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

Challenges in simulating whole virus particles and how to fix them with the SIRAH force field

Current developments in specialized software and computer power make the simulation of large molecular assemblies a technical possibility despite their computational cost. Coarse-grained (CG) approaches simplify molecular complexity and reduce computational costs while preserving intermolecular physical/chemical interactions. These methods enable virus simulations, making them more accessible to research groups with limited supercomputing resources. However, setting up and running molecular dynamics simulations of multimillion systems requires specialized molecular modeling, editing, and visualization skills. Moreover, many issues related to the computational setup, the choice of simulation engines, and the force fields that rule the intermolecular interactions require particular attention and are key to attaining a realistic description of viral systems at the fully atomistic or CG levels. Here, we provide an overview of the current challenges in simulating entire virus particles and the potential of the SIRAH force field to address these challenges through its implementations for CG and multiscale simulations.

Modulating competitive adsorption of hybrid self-assembled molecules for efficient wide-bandgap perovskite solar cells and tandems

The employment of self-assembled molecular hybrid could improve buried interface in perovskite solar cells (PSCs). However, the interplay among hybrid self-assembled monolayers (SAMs) during the deposition process has not been well-studied. Herein, we study the interaction between co-adsorbents and commonly used SAM material, [4-(3,6-dimethyl-9H-carbazol-9-yl)butyl]phosphonic acid (Me-4PACz) for wide-bandgap (WBG) PSCs. It is found that the co-adsorbent, 6-aminohexane-1-sulfonic acid (SA) tends to fill the uncovered sites without interference with Me-4PACz, ensuring the formation of a dense hole selective layer. Moreover, the use of SA/Me-4PACz mixed SAMs could effectively reduce the interfacial non-radiative recombination loss, optimize the energy alignment at the buried interface and regulate the crystallization of WBG perovskite. As a result, the 1.77 eV WBG PSCs deliver a power conversion efficiency (PCE) of 20.67% (20.21% certified) and an impressive open-circuit voltage (VOC) of 1.332 V (1.313 V certified). By combining with a 1.26 eV narrow-bandgap (NBG) PSC, we further fabricate 2-terminal all-perovskite tandem solar cells (TSCs) with a PCE of 28.94% (28.78% certified) for 0.087 cm2 and 23.92% for mini-module with an aperture area of 11.3 cm2.

Understanding dynamics in coarse-grained models. V. Extension of coarse-grained dynamics theory to non-hard sphere systems

Coarse-grained (CG) modeling has gained significant attention in recent years due to its wide applicability in enhancing the spatiotemporal scales of molecular simulations. While CG simulations, often performed with Hamiltonian mechanics, faithfully recapitulate structural correlations at equilibrium, they lead to ambiguously accelerated dynamics. In Paper I [J. Jin, K. S. Schweizer, and G. A. Voth, J. Chem. Phys. 158(3), 034103 (2023)], we proposed the excess entropy scaling relationship to understand the CG dynamics. Then, in Paper II [J. Jin, K. S. Schweizer, and G. A. Voth, J. Chem. Phys. 158(3), 034104 (2023)], we developed a theory to map the CG system into a dynamically consistent hard sphere system to analytically derive an expression for fast CG dynamics. However, many chemical and physical systems do not exhibit hard sphere-like behavior, limiting the extensibility of the developed theory. In this paper, we aim to generalize the theory to the non-hard sphere system based on the Weeks-Chandler-Andersen perturbation theory. Since non-hard sphere-like CG interactions affect the excess entropy term as it deviates from the hard sphere description, we explicitly account for the extra entropy to correct the non-hard sphere nature of the system. This approach is demonstrated for two different types of interactions seen in liquids, and we further provide a generalized description for any CG models using the generalized Gaussian CG models using Gaussian basis sets. Altogether, this work allows for extending the range and applicability of the hard sphere CG dynamics theory to a myriad of CG liquids.

Exploring an n-type conducting polymer (BBL) as a potential gas sensing material for NH3 and H2S detection

Conducting polymers (CPs) have garnered significant interest in being used as an active material in gas sensors mainly because of their structural flexibility, ease of synthesis, and enhanced performance at room temperature. The p-type CPs and their composites are mostly studied in gas sensing, which, unfortunately, exhibit limitations in terms of selectivity, stability, and sensitivity toward reducing gases. This study focuses on one of the widely studied n-type polymers, BBL(benzimidazobenzophenanthroline), as an active material for the detection of two reducing gases, namely, hydrogen sulfide (H[Formula: see text]S) and ammonia (NH[Formula: see text]), theoretically. Through molecular dynamics (MD) simulation and density functional theory (DFT) approach, we understand the adsorption behavior and selectivity of H[Formula: see text]S and NH[Formula: see text] in the BBL film. The DFT calculated adsorption energy of the preferential site at the top of a [Formula: see text] stack for H[Formula: see text]S and NH[Formula: see text] are - 0.22 eV and - 0.33 eV, respectively, and at the sides of a [Formula: see text] stack for H[Formula: see text]S and NH[Formula: see text] are - 0.42 eV and - 0.47 eV, respectively. MD simulations show that adsorption takes place in the free voids within the thin films, and the overall structure of the polymer film remained almost unaltered upon gas adsorption without any apparent swelling or significant morphological changes in the film. Our results show that BBL displays remarkable adsorption along with a higher magnitude of charge transfer for ammonia over hydrogen sulfide gas and other common gases present in the air. Moreover, both H[Formula: see text]S and NH[Formula: see text] gas adsorption happen without compromising the size of the [Formula: see text] stacked crystallites within the polymer film, which indicates, upon detection of reducing gases, the generated free electrons via the redox reactions between the gas molecules and polymer, will be able to be smoothly transported through the [Formula: see text] stack network present in the film. The detailed theoretical insights obtained from this study indicate the suitability of the n-type conducting polymer, BBL, for detecting reducing gases, NH[Formula: see text] and H[Formula: see text]S.

Room-Temperature Decomposition of the Ethaline Deep Eutectic Solvent

Environmentally benign, nontoxic electrolytes with combinatorial design spaces are excellent candidates for green solvents, green leaching agents, and carbon capture sources. We examine ethaline, a 2:1 molar ratio of ethylene glycol and choline chloride. Despite its touted green credentials, we find partial decomposition of ethaline into toxic chloromethane and dimethylaminoethanol at room temperature, limiting its sustainable advantage. We experimentally characterize these decomposition products and computationally develop a general, quantum-chemically accurate workflow to understand its decomposition. We find that fluctuations in the hydrogen bonds bind chloride near reaction sites, initiating the reaction between choline cations and chloride anions. The strong hydrogen bonds formed in ethaline are resistant to thermal perturbations, entrapping Cl in high-energy states and promoting the uphill reaction. In the design of stable green solvents, we recommend detailed evaluation of the hydrogen-bonding potential energy landscape as a key consideration for generating stable solvent mixtures.

Structural Features of the Thymol-Carvacrol Equimolar Mixture: X-Ray Scattering and Molecular Dynamics

We present a structural characterization of a low-transition-temperature mixture (LTTM), consisting of thymol and carvacrol, at an equimolar ratio. Carvacrol and thymol are natural regioisomers of terpenes. When combined at an equimolar ratio, they form a liquid mixture at room temperature, with supercooling capability and glass transition at ca. 210 K. Using small- and wide-angle X-ray scattering and molecular dynamics, we describe the structural complexity within this system. X-ray scattering reveals a low-Q peak at around 0.6 Å-1, indicating the existence of mesoscale structural heterogeneities, likely related to the segregation of polar moieties engaged in hydrogen bond (HB) interactions within an aromatic, apolar matrix. These polar interactions are predominantly a result of HBs involving thymol as the HB donor species. The liquid structure is also driven by O-H···π interactions, prevalently due to the ability of the carvacrol π-site to engage in this type of weak interaction as a HB acceptor. Besides, dispersive interactions affect the local arrangement of molecules, with a propensity of carvacrol rings to orient their first neighbors with a perpendicular orientation, while thymol tends to induce a closer approach of other thymol molecules with a preferential parallel alignment. Overall, we observed a complex structural arrangement driven by the interplay of both conventional and weak hydrogen bond interactions, with the aromatic nature of the compounds playing a pivotal role in shaping the system's architecture. Carvacrol and thymol, despite being very similar compounds, are characterized by distinctly different behavior in terms of the interactions they engage in with their neighbors, likely due to the different steric hindrance experienced by their hydroxyl groups, which are close to either a small methyl or a bulky isopropyl group, respectively. Such observations can provide useful hints to develop new solvents with tailored properties.

Solvation-mediated adsorption mechanism of solvated lithium ions at a charged solid-liquid interface for electrochemical energy storage: atomic scale investigation and insights

Ion encapsulation by solvent molecules significantly impacts ion transport and the adsorption mechanism in energy storage devices. The aim of this investigation is to analyse the adsorption mechanisms associated with the solvation shell of lithium ions near the electrode/electrolyte interface during the charging process. Simulations using molecular dynamics (MD) are conducted for LiPF6 salt in PC solvent confined in between two flat carbon electrodes. The thermodynamic and physical properties of the simulation show excellent agreement with experimental values. Results indicate that the lithium ion forms a strong tetrahedral solvation structure with PC solvent molecules. Orientation analysis reveals that the polar ends of the solvent molecules in the lithium ion solvation structure are anchored to the positive electrode, which is caused by strong attractive interactions, particularly for high surface charge densities. Meanwhile, the solvation structure and solvent molecules undergo rotation close to the negative electrode at high surface charge densities. These aforementioned phenomena lead to solvation-mediated electrostatic interactions between solvated lithium ions and the electrodes. Finally, the differential capacitance for both positive and negative electrodes decreases under these solvation-mediated electrostatic interactions. This study provides a unique intuitive image of possible implications of the solvation structure on the charging performance of energy storage devices, along with perspectives on developing electrolytes with favorable orientations.

Reshaping Interface Interactions of P. litoralis Acyltransferase for Efficient Chemoenzymatic Epoxidation in Aqueous Phase

Epoxides, a class of ethers with a three-membered ring structure, are widely used in the textile, pharmaceutical, and packaging industries. Chemoenzymatic epoxidation presents a promising method for synthesizing epoxides. However, its epoxidation efficiency is hindered by low chemoselective perhydrolysis, which is caused by the hydrolysis side reaction in the aqueous phase. In this study, a chemoenzymatic epoxidation process in the aqueous phase was developed by utilizing an acyltransferase from P. litoralis (PlAcT) for its chemoselective perhydrolysis. Crystal structure analysis, molecular dynamics simulations, and quantum mechanics calculations, along with site-specific mutagenesis, revealed that the selectivity of perhydrolysis is due to a lower energy barrier in the acyl transfer step compared to that in hydrolysis. Furthermore, the mutant PlAcTM3-2 exhibited a 7.6-fold improvement in solvent stability and a 1.3-fold increase in perhydrolysis activity compared to the wild type, achieved by reshaping interface interactions. As a result, the engineered strain Y07, harboring PlAcTM3-2, successfully synthesized compounds 3a-3n with conversions ranging from 11-99%, and the titers of compounds α-pinene oxide(3i), β-pinene oxide(3j), 3-carene oxide(3k), and limonene dioxide(3l-3) reached 55.8, 16.7, 75.2, and 21.4 g/L, respectively. These results demonstrate a sustainable method for chemoenzymatic epoxidation in the aqueous phase.

Development of molecularly imprinted polymers for the detection of human chorionic gonadotropin

Diagnostic pregnancy tests are the most widely used immunoassays for home-based use. These tests employ the well-established lateral flow assay (LFA) technique, reminiscent of affinity chromatography relying on the dual action of two orthogonal anti-hCG antibodies. Immunoassays suffer from several drawbacks, including challenges in antibody manufacturing, suboptimal accuracy, and sensitivity to adverse storing conditions. Additionally, LFAs are typically designed for single use, as the LFA technique is non-reusable. An alternative to overcome these drawbacks is to leverage molecularly imprinted polymer (MIP) technology to generate polymer-based hCG-receptors and, subsequently, non-bioreceptor-based tests. Here, we report the development of MIP nanogels for hCG detection, exploiting epitopes and magnetic templates for high-yielding dispersed phase imprinting. The resulting nanogels were designed for orthogonal targeting of two immunogenic epitopes (SV and PQ) and were thoroughly characterized with respect to physical properties, binding affinity, specificity, and sensitivity. Molecular dynamics simulations indicated a pronounced conformational overlap between the templates and the epitopes in the native protein, supporting their suitability for templating cavities for hCG recognition. Quartz crystal microbalance (QCM)-based binding tests and kinetic interaction analysis by surface plasmon resonance (SPR) revealed nanomolar dissociation constants for the MIP nanogels and their corresponding template peptides and low uptake of lutenizing hormone (LH), structurally resembling to hCG. Receptor reusability was demonstrated in the multicycle SPR sensing mode using a low pH regeneration buffer. The results suggest the feasibility of using imprinted nanogels as a class of cost-effective, stable alternatives to natural antibodies for hCG detection. We foresee applications of these binders with respect to reusable pregnancy tests and other hCG-related disease diagnostics.

Computational design to experimental validation: molecular dynamics-assisted development of polycaprolactone micelles for drug delivery

Amphiphilic diblock copolymers are used in drug delivery systems for cancer treatments. However, these carriers suffer from lower drug loading capacity, poor water solubility, and non-targeted drug release. Here, we utilized a computational approach to analyze the effect of the functional groups of the hydrophobic block on the drug-polymer interactions. To design effective drug carriers, four different amphiphilic block copolymer micelles with distinct aromatic and heteroaromatic groups at the hydrophobic core were subjected to molecular dynamics simulations. The solvent-accessible surface area, water shell, hydrogen bonding, and radius of gyration of the simulated micelles were determined. Further, we assessed the interactions between the hydrophobic block and drug molecules using linear interaction energy and non-covalent interactions. The computational studies revealed that the micelles containing a novel poly(γ-2-methoxyfuran-ε-caprolactone) (PFuCL) hydrophobic block have the highest polymer-drug interactions. From these findings, we synthesized a novel amphiphilic poly(ethylene glycol)-b-poly(γ-2-methoxyfuran(ε-caprolactone)) (PEG-b-PFuCL) block copolymer using ring-opening polymerization of FuCL monomer. The polymer was self-assembled in aqueous media to form micelles. The aromatic segment of PEG-b-PFuCL micelles enhanced the doxorubicin (DOX) loading through non-covalent interactions, resulting in a 4.25 wt% drug-loading capacity. We also showed that the hydrolysis of the ester bond allowed a faster in vitro drug release at pH 5.0 compared to pH 7.4. Cell viability experiments revealed that DOX-loaded PEG-b-PFuCL micelles show that micelles are cytotoxic and readily uptaken into MDA-MB-231 cells. Therefore, furan-substituted micelles will be an ideal drug carrier with higher polymer-to-drug interactions, enhanced drug loading, and lower premature leakage.

Ultrasonic Dispersion for Iron Recovery from Slime Tailings: Microprocesses Unveiled through Molecular Dynamics Simulations

Chemical dispersion has been commonly used to mitigate the negative effects of ultrafine particles in iron ore concentration processes. However, mechanical solutions such as ultrasound are proving to be more effective and without harmful side effects. This study compared the performance of different dispersants and ultrasound as pretreatments for reverse cationic flotation of goethite-rich slime tailings through sedimentation, dispersion, and flotation tests, along with particle size analysis. Additionally, large-scale molecular dynamics simulations were used for the first time to investigate the effects of ultrasonic shockwaves on mineral particle interactions. The results showed that ultrasonication is a superior pretreatment, enhancing particle dispersion and separation performance, cleaning mineral surfaces, and improving flotation results. Ultrasound achieved an increase in metallurgical recovery of around 9% while using only a dispersant reagent did not reach 5%. Simulations demonstrated the known effects of ultrasound, such as extreme temperature, bubble cavitation, and particle detachment, revealing the crucial microscopic mechanisms involved in particle separation by sonic waves. This study bridges experimental data with computational simulations, offering a comprehensive understanding of ultrasonication's effects on particle separation, paving the way for more efficient and sustainable processing technologies.

Hydrogen-bond induced non-linear size dependence of lysozyme under the influence of aqueous glyceline

Natural deep eutectic solvents (NADESs) are environmentally friendly green solvents and hold great promise in the pharmaceutical industry. The secondary structure of a protein, lysozyme, follows a non-monotonous behavior in aqueous glyceline (choline chloride + glycerol) as the wt. % of water is increased. However, it is unclear how the hydration affects the stability of the protein in a non-linear way. In this work, we have performed all-atom molecular dynamic simulations for 1 μs with the lysozyme protein in an aqueous glyceline deep eutectic solvent (DES) by varying the wt. % of water. The simulated radius of gyration, Rg, values can qualitatively reproduce the protein behavior such that the Rg increases initially with an increase in wt. % of water, reaches the peak at 40 wt. %, and then gradually decreases with dilution. Several other properties, including root mean square deviation, root-mean square fluctuation, secondary structure of the protein, and solvent accessible surface area, are examined to explore the NADES effect on the protein structure. Next, we analyze the hydrogen bond profile of intra-protein and among various interspecies, e.g., protein-DES, DES-DES, protein-water, and water-water. The variation in protein-protein hydrogen bonds with concentrations can qualitatively explain the non-linear conformational dependence of the protein. The radial distribution function analyses show various microscopic structures formed due to the DES and water interaction, which play a critical role in protein behavior. This study indicates that at lower wt. % of water, the protein is constrained in a strong hydrogen bond network formed by glycerol and water molecules, resulting in a lower Rg. As the wt. % of water increases, the protein-water interaction drives the protein to expand, reflecting an increasing Rg. At sufficiently higher wt. % of water, the DES constituent and the water molecules interact strongly with the protein, resulting in a decrease in Rg. Overall, the investigation offers a microscopic insight into the protein conformation in DES.

A dynamic structural unit of phase-separated heterochromatin protein 1α as revealed by integrative structural analyses

The heterochromatin protein HP1α consists of an N-terminal disordered tail (N-tail), chromodomain (CD), hinge region (HR), and C-terminal chromo shadow domain (CSD). While CD binds to the lysine9-trimethylated histone H3 (H3K9me3) tail in nucleosomes, CSD forms a dimer bridging two nucleosomes with H3K9me3. Phosphorylation of serine residues in the N-tail enhances both H3K9me3 binding and liquid-liquid phase separation (LLPS) by HP1α. We have used integrative structural methods, including nuclear magnetic resonance, small-angle X-ray scattering (SAXS), and multi-angle-light scattering combined with size-exclusion chromatography, and coarse-grained molecular dynamics simulation with SAXS, to probe the HP1α dimer and its CSD deletion monomer. We show that dynamic intra- and intermolecular interactions between the N-tails and basic segments in CD and HR depend on N-tail phosphorylation. While the phosphorylated HP1α dimer undergoes LLPS via the formation of aggregated multimers, the N-tail phosphorylated mutant without CSD still undergoes LLPS, but its structural unit is a dynamic intermolecular dimer formed via the phosphorylated N-tail and a basic segment at the CD end. Furthermore, we reveal that mutation of this basic segment in HP1α affects the size of heterochromatin foci in cultured mammalian cells, suggesting that this interaction plays an important role in heterochromatin formation in vivo.

Ab Initio Molecular Dynamics Simulations of Amino Acids and Their Ammonia-Based Analogues in Ammonia

α-Amino acids are the fundamental building blocks for complex molecular structures within the water-based biochemistry of Earth. In a hypothetical ammonia-based biochemistry, α-amino amidines may serve an equivalent role. In this study, we explore the basic properties of α-amino amidines in comparison to α-amino acids solvated in ammonia, utilizing ab initio molecular dynamics simulations. The investigation of the time-resolved molecular dipole moment reveals, in intricate detail, the relationship among the conformation, state, and magnitude of the dipole moment. Moreover, it allows for the tracking of proton-transfer reactions. In ammonia, α-amino acids tend to adopt an anionic state, with the zwitterionic state still being accessible. In contrast, the α-amino amidines remain neutral. Grotthuss diffusion is induced by the deprotonation of zwitterionic alanine. The charge transferred upon solvation serves as an indicator for the interaction strength between the solute and solvent. It is much stronger for α-amino acids, while, on average, the α-amino amidines exchange no charge with ammonia. The analyses reveal that in terms of structure, anionic α-amino acids behave very similarly to neutral α-amino amidines.

Multiscale Interfacial Structure and Organization of sII Gas Hydrate Interfaces Using Molecular Dynamics

Gas hydrate systems display complex structural arrangements in their bulk and interfacial configurations. Controlling nucleation and growth in the context of potential applications requires a characterization of these structures such that they can be manipulated at the atomic and molecular scale to fine tune macroscale applications. This work uses molecular dynamics to show the different methods of identifying interface location and thickness, the drawbacks of certain methods, and proposes improved methodology to overcome sampling issues. We characterize the interfacial position and thickness using structure and dipole-based methods at different conditions for water/sII natural gas hydrate mixtures. We find that phases with similar densities are particularly sensitive to the regression technique employed and may not resolve the thickness of the complex pre-melting layer adequately, while the dipole moments may provide better resolution. The dipole shows the complex natural of the small and compressed layer that presents on the hydrate surface. These results show that the interface is thin but dynamic and careful characterization required analysis of multiple molecular phenomena.

Extreme pH Tolerance in Peptide Coacervates Mediated by Multivalent Hydrogen Bonds for Enzyme-Triggered Oral Drug Delivery

Biopolymer-based complex coacervates hold promising prospects in the field of biomedicine. However, their low stability in environments with extreme pH and high salt concentrations, largely due to weakly charged biomacromolecules and insufficient understanding of their assembly processes, has hindered their practical applications in oral drug delivery. Here, we have developed Dopa-containing peptide-based complex coacervates that are stable across a wide range of pH (1-11) and salt concentrations. Large-scale all-atom molecular dynamics simulations reveal that multivalent hydrogen bonds control the assembly pathway of the coacervates and boost their stability. Systematic point mutations reveal that various multivalent molecular interactions can synergistically tune the properties of complex coacervates. Such peptide coacervates show high drug encapsulation efficacy and trypsin-triggered release, presenting great potential for oral drug delivery applications. Our multivalent hydrogen bond-mediated peptide coacervates provide new design principles of engineering functional coacervates for diverse applications.

Molecular dynamics simulation of synergistic behavior at the air-water interface: mixed cationic-anionic fluorocarbon-hydrocarbon surfactants

Ecological concerns surrounding conventional aqueous film-forming foam extinguishing agents, predominantly composed of long-chain fluorocarbon surfactants, have spurred the need for innovation in eco-compatible substitutes, such as short-chain fluorocarbon surfactants. Molecular dynamics simulations are a valuable tool for studying the behavior of mixed surfactant systems at the air-water interface. We have conducted molecular dynamics simulations to investigate the interfacial behavior of a mixed cationic-anionic surfactant system, including N-[3-(dimethylamino)propyl]perfluorobutanesulfonamide hydrochloride (PFB-MC) and 1-octanesulfonic acid (1-OA). The simulations explored the effects of varying PFB-MC and 1-OA ratios on aggregation and adsorption. The results indicate that the equimolar 1 : 1 ratio produced more compact aggregates at the interface and achieved the most effective reduction in surface tension and the formation of a dense interfacial film. The study highlights the competitive adsorption phenomena between surfactants and counterions at the interface, providing insights through 1D and 2D density analyses into the impact of counterbalancing ions on aggregation. An increased PFB-MC concentration resulted in decreased hydrogen bonding with water, while 1-OA showed a higher tendency for hydrogen bonding, underscoring its hydrophilicity. These findings provide valuable insights into surfactant interfacial behavior and are instrumental in the development of advanced foam extinguishing agents suitable for environmental and industrial use.

Effects of cations on the structure, dynamics and vibrational sum frequency generation spectroscopy of liquid/vapor interfaces of aqueous solutions of monovalent and divalent metal nitrates

We have employed molecular dynamics (MD) simulations and theoretical vibrational sum frequency generation spectroscopy (VSFG) to investigate the structure and interactions of water and ions at liquid/vapor interfaces of aqueous solutions of monovalent and divalent metal nitrates of NaNO3, Mg(NO3)2 and Ca(NO3)2. Structural properties, such as the number density profiles, average number of hydrogen bonds, slab radial distribution functions (SRDFs), and tetrahedral order parameter, are calculated to investigate the structure of water in bulk and at the interfaces. The ion pairing tendency is determined in terms of cation-anion SRDF and is found to be following the order Mg(NO3)2 < Ca(NO3)2 < NaNO3 both at the interfacial and bulk regions. An ionic double layer is found to be formed at the interface. A weak propensity of anions is found to be at the interface, while the cations are found to be present below the interfacial region. Three prominent features are observed in the VSFG spectrum of the liquid/vapor interfaces of metal nitrate solutions: a free (dangling) O-H peak at 3750 cm-1, a peak at 3589 cm-1 due to O-H groups hydrogen bonded to nitrates, and a broad peak at 3200-3500 cm-1 due to O-H modes hydrogen bonded to water. The charge density of cations affects the intensity of the 3200-3500 cm-1 peak. The presence of ions is found to have very little effect on the position and intensity of the dangling peak as compared to that for the neat water/vapor interface. The ionic double layers generate electric fields that reorganize and reorient the water molecules towards the vapor. This upward reorientation of water leads to a positive region in the VSFG spectrum of O-H modes which are hydrogen bonded to water in contrast to that of the neat water/vapor interface. The O-H groups hydrogen bonded to the nitrates are mostly oriented downwards and the strength of such hydrogen bonds is found to be weaker than those hydrogen bonded to water.

Mechanistic Basis for Enhanced Strigolactone Sensitivity in KAI2 Triple Mutant

Striga hermonthica is a parasitic weed that destroys billions of dollars' worth of staple crops every year. Its rapid proliferation stems from an enhanced ability to metabolize strigolactones (SLs), plant hormones that direct root branching and shoot growth. Striga's SL receptor, ShHTL7, bears more similarity to the staple crop karrikin receptor KAI2 than to SL receptor D14, though KAI2 variants in plants like Arabidopsis thaliana show minimal SL sensitivity. Recently, studies have indicated that a small number of point mutations to HTL7 residues can confer SL sensitivity to AtKAI2. Here, we analyze both wild-type AtKAI2 and SL-sensitive mutant Var64 through all-atom, long-timescale molecular dynamics simulations to determine the effects of these mutations on receptor function at a molecular level. We demonstrate that the mutations stabilize SL binding by about 2 kcal/mol. They also result in a doubling of the average pocket volume, and eliminate the dependence of binding on certain pocket conformational arrangements. While the probability of certain non-binding SL-receptor interactions increases in the mutant compared with the wild-type, the rate of binding also increases by a factor of ten. All these changes account for the increased SL sensitivity in mutant KAI2, and suggest mechanisms for increasing functionality of host crop SL receptors.

Design and Characterization of pH-Responsive DGEA-Derived Peptide Scaffolds: A Comprehensive Molecular Dynamics Simulation Study

Peptide-based, functionally active, stimuli-responsive biomaterials hold immense potential for diverse biomedical applications. Functionally active motifs of extracellular matrix (ECM) proteins, when conjugated with self-assembling peptides (SAP) or polymers, demonstrate significant promise in the development of such bioactive scaffolds. However, synthesis complexity, high associated costs, limited functionality, and potential immune responses present significant challenges. This study explores collagen-I-derived DGEA motif-based SAPs, incorporating modifications such as salt bridge pairing, charged and polar residues, hydrophobic residues, amyloidogenic sequences, and non-ECM motifs, to develop stimuli-responsive, functionally active scaffolds. Extensive molecular dynamics (MD) simulations, totaling 16.7 μs, were conducted on 20 systematically designed peptide systems. These simulations also characterized the stimuli-responsive properties of the peptides, focusing on pH and temperature responsiveness. Among the 20 designs, three peptide systems─DGEA-SBD, DGEA-SBE (salt-bridge modifications), and DGEA-F4 (with hydrophobic residue addition at the C-terminus)─successfully formed large, stable, and bioactive scaffolds. These systems exhibited enhanced aggregation (greater than 90%) and improved interpeptide hydrogen bonding (more than 30 bonds) while maintaining the accessibility of functional motifs (60-70% availability) compared to the unmodified DGEA motif. Notably, the DGEA-SBD and DGEA-SBE peptides showed a transition from small, unstable, uneven gel-like structures to large, stable, uniform, and functionally active scaffolds as the pH shifted from 3.0 to physiological pH. Comprehensive MD simulation studies demonstrated that these designed peptides exhibit increased aggregation and enhanced interpeptide hydrogen bonding while retaining their functional activity under various physiological conditions, highlighting their promising potential for biomedical applications.

The solvation of Na+ ions by ethoxylate moieties enhances adsorption of sulfonate surfactants at the air-water interface

HYPOTHESIS

Experiments show pronounced synergy in the reduction of surface tension when the nonionic surfactant Poly(oxy-1,2-ethanediyl), .alpha.-tris(1-phenylethyl)phenyl-.omega.-hydroxy- (Ethoxylated tristyrylphenol, EOT) is mixed with the anionic surfactant Sodium 4-dodecylbenzenesulfonate (NaDDBS). We hypothesize that the synergism is due to counterion (cation) effects. This would be unusual as one of the surfactants is nonionic. To test this hypothesis, the molecular mechanisms responsible need to be probed using experiments and simulations.

APPROACH

The interfacial properties of mixtures comprising EOT and NaDDBS are investigated using equilibrium molecular dynamics (MD) simulations. Free energy calculations using thermodynamic integration and umbrella sampling methods are employed to analyze the molecular interactions at surface and reveal the role of counterion solvation on the results observed. Simulation snapshots and trajectories are interrogated to confirm the findings.

FINDINGS

Simulation results indicate that the ethoxylate moieties solvate Na+ ions, forming long-lasting cation-EOT complexes. Free energy calculations suggest that these complexes are more stable at the interface than in the bulk, likely because of changes in the dielectric properties of water. The cation-EOT complexes, in turn, cause a stronger affinity between the interface and NaDDBS when EOT is present. Similar studies conducted for mixtures of EOT and cationic surfactant Dodecylammonium chloride (DAC) do not show evidence of Cl- ions solvation via the ethoxylate moieties, while the DAC headgroup was found to form hydrogen bonds with the EOT headgroup. This suggests that the mechanisms observed are likely ion specific.

Solvation Structure and Dynamics of the Thiocyanate Anion in mixed N,N-Dimethylformamide-Water Solvents: A Molecular Dynamics Approach

The solvation structure and dynamics of the thiocyanate anion at infinite dilution in mixed N, N-Dimethylformamide (DMF)-water liquid solvents was studied using classical molecular dynamics simulation techniques. The results obtained have indicated a preferential solvation of the thiocyanate anions by the water molecules, due to strong hydrogen bonding interactions between the anion and water molecules. A first hydration shell at short intermolecular distances is formed around the SCN- anion consisting mainly by water molecules, followed by a second shell consisting by both DMF and water molecules. The strong interactions between the thiocyanate anion and water molecules are further reflected upon the calculated intermittent residence lifetimes of water and DMF in the first and second solvation shells. The dependence of the reorientational relaxation times of the thiocyanate anion upon the mole fraction of DMF in the mixtures has been found to be in good agreement with experiment, revealing strong concentration effects upon these relaxation phenomena. An appreciable solvent composition effect upon the low frequency intermolecular vibrations, due to the anion-water interactions, has also been revealed by calculating the atomic velocity correlation functions and corresponding spectral densities of the anion.

Mechanistic Insight on Ethanol Driven Swelling and Disruption of Cholesterol Containing Biomimetic Vesicles From Coarse-Grained Molecular Dynamics

We have performed coarse-grained (CG) molecular dynamics (MD) simulations to delineate the impact of ethanol (EtOH) on cholesterol (CHOL) containing biomimetic bilayer and vesicle composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipids. We have first deduced the missing interaction parameters for the POPC-CHOL-EtOH-water system within the SPICA/SDK CG force-field (CG-FF). By monitoring the electron density profiles, the orientational order parameter, and reproducing the all-atom MD-derived free energy for the insertion of ethanol from the bulk aqueous phase to the hydrophobic core of the POPC-CHOL lipid bilayer, we successfully determined all the missing non-bonding interaction parameters for the POPC-CHOL-EtOH-water system. The proposed force field was applied to investigate the effect of ethanol at various concentrations on unilamellar vesicles composed of POPC and cholesterol. It was found that 40 mol% or more concentration of ethanol is required to disintegrate or rupture the POPC-CHOL vesicle membranes. While cholesterol offers some resilience against the detrimental effects of ethanol, we still observe an increase in vesicle size (swelling) and a contraction in the bilayer thickness (thinning) as ethanol concentration rises from 0 to 30 mol%. At ethanol concentrations exceeding 30 mol%, the vesicles become increasingly susceptible to disintegration due to enhanced penetration of ethanol and water molecules into the hydrophobic core of the membranes.

Enhancing Mechanical Properties of Chitosan-Silica Aerogels with Tricalcium Phosphate Nanoparticles: A Molecular Dynamics Study for Bone Tissue Engineering

Chitosan-silica aerogel nanocomposites are lightweight materials with a highly porous structure that have a wide range of applications, including drug delivery systems, tissue engineering, and insulation. These materials may be strengthened using tricalcium phosphate in chitosan-silica aerogel nanocomposites. Thus, in the present research projects, the influence of different atomic percentages of TCP (2%, 3%, and 5%) on mechanical parameters such as stress-strain, ultimate strength, and Young's modulus of chitosan-silica aerogel NCs was evaluated using molecular dynamics modeling and LAMMPS software. The findings demonstrate that the addition of tricalcium phosphate (1-3%) enhanced the ultimate strength and Young's modulus of the simulated nanocomposite from 26.968 to 43.468 GPa and from 681.145 to 1053.183 MPa, respectively. The ultimate strength and Young's modulus of the silica aerogel/chitosan nanocomposites, however, decreased to 1021.418 MPa and 42.008 GPa, respectively, with the addition more than 5% TCP.

Harnessing Pore Size in COF Membranes: A Concentration Gradient-Driven Molecular Dynamics Study on Enhanced H2/CH4 Separation

This work presents a novel approach for accurately predicting the gas transport properties of covalent organic framework (COF) membranes using a nonequilibrium molecular dynamics (NEMD) methodology called concentration gradient-driven molecular dynamics (CGD-MD). We first simulated the flux of hydrogen (H2) and methane (CH4) across two distinct COF membranes, COF-300 and COF-320, for which experimental data are available in the literature. Our CGD-MD simulation results aligned closely with the experimentally measured gas permeability and selectivity of these COF membranes. Leveraging the same methodology, we discovered promising COF candidates for H2/CH4 separation, including NPN-1, NPN-2, NPN-3, TPE-COF-I, COF-303, DMTA-TPB2, 3D-Por-COF, COF-921, COF-IM AA, TfpBDH, and PCOF-2. We then compared our findings with simulations utilizing the well-known approach that merges grand canonical Monte Carlo (GCMC) and equilibrium molecular dynamics (EMD) to predict gas adsorption and diffusion parameters in COFs. Our results showed that when the pore sizes of COF membranes are below 10 Å, the choice of the method plays a significant role in determining the performance of the membranes. The GCMC+EMD approach suggested that COFs tend to exhibit CH4 selectivity when their pore limiting diameters are below 10 Å, whereas the CGD-MD results reveal a preference for H2. Density functional theory calculations indicate that H2 has a lower affinity for three promising COFs, NPN-1, NPN-2, and NPN-3, compared to CH4, which results in H2 remaining unbound, while CH4 occupies all of the adsorption sites, thereby facilitating the selective recovery of H2 at the end of the separation process. We proposed a relationship between adsorption time and diffusion time, highlighting the critical role of selecting an appropriate simulation method. This relationship underscores how adsorption and diffusion processes interplay, impacting material performance. Overall, these insights not only improve the accuracy of predictive models but also guide the development of more efficient COF-based membrane applications for future research and industrial applications.

Atomistic insights into the humidity response of nanocellulose: a molecular dynamics study

CONTEXT

TEMPO-oxidized cellulose nanofibers (TOCNFs) show significant potential for developing high-performance resistive humidity sensors due to their hydrophilicity and structural adaptability. However, the underlying atomic-scale mechanisms governing their humidity response remain poorly understood. Using molecular dynamics simulations, this study investigates how crystal facets, nanopore widths, and humidity levels influence the surface wettability, water permeability, and swelling of TOCNFs. Our findings reveal that the (1 1 - 0) crystal facet exhibits the highest hydrophilicity, while the (100) facet is the least hydrophilic. Narrower nanopores and more hydrophilic facets enhance capillary adsorption, significantly influencing water penetration depth. Additionally, nanopore swelling is highly dependent on the crystal facet, with the (1 1 - 0) facet showing the most pronounced expansion. These insights provide a foundation for designing high-performance TOCNF-based humidity sensors.

METHODS

The humidity response of TOCNFs is simulated using the large-scale atomic molecular massively parallel simulator (LAMMPS) package with the OPLS-AA force field to describe interatomic interactions. The open-source visualization tool OVITO is employed to visualize the atomic configurations.

Ozonated Monolayer Graphene for Extended Performance and Durability in Hydrogen Fuel Cell Electric Vehicles

In the landscape of proton exchange membrane fuel cells (PEMFCs), there is a strong need for durable, low hydrogen crossover membranes that retain high current output and proton conductivity during operation. This study presents the use of UV-Ozone induced defects in graphene to eliminate the proton conductivity penalty commonly associated with traditional crossover mitigation strategies. We report a defect engineered graphene material that demonstrates an increase in hydrogen/proton selectivity of 27%, a decrease in H2 crossover of 24%, with limited to no impact on current output. Furthermore, we demonstrate a membrane that is 39% more durable than state of the art GORE Select membranes and shows no loss in performance after a 100 h accelerated stress test (AST). This study illustrates the viability of 2D material membranes to sieve between H2 and H3O+ in industrial testing conditions and serve as highly scalable and durable fuel cell membranes that represent a significant upgrade over current state of the art membranes for hydrogen fuel cell vehicles and clean energy generation.

Active-Learning Assisted General Framework for Efficient Parameterization of Force-Fields

This work presents an efficient approach to optimizing force field parameters for sulfone molecules using a combination of genetic algorithms (GA) and Gaussian process regression (GPR). Sulfone-based electrolytes are of significant interest in energy storage applications, where accurate modeling of their structural and transport properties is essential. Traditional force field parametrization methods are often computationally expensive and require extensive manual intervention. By integrating GA and GPR, our active learning framework addresses these challenges by achieving optimized parameters in 12 iterations using only 300 data points, significantly outperforming previous attempts requiring thousands of iterations and parameters. We demonstrate the efficiency of our method through a comparison with state-of-the-art techniques, including Bayesian Optimization. The optimized GA-GPR force field was validated against experimental and reference data, including density, viscosity, diffusion coefficients, and surface tension. The results demonstrated excellent agreement between GA-GPR predictions and experimental values, outperforming the widely used OPLS force field. The GA-GPR model accurately captured both bulk and interfacial properties, effectively describing molecular mobility, caging effects, and interfacial arrangements. Furthermore, the transferability of the GA-GPR force field across different temperatures and sulfone structures underscores its robustness and versatility. Our study provides a reliable and transferable force field for sulfone molecules, significantly enhancing the accuracy and efficiency of molecular simulations. This work establishes a strong foundation for future machine learning-driven force field development, applicable to complex molecular systems.

Doping Efficiency of Poly(benzodifurandione) from First Principles

Poly(benzodifurandione) (PBFDO) has emerged as a promising n-type conductive polymer (n-CP) for organic electronic applications, particularly in thermoelectrics (TE), due to its high doping efficiency and environmental stability. Unlike most high-performance p-type polymers, high-efficiency n-CPs are limited, posing a bottleneck in the TE module performance. In this study, we use first-principles electronic structure calculations to investigate the thermodynamic conditions that favor n-doping in PBFDO, focusing on the role of the temperature, chain length, and doping concentration. We compute the change in Gibbs free energy, ΔG, upon doping and explore how it varies with temperature and polymer chain length. Our results show that doping becomes more thermodynamically favorable at lower temperatures and in longer chains, with a strong dependence of ΔG on the doping level emerging as chain length increases. Notably, PBFDO can achieve favorable doping levels across various chain lengths and temperatures, with specific doping thresholds identified for different molecular weights. These findings suggest that lower synthesis temperatures could lead to more heavily doped, higher-conductivity PBFDO, and that chain length significantly influences achievable doping efficiency. This work provides insights for optimizing PBFDO doping strategies to enhance its performance in TE applications, bridging a key gap in organic semiconductor research.

Insight into the thermo-responsive phase behavior of the P1 domain of α-synuclein using atomistic simulations

Biomolecular condensate formation driven by intrinsically disordered proteins (IDPs) is regulated by interactions between various domains of the proteins. Such condensates are implicated in various neurodegenerative diseases. The presynaptic intrinsically disordered protein, α-Syn is involved in the pathogenesis of Parkinson's disease. The central non-amyloid β-component (NAC) domain in the protein is considered to be a major driver of pathogenic aggregation, although recent studies have suggested that the P1 domain from the flanking N-terminal region can act as a 'master controller' for α-Syn function and aggregation. To gain molecular insight into the phase behavior of the P1 domain itself, we investigate how assemblies of P1 (residues 36-42) chains phase separate with varying temperatures using all-atom molecular dynamics simulations. The simulations reveal that P1 is able to phase separate above a lower critical solution temperature. Formation of a condensed phase is driven by exclusion of water molecules by the hydrophobic chains. P1 chain density in the condensate is determined by weak multi-chain interactions between the residues. Moreover, tyrosine (Y39) is involved in the formation of strongest contacts between residue pairs in the dense phase. These results provide a detailed picture of condensate formation by a key segment of the α-Syn molecule.

Predicting Ionic Conductivity of Imidazolium-Based Ionic Liquid Mixtures Using Quantum-Mechanically Derived Partial Charges in the Condensed Phase

A considerable effort has been expended over the years to tune the properties of ionic liquids (ILs) by designing cations, anions, and pendant groups on the ions. A simple and effective approach to altering the properties of ILs is formulating IL-IL mixtures. However, the measurements and properties of such mixtures lag considerably behind those of pure ILs. From a molecular simulation point of view, binary IL mixtures have been investigated using charge distributions of pure ILs, which implicitly assumes that the ions of different polarizability do not influence the local electronic environment due to changing concentrations. To understand this effect, molecular dynamics (MD) simulations were conducted for a series of IL-IL mixtures containing the common cation 1-ethyl-3-methylimidazolium [C2mim] varying the composition of various combinations of anions (tetrafluoroborate [BF4] and dicyanamide [DCA], [BF4] and bis(trifluoromethanesulfonyl)imide [NTF2], [BF4] and trifluoromethanesulfonate [TFO], and [TFO] and [NTF2]). The effect of changing the electronic environment was evaluated by deriving partial charges using density functional theory (DFT) calculations in the condensed phase. It was observed that the overall charge on the cation and anion was a function of the cation-anion pairings for pure ILs. Moreover, the cation charge was found to vary linearly with anionic concentrations. Improved agreement of predicted density and ionic conductivity with experimental values was found for binary IL mixtures with this approach, in comparison to that when a fixed charge model is employed.

Comparative Study of Isomeric TFSI and FPFSI Anions in Li-Ion Electrolytes Using Quantum Chemistry and Ab Initio Molecular Dynamics

Two isomeric anions used in Li-ion conducting electrolytes, TFSI and FPFSI, have been compared through quantum-chemical calculations. The FPFSI anion has more low-energy conformers, and its asymmetry leads to an increased number of possible structures of FPFSI-Li complexes. The preferred geometry of the anion-Li ion pair for both anions is the bidentate coordination of the cation through two oxygen atoms; the binding effect is slightly weaker for the FPFSI anion. Ab initio molecular dynamics simulations for salt solutions in tetraglyme have revealed that the amount of cation-to-solvent coordination increases in the LiFPFSI electrolytes. Analysis of the vibrational spectra of anions and ion pairs and the IR spectra of electrolytes obtained from the simulations have indicated that the S-F stretching vibration of the FPFSI anion above 600 cm-1 can be used in experimental conditions to monitor the FPFSI interactions with lithium cations.

Probing Structural Variants of Irregular DNA G-Tracts (N ≤ 2) Using MspA Nanopores

Guanine-rich DNA sequences with short G-tracts (n ≤ 2) are highly prevalent and abundant in the human genome, some of which are found to be associated with diseases (Maity et al. Nucleic Acids Res. 2020, 48 (6), 3315-3327). Unlike conventional G-quadruplexes with three or more folded layers, these sequences with G2 tracts featuring two bilayered blocks remain largely unexplored. Here, we employed nanopore experiments and all-atom molecular dynamics simulations to investigate the unwinding strengths and dynamics of these bilayered blocks. Our results demonstrated that in an electric field, the tumor-targeting element AS1411, along with its derivatives AT11 and Z-G4, strongly interacted with the M2-MspA nanopore, resulting in at least two distinct populations (types I and II events) characterized by different current blockage fractions and dwell times. Despite AS1411 being well characterized with up to eight secondary structures by nuclear magnetic resonance spectroscopy, our nanopore experiments revealed only two populations. This could be reasonably explained by (i) reversible docking with high rigidity and (ii) strand separation and translocation. Notably, a new event type (type III) for Z-G4 suggested reduced susceptibility in the last layer, contributing to its increased rigidity. Furthermore, voltage-dependent dynamics revealed that Z-G4 exhibited extended dwell times for docking and partial unwinding, unlike AT11. Our in-solution nanopore experiments and MD simulation results would benefit toward understanding the folding principles of complicated structural variants by sequences consisting of multiple short G-tracts, paving the way for the rapid identification of similar-sequence nucleic acid aptamers in molecular diagnostics and targeted therapies.

Optimizing and Regulating Electric-Induced Breakup of Salt-Containing Droplets through Magnetic Field Coupling: Insights from Molecular Dynamics Simulations

Droplet electrodispersion is a fundamental phenomenon in various fields, such as electric demulsification, electrospray, and microfluidic manipulation. Electric-magnetic coupling technology, as an emerging noncontact method, shows substantial potential in modulating droplet electrohydrodynamics, yet the influence characteristics and mechanisms of coupled magnetic fields on droplet electrodispersion remain poorly understood. To address this gap, we conducted a detailed molecular dynamics simulation comparing the breakup dynamics of salt-containing droplets under a single electric field versus an electric-magnetic coupling field. Our results demonstrate that salty droplets in the electric-magnetic coupling field exhibit longer breakup response times and greater stretching deformation. This behavior is attributed to changes in ion migration speed and enrichment regions due to additional Lorentz forces. Furthermore, this effect of coupling field is observed only for ion numbers Nion > 0, with a marked attenuation at higher concentrations (Nion = 200), which is related to the hydration effect enhanced by magnetic field. When the electric capillary number Ca ranges from 0.88 to 3.91, the critical value triggering a shift in the breakup mode is enhanced in the coupling field. However, this effect diminishes as Ca approaches 8.8, at which point the coupled field no longer inhibits breakup. Additionally, as the dimensionless electric field frequency f* increases from 0.21 to 4.19, the ion migration trajectories become shorter and less able to accumulate at the interface, thereby limiting the effectiveness of the coupling field. Our study advances the fundamental understanding of salt-containing droplet breakup dynamics under an electric-magnetic coupling field and provides novel insights for controlling and suppressing electrodispersion in related technologies.

Assessing the Effect of Deep Eutectic Solvents on α-Chymotrypsin Thermal Stability and Activity

Optimizing the liquid reaction phase holds significant potential for enhancing the efficiency of biocatalytic processes since it determines reaction equilibrium and kinetics. This study investigates the influence of the addition of deep eutectic solvents on the stability and activity of α-chymotrypsin, a proteolytic enzyme with industrial relevance. Deep eutectic solvents, composed of choline chloride or betaine mixed with glycerol or sorbitol, were added in the reaction phase at various concentrations. Experimental techniques, including kinetic and fluorometry, were employed to assess the α-chymotrypsin activity, thermal stability, and unfolding reversibility. Atomistic molecular dynamics simulations were also conducted to assess the interactions and provide molecular-level insights between α-chymotrypsin and the solvent. The results showed that among all studied mixtures, adding choline chloride + sorbitol improved thermal stability up to 18 °C and reaction kinetic efficiency up to two-fold upon adding choline chloride + glycerol. Notably, the choline chloride + sorbitol system exhibited the most substantial stabilization effect, attributed to the surface preferential accumulation of sorbitol, as corroborated by the computational analyses. This work highlights the potential of tailoring liquid reaction phase of α-chymotrypsin catalyzed reaction using neoteric solvents such as deep eutectic solvents to enhance α-chymotrypsin performance and stability in industrial applications.

Microextraction of steroidal hormones from urine samples using natural deep eutectic solvents: insights into chemical interactions using molecular dynamics simulations

Natural deep eutectic solvents (NADES) are gaining significant attention in analytical chemistry due to attractive physico-chemical properties associated with sustainable aspects. They have been successfully evaluated in different fields, and applications in sample preparation have increased in the last years. However, there is a limited knowledge related to chemical interactions and mechanism of intermolecular action with specific analytes. In this regard, for the first time, this study exploited a computational investigation using molecular dynamics (MD) predictions combined with experimental data for the extraction/determination of steroidal hormones (estriol, β-estradiol, and estrone) in urine samples using NADES. The ultrasound-assisted liquid-liquid microextraction (UALLME) approach followed by high-performance liquid chromatography with diode array detection (HPLC-DAD) was employed using menthol:decanoic acid as extraction solvent. Experimental parameters were optimized through multivariate strategies, with the best conditions consisting of 3 min of extraction, 150 μL of NADES, and 3 mL of sample (tenfold diluted). According to molecular dynamics predictions confirmed by experimental data, a molar ratio that permitted the highest efficiency consisted of menthol:decanoic acid 2:1 v/v. Importantly, computational simulations revealed that van der Waals interactions were the most significant contributor to the interaction energy of analytes-NADES. Using the optimized conditions, limits of detection (LOD) ranged from 3 and 8 μg L-1, and precision (n = 3) varied from 8 to 19%. Intraday precision was evaluated at 3 concentrations: low (LOQ according to each analyte), medium (100 μg L-1), and high (750 μg L-1). Accuracy was successfully assessed through recoveries that ranged from 82 to 98%. In this case, molecular dynamics simulations proved to be an important tool for in-depth investigations of interaction mechanisms of DES with different analytes.

A molecular dynamics investigation into manipulating graphene flake spacing for increased selectivity towards short chain PFAS capture

Per- and polyfluoroalkyl substances (PFAS) are environmentally persistent contaminants that are often referred to as "Forever Chemicals". They are used in industrial and household products; however, they are resistant to degradation. Thus, PFAS contamination has become a wide-spread issue. In 2024, the EPA announced two rules regarding PFAS limiting the level of five PFAS in drinking water, and classifying PFOA and PFOS as hazardous chemicals. Adsorbent materials will be crucial to address up-concentration and removal of these species from our waterways. In our previous work, we examined five functionalized graphene flakes for PFAS capture and found that adsorption was dependent on flake clustering and functional group. Graphene oxide showed promise because the flakes generated pseudo-porous pockets. Herein, we report a new modeled material obtained by adding hydrophobic alkyl chains to graphene oxide in order to determine the impact the chains have on flake clustering and PFAS adsorption. We found that adding alkyl chains increases the propensity of capture for PFBA, a small chain PFAS that is notoriously difficult to capture. Radial distribution functions showed a large preference for PFBA and PFOA over PFOS adsorption, which is the opposite of what is typically seen in the literature for most other sorbents.

Design and theoretical calculation of chitosan derivatives: Amphiphilic chitosan micelles loaded with Chinese fir essential oil

The unique structure of chitosan-based micelles can be loaded with essential oil, so it is significant to study the modification of chitosan and the interactions between chitosan and essential oil, while molecular dynamics (MD) simulation and density functional theory (DFT) provide a solution. In this study, three kinds of amphiphilic chitosan derivatives (CSDs) were constructed by grafting of different hydrophilic and hydrophobic groups. Amphiphilic chitosan micelles loaded with Chinese fir essential oil (CFEO) were prepared by self-assembly. The aggregation behavior of CFEO component (cedrol and α-cedrene) in the solutions of chitosan and three CSDs were simulated using MD, and the mean square displacement was calculated. DFT analyzed the mechanism for regulating the molecular properties of CSDs by different modification methods, and explored the intensity and type of interaction force between cedrol/α-cedrene and three CSDs. The results show that cedrol and α-cedrene were more easily aggregated near the modified CSDs, with CS-g-PLA showing the strongest trapping ability. The grafting of polylactic acid on chitosan resulted in a significant decrease in HOMO-LUMO energy gap and an increase in reactivity activity. Widely distributed hydrogen bonding and van der Waals forces were confirmed to be the key to enhanced loading capacity.

Barrierless reactions of C2 Criegee intermediates with H2SO4 and their implication to oligomers and new particle formation

The formation of oligomeric hydrogen peroxide triggered by Criegee intermediate maybe contributes significantly to the formation and growth of secondary organic aerosol (SOA). However, to date, the reactivity of C2 Criegee intermediates (CH3CHOO) in areas contaminated with acidic gas remains poorly understood. Herein, high-level quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations are used to explore the reaction of CH3CHOO and H2SO4 both in the gas phase and at the air-water interface. In the gas phase, the addition reaction of CH3CHOO with H2SO4 to generate CH3HC(OOH)OSO3H (HPES) is near-barrierless, regardless of the presence of water molecules. BOMD simulations show that the reaction at the air-water interface is even faster than that in the gas phase. Further calculations reveal that the HPES has a tendency to aggregate with sulfuric acids, ammonias, and water molecules to form stable clusters, meanwhile the oligomerization reaction of CH3CHOO with HPES in the gas phase is both thermochemically and kinetically favored. Also, it is noted that the interfacial HPES- ion can attract H2SO4, NH3, (COOH)2 and HNO3 for particle formation from the gas phase to the water surface. Thus, the results of this work not only elucidate the high atmospheric reactivity of C2 Criegee intermediates in polluted regions, but also deepen our understanding of the formation process of atmospheric SOA induced by Criegee intermediates.

In situ valence-transited arsenic nanosheets for multi-modal therapy of colorectal cancer

Late-stage and advanced colorectal cancer (CRC) often prove to be resistant to current treatment regimens, due to the evolving tumor microenvironment. Chemotherapy-dominated multi-modal therapeutic strategies based on the specific CRC microenvironment open a new horizon for eradicating colorectal tumors. Here, in situ valence-transited arsenic nanosheets are developed as a multi-modal therapeutic platform by responding to the H2S-enriched CRC microenvironment. Carrier-free pegylated nanosheets of pentavalent arsenic (AsV), aminooxyacetic acid (AOAA), and copper ion (Cu2+) are innovatively self-assembled via coordination with high loading content and good stability. AsV in pegylated arsenic nanosheets (CAA-PEG NSs) is rapidly released and reduced to trivalent arsenic (AsIII) to exert its chemotherapy in the local tumor. Furthermore, the immunosuppressive microenvironment is thoroughly remodeled via H2S depletion of AsV to AsIII conversion and impairment of H2S production by AOAA. Additionally, the in situ produced ultrasmall CuS nanoparticles exhibit photothermal activity against CRC under the guidance of photoacoustic imaging. This multi-modal therapeutic strategy, dominated by chemotherapy, completely inhibits CRC progression and prevents its relapse.

Driving Forces of RNA Condensation Revealed through Coarse-Grained Modeling with Explicit Mg2

RNAs are major drivers of phase separation in the formation of biomolecular condensates, and can undergo protein-free phase separation in the presence of divalent ions or crowding agents. Much remains to be understood regarding how the complex interplay of base stacking, base pairing, electrostatics, ion interactions, and particularly structural propensities governs RNA phase behavior. Here we develop an intermediate resolution model for condensates of RNAs (iConRNA) that can capture key local and long-range structure features of dynamic RNAs and simulate their spontaneous phase transitions with Mg2+. Representing each nucleotide using 6-7 beads, iConRNA accurately captures base stacking and pairing and includes explicit Mg2+. The model does not only reproduce major conformational properties of poly(rA) and poly(rU), but also correctly folds small structured RNAs and predicts their melting temperatures. With an effective model of explicit Mg2+, iConRNA successfully recapitulates experimentally observed lower critical solution temperature phase separation of poly(rA) and triplet repeats, and critically, the nontrivial dependence of phase transitions on RNA sequence, length, concentration, and Mg2+ level. Further mechanistic analysis reveals a key role of RNA folding in modulating phase separation as well as its temperature and ion dependence, besides other driving forces such as Mg2+-phosphate interactions, base stacking, and base pairing. These studies also support iConRNA as a powerful tool for direct simulation of RNA-driven phase transitions, enabling molecular studies of how RNA conformational dynamics and its response to complex condensate environment control the phase behavior and condensate material properties.

SIGNIFICANCE STATEMENT

Dynamic RNAs and proteins are major drivers of biomolecular phase separation that has been recently discovered to underlie numerous biological processes and be involved in many human diseases. Molecular simulation has an indispensable role to play in dissecting the driving forces and regulation of biomolecular phase separation. The current work describes a high-resolution coarse-grained RNA model that is capable of describing the structure dynamics and complex sequence, concentration, temperature and ion dependent phase transitions of flexible RNAs. The study further reveals a central role of RNA folding in coordinating Mg2+-phosphate interactions, base stacking, and base pairing to drive phase separation, paving the road for studies of RNA-mediated phase separation in relevant biological contexts.

Proton transport in liquid phosphoric acid: the role of nuclear quantum effects revealed by neural network potential

Pure phosphoric acid exhibits high proton conductivity and is widely used in modern industry. However, its proton transport mechanism remains less understood compared to that of water, which presents a significant challenge for advancing technologies like phosphoric acid fuel cells. In this study, we utilize machine learning potentials and molecular dynamics (MD) simulations to investigate the proton diffusion mechanisms in liquid phosphoric acid systems. The neural network potentials we developed demonstrate quantum chemical accuracy and stability across a range of temperatures. Our simulations reveal continuous proton hopping between phosphoric acid anions. Moreover, the radial distribution functions and diffusion coefficients obtained from ring polymer MD-a variant of path-integral MD-exhibit improved alignment with experimental values compared to classical MD results, as ring polymer MD inherently accounts for nuclear quantum effects on proton behavior. Additionally, we employed neural networks combined with the charge equilibration method to predict the charge distribution in liquid phosphoric acid, examining the proton transport mechanism through vibrational spectra analysis.

First-Principles Molecular Dynamics Study of M3AlF6 (M= Li/Na/K) Molten Salts

The microscopic properties and Raman spectra of molten, Li3AlF6, Na3AlF6, and K3AlF6 systems were investigated using first-principles molecular dynamics combined with the Voronoi tessellation method. The results have indicated that Li+, Na+, and K+ exist in a free state, whereas Al3+ and F- form ion clusters ([AlFx]3-x) with evidence of free F- anions. The nature of the alkali metal cation does not significantly affect the average Al-F bond length (1.775 Å). The coordination numbers of Al3+ and F- are 5.22, 5.21, and 4.95 in Li3AlF6, Na3AlF6 and K3AlF6, respectively, indicating a lower content of [AlF6]3- and [AlF5]2- in K3AlF6. The self-diffusion coefficients decrease in the order Li+ > Na+ > K+, and the trend is Na3AlF6 > Li3AlF6 > K3AlF6 for Al3+ and F-. The alkali metal cation has little effect on changes in the atomic charge and spin population of Al3+. Single bonds form between Al3+ and F- and exhibit uneven bond order. The upper limits of the HOMO-LUMO gaps for Li3AlF6, Na3AlF6 and K3AlF6 are, 4.82, 2.10, and 3.51 eV, respectively, suggesting higher conductivity of Na3AlF6 relative to Li3AlF6 and K3AlF6 under superheating conditions (40 K above the liquidus temperature).

Study on the Correlation between the Microstructure and Physical Properties of ZnCl2 Aqueous Solution

This article focuses on the study of the correlation between the microstructure and physical properties of aqueous zinc chloride solutions. Macroscopic physical properties of zinc chloride aqueous solution were determined, and its microstructure was analyzed by Raman spectroscopy, molecular dynamics simulations, and density functional theory (DFT) calculations. The experimental results of macroscopic physical properties show that with the increase of ZnCl2 concentration, the conductivity of aqueous solution first increases and then decreases, and the viscosity gradually increases. Raman spectrum analysis shows that with the increase of solute concentration, double donor-acceptor (DDAA)-type hydrogen bonds are continuously destroyed and the proportion of DA-type hydrogen bonds increases. The results of molecular dynamics simulations show that with the increase of solution concentration, contact ion pairs of Zn2+-Cl- (2.28 Å) gradually appear in ZnCl2 aqueous solution, and the diffusion coefficients of Zn2+ and Cl- gradually decrease. The correlation between the Raman shift and the hydration cluster model of Zn2+ was calculated theoretically by the DFT method. With the increase of the concentration, the cluster structure of Zn2+ in aqueous solution gradually changed from [Zn(H2O)6]2+ to [ZnCl2(H2O)4]. Based on experimental data and molecular dynamics simulation results, it can be concluded that the decrease in conductivity is related to the formation of Zn2+-Cl- contact ion pairs in the solution. The interactions between Zn2+, Cl-, or contact ion pairs and water molecules, namely, hydrated ions or hydrated contact ion pairs, are the microscopic essential reason for the increase in viscosity.

Structure factor line shape model gives approximate nanoscale size of polar aggregates in pyrrolidinium-based ionic liquids

Room temperature ionic liquids (RTILs) are interesting due to their myriad uses in fields such as catalysis and electrochemistry. Their properties are intimately related to their structures, yet structural understanding is difficult to achieve. This work presents a derivation of an approximate expression for the radial distribution function, g(r). The derivation assumes a Lorentzian line shape for total structure factors, S(Q). The derived form for g(r) is used to present new equations for maxima and minima in g(r) and to define a half-length, the value of r where g(r) decays to one-half its maximum value. A detailed test of the model is presented using experimentally measured and calculated S(Q) for N-methyl-N-propylpyrrolidinium bis(trifluoromethylsulfonyl)imide (C1C3pyrrTFSI). Then, the model is extended to the series of RTILs with anions of increasing size, C1C3pyrrX (X- = Cl-, Br-, BF4-, PF6-, OTf-, TFSI-). The model predicts maxima and minima in the entire series within 4.2% of those calculated directly from molecular dynamics simulations. This reinforces our previous conclusion that distances within "polar scattering domains" responsible for the charge alternation peak in S(Q) are quantitatively related to inter-ionic distances within polar aggregates in these RTILs. The half-length is found to increase approximately linearly as anion size increases. We argue that the half-length is a measure of polar aggregate size in these RTILs.

Molecular Shells and Range of Interactions in Ionic Liquids as a Function of Temperature

Room-temperature ionic liquids (RTILs) represent a versatile class of chemical systems composed entirely of oppositely charged species whose bulk properties can be fine-tuned by adjusting molecular structures and, consequently, intermolecular interactions. Understanding the intricate dynamics between ionic species can aid in the rational design of RTILs for specific applications in a range of fields, including catalysis and electrochemistry. Here, we investigate the temperature dependence of intermolecular interactions through magnetization transfer by means of 1H-19F heteronuclear Overhauser effect spectroscopy (HOESY) for two ionic liquids, namely, [BMIM][BF4] and [BMIM][PF6]. We find that the cross-relaxation rates vary significantly over a rather small temperature range, even changing sign. Molecular dynamics (MD) simulations on neat RTIL systems replicate this behavior well and further show that the dynamic properties rather than coordination changes of RTILs account for the observed temperature behavior. Furthermore, the investigation of different coordination shells highlights the change of interaction range with temperature even to the point where inner and outer coordination shells could be in distinct motional regimes with cross-relaxation rates of opposite sign. Since temperature changes lead primarily to dynamic changes rather than structural ones, these findings underscore the versatility and high thermal stability of ionic liquids.

Unveiling the Mechanism of Action of Palmitic Acid, a Human Topoisomerase 1B Inhibitor from the Antarctic Sponge Artemisina plumosa

Cancer remains a leading cause of death worldwide, highlighting the urgent need for novel and more effective treatments. Natural products, with their structural diversity, represent a valuable source for the discovery of anticancer compounds. In this study, we screened 750 Antarctic extracts to identify potential inhibitors of human topoisomerase 1 (hTOP1), a key enzyme in DNA replication and repair, and a target of cancer therapies. Bioassay-guided fractionation led to the identification of palmitic acid (PA) as the active compound from the Antarctic sponge Artemisina plumosa, selectively inhibiting hTOP1. Our results demonstrate that PA irreversibly blocks hTOP1-mediated DNA relaxation and specifically inhibits the DNA religation step of the enzyme's catalytic cycle. Unlike other fatty acids, PA exhibited unique specificity, which we confirmed through comparisons with linoleic acid. Molecular dynamics simulations and binding assays further suggest that PA interacts with hTOP1-DNA complexes, enhancing the inhibitory effect in the presence of camptothecin (CPT). These findings identify PA as a hTOP1 inhibitor with potential therapeutic implications, offering a distinct mechanism of action that could complement existing cancer therapies.

Chemical and physical properties of orthoconic liquid crystals: 2H NMR spectroscopy and molecular dynamics simulations

In the field of chiral smectic liquid crystals, orthoconic antiferroelectric liquid crystals (OAFLCs) have attracted the interest of the scientific community due to the very high tilt angle, close to 45°, and the consequent optical properties. In the present study, the first 2H NMR investigation is reported on two samples, namely 3F5HPhF9 and 3F7HPhF8, showing the phase sequence isotropic-SmC*-SmCA* and the phase sequence isotropic-SmA-SmC*-SmCA*, respectively, when cooling from the isotropic to the crystalline phases. To this aim, the liquid crystals were doped with a small amount of deuterated probe biphenyl-4,4'-diol-d4. The trend of 2H NMR spectra versus temperature indicates the presence of very high values of the tilt of the deuterated probe in the antiferroelectric phase for both samples. The trend of the local order parameters and that of the tilt angle were compared with the results obtained for the same samples by means of different experimental techniques, namely X-ray diffraction and electrooptical measurements. Moreover, a computational study was performed on the sample labelled 3F5HPhF9 using fully atomistic classical molecular dynamics simulation of the orthoconic phase. The results obtained from the MD simulations show a very large molecular tilt of the molecules (about 42°) when packed in layers and this value is in very good agreement with experimental results. The present research aims to give additional clues about the molecular origin of the very peculiar high tilt angle of orthoconic liquid crystals in the antiferroelectric phase.

Identifying High Ionic Conductivity Compositions of Ionic Liquid Electrolytes Using Features of the Solvation Environment

Binary mixtures of ionic liquids with molecular solvents are gaining interest in electrochemical applications due to the improvement in their performance over neat ionic liquids. Dilution with suitable molecular solvents can reduce the viscosity and facilitate faster diffusion of ions, thereby yielding substantially higher ionic conductivity than that for a pure ionic liquid. Although viscosity and diffusion coefficients typically behave as monotonic functions of concentration, ionic conductivity often passes through a peak value at an optimum molar ratio of the molecular solvent to the ionic liquid. The ionic conductivity maximum is generally explained in terms of a balance between the ease of charge transport and the concentration of the charge carriers. In this work, fluctuation in the local environment surrounding an ion is invoked as a plausible explanation for the ionic conductivity mechanism with a binary mixture of 1-ethyl-3-methylimidazolium tetrafluoroborate and ethylene glycol as an example. The magnitude of the dynamism in the local environment is captured by measuring the spatial and temporal features of the solvation environment. Standard deviation in the number of ions in the solvation environment serves as a spatial feature, while the cage correlation lifetimes for oppositely charged ions within the first solvation shell serve as a temporal feature. Large standard deviations in the cluster ion population and short cage correlation lifetimes are indicators of highly dynamic ionic environment at the molecular level and consequently yield high ionic conductivity. Such compositions were found to be in good agreement with the optimum ionic liquid mole fractions obtained through experimental measurement. Short cage correlation lifetimes enable the identification of optimum mixture compositions using simulation trajectories significantly shorter than those required to implement the Nernst-Einstein or Einstein formalisms for calculating ionic conductivity. We validated the applicability of this approach across force fields and in six ionic liquid-molecular solvent electrolytes formed with combination of cations, anions, and solvents. We offer a computationally efficient approach of screening ionic liquid-molecular solvent binary mixture electrolytes to identify molar ratios that yield high ionic conductivity.

An Ultra-Stable, High-Energy and Wide-Temperature-Range Aqueous Alkaline Sodium-Ion Battery with the Microporous C4N/rGO Anode

Common anode materials in aqueous alkaline electrolytes, such as cadmium, metal hydrides and zinc, usually suffer from remarkable biotoxicity, high cost, and serious side reactions. To overcome these problems, we develop a conjugated porous polymer (CPP) in-situ grown on reduced graphene oxide (rGO) and Ketjen black (KB), noted as C4N/rGO and C4N/KB respectively, as the alternative anodes. The results show that C4N/rGO electrode delivers a low redox potential (-0.905 V vs. Ag/AgCl), high specific capacity (268.8 mAh g-1 at 0.2 A g-1), ultra-stable and fast sodium ion storage behavior (216 mAh g-1 at 20 A g-1) in 2 M NaOH electrolyte. The assembled C4N/rGO//Ni(OH)2 full battery can cycle stably more than 38,000 cycles. Furthermore, by adding a small amount of antifreeze additive dimethyl sulfoxide (DMSO) to adjust the hydrogen bonding network, the low-temperature performance of the electrolyte (0.1 DMSO/2 M NaOH) is significantly improved while hydrogen evolution is inhibited. Consequently, the C4N/rGO//Ni(OH)2 full cell exhibits an energy density of 147.3 Wh Kg-1 and ultra-high cycling stability over a wide temperature range from -70 to 45 °C. This work provides an ultra-stable high-capacity CPP-based anode and antifreeze electrolyte for aqueous alkaline batteries and will facilitate their practical applications under extreme conditions.