73 research outputs found

    The dielectric constant : reconciling simulation and experiment

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    In this paper, we present a simple correction scheme to improve predictions of dielectric constants by classical non-polarisable models. This scheme takes into account electronic polarisation effects, through the experimental refractive index of the liquid, and a possible mismatch between the potential energy surface and the dipole moment surface. We have described the latter effect by an empirical scaling factor on the point charges, the value of which was determined by fitting the dielectric constant of methanol. Application of the same scaling factor to existing benchmark datasets, comprising four different models and a wide range of compounds, led to remarkable improvements in the quality of the predictions. In particular, the observed systematic underestimation of the dielectric constant was eliminated by accounting for the two missing terms in standard models. We propose that this correction term be included in future development and validation efforts of classical non-polarisable models

    Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field

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    International audienceAll-atom molecular dynamics computer simulations were used to blindly predict the hydration free energies of a range of chloro-organic compounds as part of the SAMPL3 challenge. All compounds were parameterized within the framework of the OPLS-AA force field, using an established protocol to compute the absolute hydration free energy via a windowed free energy perturbation approach and thermodynamic integration. Three different approaches to deriving partial charge parameters were pursued: (1) using existing OPLS-AA atom types and charges with minor adjustments of partial charges on equivalent connecting atoms; (2) calculation of quantum mechanical charges via geometry optimization, followed by electrostatic potential (ESP) fitting, using Jaguar at the LMP2/cc-pVTZ(-F) level; and (3) via geometry optimization and CHelpG charges (Gaussian03 at the HF/6-31G* level), followed by two-stage RESP fitting. Protocol 3 generated the most accurate predictions with a root mean square (RMS) error of 1.2 kcal·mol −1 for the entire data set. It was found that the deficiency of the standard OPLS-AA parameters, protocol 1 (RMS error 2.4 kcal·mol −1 overall), was mostly due to compounds with more than three chlorine substituents on an aromatic ring. For this latter subset, the RMS errors were 1.4 kcal·mol −1 (protocol 3) and 4.3 kcal·mol −1 (protocol 1), respectively. We propose new OPLS-AA atom types for aromatic carbon and chlorine atoms in rings with ≥ 4 Cl-substituents that perform better than the best QM-based approach, resulting in an RMS error of 1.2 kcal·mol −1 for these difficult compounds

    Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field

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    International audienceAll-atom molecular dynamics (MD) simulations were used to predict water-cyclohexane distribution coefficients D cw of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules were parameterized with the trans-ferable all-atom OPLS-AA force field, which required the derivation of new parameters for sulfamides and heterocycles and validation of cyclohexane parameters as a solvent. The distribution coefficient was calculated from the solvation free energies of the compound in water and cyclohexane. Absolute solvation free energies were computed by an established protocol using windowed alchemical free energy perturbation with thermodynamic integration. This protocol resulted in an overall root mean square error (RMSE) in log D cw of almost 4 log units and an overall signed error of −3 compared to experimental data. There was no substantial overall difference in accuracy between simulating in NV T and NPT ensembles. The signed error suggests a systematic error but the experimental D cw data on their own are insufficient to Manuscript Click here to download Manuscript sampl5-manuscript.pdf Click here to view linked References 2 Ian M. Kenney et al. uncover the source of this error. Preliminary work suggests that the major source of error lies in the hydration free energy calculations

    Competitive Adsorption of a Multi-functional Amine and Phenol Surfactant with Ethanol on Hematite from Non-Aqueous Solution

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    Surfactants, which contain phenol and amine groups, are commonly used in industries to protect metallic surfaces, and their efficiency depends strongly on factors such as pressure and temperature, solvent properties, and the presence of other surfactants in the system. In this work, we present a molecular simulation study of the competitive adsorption between a multifunctional phenol and amine surfactant model and ethanol at the oil/solid interface formed between iso-octane and a model hematite (α-Fe2O3) slab. We show that the surfactant strongly adsorbs at the iso-octane/hematite interface in the absence of ethanol at moderate temperatures. As the concentration of ethanol is increased, the ethanol molecules compete effectively for the adsorption sites on the iron oxide surface. This competition drives the surfactant molecules to remain in the bulk solution, while ethanol forms ordered and strongly coordinated layers at the oil/solid interface, despite the well-known complete miscibility of ethanol in iso-octane in bulk under standard conditions. Potential of mean force calculations show that the free energy of adsorption of the surfactant is approximately two times larger than that for a single ethanol molecule, but the simulations also reveal that a single surfactant chain needs to displace up to five ethanol molecules to adsorb onto the surface. The end result is more favorable ethanol adsorption which agrees with the experimental analysis of similar oil/iron oxide systems also reported in this work.Industr

    Molecular-Level Insight into Charge Carrier Transport and Speciation in Solid Polymer Electrolytes by Chemically Tuning Both Polymer and Lithium Salt

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    The advent of Li-metal batteries has seen progress toward studies focused on the chemical modification of solid polymer electrolytes, involving tuning either polymer or Li salt properties to enhance the overall cell performance. This study encompasses chemically modifying simultaneously both polymer matrix and lithium salt by assessing ion coordination environments, ion transport mechanisms, and molecular speciation. First, commercially used lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) salt is taken as a reference, where F atoms become partially substituted by one or two H atoms in the −CF3 moieties of LiTFSI. These substitutions lead to the formation of lithium(difluoromethanesulfonyl)(trifluoromethanesulfonyl)imide (LiDFTFSI) and lithium bis(difluoromethanesulfonyl)imide (LiDFSI) salts. Both lithium salts promote anion immobilization and increase the lithium transference number. Second, we show that exchanging archetypal poly(ethylene oxide) (PEO) with poly(ε-caprolactone) (PCL) significantly changes charge carrier speciation. Studying the ionic structures of these polymer/Li salt combinations (LiTFSI, LiDFTFSI or LiDFSI with PEO or PCL) by combining molecular dynamics simulations and a range of experimental techniques, we provide atomistic insights to understand the solvation structure and synergistic effects that impact macroscopic properties, such as Li+ conductivity and transference number.The authors acknowledge support from the European Commission grant for Erasmus Mundus Joint Master’s Degree MESC+ under Framework Agreement Number 2018-1424/001-001-EMJMD, the EU Marie Sklodowska-Curie COFUND DESTINY project under Grant Agreement No. 945357, and the Basque Government PhD Grant. H.M. acknowledges funding from the “Departamento de Educación, Política Lingüística y Cultura del Gobierno Vasco” (Grant IT1358-22). They also thank SGI/IZO-SGIker UPV/EHU for supercomputing resources

    Difusividades de compostos bioativos em líquidos comprimidos: simulação de dinâmica molecular

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    Quercetin, a flavonoid that can be extracted from various plant sources, exhibit interesting bioactivity due to relevant antioxidant or anti-carcinogenic properties. One way of extracting this flavonoid is by solid-liquid extraction using, for example, green solvents like ethanol (EtOH) or ethyl acetate (EtOAc), which are well accepted in the food industry. Diffusivity, D12, is an important property in solid-liquid extraction, since this separation is frequently limited by mass transfer kinetics, which requires the knowledge of D12 for the accurate design and optimization of that unitary operation. The diffusivities, D12, of quercetin in ethyl acetate and ethanol were measured by the chromatographic peak broadening (CPB) method in the temperature range 30-60 °C and pressure range 1-150 bar. The diffusivities in ethanol were measured in the same laboratory by another researcher. The D12 values ranged from 3.985×10-6 to 7.826×10-6 cm2 s-1, in the case of ethanol, and 1.018×10-5 to 1.628×10-5 cm2 s-1 for ethyl acetate. The obtained D12 data followed the expected trends with temperature and pressure, namely, positive and negative derivatives, being the influence of temperature much more significant. In parallel, classical molecular dynamics (MD) simulations were performed using the GROMACS software package to estimate the diffusion coefficient in order to assess the possibility of using this computational technique to generate diffusivities for distinct pressure and temperature conditions. Different parameters sets were adopted to carry out simulations in NVT ensemble, such as the cut-off radius for short-range interactions, number of solvent and solute molecules, and simulation duration, with the objective to verify their influence on the quality of D12 estimates. The optimization of the parameters used in the MD simulations led to D12 values in good agreement with the experimental data for ethanol at 1 bar, with relative deviations less than 6.54 %. It was also shown that it is possible to obtain reliable results at higher pressures after introducing a multiplicative factor on the atoms charges of ethanol. In the case of ethyl acetate, the error at 30 °C and 1 bar was −22.51 %. Since the MD self-diffusivities of ethyl acetate also differ significantly from the experimental data, it is suggested in this work to optimize the force field parameters used to model this solvent. The agreement found between experimental and MD quercetin diffusivities in ethanol demonstrates that it is possible to obtain reliable D12 values by classical MD simulations. Further studies are suggested on the influence of different functional groups and structure of other flavonoids on D12, with a structural analysis using the radial distribution and spatial distribution function.A quercetina, um flavonoide que pode ser extraído de várias fontes vegetais, apresenta bioatividade interessante, devido às suas boas propriedades antioxidantes ou anti-carcinogénicas. Uma das técnicas de extração deste flavonoide é por extração sólido-líquido, usando, por exemplo, solventes verdes como etanol (EtOH) ou acetato de etilo (EtOAc), utilizados na indústria alimentar. A difusividade, D12, é uma propriedade importante nas extrações sólido-líquido pois, muito frequentemente, estas operações unitárias encontram-se limitadas pela cinética de transferência de massa, sendo assim relevante conhecer o coeficiente de difusão para o projeto e otimização destes processos. As difusividades da quercetina em acetato de etilo e em etanol foram medidas pelo método cromatográfico de abertura de pico (CPB), na gama de temperaturas de 303,15 a 333,15 K e de pressões de 1 a 150 bar. No caso do etanol, os valores de D12 já tinham sido medidos anteriormente, no mesmo laboratório, por outro investigador. Os valores experimentais de D12 da quercetina em etanol encontram-se entre 3,985×10-6 e 7,826×10-6 cm2 s-1, e no caso da quercetina em acetato de etilo entre 1,018×10-5 e 1,628×10-5 cm2·s-1. Os resultados experimentais obtidos seguem as dependências esperadas com a temperatura e pressão, nomeadamente, derivadas positivas e negativas, sendo a variação com a temperatura muito mais expressiva. Paralelamente, foram realizadas simulações de dinâmica molecular (MD) clássica utilizando o software GROMACS para estimar as difusividades e averiguar a possibilidade de utilizar esta técnica computacional para calcular valores de D12 noutras condições de pressão e de temperatura. Com este fim em vista, foram testados diferentes conjuntos de parâmetros em simulações no ensemble NVT, tais como o raio de corte das interações de curto alcance, número de moléculas de solvente e duração da simulação, para analisar a sua influência na exatidão das estimativas. A otimização dos parâmetros usados nas simulações de MD conduziu a valores de D12 em boa concordância com os dados experimentais no caso do etanol a 1 bar, com erro relativo inferior a 6.54 %. Foi ainda demonstrado que a pressões mais elevadas é possível obter valores fiáveis de D12, introduzindo um fator multiplicativo nas cargas dos átomos do etanol. No caso do acetato de etilo, o erro a 30 °C e 1 bar foi −22.51 %. Como os valores do coeficiente de auto-difusão do acetato de etilo, estimados por MD, diferem bastante dos valores experimentais, sugere-se neste trabalho a otimização dos parâmetros do campo de forças utilizado para modelar este solvente. A concordância entre as difusividades da quercetina em etanol medidas e estimadas por MD clássica demonstra que é realmente possível obter valores fiáveis de D12 por esta técnica computacional. Sugerem-se estudos adicionais focados em diferentes grupos funcionais e estruturas de flavonoides, através de análises estruturais usando funções de distribuição radial e de distribuição espacial.Mestrado em Engenharia Químic

    Lubricants

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    When liquids are confined into a nanometer-scale slit, the induced layering-like film structure allows the liquid to sustain non-isotropic stresses and thus be load-bearing. Such anisotropic characteristics of liquid under confinement arise naturally from the liquids’ wavenumber dependent compressibility, which does not need solidification to take place as a prerequisite. In other words, liquids under confinement can still retain fluidity with molecules being (sub-)diffusive. However, the extensively prolonged structural relaxation times can cause hysteresis of stress relaxation of confined molecules in response to the motions of confining walls and thereby rendering the quasi-static stress tensors history-dependent. In this work, by means of molecular dynamics, stress tensors of a highly confined key base-oil component, i.e., 1-decene trimer, are calculated after its relaxation from being compressed and decompressed. A maximum of 77.1 MPa normal stress discrepancy has been detected within a triple-layer boundary film. Analyses with respect to molecular morphology indicate that among the effects (e.g., confinement, molecular structure, and film density) that can potentially affect confined stresses, the ordering status of the confined molecules plays a predominant role

    Modelling water diffusion in plasticizers: development and optimization of a force field for 2,4-dinitroethylbenzene and 2,4,6-trinitroethylbenzene

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    A classical all-atom force field has been developed for 2,4,6-trinitroethylbenzene and 2,4-dinitroethylbenzene and applied in molecular dynamics simulations of the two pure and two mixed plasticizer systems. Bonding parameters and partial charges were derived through electronic and geometry optimization of the single molecules. The other required parameters were derived from values already available in the literature for generic nitro aromatic compounds, which were adjusted to reproduce to a high level of accuracy the densities of 2,4-dinitroethylbenzene, 2,4,6-trinitroethylbenzene and the energetic plasticizers K10 and R8002. This force field has been applied to both K10 and R8002, which when used as plasticizers form an energetic binder with nitrocellulose. Nitrocellulose decomposes in storage, under varying conditions, but in particular where it may become increasingly dry. Following the derivation of the force field, we have therefore applied it to calculate water diffusion coefficients for each of the different materials at 298 K and 338 K, thereby providing a starting point for understanding water behaviour in a nitrocellulose binder
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