PACKMOL: a package for building initial configurations for molecular dynamics simulations

Reliable high-PAP-1-loaded polymeric micelles for cancer therapy: preparation, characterization, and evaluation of anti-tumor efficacy

The mitochondrial potassium channel Kv1.3 is a critical therapeutic target, as its blockade induces cancer cell apoptosis, highlighting its therapeutic potential. PAP-1, a potent and selective membrane-permeant Kv1.3 inhibitor, faces solubility challenges affecting its bioavailability and antitumor efficacy. To circumvent these challenges, we developed a tumor-targeting drug delivery system by encapsulating PAP-1 within pH-responsive mPEG-PAE polymeric micelles. These self-assembled micelles exhibited high entrapment efficiency (91.35%) and drug loading level (8.30%). As pH decreased, the micelles exhibited a significant increase in particle size and zeta potential, accompanied by a surge in PAP-1 release. Molecular simulations revealed that PAE's tertiary amine protonation affected the self-assembly process, modifying hydrophobicity and resulting in larger, loosely packed particles. Furthermore, compared to free PAP-1 or PAP-1 combined with MDR inhibitors, PAP-1-loaded micelles significantly enhanced cytotoxicity and apoptosis induction in Jurkat and B16F10 cells, through mechanisms involving decreased mitochondrial membrane potential and elevated caspase-3 activity. In vivo, while free PAP-1 failed to reduce tumor size in a B16F10 melanoma mouse model, PAP-1-loaded micelles substantially suppressed tumors, reducing volume by up to 94.26%. Fluorescent-marked micelles effectively accumulated in mouse tumors, confirming their targeting efficiency. This strategy holds promise for significantly improving PAP-1's antitumor efficacy in tumor therapy.

Ionic adsorption on bulk nanobubble interfaces and its uncertain role in diffusive stability

HYPOTHESIS

Bulk nanobubbles have been proposed to improve gas exchange in a variety of applications, such as in water treatment, theragnostics, and microfluidic surface cleaning. However, there is currently no consensus regarding the mechanism responsible for their reportedly long lifetimes, which contradicts classical understanding of diffusive bubble dynamics. Recently, there has been increasing support for an electrostatic stability mechanism, following from experiments that observe negatively charged zeta potentials around nanobubbles.

SIMULATIONS

We use high-fidelity Molecular Dynamics simulations to model bulk nanobubbles under mechanical equilibrium in a sodium iodide electrolyte solution, to investigate ionic adsorption on the liquid-gas interface, and resulting zeta potential. We critically examine the hypothesised electrostatic stress underpinning this previously suggested stability mechanism, which is theorised to stabilise the nanobubbles against dissolution by counteracting the otherwise dominant effects of surface tension, however, has been too difficult to directly measure in experiments.

FINDINGS

Ions adsorb onto the liquid-gas interface, confirming an Electric Double Layer (EDL) distribution around the nanobubble with an estimated zeta potential, in accordance with experiments. However, we find no significant electrostatic stress exerted on the nanobubble surface, as any ion charge density in the EDL is completely neutralised by the rearrangement of the water molecules. As a result, the internal gas pressure is still well predicted by the standard Laplace pressure equation (with a fitted Tolman length correction ), challenging an essential assumption underlying the previously proposed theories, and we instead speculate on alternative mechanisms for electrostatic-based stability.

Facile approach developed for low-pressure separation of ethanol-water using cellulose membrane grafted with acrylic polyelectrolyte

Conventional ethanol separation from low-concentration aqueous solutions is energy-intensive and can affect flavor, highlighting the need for efficient, economical alternatives. This study presents a selective, porous polyelectrolyte membrane fabricated by grafting polyacrylate salt (PAS) onto regenerated cellulose membranes using surface-initiated atom transfer radical polymerization (SI-ATRP). The pH-responsive PAS layer enables tunable selectivity, achieving ethanol rejection rates up to 80 % for 15 vol% ethanol solutions at pressures ≤ 0.2 MPa which shows improved comprehensive separation performance and development potential compared to commercial separation membranes. In addition, molecular dynamics simulations (MDS) reveal the interactions of polyelectrolyte chain behavior and ethanol-water molecules, as well as free volume changes drive separation. This green, scalable fabrication strategy offers a potential and promising pathway for ethanol/water separation, which is desirable for applications in areas such as efficient bioethanol dehydration and processing of low-content alcoholic beverages.

Deep eutectic solvents-synergistic ultrasonic-assisted extraction of polyphenols from raspberry (Rubus idaeus L.): Optimization, mechanisms, and in vitro and cellular antioxidant activity

This study explores an innovative approach based on deep eutectic solvents (DESs)-synergistic ultrasonic-assisted extraction (UAE) of polyphenols from raspberry (RB). Choline chloride-fructose (ChCl-Fru, 2: 1) was screened and exhibited the highest amounts of active compounds. The optimal conditions for ChCl-Fru-synergistic UAE (ChCl-Fru-UAE) were obtained as follows: ultrasonic power of 360 W, liquid-to-solid ratio of 10:1, and water content in ChCl-Fru of 50 %. Eight compounds were identified in the RB extracts by HPLC-MS/MS method. SEM results revealed that UAE disrupted the surface structure of the samples, thereby facilitating the release of phenolic compounds. Molecular dynamics simulations results confirmed that ChCl-Fru significantly enhanced solute-solvent interactions, especially for delphinidin-3-O-glucoside and ellagic acid, and thus showed higher extraction efficiency. In vitro chemical and cell assays verified that ChCl-Fru-UAE demonstrated stronger antioxidant activities. Overall, ultrasonic-synergistic DESs extraction could be an eco-friendly method for recovering high-value compounds from fruits and their byproducts.

Enhancing pesticide detection: The role of serine in lipopeptide nanostructures and their self-assembly dynamics

In this research, we studied two novel lipopeptide sequences containing the amino acid serine (SPRWG) with one (compound 1) or two aliphatic tails (compound 2) to optimize the detection capabilities for organophosphate pesticides, specifically glyphosate. The study comprehensively explored how the incorporation of serine influences the physicochemical properties and supramolecular assembly of the lipopeptides, leading to enhanced interactions with glyphosate. Advanced analytical methods were employed to investigate these modifications, including fluorescence spectroscopy, circular dichroism, and small-angle X-ray scattering (SAXS). The results showed that serine significantly reduces the critical aggregation concentration, increases the hydrophilicity of the lipopeptides, and promotes the formation of distinct secondary structures-β-turns in compound 1 and β-sheets in compound 2. Moreover, isothermal titration calorimetry (ITC) and molecular dynamics confirmed the improved binding affinity with glyphosate strongly modulated by pH and pesticide load. Compound 1, with one alkyl chain, demonstrated notably higher catalytic activity and sensitivity linked to its pH equilibrium and structural features, marking it as particularly effective for acetylcholinesterase mimicry in pesticide detection. Density functional theory and molecular dynamics calculations showed that, when compared to the PRWG sequence, SPRWG has more unprotonated N-terminal sites due to a lower pKa, more beta-turn-like structures that improve stabilization. Besides promotes more hydrogen bonds between N-(phosphonomethyl)glycine (PNG, commonly known as glyphosate) and aggregates across a wide pH range and P/L; which explains its enhanced reactivity in Ellman's test and better inhibitory effects under the influence of PNG. Our results suggest that serine-functionalized lipopeptides have great potential as biomimetic sensors in environmental monitoring.

Delivery of cisplatin confined into pure and doped C240 fullerene: A molecular dynamics simulation study

In this research, we have investigated the delivery of cisplatin, as the anti-cancer drug molecule encapsulated into C240 fullerene with maximum equal number of water and carbon dioxide molecules (20H2O+20CO2) by continuously increasing the temperature from 310 to 450 K. We have determined the temperature at which the fullerene broke and the drug molecule released into the outer environment. To examine the effect of B, N, and Si doping of C240 fullerene on the bond break and release temperatures, we have also simulated the 20H2O+20CO2 mixture into 3 % doped (C233B7, C233N7, and C233Si7) and 20 % doped (C192B48, C192N48, and C192Si48) fullerenes at the same temperature range. Our results showed that there is not any bond break and consequently the drug release for the pure fullerene containing 20H2O+20CO2 mixture at any temperature. It is also observed that the N-doped fullerene shows less resistance to the breakdown, especially the C192N48 fullerene. Therefore, this N-doped C192N48 fullerene is more proper compound to use in the nano drug delivery investigations using fullerene. It is also shown that the doping fullerene is a proper way to easily destruct its structure to use in the drug delivery applications. It is also shown that the self-diffusion of the cisplatin molecule is higher in the C192N48 fullerene than the other systems. This result is in agreement with the other results and approves the C192N48 fullerene for the drug delivery purpose.

Exploring minimum free-energy pathway of GB1 dimerization in dilute and crowded solution

The intracellular crowded environment plays a major role in driving the protein-protein association reaction that entails large conformational fluctuations. A detailed understanding of the crowding influence on protein association requires characterization of transient intermediates on a free energy landscape. In this work, we explore the free energy landscape of dimerization of protein GB1 in a dilute and crowded medium by employing advanced sampling techniques, such as metadynamics and parallel tempering. Dimerization proceeds via a single dominant pathway encountering few minima in dilute solutions. However, in presence of lysozyme crowders, the free energy landscape exhibits multiple minima and multiple barriers, providing alternative pathways for dimerization. The minimum free energy pathway indicates that dimerization starts by destabilizing the N-termini of monomers in both the cases. The population of the on-pathway intermediate states in dilute medium reveals the structural modulations in GB1 conformation that eventually lead to a final dimer-like state. The presence of lysozyme crowders stabilizes new intermediates, although no stable dimer is formed. The study highlights modification of dimerization pathway by attractive protein-crowder interactions.

An artificial intelligence accelerated ab initio molecular dynamics dataset for electrochemical interfaces

Understanding atomic-scale structures at electrochemical interfaces is essential for advancing research and applications in electrochemistry. While experiments can provide detailed microscopic insights, their complexity and inefficiency often limit the large-scale generation of data. Complementing experimental approaches, computational methods, such as ab initio molecular dynamics and machine learning-accelerated molecular dynamics, offer an efficient means of obtaining microscopic information. However, despite these advancements, computational studies of interfaces have typically shared research data in isolation, often through private repositories. This practice has led to fragmented knowledge, reduced data accessibility, and limited opportunities for cross-study comparisons or large-scale meta-analyses. To overcome these challenges, we introduce ElectroFace, an artificial intelligence-accelerated ab initio molecular dynamics dataset for electrochemical interfaces. ElectroFace is designed to compile, visualize, and provide open access to interface data, fostering collaboration and accelerating progress in the field.

Ancestral evolution of oxidase activity in a class of (S)-nicotine and (S)-6-hydroxynicotine degrading flavoenzymes

Reduced flavin cofactors have the innate ability to reduce molecular oxygen to hydrogen peroxide. Flavoprotein oxidases turbocharge the reaction of their flavin cofactor with oxygen whereas flavoprotein dehydrogenases generally suppress it, yet our understanding of how these two enzyme classes control this reactivity remains incomplete. Here we used ancestral sequence reconstruction and biochemical characterization to retrace the evolution of oxidase activity in a lineage of nicotine/6-hydroxynicotine degrading enzymes of the flavoprotein amine oxidase superfamily. Our data suggest that the most ancient ancestor that gave rise to this lineage was a dehydrogenase, and that oxidase activity emerged later from within this group of dehydrogenases. We have identified the key amino acid replacements responsible for this emergence of oxidase activity, which, remarkably, span the entire protein structure. Molecular dynamics simulations indicate that this constellation of substitutions decreases the global dynamics of the protein in the evolution of oxidase function. This coincides with a dramatic restriction in the movement of a lysine residue in the active site, which more optimally positions it in front of the flavin to promote the reaction with O2. Our results demonstrate that sites distant from the flavin microenvironment can help control flavin-oxygen reactivity in flavoenzymes by modulating the conformational space and dynamics of the protein and catalytic residues in the active site.

What Are the Essential Water Molecules in Regulating Lipid Membrane Fluidity?

Living organisms often endure extreme dehydration, which disrupts the cell membrane structure and function. Dehydration can induce a fluid-to-gel phase transition in lipid bilayers, compromising their fluidity and biological role. Lipid bilayer self-assembly is governed by intricate interactions between water and lipid head groups, but which water molecules are crucial for maintaining fluidity? We address this fundamental question using molecular dynamics (MD) simulations of a liquid-ordered (Lo) lipid bilayer over a hydration range of h = 2-30. We have identified a critical threshold at hydration level h = 9, below which dehydration severely impacts lipid packing and dynamics. Water molecules hydrogen-bonded to the lipid head groups, particularly phosphate groups, play a dominant role in preserving fluidity. When outer hydration shells are lost, hydrogen bonds between lipids and water overwhelmingly strengthen, likely reducing membrane fluidity. These insights enhance our understanding of local dehydration processes, such as cell-cell fusion, and the survival mechanisms of anhydrobiotic organisms and extremophiles.

In Silico Study of Ionizable Lipid Nanoparticles Using the SPICA Force Field

Lipid nanoparticles (LNPs), composed of ionizable amino lipids, phosphatidylcholines (PC) lipids, and cholesterol, have shown promise as delivery vehicles for therapeutic oligonucleotides in various applications, including cancer immunotherapies, cellular reprogramming, genome editing, and viral vaccines (e.g., COVID-19 vaccines). However, the molecular characterization of ionizable amino lipids and their assemblies, such as LNPs, both in silico and in vitro, remains in its early stages. In particular, in silico studies on LNPs to understand their nanostructure have been limited due to the need for accurate coarse-grained (CG) models. In this study, we expand the SPICA force field to develop a more reliable and accurate explicit CG model for investigating the structure and properties of model LNPs through in silico experiments. Using this CG model, we performed molecular dynamics simulations on LNP systems with varying helper lipids and pH conditions. Our results reveal bilayer structures with double-stranded DNA (dsDNA) sandwiched between closely apposed monolayers in LNPs at pH 4, while at pH 7, dsDNA molecules are embedded within amorphous domains inside the LNPs. These in silico-optimized microstructures align well with the experimental observations obtained from small-angle X-ray scattering and cryogenic transmission electron microscopy (cryo-TEM). Additionally, a detailed analysis of LNPs containing different helper lipids explains why replacing saturated PC lipids with unsaturated PC lipids enhances the DNA transfection activity. Overall, this study provides a robust CG model for in silico studies of LNPs and offers in-depth molecular-level insights to advance their design for improved stability and efficacy.

Atomistic Insights into Ion-Driven Interactions of Calcite/Carbonated Brine/Polar Model Oil: Implications for Carbonated Smart Waterflooding

This study investigates the fundamental ion-specific (Na+, Cl-, Mg2+, and SO42-) interactions governing a polar model oil (decane + benzoic acid) at the calcite/carbonated brine interface by adopting a fully atomistic molecular dynamics (MD) simulation. By bridging molecular-scale interactions with macroscopic mechanisms, such as interfacial tension (IFT) reduction, oil viscosity, and wettability changes, this work provides the first direct mechanistic validation of phenomena that have previously been inferred only from experimental observations in carbonated smart water flooding systems. The results demonstrate that enhanced interactions between carboxylic acids and anions at the oil/brine interface significantly influence CO2 diffusion and distribution within the oleic phase, which affects the apparent oil viscosity. While variations in brine ionic composition cause only modest changes in IFT, a pronounced reduction is observed with increased concentrations of polar molecules in the oil phase. Structural analysis reveals that divalent ions (Mg2+, SO42-) are excluded from the hydration layers near the calcite surface but alter the arrangement of Na+ and Cl- ions in the hydration layer covering the calcite surface, thereby influencing wettability. Notably, SO42- neutralizes the calcite surface positive charge and facilitates Mg2+ access to the interface, promoting desorption of benzoic acid (BA) from the surface through the Mg-BA association. This highlights the cooperative role of SO42- and Mg2+ in releasing polar species from the calcite surface. The findings underscore the dominant influence of IFT over contact angle in capillary-driven recovery and show that apparent viscosity is more sensitive to CO2 content and overall salinity than specific ions. Therefore, from an industrial perspective, maintaining seawater-like salinity enriched with divalent ions offers a practical strategy to enhance the mobilization of polar acidic components during carbonated water flooding in carbonate reservoirs, supporting the design of more efficient Enhanced Oil Recovery (EOR) formulations.

From Grotthuss Transfer to Conductivity: Machine Learning Molecular Dynamics of Aqueous KOH

Accurate conductivity predictions of KOH(aq) are crucial for electrolysis applications. OH- is transferred in water by the Grotthuss transfer mechanism, thereby increasing its mobility compared to that of other ions. Classical and ab initio molecular dynamics struggle to capture this enhanced mobility due to limitations in computational costs or in capturing chemical reactions. Most studies to date have provided only qualitative descriptions of the structure during Grotthuss transfer, without quantitative results for the transfer rate and the resulting transport properties. Here, machine learning molecular dynamics is used to investigate 50,000 transfer events. Analysis confirmed earlier works that Grotthuss transfer requires a reduction in accepted and a slight increase in donated hydrogen bonds to the hydroxide, indicating that hydrogen-bond rearrangements are rate-limiting. The computed self-diffusion coefficients and electrical conductivities are consistent with experiments for a wide temperature range, outperforming classical interatomic force fields and earlier AIMD simulations.

Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN

Fuel design is usually "forward": candidate molecular structures are designed first, and then their properties are predicted for screening. Owing to the large latent space of organic molecules (1060 order), reverse design by giving target fuel properties is urgently needed. However, it is hardly realized due to the unknown complex rule of the structure-property relationship. In this work, reverse design of hydrocarbon fuels is realized based on the conditional generative adversarial network of hydrocarbon molecules. Two deep generative models, c-GAN and c-infoGAN, are established and trained for generating new candidate fuel molecules when target fuel properties are input. c-infoGAN exhibited superior generation ability in terms of the validity, uniqueness, and novelty of the as-generated molecules. JP-10, a classical hydrocarbon fuel, was rediscovered by c-infoGAN. The latent space of fuels constructed by c-infoGAN is ordered, as proved by linear interpolation and linear algebra in this high-dimensional space. Given the target of high density, low freezing point, high heating value, and large specific impulse, 27 new fuel molecules with novel structures, high diversity, and expecting properties were designed. One of the as-designed fuels was experimentally synthesized and tested, which verifies the robust design ability of c-infoGAN. This work opens new avenues for the design of new hydrocarbon fuels to meet the strict requirements of next-generation engines.

Prefilled and Concerted Ion Transport Mechanism in Hierarchical Porous Carbons for Ultra-Fast Energy Storage

Hierarchical porous structures have been extensively reported for their efficiency in achieving fast charging and high energy density in electrochemical capacitors. However, the microscopic dynamic mechanism through which hierarchical pores enhance ion transport and storage remains unclear. Here, we synthesize hierarchical mesopore-micropore carbons with varying mesopore contents of approximately 5 nm in size using a tunable "structure inheritance" strategy for comparative investigation. Advanced constant potential method molecular dynamics simulations and nuclear magnetic resonance spectroscopy are combined with electrochemical analyses to systematically investigate ion behaviors in the hierarchical- and microporous-dominant structures under the driving forces of both constant and cyclic voltages. The results indicate that a prefilled and concerted transport mode is responsible for the enhanced ion transport and storage in the hierarchical mesopore-micropore carbons. Notably, hierarchical pores exhibit a significant fast-charging enhancement, with at least a 50% reduction in response time, across various electrolytes, including aqueous, organic, water-in-salt, and ionic-liquid electrolytes. In all four tested electrolytes, the maximum power density of a typical hierarchical porous carbon is several times that of the microporous carbon. This work provides insights into how hierarchical structures improve ion transport and may promote the development of more efficient electrochemical energy storage materials and devices.

Spectroscopic insights into the thermal aging process of lithium-ion battery electrolytes

The thermal aging process of lithium-ion battery electrolyte was studied using Raman spectroscopy and fluorescence spectroscopy. The system studied is specifically a carbonate-based electrolyte containing lithium hexafluorophosphate (LiPF6). Raman spectroscopy results show that LiPF6 will decompose and produce substances with significant fluorescence effects under the thermal aging. The fluorescence spectrum results also show that the concentration of this fluorescent substance has a significant positive correlation with the intensity of thermal aging. The mechanism behind the above experimental phenomena was explained and verified by Ab Initio Molecular Dynamics (AIMD) and Density Functional Theory (DFT). AIMD confirmed that LiPF6 can decompose and polymerize into polyfluorophos-phoric acid (PFPA) with different degrees of polymerization at elevated temperature. Then, the theoretical fluorescence spectra and excited state transition of PFPA based on DFT prove that the source of the fluorescence effect is the PFPA molecule, and specifically comes from the transition of π electrons and lone pair electrons on oxygen atoms.

Removing α-H in Carboxylate-Based Electrolytes for Stable Lithium Metal Batteries

Although carboxylate esters greatly improve the cold weather performance of graphite-based lithium-ion batteries utilized in arctic expeditions, the underlying cause of the incompatibility between carboxylates and lithium (Li) anodes has not been sufficiently explained, resulting in the greatly restricted usage of carboxylate in lithium metal batteries (LMBs). Herein, we reveal the serious parasitic reactions between carboxylate α-H atoms and Li metal are the culprits that render carboxylate-based ineffectiveness for LMBs. By replacing all α-H atoms with fluorine atoms and methyl groups, we successfully construct inert carboxylates and find the ions/molecules distribution in electric-double-layer (EDL) can be manipulated at a molecular-level. The unique structure ensuring more anions are positioned closer to the Li surface in the EDL of the inert carboxylate-based electrolyte, the morphology of the deposited Li is significantly regulated and the chemical corrosion gets effectively inhibited, as a consequence of remarkable extending lifespan of carboxylate-based LMBs with routine salt concentration and few additives. More generally, using carboxylates lacking α-H atoms offer a realistic approach to increase the variety of solvents that can be used in LMBs electrolytes.

ColBuilder: flexible structure generation of crosslinked collagen fibrils

MOTIVATION

Collagen fibrils are fundamental building blocks of connective tissues, yet generating accurate molecular models of their structure remains challenging due to their hierarchical organization and complex crosslinking patterns.

RESULTS

ColBuilder has been developed to automate the generation of atomistic models of crosslinked collagen fibrils and facilitate the setup of molecular simulations. The tool integrates homology modeling, higher order structure generation and optimization to build complete fibril structures with precise control over sequence composition, crosslinking patterns, and dimensions. Users can explore different collagen sequences, manipulate crosslink chemistry through mixed ratios and densities, and generate fibrils of varying diameter and length. All-atom molecular dynamics simulations of 335nm-long fibrils validate the generated structures, showing excellent agreement with experimental measurements of D-band periodicity and force-extension behavior.

AVAILABILITY AND IMPLEMENTATION

ColBuilder is available both as an open-source command-line application and through a web interface at https://colbuilder.mpip-mainz.mpg.de.

Development of cocaine esterase W/O/W nanoemulsions by a novel low-temperature double emulsification approach for cocaine abuse treatment

Cocaine esterase is highly effective against cocaine but has a short in vivo half-life and is sensitive to temperature, limiting its clinical use. Encapsulation of cocaine esterase in water-in-oil-in-water (W/O/W) nanoemulsions offers a promising approach to improve its stability and therapeutic effectiveness. In this study, we developed a novel low-temperature double emulsification method to encapsulate the cocaine esterase mutant (E196-301) into W/O/W nanoemulsions (designated as CocE NEs). The oil phase, containing phospholipids, was cooled to room temperature under high-speed stirring before the enzyme-containing aqueous phase was added. This process prevented the precipitation of soybean phospholipids and preserved over 90 % of E196-301's enzymatic activity. Notably, the temperature stability of E196-301 has been greatly improved, E196-301 within the inner aqueous phase maintained over 90 % of its activity under temperature variations between 37 °C and 40 °C. Importantly, the in vivo half-life of E196-301 increased from 16.26 ± 1.94 min to 57.25 ± 14.71 min (3 mg/kg, i.v.). Pharmacodynamic studies revealed CocE NEs (3 mg/kg, i.v.) significantly reduced cocaine-induced locomotor sensitization in mice within 45 min, by attenuating cocaine-induced (25 mg/kg, i.p.) dopamine signaling in the brain. CocE NEs represent a promising candidate for the sustained prevention and treatment of cocaine abuse.

Covalent binding of 5-tetradecyloxy-2-furoic acid (TOFA) and c(RGDfK) and its co-delivery with Lipusu, a novel synergistic strategy to inhibit the proliferation of nasopharyngeal cancer

As the world's only commercially available paclitaxel liposome, Lipusu (Lip) has been clinically used in chemotherapy for >20 years, but the design concept of Lip remains largely unchanged since its initial development. Based on the study of Acetyl-CoA-carboxylase 1 (ACC1) in nasopharyngeal carcinoma (NPC), we proposed the concept of next-generation liposomes (NGL) utilizing lipid demand balance. In this study, we evaluated the feasibility of ACC1 and integrin αVβ3 as NPC targets, and designed 10 conjugates of 5-tetradecyloxy-2-furoic acid (TOFA) and c(RGDfK) that can bind to Lip. Considering the results of chemical parameter prediction, molecular docking, molecular dynamics simulation (MD) and other aspects, we finally selected and synthesized the compound F, and successfully constructed F-Lip by simple incubation method. Compared with Lip, F-Lip showed stronger toxicity in both HONE-1 cells and corresponding tumor-bearing mice. In conclusion, by regulating the balance of lipid demand, the toxicity of Lip can be improved so as to achieve the goal of inhibiting the proliferation of NPC. This study provides a new model for the future design and development of Lip.

Weakly solvating effect optimized hydrated eutectic electrolyte towards reliable zinc anode interfacial chemistry

The inherent issues of aqueous Zn-ion batteries, including side reactions and dendrite growth, can be effectively addressed through designing solvation structures enriched with anions to facilitate the formation of an anion-derived solid electrolyte interphase (SEI) layer. Here, the weakly solvating effect is utilized to modulate Zn2+ solvation structure for constructing an anion-derived SEI layer. Trifluoroacetamide (TFACE), with a specific weak solvating ability, serves as an ideal ligand for preparing hydrated eutectic electrolytes (HEEs) combining the anion-containing solvation structures and high ionic conductivity. The results demonstrate that coordinated anions preferentially decompose and generate an inorganic/organic hybrid SEI layer on the Zn anode, which efficiently suppresses both side reactions and dendritic growth. Such an electrolyte enables assembled Zn//polyaniline (PANI) full cells to process an impressive capacity retention, maintaining 80 % after 3000 cycles at 0.5 A g-1. This work provides a fundamental insight into building the anion-derived SEI by the weakly solvating effect and gives a viable route for designing advanced aqueous electrolytes.

Preserving fruit freshness with amyloid-like protein coatings

Addressing critical challenges in perishable fruit preservation, including hydrophobic surface treatment, protective layer adhesion on complex cuticles, and synergistic integration of preservation components, here we present an eco-friendly amyloid-like protein coating strategy developed through computer-aided molecular simulation. This system employs phase-transitioned lysozyme as an adhesive layer bonded to fruit epicuticular wax, synergized with sodium alginate and cellulose nanocrystals to form a proteinaceous barrier. Validated across 17 fruit varieties, the coating extends shelf-life by 2-5-fold through microbial inhibition, moisture loss reduction, and rot delay, while maintaining 60-98% nutrient retention, surpassing chemical preservation efficacy without toxicity risks. With edible properties, easy washability, and low cost, the coating demonstrates universal applicability for post-harvest and fresh-cut fruits. Notably, it reduces carbon dioxide emissions by 90% versus refrigeration while achieving 2.5-fold longer shelf-life. These positions the amyloid-like protein coating as a practical and sustainable approach to mitigating global food waste issues.

Mechanism of azeotrope elimination in the ethyl propionate-ethanol system using ionic liquid HMIMOAc as an entrainer: experimental and theoretical insights

Ionic liquids (ILs) are highly effective entrainers for extractive distillation of azeotropes, owing to their unique physicochemical properties. However, the intrinsic molecular mechanisms underlying the role of ILs in the azeotropic separation process remain insufficiently understood. To investigate the intrinsic causes of azeotrope elimination by ILs, the study focused on the v(O-D) region of ethanol employing both experimental and theoretical methods to investigate the microstructural properties of the ethyl propionate (EP)-ethanol azeotrope before and after separation by 1-hexyl-3-methylimidazole acetate (HMIMOAc). The key findings are as follows: (1) the interaction between HMIMOAc and ethanol is significantly stronger than that between EP and ethanol. (2) The interaction between [OAc]- in HMIMOAc and ethanol plays a critical role in eliminating the azeotrope. (3) Ethanol self-aggregates, EP-ethanol interaction complexes, and HMIMOAc-ethanol interaction complexes were identified and characterized using excess spectroscopy and quantum chemical calculations.

Molecular Mechanisms Driving the Performance of Single-Ion Conducting Polymer Electrolytes in Lithium-Based Batteries

Single-ion conducting polymer electrolytes (SICPEs) hold great potential for the next-generation batteries due to their high safety, fast charging capability, and high energy density. However, their practical application is hindered by the low ionic conductivity (IC). The addition of plasticizers has been shown to effectively enhance IC, although the underlying molecular mechanisms remain unclear. In this study, we employed atomistic molecular dynamics simulations to examine the impact of ethylene carbonate (EC) on lithium-ionic conductivity in a modified polyethylene terephthalate (mPET)-based SICPE. Our simulations reproduced experimental IC values and revealed a similar IC trend with varying EC concentrations, including a notable transition at 50 wt % EC. This enhancement in IC appears to be associated with increased EC diffusion and the preferential coordination of the lithium ions with the oxygen atoms in EC. Analysis of the local oxygen coordination environment around lithium ions further explains the IC transition observed at 50 wt % EC. These findings provide insights into the molecular mechanisms by which EC enhances IC in mPET-based SICPEs, primarily through changes in the local oxygen environment surrounding lithium ions. This study contributes to the design of improved SICPEs with plasticizers, supporting advancements in lithium-ion battery technology.

Unraveling the Mechanical Behavior of Softwood Secondary Cell Walls through Atomistic Simulations

The plant cell wall (PCW) is a remarkable biomaterial, endowing plants with strength, stiffness, and defense against pathogens and chemical agents. This complex structure, mainly composed of cellulose in a matrix of hemicellulose, lignin, and water, exhibits impressive mechanical properties. However, the link between its molecular architecture and macroscopic mechanics is not fully understood. This study uses molecular dynamics simulations to examine the nanomechanical behavior of spruce wood's S2 layer. Multicomponent models including cellulose, hemicellulose (xylan and mannan), lignin, and water were developed. Simulations showed that water acts as a "molecular lubricant", mediating critical interactions between the components of the system. Tension and compression tests on the models displayed realistic mechanical behavior. Our results show that cellulose microfibrils bear the primary load, while lignin dissipates stress under compression. These findings offer new insights into the relationship between the molecular structure and mechanical function in this complex biomaterial.

Creating Coarse-Grained Systems with COBY: Toward Higher Accuracy of Complex Biological Systems

Current trends in molecular modeling are geared toward increasingly realistic representations of the biological environments reflected in larger, more complex systems. The complexity of the system-building procedure is ideally handled by software that converts user-provided descriptors into system coordinates. This, however, is not a trivial task, as building algorithms use simplifications that result in inaccuracies in the system properties. We created COBY, a coarse-grained system builder that can create a large variety of systems in a single command call with an improved accuracy of the complex membrane and solvent building procedures. COBY also contains features for building diverse systems in a single step, and has functionalities aiding force field development. COBY is an open-source software written in Python 3, and the code, documentation, and tutorials are hosted at https://github.com/MikkelDA/COBY.

Deconstructing 1H NMR Chemical Shifts in Strong Hydrogen Bonds: A Computational Investigation of Solvation, Dynamics, and Nuclear Delocalization Effects

This study provides the first quantitative dissection of the factors influencing 1H NMR chemical shifts δH in strong hydrogen-bonded systems, focusing on solvation, nuclear dynamics, and nuclear delocalization. A novel computational framework was developed, combining static quantum chemical calculations (nonrelativistic and relativistic), ab initio molecular dynamics (AIMD), and three-dimensional numerical solutions of the Schrödinger equation. This multiscale approach was applied to three model systems: the bifluoride anion (FHF)-, the Zundel cation (H5O2)+, and the pyridine-pyridinium cation (PyHPy)+. Our results reveal that nuclear dynamics and delocalization are the dominant factors determining δH in complexes with short, strong hydrogen bonds. Solvation effects, while critical for defining the hydrogen-bonding environment, play a secondary role. By isolating the contributions of each factor, we demonstrate that traditional methods often underestimate the quantum mechanical nature of the proton. The application of three-dimensional Schrödinger equation solutions represents a significant methodological advancement, enabling deeper insights into proton behavior in hydrogen bonds. This work not only enhances our understanding of NMR parameters in challenging systems but also establishes a robust framework for modeling complex interactions in chemical and biological environments.

Electron displacement polarization of high-dielectric constant fiber separators enhances interface stability

The electrostatic effects of separators under the internal electric field are often overlooked, leading to the unreliability of traditional theoretical models. Here we introduce the dielectric constant as a descriptor and develop a high dielectric constant fiber separator primarily composed of phosphorylated cellulose. Under the internal electric field, the intense electron displacement polarization within the high dielectric constant separator enhances the charge transfer kinetics and optimizes the solvation structure, thus mitigating the formation of amorphous organic oligomers at the solid-electrolyte interphase. Furthermore, the separator induces the formation of LiF, thereby forming a robust and low-resistance solid-electrolyte interphase. The separator exhibits high ionic conductivity (0.76 mS cm-1 at 25 °C) and Li+ transference number (0.68). Consequently, the Li||LiFePO4 pouch cell with the prepared separator achieve high specific energy exceeding 350 Wh kg-1 (relative to the mass of pouch cells) under practical quantities of active materials and electrolyte.

Insights into the mobility of rare earth complexes in groundwater-rock interactions: A geochemical view from modeling of computational chemistry

This study investigates the prediction and stability of novel complexes of rare earth elements (REE) under simulated groundwater and hydrothermal conditions. The electronic structure properties of the REE complexes LnX3 and Ln2Y3, with Ln = La, Lu; X = Cl-, F-, (HCO3)-, (AlO2)-, and Y = (SO4)2-, (CO3)2- were explored using density functional theory (DFT) including relativistic effects. The nature of the bonding in the complexes was assessed via the theory of atoms in molecules. Evidence shows that relativistic contributions play a significant role in stabilization energy and bonding distance, especially in La-complexes, where bond distances shrink by 0.64-6.82 %. Formation energies were calculated to identify the most stable configurations, being the most stable Ln2 (SO4)3. Molecular electrostatic potential (MEP) was analyzed to predict the acidic or basic behavior of the complexes. Ab initio molecular dynamics (AIMD) simulations were also performed for models with the first solvation shell, and also for models representing massive systems. In large-scale systems at 300 °C, the stability varies by element. For La, the most stable is La2(CO3)3, while for Lu, it is Lu2(SO4)3 ≈ Lu2(CO3)3. It evidences the feasibility of the existence of the REE complexes in aqueous media. These results give insight into the mobility and stability that these complexes may present in water-rock interaction processes of groundwater and environmental systems.

Soybean Lectin Cross-Links Membranes by Binding Sulfatide in a Curvature-Dependent Manner

Soybean (Glycine max) is a key source of plant-based protein, yet its nutritional value is impacted by antinutritional factors, including lectins. Whereas soybean lectin is known to bind N-acetyl-d-galactosamine (GalNAc), its lipid interactions remain unexplored. Using a novel purification method, we isolated lectin from soybean meals and characterized its interactions with GalNAc and the glycosphingolipid sulfatide. Isothermal titration calorimetry revealed micromolar affinity for GalNAc, whereas most GalNAc derivatives displayed weak or no binding. Lectin exhibited high-affinity binding to sulfatide in a membrane curvature-dependent manner. Binding of lectin to sulfatide promoted cross-linking of sulfatide-containing vesicles. Whereas sulfatide interaction was independent of GalNAc binding, suggesting distinct binding sites, vesicle cross-linking was inhibited by the sugar. Molecular dynamics simulations identified a consensus sulfatide-binding site in lectin. These findings highlight the dual ligand-binding properties of soybean lectin and may provide strategies to mitigate its antinutritional effects and improve soybean meal processing.

CrypToth: Cryptic Pocket Detection through Mixed-Solvent Molecular Dynamics Simulations-Based Topological Data Analysis

Some functional proteins undergo conformational changes to expose hidden binding sites when a binding molecule approaches their surface. Such binding sites are called cryptic sites and are important targets for drug discovery. However, it is still difficult to correctly predict cryptic sites. Therefore, we introduce an advanced method, CrypToth, for the precise identification of cryptic sites utilizing the topological data analysis such as persistent homology method. This method integrates topological data analysis and mixed-solvent molecular dynamics (MSMD) simulations. To identify hotspots corresponding to cryptic sites, we conducted MSMD simulations using six probes with different chemical properties: dimethyl ether, benzene, phenol, methyl imidazole, acetonitrile, and ethylene glycol. Subsequently, we applied our topological data analysis method to rank hotspots based on the possibility of harboring cryptic sites. Evaluation of CrypToth using nine target proteins containing well-defined cryptic sites revealed its superior performance compared with recent machine-learning methods. As a result, in seven of nine cases, hotspots associated with cryptic sites were ranked the highest. CrypToth can explore hotspots on the protein surface favorable to ligand binding using MSMD simulations with six different probes and then identify hotspots corresponding to cryptic sites by assessing the protein's conformational variability using the topological data analysis. This synergistic approach facilitates the prediction of cryptic sites with a high accuracy.

Identification of non-charged 7.44 analogs interacting with the NHR2 domain of RUNX1-ETO with improved antiproliferative effect in RUNX-ETO positive cells

The RUNX1/ETO fusion protein is a chimeric transcription factor in acute myeloid leukemia (AML) created by chromosomal translocation t(8;21)(q22;q22). t(8;21) abnormality is associated with 12% of de novo AML cases and up to 40% in the AML subtype M2. Previously, we identified the small-molecule inhibitor 7.44, which interferes with NHR2 domain tetramerization of RUNX1/ETO, restores gene expression down-regulated by RUNX1/ETO, inhibits proliferation, and reduces RUNX1/ETO-related tumor growth in a mouse model. However, despite favorable properties, 7.44 is negatively charged at physiological pH and was predicted to have low to medium membrane permeability. Here, we identified M23, M27, and M10 as non-charged analogs of 7.44 using ligand-based virtual screening, in vivo hit identification, biophysical and in vivo hit validation, and integrative modeling and ADMET predictions. All three compounds interact with the NHR2 domain, have KD, app values of 39-114 µM in Microscale Thermophoresis experiments, and IC50 values of 33-77 µM as to cell viability in RUNX1/ETO-positive KASUMI cells, i.e., are ~ 5 to 10-fold more potent than 7.44. M23 is ~ 10-fold more potent than 7.44 in inhibiting cell proliferation of RUNX1/ETO-positive cells. Biological characterization of M23 in relevant RUNX1/ETO-positive -and negative cell lines indicates that M23 induces apoptosis and promotes differentiation in RUNX1/ETO-positive AML cells. M23 and M27 are negligibly protonated or in a ~ 1:1 ratio at physiological pH, while M10 has no (de-)protonatable group. The non-protonated species are predicted to be highly membrane-permeable, along with other favorable pharmacokinetic and toxicological properties. These compounds might serve as lead structures for compounds inhibiting RUNX1/ETO oncogenic function in t(8;21) AML.

Inorganic Hydrogels can be Flexible and Highly Extensible

Inorganic hydrogels have great potential in many applications as sustainable materials, but lack flexibility due to rigid network structures. Here, a novel strategy is proposed-an inorganic polymer hydrogel, prepared by crosslinking long-chain polyphosphate (LPP) with M2+ ions (Ca2+, Mn2+, Mg2+, Ni2+), which effectively address the rigidity and fragility issues commonly associated with traditional inorganic gels. With the most stable hydration shell among those ions, Ni2+ tends to interact indirectly with LPP through hydrogen bonds rather than coordination bonds. The unique Ni2+-phosphate interaction endows the Ni-LPP hydrogels with ultrahigh elongation at break (≈15 000×). Further experiments reveal that the Ni2+-phosphate motif can be applied to other hydrogels as an extension enhancement factor. The highly extensible, good conductive (1.06 ± 0.08 S m-1), self-healing (within 30 s and without stimulation), arbitrarily shapeable, and nonflammable Ni-LPP inorganic hydrogel indicates a bright future in flexible electronics, environmental remediation, and beyond.

Multi-Agent-Network-Based Idea Generator for Zinc-Ion Battery Electrolyte Discovery: A Case Study on Zinc Tetrafluoroborate Hydrate-Based Deep Eutectic Electrolytes

Aqueous deep eutectic electrolytes (DEEs) offer great potential for low-cost zinc-ion batteries but often have limited performance. Discovering new electrolytes is therefore crucial, yet time-consuming and resource-intensive. In response, this work presents a Large Language Model (LLM)-based multi-agent network that proposes DEE compositions for zinc-ion batteries. By analyzing academic papers from the DEE field, the network identifies innovative, inexpensive, and sustainable Lewis bases to pair with Zn(BF4)2·xH2O. A Zn(BF4)2·xH2O-ethylene carbonate (EC) system demonstrates high conductivity (10.6 mS cm-1) and a wide electrochemical stability window (2.37 V). The optimized electrolyte enables stable zinc stripping/plating, achieves outstanding rate performance (81 mAh g-1 at 5 A g-1), and supports 4000 cycles in Zn||polyaniline cells at 3 A g-1. Spectroscopic analyses and simulations reveal that EC coordinates to Zn2+ , mitigating water-induced corrosion, while a fluorine-rich hybrid organic/inorganic solid electrolyte interphase enhances stability. This work showcases a pioneering LLM-driven approach to electrolyte development, establishing a new paradigm in materials research.

Understanding Solute-Hydrotrope Aggregation in Aqueous Solutions: A Molecular Dynamics Approach

Hydrotropy is a phenomenon where an amphiphilic molecule (i.e., the hydrotrope) is able to enhance the aqueous solubility of a hydrophobic solute. Understanding the molecular mechanisms behind this phenomenon is crucial to designing new hydrotropes aimed at enhancing the aqueous solubility of specific target solutes. This study investigates the hydrotropic behavior of 1,2-alkanediols in enhancing the aqueous solubility of syringic acid using molecular dynamics (MD) simulations. The analysis carried out here employs several computational methods, including Kirkwood-Buff integrals, solvation free energies, radial distribution functions, and hydrogen bonding number. The solvation free energy results reported in this work help explain the thermodynamic favorability of syringic acid solubilization in the presence of 1,2-alkanediols, aligning with experimental trends. In addition, MD simulations reveal a pronounced affinity between syringic acid and 1,2-alkanediols, particularly at low hydrotrope concentrations. This high affinity is driven by the alkyl chain of each hydrotrope when water is the main solvent, resulting in an increase in the solubility of the solute as the length of the hydrotrope alkyl chain increases. However, a shift in the solubilization mechanism is seen when water is no longer the main solvent, with the hydrogen bonding capabilities of the hydrotrope playing a larger role than its alkyl chains. Under low water concentration conditions, longer alkyl chains in the hydrotrope have difficulty forming hydrogen bonds, leading to an opposite trend compared to lower hydrotrope concentrations. This different behavior with composition results in a maximum solubility for systems with long alkyl chains at intermediate hydrotrope concentrations.

Tailoring the Regioselectivity of Lentinula edodes O-Methyltransferases for Precise O-Methylation of Flavonoids

A novel O-methyltransferase, LeOMT4, from Lentinula edodes was identified, expressed, and characterized. Although its catalytic activity was lower than that of the previously reported LeOMT2, LeOMT4 displayed strong regioselectivity for the meta-hydroxy group across different catecholic compounds, producing e.g., ferulic acid with an almost exclusive regioisomeric ratio of 98:2 and homoeriodictyol with a ratio of 82:18 (3'-product:4'-product). Leveraging the high sequence and predicted structural similarity between LeOMT2 and LeOMT4, key sites for the tailoring of LeOMT2 were identified through site-directed mutagenesis. This approach aimed for robust mutants retaining the high specific activity of LeOMT2, while enhancing regioselectivity. A single amino acid substitution, F182Y, enabled a regioisomeric ratio of 91:9 for the production of homoeriodictyol. Notably, another single amino acid substitution, I53M reversed the regioselectivity to 2:98 in favor of hesperetin. This strategy enables the selective production of sought-after pharmacologically active flavonoids (butein) and flavor-active flavonoids (homoeriodictyol, hesperetin, hesperetin dihydrochalcone).

Point defect formation at finite temperatures with machine learning force fields

Point defects dictate the properties of many functional materials. The standard approach to modelling the thermodynamics of defects relies on a static description, where the change in Gibbs free energy is approximated by the internal energy. This approach has a low computational cost, but ignores contributions from atomic vibrations and structural configurations that can be accessed at finite temperatures. We train a machine learning force field (MLFF) to explore dynamic defect behaviour using Te+1 i and V +2 Te in CdTe as exemplars. We consider the different entropic contributions (e.g., electronic, spin, vibrational, orientational, and configurational) and compare methods to compute the defect free energies, ranging from a harmonic treatment to a fully anharmonic approach based on thermodynamic integration. We find that metastable configurations are populated at room temperature and thermal effects increase the predicted concentration of Te+1 i by two orders of magnitude - and can thus significantly affect the predicted properties. Overall, our study underscores the importance of finite-temperature effects and the potential of MLFFs to model defect dynamics at both synthesis and device operating temperatures.

Water-in-Salt Electrolyte Stabilizes Pyrazine Radical: Suppression of Its Aggregation by Interaction between Pyrazine and Li(H2O)n. J Am Chem Soc 2025;147:16812-16825. [PMID: 40327745 DOI: 10.1021/jacs.4c09561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Stabilizing radical intermediates of redox-active organic molecules in aqueous media is crucial for advancing applications in energy storage, catalysis, and electrosynthesis. This study investigates the stabilization of protonated radical intermediates of pyrazine derivatives in water-in-salt electrolytes (WISEs) with 7-8 m LiTFSI. Strong interactions between pyrazine derivatives and Li+-coordinated water (Li(H2O)n+) in WISEs prevent molecular aggregation and protect radical intermediates from disproportionation and oxygen-induced degradation. Voltammetric results show that higher concentrations of LiTFSI enhance both the stability and redox reversibility of dimethylpyrazine (DMP) radical intermediates, with protonation identified as a key stabilizing factor. Notably, these stabilizing effects were absent in solutions containing concentrated LiCl or LiNO3. Fourier-transform infrared (FTIR) spectroscopy and molecular dynamics (MD) simulations confirmed reduced DMP aggregation in LiTFSI-based electrolytes, driven by interactions with Li(H2O)n+, while no similar solvation structure modification occurred with LiNO3. The protonated radical intermediates in LiTFSI-based WISEs exhibited greater resistance to oxygen-induced degradation compared to conventional acidic solutions. Additionally, substitution of methyl or ethyl groups on the pyrazine ring destabilized the corresponding radical intermediates in LiTFSI-based WISEs, primarily due to the alkyl inductive effect, as evidenced by electrochemical and UV-visible absorption spectroscopy. Charge-discharge tests in an H-cell further demonstrated significantly improved Coulombic efficiency of pyrazine redox reactions in LiTFSI-based WISEs compared to acidic Salt-in-Water electrolytes, underscoring the importance of radical intermediate stabilization.

Anion Redistribution in Solvation Structure Enables a Stable Graphite Cathode in Dual-Ion Batteries

The electrochemical properties of anions as carriers in graphite-based dual-ion batteries (GDIBs) play an important role in achieving long cycling stability and high-rate performance. However, anion behavior in the electrolyte was neglected in previous studies. To balance high voltage and fast conduction, the anion behavior after introducing diluent in a highly concentrated electrolyte|high concentrated electrolyte (HCE) to form locally highly concentrated electrolyte|locally high concentrated electrolyte (LHCE) in GDIBs was deeply investigated. In contrast to the highly aggregated coordinated ion pairs in the HCE, more free anions can be attained in the LHCE without significant reunion. These free anions can rapidly migrate to the electrode surface under the electric field drive and then intercalate between graphite layers with a lower energy barrier. Meanwhile, an inorganic-rich interfacial layer with rapid ion conduction and a thinner thickness can be formed to prevent further decomposition of anions and stabilize the structure of the cathode. As a consequence, the dual-graphite DIBs achieved a superior capacity of 98.3% after 1000 cycles at a high rate of 200 mA g-1 in LHCE, and the corresponding pouch cells exhibited a stable cycling process. This work advances the understanding of anion chemistry, enabling the regulation of the anion status to enhance the electrochemical performance of GDIBs.

How to Control the Release Behavior of Insect Sex Pheromones Using Nanomicro Fiber: Insights from Experiment and Molecular Dynamics Simulation

Polymer-based electrospun fibers can effectively sustain pheromone release for pest control, yet their regulatory mechanisms remain unclear. In this study, fibers from various polymers were loaded with multicomponent sex pheromones of Grapholitha molesta and characterized. Release tests showed that poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (PHB) fibers released 90% of pheromones in 81.93 days, compared to 14.01 days for polycaprolactone fibers. Molecular dynamics (MD) simulations revealed that pheromones diffused through the polymer network via vibrations, cavity formation, and jumping. PHB fibers exhibited the lowest diffusion coefficient (0.0064 × 10-9 m2 s-1) and highest activation energy (24.56 kJ mol-1). Additionally, PHB exhibited good crystallinity and crystal arrangement, thereby enhancing the restriction on pheromone molecules. By combining MD simulations with experimental studies, molecular structure, intermolecular forces, and crystallinity were identified as the main factors regulating the release behavior of these polymer fibers. Finally, trapping experiments confirmed their effectiveness, indicating that release studies can guide field applications.

Anomalous Piezochromic Luminescence in Covalent Triazine Frameworks via Molecular Insertion: Blueshifted and Enhanced Emission

Piezochromic materials typically exhibit pressure-induced redshifted and quenched emission due to enhanced intermolecular π-π stacking and molecular planarization. Consequently, achieving blueshifted and enhanced emission in π-conjugated systems remains a significant challenge. Here, we report anomalous piezochromic luminescence in covalent triazine frameworks (CTFs) via molecular insertion. Upon introducing methanol into the nanopores of CTFs, a blueshift in emission from 507.0 to 485.5 nm, accompanied by enhanced intensity, is observed under compression up to 1.22 GPa, distinctly contrasting the redshifted and quenched emission typically observed in compressed pristine CTFs and other crystalline porous materials (CPMs). Combined experimental and theoretical analyses reveal that methanol can weaken the interlayer π-π stacking and intralayer conjugation of CTFs by forming weak interactions with CTFs, such as hydrogen bonding, to realize the interlayer slip and intralayer distortions of CTFs, which results in the blueshifted and enhanced emission. This strategy also proves effective with other molecular insertions, offering a general approach to achieving anomalous piezochromic luminescence in CTFs. Our findings establish molecular insertion as a robust method for engineering pressure-responsive luminescent materials and provide valuable insights for the design of advanced optical sensors and stimuli-responsive systems.

Harnessing Solvation Chemistry of Pentavalent Vanadium for Wide-Temperature Range Vanadium Flow Batteries

Vanadium flow batteries (VFBs) are safe, cost-effective, and scalable solutions for storing renewable energies. However, the poor thermal stability of pentavalent vanadium [V(V)] electrolyte, manifested as V2O5 precipitation at high temperatures, leads to more critical heat management, low energy density, and even low reliability. The unclear dynamic solvation chemistry of V(V) ions brings difficulties in solving the above issues intrinsically. Herein, we investigated solvation structures and dynamic evolution of V(V) electrolyte using ab initio molecular dynamics (AIMD) and in situ liquid time-of-flight secondary ion mass spectrometry (ToF-SIMS). For the first time, we clarified the transformation from [VO2(H2O)3]+ to VO(OH)3, identifying the second deprotonation as the rate-determining step. Based on this, we developed stabilization strategies through anion coordination and proton concentration control. The incorporation of HCl and trifluoromethanesulfonic acid improved the thermal stability of V(V) electrolytes remarkably. The optimized electrolyte showed no precipitation during 30-day static tests at 50 °C, enabling stable cycling performance of 3000 cycles in VFB single cells. Further demonstration in a kW-scale stack achieved over 1000 cycles, validating the scalability and viability. Our work provides insights into the solvation chemistry of V(V) species, paving the way to improve the reliability and energy density of a VFB system.

Interatomic Interactions and Ion-Transport in a Polyoligomeric Silsesquioxane-Based Multi-Ionic Salt Electrolyte for Lithium-Ion Batteries

Polyoligomeric silsesquioxane (POSS) tailored with trifluoromethanesulfonylimide-lithium and solvated in tetraglyme (G4) is a potential electrolyte for Li-ion batteries. Using classical MD simulations, at different G4/POSS(-LiNSO2CF3)8 molar ratios, the interactions of Li+ ions with the oxygen atoms of G4 and, oxygen/nitrogen sites of the pendant tails, the behaviour of POSS(--NSO2CF3)8, and the mobility of species are investigated. The RDFs showed that there exist competing interactions of the O(G4), O(POSS), and N(POSS) sites with Li+ ions. The lifetime analysis indicated that Li+- - -O(POSS) and Li+- - -N(POSS) interactions are longer-lived compared to Li+- - -O(G4). The morphological changes of the POSS tails upon interaction with Li+ ions were analysed using rotational lifetimes, coiling, and end-to-end distances. The ion-speciation analysis indicated the presence of solvent-separated ion pairs (SSIPs), contact ion pairs (CIPs), and higher-order ion clusters, with SSIPs being the more dominant species at 32/1. The self-diffusion coefficients for the 32/1 system, which showed the least cation-anion interaction, followed the trend:D G 4 > D L i + > D F P O S S > D P O S S ${{D}_{G4}\char62 {D}_{Li+}\char62 {D}_{F\left(POSS\right)}\char62 {D}_{POSS}}$ . The computed cationic transference number (t+) using theD F P O S S ${{D}_{F\left(POSS\right)}}$ is consistent with NMR experimental data. The t+ (and the trends with temperature) computed using theD P O S S ${{D}_{POSS}}$ and ionic conductivities are in good agreement.

Demonstration of a Chemical Recycling Concept for Polybutylene Succinate Containing Waste Substrates via Coupled Enzymatic/Electrochemical Processes

Chemical recycling of polymer waste is a promising strategy to reduce the dependency of chemical industry on fossil resources and reduce the increasing quantities of plastic waste. A common challenge in chemical recycling processes is the costly downstream separation of reaction products. For polybutylene succinate (PBS) no effective recycling concept has been implemented so far. In this work we demonstrate a promising recycling concept for PBS, avoiding costly purification steps. We developed a sequential process, coupling enzymatic hydrolysis of PBS with an electrochemical reaction step. The enzymatic step efficiently hydrolyses PBS in its monomers, succinic acid and 1,4-butanediol. The electrochemical step converts succinic acid into ethene as final product. Ethene is easily separated from the reaction solution as gaseous product, together with hydrogen as secondary product, while 1,4-butanediol remains in the aqueous solution. Both reaction steps operate in aqueous solvent and benign reaction conditions. Furthermore, the influence of electrolyte components on the electrochemical step was unraveled by applying molecular dynamic simulations. The final coupled process achieves a total ethene productivity of 91 μmol/cm2 over a duration of 8 hours, with 1110 μmol/cm2 hydrogen and 77 % regained 1,4-butanediol as valuable secondary products.

Molecular Dynamics of High-Pressure Liquid Water: Going from Ambient to Near-Critical Temperatures

The properties of high-pressure liquid water were investigated along the isobar of 25 MPa and in the temperature range 298.15-623.15 K using classical molecular dynamics simulations. Particular attention has been given to the changes in the local structural and related dynamic properties of liquid water. The results obtained have revealed noticeable changes in the shape of the calculated radial distribution functions, as well as the existence of local extrema or crossovers in several structural descriptors and entropic quantities at temperatures around 423.15 K and 498.15 K, where also significant changes in the hydrogen bond network of liquid water have also been observed. The temperature dependence of translational, reorientational, and hydrogen bond dynamics of liquid water has also been investigated by calculating the translational self-diffusion and the corresponding O-H vector Legendre reorientational correlation times and hydrogen bond lifetimes. The corresponding activation energies for each investigated relaxation process have also been presented and discussed.

Water Clustering Modulates Activity and Enables Hydrogenated Product Formation during Carbon Monoxide Electroreduction in Aprotic Media

Water solvation plays a critical role in a wide range of electrochemical transformations, but its role is often convoluted since water is typically used as both a solvent and a proton source. Here, we experimentally control water speciation and activity using aprotic solvent media during the carbon monoxide reduction reaction (CORR). Remarkably, we show that aprotic solvents that support microheterogeneous water-water clusters lead to significant amounts of CORR products (methane and ethylene) with a maximum ethylene Faradaic efficiency of 22% in acetonitrile (χH2O = 0.2). In contrast, microhomogeneous systems-where water integrates into the solvents' intermolecular binding network and has lower activity-primarily support the undesired hydrogen evolution reaction (HER). Insights gained expand our understanding of water activity and nonaqueous electrolyte design for other important transformation reactions beyond CO reduction, such as CO2RR and HER.

Study on the self-diffusion coefficients of binary mixtures of supercritical water and H2, CO, CO2, CH4 confined in carbon nanotubes

Nano-confined binary mixtures are prevalent in the chemical industry, geology, and energy sectors. Investigating their mass transfer behavior can enhance process intensification. This study examines the confined self-diffusion coefficients of binary mixtures of supercritical water (SCW) with H2, CO, CO2 and CH4 in carbon nanotubes (CNT) using molecular dynamics (MD) simulations at temperatures of 673-973 K, a pressure of 25-28 MPa, solute molar concentrations of 0.01-0.3, and CNT diameters of 9.49-29.83 Å. We developed a novel machine learning (ML) clustering method to optimize abnormal MSD-t data, effectively extracting information and providing algorithmic enhancements for calculating the diffusion coefficient. We analyzed the effects of temperature, solute molar concentration, and CNT diameter on the confined self-diffusion coefficient and energy input. Results indicate that over 60 % of the solute energy input derives from the Lennard-Jones effect of the CNT wall. The confined self-diffusion coefficient of solutes increases linearly with temperature, saturates with increasing CNT diameter, and remains relatively constant with varying concentration. Finally, based on the unique relationship between CNTs and the confined self-diffusion coefficient, we developed a new mathematical model for prediction. The regression line exhibits an R2 value of 0.9789, offering a new method for predicting the properties of nano-confined fluids.

The Impact of Permeation Enhancers on Transcellular Permeation of Small Molecule Drugs

Passive permeation through an epithelial membrane may be enhanced by using a class of amphiphilic molecules known as permeation enhancers (PEs). PEs have been studied in clinical trials and used in coformulations with peptides and small molecule drugs, and yet, an understanding of the permeant-PE interactions leaves much to be desired. This manuscript uses all-atom molecular dynamics (MD) simulations to showcase the effects of sodium caprate (C10) and salcaprozate sodium (SNAC), two commonly applied PEs, on membrane properties and the free energy profiles of five small molecule drugs (mannitol, atenolol, ketoprofen, decanedecaol, mucic acid). Our results show that both C10 and SNAC make the lipid molecules pack more densely, but C10 increases the lipid lateral diffusivity while SNAC decreases it. The change in the lipid order parameter also shows both PEs increasing the order near the lipid heads, possibly due to the dense packing in the membrane. A decrease in the central barrier of the permeation free energy was observed by embedding PEs into a lipid bilayer and SNAC is more efficient in doing so than C10. Neither SNAC nor C10 has a large impact on the diffusion coefficient of the small molecules. The analysis of the MD simulations revealed that PEs make the membrane tail region more hydrophilic by forming hydrogen bonds with small molecule drugs, i.e., decreasing the central barrier of the permeation free energy. While this study was only limited to small molecule drugs, this lays the groundwork for future studies to which the effects of the PEs in the permeation of macromolecules and peptides may be observed.

A Theoretical Kinetic Study of Nitrocyclohexane Combustion: Thermal Decomposition Behavior and H-Atom Abstraction

Nitrocyclohexane (NCH) is regarded as a highly promising energetic liquid fuel and additive for pulse detonation engines (PDEs) due to its excellent ignition performance and rapid energy release characteristics. Developing a detailed kinetic model for NCH is crucial for understanding its combustion characteristics and accurately predicting its behavior under actual operating conditions. In this study, reactive molecular dynamics (RMD) simulations were performed employing the ReaxFF-lg force field and the canonical (NVT) ensemble to investigate the temperature-dependent kinetic behavior of NCH. The results indicate that the initial decomposition of NCH is primarily driven by C-N bond rupture, followed by C-H bond cleavage, H atom abstraction, and other reactions, with H-abstraction playing a more significant role at lower temperatures. Subsequently, a systematic investigation of H-abstraction at seven sites in NCH involving six small species (Ḣ, ȮH, ĊN, HȮ2, NO2, and O2) was conducted at the QCISD(T)/cc-pVXZ(X = D,T)//MP2/cc-pVXZ (X = D,T,Q)//M06-2X/6-311++G(d,p) level of theory. The calculations reveal that there are minimal differences in reactivity between axial and equatorial H-abstraction, which proceed as parallel reaction channels. Compared to H-abstraction at nitro-substituted, meta, and para positions on the NCH ring, ortho H-abstraction reactions exhibit relatively lower rate coefficients. The obtained kinetic parameters in Arrhenius form and thermodynamic data in NASA polynomial format, covering a wide temperature range (298.15-2000 K), can be directly utilized for the development of the NCH kinetic mechanism.

Exploring the Local Structure of Molten NaF-ZrF4 through In Situ XANES/EXAFS and Molecular Dynamics

Molten salts are critical materials for advanced energy systems, particularly in molten salt reactors (MSRs), due to their exceptional thermophysical and chemical properties. While significant progress has been made in understanding their macroscopic behaviors, detailed knowledge of their atomic structures remains limited, particularly in fluoride-based salts with high zirconium concentrations. This study investigates the atomic structure and thermophysical properties of NaF-ZrF4 salt mixtures (53-47 and 56-44 mol %) using an integrated experimental and computational approach. X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectroscopy were employed to probe the local environment of Zr atoms across temperatures from 530 to 700 °C, revealing changes in coordination states and bond distances. Complementary ab initio molecular dynamics (AIMD) and neural network-based molecular dynamics (NNMD) simulations were validated against experimental data to elucidate short- and intermediate-range ordering in the melt. The results highlight a temperature-driven transition toward lower Zr coordination numbers and increased structural distortion, providing insights into the fluoroacidity and potential corrosiveness of these salts. This comprehensive understanding of the NaF-ZrF4 structure supports the development of more reliable models for molten salts, aiding advancements in next-generation nuclear reactors and energy systems.