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

A self-assembled protein β-helix as a self-contained biofunctional motif

Nature constructs matter by employing protein folding motifs, many of which have been synthetically reconstituted to exploit function. A less understood motif whose structure-function relationships remain unexploited is formed by parallel β-strands arranged in a helical repetitive pattern, termed a β-helix. Herein we reconstitute a protein β-helix by design and endow it with biological function. Unlike β-helical proteins, which are contiguous covalent structures, this β-helix self-assembles from an elementary sequence of 18 amino acids. Using a combination of experimental and computational methods, we demonstrate that the resulting assemblies are discrete cylindrical structures exhibiting conserved dimensions at the nanoscale. We provide evidence for the structures to form a carpet-like three-dimensional scaffold promoting and inhibiting the growth of human and bacterial cells, respectively, while being able to mediate intracellular gene delivery. The study introduces a self-assembled β-helix as a self-contained bio- and multi-functional motif for exploring and exploiting mechanistic biology.

Discrepant Effects of Hydrated and Neat Reline on the Conformational Stability of a Knotted Protein

Although knotted proteins are rare in number, their peculiar topology has long intrigued the scientific community. In this study, we have explored the conformational stability of a trefoil-knotted protein, YbeA, in reline (choline chloride:urea in a 1:2 ratio), a well-characterized deep eutectic solvent, using classical molecular dynamics simulation. Deep eutectic solvents (DESs) are explored as a reliable alternative to conventional solvents, effectively altering a protein's structural stability and activity, either stabilizing its native state or disordering its conformation depending on the relevant interactions involved. Here, using pure and hydrated concentrations of reline, we observe the conflicting effect of the DES on the knotted protein's stability. Our studies at room temperature and elevated temperatures show that in pure reline, the protein is conformationally stable and rigid. In contrast, the protein tends to lose its structural integrity in hydrated reline. The stable knotted topology also gets untied as the protein, solvated in hydrated reline, is exposed to an elevated temperature. Using Minimum Distance Distribution Functions and Kirkwood-Buff Integrals, we analyzed the solvation pattern of the DES constituents around the protein. We expect that this study will lead to more effective strategies in developing tailored solvent systems for comprehending the conformational behavior of knotted proteins.

A coarse-grained model for aqueous two-phase systems: Application to ferrofluids

Aqueous two-phase systems (ATPSs), phase-separating solutions of water soluble but mutually immiscible molecular species, offer fascinating prospects for selective partitioning, purification, and extraction. Here, we formulate a general Brownian dynamics based coarse-grained simulation model for an ATPS of two water soluble but mutually immiscible polymer species. Including additional solute species into the model is straightforward, which enables capturing the assembly and partitioning response of, e.g., nanoparticles (NPs), additional macromolecular species, or impurities in the ATPS. We demonstrate that the simulation model captures satisfactorily the phase separation, partitioning, and interfacial properties of an actual ATPS using a model ATPS in which a polymer mixture of dextran and polyethylene glycol (PEG) phase separates, and magnetic NPs selectively partition into one of the two polymeric phases. Phase separation and NP partitioning are characterized both via the computational model and experimentally, under different conditions. The simulation model captures the trends observed in the experimental system and quantitatively links the partitioning behavior to the component species interactions. Finally, the simulation model reveals that the ATPS interface fluctuations in systems with magnetic NPs as a partitioned species can be controlled by the magnetic field at length scales much smaller than those probed experimentally to date.

Unveiling the Interactions of Doxorubicin with the Lipid Components of Liposomes for Its Delivery

The characterization of drug/lipid interactions is key to developing novel and more efficient drug delivery systems. In this work, we combine electrochemical measurements, attenuated total reflection (ATR) spectroscopy, and molecular dynamics simulations to unveil the interacting mechanisms of doxorubicin (DOX) with lipid monolayers and bilayers containing a cytidine derivative nucleolipid, which serve as a model system of previously developed liposomes for DOX delivery. The nucleolipid was included in the liposome formulation to take advantage of its molecular recognition capabilities and its capacity to anchor gold nanoparticles. The compression isotherms of the Langmuir monolayers and interfacial capacitance measurements on a gold electrode modified with hybrid bilayers in the presence of DOX demonstrate the interaction of the drug with the nucleolipid polar heads. This is confirmed by computational simulations of a solvated DOX/bilayer complex, which show that the adsorption process is driven by stacking and electrostatic interactions involving the aromatic and nonaromatic moieties of DOX, respectively. Moreover, both ATR spectra of supported bilayers on silicon and simulations show that the presence of DOX does not significantly affect the tilt angles of the lipids. The system studied in this work is a promising therapeutic option for cancer treatment. The combined methodology applied to this study can serve as a reference for other studies of drug-carrier interactions.

Structural transitions at the bilayer graphene-methanol interface from ab initio molecular dynamics

The precise tailoring of the atomic architecture of 2D carbon-based materials, which results in the modulation of their physical properties, promises to open new pathways for the design of technological devices in electronics, spintronics and energy storage. High-pressure conditions can lead to the synthesis of complex materials starting from multi-layer graphene, often relying on chemical transformations at the interface between carbon and pressure-transmitting media like water or alcohol. Unfortunately, the experimental characterization of molecular-scale mechanisms at interfaces is very challenging. On the other side, the sheer cost of ab initio simulations strongly limited, so far, the computational works in literature to simplified models that, often, do not capture the complexity of the materials and finite-temperature effects. In this work, we provide for the first time an extensive computational study of complex, realistic models of bilayer graphene-methanol interfaces at high pressure and finite temperature. Our simulations allow fundamental insight to be gained on several questions raised from previous experimental works about structural, electronic and reactivity properties of this challenging material. The exploitation of state-of-the-art enhanced sampling techniques combined with topological electronic descriptors allowed characterization of barrier-activated functionalization processes, unveiling a major catalytic effect of carbon defects and pressure towards sp3 formation.

Multiscale modeling of charge transfer in hole-transporting materials: Linking molecular morphology to charge mobility

Hole-transporting materials (HTMs) play a pivotal role in the performance and stability of organic electronic devices by enabling efficient hole transport. This study employs a multiscale approach to explore the relationship between molecular morphology and charge transfer properties in four HTM molecules. By combining quantum mechanical calculations, molecular dynamics simulations, and kinetic Monte Carlo modeling, we analyze key structural features such as radial distribution functions, principal axis orientations, and non-covalent interactions. Our findings reveal that molecular size and substituent effects significantly influence non-covalent interactions and molecular alignments, thereby affecting charge transport pathways. Charge transfer rates and energetic disorder were modeled using the master equation, and mobilities were computed, showing satisfactory agreement with experimental data. This comprehensive analysis provides valuable insights into the design of HTMs for organic electronic devices, emphasizing the importance of molecular architecture in optimizing charge mobility and minimizing energy losses.

CrypTothML: An Integrated Mixed-Solvent Molecular Dynamics Simulation and Machine Learning Approach for Cryptic Site Prediction

Cryptic sites, which are transient binding sites that emerge through protein conformational changes upon ligand binding, are valuable targets for drug discovery, particularly for allosteric modulators. However, identifying these sites remains challenging because they are often discovered serendipitously when both ligand-binding (holo) and ligand-free (apo) states are experimentally determined. Here, we introduce CrypTothML, a novel framework that integrates mixed-solvent molecular dynamics (MSMD) simulations and machine learning to predict cryptic sites accurately. CrypTothML first identifies hotspots through MSMD simulations using six chemically diverse probes (benzene, dimethyl-ether, phenol, methyl-imidazole, acetonitrile, and ethylene glycol). A machine learning model then ranks these hotspots based on their likelihood of being cryptic sites, incorporating both hotspot-derived and protein-specific features. Evaluation on a curated dataset demonstrated that CrypTothML outperforms recent machine learning-based methods, achieving an AUC-ROC of 0.88 and successfully identifying cryptic sites missed by other methods. Additionally, CrypTothML ranked cryptic sites as the top prediction more frequently than existing methods. This approach provides a powerful strategy for accelerating drug discovery and designing allosteric drugs.

Novel Anti-MRSA Peptide from Mangrove-Derived Virgibacillus chiguensis FN33 Supported by Genomics and Molecular Dynamics

Antimicrobial resistance (AMR) is a global health threat, with methicillin-resistant Staphylococcus aureus (MRSA) being one of the major resistant pathogens. This study reports the isolation of a novel mangrove-derived bacterium, Virgibacillus chiguensis FN33, as identified through genome analysis and the discovery of a new anionic antimicrobial peptide (AMP) exhibiting anti-MRSA activity. The AMP was composed of 23 amino acids, which were elucidated as NH3-Glu-Gly-Gly-Cys-Gly-Val-Asp-Thr-Trp-Gly-Cys-Leu-Thr-Pro-Cys-His-Cys-Asp-Leu-Phe-Cys-Thr-Thr-COOH. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) for MRSA were 8 µg/mL and 16 µg/mL, respectively. FN33 AMP induced cell membrane permeabilization, suggesting a membrane-disrupting mechanism. The AMP remained stable at 30-40 °C but lost activity at higher temperatures and following exposure to proteases, surfactants, and extreme pH. All-atom molecular dynamics simulations showed that the AMP adopts a β-sheet structure upon membrane interaction. These findings suggest that Virgibacillus chiguensis FN33 is a promising source of novel antibacterial agents against MRSA, supporting alternative strategies for drug-resistant infections.

Exploring the Interfacial Formation between Aqueous Slabs and a Hydrophobic Membrane

Molecular dynamics simulations were used to study the interfacial formation between pure and saline aqueous slabs and hydrophobic polytetrafluoroethylene (PTFE) surfaces, both porous and nonporous. The simulations revealed that the formation of transient water vapor bridges between the slabs and the hydrophobic surface facilitated initial contact by lowering the energy barrier, ultimately leading to surface adherence. The presence of saline aqueous slabs slowed the contact process and influenced the dynamics of the vapor-phase bridges. Additionally, porous PTFE surfaces accelerated the initial contact of the aqueous slabs and exhibited distinctive ion concentration gradients, particularly at the pore centers, indicating localized salinity. Structural deformations, such as bending and pore contact angles, were quantified, providing new insights into the nano-structural changes during the interactions between the slabs and PTFE surfaces.

Exact Two-Component Relativistic Polarizable Density Embedding

We have implemented the fragment-based polarizable density embedding (PDE) model within a relativistic framework building on the eXact 2-Component (X2C) relativistic Hamiltonian, thereby taking the PDE method to a relativistic framework. The PDE model provides a robust solution to the electron-leakage problem, and we show that this newly implemented model offers an accurate way to model solvated systems possessing significant relativistic effects. To demonstrate the model's performance, we perform comparative calculations of the K- and L2,3-edge spectra of water-solvated cysteine (both protonated and deprotonated) with the X2C Hamiltonian. Particularly, with counterions such as Na+ in the solvent, electron leakage clearly shows in the older polarizable embedding model through spurious peaks in the spectra. However, when the PDE model is employed, these spurious peaks disappear.

Surveying Enzyme Crystal Structures Reveals the Commonality of Active-Site Solvent Accessibility and Enzymatic Water Networks

Despite the demonstrable dependence of enzyme functionality on solvation, the notion of water being directly chemically required for catalysis inside active sites remains unexplored. Here we report that over 99% of 1013 enzyme crystals obtained by X-ray crystallography with high resolution (<1.5 Å) contain continuous chains of water linking residues within the active site to bulk water. Also reported are the findings which inspired this study-that electric fields experienced by water hydrogen atoms are on average twice as strong in the active sites of both chains of bacterial polynucleotide kinase (PDB 4QM6) structures compared to those in bulk water. These results point to the possibility that water molecules within active sites may be paramount to the immense catalytic power of enzymes, especially for mechanisms requiring hydronium or hydroxide ions.

Mechanically Activated Starch Reticular Nanostructure Traps Ferulic Acid as a Structural and Functional Cargo

Upon the scalable utilization of polyphenols, the design of their composites with polymers has received a great deal of attention. However, the starch polymer has a weak loading of hydrophobic polyphenols typically through noncovalent interactions without biochemical catalysts. Here, we tailor a reticular starch nanostructure from a starch nanosphere precursor (preSNS) that traps ferulic acid (FA) via esterification. The preSNS-FA network is activated by a green physical method via dynamic high-pressure microfluidization, exhibiting an exceptionally higher content of FA (∼38.0%) compared with the conventional starch group (only ∼1.5%). SEM, FTIR, XRD, 13C NMR, 1H NMR, and XPS results as well as molecular dynamics simulation comprehensively confirm the changes in architecture and hydrogen bonding modes with the formation of -COOR-. The preSNS-FA network also has an enzymatic hydrolysis resistance (up to 83.8%). Collectively, this work establishes a high-performance and catalyst-free synthetic route toward an esterified polyphenol complex network with potential applications in nutrient delivery, food packaging, and agriculture fields.

Semaglutide Aggregates into Oligomeric Micelles and Short Fibrils in Aqueous Solution

Semaglutide is a lipopeptide with important applications in the treatment of diabetes, obesity, and other conditions. This class of drug (glucagon-like peptide-1 agonists and other lipidated peptides) may be susceptible to aggregation due to the tendency of lipopeptides to self-assemble into various nanostructures. Here, we show using cryogenic-TEM, small-angle X-ray scattering, and molecular dynamics simulations that semaglutide in aqueous solution undergoes slow aggregation into spherical micelles in water at sufficiently high concentration. A small population of needle-shaped fibril aggregates is also observed. At a lower concentration, dimer and trimer structures are formed. The micelles, once formed, are stable toward further aging. The aggregation influences the effect of semaglutide on the permeability of an epithelial gut model membrane of Caco-2 cells. These findings are expected to be important in understanding the long-term stability of semaglutide solutions and the potential effects of aggregation on therapeutic efficacy.

How Are Plastoglobules Formed in Green Algae?

Plastoglobules are droplet-like organelles with a hydrophobic core of neutral lipids surrounded by a lipid monolayer, usually found in the chloroplasts of most plants and green algae. They not only serve as lipid storage units in the thylakoid membranes but are also involved in many cellular processes, including photoprotection, metabolite synthesis, protein recruitment, and chloroplast differentiation. Unlike lipid droplets, which nucleate, grow, and subsequently detach from the endoplasmic reticulum (ER) membrane, plastoglobules remain permanently coupled to the stromal side of the thylakoid membrane. In this study, we employ molecular dynamics simulations to investigate the growth mechanism of plastoglobules in a model thylakoid membrane of Dunaliella algae. Our findings suggest that significant membrane remodeling, likely driven by the thylakoid membrane proteins, is essential for the directional growth and stability of the plastoglobules.

Conductivity and Diffusivity of Ions in Aqueous MgCl2 from Equilibrium and Nonequilibrium Simulations

Advanced electrochemical energy storage technologies require new electrolytes to be considered, so efficient computational characterization of ionic conductivity in a range of systems is of importance. In this manuscript we compare different equilibrium (EMD) and nonequilibrium molecular dynamics (NEMD) simulation algorithms to determine ionic conductivities. Aqueous magnesium ion batteries utilizing magnesium chloride as the electrolyte are a promising alternative to conventional lithium-ion batteries, so we focus on magnesium chloride electrolytes to demonstrate our results. We show the importance of accounting for ionic correlations and find that NEMD algorithms can provide more efficient calculations of ionic conductivity than EMD algorithms when ionic correlations need to be accounted for. In contrast, diffusivities and Nernst-Einstein conductivities can be determined more efficiently with EMD algorithms in the highly conductive systems considered here. We also demonstrate that the alignment of the water molecules due to the applied field in NEMD simulations is small at typical field strengths and has no impact on the calculated conductivities. Comparison of the results for the conductivity of different ions and their coupling provides insight into how force fields might be improved.

DL_POLY Quantum 2.1: A Suite of Real-Time Path Integral Methods for the Simulation of Dynamical Properties and Vibrational Spectra

DL_POLY Quantum 2.1 is introduced here as a highly modular, sustainable, and scalable general-purpose molecular dynamics (MD) simulation software for large-scale long-time MD simulations of condensed phase and interfacial systems with the essential nuclear quantum effects (NQEs) included. The new release improves upon version 2.0 through the introduction of several emerging real-time path integral (PI) methods, including fast centroid molecular dynamics (f-CMD) and fast quasi-CMD (f-QCMD) methods, as well as our recently introduced hybrid CMD (h-CMD) method for the accurate and efficient simulation of vibrational infrared spectra. Several test cases, including liquid bulk water at 300 K and ice Ih at 150 K, are used to showcase the performance of different implemented PI methods in simulating the infrared spectra at both ambient conditions and low temperatures where NQEs become more apparent. Additionally, using different salt-in-water (i.e., dilute) and water-in-salt (i.e., concentrated) lithium bis(trifluoromethanesulfonyl)imide (Li-TFSI) aqueous electrolyte solutions, we demonstrate the applicability of our recently introduced h-CMD method implemented in DL_POLY Quantum 2.1 for the large scale simulation of infrared (IR) spectra of complex heterogeneous systems. We show that h-CMD can overcome the curvature problem of CMD and the artificial broadening of T-RPMD for the accurate simulation of the vibrational spectra of complex, heterogeneous systems with NQEs included.

Enhanced oil recovery promoted by aqueous deep eutectic solvents on silica and calcite surfaces: a molecular dynamics study

Enhanced oil recovery (EOR) plays a critical role in optimizing oil extraction from existing fields to satisfy global energy demands while mitigating environmental impact. One promising EOR technique involves injecting water with reduced surface tension utilizing deep eutectic solvents (DESs). Despite early experimental support, the efficacy of aqueous-DES EOR varies and depends on factors such as connate water saturation, water salinity, and reservoir wettability. The recovery mechanisms for aqueous DESs are poorly understood due to the intricate nature of oil components and reservoir formation. In this paper, we investigate the role of DESs in the EOR process through molecular dynamics (MD) simulations. Three different types of DES molecules, such as choline chloride : urea (ChCl : U), choline chloride : ethylene glycol (ChCl : EG), and menthol : salicylic acid (M : SA) are used, for the recovery of dodecane (C12H26) oil from silica and calcite confined surfaces. We have demonstrated the structural characteristics of these systems by examining various physical properties, including interaction energies, density profiles, hydrogen bonds, and interfacial tension (IFT). Different concentrations (10 and 25 wt%) of DESs have been considered to unravel the effect of concentration on oil removal. The wettability of the substrate and the IFT between oil and aqueous DESs are critical physical properties that play a crucial role in influencing EOR phenomena. The IFT between water and oil decreases with the addition of DESs for all DES molecules, leading to a shift in surface behavior from oleophilic to oleophobic and ultimately facilitating the removal of oil from the substrate. Additionally, hydrogen bond formation between DESs and water has been calculated to elucidate its influence on the water/oil interface and substrate wettability. The study provides insights into the fundamental aspects of EOR processes for more effective and sustainable oil extraction.

Elucidating the microscopic properties of a β-barrel protein and the solvent confined in and around it

Intracellular lipid binding proteins (iLBPs) possess different characteristics, including a rigid protein structure consisting of a β-barrel, an α-helix cap, and a substantial internalized water cluster. Despite X-ray crystallographic research providing insights into the three-dimensional structures of iLBPs, the protein conformations, and the function of the internal water molecules inside the protein remain uncertain. In this study, we conducted molecular dynamics (MD) simulations on free (apo) and oleate-bound (holo) rat liver fatty acid binding proteins (rLFABPs), which are common intracellular lipid binding proteins (iLBPs) found in the liver of rats. Efforts have been made to obtain a comprehensive microscopic understanding of the conformational motions of different segments of the protein, namely, the β-strands, the helix-turn-helix (HTH) motif, and the loop regions, along with the impact of ligand binding on the microscopic structure and ordering of water molecules confined within the core and at the exterior surface of the protein. The calculations revealed fluctuating nature of the HTH region, characterized by the development and disruption of distinct secondary structural components. Furthermore, the coexistence of spatially heterogeneous ordered and disordered water molecules within the core regions of the apo and holo forms has been observed. A high degree of ordering of core water molecules has been attributed to those that are doubly coordinated. In contrast, the randomly oriented ones are found to be surrounded by three neighboring water molecules in their first coordination shells. Such non-uniform ordering of core water molecules suggests their important role in the ligand binding process for this class of proteins.

Advancing lithium metal electrode beyond 99.9% coulombic efficiency via super-saturated electrolyte with compressed solvation structure

Lithium metal negative electrode is pivotal for advancing high-energy-density lithium batteries. Despite their promise, the inherent poor interfacial stability of electrolytes on lithium metal and the repeated reconstruction of the solid electrolyte interphase lead to continuous consumption of active Li and electrolyte, causing rapid failure of Li metal batteries under practical conditions. Here, we propose compressing the spacing between Li ions and anions to recruit more anions around Li ions, forming tighter solvation clusters, and then achieving the super-saturated electrolyte with a 16 M Li salt concentration in the solvent phase. This compressed solvation structure electrolyte demonstrates enhanced stability towards Li metal negative electrode, attaining more than 99.9% coulombic efficiency in Li||Cu cells and enabling long cycling life in lean-Li Li metal full cells. Designed with a positive electrode material proportion of 68%, our Li metal pouch cell achieves a specific energy of 510.3 Wh kg-1 (based on the total mass of the cell) and maintains stable cycling over 100 cycles.

On the modeling of hydrocarbon combustion in external electric fields with reactive molecular dynamics

The use of electric fields may provide a mechanism to enable fuel-flexible technologies in aviation. The development of such technologies requires methodologies able to accurately quantify electric field effects on chemical reactions at the molecular level. This work provides a comprehensive assessment of methodologies used in the framework of reactive molecular dynamics (MD) with the reactive force field ReaxFF. The focus is on the computation of atomic charges, the method used for equilibration, and the use of global thermostats for hydrocarbon combustion in an external electric field. The charge equilibration method (QEq) and the charge transfer with polarization current equilibration method (QTPIE) were analyzed for the computation of atomic charges. For the fuel-oxygen system investigated, QEq leads to molecules with a sizable spurious net charge. QTPIE leads to more accurate molecular charges but at the cost of underestimating some atomic charges. This leads to faster combustion kinetics with QEq compared with QTPIE. A two-step equilibration procedure provides a more equilibrated system compared to widely used equilibration procedures. Furthermore, using a global thermostat with an external electric field results in an artificial reduction in fuel and oxygen first-order reaction rates. These artificial effects can be avoided by not using a thermostat, but at the expense of electric-field-induced heating. Applying an external electric field without a global thermostat accelerates combustion much more with QEq compared with QTPIE, due to the larger charges predicted by QEq. This study reveals several simulation artifacts that affect reactive MD of fuel combustion and contributes toward the more accurate modeling of fuel combustion in external electric fields.

Unveiling the Entropic Effect of Electrolytes on Kinetics and Cyclability for Practical Lithium-Sulfur Batteries

Lithium-sulfur (Li-S) batteries under low-temperature and lean electrolyte conditions for practical application are hindered by a sluggish conversion reaction, low sulfur utilization, and cycling stability. Herein, we designed a high-entropy (HE) electrolyte by mixing three Li salts. The HE electrolyte simultaneously improves lithium sulfide (Li2S) conversion reaction kinetics, sulfur utilization, and cyclability due to the anticlustering effect on lithium polysulfides, three-dimensional Li2S growth, and robust anion-derived solid electrolyte interphase layer formation, respectively. Consequently, the HE electrolyte exhibits a high initial reversible capacity (1159.9 mAh g-1) and cycling stability for 40 cycles under a low electrolyte-to-sulfur ratio (3.5 μL mg-1) at the pouch cell level. In addition, the Li-S cell with HE electrolyte exhibits high cycling stability with a capacity decay of 0.01% per cycle during 200 cycles at -15 °C.

Computational study of diol camptothecin drug delivery process using MPEG-1-based nanosome structure: molecular dynamics approach

In recent years, the drug delivery process has become important for effective treatments of various diseases. However, drug carrier design is a complex procedure and many of designed structures do not perform well. Nanostructures are promising systems for effective drug delivery process. Between nanostructures, nanosomes are effective vesicles of spherical shape that can be created from different self-assembled nanosize components. It is expected the appropriate design of nanosome-based samples, introduced a suitable drug carrier for clinical applications. In current research, we introduced macrophage-expressed gene (MPEG-1) protein-based nanosome performance in diol camptothecin (CPT(OH)2) drug delivery process in aqueous environment for the first time. The molecular dynamics (MD) method implemented for this purpose by using dreiding force field. Our MD simulations were performed two main phases. In the first phase, defined samples equilibrated at initial condition (T0 = 300 K and P0 = 1 bar). Then, drug delivery performance of equilibrated samples was reported. Computational outputs predicted atomic stability of samples in standard condition. This performance is conducted from kinetic and potential energies convergence in equilibrium phase. Also, drug delivery process was detected after 0.12 ns in aqueous environment. Numerically, drug delivery ratio reached to 66%. Furthermore, zeta potential converged to -2.20 mV after 100 ns. From these outputs, we concluded MPEG-1-based nanosome can be used in actual cases for drug delivery in clinical applications.

Biodegradable Carrier-Free Nanomedicine via Self-Assembly of Pure Drug Molecules for Triple Sensitization of Radiotherapy

Radiotherapy (RT) has been one of the most widely applied cancer treatments, while radiotherapy resistance remains a major limitation. Herein, we synthesized a biodegradable AID nanomedicine incorporating atovaquone (ATO), new indocyanine green (IR820), and doxorubicin (DOX) via π-π stacking and hydrophobic interactions, along with high drug loading efficiency and long-term stability. The AID nanomedicine effectively reduces the activity of mitochondrial electron transport chain complexes I/II/III/IV/V, disrupts the mitochondrial oxidative respiratory chain, and decreases oxygen consumption, thereby alleviating the hypoxic microenvironment within the tumor. Moreover, mild hyperthermia induced by IR820 improves intratumor blood flow, thereby enhancing the radiotherapeutic efficiency. Additionally, DOX-triggered chemotherapy further sensitizes the tumor to radiotherapy, achieving triple sensitization. Our findings demonstrate that AID nanomedicine, combined with near-infrared (NIR) and radiotherapy, significantly suppresses tumor growth in vivo without noticeable side effects. In conclusion, our work presents a self-assembling nanomedicine with excellent biocompatibility, showing great potential for future development in triple radiotherapy sensitization.

Role of Adsorption-Induced Deformation on Gas Self-Diffusivity in a Flexible Microporous Coal Matrix

Adsorption-induced deformation has long been underappreciated in gas transport studies of microporous coal, yet it strongly influences pore configurations and diffusive pathways. Here, a hybrid grand canonical Monte Carlo (GCMC)/molecular dynamics (MD) approach and equilibrium MD (EMD) simulations are employed to investigate how matrix flexibility reshapes pore structures and, in turn, impacts CH4 and CO2 self-diffusion in connected pore networks under various gas loadings. The results show that coal matrix deformation enhances adsorption, with CO2 exhibiting greater uptake and volumetric strain than CH4. A universal linear relationship emerges among gas loading, free volume ratio, and self-diffusion coefficients for both rigid and flexible matrices. In flexible matrices, this linearity features a gentler slope, indicating reduced diffusion sensitivity to diminishing free volume with loadings. By comparing geometrical and effective tortuosity, it is revealed that strongly adsorbing CO2 induces significant swelling and complex local rearrangements at elevated loadings, pushing geometrical tortuosity far beyond rigid-matrix levels, whereas CH4─with weaker adsorption─drives smaller, more uniform structural adjustments that only mildly increase geometrical tortuosity. These differences in tortuosity directly reflect changes in path complexity, which in turn governs self-diffusion behavior. Collectively, the findings clarify the dynamic coupling between gas adsorption, matrix deformation, and self-diffusivity in microporous coal, offering critical guidance for enhanced gas recovery and CO2 sequestration strategies that rely on accurate modeling of gas transport in deformable media.

Spontaneous aqueous defluorination of trifluoromethylphenols: substituent effects and revisiting the mechanism

Trifluoromethylphenols (TFMPs) are environmental contaminants that exist as transformation products of aryl-CF3 pharmaceuticals and agrochemicals. Their -CF3 moiety raises concerns as it may form problematic fluorinated transformation products such as the persistent pollutant trifluoroacetic acid (TFA). This study investigates the hydrolysis and spontaneous defluorination mechanisms of 2-TFMP, 3-TFMP, 4-TFMP, and 2-Cl-4-TFMP under environmentally relevant aqueous conditions, and under alkaline pH to investigate the mechanism of defluorination. 3-TFMP did not undergo hydrolysis. The other TFMPs reacted to primarily form the corresponding hydroxybenzoic acids and fluoride. High-resolution mass spectrometry identified a benzoyl fluoride intermediate in the hydrolysis of 4-TFMP and other dimer-like transformation products of the 4- and 2-Cl-4-TFMP. Density functional theory calculations revealed that the key defluorination step likely proceeds via an E1cb mechanism, driven by β-elimination. Experimental and computational results demonstrated substituent-dependent differences in reactivity, and the importance of the deprotonation of TFMPs for the hydrolysis reaction to proceed. These findings provide mechanistic insights into the complete defluorination of TFMPs and broader implications for the environmental defluorination of other PFAS.

General fabrication of bioactive dissolving microneedles from whole grain seeds derived starch for transdermal application

Dissolving microneedles (DMNs) have gained increasing attraction for transdermal drug delivery. However, their manufacture is limited due to the lack of suitable fabricating materials. It is highly demanded to explore new materials for DMN preparation. Herein, we were the first to discover that natural grain powders were promising material candidates for DMN manufacture. MD was first used to determine the solvent to prepare microneedles. Then, mold method was used to fabricate five grain seed powders into microneedles. Afterwards, FTIR, XRD, MTT, live/dead assay and antioxidative assays (DPPH and Fenton) were applied to assess the chemical and biological properties of the microneedles. Finally, both in vitro and in vivo experiments were used to assess the transdermal effects of the microneedles. The results demonstrated that the microneedles had excellent biosafety with >90 % of living cells and <5 % of hemolysis rate. Also, the microneedles displayed up to 100 % eradication of free radicals, implying their good antioxidative capabilities. The transdermal study demonstrated that the microneedles could pierce mouse skins and undergo completely and fast dissolving in the skin as quickly as 30 s. This work will motivate more attempts to develop novel transdermal microneedles from natural products for biological applications.

Pulsed electric fields disaggregating chlorophyll aggregates and boosting its biological activity

Chlorophyll molecules in solution spontaneously form chlorophyll aggregates due to intermolecular interactions such as hydrophobic bonding and π-π stacking, which reduce the biological activity of the chlorophyll solution. In this study, it was explored the mechanism of pulsed electric fields (PEF) parameters on the structure and biological activity of chlorophyll aggregates. The results showed that the microstructure of chlorophyll aggregates can be changed, leading to the formation of smaller particles by adjusting parameters during PEF treatment. Moreover, the smaller chlorophylls aggregates exhibited the stronger antioxidant and anti-inflammatory activities in vitro compared to control (without PEF treatment). Moreover, PEF treatment also induced changes in the microscopic state of chlorophylls confirmed by SEM. Molecular dynamics (MD) simulations indicated that PEF treatment increased the radius of gyration and solvent-accessible surface area (SASA) of chlorophyll aggregates while decreasing their density compared to untreated sample. These results suggested that PEF treatment can disrupt the interaction between chlorophyll molecules, leading to the disaggregation of chlorophyll aggregates and enhancing its bioactivity.

Reactive amino acid-derived deep eutectic solvents for tailored lignin modification

The heterogeneous structure and characteristic variability of industrial lignin present key challenges that hinder its use in numerous advanced scenarios. Herein, we explore amino acid-derived deep eutectic solvents (AADESs) featuring diverse side chain structures (glycine, alanine, valine, lysine (Lys), and proline) and serving as reactive media for modifying alkali lignin. For the first time, quantum chemistry and molecular dynamics simulations were employed to demonstrate the formation mechanism of AADESs. Among all the considered systems, the Lys-based system proved to be the most stable system owing to its strong nucleophilicity. Unlike choline chloride-based DES, the strong nucleophilicity of Lys could induce nanocrystallization and targeted modification of α-OH to attach phenolic hydroxyl in lignin. Breaking the β-O-4 and β-β linkages within lignin increased the phenolic hydroxyl content of the lignin by up to ~50 %. Additionally, the -NH2 of amino acids can further increase the reactive sites of lignin, improve thermal stability, and facilitate further chemical modification. The reactivity of AADESs was notably influenced by the nucleophilicity of the side chains of amino acids, as also supported by the simulations. Overall, this research provides in-depth insights into lignin modification within sustainable and reactive solvents, advancing lignin valorization for high-end applications.

Biphenylene Coordination and Ring-Opening by Alkali-Metal Nickelates

The pre-coordination of substrates to heterobimetallic complexes plays a key role in facilitating challenging bond activations and catalytic reactions. Herein, we report a family of low-valent phenyl-alkali-metal nickelates containing a η4-coordinated biphenylene ligand and demonstrate how the coordination and solvation preferences of the alkali-metal cation (Li, Na, or K) influence the rate of C─C bond oxidative addition at nickel through combined structural, spectroscopic and computational studies. The rate of C─C bond cleavage can be further manipulated by replacing the two phenyl-carbanionic ligands with a cyclic 2,2'-biphenyl scaffold, which affords thermally stable and symmetric spirocyclic nickelates upon ring-opening.

Comprehensive picture of β-barrel transformation in the fibrillogenesis of odorant-binding proteins

Protein dysfunction can be caused by its fibrillogenesis, which is often initiated by rather subtle structural changes. In the case of odorant-binding proteins (OBPs), fibrillogenesis triggering is mediated by local melting of the peripheral C-terminal domain while maintaining the integrity of the bulk of the molecule, the β-barrel. This work is focused on establishing the sequence and duration of structural transformations of OBPs' β-barrel during fibrillogenesis. We found that β-barrel transformation requires oligomerization of OBPs monomers with unlocked C-terminus, whose formation precedes the fibrillogenesis initiation. The fibrillogenesis lag phase involves the gradual bond weakening within the β-barrel without its destruction. During this phase, oligomeric molecules first experience partial disruption of contacts near the β1-strand, followed by its disorganization and the opening of the internal protein cavity. In the exponential phase, complete β-barrel reorganization in aggregates lasts as long as the lag phase, accompanied by the sequential appearance of prefibrillar forms with cytotoxicity and mature amyloid fibrils. Our findings suggest similarities in the intermediate states accumulated during fibrillogenesis as well as common mechanisms and sequence of structural transitions for proteins of β-barrel topology. This contributes to the identification of relevant targets and possible ways to inhibit amyloidogenesis of these proteins.

A simple co-assembly strategy to control the dimensions of nanoparticles for enhanced synergistic therapy

Despite phthalocyanine has excellent photodynamic and photothermal effects as a photosensitizer and photothermal agent, hydrophobicity and aggregation limits its biological application. In this paper, phthalocyanine-cyanine co-assembled nanoparticles were designed to modulate the dimensions and morphology by introducing water-soluble cyanine. The cyanine had the ability to transform the nanomaterials from microrods to nanospheres, thus successfully constructing photoactivated nanomedicines. Their appropriate size effect and improved water solubility conferred the nanoparticles with extended blood circulation time and tumor accumulation capacity. Meanwhile, the fluorescence effect of cyanine enabled the nanoparticles to have the ability of fluorescence imaging. The nanoparticles achieved enhanced PDT/PTT synergistic effect under single laser induction, especially the generation of type I photodynamics.

Molecular Recognition and Chiral Discrimination from NMR and Multi-Scale Simulations

Chiral molecules are particularly interesting to the pharmaceutical and agrochemical sectors due to their chemical and physical properties. Separation and identification of enantiomers are critical for a broad range of compounds, and discriminating stereoisomers in solution remains a key analytical challenge. Nuclear Magnetic Resonance (NMR) with Matrix-Assisted Diffusion-Ordered Spectroscopy (MAD), in the presence of chiral resolving agents, has emerged as a tool to explore these chiral mixtures. However, insight into the intermolecular interactions that lead to chiral recognition is still limited. Here, we combine experimental MAD studies with computational approaches to investigate the enantioselective discrimination of Mandelic Acid (MA) enantiomers using (R)-BINOL and (S)-BINOL. Molecular dynamics simulations explain the differences in diffusion coefficients for heterochiral complexes. Furthermore, quantum mechanical calculations confirmed enantioselective binding preferences due to differences in Gibbs free energies, highlighting the fundamental interactions and structural criteria that explain the NMR shielding and the diffusion trends. This integrated approach bridges experimental and theoretical studies, offering a comprehensive understanding of chiral recognition mechanisms and elucidating the observed heterochiral preference of BINOL for MA enantiomers. Our findings advance the field of chiral analysis and lay a foundation for future developments for identifying stereoisomers and recognition modes underlying enantioselective binding.

Designing Advanced Electrolytes for High-Voltage High-Capacity Disordered Rocksalt Cathodes

Lithium (Li)-excess transition metal oxide materials which crystallize in the cation-disordered rock salt (DRX) structure are promising cathodes for realizing low-cost, high-energy-density Li batteries. However, the state-of-the-art electrolytes for Li-ion batteries cannot meet the high-voltage stability requirement for high-voltage DRX cathodes, thus new electrolytes are urgently demanded. It has been reported that the solvation structures and properties of the electrolytes critically influence the performance and stability of the batteries. In this study, the structure-property relationships of various electrolytes with different solvent-to-diluent ratios are systematically investigated through a combination of theoretical calculations and experimental tests and analyses. This approach guides the development of electrolytes with unique solvation structures and characteristics, exhibiting high voltage stability, and enhancing the formation of stable electrode/electrolyte interphases. These electrolytes enable the realization of Li||Li1.094Mn0.676Ti0.228O2 (LMTO) DRX cells with improved performance compared to the conventional electrolyte. Specifically, Li||LMTO cells with the optimized advanced controlled-solvation electrolyte deliver higher specific capacity and longer cycle life compared to cells with the conventional electrolyte. Additionally, the investigation into the structure-property relationship provides a foundational basis for designing advanced electrolytes, which are crucial for the stable cycling of emerging high-voltage cathodes.

Tailored bamboo fractionation with ternary deep eutectic solvent system to maximize biorefinery toward enzymatic saccharification and lignin recovery

Six different ternary deep eutectic solvent (DES) of tetraethylammonium chloride (TEAC)/oxalic acid (OA)-polyols were synthesized to improve the production of fermentable sugars and lignin by-products. The bamboo fractionation and bioconversion of cellulose residues can be enhanced by the ternary DES pretreatment, and its increasing efficiency was positively related to the alkyl carbon chain length and hydroxyl number of polyols in the hydrogen bond donor. The 1,4-butanediol (BDO)-assisted DES pretreatment showed excellent performance in achieving high xylan removal (86.7 %) and delignification (91.98 %). The pretreated bamboo was used for enzymatic hydrolysis and ethanol fermentation, with glucose yield and ethanol production of 76.13 % and 16.17 g/L, which was significantly improved by 30 % and 48 % compared to bamboo treated with corresponding binary TEAC/OA. The characterization of trinary pretreated bamboo revealed that the addition of polyols helped to protect the β-O-4 substructure of lignin, reduce the recondensation of lignin fragments, and thus enhance enzyme digestibility. Furthermore, 37.9% of lignin with high purity and highly active hydroxyl substructures was recovered. The proposed novel TEAC/OA-BDO DES mixture has great potential as an effective pretreatment solvent for future bamboo biorefinery.

Compensating K Ions Through an Organic Salt in Electrolytes for Practical K-Ion Batteries

K-ion batteries face significant challenges due to a severe shortage of active K ions, with cathode materials typically containing less than 70% K ions and first-cycle irreversible reactions consuming up to 20% more. Conventional K-ion compensation methods fail to supply sufficient K ions without compromising cell integrity. To address this, we introduce potassium sulfocyanate (KSCN) as an electrolyte additive capable of delivering up to 100% active K ions. During initial charging, KSCN undergoes oxidative decomposition at 3.6 V, releasing active K ions and forming the cosolvent thiocyanogen ((SCN)2). This molecule, meeting diverse electrochemical properties, was identified using unsupervised machine learning and cheminformatics. The approach demonstrated full KSCN conversion and excellent compatibility with all cell components. The presence of (SCN)2 cosolvent enhanced the rate capability of anodes by promoting K-ion desolvation. In a hard carbon|K0.5Mg0.15[Mn0.8Mg0.05]O2 pouch cell, this approach tripled the capacity through supplying 58% active K ions, showcasing a practical solution for active K-ion compensation in K-ion batteries.

Na-Hybridized LiNbO3 Nanocrystal-Glass Composites for Ultra-Short Optical Pulse Detection

LiNbO3 nanocrystal-glass composites (LiNbO3-NGC), characterized by its unique 3D random domain structure, have shown great promise for significant applications, such as femtosecond pulse monitoring and full-color 3D displays. However, the nonlinear response of the LiNbO3-NGC is greatly suppressed by the defects, and effective manipulation of these defects remains a long-standing challenge. In this study, a Na-hybridization strategy is proposed to control defects in the LiNbO3-NGC to enhance its nonlinear properties and realizing its practical application for ultrashort optical pulse monitoring. The findings reveal that the incorporation of Na ions effectively reduces the defects within the composite, resulting in significantly improved nonlinear effects. By using this hybridized LiNbO3-NGC, the transverse second-harmonic generation is achieved. An ultrashort optical pulse system is also constructed and successfully applied it for real-time quantitative measurement of the duration, distribution, and front tilting of optical pulses in the 10-15 s scale. These results not only present an excellent example about defect engineering in nonlinear LiNbO3-NGC but also point to practical applications for the measurement of extreme physical parameters.

Local Structure and Ionic Diffusion in LiF-BeF2-ThF4 Molten Salts: Insights from Ab Initio Molecular Dynamics

Understanding the local structure and ionic diffusion in LiF-BeF2-ThF4 (FLiBeTh) is critical for designing fourth-generation nuclear reactors. However, high-temperature experiments with these salts are often associated with radioactivity and toxicity. Computational simulations provide a safe and efficient method for exploring these materials. In this study, ab initio molecular dynamics (AIMD) simulations were used to analyze the 2LiF-BeF2 system with ThF4 additions ranging from 0 to 18.18 mol % at 973 K. We calculated the radial distribution function (RDF), angular distribution function (ADF), coordination number (CN), mean square displacement (MSD), and anion residence ratio r(t) to investigate the impact of ThF4 concentration on the local structure and ionic diffusion. We found that increasing concentrations of ThF4 have little impact on the structure of the cation first coordination shells. The RDF indicates short-range order in the structure of the molten salts. Additionally, the CN and its distribution indicate that Li+ is primarily tetra- and penta-coordinated, Be2+ is tetra-coordinated, and Th4+ is octa-coordinated. ADF analysis reveals that while the first coordination shells of Be2+ tend toward a regular tetrahedral configuration, Li+ exhibits a distorted octahedral structure, often with one or two anionic cavities. In terms of ionic diffusion, the mean square displacement (MSD) indicate that ionic diffusion rates order as follows: Li+ > F- > Be2+ > Th4+. The r(t) indicates that Be-F coordination shell is the most stable, followed by Th-F, with Li-F being the most dynamic. As ThF4 concentration increases, there is a decrease in the total MSD of the molten salt, suggesting a reduction in overall ionic diffusion. The results from the AIMD simulations align closely with experimental and other simulation data, thereby confirming the reliability of this work. Overall, this study provides insights into the FLiBeTh molten salt, supporting the development of fourth-generation nuclear reactor fuels.

Molecular dynamics exploration of the barrier properties of small gas molecules in the semicrystalline parylene C

Poly(chloro-p-xylylene) (parylene C) is recognized for its outstanding chemical resistance, high thermal stability, biocompatibility, and superior permeability barrier properties. This material predominantly exists in a semicrystalline state. Despite its significance, theoretical studies simulating the semicrystalline parylene C system are scarce. This study aims to elucidate the relationship between the semicrystalline structures and the barrier properties of parylene C through a molecular dynamics approach. Semicrystalline parylene C with 10-50% aligned regions were constructed, which exhibited a degree of crystallinity ranging from 17% to 44%. We discovered that increased aligned chains could significantly alter the material's structure and morphology. These changes could further lead to variations in the density, fractional free volume, and pore size distribution of parylene C, thus affecting its glass transition temperature, permeability barrier and mechanical properties. Additionally, the relative values of gas permeability coefficients closely match experimental data. The insights into the structure-property relationship presented in this work could offer valuable guidance for developing functionalized and structured parylene C as coating materials.

Boosting Reaction Kinetics with Viscous Nanowire Dispersions

Higher viscosity typically slows chemical reactions by restricting molecular movement, while stirring accelerates reactions by enhancing reactant diffusion and collisions. However, in this study, we reveal that reaction rates in nanowire dispersions─with microscopic viscosity ∼300 times that of decane, can be enhanced by over an order of magnitude. Counterintuitively, stirring slows the reaction with higher stirring rates causing even greater deceleration. This phenomenon is observed in both photo- and thermally activated cyclic reactions. Molecular dynamics simulations and confocal laser scanning microscopy suggest that aliphatic chains grafted onto nanowires interact with anisotropic molecules, increasing their local concentrations near the nanowires. Notably, azobenzene photoisomerization is completely inhibited in the nanowire dispersion, despite completing within 30 s in the absence of nanowires. We propose that the aliphatic chains align reactive molecules directionally, while the confined space prevents bulky cis-isomer formation. These findings show that nanowires not only harvest and orient reactive molecules but also exclude bulky products, significantly enhancing the reaction kinetics in confined systems.

In silico cooling rate dependent crystallization and glass transition in n-alkanes

n-Alkanes (CnH2n+2) are linear chain compounds spanning length-scales from small molecules to polymers. Intermediate length alkanes (say, n = 10-20) have attracted much interest as organic phase change materials (PCM) for storing energy as latent heat. The cooling rate (γ) determines both the latent heat and temperature of crystallization. While slow cooling of the liquid leads to the crystalline state, rapid cooling leads to a glassy state (glass transition temperature Tg). Albeit scant theoretical investigations concerning the vitrification processes, the role of molecular conformations therein remains completely unexplored. Our work presents an all-atom molecular dynamics study of (a) cooling intermediate length alkanes (n = 12 and 16) at seven different rates, and (b) rapidly cooling 14 n-alkanes (4 ≤ n ≤ 50) for determining Tg(n). We find that for linear molecules the end-to-end distance (Ree) is of special relevance: the crystal is composed solely of fully stretched molecules (maximal Ree). Hence one may define the "degree of crystallization" as the area under the maximal Ree peak in the Ree distribution. Other peaks in the distribution represent conformations that existed in the supercooled liquid just before vitrification. A peak for the shortest, hairpin rotamer appears only for n ≥ n0 = 18, and is also manifested in the minimum of Rg/Ree(n) for liquid n-alkanes. The dependence of Tg on n is represented as two intersecting Ueberreiter and Kanig equations, intersecting near n0 = 18. Extrapolation gives the asymptotic n → ∞ limit of Tg, T∞g = 250 K, which is probably its most accurate estimate obtained theoretically todate.

Unveiling molecular interactions in glycerol-based deep eutectic solvents

Elucidating the liquid structure of deep eutectic solvents (DES) is crucial to understand how local interactions determine their properties. In this work, the impact of the anion on the liquid structure and local interactions was investigated for mixtures of tetrabutylammonium chloride and bromide ([N4444]Cl and [N4444]Br) with glycerol (Gly). The phase behavior was explored across various compositions using differential scanning calorimetry (DSC) showing that these mixtures form a (meta)stable liquid at room temperature and xsalt = 0.25. At this composition, infrared spectroscopy (IR) revealed strong hydrogen bonding between glycerol and the anion that is more pronounced for chloride than bromide. This finding is supported by the enthalpy of mixing measurements and by quantum chemical calculations. Molecular dynamics (MD) simulations demonstrated that intermolecular hydrogen bonds between glycerol molecules persist, maintaining a long-range liquid structure even in the presence of salt. Far-infrared spectroscopy (FIR) combined with MD simulations revealed changes in local intermolecular dynamics due to a confinement effect caused by the strong anion-glycerol interactions. These results highlight the critical influence of local interactions driven by the anion on DES properties.

Optimizing Amphoteric Cellulose Additives with Complexation-Adsorption Mechanisms to Stabilize the Zn Anode

The growth of Zn dendrites and interfacial side reactions are two critical challenges impeding the commercial application of aqueous zinc batteries (AZBs). The amphoteric electrolyte additive is considered a convenient and efficient strategy to stabilize the Zn anode. However, most studies overlook the critical impacts of their charge compositions and the corresponding mechanisms on Zn2+ electroplating behavior. Here, we use amphoteric cellulose as an exemplary research object, as the number of positive/negative groups can be easily and effectively controlled. We elucidate in detail the interplay between the complexation and adsorption mechanisms of the amphoteric cellulose additive in AZBs. Specifically, the amphoteric cellulose additive not only guides and regulates Zn2+ deposition but also forms a uniform protective layer on the Zn surface. As a result, the optimal additive enables dendrite-free and side-reaction-suppressed AZBs, leading to a Zn||Zn cell with a high depth of discharge of 68.4%, and a Zn||NH4V4O10 cell with a high reversible specific capacity of 310 mAh g-1. This work demonstrates a promising strategy by elucidating the role of charge composition in electrolyte additive design, advancing the development of stable AZBs.

Revealing the Nature of Non-Covalent Interactions in Ionic Liquids by Combined Pulse EPR and 19F NMR Spectroscopy

Ionic liquids (ILs) are a unique class of compounds that have attracted interest for numerous and diverse applications, ranging from solvents for sustainable synthesis to sustainable electrolytes. Understanding their nanostructure and solute-solvent interactions is a prerequisite to harnessing the full potential of ILs. It has been proposed that ILs solvate non-polar solutes via their alkyl chains through the formation of nanoscale structures, such as micelles. Here, we determine the non-covalent interactions responsible for such nanostructuring in ILs. We use pulse electron paramagnetic resonance (EPR), paramagnetic relaxation enhancement (PRE) NMR, molecular dynamics (MD), and density functional theory (DFT) calculations in combination with ILs tailored to probe specific interactions through spin and isotopic labelling. Inter- and intramolecular cation-anion interactions are probed by electron-nuclear double resonance (ENDOR) and 19F PRE experiments and show that nitroxide solutes associate with the polar domains of the imidazolium cation through weak hydrogen bonding with the imidazolium ring protons, as supported by MD simulations. Thus, this study reveals a less structured nanostructure than a micellar picture might suggest, but with clear IL cation-solute interactions. Our methodology to reveal nanostructure not only has implications for ILs but is also applicable to other soft matter systems.

Interfacial Separations by a Polydimethylsiloxane Layer. Molecular Modeling of Coated Stir Bar Extraction of Organics from Aqueous Solutions

Separation processes relying on interfacial interactions, such as the stir bar sorptive extraction represent one of the most critical methods of analyte trace organic detection and extraction in environmental, food, and biomedical samples. While the use of polydimethylsiloxane (PDMS) as a sorptive coating in SBSE has exhibited high sensitivity and efficiency; the molecular mechanisms involved are less explored. We report molecular simulation studies using molecular dynamics (MD) to investigate the absorption of organic compounds including phenol, chlorophenol, guaiacol, benzyl alcohol, and phenethyl alcohol at the aqueous-PDMS interface, and focus on temperature-dependent behavior. By employing an appropriate force field for PDMS, organic compounds, and water, these simulations directly predict PDMS-water partition coefficients, log P [PDMS/water], diffusion coefficients, and solubilities in the PDMS phase without relying on octanol-water partitioning as a surrogate. An important result of the MD simulations in this work is our ability to predict the temperature dependence of the log p(PDMS/water). Results reveal a nonmonotonic temperature-dependent sorption trend for log P [PDMS/water] values. However, we find that with increasing temperature, the absolute number of organic molecules in the PDMS phase increases, driven by enhanced molecular diffusion and PDMS's significant sorption capacity. The findings demonstrate that performing SBSE at elevated temperatures can enhance analyte uptake, improving the analytical sensitivity of trace level extractions, where achieving sufficient analyte concentration in the sorptive phase is critical for reliable detection and quantification in a wide variety of applications in environmental monitoring, food safety, and biomedical analysis. These simulations predict that temperature is a good parameter for the optimization of operating conditions of SBSE. Our results also highlight the ability of MD simulations to reliably capture complex molecular level interactions governing SBSE performance, aligning well with experimental trends and observed behaviors.

Lipid-Derived Electrophiles Modify Proteins and Alter Their Interfacial Behavior: The Distinct Mediating Role of the Interface

In interface-dominated systems (IDSs), lipid peroxidation (LPO) and interfacial protein arrangement commonly coexist. Although lipid-derived electrophiles (LDEs), especially α,β-unsaturated aldehydes, extensively modify proteins, the specific role of interfaces in promoting such modification and its effect on protein behavior remains unclear. Here, we synthesized a yne-ACR probe to simulate LDEs and investigated its modification effect on whey protein (WP) in an IDS model comprising n-hexadecane (Hex) and water. Interface hydromechanics results reveal that the interface distinctly mediates protein modification by yne-ACR in the IDS model. Both the yne-ACR concentration and interfacial properties significantly affect protein interfacial behavior. The interface offers a unique environment for protein modification by yne-ACR, differing from homogeneous systems and producing varied aggregation behaviors between interfacial and nonadsorbed proteins. Chemical proteomic profiling identified 209 modified proteins at the interface compared to 156 in nonadsorbed systems, highlighting increased susceptibility of interfacial proteins to yne-ACR modification and subsequent changes in aggregation patterns. All-atom molecular dynamics (MD) simulations indicate that yne-ACR modification disrupts the stability of protein aggregates at interfaces, promoting redistribution between the interface and the bulk phases and modifying interfacial activity. These findings clarify how LDEs modify proteins in IDSs and their subsequent effects on interfacial behavior.

Influence of Water/Ethanol Mixing Ratio on Gemcitabine Binding to Cucurbit-7-uril Based on Molecular Dynamics Simulations and Three-Dimensional Reference Interaction Site Model

Accurate binding affinities of the cucurbit-7-uril-gemcitabine (CB7-GEM) complex in pure water and ethanol/water-mixed solvents were obtained by combining molecular dynamics simulations and three-dimensional reference interaction site model (3D-RISM) calculations. Point charges of CB7 and GEM molecules, depending on solvent mixture ratios, were determined using 3D-RISM self-consistent field (3D-RISM-SCF) calculations. The calculated binding affinities reveal that the most preferable CB7-GEM complex forms in the pure water system. The complexes in the mixed solvents show lower stability at higher ethanol ratios. Stable conformations at different solvent concentrations appear to be a key factor in the obtained trend of binding affinity enhancement. Conformations in the high-water fractions, associated with higher complex stability, exhibit lower internal energies than those in high-methanol fractions. Disruption of hydrogen-bonding formation also plays a crucial role in the solvation free energies. An explicit solvent model is crucial for accurate calculations of CB7-GEM complexes in these binary mixtures, providing results comparable to the experiments.

Thermo-Mechanical Properties of Cis-1,4-Polyisoprene: Influence of Temperature and Strain Rate on Mechanical Properties by Molecular Dynamic Simulations

Cis-1,4-polyisoprene is a widely used elastomer that demonstrates particular thermal and mechanical characteristics, in which the latter is influenced by temperature and strain rate. Molecular dynamic simulations were used to obtain thermal conductivities, glass transition temperatures (Tg), and tensile deformation. Thermal conductivities were calculated by applying the Green-Kubo method, and a decrease in thermal conductivity was observed with increasing temperature. Density-temperature relations were used to calculate Tg, which indicates the transition from the glassy to the rubbery state of the material, and this temperature influences mechanical properties. Investigation of the mechanical properties under uniaxial tensile deformation for constant strain rates indicates an increase in the stiffness and strength of the material at lower temperatures, while increasing molecular mobility at higher temperatures results in reducing these properties. The influence of strain rates at constant temperature highlighted the viscoelastic nature of the structure; increasing strain rates resulted in increases in stiffness, strength, elongation at maximum strength, and elongation at break because of restricted molecular relaxation time. The united-atom force field contributes to higher computational efficiency, which is suitable for large-scale simulations. These results provide important information on the thermo-mechanical properties and tunability of cis-1,4-polyisoprene, which supports applications in the production of interactive fiber rubber composites.

Atomistic Modeling of Cross-Linking in Epoxy-Amine Resins: An Open-Source Protocol

Atomistic modeling has become an extensively used method for studying thermosetting polymers, particularly in the analysis and development of high-performance composite materials. Despite extensive research on the topic, a widely accepted, standardized, flexible, and open-source approach for simulating the cross-linking process from precursor molecules has yet to be established. This study proposes, tests, and validates a Molecular Dynamics (MD) protocol to simulate the cross-linking process of epoxy resins. We developed an in-house code based on Python and LAMMPS, enabling the generation of epoxy resin structures with high degrees of cross-linking. In our work, the epoxy network is dynamically formed within the MD simulations, modeling the chemical bonding process with constraints based on the distance between the reactive sites. To validate our model against experimental data from the literature, we then computed the density, thermal conductivity, and elastic response. The results show that the produced structures align well with experimental evidence, validating our method and confirming its feasibility for further analyses and in silico experiments. Beyond the case study presented in this work, focusing on bisphenol A diglycidyl ether (DGEBA) epoxy resin and diethylenetriamine (DETA) as curing agents in a 5:2 ratio, our approach can be easily adapted to investigate different epoxy resins.

Physical Stability and Molecular Mobility of Resveratrol in a Polyvinylpyrrolidone Matrix

The physical stability, molecular mobility, and appearance of nanocrystalline resveratrol in a polyvinylpyrrolidone (PVP) matrix were investigated. Two formulations with resveratrol loadings of 30% and 50% were prepared and characterized using powder X-ray diffraction (PXRD) and time-domain nuclear magnetic resonance (TD-NMR). Samples were studied over time (up to 300 days post-preparation), across temperatures (80-300 K), and under varying humidity conditions (0% and 75% relative humidity). The results demonstrate that the 30% resveratrol-PVP sample is a homogeneous amorphous solid dispersion (ASD), while the 50% resveratrol-PVP sample contained resveratrol nanocrystals measuring about 40 nm. NMR measurements and molecular dynamics (MD) simulations revealed that incorporation of resveratrol into the polymer matrix modifies the system's dynamics and mobility compared to the pure PVP polymer. Additionally, MD simulations analyzed the hydrogen bonding network within the system, providing insights for a better understanding of the physical stability of the ASD under different conditions.