Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

Cubosome lipid nanocarriers for delivery of ultra-short antimicrobial peptides

HYPOTHESIS

Although antimicrobial peptides (AMPs) are a promising class of new antibiotics, their inherent susceptibility to degradation requires nanocarrier-mediated delivery. While cubosome nanocarriers have been extensively studied for delivery of AMPs, we do not currently understand why cubosome encapsulation improves antimicrobial efficacy for some compounds but not others. This study therefore aims to investigate the link between the mechanism of action and permeation efficiency of the peptides, their encapsulation efficacy, and the antimicrobial activity of these systems.

EXPERIMENTS

Encapsulation and delivery of Indolicidin, and its ultra-short derivative, Priscilicidin, were investigated using SAXS, cryo-TEM and circular dichroism. Molecular dynamics simulations were used to understand the loading of these peptides within cubosomes. The antimicrobial efficacy was assessed against gram-negative (E. coli) and gram-positive (MRSA) bacteria.

FINDINGS

A high ionic strength solution was required to facilitate high loading of the cationic AMPs, with bilayer encapsulation driven by tryptophan and Fmoc moieties. Cubosome encapsulation did not improve the antimicrobial efficacy of the AMPs consistent with their high permeation, as explained by a recent 'diffusion to capture model'. This suggests that cubosome encapsulation may not be an effective strategy for all antimicrobial compounds, paving the way for improved selection of nanocarriers for AMPs, and other antimicrobial compounds.

CYCLOPEp Builder: Facilitating cyclic peptide and nanotube research through a user-friendly web platform

The study of cyclic peptides (CPs) and self-assembling cyclic peptide nanotubes (SCPNs) is pivotal in advancing applications in diverse fields such as biomedicine, nanoelectronics, and catalysis. Recognizing the limitations in the experimental study of these molecules, this article introduces CYCLOPEp Builder, a comprehensive web-based application designed to facilitate the design, simulation, and visualization of CPs and SCPNs. The tool is engineered to generate molecular topologies, essential for conducting Molecular Dynamics simulations that span All-Atom to Coarse-Grain resolutions. CYCLOPEp Builder's user-friendly interface simplifies the complex process of molecular modeling, providing researchers with the ability to readily construct CPs and SCPNs. The platform is versatile, equipped with various force fields, and capable of producing structures ranging from individual CPs to complex SCPNs with different sequences, offering parallel and antiparallel orientations among them. By enhancing the capacity for detailed visualization of molecular assemblies, CYCLOPEp Builder improves the understanding of CP and SCPN molecular interactions. This tool is a step forward in democratizing access to sophisticated simulations, offering an invaluable resource to the scientific community engaged in the exploration of supramolecular structures. CYCLOPEp is accessible at http://cyclopep.com/.

A shared mechanism for TNP-ATP recognition by members of the P2X receptor family

P2X receptors (P2X1-7) are non-selective cation channels involved in many physiological activities such as synaptic transmission, immunological modulation, and cardiovascular function. These receptors share a conserved mechanism to sense extracellular ATP. TNP-ATP is an ATP derivative acting as a nonselective competitive P2X antagonist. Understanding how it occupies the orthosteric site in the absence of agonism may help reveal the key allostery during P2X gating. However, TNP-ATP/P2X complexes (TNP-ATP/human P2X3 (hP2X3) and TNP-ATP/chicken P2X7 (ckP2X7)) with distinct conformations and different mechanisms of action have been proposed. Whether these represent species and subtype variations or experimental differences remains unclear. Here, we show that a common mechanism of TNP-ATP recognition exists for the P2X family members by combining enhanced conformation sampling, engineered disulfide bond analysis, and covalent occupancy. In this model, the polar triphosphate moiety of TNP-ATP interacts with the orthosteric site, while its TNP-moiety is deeply embedded in the head and dorsal fin (DF) interface, creating a restrictive allostery in these two domains that results in a partly enlarged yet ion-impermeable pore. Similar results were obtained from multiple P2X subtypes of different species, including ckP2X7, hP2X3, rat P2X2 (rP2X2), and human P2X1 (hP2X1). Thus, TNP-ATP uses a common mechanism for P2X recognition and modulation by restricting the movements of the head and DF domains which are essential for P2X activation. This knowledge is applicable to the development of new P2X inhibitors.

Randomly methylated β-cyclodextrin improves water - solubility, cellular protection and mucosa permeability of idebenone

Neurodegenerative diseases such as Alzheimer's are very common today. Idebenone (IDE) is a potent antioxidant with good potential for restoring cerebral efficiency in cases of these and other medical conditions, but a serious drawback for the clinical use of IDE in neurological disorders lies in its scarce water solubility, which greatly inhibits its bioavailability. In this work, we prepared the inclusion complex of IDE with randomly methylated β-cyclodextrin (RAMEB), resulting in improved water solubility of the included drug; then its in vitro biological activity and ex vivo permeability was evalutated. The solid complex was characterized through FT-IR spectroscopy, Thermogravimetric analysis (TGA) and Differential Scanning Calorimetry (DSC). A 78-fold improvement of the solubility of IDE in water resulted, together with a strong 1:1 host-guest interaction (association constant of 12630 M-1), and dissolution of the complex within 15 min, all evidenced during the in-solution studies. Biological in vitro studies were then performed on differentiated human neuroblastoma cells (SH-SY5Y) subjected to oxidative stress. Pretreatment with IDE/RAMEB positively affected cell viability, promoted the nuclear translocation of Nrf2, and increased the levels of GSH as well as those of the endogenous antioxidant enzymes Mn-SOD and HO-1. Lastly, the complexation significantly improved the permeation of IDE through isolated rat nasal mucosa.

Advancing plant cell wall modelling: Atomistic insights into cellulose, disordered cellulose, and hemicelluloses - A review

The complexity of plant cell walls on different hierarchical levels still impedes the detailed understanding of biosynthetic pathways, interferes with processing in industry and finally limits applicability of cellulose materials. While there exist many challenges to readily accessing these hierarchies at (sub-) angström resolution, the development of advanced computational methods has the potential to unravel important questions in this field. Here, we summarize the contributions of molecular dynamics simulations in advancing the understanding of the physico-chemical properties of natural fibres. We aim to present a comprehensive view of the advancements and insights gained from molecular dynamics simulations in the field of carbohydrate polymers research. The review holds immense value as a vital reference for researchers seeking to undertake atomistic simulations of plant cell wall constituents. Its significance extends beyond the realm of molecular modeling and chemistry, as it offers a pathway to develop a more profound comprehension of plant cell wall chemistry, interactions, and behavior. By delving into these fundamental aspects, the review provides invaluable insights into future perspectives for exploration. Researchers within the molecular modeling and carbohydrates community can greatly benefit from this resource, enabling them to make significant strides in unraveling the intricacies of plant cell wall dynamics.

Molecular Dynamics Simulation Study on the Structural and Thermodynamic Analysis of Oxidized and Unoxidized Forms of Polyaniline

The conducting polymer polyaniline (PANI) has shown significant interest for the development of electrified membranes (EMs) with superior antifouling characteristics. However, the blending and doping of PANI with other polymers and nanomaterials highly influence the properties of the membrane surface. PANI exists in two forms: oxidized, known as emeraldine salt (ES), and unoxidized, referred to as emeraldine base (EB). Therefore, understanding the different forms of PANI and the variations between the oxidized and unoxidized forms along the length of the polymer chain is intriguing. In this paper, we present the design of a novel copolymer consisting of EB and ES monomers with varying charge densities and different segmental arrangements. We present various intra- and intermolecular structural properties of the PANI chains using all-atom molecular dynamics (MD) simulations. Herein, we present a detailed conformational free energy analysis to understand the conformational transitions of the PANI chains. Our results show increased radius of gyration (Rg) values with increased charge density. Furthermore, we also present the H-bonding, free energy analysis, reduced density gradient (RDG), and solvent-accessible surface area (SASA) values for the observed conformational transitions of PANI. Therefore, these observations are crucial in understanding the complex behavior of chains for designing target-specific polymeric materials.

Origin of Pressure Resistance in Deep-Sea Lactate Dehydrogenase

High hydrostatic pressure has a dramatic effect on biochemical systems, as exposure to high pressure can result in structural perturbations ranging from dissociation of protein complexes to complete denaturation. The deep ocean presents an interesting paradox since it is teeming with life despite the high-pressure environment. This is due to evolutionary adaptations in deep-sea organisms, such as amino acid substitutions in their proteins, which aid in resisting the denaturing effects of pressure. However, the physicochemical mechanism by which these substitutions can induce pressure resistance remains unknown. Here, we use molecular dynamics simulations to study pressure-adapted lactate dehydrogenase from the deep-sea abyssal grenadier (Coryphaenoides armatus), in comparison with that of the shallow-water Atlantic cod (Gadus morhua). We examined structural, thermodynamic and volumetric contributions to pressure resistance, and report that the amino acid substitutions result in a decrease in volume of the deep-sea protein accompanied by a decrease in thermodynamic stability of the native protein. Our simulations at high pressure also suggest that differences in compressibility may be important for understanding pressure resistance in deep-sea proteins.

Electric-field-induced structure and dynamics of an ethanol-water mixture in hydrophobic-hydrophilic nanochannels

Understanding the behavior of confined fluid mixtures under external electric fields is essential for advancing scientific knowledge and improving a wide range of technological applications, from energy systems to biological processes. An electric field has been widely used to investigate the phase transition of water and modification of interfacial water at the nanoscale. However, the structure and dynamics of the interfacial layer in complex confined fluid mixtures, such as ethanol-water mixtures, remain unexplored under the influence of an electric field. In this study, we explore the structural and dynamic behavior of binary ethanol-water mixtures confined within slit-like hydrophilic (mica) and hydrophobic (graphene) nanochannels under an external electric field using classical molecular dynamics (MD) simulations. We find two distinct interfacial water layers near the hydrophilic mica surface, and a more pronounced sharp peak appears near the hydrophobic graphene sheet with increasing electric field. The density maxima of the -OH and -CH3 groups of ethanol shift towards and away from the graphene surface with an increasing electric field. Our simulations reveal that the electric field strongly impacts the inter and intralayer hydrogen bonding among water and ethanol molecules. The diffusion coefficient of water slightly increases with the electric field and then reduces with an electric field for a lower concentration of ethanol. This finding reveals that the electric field influences the desorption of interfacial water near the hydrophilic mica surface, which can be an implication for diverse technological applications like modifying surface wettability.

Molecular Simulations of Thermal Transport across Iron Oxide-Hydrocarbon Interfaces

The rational design of dielectric fluids for immersion cooling of batteries requires a molecular-level understanding of the heat flow across the battery casing/dielectric fluid interface. Here, we use nonequilibrium molecular dynamics (NEMD) simulations to quantify the interfacial thermal resistance (ITR) between hematite and poly-α-olefin (PAO), which are representative of the outer surface of the steel battery casing and a synthetic hydrocarbon dielectric fluid, respectively. After identifying the most suitable force fields to model the thermal properties of the individual components, we then compared different solid-liquid interaction potentials for the calculation of the ITR. These potentials resulted in a wide range of ITR values (4-21 K m2 GW-1), with stronger solid-liquid interactions leading to lower ITR. The increase in ITR is correlated with an increase in density of the fluid layer closest to the surface. Since the ITR has not been experimentally measured for the hematite/PAO interface, we validate the solid-liquid interaction potential using the work of adhesion calculated using the dry-surface method. The work of adhesion calculations from the simulations were compared to those derived from experimental contact angle measurements for PAO on steel. We find that all of the solid-liquid potentials overestimate the experimental work of adhesion. The experiments and simulations can only be reconciled by further reducing the strength of the interfacial interactions. This suggests some screening of the solid-liquid interactions, which may be due to the presence of an interfacial water layer between PAO and steel in the contact angle experiments. Using the solid-liquid interaction potential that reproduces the experimental work of adhesion, we obtain a higher ITR (33 K m2 GW-1), suggesting inefficient thermal transport. The results of this study demonstrate the potential for NEMD simulations to improve understanding of the nanoscale thermal transport across industrially important interfaces. This study represents an important step toward the rational design of more effective fluids for immersion cooling systems for electric vehicles and other applications where thermal management is of high importance.

Nanoscale Structures of Tough Microparticle-Based Films Investigated by Synchrotron X-Ray Scattering and All-Atom Molecular-Dynamics Simulation

In this study, the nanoscale structures of microparticle-based films are revealed by synchrotron small-angle X-ray scattering (SAXS) and all-atom molecular-dynamics (AA-MD) simulations. The microparticle-based films consisting of the simplest acrylate polymer microparticles are applied as a model because the films are formed without additives and organic solvents and exhibit high toughness properties. The characteristic interfacial thickness (tinter) obtained from the SAXS analysis reflects the mixing degree of polymer chains on the microparticle surface in the film. The cross-linking density of inner microparticles is found to be strongly correlated to not only several properties of individual microparticles, such as swelling ratio and radius of gyration, but also the tinter and toughness of the corresponding films. Therefore, the tinter and toughness values follow a linear relationship because the cross-linking restricts the mixing of polymer chains between their surfaces in the film, which is a unique feature of microparticle-based films. This characteristic also affects their deformation behavior observed by in situ SAXS during tensile testing and their density profiles calculated by AA-MD simulations. This work provides a general strategy for material design to control the physical properties and structures of their films for advanced applications, including volatile organic compound-free sustainable coatings and adhesives.

Experimental and simulation study of reverse micelles formed by aerosol-OT and water in non-polar solvents

The formation of reverse micelles by aerosol-OT [sodium bis(2-ethylhexyl) sulfosuccinate] in hydrocarbon solvents, and in the presence of water, is studied using a combination of atomistic molecular-dynamics simulations and small-angle neutron scattering (SANS). There have been many previous studies of aerosol-OT and its self-assembly in both water and non-aqueous solvents, but this work is focused on a combined experimental and simulation study of reverse-micelle formation. The effects of hydration (with water-to-surfactant molar ratios in the range 0-60) and solvent (cyclohexane and n-dodecane) are investigated. A force field is adapted that results in spontaneous formation of reverse micelles starting from completely randomized configurations. The computed dimensions of the reverse micelles compare very favourably with those determined in SANS experiments, providing validation of the simulation model. The kinetics of reverse-micelle formation are studied with a 50-ns, 1.7-million-atom system which contains, in the steady state, about 50 reverse micelles. The internal structures of reverse micelles are characterized with mass density profiles, and the effects of solvent, and the structural crossover from highly structured water to 'bulk' water in the core, are detailed. The corresponding changes in the molecular reorientation times of sequestered water are also determined. Overall, the combination of experiment and simulation gives a detailed picture of reverse-micelle self-assembly and structure.

Li-ion solvation structure at electrified solid-liquid interface: Understanding solvation structure dynamics and its role in electrochemical energy storage through binary ethylene carbonate and dimethyl carbonate solvent

Binary solvent electrolytes can provide interpretations for designing advanced electrolytes of next generation batteries. This study investigates the adsorption mechanisms of solvated lithium ions in binary solvents near charged electrodes. Molecular dynamic simulations are performed for lithium hexafluorophosphate (LiPF6) in ethylene carbonate and dimethyl carbonate (EC:DMC) solvent sandwiched between two electrodes. Results show that lithium ions form a tetrahedral solvation structure with two EC and two DMC molecules. The solvated lithium ion shows anti-electrostatic interaction with electrodes. This can be attributed to the electrostatic attraction of the polar end of the DMC molecule, which keeps the cation anchored to the positive electrode. Meanwhile, the solvation structure adopts a fix orientation at the negative electrode, which leads to unchanged electrostatic interaction at high charge density. Finally, EC molecules are swapped by DMC molecules near the negative electrode at high charge density. This leads to a decrease in local relative permittivity and, therefore, a decrease in differential capacitance. The differential capacitance of the positive electrode continuously decreases with increasing charge density. This is caused by the partial anchoring of solvent molecules holding the cations, which cancels the adsorption of anions near the positive electrode. This study provides insights into designing better electrolytes for efficient battery performance.

The adsorption of drugs on nanoplastics has severe biological impact

Micro- and nanoplastics can interact with various biologically active compounds forming aggregates of which the effects have yet to be understood. To this end, it is vital to characterize these aggregates of key compounds and micro- and nanoplastics. In this study, we examined the adsorption of the antibiotic tetracycline on four different nanoplastics, made of polyethylene (PE), polypropylene (PP), polystyrene (PS), and nylon 6,6 (N66) through chemical computation. Two separate approaches were employed to generate relevant conformations of the tetracycline-plastic complexes. In the first approach, we folded the plastic particle from individual polymer chains in the presence of the drug through multiple separate simulated annealing setups. In the second, more biased, approach, the neat plastic was pre-folded through simulated annealing, and the drug was placed at its surface in multiple orientations. The former approach was clearly superior to the other, obtaining lower energy conformations even with the antibiotic buried inside the plastic particle. Quantum chemical calculations on the structures revealed that the adsorption energies show a trend of decreasing affinity to the drug in the order of N66> PS> PP> PE. In vitro experiments on tetracycline-sensitive cell lines demonstrated that, in qualitative agreement with the calculations, the biological activity of tetracycline drops significantly in the presence of PS particles. Preliminary molecular dynamics simulations on two selected aggregates with each plastic served as first stability test of the aggregates under influence of temperature and in water. We found that all the selected cases persisted in water indicating that the aggregates may be stable also in more realistic environments. In summary, our data show that the interaction of micro- and nanoplastics with drugs can alter drug absorption, facilitate drug transport to new locations, and increase local antibiotic concentrations, potentially attenuating antibiotic effect and at the same time promoting antibiotic resistance.

Behavior of Trapped Molecules in Lantern-Like Carcerand Superphanes

Superphanes are a group of organic molecules from the cyclophane family. They are characterized by the presence of two parallel benzene rings joined together by six bridges. If these bridges are sufficiently long, the superphane cavity can be large enough to trap small molecules or ions. Using ab initio (time scale of 80 ps) and classical (up to 200 ns) molecular dynamics (MD) methods, we study the behavior of five fundamental molecules (M = H2O, NH3, HF, HCN, MeOH) encapsulated inside the experimentally reported lantern-like superphane and its two derivatives featuring slightly modified side bridges. The main focus is studying the dynamics of hydrogen bonds between the trapped M molecule and the imino nitrogen atoms of the side chains of the host superphane. The length of the N···H hydrogen bond increases in the following order: HF < HCN < H2O < MeOH < NH3. The mobility of the trapped molecule and its preferred position inside the superphane cage depend not only on the type of this molecule but also largely on the in/out conformational arrangement of the imino nitrogens in the side chains of the superphane. Their inward-pointing positions allow the formation of strong N···H hydrogen bonds. For this reason, these nitrogens are the preferred sites of interaction. The mobility of the molecules and their residence times on each side of the superphane have been explained by referring to the symmetry and conformation of the given superphane cage. All force field MD simulations have shown that the encapsulated molecule remained inside the superphane cage for 200 ns without any escape event to the outside. Moreover, our simulations based on some endohedral complexes in the water box also showed no exchange event. Thus, the superphanes we study are true carcerand molecules. We attribute this property to the hydrophobic side chains and their pinwheel arrangement, which makes the side walls of the studied superphanes fairly impenetrable to small molecules.

Molecular dynamics insights into the dynamical behavior of structurally modified water in aqueous deep eutectic solvents (ADES)

Recent studies have demonstrated that the presence of water in deep eutectic solvents (DESs) significantly affects their dynamics, structure, and physical properties. Although the structural changes due to the addition of water are well understood, the microscopic dynamics of these changes have been rarely studied. Here, we performed molecular dynamics simulation of 30% (v/v) (∼0.57 molar fraction) water mixture of DES containing CH3CONH2 and NaSCN/KSCN at various salt fractions to understand the microscopic structure and dynamics of water. The simulated results reveal a heterogeneous environment for water molecules in aqueous DES (ADES), which is influenced by the nature of the cation. The diffusion coefficients of water in ADESs are significantly lower than that in neat water and concentrated aqueous NaSCN/KSCN solution. When Na+ ions are replaced by K+ ions in the ADES system, the diffusion coefficient increases, which is consistent with the measured nuclear magnetic resonance data. Self-dynamic structure factor for water and other simulated dynamic quantities, such as reorientation, hydrogen-bond, and residence time correlation functions, show markedly slower dynamics inside ADES than in the neat water and aqueous salt solution. Moreover, these dynamics become faster when Na+ ions in ADES are replaced by K+ ions. The results suggest that the structural environment of water in Na+-rich ADES is rigid due to the presence of cation-bound water and geometrically constrained water. The medium becomes less rigid as the KSCN fraction increases due to the relatively weaker interaction of K+ ions with water than Na+ ions, which accelerates the dynamical processes.

Covalent organic framework membranes with vertically aligned nanorods for efficient separation of rare metal ions

Covalent organic frameworks (COFs) have emerged as promising platforms for membrane separations, while remaining challenging for separating ions in a fast and selective way. Here, we propose a concept of COF membranes with vertically aligned nanorods for efficient separation of rare metal ions. A quaternary ammonium-functionalized monomer is rationally designed to synthesize COF layers on porous substrates via interfacial synthesis. The COF layers possess an asymmetric structure, in which the upper part displays vertically aligned nanorods, while the lower part exhibits an ultrathin dense layer. The vertically aligned nanorods enlarge contact areas to harvest water and monovalent ions, and the ultrathin dense layer enables both high permeability and selectivity. The resulting membranes exhibit exceptional separation performances, for instance, a Cs+ permeation rate of 0.33 mol m-2 h-1, close to the value in porous substrates, and selectivities with Cs+/La3+ up to 75.9 and 69.8 in single and binary systems, highlighting the great potentials in the separation of rare metal ions.

Machine Learnable Language for the Chemical Space of Nanopores Enables Structure-Property Relationships in Nanoporous 2D Materials

The synthesis of nanoporous two-dimensional (2D) materials has revolutionized fields such as membrane separations, DNA sequencing, and osmotic power harvesting. Nanopores in 2D materials significantly modulate their optoelectronic, magnetic, and barrier properties. However, the large number of possible nanopore isomers makes their study onerous, while the lack of machine-learnable representations stymies progress toward structure-property relationships. Here, we develop a language for nanopores in 2D materials, called STring Representation Of Nanopore Geometry (STRONG), that opens the field of 2D nanopore informatics. We show that STRONGs are naturally suited for machine learning via recurrent neural networks, predicting formation energies/times of arbitrary nanopores and transport barriers for CO2, N2, and O2 gas molecules, enabling structure-property relationships. The machine learning models enable the discovery of specific nanopore topologies to separate CO2/N2, O2/CO2, and O2/N2 gas mixtures with high selectivity ratios. We also enable the rapid enumeration of unique configurations of stable, functionalized nanopores in 2D materials via STRONGs, allowing systematic searching of the vast chemical space of nanopores. Using the STRONGs approach, we find that a mix of hydrogen and quinone functionalization results in the most stable functionalized nanopore configuration in graphene, a discovery made feasible by expedited chemical space exploration. Additionally, we also unravel the STRONGs approach as ∼1000 times faster than graph theory algorithms to distinguish nanopore shapes. These advances in the language-based representation of 2D nanopores will accelerate the tailored design of nanoporous materials.

Microscopic Structure of Neat Linear Alkylamine Liquids: An X-Ray Scattering and Computer Simulation Study

Linear amines, from propylamine to nonylamine, are studied under ambient conditions by X-ray scattering and molecular dynamics simulations of various force field models. The major finding is that the prepeak in alkylamines is about 1 order of magnitude weaker than that in alkanols, hence suggesting much weaker hydrogen bonding-induced clustering of the amine groups than for the hydroxyl groups. Computer simulation studies reveal that the OPLS-UA model reproduces the prepeak, but with larger amplitudes, while the GROMOS-UA and CHARMM-AA force fields show almost no prepeak. Simulations of all models show the existence of hydrogen-bonded clusters, equally confirmed by the prominent prepeak of the structure factor between the nitrogen atoms. The hydrogen bond strength, as modeled by the Coulomb association in classical force field models, is about the same order of magnitude for both systems. Then, one may ask what is the origin of the weaker prepeak in alkylamines? Simulation data reveal that the existence of the prepeak is controlled through the cancellation of the positive contributions from the charged group correlations by the negative contributions from the cross charged-uncharged correlations. The C2v symmetry of the amine headgroup hinders clustering, which favors cross correlations with the tail atoms. This is opposite to alkanols where the symmetry of the hydroxyl headgroup favors clustering and hinders cross correlations with the alkyl tail. This competition between charged and uncharged atomic groups appears as a general mechanism to explain the existence of scattering prepeaks, including their position and amplitude.

Inhibition of Pseudomonas aeruginosa Carbonic Anhydrases, Exploring Ciprofloxacin Functionalization Toward New Antibacterial Agents: An In-Depth Multidisciplinary Study

Ciprofloxacin (CPX) is one of the most employed antibiotics in clinics to date. However, the rise of drug-resistant bacteria is dramatically impairing its efficacy, especially against life-threatening pathogens, such as Pseudomonas aeruginosa. This Gram-negative bacterium is an opportunistic pathogen, often infecting immuno-compromised patients with severe or fatal outcomes. The evidence of the possibility of exploiting Carbonic Anhydrase (CA, EC: 4.2.1.1) enzymes as pharmacological targets along with their role in P. aeruginosa virulence inspired the derivatization of CPX with peculiar CA-inhibiting chemotypes. Thus, a large library of CPX derivatives was synthesized and tested on a panel of bacterial CAs and human isoenzymes I and II. Selected derivatives were evaluated for antibacterial activity, revealing bactericidal and antibiofilm properties for some compounds. Importantly, promising preliminary absorption, distribution, metabolism, and excretion (ADME) properties in vitro were found and no cytotoxicity was detected for some representative compounds when tested in Galleria mellonella larvae.

Heterogeneous Li coordination in solvent-in-salt electrolytes enables high Li transference numbers

The transport properties and the underlying coordination structure of a ternary electrolyte consisting of lithium bis(trifluoromethanesulfonyl)imide (LiTFSI), 1,2-dimethoxyethane (DME), and 1,3-dioxolane (DOL) is studied over a wide concentration range, up to that of a Solvent-in-Salt (SiS) electrolyte. Among other advantages for next-generation battery applications, SiS electrolytes offer a high lithium transference number (tLi) of 0.73. We analyze the transport mechanism by electrophoretic NMR (eNMR), providing the mobilities (μi) of all species. Intriguingly, in the SiS region, the mobility of the neutral species DME exceeds the cation mobility (μDME > μLi), suggesting a heterogeneous transport mechanism, where the Li+ mobility is averaged over different species. Based on Raman spectroscopy, NMR spectroscopy and MD simulations, we derive a model for a concentration-dependent Li+ coordination environment with a heterogeneous Li+ coordination in the SiS region, where the 1st coordination shell either consists of TFSI- and DOL only, or of DME, TFSI-, and DOL. Lithium ions partially coordinated by DME migrate faster in an electric field, in contrast to lithium ions solely coordinated by anions and DOL molecules, explaining the peculiarity of the rapidly migrating neutral DME molecules. Further, DME is identified as an exclusively bidentate ligand, while TFSI- and DOL act as bridging ligands coordinating different Li+ ions. Thus, Li+ coordination heterogeneity is the basis for Li+ transport heterogeneity and for achieving very high Li+ transference numbers. In addition, an effective dynamic decoupling of Li+ and anions occurs with an Onsager coefficient σ+- ≈ 0. These results provide a deeper understanding of the very efficient lithium-ion transport in SiS electrolytes, with the potential to bring further improvements for battery applications.

Effect of Inorganic Additive Strategy on the Stability of VO2+ in Vanadium Redox Flow Battery Electrolyte by Molecular Dynamics

Inorganic ions are considered to be effective additives to improve the temperature stability of all-vanadium redox flow batteries. In this study, molecular dynamics simulation has been performed to study the solvation structure and dynamic properties of VO2+ in the positive electrolyte by doping Na+, K+, and NH4+ in the presence of V2O5 precipitation. The results show that VO2+ ions aggregate into chainlike clusters in the electrolyte due to the induction of SO42-. The additives, which are stable in the solvation layers of VO2+, can work as protective shells to inhibit cluster growth. NH4+ is a superior dispersant compared with Na+ and K+ as it can stably exist in both the first solvation layer and the second solvation layer of VO2+. This work performed the molecular dynamics simulation of the electrolyte of vanadium redox flow batteries, and it gives some insights into the theoretical study of the modification of the cathode electrolyte.

Hydrophilic Chain Length for Octylphenol Polyoxyethylene Ether Adsorption at the n-Hexadecane-Water Interface: Theoretical and Experimental Study

With the advancement of technologies for developing tight and shale reservoirs, nonionic surfactants have garnered significant attention due to their remarkable properties. The structure of these surfactants plays a crucial role in determining the characteristics of the oil-water interface, particularly influencing emulsification behavior and crude oil recovery. This study investigates the effect of varying the number of hydrophilic polar groups (n = 10, 20, 30, 50) in octylphenol polyoxyethylene ether (OP-n) on its adsorption behavior at the n-hexadecane-water interface using molecular dynamics simulation. The impact of these variations on interfacial properties was further analyzed through measurements of interfacial tension and observations of emulsion droplet morphology. The study results indicate that variations in the number of hydrophilic polar groups significantly affect interfacial properties. Increasing the number of hydrophilic polar groups led to a notable increase in the thickness of the n-hexadecane or water phase, as well as the thickness of the water or oil layer and the surfactant layer. Moreover, when the number of hydrophilic polar groups reached 20, the OP-n molecules exhibited a more curled conformation at the interface, enhancing their ability to encapsulate water and resulting in a decrease in the diffusion coefficient of the molecules in each phase. Additionally, interfacial tension was found to be positively correlated with the number of hydrophilic polar groups and remained unchanged beyond a certain emulsion diameter. This study provides a theoretical basis and reference data for optimizing surfactant structures to improve crude oil recovery.

Decomposition and Growth Pathways for Ammonium Nitrate Clusters and Nanoparticles

Understanding the formation and decomposition mechanisms of aerosolized ammonium nitrate species will lead to improvements in modeling the thermodynamics and kinetics of aerosol haze formation. Studying the sputtered mass spectra of cation and anion ammonium nitrate clusters can provide insights as to which growth and evaporation pathways are favored in the earliest stages of nucleation and thereby guide the development and use of accurate models for intermolecular forces for these systems. Simulated annealing Monte Carlo optimization followed by density functional theory optimizations can be used reliably to predict minimum-energy structures and interaction energies for the cation and anion clusters observed in mass spectra as well as for neutral nanoparticles. A combination of translational and rotational mag-walking and sawtooth simulated annealing methods was used to find optimum structures of the various heterogeneous clusters identifiable in the mass spectra. Following these optimizations with ωB97X-D3 density functional theory calculations made it possible to rationalize the pattern of peaks in the mass spectra through computation of the binding energies of clusters involved in various growth and dissociation pathways. Testing these calculations against CCSD(T) and MP2 predictions of the structures and binding energies for small clusters demonstrates the accuracy of the chosen model chemistry. For the first time, the peaks corresponding with all detectable species in both the positive and negative ion mass spectra of ammonium nitrate are identified with their corresponding structures. Thermodynamic control of particle growth and decomposition of ions due to loss of ammonia or nitric acid molecules is indicated. Structures and interaction energies for larger (NH4NO3)n nanoparticles are also presented, including the prediction of new particle morphologies with trigonal pyramidal character.

Exploring the Interaction of Human α-Synuclein with Polyethylene Nanoplastics: Insights from Computational Modeling and Experimental Corroboration

Plastics, particularly microplastics (MPs) and nanoplastics (NP), have become major environmental and health concerns due to their high chemical stability. The highly hydrophobic plastics enter living organisms through reversible interactions with biomolecules, forming biocoronas. Following recent reports on plastics breaching the blood-brain barrier, the binding behavior of human α-synuclein (hαSn) with polyethylene-based (PE) plastics was evaluated by using molecular dynamics simulations and experimental methods. The results provided three important findings: (i) hαSn transitions from an open helical to a compact conformation, enhancing intramolecular interactions, (ii) nonoxidized PE NPs (NPnonox) rapidly adsorb hαSn, as supported by experimental data from dynamic light scattering and adsorption isotherms, altering its structure, and (iii) the oxidized NP (NPox) failed to capture hαSn. These interactions were dominated by the N-terminal domain of hαSn, with major contributions from hydrophobic amino acids. These findings raise concerns about the potential pharmacological effects of NP-protein interactions on human health.

Strong Lewis-acid coordinated PEO electrolyte achieves 4.8 V-class all-solid-state batteries over 580 Wh kg-1

Polyethylene oxide (PEO) based electrolytes critically govern the security and energy density of solid-state batteries, but typically suffer from poor oxidation resistance at high voltages, which limits the energy density of batteries. Here, we report a Lewis-acid coordinated strategy to significantly improve the cyclic stability of 4.8 V-class PEO-based battery. The introduced Mg2+ and Al3+ with strong electron-withdrawing capability weaken the electron density of ether oxygen (EO) chains via chelation in the coordination structure, resulting in a locally limited interaction between the EO chains and the surface of cathodes at high state of charge. The batteries using Lewis-acid coordinated electrolytes and Ni-rich cathodes achieve high voltage stability of 4.8 V over 300 cycles. Further, the realization of industrial-scale electrolyte membranes, and Ah-level pouch cells over 586 Wh kg‒1 with good cyclic stability, suggests the potential of our strategy in practical applications of all-solid-state batteries.

Anion Selectivities in Zwitterion Grafted Nanopores: Effect of Zwitterion Architecture

The separation of ions of similar charge is a crucial challenge in many applications, from water treatment to precious metal recovery. Membranes with cross-linked zwitterionic amphiphilic copolymer (ZAC-X) selective layers, which feature self-assembled, zwitterion-lined nanodomains for permeation, offer unique permselectivity between monovalent anions (e.g., Cl-/F-). This has motivated studies on the mechanisms of transport and selectivity in this family of materials. In this study, we conducted molecular dynamics simulations of aqueous salt solutions within zwitterion-functionalized nanopores to elucidate the influence of dipole orientation of the ZI ligands on anion diffusivities, partitioning, and permeabilities. Our model compares systems with contrasting ZI organization: surface-cation-anion (S-ZI+-ZI-, Motif A) and surface-anion-cation (S-ZI--ZI+, Motif B). Our results reveal that Motif A exhibits less pronounced ion pairing due to a spatial separation in the radial profiles of cations and anions. Motif B demonstrates prominent ion pairing for smaller anions owing to their overlap with cation distributions. Further, our potential of mean force profiles reveals that anion partitioning increases with anion size in both ligand motifs, whereas Motif B exhibits significantly higher partitioning selectivity toward larger anions compared to Motif A. Our results for ion diffusivities show that the self-diffusivities of both anions and cations are lower for Motif B compared to Motif A. Such trends in anion partitioning and diffusivities can be explained by differences in the interactions and steric hindrance experienced by the anionic species in Motifs A and B. Finally, our results for anion permselectivity, obtained by combining partitioning and diffusivity, indicate that partitioning trends dominate over diffusivity trends. Consequently, anion permeability increases with anion size, and ligand Motif B yields much higher permselectivity toward larger anions compared to ligand Motif A.

Homology modelling, molecular docking studies and synthesis of aminopyrimidines as inhibitors for deoxynucleoside kinase analogues in cancer chemoprevention

The development of alternative anticancer agents with minimal side effects has become more critical due to the rising recurrence of mammalian malignancies and the severe side effects of chemotherapeutic treatments. Kinases are an essential target for neostatic impact as they play an important role in the modulation of growth factor signalling. Our work aims to screen novel nine-series of thiazole-based aminopyrimidines and sulphaminopyrimidines against the enzymes mitochondrial thymidine kinase 2, deoxyguanosine kinase (2OCP), deoxycytidine kinase (2QRN) and thymidylate kinase (1E2Q) by molecular docking, synthesise and to study their in vitro inhibitory studies. The synthesised compounds were characterised by Infrared, Nuclear magnetic resonance and Mass spectroscopy. In silico studies, compound 4c stands out among the series, with a reported docking score ranging from -6 to -8 Kcal/mol against all the analogue kinases. The in vitro cytotoxicity assay against human small-cell lung carcinoma (A-549) has shown that 5c (IC50 = 53.9 µM) has an excellent cytotoxic effect over 4c (IC50= 68.68 µM). The reason might be the presence of the benzene sulphonamide group, which enhances their anticancer action. To conclude, the compounds 4c and 5c were found to be potent inhibitors of the deoxynucleoside kinases. In vivo studies must further verify these to prove their potent neostatic effect.

Chemically Transferable Electronic Coarse Graining for Polythiophenes

Recent advances in machine-learning-based electronic coarse graining (ECG) methods have demonstrated the potential to enable electronic predictions in soft materials at mesoscopic length scales. However, previous ECG models have yet to confront the issue of chemical transferability. In this study, we develop chemically transferable ECG models for polythiophenes using graph neural networks. Our models are trained on a data set that samples over the conformational space of random polythiophene sequences generated with 15 different monomer chemistries and three different degrees of polymerization. We systematically explore the impact of coarse-grained representation on ECG accuracy, highlighting the significance of preserving the C-β coordinates in thiophene. We also find that integrating unique polymer sequences into training enhances the model performance more efficiently than augmenting conformational sampling for sequences already in the training data set. Moreover, our ECG models, developed initially for one property and one level of quantum chemical theory, can be efficiently transferred to related properties and higher levels of theory with minimal additional data. The chemically transferable ECG model introduced in this work will serve as a foundation model for new classes of chemically transferable ECG predictions across chemical space.

Mechanistic Insights of Amino Acid Binding to Hydroxyapatite: Molecular Dynamics Charts Future Directions in Biomaterial Design

Extensive efforts have been made to improve the understanding of hard tissue regeneration, essential for advancing medical applications like bone graft materials. However, the mechanisms of bone biomineralization, particularly the regulation of hydroxyapatite growth by proteins/peptides, remain debated. Small biomolecules such as amino acids are ideal for studying these mechanisms due to their simplicity and relevance as protein/peptide building blocks. This study investigates the binding affinity of four amino acids including glycine (Gly), proline (Pro), lysine (Lys), and aspartic acid (Asp) to the hydroxyapatite (HAP) (100) surface through molecular dynamics simulations. Our findings reveal that aspartic acid exhibits the most energetically favorable binding affinity, attributed to its additional carboxylate group (-COO-), which facilitates stronger interactions with Ca2+ ions on the HAP surface compared to other amino acids with single carboxylate groups. This highlights the critical role of specific functional groups in modulating binding strength, emphasizing that the presence of multiple binding sites in amino acids enhances binding stability. Interestingly, the study also uncovers the significance of water-mediated interactions, as the compact water layer above the HAP surface acts as a barrier, complicating direct binding and underscoring the need to consider solvation effects in simulations. Glycine, due to its small size, demonstrates a unique ability to penetrate this tightly bound water monolayer, suggesting that molecular size influences binding dynamics. These simulations offer detailed insights into the atomic-level interactions, providing a deeper understanding of binding affinity and stability. These insights are pertinent for designing peptides or proteins with enhanced interactions with biomaterials, particularly in mimicking natural bone-binding processes.

ANI/EFP: Modeling Long-Range Interactions in ANI Neural Network with Effective Fragment Potentials

Deep learning Neural Networks (NN) have been developed in the field of molecular modeling for the purpose of circumventing the high computational cost of quantum-mechanical calculations while rivaling their accuracies. Although these networks have found great success, they generally lack the ability to accurately describe long-range interactions, which makes them unusable for extended molecular systems. Herein, we provide a method for partially retraining the deep learning general-use neural network ANI, in which the long-range interactions are represented via atomic electrostatic potentials. The electrostatic potentials, generated with polarizable effective fragment potentials (EFP), are used as an additional input feature for the network. This new ANI/EFP network can predict solute-solvent interaction energies on a trained data set with a kcal/mol accuracy. It also shows promise in predicting the interaction energies of a solute in solvent environments that have not been included in a training data set. The proposed protocol can be taken as an example and further developed, leading to highly accurate and transferable neural network potentials capable of handling long-range interactions and extended molecular systems.

Online SFE-SFC-MS/MS analysis of pyraclostrobin and chiral mefentrifluconazole residues in mango and mango juice

This study established an on-line SFE-SFC-MS/MS method for the determination of mefentrifluconazole (MFZ) enantiomers and pyraclostrobin (PY) in mango and mango juice. Key parameters of SFC separation and SFE extraction have been optimized for high efficiency, sensitivity, and environmental friendliness. Enthalpy controlled enantioseparations of MFZ were recognized by thermodynamic analysis. Molecular docking estimated the enantiomeric recognition of MFZ enantiomers binding to the chiral stationary phase. The mean recoveries (RSDs) were in the range of 94.5-106.8 % (4.2-15.4 %), 91.1-103 % (3.6-10.3 %), 94.7-102.7 % (3.8-9.8 %), and 93.2-106.9 % (4.1-12.1 %) for R-MFZ, S-MFZ, racemic MFZ, and PY under 3 spiked levels of interday assays (n = 15). The LOQs of R-MFZ, S-MFZ, and PY were 0.5, 0.5, and 1 μg kg-1. The method was further applied to real samples in Guangxi Province, China with low acute and chronic dietary risk for MFZ and PY in mango and mango juice.

Inhibition of early RNA replication in Chikungunya and Dengue virus by lycorine: In vitro and in silico studies

Arboviruses such as chikungunya virus (CHIKV) and dengue virus (DENV) collectively afflict millions of individuals worldwide particularly in endemic countries like India, leading to substantial morbidity and mortality. With the lack of effective vaccines for both CHIKV and DENV in India, the search for antiviral compounds becomes paramount to control these viral infections. In line with this, our investigation was focused on screening natural compounds for their potential antiviral activity against CHIKV and DENV. Using different assays, including plaque assay, immunofluorescence, and reverse transcription-quantitative real-time PCR (qRT-PCR), out of 109 natural compounds tested, we confirmed lycorine's in vitro antiviral activity against CHIKV and DENV at low micromolar concentrations in different cell types. Time of addition assays indicated that lycorine does not impede viral entry. Additionally, qRT-PCR results along with time of addition assay suggested that lycorine interferes with the synthesis of negative strand viral RNA. Molecular docking analysis was done to understand the mode of inhibition of viral replication. The results revealed that the most likely binding site with the highest binding affinity of lycorine, was at the palm and finger domains, in the vicinity of the catalytic site of CHIKV and DENV RNA-dependent RNA polymerase (RdRp). Collectively, our data underscores the potential of lycorine to be developed as a direct acting inhibitor for DENV and CHIKV, addressing the critical need of requirement of an antiviral in regions where these viruses pose significant public health threats.

Identification of new leads against ubiquitin specific protease-7 (USP7): a step towards the potential treatment of cancers

Ubiquitin-specific protease-7 (USP7) is an important drug target as it regulates multiple proteins and genes (such as MDM2 and p53) with roles in cancer progression. Its inhibition can hinder the function of oncogenes, increase tumor suppression, and enhance immune response. The current study was designed to express USP7 in a prokaryotic system, followed by screening of small molecules against it using biophysical methods, primarily STD-NMR technique. Among them, 12 compounds showed interaction with USP7 as inferred from NMR-based screening. These compounds further caused destabilization of USP7 by reducing its melting temperature (T m) up to 6 °C in thermal shift assay. Molecular docking and simulation studies revealed that these compounds bind to the putative substrate binding pocket of USP7 and thus may block the entry of the substrate. Four compounds i.e., 4-hydroxy-diphenyl amine (2), phenyl-(2,3,4-trihydroxyphenyl) methanone (3), 4'-amino-2',5'-diethoxy benzanilide (5), and hydroquinone (12), showed anti-cancer activity against colorectal cancerous cells (HCT116) with IC50 values in the range of 31-143 μM. These compounds also down-regulated the mRNA expression of the MDM2 gene and up-regulated the mRNA expression of the p53 gene in HCT116 cells, as studied using qPCR analysis. This study thereby identifies several negative modulators of USP7 that can be studied further as potential anti-cancer agents.

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.

In Silico Evaluation and Experimental Validation of Interfacial Properties in 3-5 Residue Peptides

Predicting the interfacial properties of peptides is important for replacing oil-derived surfactants in cosmetics, oil, and agricultural applications. This work validated experimentally the estimations of surface tension at the critical micelle concentration (STCMC) of six peptides performed through a random forest (RF) model in a previous contribution. In silico interfacial tensions of the peptides were obtained in the system decane-water, and dilational experiments were applied to elucidate the foaming potential. The RF model accurately classified the peptides into high and low potential to reduce the STCMC. The simulations at the decane-water interface correctly identified peptides with high, intermediate, and low interfacial properties, and the dilational rheology allowed the estimation of the possible potential of three peptides to produce foams. This study sets the basis for identifying surface-active peptides, but future work is necessary to improve the estimations and the correlation between dilational properties and foam stabilization.

Does Positron Attachment Take Place in Water Solution?

We performed a computational study of positron attachment to hydrated amino acids, namely glycine, alanine, and proline in the zwitterionic form. We combined the sequential quantum mechanics/molecular mechanics (s-QM/MM) method with various levels of any particle molecular orbital (APMO) calculations. Consistent with previous studies, our calculations indicate the formation of energetically stable states for the isolated and microsolvated amino acids, in which the positron localizes around the carboxylate group. However, for the larger clusters, composed of 7 to 40 water molecules, hydrogen bonding between the solute and solvent molecules disfavors positron attachment to the amino acids, giving rise to surface states in which the positron is located around the water-vacuum interface. The analysis of positron binding energies, positronic orbitals, radial probability distributions, and annihilation rates consistently pointed out the change from positron-solute to positron-solvent states. Even with the inclusion of an electrostatic embedding around the aggregates, the positrons did not localize around the solute. Positron attachment to molecules in the gas phase is a well-established fact. The existence of hydrated positronic molecules could also be expected from the analogy with transient anion states, which are believed to participate in radiation damage. Our results indicate that positron attachment to hydrated biomolecules, even to zwitterions with negatively charged carboxylated groups, would not take place. For the larger clusters, in which positron-water interactions are favored, the calculations indicate an unexpectedly large contribution of the core orbitals to the annihilation rates, between 15 and 20%. Finally, we explored correlations between positron binding energies (PBEs) and dipole moments, as well as annihilation rates and PBEs, consistent with previous studies for smaller clusters.

Machine learning models to identify lead compound and substitution optimization to have derived energetics and conformational stability through docking and MD simulations for sphingosine kinase 1

Sphingosine kinases (SphKs) are a group of important enzymes that circulate at low micromolar concentrations in mammals and have received considerable attention due to the roles they play in a broad array of biological processes including apoptosis, mutagenesis, lymphocyte migration, radio- and chemo-sensitization, and angiogenesis. In the present study, we constructed three classification models by four machine learning (ML) algorithms including naive bayes (NB), support vector machine (SVM), logistic regression, and random forest from 395 compounds. The generated ML models were validated by fivefold cross validation. Five different scaffold hit fragments resulted from SVM model-based virtual screening and docking results indicate that all the five fragments exhibit common hydrogen bond interaction a catalytic residue of SphK1. Further, molecular dynamics (MD) simulations and binding free energy calculation had been carried out with the identified five fragment leads and three cocrystal inhibitors. The best 15 fragments were selected. Molecular dynamics (MD) simulations showed that among these compounds, 7 compounds have favorable binding energy compared with cocrystal inhibitors. Hence, the study showed that the present lead fragments could act as potential inhibitors against therapeutic target of cancers and neurodegenerative disorders.

Charge Scaling in Classical Force Fields for Lithium Ions in Polymers

Polymer electrolytes are of interest for applications in energy storage. Molecular simulations of ion transport in polymer electrolytes have been widely used to study the conductivity in these materials. Such simulations have generally relied on classical force fields. A peculiar feature of such force fields has been that in the particular case of lithium ions (Li+), their charge must be scaled down by approximately 20% to achieve agreement with experimental measurements of ion diffusivity. In this work, we present first-principles calculations that serve to justify the charge-scaling factor and van der Waals interaction parameters for Li+ diffusion in poly(ethylene glycol) (PEO) with bistriflimide (TFSI-) counterions. Our results indicate that a scaling factor of 0.79 provides good agreement with DFT calculations over a relatively wide range of Li+ concentrations and temperatures, consistent with past reports where that factor was adjusted by trial and error. We also show that such a scaling factor leads to diffusivities that are in quantitative agreement with experimental measurements.

Chelator-Assisted Precipitation-Based Separation of the Rare Earth Elements Neodymium and Dysprosium from Aqueous Solutions

The rare earth elements (REEs) are critical resources for many clean energy technologies, but are difficult to obtain in their elementally pure forms because of their nearly identical chemical properties. Here, an analogue of macropa, G-macropa, was synthesized and employed for an aqueous precipitation-based separation of Nd3+ and Dy3+. G-macropa maintains the same thermodynamic preference for the large REEs as macropa, but shows smaller thermodynamic stability constants. Molecular dynamics studies demonstrate that the binding affinity differences of these chelators for Nd3+ and Dy3+ is a consequence of the presence or absence of an inner-sphere water molecule, which alters the donor strength of the macrocyclic ethers. Leveraging the small REE affinity of G-macropa, we demonstrate that within aqueous solutions of Nd3+, Dy3+, and G-macropa, the addition of HCO3 - selectively precipitates Dy2(CO3)3, leaving the Nd3+-G-macropa complex in solution. With this method, remarkably high separation factors of 841 and 741 are achieved for 50 : 50 and 75 : 25 mixtures. Further studies involving Nd3+:Dy3+ ratios of 95 : 5 in authentic magnet waste also afford an efficient separation as well. Lastly, G-macropa is recovered via crystallization with HCl and used for subsequent extractions, demonstrating its good recyclability.

A molecular dynamics simulation study of EthylChlorophyllide A molecules confined in a SiO2 nanoslit

This paper investigates the dynamic behavior of EthylChlorophyllide A (EChlideA) molecules in a methanol solution confined within a 4 nm silica nanoslit, using molecular dynamics simulations over a duration of 1 ms. Three systems, containing 1, 2, and 4 solutes, were studied at 298 K. The results demonstrate that EChlideA molecules predominantly adsorb onto the silica surfaces, driven by specific interactions between chlorin ring's methyl group and the hydroxyl groups of the silica. This adsorption leads to stable binding, particularly in less crowded environments, as indicated by the potential of mean force analysis. Higher molecular concentrations, such as those with four EChlideA molecules, introduce variation in binding strength due to molecular aggregation and complex interactions. The orientation analysis reveals that the chlorin ring tends to align parallel to the surface, requiring rotational adjustments during surface diffusion. In addition, solvent coordination around the Mg ion remains consistent under bulk conditions, although with some variation in higher concentrations. This study also highlights a decrease in linear diffusion and an increase in rotational relaxation times for EChlideA molecules within the confined nanoslit, reflecting the influence of molecular concentration and arrangement on their dynamics. These findings provide valuable insights into the role of surface interactions, molecular orientation, and solvent coordination in confined environments, offering implications for the design of nanoscale systems.

The impact of acyl-CoA:cholesterol transferase (ACAT) inhibitors on biophysical membrane properties depends on membrane lipid composition

Acyl-coenzyme A: cholesterol acyltransferases are enzymes which are involved in the homeostasis of cholesterol. Impaired enzyme activity is associated with the occurrence of various diseases like Alzheimer's disease, atherosclerosis, and cancers. At present, mitotane is the only inhibitor of this class of enzymes in clinical use for the treatment of adrenocortical carcinoma but associated with common and severe adverse effects. The therapeutic effect of mitotane depends on its interaction with cellular membranes. The search for less toxic but equally effective compounds is hampered by an incomplete understanding of these biophysical properties. In the present study, the interaction of the three ACAT inhibitors nevanimibe, Sandoz 58-035, and AZD 3988 with membranes has been investigated using lipid model membranes in conjunction with biophysical experimental (NMR, ESR, fluorescence) and theoretical (MD simulations) approaches. The data show, that the drugs (i) incorporate into lipid membranes, (ii) differently influence the structure of lipid membranes; (iii) affect membrane structure depending on the lipid composition; and (iv) do not cause hemolysis of red blood cells. The results are discussed with regard to the use of the drugs, in particular to better understand their efficacy and possible side effects.

Diffusivity of CO2 in H2O: A Review of Experimental Studies and Molecular Simulations in the Bulk and in Confinement

An in-depth review of the available experimental and molecular simulation studies of CO2 diffusion in H2O, which is a central property in important industrial and environmental processes, such as carbon capture and storage, enhanced oil recovery, and in the food industry is presented. The cases of both bulk and confined systems are covered. The experimental and molecular simulation data gathered are analyzed, and simple and computationally efficient correlations are devised. These correlations are applicable to conditions from 273 K and 0.1 MPa up to 473 K and 45 MPa. The available experimental data for diffusion coefficients of CO2 in brines are also collected, and their dependency on temperature, pressure, and salinity is examined in detail. Other engineering models and correlations reported in literature are also presented. The review of the simulation studies focuses on the force field combinations, the data for diffusivities at low and high pressures, finite-size effects, and the correlations developed based on the Molecular Dynamics data. Regarding the confined systems, we review the main methods to measure and compute the diffusivity of confined CO2 and discuss the main natural and artificial confining media (i.e., smectites, calcites, silica, MOFs, and carbon materials). Detailed discussion is provided regarding the driving force for diffusion of CO2 and H2O under confinement, and on the role of effects such as H2O adsorption on hydrophilic confining media on the diffusivity of CO2. Finally, an outlook of future research paths for advancing the field of CO2 diffusivity in H2O at the bulk phase and in confinement is laid out.

All-atom molecular dynamics simulations showing the dynamics of small organic molecules in water-solvated polyelectrolyte brush layers

Polyelectrolyte brushes can introduce functionality to surfaces and because of this, these brushes have been studied extensively. In many applications, these brushes are used in solutions that contain a variety of molecules. While the interaction between polyelectrolyte brushes and molecules has been studied via coarse-grained simulations and experiments, such interaction has not been studied in molecular detail. An understanding of interactions in such molecular detail may prove crucial in the design of future brush coatings that can enable desired adsorption of different organic and biological molecules. Therefore, we present a first all-atom molecular dynamics simulations study of poly(sodium acrylate) brushes in contact with a small organic molecule, γ-butyrolactone. Within this molecular framework, we study the interaction of this lactone molecule with the brush layer and study the ensuing absorption and dynamics of the lactone inside the brush layer. The lactone is found to prefer to remain in the bulk solution; however, when absorbed, lactone molecules are found to have significantly reduced mobilities as compared to that in the bulk solution and are able to massively influence the properties of the brush-entrapped water molecules. These findings provide unprecedented details about the absorption-driven changes to molecular structure and dynamics of the lactone molecules and the water molecules inside the brush layer and can only be uncovered by our all-atom MD simulations. Such explicit and atomistically-resolved information, taking into account the specific chemical nature of the interacting systems, is rare in the context of designing polymer and PE brush-based coatings. Thus, we anticipate that our findings will be crucial in the design of future brush coatings aimed at providing adsorption platforms for different organic and biomolecules.

3,8-Disubstituted Pyrazolo[1,5-a]quinazoline as GABAA Receptor Modulators: Synthesis, Electrophysiological Assays, and Molecular Modelling Studies

As a continuation of our study in the field of GABAA receptor modulators, we report the design and synthesis of new pyrazolo[1,5-a]quinazoline (PQ) bearing at the 8-position an oxygen or nitrogen function. All the final compounds and some intermediates, showing the three different forms of the pyrazolo[1,5-a]quinazoline scaffold (5-oxo-4,5-dihydro, -4,5-dihydro, and heteroaromatic form), have been screened with an electrophysiological technique on recombinant GABAAR (α1β2γ2-GABAAR), expressed in Xenopus laevis oocytes, by evaluating the variation in produced chlorine current, and permitting us to identify some interesting compounds (6d, 8a, 8b, and 14) on which further functional assays were performed. Molecular modelling studies (docking, minimization of complex ligand-receptor, and MD model) and a statistical analysis by a Hierarchical Cluster Analysis (HCA) have collocated these ligands in the class corresponding to their pharmacological profile. The HCA results are coherent with the model we recently published (Proximity Frequencies), identifying the residues γThr142 and αHis102 as discriminant for the agonist and antagonist profile.

Role of EDTA protonation in chelation-based removal of mercury ions from water

A robust method of hazardous metal ion removal from an aqueous environment involves the use of chelating agents, such as ethylenediaminetetraacetic acid (EDTA). Here, we focus on mercury (Hg2+) uptake by EDTA using both molecular dynamics and density functional theory simulations. Our results indicate that the deprotonation of the EDTA carboxylate groups improves the localization of negative charge on the deprotonated sites. This mechanism facilitates charge transfer between the metal ions and EDTA, and provides a stronger and more stable EDTA-Hg2+ complex formation improving the efficiency of the chelation process. The best metal removal conditions are achieved using the fully deprotonated form of EDTA, which naturally occurs at pH levels above 3.

Binding Mechanism of the Active Form of Molnupiravir to RdRp of SARS-CoV-2 and Designing Potential Analogues: Insights from Molecular Dynamics Simulations

Molnupiravir, an FDA-approved nucleoside prodrug for treating COVID-19, converts into N4-hydroxycytidine triphosphate (NHC-TP), which integrates into SARS-CoV-2 RNA by its RNA-dependent RNA polymerase (RdRp) causing lethal mutations in viral proteins. Due to the risk of RdRp-mediated drug resistance and potential off-target effects on host polymerases (e.g., human polymerase II/HPolII), it is crucial to understand NHC-TP interactions at polymerase active sites for developing new, resistance-proof treatments. In this study, we used molecular dynamics (MD) simulations to probe key interactions between NHC-TP and SARS-CoV-2 RdRp and designed novel NHC-TP analogues with greater selectivity for SARS-CoV-2 RdRp over HPolII by a virtual screening workflow. We docked NHC-TP to a modified SARS-CoV-2 RdRp-Remdesivir triphosphate structure (PDB ID: 7BV2) and generated 71 NHC-TP analogues with bulky substituents to increase the interaction with RdRP and to reduce HPolII incorporation. MD simulations assessed the stability, binding affinity, and site interactions of these analogues. The top 7 candidates, with favorable ADMET properties, likely inhibit replication via potential dual mechanisms (the replicative stalling and the induction of lethal mutations) while maintaining selectivity for SARS-CoV-2 RdRp.

Exploring Niclosamide as a Multi-target Drug Against SARS-CoV-2: Molecular Dynamics Simulation Studies on Host and Viral Proteins

Niclosamide has emerged as a promising repurposed drug against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In vitro studies suggested that niclosamide inhibits the host transmembrane protein 16F (hTMEM16F), crucial for lipid scramblase activity, which consequently reduces syncytia formation that aids viral spread. Based on other in vitro reports, niclosamide may also target viral proteases such as papain-like protease (PLpro) and main protease (Mpro), essential for viral replication and maturation. However, the precise interactions by which niclosamide interacts with these multiple targets remain largely unclear. Docking and molecular dynamics (MD) simulation studies were undertaken based on a homology model of the hTMEM16F and available crystal structures of SARS-CoV-2 PLpro and Mpro. Niclosamide was observed to bind stably throughout a 400 ns MD simulation at the extracellular exit gate of the hTMEM16F tunnel, forming crucial interactions with residues spanning the TM1-TM2 loop (Gln350), TM3 (Phe481), and TM5-TM6 loop (Lys573, Glu594, and Asp596). Among the SARS-CoV-2 proteases, niclosamide was found to interact effectively with conserved active site residues of PLpro (Tyr268), exhibiting better stability in comparison to the control inhibitor, GRL0617. In conclusion, our in silico analyses support niclosamide as a multi-targeted drug inhibiting viral and host proteins involved in SARS-CoV-2 infections.

Molecular permeation through large pore channels: computational approaches and insights

Computational methods such as molecular dynamics (MD) have illuminated how single-atom ions permeate membrane channels and how selectivity among them is achieved. Much less is understood about molecular permeation through eukaryotic channels that mediate the flux of small molecules (e.g. connexins, pannexins, LRRC8s, CALHMs). Here we describe computational methods that have been profitably employed to explore the movements of molecules through wide pores, revealing mechanistic insights, guiding experiments, and suggesting testable hypotheses. This review illustrates MD techniques such as voltage-driven flux, potential of mean force, and mean first-passage-time calculations, as applied to molecular permeation through wide pores. These techniques have enabled detailed and quantitative modeling of molecular interactions and movement of permeants at the atomic level. We highlight novel contributors to the transit of molecules through these wide pathways. In particular, the flexibility and anisotropic nature of permeant molecules, coupled with the dynamics of pore-lining residues, lead to bespoke permeation dynamics. As more eukaryotic large-pore channel structures and functional data become available, these insights and approaches will be important for understanding the physical principles underlying molecular permeation and as guides for experimental design.

Hydrogen-Bonded Ionic Co-Crystals for Fast Solid-State Zinc Ion Storage

The development of new ionic conductors meeting the requirements of current solid-state devices is imminent but still challenging. Hydrogen-bonded ionic co-crystals (HICs) are multi-component crystals based on hydrogen bonding and Coulombic interactions. Due to the hydrogen bond network and unique features of ionic crystals, HICs have flexible skeletons. More importantly, anion vacancies on their surface can potentially help dissociate and adsorb excess anions, forming cation transport channels at grain boundaries. Here, it is demonstrated that a HIC optimized by adjusting the ratio of zinc salt and imidazole can construct grain boundary-based fast Zn2+ transport channels. The as-obtained HIC solid electrolyte possesses an unprecedentedly high ionic conductivity at room and low temperatures (≈11.2 mS cm-1 at 25 °C and ≈2.78 mS cm-1 at -40 °C) with ultra-low activation energy (≈0.12 eV), while restraining dendrite growth and exhibiting low overpotential even at a high current density (<200 mV at 5.0 mA cm-2) during Zn symmetric cell cycling. This HIC also allows solid-state Zn||covalent organic framework full cells to work at low temperatures, providing superior stability. More importantly, the HIC can even support zinc-ion hybrid supercapacitors to work, achieving extraordinary rate capability and a power density comparable to aqueous solution-based supercapacitors. This work provides a path for designing facilely prepared, low-cost, and environmentally friendly ionic conductors with extremely high ionic conductivity and excellent interface compatibility.

Hiding in plain sight: Optimizing topoisomerase IIα inhibitors into Hsp90β selective binders

Due to their impact on several oncogenic client proteins, the Hsp90 family of chaperones has been widely studied for the development of potential anticancer agents. Although several Hsp90 inhibitors have entered clinical trials, most were unsuccessful because they induced a heat shock response (HSR). This issue can be circumvented by using isoform-selective inhibitors, but the high similarity in the ATP-binding sites between the isoforms presents a challenge. Given that Hsp90 shares a conserved Bergerat fold with bacterial DNA gyrase B and human topoisomerase IIα, we repurposed our ATP-competitive inhibitors of these two proteins for Hsp90 inhibition. We virtually screened a library of in-house inhibitors and identified eleven hits for evaluation of Hsp90 binding. Among these, compound 11 displayed low micromolar affinity for Hsp90 and demonstrated a 12-fold selectivity for Hsp90β over its closest isoform, Hsp90α. Out of 29 prepared analogs, 16 showed a preference for Hsp90β over Hsp90α. Furthermore, eleven of these compounds inhibited the growth of several cancer cell lines in vitro. Notably, compound 24e reduced intracellular levels of Hsp90 client proteins in MCF-7 cells, leading to cell cycle arrest in the G0/G1 phase without inducing HSR. This inhibitor exhibited at least a 27-fold preference for Hsp90β and was selective against topoisomerase IIα, a panel of 22 representative protein kinases, and proved to be non-toxic in a zebrafish larvae toxicology model. Finally, molecular modeling, corroborated by STD NMR studies, and the binding of 24e to the S52A mutant of Hsp90α confirmed that the serine to alanine switch drives the selectivity between the two cytoplasmic isoforms.