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Entropy of Simulated Liquids Using Multiscale Cell Correlation.

ABSTRACT: Accurately calculating the entropy of liquids is an important goal, given that many processes take place in the liquid phase. Of almost equal importance is understanding the values obtained. However, there are few methods that can calculate the entropy of such systems, and fewer still to make sense of the values obtained. We present our multiscale cell correlation (MCC) method to calculate the entropy of liquids from molecular dynamics simulations. The method uses forces and torques at the molecule and united-atom levels and probability distributions of molecular coordinations and conformations. The main differences with previous work are the consistent treatment of the mean-field cell approximation to the approriate degrees of freedom, the separation of the force and torque covariance matrices, and the inclusion of conformation correlation for molecules with multiple dihedrals. MCC is applied to a broader set of 56 important industrial liquids modeled using the Generalized AMBER Force Field (GAFF) and Optimized Potentials for Liquid Simulations (OPLS) force fields with 1.14*CM1A charges. Unsigned errors versus experimental entropies are 8.7 J K - 1 mol - 1 for GAFF and 9.8 J K - 1 mol - 1 for OPLS. This is significantly better than the 2-Phase Thermodynamics method for the subset of molecules in common, which is the only other method that has been applied to such systems. MCC makes clear why the entropy has the value it does by providing a decomposition in terms of translational and rotational vibrational entropy and topographical entropy at the molecular and united-atom levels.

SUBMITTER: Ali HS

PROVIDER: S-EPMC7515279 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Entropy of Simulated Liquids Using Multiscale Cell Correlation.

Ali Hafiz Saqib HS Ali Hafiz Saqib HS Higham Jonathan J Henchman Richard H RH

Entropy (Basel, Switzerland) 20190731 8

Accurately calculating the entropy of liquids is an important goal, given that many processes take place in the liquid phase. Of almost equal importance is understanding the values obtained. However, there are few methods that can calculate the entropy of such systems, and fewer still to make sense of the values obtained. We present our multiscale cell correlation (MCC) method to calculate the entropy of liquids from molecular dynamics simulations. The method uses forces and torques at the molec ...[more]

PMID: 33267464

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Project description:This study investigated the relationship between lead (Pb) speciation determined using Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy in <10 μm particulate matter (PM10) from mining/smelting impacted Australian soils (PP, BHK5, BHK6, BHK10 and BHK11) and inhalation exposure using two simulated lung fluids [Hatch's solution, pH 7.4 and artificial lysosomal fluid (ALF), pH 4.5]. Additionally, elemental composition of Pb rich regions in PP PM10 and the post-bioaccessibility assay residuals were assessed using a combination of Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray Spectroscopy (EDX) to provide insights into how extraction using simulated lung fluids may influence Pb speciation in vitro. Correlation between Pb speciation (weighted %) and bioaccessibility (%) was assessed using Pearson r (α = 0.1 and 0.05). Lead concentration in PM10 samples ranged from 782 mg/kg (BHK6) to 7796 mg/kg (PP). Results of EXAFS analysis revealed that PP PM10 was dominated by Pb adsorbed onto clay/oxide, while the four BHK PM10 samples showed variability in the weighted % of Pb adsorbed onto clay/oxide and organic matter bound Pb, Pb phosphate, anglesite and galena. When bioaccessibility was assessed using different in vitro inhalation assays, results varied between samples and between assays, Pb bioaccessibility in Hatch's solution ranged from 24.4 to 48.4%, while in ALF, values were significantly higher (72.9-96.3%; p < 0.05). When using Hatch's solution, bioaccessibility outcomes positively correlated to anglesite (r:0.6246, p:0.0361) and negatively correlated to Pb phosphate (r: -0.9610, p:0.0041), organic bound Pb (r: -0.7079, p: 0.0578), Pb phosphate + galena + plumbojarosite (r: -0.9350, p: 0.0099). No correlation was observed between Pb bioaccessibility (%) using Hatch's solution and weighted % of Pb adsorbed onto clay/oxide and between bioaccessibility (%) using ALF and any Pb species. SEM and EDX analysis revealed that a layer of O-Pb-Ca-P-Si-Al-Fe formed during the in vitro extraction using Hatch's solution.

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Entropy of Simulated Liquids Using Multiscale Cell Correlation.

Publications

Entropy of Simulated Liquids Using Multiscale Cell Correlation.

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