Atomistic molecular dynamics simulation of diffusion in binary liquid n-alkane mixtures

The effect of functional groups on the glass transition temperature of atmospheric organic compounds: a molecular dynamics study

Organic compounds constitute a substantial part of atmospheric particulate matter not only in terms of mass concentration but also in terms of distinct functional groups. The glass transition temperature provides an indirect way to investigate the phase state of the organic compounds, playing a crucial role in understanding their behavior and influence on aerosol processes. Molecular dynamics (MD) simulations were implemented here to predict the glass transition temperature (Tg) of atmospherically relevant organic compounds as well as the influence of their functional groups and length of their carbon chain. The cooling step used in the simulations was chosen to be neither too low (to supress crystallization) nor too high (to avoid Tg overprediction). According to the MD simulations, the predicted Tg is sensitive to the functional groups as follows: carboxylic acid (-COOH) > hydroxyl (-OH) and (-COOH) > carbonyls (-CO). Increasing the number of carbon atoms leads to higher Tg for the linearly structured compounds. Linear compounds with lower molecular weight were found to exhibit a lower Tg. No clear correlation between O : C and Tg was observed. The architecture of the carbon chain (linear, or branched, or ring) was also found to impact the glass transition temperature. Compounds containing a non-aromatic carbon ring are characterized by a higher Tg compared to linear and branched ones with the same number of carbon atoms.

Interface and Interphase in Polymer Nanocomposites with Bare and Core-Shell Gold Nanoparticles

Metal nanoparticles are used to modify/enhance the properties of a polymer matrix for a broad range of applications in bio-nanotechnology. Here, we study the properties of polymer/gold nanoparticle (NP) nanocomposites through atomistic molecular dynamics, MD, simulations. We probe the structural, conformational and dynamical properties of polymer chains at the vicinity of a gold (Au) NP and a functionalized (core/shell) Au NP, and compare them against the behavior of bulk polyethylene (PE). The bare Au NPs were constructed via a systematic methodology starting from ab-initio calculations and an atomistic Wulff construction algorithm resulting in the crystal shape with the minimum surface energy. For the functionalized NPs the interactions between gold atoms and chemically adsorbed functional groups change their shape. As a model polymer matrix we consider polyethylene of different molecular lengths, from the oligomer to unentangled Rouse like systems. The PE/Au interaction is parametrized via DFT calculations. By computing the different properties the concept of the interface, and the interphase as well, in polymer nanocomposites with metal NPs are critically examined. Results concerning polymer density profiles, bond order parameter, segmental and terminal dynamics show clearly that the size of the interface/interphase, depends on the actual property under study. In addition, the anchored polymeric chains change the behavior/properties, and especially the chain density profile and the dynamics, of the polymer chain at the vicinity of the Au NP.

A blob model to parameterize polymer hole free volumes and solute diffusion

Solute diffusion in solid polymers has tremendous applications in packaging, reservoir, and biomedical technologies but remains poorly understood. Diffusion of non-entangled linear solutes with chemically identical patterns (blobs) deviates dramatically in polymers in the solid-state (α_lin > 1, Macromolecules 2013, 46, 874) from their behaviors in the molten state (α_lin = 1, Macromolecules, 2007, 40, 3970). This work uses the scale invariance of the diffusivities, D, of linear probes D(N·M_blob + M_anchor,T,T_g) = N^{-α_lin(T,T_g)}D(M_blob + M_anchor,T,T_g) comprising N identical blobs of mass M_blob and possibly one different terminal pattern (anchor of mass M_anchor) to evaluate the amounts of hole-free volume in seven polymers (aliphatic, semi-aromatic and aromatic) over a broad range of temperatures (-70 K ≤T-T_g≤ 160 K). The new parameterization of the concept of hole-free volumes opens the application of the free-volume theory (FVT) developed by Vrentas and Duda to practically any polymer, regardless of the availability of free-volume parameters. The quality of the estimations was tested with various probes including n-alkanes, 1-alcohols, n-alkyl acetates, and n-alkylbenzene. The effects of enthalpic and entropic effects of the blobs and the anchor were analyzed and quantified. Blind validation of the reformulated FVT was tested successfully by predicting from first principles the diffusivities of water and toluene in amorphous polyethylene terephthalate from 4 °C to 180 °C and in various other polymers. The new blob model would open the rational design of additives with controlled diffusivities in thermoplastics.

Fluid-solid phase transition of n-alkane mixtures: Coarse-grained molecular dynamics simulations and diffusion-ordered spectroscopy nuclear magnetic resonance

Wax appearance temperature (WAT), defined as the temperature at which the first solid paraffin crystal appears in a crude oil, is one of the key flow assurance indicators in the oil industry. Although there are several commonly-used experimental techniques to determine WAT, none provides unambiguous molecular-level information to characterize the phase transition between the homogeneous fluid and the underlying solid phase. Molecular Dynamics (MD) simulations employing the statistical associating fluid theory (SAFT) force field are used to interrogate the incipient solidification states of models for long-chain alkanes cooled from a melt to an arrested state. We monitor the phase change of pure long chain n-alkanes: tetracosane (C₂₄H₅₀) and triacontane (C₃₀H₆₂), and an 8-component surrogate n-alkane mixture (C₁₂-C₃₃) built upon the compositional information of a waxy crude. Comparison to Diffusion Ordered Spectroscopy Nuclear Magnetic Resonance (DOSY NMR) results allows the assessment of the limitations of the coarse-grained models proposed. We show that upon approach to freezing, the heavier components restrict their motion first while the lighter ones retain their mobility and help fluidize the mixture. We further demonstrate that upon sub-cooling of long n-alkane fluids and mixtures, a discontinuity arises in the slope of the self-diffusion coefficient with decreasing temperature, which can be employed as a marker for the appearance of an arrested state commensurate with conventional WAT measurements.

Application of Reverse Nonequilibrium Molecular Dynamics to the Calculation of the Mutual Diffusion Coefficient of Alkane Mixtures

In a recent publication, a reverse nonequilibrium molecular dynamics (RNEMD) method was presented for computing the mutual diffusion coefficient of liquid mixtures. A concentration gradient and a subsequent mass flux are induced in the system by suitably exchanging molecules in different regions. The algorithm has been successfully tested on Lennard-Jones mixtures and molecular fluid mixtures with molecules having the same number of particles. In this work, a modification is made to the RNEMD method to determine the mutual diffusion coefficient of binary liquid mixtures with molecules having different sizes and masses. To migrate molecules of a different type, the splitting method has been used in this work. Investigation of the resulting steady-state mass fraction profile allows the evaluation of the mutual diffusion coefficient. For validation, the mutual diffusion coefficients of ethane-propane and ethane-pentane liquid mixtures at different compositions and temperatures have been obtained using this method. The mutual diffusion coefficients obtained from the RNEMD simulations are within the error bars of values obtained by equilibrium molecular dynamics for the identical model and conditions. The excess energy released due to the exchange of molecules is efficiently removed by strongly coupling a local thermostat in the region around the insertion point. There is no heating of the analysis region.

Structure and Mass Transport Characteristics at the Intrinsic Liquid-Vapor Interfaces of Alkanes

In this paper, an instantaneous interface definition has been used to study the intrinsic structure and self-diffusion coefficient in the vicinity of the liquid-vapor interfaces of decane and tetracosane at three different temperatures using molecular dynamics simulations, and the results have been compared with those obtained on the basis of the conventional Gibbs dividing surface (time- and space-averaged interface). The alkane molecules were modeled using the united atom NERD force field. Partial layered structures of alkane molecules at the liquid-vapor interface are observed as a pinned structure of alkane liquids based on the intrinsic interface. This kind of characteristic has not been observed in the density profiles obtained based on the Gibbs dividing surface. By examining the orientation order parameter and radius of gyration of the alkane molecules, it was observed that the alkane molecules were preferentially oriented to be more parallel to the intrinsic interface than to the Gibbs dividing surface, and the shape of the alkane molecules is slightly changed in the vicinity of the liquid-vapor interfaces. The self-diffusion coefficient parallel to the intrinsic interface was examined using the Green-Kubo relation, where the projection of the velocity in the parallel direction to the local intrinsic interface is used in the velocity correlation function. It was found that the self-diffusion coefficient in the direction parallel to the intrinsic interface changes as the position approaches the interface in a more obvious manner as compared with the self-diffusion coefficient obtained with respect to the Gibbs dividing surface. These results suggest that the use of an instantaneous interface definition allowed us to capture sharp variations in transport properties which are originating due to steeper structure at the liquid-vapor interfaces.

Mass transport and structure of liquid n-alkane mixtures in the vicinity of α-quartz substrates

The asymmetric self-diffusion characteristics of binary n-alkane mixtures in the first adsorption layer near α-quartz substrate were demonstrated and discussed.

Tracer diffusion in a crowded cylindrical channel

Based on a coarse-grained model, we carry out molecular dynamics simulations to analyze the diffusion of a small tracer particle inside a cylindrical channel whose inner wall is covered with randomly grafted short polymeric chains. We observe an interesting transient subdiffusive behavior along the cylindrical axis at high attraction between the tracer and the chains, however, the long-time diffusion is always normal. This process is found to be enhanced for the case that we immobilize the grafted chains, i.e., the subdiffusive behavior sets in at an earlier time and spans over a longer time period before becoming diffusive. Even if the grafted chains are replaced with a frozen sea of repulsive, nonconnected particles in the background, a transient subdiffusion is observed. The intermediate subdiffusive behavior only disappears when the grafted chains are replaced with a mobile background sea of mutually repulsive particles. Overall, the long-time diffusion coefficient of the tracer along the cylinder axis decreases with an increase in system volume fraction, the strength of the attraction between the tracer and the background, and also on freezing the background.

Dynamic heterogeneity in fully miscible blends of polystyrene with oligostyrene

Binary blends of polystyrene with oligostyrene are perfectly miscible (χ=0) yet dynamically heterogeneous. This is evidenced by independent probing of the dipole relaxation perpendicular to the backbone by dielectric spectroscopy and molecular dynamics. The self-concentration model with a single intramolecular length scale qualitatively describes the slower segmental dynamics. A quantitative comparison based on MD, however, requires a composition-dependent length scale. The pertinent dynamic length scale that best describes the slow segmental dynamics in miscible blends relates to both intra- and intermolecular contributions.

Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient

In this work, we have evaluated how well the general assisted model building with energy refinement (AMBER) force field performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, five organic compounds in aqueous solutions, four proteins in aqueous solutions, and nine organic compounds in nonaqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned errors and the root mean square errors are 0.137 and 0.171 × 10(-5) cm(-2) s(-1), respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for eight organic solvents with experimental data (R(2) = 0.784), four proteins in aqueous solutions (R(2) = 0.996), and nine organic compounds in nonaqueous solutions (R(2) = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide, and cyclohexane have been studied. The major molecular dynamics (MD) settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution.

Molecular dynamics simulations of functional group effects on solvation thermodynamics of model solutes in decane and tricaprylin

Triglycerides and related fatty acid esters constitute a large percentage of the lipid excipients employed in the development of lipid-based drug formulations. Computer simulations can provide useful information on the structural, dynamic, and thermodynamic properties of these systems and may ultimately be valuable in predicting relative drug solubilities in lipid vehicles. This study utilized all-atom molecular dynamics simulations to explore the solvation of several model solutes in lipid vehicles. First, a combined thermodynamic perturbation and integration approach was employed to calculate functional group contributions to the free energy of transfer from n-decane to tricaprylin for a set of polar substituents attached to the 9-position of anthracene. A scaling factor of 0.79 for all atomic charges in the dry lipid (where the unscaled charges were obtained at the level of the HF/6-31G* basis set) was necessary in order to match the calculated group contributions to the free energies of transfer with their experimental values at 37 degrees C. A second set of simulations was performed in water-saturated tricaprylin containing a single molecule of benzamide to explore the state of organization of solvent molecules, the distribution of water molecules, and the local environment surrounding the solute. Radial distribution functions revealed evidence of local structure in the liquid triglyceride. The dissolved water was found to exist approximately 50% as monomers and 50% as self-associated species. Substantial hydrogen-bonding of benzamide with ester carbonyl oxygen atoms was observed.

Response to comment by Almeida et al.: free area theories for lipid bilayers--predictive or not?

Free area theories for lateral diffusion in lipid bilayers are reviewed and discussed. It has been suggested by Almeida et al. that free area theories yield quantitative predictions for lateral diffusion coefficients of lipids. We investigate the plausibility of this suggestion by first sketching what is to be expected of a quantitative theory with predictive power, and subsequently examining whether existing free area theories comply with these expectations. Our conclusion is that current free area theories for lipid bilayers are not quantitative theories with predictive power. They involve a number of adjustable parameters, all of which are not estimated independently, but derived from fitting the theory to the very data whose behavior the theory is supposed to predict. Further, the interpretation and behavior of some of the parameters are ambiguous. The best example is the so-called activation barrier, whose qualitative behavior with the cholesterol concentration in a DMPC bilayer varies depending on the experimental method used to generate the input data and the exact assumptions made to formulate the theory. Independent determination of the activation barrier from numerical simulations or experiments appears to be very difficult.