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The vapor-liquid equilibrium of binary mixtures of xenon + S[F.sub.6] was measured at nine temperatures from 235.34 to 295.79 K and pressure up to 6.5 MPa. The mixture critical line is continuous between the critical points of the pure components, hence the system is classified as type 1 phase behavior in the scheme of van Konynenburg and Scott.

Ab initio quantum chemical calculations were carried out to determine the structural properties as well as the intramolecular potentials for alkyl-substituted polyhedral oligomeric silsequioxane (POSS) macromolecules. The results indicated that the length of the linear hydrocarbon chain does not affect the structural or electronic properties of the POSS cage to which it is covalently bound.

An experimental and theoretical study of the thermodynamic properties of semifluorinated alkanes is performed. The results are interpreted using the SAFT-VR equation of state and the results are able to predict the thermodynamic behavior of the perfluoroalkylalkanes.

A charge-transfer reactive (CTR) force field along with other force fields taken from literature is used to predict the thermophysical properties of polyhedral oligomeric silsesquioxanes (POSS). All the force fields tested performed satisfactorily, but results indicate that the literature force field Hybrid-COMPASS and CTR predict structural properties of systems that contain POSS monomers, through molecular simulation.

The infinite dilution properties of two water +n-alkane mixtures by using a statistical associating fluid theory (SAFT) are presented. Recent theoretical and simulation studies suggest an unexpected shift in the solubility of n-alkanes in near critical water.

A study of the thermodynamic functions of the liquid mixtures xenon + n-butane and xenon + isobutane is presented. It is shown that the mixtures have a similar behavior to that of other xenon + alkane mixtures.

Measurements of total vapor pressures for liquid mixtures of xenon + propane at 161.40, 182.34 and 195.49 K and of xenone + ethane at 161.40 and 182.34 K reveal negative deviations from Raoult's law at all temperatures. The thermodynamics of the two liquid mixtures are further discussed.

The statistical associating fluid theory for chain molecules with attractive potentials for variable range was used to investigate the fluid-phase equilibria of the methane + n-hexane system. The system was found to exhibit a type V phase behavior, in which the two components display partial miscibility. The region of liquid-liquid immiscibility was accurately predicted by using the Lorentz-Berthelot mixing rules.

A statistical associating fluid theory for potential of variable range is developed to model dipolar fluids (SAFT-VR+D) and the high-pressure phase diagram of hydrogen sulfide + n-alkane binary mixtures is examined. The SAFT-VR+D theory has explored and predicted the effect of temperature and the molecular weight of the hydrocarbon component on the solubility of [H.sub.2]S in the n-alkanes.

The equilibrium molecular dynamics simulation results for polyhedral oligomeric silsesquioxanes (POSS) monomers dissolved in liquid normal hexane at 300 K and at 400 K are reported.

The statistical associating fluid theory for potentials of variable range (SAFT-VR) equation of state is extended to account for quadrupolar interactions by using a Pade-approximation term derived from perturbation theory. The inclusion of the quadrupolar interaction into the SAFT-VR equation improves the predictive ability of the SAFT-VR EOS when studying the phase behavior of alkane + nitrogen systems and reduces the need to use effective parameters by explicitly including at the molecular level interactions due to the quadrupole moment.

Molecular-simulation results for POSS-POSS radial distribution functions (where POSS=polyhedral oligomeric silsesquioxane), potentials of mean force, and self-diffusion coefficients for POSS monomers dissolved in poly(dimethylsiloxane) are presented. Results demonstrate that it is possible to modulate the effective POSS-POSS interaction by increasing the temperature or by substituting by hydrogen atoms in the POSS monomer with methyl groups.

A new apparatus, based on the static and analytical method, is developed for the study of vapor-liquid or vapor-liquid-liquid equilibrium. The equilibrium vapor pressures of (xenon + methane) binary mixtures are measured and the results have been correlated by the Peng-Robinson equation of state.

Statistical associating fluid theory for potentials of variable attractive range (SAFT-VR) is used in studying high-pressure equilibria in perfluoro-(n)-alkane + (n)-alkane binary mixtures. These compounds undergo large positive deviations from Raoult's Law while the phase behavior changes from type II to type III. The perfluoro-n-alkane and n-alkane molecules are assumed to be attractive spherical segments tangentially bonded together to form chains. The critical lines predicted by SAFT-VR for the mixtures are in close agreement with experimental data.

We have developed a multi-input E( n ) equivariant graph convolution-based model designed for the prediction of chemical properties that result from the interaction of heterogeneous molecular structures. By incorporating spatial features and constraining the functions learned from these features to be equivariant to E( n ) symmetries, the interactional-equivariant graph neural network (IEGNN) can efficiently learn from the 3D structure of multiple molecules. To verify the IEGNN's capability to learn interactional properties, we tested the model's performance on three molecular data sets, two of which are curated in this study and made publicly available for future interactional model benchmarking. To enable the loading of these data sets, an open-source data structure based on the PyTorch Geometric library for batch loading multigraph data points is also created. Finally, the IEGNN's performance on a data set consisting of an unknown interactional relationship (the frictional properties resulting between monolayers with variable composition) is examined. The IEGNN model developed was found to have the lowest mean absolute percent error for the predicted tribological properties of four of the six data sets when compared to previous methods.

MoSDeF-GOMC is a python interface for the Monte Carlo software GOMC to the Molecular Simulation Design Framework (MoSDeF) ecosystem. MoSDeF-GOMC automates the process of generating initial coordinates, assigning force field parameters, and writing coordinate (PDB), connectivity (PSF), force field parameter, and simulation control files. The software lowers entry barriers for novice users while allowing advanced users to create complex workflows that encapsulate simulation setup, execution, and data analysis in a single script. All relevant simulation parameters are encoded within the workflow, ensuring reproducible simulations. MoSDeF-GOMC's capabilities are illustrated through a number of examples, including prediction of the adsorption isotherm for CO 2 in IRMOF-1, free energies of hydration for neon and radon over a broad temperature range, and the vapor-liquid coexistence curve of a four-component surrogate for the jet fuel S-8. The MoSDeF-GOMC software is available on GitHub at https://github.com/GOMC-WSU/MoSDeF-GOMC.

Molecular dynamics simulations of mixtures of the ceramide nonhydroxy-sphingosine (NS), cholesterol, and a free fatty acid are performed to gain molecular-level understanding of the structure of the lipids found in the stratum corneum layer of skin. A new coarse-grained force field for cholesterol was developed using the multistate iterative Boltzmann inversion (MS-IBI) method. The coarse-grained cholesterol force field is compatible with previously developed coarse-grained force fields for ceramide NS, free fatty acids, and water and validated against atomistic simulations of these lipids using the CHARMM force field. Self-assembly simulations of multilayer structures using these coarse-grained force fields are performed, revealing that a large fraction of the ceramides adopt extended conformations, which cannot occur in the single bilayer in water structures typically studied using molecular simulation. Cholesterol fluidizes the membrane by promoting packing defects, and an increase in cholesterol content is found to reduce the bilayer thickness due to an increase in interdigitation of the C 24 lipid tails, consistent with experimental observations. Using a reverse-mapping procedure, a self-assembled coarse-grained multilayer system is used to construct an equivalent structure with atomistic resolution. Simulations of this atomistic structure are found to closely agree with experimentally derived neutron scattering length density profiles. Significant interlayer hydrogen bonding is observed in the inner layers of the atomistic multilayer structure that are not found in the outer layers in contact with water or in equivalent bilayer structures. This work highlights the importance of simulating multilayer structures, as compared to the more commonly studied bilayer systems, to enable more appropriate comparisons with multilayer experimental membranes. These results also provide validation of the efficacy of the MS-IBI derived coarse-grained force fields and the framework for multiscale simulation.

The structural properties of two- and three-component gel-phase bilayers were studied using molecular dynamics simulations. The bilayers contain distearoylphosphatidylcholine (DSPC) phospholipids mixed with alcohols and/or fatty acids of varying tail lengths, with carbon chain lengths of 12, 16, and 24 studied. Changes in both headgroup chemistry and tail length are found to affect the balance between steric repulsion and van der Waals attraction within the bilayers, manifesting in different bilayer structural properties. Lipid components are found to be located at different depths within the bilayer depending on both chain length and headgroup chemistry. The highest bilayer ordering and lowest area per tail are found in systems with medium-length tails. While longer tails can enhance van der Waals attractions, the increased tail-length asymmetry is found to induce disorder and reduce tail packing. Bulkier headgroups further increase steric repulsion, as reflected in increased component offsets and reduced tail packing. These findings help explain how bilayer composition affects the structure of gel-phase bilayers.

We demonstrate how the recently developed Python-based Molecular Simulation and Design Framework (MoSDeF) can be used to perform molecular dynamics screening of functionalized monolayer films, focusing on tribological effectiveness. MoSDeF is an open-source package that allows for the programmatic construction and parametrization of soft matter systems and enables TRUE (transferable, reproducible, usable by others, and extensible) simulations. The MoSDeF-enabled screening identifies several film chemistries that simultaneously show low coefficients of friction and adhesion. We additionally develop a Python library that utilizes the RDKit cheminformatics library and the scikit-learn machine learning library that allows for the development of predictive models for the tribology of functionalized monolayer films and use this model to extract information on terminal group characteristics that most influence tribology, based on the screening data.

Despite the ubiquity of nanoparticles in modern materials research, computational scientists are often forced to choose between simulations featuring detailed models of only a few nanoparticles or simplified models with many nanoparticles. Herein, we present a coarse-grained model for amorphous silica nanoparticles with parameters derived via potential matching to atomistic nanoparticle data, thus enabling large-scale simulations of realistic models of silica nanoparticles. Interaction parameters are optimized to match a range of nanoparticle diameters in order to increase transferability with nanoparticle size. Analytical functions are determined such that interaction parameters can be obtained for nanoparticles with arbitrary coarse-grained fidelity. The procedure is shown to be extensible to the derivation of cross-interaction parameters between coarse-grained nanoparticles and other moieties and validated for systems of grafted nanoparticles. The optimization procedure used is available as an open-source Python package and should be readily extensible to models of non-silica nanoparticles.

Interfacial properties of n-alkylsilane monolayers on silica have been investigated with molecular dynamics simulations using both reactive and classical (i.e., nonreactive) force fields. A synthesis mimetic simulation (SMS) procedure using the reactive force field ReaxFF has been developed to mimic the experimental processing of silicon wafers involved in the preparation of alkylsilane monolayers; in the SMS procedure, amorphous silica surfaces are generated and exposed to hydrogen peroxide (H2O2) to create a hydroxide surface layer. Alkylsilane monolayers are then assembled on these surfaces, and their behavior is studied. To investigate the impact of the SMS procedure on monolayer properties, simulations have also been performed using more idealized monolayers assembled on crystalline surfaces and non-H2O2-processed amorphous surfaces. The simulations reported here demonstrate that processing-induced silica surface roughness plays a key role in the structure and frictional performance of monolayers. Furthermore, ignoring these effects results in a significant underestimation of the coefficient of friction and an overestimation of the orientational ordering of the monolayers.

The vapor pressure of four liquid perfluoroalkylalkanes (CF3(CF2)n(CH2)mCH3; n = 3, m = 4,5,7; n = 5, m = 5) was measured as a function of temperature between 278 and 328 K. Molar enthalpies of vaporization were calculated from the experimental data, and the results were compared with data from the literature for the corresponding alkanes and perfluoroalkanes. The heterosegmented statistical associating fluid theory was used to interpret the results at the molecular level both with and without the explicit inclusion of the dipolar nature of the molecules. Additionally, ab initio calculations were performed for all perfluoroalkylalkanes studied to determine the dipole moment to be used in the theoretical calculations. We demonstrate that the inclusion of a dipolar term is essential for describing the vapor-liquid equilibria of perfluoroalkylalkanes. It is also shown that vapor-liquid equilibria in these compounds result from a subtle balance between dipolar interactions, which decrease the vapor pressure, and the relatively weak dispersive interactions between the hydrogenated and fluorinated segments.

Ceramides are known to be a key component of the stratum corneum, the outermost protective layer of the skin that controls barrier function. In this work, molecular dynamics simulations are used to examine the behavior of ceramide bilayers, focusing on non-hydroxy sphingosine (NS) and non-hydroxy phytosphingosine (NP) ceramides. Here, we propose a modified version of the CHARMM force field for ceramide simulation, which is directly compared to the more commonly used GROMOS-based force field of Berger (Biophys. J. 1997, 72); while both force fields are shown to closely match experiment from a structural standpoint at the physiological temperature of skin, the modified CHARMM force field is better able to capture the thermotropic phase transitions observed in experiment. The role of ceramide chemistry and its impact on structural ordering is examined by comparing ceramide NS to NP, using the validated CHARMM-based force field. These simulations demonstrate that changing from ceramide NS to NP results in changes to the orientation of the OH groups in the lipid headgroups. The arrangement of OH groups perpendicular to the bilayer normal for ceramide NP, verse parallel for NS, results in the formation of a distinct hydrogen bonding network, that is ultimately responsible for shifting the gel-to-liquid phase transition to higher temperature, in direct agreement with experiment.

In nature, processive and non-processive cellulase enzymes deconstruct cellulose to soluble sugars. From structural studies, the consensus is that processive cellulases exhibit tunnels lined with aromatic and polar residues, whereas non-processive cellulases exhibit open clefts with fewer ligand contacts. To gain additional insight into the differences between processive and non-processive cellulases, we examine the glycoside hydrolase family 7 (GH7) cellobiohydrolase, Cel7A, and the endoglucanase, Cel7B, from Trichoderma reesei with molecular simulation. We compare properties related to processivity and compute the binding affinity changes for mutation of four aromatic residues lining the Cel7A active site tunnel and Cel7B cleft to alanine. For the wild-type enzymes, dissimilar behavior is observed at nearly every glucopyranose-binding site from -7 to +2, except in the -2 site, suggesting that the structural differences directly around the catalytic center and at the active site tunnel entrances and exits may all contribute to processivity in GH7s. Interestingly, the -2 site is similar in both enzymes, likely due to the significant conformational change needed in the cellodextrin ligand near this site for catalysis. Moreover, aromatic residue mutations in the Cel7A and Cel7B active sites display only small differences in binding affinity, but the ligand flexibility and enzyme-ligand interactions are only locally affected in Cel7A, whereas the entire ligand is significantly affected when any aromatic residue is mutated in Cel7B.

Because of small surface area to volume ratios nanoscale devices can exhibit dominant surface forces that can quickly degrade unlubricated contacting surfaces. While fluorinated materials have been widely used as lubricants, because of their low critical surface tension and high thermal and mechanical stability, fluorinated monolayer coatings, which are suitable for lubricating nanoscale devices, are less effective as lubricants. Although fluorinated monolayers are more stable than their hydrocarbon counterparts against elevated temperature and humidity, they are known to exhibit higher frictional forces. To overcome this issue, here we study mixed monolayers composed of both hydrocarbon and fluorocarbon chains. Hydrocarbon-based monolayers have been widely studied and shown to improve frictional properties and device life. To investigate the frictional behavior of mixed fluorocarbon/hydrocarbon monolayers, molecular dynamics simulations of pure hydrogenated and fluorinated chains and mixed fluorinated/hydrogenated chains on silica surfaces have been performed. The adhesion and friction between the nanoconfined monolayers as a function of normal load, chain length, and chemical composition of the monolayer coating have been investigated, and mixed fluorocarbon/hydrocarbon monolayers found to outperform both pure fluorocarbon and pure hydrocarbon monolayers. Surface coverage was found to have a significant effect on the performance of all systems studied with higher surface coverage resulting in lower frictional forces. The simulations also show that when the hydrocarbon chains in the monolayer are longer than the fluorocarbon chains, a liquidlike layer is formed by the longer hydrocarbon chains that protrudes above the shorter fluorocarbon chains and aids in friction reduction. A frictional load dependence is also seen in these mixed monolayer systems because of repulsive interactions between the fluorocarbon base layer and the hydrocarbon liquidlike layer. A chain length difference of eight carbons between the base layer and the liquidlike layer was found to provide the lowest friction, while both a larger (because of increased entanglement) and a smaller (insufficient atoms between the contacting base layers to form a liquidlike layer) chain length difference increased friction.

We report the frictional performance and long-term tribological stability of various alkyl silane monolayer films on silicon by using pin-on-disk tribometry at ambient conditions. We show that the durability of monolayers derived from n-alkyltrichlorosilanes on silicon increases exponentially with the chain length of the silane precursor, which we relate to the cohesive energy of these monolayers through molecular dynamics simulations. X-ray photoelectron spectroscopy (XPS) was used to show that tribological damage consisted of the loss of molecular components that could be partially replaced upon exposure to a solution containing perfluorinated silane precursors. For monolayers derived from n-octadecyltrichlorosilane, a critical load was identified to be approximately 250 mN (200 MPa), above which failure of films occurred within 100 cycles of testing. Monolayers with hydroxyl surfaces exhibited reduced stabilities due to stronger tip-surface interactions. Monolayers with the capability for cross-linking exhibited much greater stabilities than monolayers where cross-linking was limited or prevented. Collectively, these results demonstrate that the mechanical durability of monolayers when subjected to a tribological load is greatly enhanced by maximizing dispersional interactions and cross-linking and minimizing tip-surface interactions.

This Article presents a quantitative comparison of the frictional performance for monolayers derived from n-alkanethiolates on gold and n-alkyl trichlorosilanes on silicon. Monolayers were characterized by pin-on-disk tribometry, contact angle analysis, ellipsometry, and electrochemical impedance spectroscopy (EIS). Pin-on-disk microtribometry provided frictional analysis at applied normal loads from 10 to 1000 mN at a speed of 0.1 mm/s. At low loads (10 mN), methyl-terminated n-alkanethiolate self-assembled monolayers (SAMs) exhibited a 3-fold improvement in coefficient of friction over SAMs with hydroxyl- or carboxylic-acid-terminated surfaces. For monolayers prepared from both n-alkanethiols on gold and n-alkyl trichlorosilanes on silicon, a critical chain length of at least eight carbons is required for beneficial tribological performance at an applied load of 9.8 mN. Evidence for disruption of chemisorbed alkanethiolate SAMs with chain lengths n

The effect of 1-n-butyl-3-methylimidazolium nitrate ionic liquid (IL) on the shear dynamics and tribological properties of contacting ordered alkylsilane self-assembled monolayers (SAM) on SiO(2) surfaces was studied using molecular dynamics simulation. Use of the IL as a lubricant was found to reduce the friction between the contacting monolayers in the studied range of applied loads. At low applied loads, complex behavior in the dependency of the frictional force on the normal load in both lubricated and dry monolayers is observed and is shown to be due to the rearrangement of the SAM chains under shear. In contrast, this dependency was found to be linear at high normal loads. The simulations also indicate that the ordering of the SAM chains may be disrupted by penetrating lubricant molecules, suggesting that the IL could incorporate into a damaged area of the SAM coating and restore tribological properties. To our knowledge, this is the first simulation study of the effect of an IL lubricant on the frictional dynamics of SAMs.

A statistical associating fluid theory for potential of variable range has been recently developed to model dipolar fluids (SAFT-VR+D) [Zhao and McCabe, J. Chem. Phys. 2006, 125, 104504]. The SAFT-VR+D equation explicitly accounts for dipolar interactions and their effect on the thermodynamics and structure of a fluid by using the generalized mean spherical approximation (GMSA) to describe a reference fluid of dipolar square-well segments. In this work, we apply the SAFT-VR+D approach to real mixtures of dipolar fluids. In particular, we examine the high-pressure phase diagram of hydrogen sulfide+n-alkane binary mixtures. Hydrogen sulfide is modeled as an associating spherical molecule with four off-center sites to mimic hydrogen bonding and an embedded dipole moment (micro) to describe the polarity of H2S. The n-alkane molecules are modeled as spherical segments tangentially bonded together to form chains of length m, as in the original SAFT-VR approach. By using simple Lorentz-Berthelot combining rules, the theoretical predictions from the SAFT-VR+D equation are found to be in excellent overall agreement with experimental data. In particular, the theory is able to accurately describe the different types of phase behavior observed for these mixtures as the molecular weight of the alkane is varied: type III phase behavior, according to the scheme of classification by Scott and Konynenburg, for the H2S+methane system, type IIA (with the presence of azeotropy) for the H2S+ethane and+propane mixtures; and type I phase behavior for mixtures of H2S and longer n-alkanes up to n-decane. The theory is also able to predict in a qualitative manner the solubility of hydrogen sulfide in heavy n-alkanes.

Ab initio quantum mechanical calculations have been performed to establish the potentials for alkyl-substituted polyhedral oligomeric silsesquioxane (POSS) monomers RxH8-x(SiO1.5)8. More specifically, we have examined the unsubstituted POSS (SiO1.5H)8 cage as well as linear and cyclic alkyl-substituted cages where one of the terminating hydrogen atoms is replaced by a hydrocarbon group, that is, R1H7(SiO1.5)8. The results for the minimum-energy configurations indicate that the presence of the linear hydrocarbon chains and cyclic intermediates have very little effect on the structure of the POSS cage. Although the POSS monomeric cage does influence the partial charges of the first few carbon atoms covalently bound to the POSS monomer, its effect on the structural properties of the alkyl chain is small. Differences arise, however, for cyclic alkyl substitutents bound to the POSS cage due to the repulsive interactions between the POSS cage and bulkier cyclic intermediates that result upon rotation of the Si-C-C-C dihedral angles. The interatomic potentials for these rotational, or torsional, terms need to be modified slightly in order to appropriately simulate sterically hindered substitutents on the cage. Our results suggest that combining an atomistic force field independently developed to describe silsesquioxanes with an independent atomistic model developed to describe hydrocarbon chains can be used in classical molecular simulation studies of most alkyl-silsesquioxanes. This avoids the need to develop specific force fields for each substituted POSS cage studied and opens up the possibility of using molecular simulation to probe the thermodynamic and structural properties of these unique nanoscale building blocks.

The phase behavior of nitrogen + n-alkanes is studied within the framework of the statistical associating fluid theory for potentials of variable range (SAFT-VR). The effect of the quadrupole moment of nitrogen on the phase behavior is considered through an extension of the SAFT-VR equation that includes an additional contribution to the Helmholtz free energy due to quadrupolar interactions. A significant improvement in the description of the phase diagram of the binary mixtures of nitrogen with different n-alkanes is obtained with the new approach when compared to predictions from the original SAFT-VR EOS (i.e., without the quadrupolar term). The experimental value for the quadrupole moment of nitrogen is used in the new equation; thus, no additional parameters are employed. Given the nonideal nature of the binary mixtures, a binary interaction parameter is needed to describe the full-phase diagram and high-pressure critical lines of these systems; however, this can be fitted to a single system and successfully used to predict the phase behavior of other binary mixtures without additional fitting. Furthermore, only a single, transferable, cross-energy parameter is required when the quadrupolar term is considered, whereas a cross-range parameter is also needed with the original SAFT-VR approach. The inclusion of the quadrupolar term in the equation of state therefore reduces the need to use effective parameters by explicitly including at the molecular level interactions due to the quadrupole moment.

The SAFT-VRX equation of state combines the SAFT-VR equation with a crossover function that smoothly transforms the classical equation into a nonanalytical form close to the critical point. By a combinination of the accuracy of the SAFT-VR approach away from the critical region with the asymptotic scaling behavior seen at the critical point of real fluids, the SAFT-VRX equation can accurately describe the global fluid phase diagram. In previous work, we demonstrated that the SAFT-VRX equation very accurately describes the pvT and phase behavior of both nonassociating and associating pure fluids, with a minimum of fitting to experimental data. Here, we present a generalized SAFT-VRX equation of state for binary mixtures that is found to accurately predict the vapor-liquid equilibrium and pvT behavior of the systems studied. In particular, we examine binary mixtures of n-alkanes and carbon dioxide + n-alkanes. The SAFT-VRX equation accurately describes not only the gas-liquid critical locus for these systems but also the vapor-liquid equilibrium phase diagrams and thermal properties in single-phase regions.