Extension of the LOPLS-AA Force Field for Alcohols, Esters, and Monoolein Bilayers and its Validation by Neutron Scattering Experiments

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.

Mesoscopic Structure of Lipid Nanoparticle Formulations for mRNA Drug Delivery: Comirnaty and Drug-Free Dispersions

Lipid nanoparticles (LNPs) produced by antisolvent precipitation (ASP) are used in formulations for mRNA drug delivery. The mesoscopic structure of such complex multicomponent and polydisperse nanoparticulate systems is most relevant for their drug delivery properties, medical efficiency, shelf life, and possible side effects. However, the knowledge on the structural details of such formulations is very limited. Essentially no such information is publicly available for pharmaceutical dispersions approved by numerous medicine agencies for the use in humans and loaded with mRNA encoding a mimic of the spike protein of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) as, e.g., the Comirnaty formulation (BioNTech/Pfizer). Here, we present a simple preparation method to mimic the Comirnaty drug-free LNPs including a comparison of their structural properties with those of Comirnaty. Strong evidence for the liquid state of the LNPs in both systems is found in contrast to the designation of the LNPs as solid lipid nanoparticles by BioNTech. An exceptionally detailed and reliable structural model for the LNPs i.a. revealing their unexpected narrow size distribution will be presented based on a combined small-angle X-ray scattering and photon correlation spectroscopy (SAXS/PCS) evaluation method. The results from this experimental approach are supported by light microscopy, 1H NMR spectroscopy, Raman spectroscopy, cryogenic electron microscopy (cryoTEM), and simultaneous SAXS/SANS studies. The presented results do not provide direct insights on particle formation or dispersion stability but should contribute significantly to better understanding the LNP drug delivery process, enhancing their medical benefit, and reducing side effects.

Molecular dynamics studies of the solubility behavior of carbon dioxide (CO2 ), difluoromethane (R-32), 1-chloro-3,3,3-trifluoropropene (R-1233zd(E)) and 2,3,3,3-tetrafluoro-1-propene (R-1234yf) in pentaerythritol tetra(2-ethylhexanoate) (PEB8), pentaerythritol tetrabutyrate (PEC4) and pentaerythritol tetraoctanoate (PEC8)

To reduce the climate impact of thermal engines such as heat pumps or refrigeration machines, refrigerants with a low global warming potential need to be paired with fitting lubricants. As the contamination of those liquid components influences the efficiency and lifetime of these machines, knowledge about their solubility behavior is of great interest. Molecular simulations offer mighty tools to investigate these solubilities while giving structural insight into the systems. Here the solubility behavior of CO2 , R-32, R-1233zd(E), and R-1234yf in PEB8, PEC4, and PEC8 is compared through the solvation free energy ∆GSolv obtained by molecular dynamics simulations. To derive ∆GSolv at low computational cost, an iterative method is used to find an optimal number and distribution of intermediate states. The resulting distributions are investigated with regard to different parameters of the employed softcore-potential. ∆GSolv values for the different refrigerant-lubricant pairings at different temperatures are provided, followed by a structural analysis.

Molecular dynamics simulations for interfacial structure and affinity between carboxylic acid-modified Al2O3 and polymer melts

Controlling the dispersion state of nanoparticles in a polymer matrix is necessary to produce polymer nanocomposites. The surface modification of nanoparticles is used to enable their dispersion in polymers. Moreover, molecular dynamics (MD) simulations are useful for revealing the interfacial properties between nanoparticles and polymers to aid in the design of materials. In this study, the effect of surface coverage, modifier length, and polymer species on the interfacial structure and affinity between surface-modified Al2O3 and polymer melts were investigated using all-atom MD simulations. Hexanoic, decanoic, and tetradecanoic acids were used as surface modifiers, and polypropylene (PP), polystyrene (PS), and poly (methyl methacrylate) (PMMA) were used as polymers. The work of adhesion Wadh and the work of immersion Wimm were selected as quantitative measures of affinity. Wadh was calculated using the phantom-wall approach, and Wimm was calculated by simply subtracting the surface tension of polymers γL from Wadh. The results showed that Wadh and Wimm were improved by surface modification with low coverage, owing to a good penetration of the polymer. The effect of modifier length on Wadh and Wimm was small. Whereas Wadh increased in the following order: PP < PS < PMMA, Wimm increased as follows: PMMA < PS < PP. Finally, the trend of Wadh and Wimm was organized using the Flory-Huggins interaction parameter χ between the modifier and the polymer. This study demonstrates that the interfacial affinity can be improved by tuning the surface coverage and modifier species depending on the polymer matrix.

Influence of Ethanol Parametrization on Diffusion Coefficients Using OPLS-AA Force Field

Molecular dynamics simulations employing the all-atom optimized potential for liquid simulations (OPLS-AA) force field were performed for determining self-diffusion coefficients (D11) of ethanol and tracer diffusion coefficients (D12) of solutes in ethanol at several temperature and pressure conditions. For simulations employing the original OPLS-AA diameter of ethanol's oxygen atom (σOH), calculated and experimental diffusivities of protic solutes differed by more than 25%. To correct this behavior, the σOH was reoptimized using the experimental D12 of quercetin and of gallic acid in liquid ethanol as benchmarks. A substantial improvement of the calculated diffusivities was found by changing σOH from its original value (0.312 nm) to 0.306 nm, with average absolute relative deviations (AARD) of 3.71% and 4.59% for quercetin and gallic acid, respectively. The new σOH value was further tested by computing D12 of ibuprofen and butan-1-ol in liquid ethanol with AARDs of 1.55% and 4.81%, respectively. A significant improvement was also obtained for the D11 of ethanol with AARD = 3.51%. It was also demonstrated that in the case of diffusion coefficients of non-polar solutes in ethanol, the original σOH=0.312 nm should be used for better agreement with experiment. If equilibrium properties such as enthalpy of vaporization and density are estimated, the original diameter should be once again adopted.

Computing Viscosities of Mixtures of Ester-Based Lubricants at Different Temperatures

Synthetic esters are used as lubricants for applications at high temperatures, but their development can be a trial and error process. In this context, molecular dynamics simulations could be used as a tool to investigate the properties of new lubricants, in particular viscosity. We employ nonequilibrium molecular dynamics (NEMD) simulations to predict bulk Newtonian viscosities of a set of mixtures of two esters, di(2-ethylhexyl) sebacate (DEHS) and di(2-ethylhexyl) adipate (DEHA) at 293 and 343 K as well as equilibrium molecular dynamics (EMD) and NEMD at 393 K and compare these to experimental measurements. The simulations predict mixture densities within 5% of the experimental values, and we are able to retrieve between 99% and 75% of the experimental viscosities for all ranges of temperature. Experimental viscosities show a linear trend which we are able to capture using NEMD at low temperature and EMD at high temperature. Our work shows that, using EMD and NEMD simulations, and the workflows we developed, we can obtain reliable estimates of the viscosities of mixtures of industrially relevant ester-based lubricants at different temperatures.

Individual adsorption of low volatility pheromones: Amphiphilic molecules on a clean water-air interface

Environmental conditions can alter olfactory scent and chemical communication among biological species. In particular, odorant molecules interact with aerosols. Thermodynamics variables governing the adsorption from air to water surface of bombykol, the most studied pheromone, and of three derivative molecules, bombykal, bombykoic acid, and bombykyle acetate, are computed by steered and un-biased molecular dynamics in order to compare the role of their polar head group on adsorption on aqueous aerosols. When adsorbed, the molecule center of mass stands at about 1.2 Å from the interface and oscillates on the same length scale, trapped in an energy well. Gibbs energy of adsorption and desorption time of bombykol are found to be 9.2 k_BT and 59 µs, respectively. The following ordering between the molecules is observed, reading from the more to the least adsorbed: bombykoic acid > bombykol > bombykoic acetate > bombykal. It originates from a complex interplay of entropy and enthalpy. The entropy and enthalpy of adsorption are discussed in the light of structural arrangement, H-bonding, and hydrophilic tail positioning of the molecules at the interface. Our results show that, when dispersed in the air, pheromones adsorb on aqueous aerosols. However, the individual residence time is quite short on pure water surfaces. Aerosols can, therefore, only have a decisive influence on chemical communication through collective effects or through their chemical composition that is generally more complex than that of a pure water surface.

Tuning curvature and phase behavior of monoolein bilayers by epigallocatechin-3-gallate: Structural insight and cytotoxicity

The use of glyceryl monooleate (GMO)-based nanoparticles has not yet been explored in overcoming the low bioavailability of Epigallocatechin-3-gallate (EGCG), a green tea polyphenol with a known anticancer activity. Since the inclusion of a guest molecule can affect the curvature and the supramolecular structure of fully hydrated GMO-based phase, the phase behavior of bulk and dispersed liquid crystalline systems containing EGCG were explored by Small Angle Neutron Scattering and X-Ray Diffraction experiments. Molecular Dynamic Simulations showed how the interaction of EGCG with polar heads of GMO strongly affects the curvature and packing of GMO phase. The EGCG encapsulation efficiency was determined in the nanodispersions and their size studied by Dynamic Light Scattering and Atomic Force Microscopy. A nanodispersed formulation has been optimized with a cytotoxic effect more than additive of GMO and EGCG.

Revisiting Polymer-Particle Interaction in PEO Solutions

We have measured the electrophoretic mobility and diffusion coefficient of carboxylate-modified and sulfate-modified polystyrene latex particles in poly(ethylene oxide) aqueous solutions. Carboxylate-modified polystyrene particles have shown a bound polymeric layer as the surface net charge vanishes even at very low poly(ethylene oxide) concentration. The polymeric layer causes a lower electrophoretic mobility and slower Brownian diffusion than that corresponding to the bare particles. We show that the diffusion is the result of a significantly increased effective particle size 2r_heff = 30 nm. This bound layer is not present in sulfate-modified polystyrene latex particles. The interaction between the carboxylate-modified particle surface and the macromolecules has been confirmed by means of atomistic computer simulations. The grafted acrylate copolymers, which come from the preparation procedure of the latex particles, confer more hydrophobic surface ready to interact with the polymer. The simulations suggest that the interaction is modulated not only by the nature of the acrylic acid monomer but also by the length of the grafted copolymer. Our results have important implications for particle selection in microrheology experiments.

Lipid Dynamics in Membranes Slowed Down by Transmembrane Proteins

Lipids and proteins, as essential components of biological cell membranes, exhibit a significant degree of freedom for different kinds of motions including lateral long-range mobility. Due to their interactions, they not only preserve the cellular membrane but also contribute to many important cellular functions as e.g., signal transport or molecular exchange of the cell with its surrounding. Many of these processes take place on a short time (up to some nanoseconds) and length scale (up to some nanometers) which is perfectly accessible by quasielastic neutron scattering (QENS) experiments and molecular dynamics (MD) simulations. In order to probe the influence of a peptide, a transmembrane sequence of the transferrin receptor (TFRC) protein, on the dynamics of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) large unilamellar vesicles (LUVs) on a nanosecond time scale, high-resolution QENS experiments and complementary MD simulations have been utilized. By using different scattering contrasts in the experiment (chain-deuterated lipids and protonated lipids, respectively), a model could be developed which allows to examine the lipid and peptide dynamics separately. The experimental results revealed a restricted lipid lateral mobility in the presence of the TFRC transmembrane peptides. Also the apparent self-diffusion coefficient of the lateral movement of the peptide molecules could be determined quantitatively for the probed short-time regime. The findings could be confirmed very precisely by MD simulations. Furthermore, the article presents an estimation for the radius of influence of the peptides on the lipid long-range dynamics which could be determined by consistently combining results from experiment and simulation.

Mutual and Thermal Diffusivities as well as Fluid-Phase Equilibria of Mixtures of 1-Hexanol and Carbon Dioxide

This work contributes to an improved understanding of the fluid-phase behavior and diffusion processes in mixtures of 1-hexanol and carbon dioxide (CO₂) at temperatures around the upper critical end point (UCEP) of the system. Raman spectroscopy and dynamic light scattering were used to determine the composition at saturation conditions as well as Fick and thermal diffusivities. An acceleration of the Fick diffusive process up to CO₂ mole fractions of about 0.2 was found, followed by a strong slowing-down approaching vapor-liquid-liquid equilibrium or critical conditions. The acceleration of the Fick diffusive process vanished at temperatures much higher than the UCEP. Experimental Fick diffusivity data were compared with predictions from equilibrium molecular dynamics simulations and excess Gibbs energy calculations using interaction parameters from the literature. Both theoretical methods were not able to predict that the thermodynamic factor is equal to zero at the spinodal composition, stressing the need for new methodologies under such conditions. Thus, new sets of temperature-dependent interaction parameters were developed for the nonrandom two-liquid model, which improve the prediction of the Fick diffusion coefficient considerably. The link between the Fick diffusion coefficient and the nonrandomness of the liquid phases is also discussed.

Density and viscosity of a polyol ester lubricant: Measurement and molecular dynamics simulation

Polyol ester (POE) is the main component of many refrigeration lubricants. In this work, the density and the viscosity of a typical, pure polyol ester, pentaerythritol tetrahexanoate (PEC6), were measured over 258.15 K to 373.15 K and predicted with molecular dynamics simulations. Nonequilibrium molecular dynamics (NEMD) was employed to compute the shear viscosities for different shear rates. The Eyring model was used to fit the shear viscosities and to extrapolate to the Newtonian viscosity. A protocol was proposed to perform a NEMD-Eyring fit for a low-error, reproducible and robust Newtonian viscosity calculation. Three force fields, i.e., OPLS, LOPLS, and DREIDING, were tested in terms of their density and viscosity prediction accuracy. OPLS gave the best density prediction (within ± 0.2 %), while LOPLS showed the best viscosity prediction accuracy (within - 4 % to 20 %). This work illustrates the value of molecular simulation in predicting lubricant properties and its potential in guiding the design of POE lubricants for desired properties.

Diffusivities in 1-Alcohols Containing Dissolved H2, He, N2, CO, or CO2 Close to Infinite Dilution

The influence of the strength of intermolecular interactions on mass diffusive processes remains poorly understood for mixtures of associative liquids with dissolved gases. For contributing to a fundamental understanding of the interplay between liquid structures and mass diffusivities in such systems, dynamic light scattering, Raman spectroscopy, and molecular dynamics simulations were used in this work. As model systems, binary mixtures consisting of the gases hydrogen, helium, nitrogen, carbon monoxide, or carbon dioxide dissolved in ethanol, 1-hexanol, or 1-decanol were selected. Experiments and simulations were performed at macroscopic thermodynamic equilibrium close to infinite dilution of solute for temperatures between 303 and 423 K. The Fick diffusion coefficients and self-diffusivities of the gas solutes increase with increasing temperature, decreasing alkyl chain length of the 1-alcohols, and decreasing molar mass of the solutes except for helium and hydrogen showing the opposite behavior. The analysis of the liquid structure of the mixtures showed that the fraction of hydrogen-bonded alcohol molecules decreases with increasing alkyl chain length and temperature. From the obtained structure-property relationships, a new correlation was developed to predict mass diffusivities in binary mixtures consisting of n-alkanes or 1-alcohols with dissolved gases close to infinite dilution within 10% on average.

Independence between friction and velocity distribution in fluids subjected to severe shearing and confinement

Lubricated friction at high shear and high enough pressure becomes saturated, independently of the velocity profile in the lubricant thickness.

On the effect of confined fluid molecular structure on nonequilibrium phase behaviour and friction

Atomistic simulations and tribology experiments uncover the effect of molecular structure on the flow and friction behaviour of confined films under extreme conditions.

Membrane pore formation in atomistic and coarse-grained simulations

Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.