Combined Molecular Dynamics Research Articles

Mechanistic insights into the electron attachment process to guanosine in the presence of arginine.

The attachment of low-energy electrons (LEEs) to DNA biomolecules leads to irreversible damage. However, the behavior of this interaction can be influenced by the presence of amino acids. Herein, we have delved into the mechanism of electron attachment to the guanosine in the presence of arginine. This study used combined molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) approaches to collect and optimize the geometries having hydrogen-bonds (H-bonds) between guanosine and arginine, respectively, followed by atom centered density matrix propagation (ADMP) simulations to assess the electron attachment ability of guanine with and without arginine. The vertical detachment energy (VDE) and natural population analysis (NPA) suggest that the electron attached to guanosine occurs more readily due to the H-bonds between guanosine and arginine. The singly occupied molecular orbitals (SOMOs), VDE, and NPA from ADMP results corroborated the idea that in the presence of arginine, the electron effectively attached to the guanosine moiety while the auto detachment process becomes less probable in the case of arg-guanosine (two-H bonds). However, in the presence of arginine, the dissociative electron attachment (DEA) process for guanosine is exothermic, while in the absence of arginine, it is endothermic. This study provides new insight into the process of radiation damaging biological systems by elucidating the DEA to DNA subunits in the presence of amino acids, paving the way for a deeper understanding of radiation-induced damage in biological systems.

Probing laser-induced structural transformation of lignin into few-layer graphene

The combined experimental study and molecular dynamics simulations elucidate laser-induced structural transformation of lignin into few-layer graphene.

A combined AIMD and DFT study of the low-energy radiation responses of GaN.

Although GaN is a promising candidate for semiconductor devices, degradation of GaN-based device performance may occur when the device is bombarded by high-energy charged particles during its application in aerospace, astronomy, and nuclear-related areas. It is thus of great significance to explore the influence of irradiation on the microstructure and electronic properties of GaN and to reveal the internal relationship between the damage mechanisms and physical characteristics. Using a combined density functional theory (DFT) and ab initio molecular dynamics (AIMD) study, we explored the low-energy recoil events in GaN and the effects of point defects on GaN. The threshold displacement energies (Eds) significantly depend on the recoil directions and the primary knock-on atoms. Moreover, the Ed values for nitrogen atoms are smaller than those for gallium atoms, indicating that the displacement of nitrogen dominates under electron irradiation and the created defects are mainly nitrogen vacancies and interstitials. The formation energy of nitrogen vacancies and interstitials is smaller than that for gallium vacancies and interstitials, which is consistent with the AIMD results. Although the created defects improve the elastic compliance of GaN, these radiation damage states deteriorate its ability to resist external compression. Meanwhile, these point defects lead the Debye temperature to decrease and thus increase the thermal expansion coefficients of GaN. As for the electronic properties of defective GaN, the point defects have various effects, i.e., VN (N vacancy), Gaint (Ga interstitial), Nint (N interstitial), and GaN (Ga occupying the N lattice site) defects induce the metallicity, and NGa (N occupying the Ga lattice site) defects decrease the band gap. The presented results provide underlying mechanisms for defect generation in GaN, and advance the fundamental understanding of the radiation resistances of semiconductor materials.

Adsorption of molecular hydrogen on Be3Al2(SiO3)6-beryl: theoretical insights for catalysis, hydrogen storage, gas separation, sensing, and environmental applications.

Employing a combination of Density Functional Theory (DFT) calculations and Molecular Dynamics (MD) simulations, the adsorption of molecular hydrogen (H2) on Be3Al2(SiO3)6-beryl, a prominent silicate mineral, has been studied. The crystal structure of beryl, which consists of interconnected tetrahedral and octahedral sites, provides a fascinating framework for comprehending H2 adsorption behavior. Initial investigation of the interaction between H2 molecules and the beryl surface employed DFT calculations. We identified favorable adsorption sites and gained insight into the binding mechanism through extensive structural optimizations and energy calculations. H2 molecules preferentially adsorb on the exposed oxygen atoms surrounding the octahedral sites, producing weak van der Waals interactions with the beryl surface, according to our findings. To further investigate the dynamic aspects of H2 adsorption, MD simulations employing a suitable force field were conducted. To precisely represent interatomic interactions within the Be3Al2(SiO3)6-beryl-H2 system, the force field parameters were meticulously parameterized. By subjecting the system to a variety of temperatures, we were able to obtain valuable information about the stability, diffusion, and desorption kinetics of H2 molecules within the beryl structure. The comprehensive understanding of the H2 adsorption phenomenon on Be3Al2(SiO3)6-beryl is provided by the combined DFT and MD investigations. The results elucidate the mechanisms underlying H2 binding, highlighting the role of surface oxygen atoms and the effect of temperature on H2 dynamics. This research contributes to a fundamental understanding of hydrogen storage and release in beryllium-based silicates and provides valuable guidance for the design and optimization of materials for hydrogen storage, catalysis, gas separation, sensing and environmental applications.

Analogs of α-conotoxin PnIC selectively inhibit α7β2- over α7-only subtype nicotinic acetylcholine receptors via a novel allosteric mechanism.

This study was undertaken to identify and characterize the first ligands capable of selectively identifying nicotinic acetylcholine receptors containing α7 and β2 subunits (α7β2-nAChR subtype). Basal forebrain cholinergic neurons express α7β2-nAChR. Here, they appear to mediate neuronal dysfunction induced by the elevated levels of oligomeric amyloid-β associated with early Alzheimer's disease. Additional work indicates that α7β2-nAChR are expressed across several further critically important cholinergic and GABAergic neuronal circuits within the central nervous system. Further studies, however, are significantly hindered by the inability of currently available ligands to distinguish heteromeric α7β2-nAChR from the closely related and more widespread homomeric α7-only-nAChR subtype. Functional screening using two-electrode voltage-clamp electrophysiology identified a family of α7β2-nAChR-selective analogs of α-conotoxin PnIC (α-CtxPnIC). A combined electrophysiology, functional kinetics, site-directed mutagenesis, and molecular dynamics approach was used to further characterize the α7β2-nAChR selectivity and site of action of these α-CtxPnIC analogs. We determined that α7β2-nAChR selectivity of α-CtxPnIC analogs arises from interactions at a site distinct from the orthosteric agonist-binding site shared between α7β2- and α7-only-nAChR. As numerous previously identified α-Ctx ligands are competitive antagonists of orthosteric agonist-binding sites, this study profoundly expands the scope of use of α-Ctx ligands (which have already provided important nAChR research and translational breakthroughs). More immediately, analogs of α-CtxPnIC promise to enable, for the first time, both comprehensive mapping of the distribution of α7β2-nAChR and detailed investigations of their physiological roles.

On the origin of the electronic and magnetic circular dichroism of naphthyl C-glycosides: Anomeric configuration

Aryl C-glycosides, in which the glycosidic bond is changed to a carbon–carbon bond, are an important family of biologically-active compounds. They often serve as secondary metabolites or exhibit antibiotic and cytostatic activities. Their stability to hydrolysis has made them attractive targets for new drugs. Their conformational behavior often strongly influences the resulting function. Their detailed structural and conformational description is thus highly desirable.This work studies the structure of three different naphthyl C-glycosides using UV–vis absorption as well as electronic and magnetic circular dichroism. It also describes their conformational preferences using a combination of molecular dynamics and DFT calculations. The reliability of these preferences has been verified by simulations of spectral properties and a comparison with their measured spectra. In particular, ECD spectroscopy has been shown to distinguish easily between α- and β-pseudoanomers of aryl C-glycosides. Computer simulations and spectral decomposition have revealed how the resulting ECD patterns of the naphthyl glycosides studied are influenced by different conformer populations. In conclusion, reliable ECD patterns cannot be calculated by separating the naphthyl rotation from other conformational motions. MCD patterns have been similar for all the naphthyl C-glycosides studied. No clear diagnostic features have been found for either the pseudoanomeric configuration or the preferred hydroxymethyl rotamer. Nevertheless, the work has demonstrated the potential of MCD for the study of aryl glycosides interacting with proteins.

A method to improve the barrier performance of flexible riser internal pressure sheath—Heat transfer experiment and simulation

AbstractA considerable amount of acidic gas penetrates into the annulus between the internal pressure sheath and the outer protective sheath during the service of flexible risers, which will inevitably lead to corrosion of the metal functional layer. Many researchers have modified nanocomposites from the mass transfer perspective to reduce the materials' permeability coefficient. While permeation is an integrated process of heat and mass transfer process, heat distribution directly impacts gas permeation. Herein, the thermal conductivity of flexible riser liner materials is predicted for the first time by a combination of molecular dynamics and experiments, and then the radial temperature distribution under different seawater temperatures and internal fluid temperatures is investigated by finite element analysis. Finally, the effect of temperature distribution on the permeation coefficient was analyzed. The results demonstrate that the thermal conductivity can be predicted by molecular dynamics simulation, and the thermal conductivity of (polyvinylidene difluoride) PVDF/TiO2 decreases, while the thermal conductivity of PVDF/carbon nanotube (CNT) increases compared with pure PVDF. The temperature distribution of the internal pressure sheath material decreases when condensate water is present. As the fluid temperature rises from 30 to 110°C, the maximum increase ratio in the permeability of PVDF/CNT over PVDF increased from 3.6% to 14.8%, and the maximum decrease ratio of PVDF/TiO2 permeability coefficient compared with PVDF is from 1.2% to 4.6%. The results present a new idea to improve the barrier properties of materials by decreasing thermal conductivity.

Probing binding and occlusion of substrate in the human creatine transporter-1 by computation and mutagenesis.

In chordates, energy buffering is achieved in part through phosphocreatine, which requires cellular uptake of creatine by the membrane-embedded creatine transporter (CRT1/SLC6A8). Mutations in human slc6a8 lead to creatine transporter deficiency syndrome, for which there is only limited treatment. Here, we used a combined homology modeling, molecular dynamics, and experimental approach to generate a structural model of CRT1. Our observations support the following conclusions: contrary to previous proposals, C144, a key residue in the substrate binding site, is not present in a charged state. Similarly, the side chain D458 must be present in a protonated form to maintain the structural integrity of CRT1. Finally, we identified that the interaction chain Y148-creatine-Na+ is essential to the process of occlusion, which occurs via a "hold-and-pull" mechanism. The model should be useful to study the impact of disease-associated point mutations on the folding of CRT1 and identify approaches which correct folding-deficient mutants.

Molecular insights into the CO2 absorption mechanism by superbase protic ionic liquids by a combined density functional theory and molecular dynamics approach

Protic ionic liquids (PILs) are emerging as a new class of sustainable and efficient solvents for CO2 capture, requiring a fundamental understanding of their properties for their optimal design. To obtain a molecular-level understanding of the mechanism behind CO2 absorption in this class of absorbents, we selected four novel and high-efficient PILs prepared from superbase 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) and 1,5-diazabicyclo[4.3.0]-5-nonene (DBN) as cations, with imidazole (Im) and pyrazole (Pyr) as anions. Density functional theory (DFT) and molecular dynamics (MD) simulations were used to quantify their interactions and reaction mechanisms as well as the dynamics of the CO2 absorption process. Results indicate that CO2 primarily interacts with the anions of PILs through van der Waals forces, while the cations and anions of PILs mainly engage in strong hydrogen-bonding interactions. Additionally, the anions primarily serve as the absorption reaction sites for CO2, with their molecule centers of mass being the closest. Meanwhile, reaction with CO2 requires overcoming a relatively low energy barrier (i.e., ∼35–40 kJ·mol−1), making them more favorable for regeneration than benchmark solvents. Notably, MD simulations have also shown that CO2 molecules are preferentially accumulating at the gas/PILs interfaces and that chemisorption is leading the CO2 capture at low pressures in these PILs. Among the studied systems [DBUH][Pyr] is the most reacting system with CO2, while [DBUH][Pyr] shows the lower regeneration energy. The findings would shed more light on understanding and designing PILs for CO2 capture.

Molecular dynamics study on the effect of inorganic salts on the wettability of surfactants on bituminous coal: Sodium dodecyl sulfate and sodium chloride as representatives

To further enhance the wetting ability of surfactants to coal, the mechanism of improving the wetting performance of SDS to bituminous coal by the addition of inorganic salt NaCl was studied through a combination of molecular dynamics (MD) simulation with experimental measurements. In the experiment part, the surface tensions of the mixed NaCl-SDS solutions and the contact angles on the bituminous coal surface were measured. Furthermore, MD simulations were conducted to investigate the adsorption characteristics and wetting mechanism of a mixed NaCl-SDS solution on the coal surface at the atomic scale. In this process, the static potentials of the H2O molecule, coal molecule and SDS molecule were calculated, and the number of hydrogen bonds (H-bonds) formed throughout the whole simulation process, the average H-bond length, the relative concentration distribution (RCD) curve and the mean square displacement (MSD) curve were obtained. The experimental results showed that the surface tension and contact angle were both decreased by the addition of sodium chloride in mixed solutions. When 0.6 mol/L NaCl was added, the surface tension and contact angle reached the minima of 30.45 mN/m and 13.01°, respectively. The MD simulation results showed that, after the addition of NaCl, diffusion and migration of H2O molecules were limited, the number of H-bonds increases, the average bond length decreased, the sorption between H2O molecules and coal molecules was enhanced, and the hydrophilicity of coal surface was improved, which meant that the wetting ability of SDS solution to bituminous coal was enhanced by adding NaCl. The effect of the added NaCl in improving the wettability of SDS on coal was explored from two perspectives with macroscopic experiments and microcosmic simulations, and the added NaCl improved the effects of dust suppressants, and played a key role in preventing dust hazards in coal mines.

Fluorine-free and hot water repellent superhydrophobic palygorskite: A combined experimental and molecular dynamics study

The present work investigates the wettability of dodecyltrimethoxysilane (DTMS) functionalized palygorskite (PAL) using both experimental and molecular dynamics approaches. The best superhydrophobicity was achieved at a PAL/DTMS ratio of 0.60 g/mL. Changes in wettability were simulated by varying the DTMS grafting ratio from perspectives of contact angle, interaction energy, the water molecule’s distribution characteristics, and hydrogen bonds. The results show that DTMS grafting promotes hydrophobicity, whereas excess grafting ratio declines hydrophobicity due to roughness decrease. The hot water resistance was analyzed from interaction energy, diffusion behavior, and cohesion energy, and the findings are consistent with the experimental results.

Unraveling the structural and dynamic heterogeneities of hydroxyl-functionalized di-cationic ionic liquids (HFDILs): An integrated ab initio and molecular dynamics approach

This study comprehensively investigates the effects of hydroxyl groups in side chains and cation symmetry on intra- and inter-molecular structures, dynamics, and thermodynamic properties of two hydroxyl-functionalized di-cationic ionic liquids (HFDILs). Using a combination of molecular dynamics (MD) simulations and quantum chemistry (QC) calculations, we compare the influence of these effects on various properties with corresponding non-hydroxyl DILs reported in previous works. The structure of HFDILs is explored using angle distribution, radial distribution, spatial distribution, and combined distribution functions. Also, the averaged noncovalent interaction (aNCI) analysis is used to characterize the weak noncovalent interactions in fluctuating environment of HFDILs. Results showed that the oxygen atoms of anion have the strongest interaction with the hydrogen atom of hydroxyl group, followed by the hydrogen atom at the top of the imidazolium ring. Domain analysis and Voronoi calculations are performed to investigate the number of polar and non-polar subunits, revealing that symmetric HFDILs with two hydroxyl groups in their side chains have greater structural heterogeneity than asymmetric ones with only one hydroxyl group due to the larger accumulation of non-polar subunits. To investigate dynamical heterogeneity, we calculate the non-Gaussian parameter, van Hove correlation, hydrogen bond, ion pair, ion cage, and reorientation dynamics. Results indicated that symmetric HFDILs have slower dynamics, greater dynamic heterogeneity, and more stability than asymmetric ones. Finally, the structure and strength of ion triplet interactions are examined using quantum mechanical methods, revealing that symmetric HFDILs are more stable than asymmetric ones. This study provides valuable information for understanding DILs and their potential applications in various fields.

Elevator-like movements of prestin mediate outer hair cell electromotility

The outstanding acuity of the mammalian ear relies on cochlear amplification, an active mechanism based on the electromotility (eM) of outer hair cells. eM is a piezoelectric mechanism generated by little-understood, voltage-induced conformational changes of the anion transporter homolog prestin (SLC26A5). We used a combination of molecular dynamics (MD) simulations and biophysical approaches to identify the structural dynamics of prestin that mediate eM. MD simulations showed that prestin samples a vast conformational landscape with expanded (ES) and compact (CS) states beyond previously reported prestin structures. Transition from CS to ES is dominated by the translational-rotational movement of prestin’s transport domain, akin to elevator-type substrate translocation by related solute carriers. Reversible transition between CS and ES states was supported experimentally by cysteine accessibility scanning, cysteine cross-linking between transport and scaffold domains, and voltage-clamp fluorometry (VCF). Our data demonstrate that prestin’s piezoelectric dynamics recapitulate essential steps of a structurally conserved ion transport cycle.

Effect of thermal fluctuations on the electronic excitation energies of linear polyenes: A combined molecular dynamics and TD‐DFT study

AbstractIn the present study, thermally averaged electronic excitation energies (the so‐called dynamic approach) are quantitatively assessed for a model molecular system composed of a series of increasingly longer chains of simple linear polyenes. The molecular dynamics trajectories are calculated using the semi‐empirical “Geometry, Frequency, Noncovalent, eXtended Tight Binding” (GFN2‐xTB) method, while TD‐DFT vertical excitation energies of selected snapshots are obtained with the spin‐component‐scaled double hybrid density functional SCS‐wPBEPP86. Boltzmann weighted average excitation energies were then calculated in order to take into account the contribution of thermal motions. Excitation energies via the dynamic approach are compared with that of the static approach in which thermal fluctuations are not considered. The differences between the dynamic and the static approaches were found to be around the range to eV for polyenes up to 44 carbon atoms. This range of errors is relatively small in comparison with typical errors produced by using different density functionals and/or basis sets. Therefore, the electronic excited states of small to medium lengths of linear polyenes (less than 50 carbon atoms) can be safely modeled via the static approach. However, extrapolation of the results to longer polyenes indicates that the difference between both approaches is estimated to be 0.05 eV for polyenes containing 100 carbon atoms, which suggests that considering thermal motions in the calculations of excitation energies is recommended for such long conjugated molecular systems.

Molecular mechanism of EAG1 channel inhibition by imipramine binding to the PAS domain

Ether-a-go-go (EAG) channels are key regulators of neuronal excitability and tumorigenesis. EAG channels contain an N-terminal Per-Arnt-Sim (PAS) domain that can regulate currents from EAG channels by binding small molecules. The molecular mechanism of this regulation is not clear. Using surface plasmon resonance and electrophysiology we show that a small molecule ligand imipramine can bind to the PAS domain of EAG1 channels and inhibit EAG1 currents via this binding. We further used a combination of molecular dynamics (MD) simulations, electrophysiology, and mutagenesis to investigate the molecular mechanism of EAG1 current inhibition by imipramine binding to the PAS domain. We found that Tyr71, located at the entrance to the PAS domain cavity, serves as a "gatekeeper" limiting access of imipramine to the cavity. MD simulations indicate that the hydrophobic electrostatic profile of the cavity facilitates imipramine binding and in silico mutations of hydrophobic cavity-lining residues to negatively charged glutamates decreased imipramine binding. Probing the PAS domain cavity-lining residues with site-directed mutagenesis, guided by MD simulations, identified D39 and R84 as residues essential for the EAG1 channel inhibition by imipramine binding to the PAS domain. Taken together, our study identified specific residues in the PAS domain that could increase or decrease EAG1 current inhibition by imipramine binding to the PAS domain. These findings should further the understanding of molecular mechanisms of EAG1 channel regulation by ligands and facilitate the development of therapeutic agents targeting these channels.

In-situ gelation based on rapid crosslinking: A versatile bionic water-based lubrication strategy

Hydrogel is emerging as a new water-based lubricant due to its enhanced load-bearing capacity and lubrication effect in industrial process and biological application. But the loss and degradation issues in long-term usage become a bottleneck for its further development. Hence how to realize the continuous supplement of hydrogel lubricant in the friction process with an instant response to shear stress becomes a highly expected goal. In this study, inspired by the regeneration of cartilage, a surface engineering strategy is first put forward based on chemically active interface and cross-linking gelation, in which Borax as cross-linking agent is released in-situ with the grinding debris in friction process from polyimide/Borax composite coating into the polyvinyl alcohol (PVA) solution, followed with instant gelation to form effective lubrication mediate layer between contact interface. The combined experimental and molecular dynamics simulation studies suggest that the enhanced intermolecular interaction in hydrogel layer which highly depends on cross-linking degree, together with hydrodynamic effect is responsible for the excellent lubrication and high adaptability to various working condition even under the high contact stress of 175.90 MPa. The similar tribological performances in other chemically active interface-fluid combination systems demonstrate the versatility of this facile strategy.

Research on Representative Volume Element Fex-Cy High-Temperature Mechanical Model Based on Response Surface Analysis

In this research, a multi-scale representative volume element method is introduced that combines the temperature and stress fields to analyze the force field distribution around microcracks in low-carbon steel using a combination of molecular dynamics and finite element analysis. Initially, an orthogonal experimental design was used to design the molecular dynamics simulation experiments. Next, a nano-level uniaxial tensile test model for mild steel was established based on the experimental design, and the uniaxial tensile behavior of low-carbon steel was investigated using molecular dynamics. Lastly, mathematical models of the modulus of elasticity E and yield strength Q of mild steel at a high temperature were obtained statistically using the response surface methodology. Meanwhile, a finite element model with a coupled temperature–stress field was established to investigate the force field distribution around the microscopic defects, and the microscopic crack stress concentration coefficient K was revised. The results indicate that regardless of the location of microcracks within the structure, the stress distribution due to size effects should be considered under high-temperature loading.

Elucidating Interfacial Dynamics of Ti-Al Systems Using Molecular Dynamics Simulation and Markov State Modeling.

Due to their remarkable mechanical and chemical properties, Ti-Al-based materials are attracting considerable interest in numerous fields of engineering, such as automotive, aerospace, and defense. With their low density, high strength, and resistance to corrosion and oxidation, these intermetallic alloys and metal-compound composites have found diverse applications. However, additive manufacturing and heat treatment of Ti-Al alloys frequently lead to brittleness and severe formation of defects. The present study delves into the interfacial dynamics of these Ti-Al systems, particularly focusing on the behavior of Ti and Al atoms in the presence of TiAl3 grain boundaries under experimental heat treatment conditions. Using a combination of molecular dynamics and Markov state modeling, we scrutinize the kinetic processes involved in the formation of TiAl3. The molecular dynamics simulation indicates that at the early stage of heat treatment, the predominating process is the diffusion of Al atoms toward the Ti surface through the TiAl3 grain boundaries. Markov state modeling identifies three distinct dynamic states of Al atoms within the Ti/Al mixture that forms during the process, each exhibiting a unique spatial distribution. Using transition time scales as a qualitative measure of the rapidness of the dynamics, it is observed that the Al dynamics is significantly less rapid near the Ti surface compared to the Al surface. Put together, the results offer a comprehensive understanding of the interfacial dynamics and reveal a three-stage diffusion mechanism. The process initiates with the premelting of Al, proceeds with the prevalent diffusion of Al atoms toward the Ti surface, and eventually ceases as the Ti concentration within the mixture progressively increases. The insights gained from this study could contribute significantly to the control and optimization of manufacturing processes for these high-performing Ti-Al-based materials.

Combined density functional theory and molecular dynamics analyses on Lithium/Sodium ion interaction and diffusion in gel polymer electrolytes with poly-vinylidene fluoride scaffold, propylene carbonate/Ionic Liquid solvent, and perchlorate salt

Choice of a proper electrolyte is very crucial to enhance the overall performance of a metal-ion battery. In this work, dispersion corrected density functional theory and classical molecular dynamics simulations are carried out to explore the metal ion (Li+ and Na+) interaction and diffusion through polyvinylidene fluoride (PVDF)-based gel polymer electrolytes. Four types of polymer/solvent/salt electrolyte systems are investigated considering PVDF scaffold for each case, and conventionally used propylene carbonate and rarely used, albeit cheaper, ionic liquid [BMIM][ClO4] as solvent, along with metal perchlorate salts LiClO4 and NaClO4. Inter-unit interactions within the electrolyte clusters, electrolyte uptake, and electrochemical stability of the electrolytes are explained by gas-phase DFT analyses, considering the polymer/solvent/salt components in 1:1:1 molecular ratio. Diffusion of the ions and ionic conductivity of the electrolytes are explored by MD simulation referring to two different size and time scales. From the DFT-based non-bonding interaction analyses, metal ions are found to exhibit strong non-covalent interactions with the adjacent O and F atoms, where the O atoms are parts of PC and [ClO4]- ions, and F atoms are from the PVDF chains. [BMIM]+, [ClO4]-, and PVDF are found to interact through weak van der Waals type hydrogen bonds. Both DFT and MD calculations suggest that, Li+ and Na+ ions are primarily coordinated with [ClO4]- ions. Dynamics studies confirm that for PVDF/IL/salt, total ionic conductivity is predominated by [BMIM]+ and [ClO4]-, exhibiting lower metal ion diffusivity as compared to PC-containing electrolytes. For both Li- and Na-ion systems, owing to the availability of higher number of charge carriers, electrolytes containing ILs show higher ionic conductivity compared to those containing PC as the solvent.

A Computational Chemistry Approach to the Molecular Design of SiO2 Nanoparticles Coated with Stearic Acid and Sodium Stearate in Ethanol Solvent.

Preparation of hydrophobic SiO2 nanoparticles (NPs) coated with different surfactants is important due to their potential application in different fields of chemistry. In this work, a combined experimental and Molecular Dynamics (MD) simulation approach, is advanced to characterize the adsorption process, in ethanol as a solvent, of stearic acid and sodium stearate on SiO2 spherical NPs with different ionization degrees (0%, 10%, and 23.3%). The main objective is to gain molecular insight into the factors involved in the preparation of hydrophobic coated NPs, which involves the intervention of ion-dipole, electrostatic, and hydrogen bond-type interactions depending on the surfactants and the nature SiO2 NPs. Our results demonstrate that the SiO2 NPs have a good affinity for ethanol solvent medium., as confirmed through the analysis of the Radial Distribution Functions (RDFs)), which indicates that hydrogen bonds are formed at a distance of ∼0.192 nm between ethanol and SiO2 NPs. The presence of Na+ ions reduce the electrostatic repulsion between the -COO- and -SiO- groups in NPs with degrees of ionization of 10% and 23.3%, because it acts as a bridge and thus favors the adsorption between the silanol and carboxylic groups. The investigation of the Potentials of Mean Force (PMFs) suggests that the adsorption on these NPs, is a spontaneous process compared with the case with 0% ionization degree. The experimental coating of the NPs was studied using Atomic Force Microscopy (AFM), a technique that allows the indirect measure of the Work of Adhesion (Wadh), a key quantity to estimate the energy needed to separate the interfaces AFM tip-sample. The experimental values of Wadh for the pure SiO2 NPs and two modified SiO2 NPs correspond to 2.01 J/m2, 1.72 J/m2 and 1.43 J/m2, respectively. The main conclusion is that the interaction energies between surfactants and SiO2 NPs, estimated from MD simulations, and the Wadh obtained from AFM measurements are correlated, in the sense that the reduction in the Wadh, in a solvent-free environment, corresponds to an increment of the interaction energy in the presence of the solvent. This reduction in Wadh is also associated with the fact that the nature of the coating of the SiO2 NPs surfaces increases the NPs hydrophobicity. Our analysis provides a path for the computational design and the prediction of hydrophobicity of coated NPs, which is the main focus of our work.