mechanisms by which cations direct the nucleation towards specific zeolites is not known. Elucidating these mechanisms is key to realize new zeolites for catalysis and separations, and is the focus of this project. This project developed and implemented a synergistic, data-driven computational and experimental approach to resolve the molecular pathways of nucleation, growth, and polymorph selection of zeolites and the role of organic cations in directing their formation. The project developed computationally efficient and accurate models for the study of the nucleation and growth of pure silica zeolites in molecular simulations, using machine learning with data from experiments. Simulations with these models were integrated with scanning tunneling electron microscopy, computer vision, and deep learning to unveil the molecular pathways of formation of a zeolite. Of particular interest in this project was to elucidate the role of amorphous precursors in the nucleation of the zeolite. Previous experiments indicate that zeolites are born within non-crystalline aggregates in which the silicates and organic cations have local and medium range order similar to that of the zeolite. The organic cations that direct the formation of zeolites and those that direct the formation of ordered mesoporous silicas are similar. We hypothesized that the frustrated attraction that for large organic cations leads to the formation of stable mesophases that direct the synthesis of mesoporous silicas, could promote the formation of metastable mesophases that can assist in the nucleation and polymorph selection of zeolites. The simulations resolved how structure directing agents build crystalline order and showed that mesoscopic pre-ordering occurs is not required to facilitate the nucleation of zeolites, because the synthesis occurs at high driving forces, where the barriers for nucleation are negligible. This project unveiled that polymorph selection in zeolite synthesis occurs after nucleation, opening a distinct area of control through the kinetics of growth and not through nucleation barriers.

36 MATERIALS SCIENCE↗

Viscous flow properties and hydrodynamic diameter of phenothiazine-based redox-active molecules in different supporting salt environments

We report viscous flow properties of a redox-active organic molecule, N-(2-(2-methoxyethoxy)ethyl)phenothiazine (MEEPT), a candidate for non-aqueous redox flow batteries, and two of its radical cation salts. A microfluidic viscometer enabled the use of small sample volumes in determining viscosity as a function of shear rate and concentration in the non-aqueous solvent, acetonitrile, both with and without supporting salts. All solutions tested show Newtonian behavior over shear rates of up to 30 000 s−1, which was rationalized by scaling arguments for the diffusion-based relaxation time of a single MEEPT molecule without aggregation. Neat MEEPT is flowable but with a large viscosity (412 mPa⋅s at room temperature), which is ∼1000 times larger than that of acetonitrile. MEEPT solutions in acetonitrile have low viscosities; at concentrations up to 0.5 M, the viscosity increases by less than a factor of two. From concentration-dependent viscosity measurements, molecular information was inferred from intrinsic viscosity (hydrodynamic diameter) and the Huggins coefficient (interactions). Model fit credibility was assessed using the Bayesian Information Criterion. It is found that the MEEPT and its charged cations are “flowable” and do not flocculate at concentrations up to 0.5 M. MEEPT has a hydrodynamic diameter of around 8.5 Å, which is almost insensitive to supporting salt and state of charge. This size is comparable to molecular dimensions of single molecules obtained from optimized structures using density functional theory calculations. The results suggest that MEEPT is a promising candidate for redox flow batteries in terms of its viscous flow properties.

Wang, Yilin (ORCID:0000000316102995)↗

Shape-persistent phthalocyanine cages

Phthalocyanine (Pc), an electro-redox active moiety, has many attractive properties stemming from its large aromatic system and ability to act as a catalyst in electrochemical reactions, such as the CO 2 reduction reaction (CO 2 RR). However, due to the synthetic challenge related to geometric requirements and poor solubility (strong aggregation), discrete shape-persistent cages consisting of site-isolated, readily accessible Pc moieties have not been available. Here, we report the synthesis of Zn- and Ni-metallated Pc-based molecular cages via one-step dynamic spiroborate linkage formation in high yields. The ZnPc cage structure is unambiguously elucidated at the atomic level by single-crystal X-ray diffraction. Moreover, owing to the site-isolated redox-active metal centers, readily accessible intrinsic cavity, and shape-persistent backbone, the Ni-metallated Pc (NiPc) cage exhibits high catalytic efficiency, selectivity, and stability, superior to the non-caged control molecules in electrocatalytic CO 2 RR.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Transcriptomics-based Machine Learning (ML) Analysis Predicts Space-Exposed Murine Livers

NASA has employed high-throughput molecular assays to identify sub-cellular changes impacting human physiology during spaceflight. Machine learning (ML) methods hold the promise to improve our ability to identify important signals within highly dimensional molecular data. However, the inherent limitation of study subject numbers within a spaceflight mission minimizes the utility of ML approaches. To overcome the sample power limitations, data from multiple spaceflight missions must be aggregated while appropriately addressing intra- and inter-study variabilities. Here we describe an approach to log transform, scale and normalize data from six heterogeneous, mouse liver derived transcriptomics datasets (ntotal=137) which enabled ML-methods to perform well (AUC ≥ 0.87) in classifying spaceflown vs ground control animals rather than mission-of-origin. Concordance was found between liver-specific biological processes identified from harmonized ML-based analysis and study-by-study classical omics analysis. This work demonstrates the feasibility of applying ML methods on integrated, heterogeneous datasets of small sample size.

Machine Learning↗

Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment

Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins and are packed full of enzyme cargoes and metabolites as they fulfill their function. Coupling together recent SAXS and proteomics work, it is possible to develop molecular models for these microcompartments and interrogate enzyme and metabolite dynamics within. Our primary goal of this study is to quantify the permeability of metabolite glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP) across the BMC shell through classical molecular dynamics simulation. The Haliangium ochraceum model of BMC shell (PDB: 6MZX) was used to model an intact BMC of approximately 10 million atoms. Working at this scale presented its own challenges in managing large data sets, with multiple challenges and hardware advances discussed that facilitated this work. Over approximately 750 ns of aggregate simulation, we see multiple permeation events for these metabolites that were added at high concentration through the pores present within BMC shell tiles. When compared to independent permeability estimates for the same metabolites determined through replica exchange umbrella sampling simulations, the permeabilities varied by approximately 3 orders of magnitude. Regardless, the permeability coefficients for both G3P and DHAP are highly similar and very high, such that only very small concentration gradients can be maintained across the BMC shell between the cytosol and BMC interior. The large simulation systems also facilitated comparisons for molecular diffusivity in the crowded environment within the BMC shell. By our estimates, the viscosity within a packed BMC shell is at least 10-fold higher than it would be in neat solution and is the real driver for varying permeability estimates we obtained through simulation. These findings will be used as design inputs for future bioengineering efforts to make products from BMCs, highlighting how permeable BMC shells can be.

Diffusion↗

Barrierless nucleation in glassy precursors drives zeolite formation

Zeolites are crystalline, microporous silicates widely used in catalysis and separations, yet the molecular mechanisms of their formation remain unresolved. Experiments indicate that hydrothermal synthesis of silica zeolites from clear solution proceeds through amorphous nanoaggregates that gradually develop zeolite order in an apparently continuous amorphous to crystal transformation. Here, we combine molecular simulations with advanced algorithms that identify zeolite order and computer vision to elucidate the pathway from clear solution to zeolite nanocrystal. We show that at conditions of hydrothermal synthesis of silica zeolites, the transformation of precursor aggregate into zeolite is not limited by nucleation barriers but by the slow dynamics of reorganization in the glassy precursor matrix. The negligible nucleation barriers result in spinodal-like crystallization that leads to a gradual formation of a mosaic of small crystallites that explain the seemingly continuous character of zeolite crystallization and the catalytic activity of X-ray amorphous, protozeolites and embryonic zeolites. We find that zeolite-like porosity and short-range order emerge early within glassy precursors, well before crystallinity is detected in transmission electron microscopy (TEM) images or X-ray diffraction. The nanoaggregate’s temperature-size phase diagram reveals a convergence of the zeolite–amorphous equilibrium and maximum crystallization rate at ~3 nm diameter nanoparticle diameters and ~200 °C. This convergence signals the termination of the first-order amorphous-to-zeolite transition. Our results provide a unifying framework for understanding nucleation of silica zeolites from solution and suggest that barrierless nucleation may govern the formation of other nanoparticle systems, including minerals and oxides synthesized far below their bulk melting points.

36 MATERIALS SCIENCE↗

Transport Phenomena in Low Temperature Lithium-Ion Battery Electrolytes

Lithium-ion batteries face low temperature performance issues, limiting the adoption of technologies ranging from electric vehicles to stationary grid storage. This problem is thought to be exacerbated by slow transport within the electrolyte, which in turn may be influenced by ion association, solvent viscosity, and cation transference number. How these factors collectively impact low temperature transport phenomena, however, remains poorly understood. Here we show using all-atom classical molecular dynamics (MD) simulations that the dominant factor influencing low temperature transport in LP57 (1 M LiPF 6 in 3:7 ethylene carbonate (EC)/ethyl methyl carbonate (EMC)) is solvent viscosity, rather than ion aggregation or cation transference number. We find that ion association decreases with decreasing temperature, while the cation transference number is positive and roughly independent of temperature. In an effort to improve low temperature performance, we introduce γ -butyrolactone (GBL) as a low viscosity co-solvent to explore two alternative formulations: 1 M LiPF 6 in 15:15:70 EC/GBL/EMC and 3:7 GBL/EMC. While GBL reduces solution viscosity, its low dielectric constant results in increased ion pairing, yielding neither improved bulk ionic conductivity nor appreciably altered ion transport mechanisms. We expect that these results will enhance understanding of low temperature transport and inform the development of superior electrolytes.

25 ENERGY STORAGE↗

Unraveling the Heterogeneous but Ordered Microstructure of the Nonionic Deep Eutectic Solvent Formed by Lauric Acid and N -Methylacetamide

The nonionic deep eutectic solvent, formed by lauric acid (LA) and N-methylacetamide (NMA), has been shown to have a heterogeneous molecular structure in which the LA and NMA form nonpolar and polar domains, respectively. Previous vibrational spectroscopy experiments demonstrated that the ability of the LA domains to solvate compounds was limited to long carbon chains, whereas other nonpolar molecules, such as W(CO) 6 , were found to be solvated by both LA and NMA. These experiments were not fully compatible with the previously proposed micelle-like structure of the nonpolar domains of the LA-NMA DES. In this work, the modeling of the DES molecular structure is pursued using classical molecular dynamics simulations. The new classical model reproduces both the SAXS structural factors and the previously experimentally derived interaction map for these LA-NMA DESs. In addition, the simulation also shows that LA-NMA DESs form highly organized LA aggregates that are difficult to disorganize. Further evidence of the correct description provided by the newly derived model is obtained using a moderately polar probe: chloroform-d. Computations using the classical model have a good agreement with the solvation behavior of the probe derived from experiments, in which the location of the probe is found to be mostly within the polar domain of the DES. The computational model also demonstrates that the probe solvation is a consequence of the tightly packed LA structure, which causes nonpolar molecules to be located at the interphase of the DES nonpolar domains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hydrodynamically Controlled Self‐Organization in Mixtures of Active and Passive Colloids

Abstract Active particles are known to exhibit collective behavior and induce structure in a variety of soft‐matter systems. However, many naturally occurring complex fluids are mixtures of active and passive components. The authors examine how activity induces organization in such multi‐component systems. Mixtures of passive colloids and colloidal micromotors are investigated and it is observed that even a small fraction of active particles induces reorganization of the passive components in an intriguing series of phenomena. Experimental observations are combined with large‐scale simulations that explicitly resolve the near‐ and far‐field effects of the hydrodynamic flow and simultaneously accurately treat the fluid–colloid interfaces. It is demonstrated that neither conventional molecular dynamics simulations nor the reduction of hydrodynamic effects to phoretic attractions can explain the observed phenomena, which originate from the flow field that is generated by the active colloids and subsequently modified by the aggregating passive units. These findings not only offer insight into the organization of biological or synthetic active–passive mixtures, but also open avenues to controlling the behavior of passive building blocks by means of small amounts of active particles.

36 MATERIALS SCIENCE↗

Fluid models and simulations of biological cell phenomena

The dynamics of coated droplets are examined within the context of biofluids. Of specific interest is the manner in which the shape of a droplet, the motion within it as well as that of aggregates of droplets can be controlled by the modulation of surface properties and the extent to which such fluid phenomena are an intrinsic part of cellular processes. From the standpoint of biology, an objective is to elucidate some of the general dynamical features that affect the disposition of an entire cell, cell colonies and tissues. Conventionally averaged field variables of continuum mechanics are used to describe the overall global effects which result from the myriad of small scale molecular interactions. An attempt is made to establish cause and effect relationships from correct dynamical laws of motion rather than by what may have been unnecessary invocation of metabolic or life processes. Several topics are discussed where there are strong analogies droplets and cells including: encapsulated droplets/cell membranes; droplet shape/cell shape; adhesion and spread of a droplet/cell motility and adhesion; and oams and multiphase flows/cell aggregates and tissues. Evidence is presented to show that certain concepts of continuum theory such as suface tension, surface free energy, contact angle, bending moments, etc. are relevant and applicable to the study of cell biology.

Greenspan, H. P.↗

Decomposition of liquid-liquid extraction organic phase structure into critical and pre-peak contributions

Solution nanostructure induced by amphiphile self-association plays an important role in various chemical and physical processes, including liquid-liquid extraction (LLE). Small angle scattering techniques are an essential means of probing this structure, but, due to non-uniqueness of scattering patterns, their interpretation is not trivial. Here, in this study, we decompose small angle x-ray scattering (SAXS) patterns for a range of binary LLE organic phases into two components: Ornstein-Zernike and pre-peak contributions resulting from, respectively, critical concentration fluctuations and packing of the amphiphilic extractant molecules in the nonpolar aliphatic diluent. While we previously applied Ornstein-Zernike scattering models to similar organic phases, including the pre-peak explicitly in the fit allows us to measure weak fluctuations at high extractant concentration and simultaneously obtain information on the position and intensity of the correlation peak related to amphiphile packing. Scattering patterns and partial structure factors calculated from molecular dynamics simulations support this interpretation. We demonstrate how this minimal scattering model describes nanostructuring for a large number of extractant types over their entire extractant/diluent composition ranges, suggesting simple and universal behavior. The straightforward assignment of these structural contributions facilitates the comparison of these features between different classes of extractant molecules and will enable further studies of organic phase aggregation. Applicability to more complex, process-relevant organic phases is illustrated with post-contact organic phases containing significant quantities of extracted lanthanide nitrate salt, which we find are readily described by this model.

74 ATOMIC AND MOLECULAR PHYSICS↗

Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates

Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (μ) are necessary to optimize coupling within dye aggregates. Extinction coefficients (ε) can be used to determine the μ of dyes, and so dyes with a large ε (>150,000 M –1 cm –1 ) should be engineered or identified. However, dye properties leading to a large ε are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations, can be time-consuming. In order to screen large datasets of molecules for desirable properties (i.e., large ε and μ), a computational workflow was established using machine learning (ML), DFT, time-dependent (TD-) DFT, and molecular dynamics (MD). ML models were developed through training and validation on a dataset of 8802 dyes using structural features. A Classifier was developed with an accuracy of 97% and a Regressor was constructed with an R2 of above 0.9, comparing between experiment and ML prediction. Using the Regressor, the ε values of over 18,000 dyes were predicted. The top 100 dyes were further screened using DFT and TD-DFT to identify 15 dyes with a μ relative to a reference dye, pentamethine indocyanine dye Cy5. Two benchmark MD simulations were performed on Cy5 and Cy5.5 dimers, and it was found that MD could accurately capture experimental results. The results of this study exhibit that our computational workflow for identifying dyes with a large μ for excitonic applications is effective and can be used as a tool to develop new dyes for excitonic applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

NaCl aggregation in water at elevated temperatures and pressures: Comparison of classical force fields

The properties of water vary dramatically with temperature and density. This can be exploited to control its effectiveness as a solvent. Thus, supercritical water is of keen interest as solvent in many extraction processes. The low solubility of salts in lower density supercritical water has even been suggested as a means of desalination. The high temperatures and pressures required to reach supercritical conditions can present experimental challenges during collection of required physical property and phase equilibria data, especially in salt-containing systems. Molecular simulations have the potential to be a valuable tool for examining the behavior of solvated ions at these high temperatures and pressures. However, the accuracy of classical force fields under these conditions is unclear. We have, therefore, undertaken a parametric study of NaCl in water, comparing several salt and water models at 200 bar–600 bar and 450 K–750 K for a range of salt concentrations. We report a comparison of structural properties including ion aggregation, hydrogen bonding, density, and static dielectric constants. All of the force fields qualitatively reproduce the trends in the liquid phase density. An increase in ion aggregation with decreasing density holds true for all of the force fields. The propensity to aggregate is primarily determined by the salt force field rather than the water force field. This coincides with a decrease in the water static dielectric constant and reduced charge screening. While a decrease in the static dielectric constant with increasing NaCl concentration is consistent across all model combinations, the salt force fields that exhibit more ionic aggregation yield a slightly smaller dielectric decrement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗