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The sustainable development encompasses the search for new materials for energy storage, gas capture, separation, and solvents in industrial processes that can substitute conventional ones in an efficient and clean manner. Ionic liquids (ILs) emerged and have been advanced as alternative materials for such applications, but an obstacle is their hygroscopicity and the effects on their physical properties in the presence of humidity. Several industrial processes depend on the aqueous interfacial properties, and the main focus of this work is the water/IL interface. The behavior of the aqueous ionic liquids at the water-vacuum interface is representative for their water interfacial properties. Using X-ray photoelectron spectroscopy in combination with molecular dynamics simulations we investigate four aqueous IL systems, and provide molecular level insight on the interfacial behaviour of the ionic liquids, such as ion-pair formation, orientation and surface concentration. We find that ionic liquids containing a chloride anion have a lowered surface enrichment due to the low surface propensity of chloride. In contrast, the ionic liquids containing a bistriflimide anion are extremely surface-enriched due to cooperative surface propensity between the cations and anions, forming a two-dimensional ionic liquid on the water surface at low concentrations.
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The increasing oxidative stress demands potential chemical compounds derived from natural resources with good antioxidant activity to overcome adverse health issues. In this context, we investigated the antioxidant properties of four dibenzopyrone phenolic compounds obtained from the endophytic fungus Alternaria alternata: altenusin, altenusin B, alterlactone, and dehydroaltenusin using DFT calculations. Our investigation focused on understanding the structure-antioxidant property relationship. It delved into probing the activity by modelling the antioxidant mechanisms. The computed transition states and thermochemical parameters, along with the structural attributes, indicate that altenusin B has good antioxidant efficacy among the four compounds, and it follows the HAT mechanism in an aqueous phase. Remarkably, our findings indicate that altenusin B exhibits potent HOOË radical scavenging properties, characterized by the computed high rate constant. The molecular docking studies of these compounds with the pro-oxidant enzyme xanthine oxidase (XO) gave insights into the binding modes of the compounds in the protein environment. Furthermore, molecular dynamics (MD) simulations were employed to study the interaction and stability of the compounds inside the XO enzyme. Our exploration sheds light on the radical scavenging potential of the -OH sites and the underlying antioxidant mechanisms that underpin the compounds' effective antioxidant potential.
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Alternaria , Antioxidantes , Compuestos de Bifenilo , Antioxidantes/farmacología , Antioxidantes/química , Simulación del Acoplamiento Molecular , Alternaria/química , Fenoles/química , Modelos TeóricosRESUMEN
Understanding excited-state intramolecular proton transfer (ESIPT) is essential for designing organic molecules to enhance photophysical and luminophore properties in the development of optoelectronic devices. In this context, an attempt has been made to understand the impact of substituents on the ESIPT process of 2-(oxazolinyl)-phenol. Electron donating (EDG: -NH2, -OCH3, and -CH3) and electron withdrawing (EWG: -Cl, -Br, -COOH, -CF3, -CN, and -NO2) substitutions have been computationally designed and screened through density functional theory (DFT) and time-dependent density-functional theory (TDDFT) calculations. Furthermore, the ground state intramolecular proton transfer and ESIPT mechanisms of these designed luminophores are explored using the transition state theory. The results reveal that molecules with EDG show higher absorption and emission peaks than molecules with EWG and also indicate that the mobility of charge carriers in 2-(oxazolinyl)-phenol derivatives is significantly influenced by substituents. We found that the EWGs decrease the reorganization energy and increase the vertical ionization potential and electron affinity values, as well as the highest occupied molecular orbital-lowest unoccupied molecular orbital gap, compared to the EDG substituted molecules. Significantly, the excited state (S1) of the keto emission (K) form shows notably larger values for the EDG substitutions. The intersystem crossing pathway efficiency weakens with reduced spin-orbit coupling matrix element in the enol form with electron-donating substituents and vice versa in the keto form during S1-T3 transitions. Our research links intramolecular proton transfers and triplet generation, making these substituted molecules appealing for optoelectronic devices. Introducing EDGs, such as -NH2, boosts the ESIPT reaction in 2-(oxazolinyl)-phenol. This study guides designing ESIPT emitters with unique photophysical properties.
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Electrochemical Double Layer Capacitors (EDLCs) with ionic liquid electrolytes outperform conventional ones using aqueous and organic electrolytes in energy density and safety. However, understanding the electrochemical behaviors of ionic liquid electrolytes under compressive/tensile strain is essential for the design of flexible EDLCs as well as normal EDLCs, which are subject to external forces during assembly. Despite many experimental studies, the compression/stretching effects on the performance of ionic liquid EDLCs remain inconclusive and controversial. In addition, there is hardly any evidence of prior theoretical work done in this area, which makes the literature on this topic scarce. Herein, for the first time, we developed an atomistic model to study the processes underlying the electrochemical behaviors of ionic liquids in an EDLC under strain. Constant potential non-equilibrium molecular dynamics simulations are conducted for EMIM BF4 placed between two graphene walls as electrodes. Compared to zero strain, low compression of the EDLC resulted in compromised performance as the electrode charge density dropped by 29%, and the performance reduction deteriorated significantly with a further increase in compression. In contrast, stretching is found to enhance the performance by increasing the charge storage in the electrodes by 7%. The performance changes with compression and stretching are due to changes in the double-layer structure. In addition, an increase in the value of the applied potential during the application of strain leads to capacity retention with compression revealed by the newly performed simulations.
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Metal-organic frameworks (MOFs) constitute a class of three-dimensional porous materials that have shown applicability for carbon dioxide capture at low pressures, which is particularly advantageous in dealing with the well-known environmental problem related to the carbon dioxide emissions into the atmosphere. In this work, the effect of changing the metallic center in the inorganic counterpart of MIL-53 (X), where X = Fe3+, Al3+, and Cu2+, has been assessed over the ability of the porous material to adsorb carbon dioxide by means of first-principles theory. In general, the non-spin polarized computational method has led to adsorption energies in fair agreement with the experimental outcomes, where the carbon dioxide stabilizes at the pore center through long-range interactions via oxygen atoms with the axial hydroxyl groups in the inorganic counterpart. However, spin-polarization effects in connection with the Hubbard corrections, on Fe 3d and Cu 3d states, were needed to properly describe the metal orbital occupancy in the open-shell systems (Fe- and Cu-based MOFs). This methodology gave rise to a coherent high-spin configuration, with five unpaired electrons, for Fe atoms leading to a better agreement with the experimental results. Within the GGA+U level of theory, the binding energy for the Cu-based MOF is found to be Eb = -35.85 kJ/mol, which is within the desirable values for gas capture applications. Moreover, it has been verified that the adsorption energetics is dominated by the gas-framework and internal weak interactions.
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The world desperately needs new technologies and solutions for gas capture and separation. To make this possible, molecular modeling is applied here to investigate the structural, thermodynamic, and dynamical properties of a model for the poly(urethane urea) (PUU) oligomer model to selectively capture CO2 in the presence of CH4. In this work, we applied a well-known approach to derive atomic partial charges for atoms in a polymer chain based on self-consistent sampling using quantum chemistry and stochastic dynamics. The interactions of the gases with the PUU model were studied in a pure gas based system as well as in a gas mixture. A detailed structure characterization revealed high interaction of CO2 molecules with the hard segments of the PUU. Therefore, the structural and energy properties explain the reasons for the greater CO2 sorption than CH4. We find that the CO2 sorption is higher than the CH4 with a selectivity of 7.5 at 298 K for the gas mixture. We characterized the Gibbs dividing surface for each system, and the CO2 is confined for a long time at the gas-oligomer model interface. The simulated oligomer model showed performance above the 2008 Robeson's upper bound and may be a potential material for CO2/CH4 separation. Further computational and experimental studies are needed to evaluate the material.
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The harmonic angle bending potential is used in many force fields for (bio)molecular simulation. The force associated with this potential is discontinuous at angles close to 180°, which can lead to numeric instabilities. Angle bending of linear groups, such as alkynes or nitriles, or linear molecules, such as carbon dioxide, can be treated by a simple harmonic potential if we describe the fluctuations as a deviation from a reference position of the central atom, the position of which is determined by the flanking atoms. The force constant for the linear angle potential can be derived analytically from the corresponding force constant in the traditional potential. The new potential is tested on the properties of alkynes, nitriles, and carbon dioxide. We find that the angles of the linear groups remain about 2° closer to 180° using the new potential. The bond and angle force constants for carbon dioxide were tuned to reproduce the experimentally determined frequencies. An interesting finding was that simulations of liquid carbon dioxide under pressure with the new flexible model were stable only when explicitly modeling the long-range Lennard-Jones (LJ) interactions due to the very long-range nature of the LJ interactions (>1.7 nm). In the other tested liquids, we find that a Lennard-Jones cutoff of 1.1 nm yields similar results as the particle mesh Ewald algorithm for LJ interactions. Algorithmic factors influencing the stability of liquid simulations are discussed as well. Finally, we demonstrate that the linear angle potential can be used in free energy perturbation calculations.
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Classical molecular dynamics simulations were performed on twelve different ionic liquids containing aprotic heterocyclic anions doped with Li+. These ionic liquids have been shown to be promising electrolytes for lithium ion batteries. Self-diffusivities, lithium transference numbers, densities, and free volumes were computed as a function of lithium concentration. The dynamics and free volume decreased with increasing lithium concentration, and the trends were rationalized by examining the changes to the liquid structure. Of those examined in the present work, it was found that (methyloxymethyl)triethylphosphonium triazolide ionic liquids have the overall best performance.
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The properties of five deep eutectic solvents prepared based on the selection of choline chloride ionic liquid as hydrogen bond acceptor, which are mixed with several hydrogen bond donors with selected molecular features, were studied theoretically at graphene interfaces via both density functional theory and classical molecular dynamics methods. Molecular structuring at the interfaces, angular orientation, densification, and dynamic properties were analyzed upon adsorption on the graphene surface and when the deep eutectic solvents were confined between two graphene sheets and analyzed in terms of the role of the type of hydrogen bond donor for each solvent. Likewise, the behavior of deep eutectic solvent nanodroplets on graphene was simulated leading to the calculation of contact angles and nanowetting with further studies considering the effect of an external electric field on nanodroplet properties.
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Despite the innumerous papers regarding the study of the ionic liquids as a potential candidate for CO2 capture, many details concerning the structure and dynamics of CO2 in the system are still to be revealed, i.e., the correlation between the local environment structure and the dynamic properties of the substance. This present work relied on the performance of molecular dynamics both for the neat [C2mim][Tf2N] and [C2mim][Tf2N]/CO2 mixtures in an attempt to elucidate the local environment of CO2 and their effects on the dynamic properties of [C2mim][Tf2N]. A slight change in the orientation of the cation and anion could be observed, which was correlated to the cation and anion moving away from each other in order to receive the carbon dioxide. The gas molecules pushed both the cation and the anion away to create sufficient void to its accommodation. The diffusion coefficient of [C2mim]+ is higher than [Tf2N]- regardless the increase of the CO2 concentration. The addition of CO2 in the ionic liquid has shown an increase of 4-5 times for the diffusivity of ions, which was related to the decrease of cation-anion interaction strength. The transport properties' results showed that the addition of CO2 in the ionic liquid generates the fluidization of the system, decreasing the viscosity as a consequence of the local environment structure changing. Likewise, the effect of the type of anion and cation on the system properties was studied considering [Ac]- and [BMpyr]+ ions, showing large effects by the change of anion to [Ac]- which rise from the strong [C2mim]+-[Ac]- interaction, which conditions the solvation of ions by CO2 molecules.
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Among the alternative host materials for solid polymer electrolytes (SPEs), polycarbonates have recently shown promising functionality in all-solid-state lithium batteries from ambient to elevated temperatures. While the computational and experimental investigations of ion conduction in conventional polyethers have been extensive, the ion transport in polycarbonates has been much less studied. The present work investigates the ionic transport behavior in SPEs based on poly(trimethylene carbonate) (PTMC) and its co-polymer with ε-caprolactone (CL) via both experimental and computational approaches. FTIR spectra indicated a preferential local coordination between Li(+) and ester carbonyl oxygen atoms in the P(TMC20CL80) co-polymer SPE. Diffusion NMR revealed that the co-polymer SPE also displays higher ion mobilities than PTMC. For both systems, locally oriented polymer domains, a few hundred nanometers in size and with limited connections between them, were inferred from the NMR spin relaxation and diffusion data. Potentiostatic polarization experiments revealed notably higher cationic transference numbers in the polycarbonate based SPEs as compared to conventional polyether based SPEs. In addition, MD simulations provided atomic-scale insight into the structure-dynamics properties, including confirmation of a preferential Li(+)-carbonyl oxygen atom coordination, with a preference in coordination to the ester based monomers. A coupling of the Li-ion dynamics to the polymer chain dynamics was indicated by both simulations and experiments.
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This paper presents atomistic molecular dynamics simulation studies of lithium bis(trifluoromethane)sulfonylimide (LiTFSI) in a blend of 1-ethyl-3-methylimidazolium (EMIm)-TFSI and poly(ethylene oxide) (PEO), which is a promising electrolyte material for Li- and Li-ion batteries. Simulations of 100 ns were performed for temperatures between 303 K and 423 K, for a Li:ether oxygen ratio of 1:16, and for PEO chains with 26 EO repeating units. Li(+) coordination and transportation were studied in the ternary electrolyte system, i.e., PEO16LiTFSIâ 1.0 EMImTFSI, by applying three different force field models and are here compared to relevant simulation and experimental data. The force fields generated significantly different results, where a scaled charge model displayed the most reasonable comparisons with previous work and overall consistency. It is generally seen that the Li cations are primarily coordinated to polymer chains and less coupled to TFSI anion. The addition of EMImTFSI in the electrolyte system enhances Li diffusion, associated to the enhanced TFSI dynamics observed when increasing the overall TFSI anion concentration in the polymer matrix.
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Suministros de Energía Eléctrica , Electrólitos/química , Imidazoles/química , Líquidos Iónicos/química , Compuestos de Litio/química , Polietilenglicoles/química , Sulfonamidas/química , Difusión , Simulación de Dinámica Molecular , Estructura Molecular , TemperaturaRESUMEN
Emissions of greenhouse gases due to human activities have been well documented as well as the effects on global warming resulting from it. Efforts to reduce greenhouse gases at the source are crucial to curb climate change, but due to insignificant economic incentives to reduce usage of fossil fuels, not a lot of progress has been made by this route. This necessitates additional measures to reduce the occurrence of greenhouse gases in the atmosphere. Here we used theoretical methods to study the solubility of carbon dioxide in ionic liquids (ILs) since sequestration of CO2 in ILs has been proposed as a possible technology for reducing the emissions of CO2 to the atmosphere. Ionic liquids form a class of solvents with melting temperatures below 100 °C and, due to very low vapor pressures, which are not volatile. We have performed molecular dynamics (MD) simulations of 1-ethyl-3-methylimidazolium (C2mim) bis(trifluoromethylsulfonyl)imide (Tf2N) and its mixtures with carbon dioxide in order to investigate the CO2 concentration effect on the CO2-cation and CO2-anion interactions. A systematic investigation of CO2 concentration effects on resulting equilibrium liquid structure, and the local environment of the ions is provided. The Quantum Theory of Atoms in Molecules (QTAIM) was used to determine the interaction energy for CO2-cation and CO2-anion complexes from uncorrelated structures derived from MD simulations. A spatial distribution function analysis demonstrates the specific interactions between CO2 and the ionic liquid. Our findings indicate that the total volume of the system increases with the CO2 concentration, with a molar volume of CO2 of about 0.038 L/mol, corresponding to liquid CO2 under a pressure of 100 bar. In other words, the IL effectively pressurizes the CO2 inside its matrix. The thermodynamics of CO2 solvation in C2 min-Tf2N were computed using free energy techniques, and the solubility of CO2 is found to be higher in this IL (-3.7 ± 1 kcal/mol) than in water (+0.2 kJ/mol), predominantly due to anion-CO2 interactions.
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Dióxido de Carbono/química , Imidazoles/química , Imidas/química , Líquidos Iónicos/química , Secuestro de Carbono , Simulación de Dinámica Molecular , SolubilidadRESUMEN
Zirconia oxide (ZrO2) is a material that has aroused great interest in the scientific community for its general use in various technological applications, such as fuel cells, solar cells, electronic devices, catalysis, dental biomaterial and ceramics. When it is applied as a catalyst, the doping and vacancy effects of their crystalline phases are important properties to guide new developments. This work investigates tetragonal and monoclinic crystalline phases of the Zn-doped ZrO2 by periodic density functional calculations. Changes in the electronic and acid-basic properties were performed by Bader charge analysis, the density of states calculations (DOS) and the projected density of states (PDOS). The formation of oxygen vacancies was also evaluated. The calculated oxygen vacancy formation energies indicate that it is much easier to generate oxygen vacancy in the Zn-doped ZrO2 than in the pure material; in addition, oxygen vacancy formation is favored in the monoclinic phase. Bader charge analyses and projected density of states indicated that the doping of ZrO2 with Zn creates more basic and acid sites. The most stable material is the Zn-doped 3-fold coordinated Zr atom of the m-ZrO2, which can be used for future developments and applications.
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Plants from the Garcinia genus have been used worldwide due to their therapeutic properties. Among the various metabolites isolated from this genus, 7-epi-clusianone, a tetraprenylated benzophenone, stands out for its wide range of identified biological activities. This benzophenone can exist in five tautomeric forms, although the benzene-d6 and chloroform-d3 solution nuclear magnetic resonance (NMR) spectra revealed only two tautomeric forms (B and C) in equilibrium, with concentration ratio depending on the solvent in which the spectrum was obtained. Calculated energy values suggested that tautomeric forms B and E would be prevalent in benzene-d6 solution, in contrast to the experimental data. Considering this conflicting result, we employed the statistical DP4 + method based on 13C and 1H NMR chemical shift calculations, in the gas phase and in benzene-d6 solution, to confirm that the B and C tautomeric forms of 7-epi-clusianone are the most prevalent in the experimental conditions.
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Benceno , Benzofenonas , Benzoquinonas , Espectroscopía de Resonancia Magnética , Modelos Teóricos , Conformación MolecularRESUMEN
Structural and dynamical properties of liquid trimethylphosphine (TMP), (CH(3))(3)P, as a function of temperature is investigated by molecular dynamics (MD) simulations. The force field used in the MD simulations, which has been proposed from molecular mechanics and quantum chemistry calculations, is able to reproduce the experimental density of liquid TMP at room temperature. Equilibrium structure is investigated by the usual radial distribution function, g(r), and also in the reciprocal space by the static structure factor, S(k). On the basis of center of mass distances, liquid TMP behaves like a simple liquid of almost spherical particles, but orientational correlation due to dipole-dipole interactions is revealed at short-range distances. Single particle and collective dynamics are investigated by several time correlation functions. At high temperatures, diffusion and reorientation occur at the same time range as relaxation of the liquid structure. Decoupling of these dynamic properties starts below ca. 220 K, when rattling dynamics of a given TMP molecules due to the cage effect of neighbouring molecules becomes important.
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Herein, molecular modeling techniques were used with the main goal to obtain candidates from a drug database as potential targets to be used against SARS-CoV-2. This novel coronavirus, responsible by the COVID-19 outbreak since the end of 2019, became a challenge since there is not vaccine for this disease. The first step in this investigation was to solvate the isolated S-protein in water for molecular dynamics (MD) simulation, being observed a transition from "up" to "down" conformation of receptor-binding domain (RBD) of the S-protein with angle of 54.3 and 43.0 degrees, respectively. The RBD region was more exposed to the solvent and to the possible drugs due to its enhanced surface area. From the equilibrated MD structure, virtual screening by docking calculations were performed using a library contained 9091 FDA approved drugs. Among them, 24 best-scored ligands (14 traditional herbal isolate and 10 approved drugs) with the binding energy below -8.1 kcal/mol were selected as potential candidates to inhibit the SARS-CoV-2 S-protein, preventing the human cell infection and their replication. For instance, the ivermectin drug (present in our list of promise candidates) was recently used successful to control viral replication in vitro. MD simulations were performed for the three best ligands@S-protein complexes and the binding energies were calculated using the MM/PBSA approach. Overall, it is highlighted an important strategy, some key residues, and chemical groups which may be considered on clinical trials for COVID-19 outbreak. [Formula: see text]Communicated by Ramaswamy H. Sarma.
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COVID-19 , Preparaciones Farmacéuticas , Reposicionamiento de Medicamentos , Humanos , Simulación del Acoplamiento Molecular , SARS-CoV-2RESUMEN
Microtubules have been widely studied in recent decades as an important pharmacological target for the treatment of cancer especially due to its key role in the mitosis process. Among the constituents of the microtubules, αß-tubulin dimers stand out in view of their four distinct interaction sites, including the so-called colchicine binding site (CBS) - a promising target for the development of new tubulin modulators. When compared to other tubulin sites, targeting the CBS is advantageous because this site is able to host ligands with lower molecular volume and lipophilicity, thus reducing the chances of entailing the phenomenon of multiple drug resistance (MDR) - one of the main reasons of failure in chemotherapy. However, colchicine, the first ligand ever discovered with affinity towards the CBS, despite modulating the action of microtubules, has shown toxicity in clinical studies. Therefore, in order to expand the known chemical space of scaffolds capable of interacting with CBS and to design non-toxic colchicine binding site inhibitors, we conducted a robust virtual screening pipeline. This has been rigorously validated and consisted of ligand- and structure-based methodologies, which allowed us to select four promising CBS inhibitors called tubLCQF1-4. These four compounds were also evaluated with long trajectories molecular dynamics simulations and respective results were used for the theoretical determination of the free energy released in the formation of the complexes, using the Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) methodology.
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Colchicina , Simulación de Dinámica Molecular , Sitios de Unión , Simulación del Acoplamiento Molecular , Moduladores de Tubulina/farmacologíaRESUMEN
Increasing the ionic conductivity has for decades been an overriding goal in the development of solid polymer electrolytes. According to fundamental theories on ion transport mechanisms in polymers, the ionic conductivity is strongly correlated to free volume and segmental mobility of the polymer for the conventional transport processes. Therefore, incorporating plasticizing side chains onto the main chain of the polymer host often appears as a clear-cut strategy to improve the ionic conductivity of the system through lowering of the glass transition temperature (T g). This intended correlation between T g and ionic conductivity is, however, not consistently observed in practice. The aim of this study is therefore to elucidate this interplay between segmental mobility and polymer structure in polymer electrolyte systems comprising plasticizing side chains. To this end, we utilize the synthetic versatility of the ion-conductive poly(trimethylene carbonate) (PTMC) platform. Two types of host polymers with side chains added to a PTMC backbone are employed, and the resulting electrolytes are investigated together with the side chain-free analogue both by experiment and with molecular dynamics (MD) simulations. The results show that while added side chains do indeed lead to a lower T g, the total ionic conductivity is highest in the host matrix without side chains. It was seen in the MD simulations that while side chains promote ionic mobility associated with the polymer chain, the more efficient interchain hopping transport mechanism occurs with a higher probability in the system without side chains. This is connected to a significantly higher solvation site diversity for the Li+ ions in the side-chain-free system, providing better conduction paths. These results strongly indicate that the side chains in fact restrict the mobility of the Li+ ions in the polymer hosts.
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Lithium-metal batteries are promising candidates to fulfill the future performance requirements for energy storage applications. However, the tendency to form metallic dendrites and the undesirable side reactions between the electrolyte and the Li electrode lead to poor performance and safety issues in these batteries. Therefore, understanding the interfacial properties and the Li-metal surface/electrolyte interactions is crucial to resolve the remaining obstacles and make these devices feasible. Here, we report a computational study on the interface effects in ternary polymer electrolytes composed by poly(ethylene oxide) (PEO), lithium salts, and different ionic liquids (ILs) confined between two Li-metal slabs. Atomistic simulations are used to characterize the local environment of the Li+ ions and the transport properties in the bulk and at the interface regions. Aggregation of ions at the metal surface is seen in all investigated systems; the structure and composition are directly correlated to the IL components. The strong interactions between the electrolyte species and the Li-metal atoms result in the structuring of the electrolyte at the interface region, in which comparatively small and flat ions result in a well-defined region with extensive Li+ populations and high self-diffusion coefficients. In contrast, large ions such as [P222mom]+ increase the PEO density in the bulk due to large steric effects at the interface. Therefore, the choice of specific ILs in ternary polymer electrolytes can tune the structure-dynamic properties at the Li-metal surface/electrolyte interface, controlling the SEI formation at the electrode surface, and thereby improve battery performance.