Molecular Structure Inhibiting Synergism in Charged Surfactant Mixtures: An Atomistic Molecular Dynamics Simulation Study.

Synergistic and nonsynergistic surfactant-water mixtures of sodium dodecyl sulfate (SDS), lauryl betaine (C12B), and cocoamidopropyl betaine (CAPB) systems are studied using molecular simulation to understand the role of interactions among headgroups, tailgroups, and water on structural and thermodynamic properties at the air-water interface. SDS is an anionic surfactant, while C12B and CAPB are zwitterionic; CAPB differs from C12B by an amide group in the tail. While the lowest surface tensions at high surface concentrations in the SDS-C12B synergistic system could not be reproduced by simulation, estimated partitioning between surface and bulk shows trends consistent with synergism. Structural analysis shows the influence of the SDS headgroup pulling C12B to the surface, resulting in closely packed structures compared to their respective homomolecular-surfactant systems. The SDS-CAPB system, on the other hand, is nonsynergistic when the surfactants are mixed on account of the tilted structure of the CAPB tail. The translational excess entropy due to the tailgroup interactions discriminates between the synergistic and nonsynergistic systems. The implications of such interactions on surfactant effects in complex, multicomponent atmospheric aerosols are discussed.

ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.

Non-structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism for translocation has been proposed based on crystal structures and single molecule experiments. We here perform atomistic molecular dynamics in explicit solvent on the microsecond time scale of the available experimental structures. We also construct and simulate putative intermediates for the translocation process, and we perform non-equilibrium targeted simulations to estimate their relative stability. For each of the simulated structures we carefully characterize the available conformational space, the ligand binding pocket, and the RNA binding cleft. The analysis of the hydrogen bond network and of the non-equilibrium trajectories indicates an ATP-dependent stabilization of one of the protein conformers. Additionally, enthalpy calculations suggest that entropic effects might be crucial for the stabilization of the experimentally observed structures.

The effect of anaesthetics on the properties of a lipid membrane in the biologically relevant phase: a computer simulation study.

Molecular dynamics simulations of the fully hydrated neat dipalmitoylphosphatidylcholine (DPPC) membrane as well as DPPC membranes containing four different general anaesthetic molecules, namely chloroform, halothane, diethyl ether and enflurane, have been simulated at two different pressures, i.e., at 1 bar and 1000 bar, at the temperature of 310 K. At this temperature the model used in this study is known to be in the biologically most relevant liquid crystalline (Lα) phase. To find out which properties of the membrane might possibly be related to the molecular mechanism of anaesthesia, we have been looking for properties that change in the same way in the presence of any general anaesthetic molecule, and change in the opposite way by the increase of pressure. This way, we have ruled out the density distribution of various groups along the membrane normal axis, orientation of the lipid heads and tails, self-association of the anaesthetics, as well as the local order of the lipid tails as possible molecular reasons of anaesthesia. On the other hand, we have found that the molecular surface area, and hence also the molecular volume of the membrane, is increased by the presence of any anaesthetic molecule, and decreased by the pressure, in accordance with the more than half a century old critical volume hypothesis. We have also found that anaesthetic molecules prefer two different positions along the membrane normal axis, namely the middle of the membrane and the outer edge of the hydrocarbon region, close to the polar headgroups. The increase of pressure is found to decrease the former, and increase the latter preference, and hence it might also be related to the pressure reversal of anaesthesia.

The molecular scale mechanism of deposition ice nucleation on silver iodide.

Heterogeneous ice nucleation is a ubiquitous process in the natural and built environment. Deposition ice nucleation, i.e. heterogeneous ice nucleation that - according to the traditional view - occurs in a subsaturated water vapor environment and in the absence of supercooled water on the solid, ice-forming surface, is among the most important ice formation processes in high-altitude cirrus and mixed-phase clouds. Despite its importance, very little is known about the mechanism of deposition ice nucleation at the microscopic level. This study puts forward an adsorption-based mechanism for deposition ice nucleation through results from a combination of atomistic simulations, experiments and theoretical modelling. One of the most potent laboratory surrogates of ice nucleating particles, silver iodide, is used as a substrate for the simulations. We find that water initially adsorbs in clusters which merge and grow over time to form layers of supercooled water. Ice nucleation on silver iodide requires at minimum the adsorption of 4 molecular layers of water. Guided by the simulations we propose the following fundamental freezing steps: (1) Water molecules adsorb on the surface, forming nanodroplets. (2) The supercooled water nanodroplets merge into a continuous multilayer when they grow to about 3 molecular layers thick. (3) The layer continues to grow until the critical thickness for freezing is reached. (4) The critical ice cluster continues to grow.

Molecular dynamics simulations of the water adsorption around malonic acid aerosol models.

Water nucleation around a malonic acid aggregate has been studied by means of molecular dynamics simulations in the temperature and pressure range relevant for atmospheric conditions. Systems of different water contents have been considered and a large number of simulations have allowed us to determine the phase diagram of the corresponding binary malonic acid-water systems. Two phases have been evidenced in the phase diagrams corresponding either to water adsorption on a large malonic acid grain at low temperatures, or to the formation of a liquid-like mixed aggregate of the two types of molecules, at higher temperatures. Finally, the comparison between the phase diagrams simulated for malonic acid-water and oxalic acid-water mixtures emphasizes the influence of the O : C ratio on the hydrophilic behavior of the aerosol, and thus on its ability to act as a cloud condensation nucleus, in accordance with recent experimental conclusions.

Lateral dynamics of surfactants at the free water surface: a computer simulation study.

Molecular dynamics simulations of the adsorption layer of five different surfactant molecules, i.e., pentyl alcohol, octyl alcohol, dodecyl alcohol, sodium dodecyl sulfate, and dodecyl trimethyl ammonium chloride are performed at the free surface of their aqueous solution at two surface densities, namely 1 and 4 µmol/m(2) at 298 K. The results are analyzed in terms of the two-dimensional single molecule dynamics, in particlular, lateral diffusion of the surfactants at the liquid surface, in order to distinguish between two possible adsorption scenarios, namely the assumptions of localized and mobile surfactants. The obtained results, in accordance with the dynamical nature of the liquid phase and liquid surface, clearly support the latter scenario, as the time scale of lateral diffusion of the surfactant molecules is found to be comparable with that of the three-dimensional diffusion of water in the bulk liquid phase. The mechanism of this lateral diffusion is also investigated in detail by calculating binding energy distribution of the water molecules in the first hydration shell of the surfactant headgroups and that of the nonfirst shell surface waters, and by calculating the mean residence time of the water molecules in the first hydration shell of the surfactant headgroups. This time is found to be at least an order of magnitude smaller than the characteristic time of the lateral diffusion of the surfactants, revealing that surfactant molecules move without their first shell hydration water neighbors at the surface.

Adsorption of acetaldehyde on ice as seen from computer simulation and infrared spectroscopy measurements.

Detailed investigation of the adsorption of acetaldehyde on I(h) ice is performed under tropospheric conditions by means of grand canonical Monte Carlo computer simulations and compared to infrared spectroscopy measurements. The experimental and simulation results are in a clear accordance with each other. The simulations indicate that the adsorption process follows Langmuir behavior in the entire pressure range of the vapor phase of acetaldehyde. Further, it was found that the adsorption layer is strictly monomolecular, and the adsorbed acetaldehyde molecules are bound to the ice surface by only one hydrogen bond, typically formed with the dangling H atoms at the ice surface, in agreement with the experimental results. Besides this hydrogen bonding, at high surface coverages dipolar attraction between neighboring acetaldehyde molecules also contributes considerably to the energy gain of the adsorption. The acetaldehyde molecules adopt strongly tilted orientations relative to the ice surface, the tilt angle being scattered between 50° and 90° (i.e., perpendicular orientation). The range of the preferred tilt angles narrows, and the preference for perpendicular orientation becomes stronger upon saturation of the adsorption layer. The CH(3) group of the acetaldehyde molecules points as straight away from the ice surface within the constraint imposed by the tilt angle adopted by the molecule as possible. The heat of adsorption at infinitely low coverage is found to be -36 ± 2 kJ/mol from the infrared spectroscopy measurement, which is in excellent agreement with the computer simulation value of -34.1 kJ/mol.

Anesthetic molecules embedded in a lipid membrane: a computer simulation study.

The effect of four general anesthetic molecules, i.e., chloroform, halothane, diethyl ether and enflurane, on the properties of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) membrane is studied in detail by long molecular dynamics simulations. Furthermore, to address the problem of pressure reversal, the effect of pressure on the anesthetic containing membranes is also investigated. In order to ensure sufficient equilibration and adequate sampling, the simulations performed have been at least an order of magnitude longer than the studies reported previously in the literature on general anesthetics. The results obtained can help in resolving several long-standing contradictions concerning the effect of anesthetics, some of which were the consequence of too short simulation time used in several previous studies. More importantly, a number of seeming contradictions are found to originate from the fact that different anesthetic molecules affect the membrane structure differently in several respects. In particular, halothane, being able to weakly hydrogen bound to the ester group of the lipid tails, is found to behave in a markedly different way than the other three molecules considered. Besides, we also found that two changes, namely lateral expansion of the membrane and increasing local disorder in the lipid tails next to the anesthetic molecules, are clearly induced by all four anesthetic molecules tested here in the same way, and both of these effects are reverted by the increase in pressure.

Surface properties of the polarizable Baranyai-Kiss water model.

The water surface properties using the Baranyai-Kiss (BK) model [A. Baranyai and P. T. Kiss, J. Chem. Phys. 133, 144109 (2010)] are studied by molecular dynamics simulation, and compared to popular rigid water potentials, namely to the extended simple point charge (SPC/E) and the transferable interaction potential with 4 points (TIP4P) models. The BK potential is a polarizable model of water with three Gaussian charges. The negative charge is connected to its field-free position by a classical harmonic spring, and mechanical equilibrium is established between this spring force and the force due to the charge distribution of the system. The aim of this study is, on the one hand, to test the surface properties of the new model, and on the other hand, to identify differences between the models listed above. The obtained results reveal that the BK model reproduces very well a number of properties corresponding to liquid-vapor equilibrium, such as the coexisting liquid and vapor densities, saturated vapor pressure or surface tension. Further, this model reproduces excellently the critical point of water even in comparison with a large number of widely used polarizable and nonpolarizable models. The structural properties of the liquid surface of BK water turns out to be very similar to that of the SPC/E model, while the surface of TIP4P water is found to be somewhat less ordered. This finding is related to the fact that the critical temperature of the TIP4P model is lower than that of either SPC/E or BK.

Computer Simulation of the Surface of Aqueous Ionic and Surfactant Solutions.

The surface of aqueous solutions of simple salts was not the main focus of scientific attention for a long while. Considerable interest in studying such systems has only emerged in the past two decades, following the pioneering finding that large halide ions, such as I-, exhibit considerable surface affinity. Since then, a number of issues have been clarified; however, there are still several unresolved points (e.g., the effect of various salts on lateral water diffusion at the surface) in this respect. Computer simulation studies of the field have largely benefited from the appearance of intrinsic surface analysis methods, by which the particles staying right at the boundary of the two phases can be unambiguously identified. Considering complex ions instead of simple ones opens a number of interesting questions, both from the theoretical point of view and from that of the applications. Besides reviewing the state-of-the-art of intrinsic surface analysis methods as well as the most important advances and open questions concerning the surface of simple ionic solutions, we focus on two such systems in this Perspective, namely, the surface of aqueous mixtures of room temperature ionic liquids and that of ionic surfactants. In the case of the former systems, for which computer simulation studies have still scarcely been reported, we summarize the theoretical advances that could trigger such investigations, which might well be of importance also from the point of view of industrial applications. Computer simulation methods are, on the other hand, widely used in studies of the surface of surfactant solutions. Here we review the most important theoretical advances and issues to be addressed and discuss two areas of applications, namely, the inclusion of information gathered from such simulations in large scale atmospheric models and the better understanding of the airborne transmission of viruses, such as SARS-CoV-2.

Water adsorption around oxalic acid aggregates: a molecular dynamics simulation of water nucleation on organic aerosols.

The phase behaviour of binary oxalic acid-water mixtures has been investigated by means of computer simulation techniques. Such mixtures play an important role in atmospheric processes, since the hydrogen bonding ability of oxalic acid molecules allows them to form aerosol particles. Water can in turn be readily adsorbed on the surface of such aerosol particles, which results in the formation of small ice grains. These grains are thus considered to be acting as cloud condensation nuclei, giving rise to the formation of ice clouds.

Molecular dynamics simulation of the adsorption of oxalic acid on an ice surface.

The adsorption properties of oxalic acid molecules on the surface of hexagonal ice are investigated by means of molecular dynamics simulations performed at tropospheric temperatures. Although the oxalic acid-water interaction is strong at low coverage, due to the possible formation of a large number of hydrogen bonds between the adsorbed oxalic acid and the surface water molecules, the results of the simulations at finite coverage show the predominant role played by the oxalic acid-oxalic acid lateral interactions in the adsorption/desorption process. These interactions are even stronger than the water-water or water-oxalic acid interactions. With increasing temperature these strong lateral interactions favor the formation of oxalic acid aggregates on the ice surface, with the concomitant departure of water molecules through the ducts in the adsorbed layer created by the aggregation process. These results support conclusions of experimental data on the oxalic acid-ice interactions. Moreover, in comparison to previously obtained results for formic and acetic acid adsorbed on ice, the present study suggests that not only the organic functionality is of importance for atmospheric implications of partially oxidized hydrocarbons (POH) interactions with ice, but also the balance between water-ice, water-POH, and POH-POH interactions.

Adsorption of hydroxyacetone on pure ice surfaces.

The adsorption of hydroxyacetone molecules at the surface of ice is investigated by means of flow-tube reactor measurements in the temperature range: 213-253 K. The number of molecules adsorbed per surface unit is conventionally plotted as a function of the absolute gas concentration of hydroxyacetone and is compared to that previously obtained for acetone and ethanol. The enthalpy of adsorption and the monolayer capacity at the ice surface are determined. In addition, molecular dynamics simulations are performed to support the experimental results. However, it is shown that the available interaction potential between hydroxyacetone and ice is not accurate enough to allow a robust detailed analysis of the adsorption process. Finally, a rapid estimation of the hydroxyacetone partitioning between the gas phase and ice shows that in the densest ice clouds, up to 29% of hydroxyacetone could be adsorbed on pure ice surfaces at 203 K.

Molecular dynamics simulation and identification of the truly interfacial molecules (ITIM) analysis of the liquid-vapor interface of dimethyl sulfoxide.

The liquid-vapor interface of dimethyl sulfoxide (DMSO) is investigated by molecular dynamics computer simulation and by the novel method of the identification of the truly interfacial molecules (ITIM). With this method, it is possible to consider in the analysis specifically those molecules that are located right at the boundary of the two phases. The obtained results show that the orientation of the surface molecules is driven by the requirement that these molecules should be able to maintain their strong dipole-dipole and pi-pi interactions with each other, such as in the bulk liquid phase. This requirement leads to the preference of the polar S=O double bonds for laying parallel with the surface, and of the apolar CH(3) groups for pointing rather flatly out of the liquid phase. As a result, the surface of liquid DMSO is only mildly corrugated, in terms of the molecular size. Similarly to the bulk liquid phase, the DMSO molecules are also found to form long dipole chains of head-to-tail oriented neighbors even within the surface layer. The results also indicate that, at least from the point of view of the dynamics of the individual molecules, the division of the system beneath the truly surface layer into further subsurface molecular layers is already physically meaningless.

Free energy of mixing of pyridine and its methyl-substituted derivatives with water, as seen from computer simulations.

The free energies of mixing of pyridine, 2-methylpyridine, and 2,6-dimethylpyridine with water have been calculated at 298 K for systems containing 1, 5, and 50 mol % pyridine or its derivative by the method of thermodynamic integration. The obtained results show that the trend of the free energy of mixing of these compounds with water, observed previously at infinite dilution, clearly vanishes at 1 mol % and reverses at higher pyridine concentrations. Thus, in the 5 and 50 mol % systems, the free energy of mixing increases with increasing number of methyl groups. A similar trend is observed for the entropic component of the free energy of mixing at any composition, indicating that, above 1 mol % pyridine content, the entropic term becomes dominant and determines the order of the free energies of mixing of these compounds with water. The fact that this order is in clear accordance with the experimentally observed order of the ease of miscibility of these compounds with water at concentrations above 1 mol % suggests that the entropy of mixing plays a decisive role in the mixing behavior of methyl-substituted pyridines with water.

Water Activity from Equilibrium Molecular Dynamics Simulations and Kirkwood-Buff Theory.

Water activity and related thermodynamic properties are calculated for several aqueous solutions using equilibrium molecular dynamics in conjunction with the recent extension of the Kirkwood-Buff (KB) theory for closed systems. The general applicability of this method is evaluated on aqueous mixtures of ethanol, glyoxal, malonic acid, and NaCl, which represent different types of condensed-phase interactions. Solution microstructures are analyzed using KB integrals and cluster analysis to identify molecular associations due to hydrophobic interactions, hydrate formation, hydrogen bonding, or electrostatic forces affecting solution nonideality in the different systems. Activity estimation by this implementation-subvolume-KB molecular dynamics, or SKBMD, simulation-agrees well with experimental measurements and UNIFAC calculations over a wide range of nonideality, with the exception of the malonic acid/water system. Systematic deviations for this system are attributed to the deficiency of the standard OPLS force field, and are partially remediated with a Non-Bonded FIX (NBFIX) correction to reduce its extensive hydrogen-bonded clustering. Comparison of water and solute excess chemical potentials against other molecular simulation techniques for NaCl/water mixtures shows the SKBMD method to be competitive in performance with those requiring additional external constraints or computational complexity. Equilibrium molecular dynamics and KB theory can therefore be suitable for estimation of solution properties and testing the suitability of force fields, though strongly associating components leading to large and long-lived molecular clusters (either in reality or as a result of a bias in atom-atom potentials) can lead to inefficient sampling and higher estimation errors.

Immersion depth of surfactants at the free water surface: a computer simulation and ITIM analysis study.

The adsorption layer of five different surfactants, namely, pentanol, octanol, dodecanol, dodecyl trimethyl ammonium chloride, and sodium dodecyl sulfate, has been analyzed on the basis of molecular dynamics simulation results at two surface densities, namely, 1 and 4 µmol/m(2). The analyses have primarily focused on the question of how deeply, in terms of atomistic layers, the different surfactant molecules are immersed into the aqueous phase. The orientation and conformation of the surfactant molecules have also been analyzed. The obtained results reveal a clear difference between the immersion behavior of the alcoholic and ionic surfactants. Thus, alcoholic surfactants are found to be located right at the water surface, their apolar tails not being considerably immersed into the aqueous phase and the alcoholic headgroups being preferentially located in the surface layer of water. Ionic surfactants are immersed several layers deep into the aqueous phase, with headgroup atoms reaching the sixth-eighth and tail carbon atoms reaching the third-fourth subsurface layer in several cases. The observed difference is related, on the one hand, to the ability of the alcoholic surfactants of substituting surface water molecules in their lateral hydrogen bonding network at the water surface and that of their apolar tails for replacing dangling hydrogens and, on the other hand, to the energetic gain of the ionic headgroups if they are fully hydrated rather than being in contact with hydrocarbon tail groups.

Calculation of the intrinsic solvation free energy profile of an ionic penetrant across a liquid-liquid interface with computer simulations.

We introduce the novel concept of an intrinsic free energy profile, allowing one to remove the artificial smearing caused by thermal capillary waves, which renders difficulties for the calculation of free energy profiles across fluid interfaces in computer simulations. We apply this concept to the problem of a chloride ion crossing the interface between water and 1,2-dichloroethane and show that the present approach is able to reveal several important features of the free energy profile which are not detected with the usual, nonintrinsic calculations. Thus, in contrast to the nonintrinsic profile, a free energy barrier is found at the aqueous side of the (intrinsic) interface, which is attributed to the formation of a water "finger" the ion pulls with itself upon approaching the organic phase. Further, by the presence of a nonsampled region, the intrinsic free energy profile clearly indicates the coextraction of the first hydration shell water molecules of the ion when entering the organic phase.

Competitive adsorption of surfactants and polymers at the free water surface. A computer simulation study of the sodium dodecyl sulfate-poly(ethylene oxide) system.

Competitive adsorption of a neutral amphiphilic polymer, namely poly(ethylene oxide) (PEO) and an ionic surfactant, i.e., sodium dodecyl sulfate (SDS), is investigated at the free water surface by computer simulation methods at 298 K. The sampled equilibrium configurations are analyzed in terms of the novel identification of the truly interfacial molecules (ITIM) method, by which the intrinsic surface of the aqueous phase (i.e., its real surface corrugated by the capillary waves) instead of an ideally flat surface approximating its macroscopic surface plane, can be taken into account. In the simulations, the surface density of SDS is gradually increased from zero up to saturation, and the structural, dynamical, and energetic aspects of the gradual squeezing out of the PEO chains from the surface are analyzed in detail. The obtained results reveal that this squeezing out occurs in a rather intricate way. Thus, in the presence of a moderate amount of SDS the majority of the PEO monomer units, forming long bulk phase loops in the absence of SDS, are attracted to the surface of the solution. This synergistic effect of SDS of moderate surface density on the adsorption of PEO is explained by two factors, namely by the electrostatic attraction between the ionic groups of the surfactant and the moderately polar monomer units of the polymer, and by the increase of the conformational entropy of the polymer chain in the presence of the surfactant. This latter effect, thought to be the dominant one among the above two factors, also implies the formation of similar polymer/surfactant complexes at the interface than what are known to exist in the bulk phase of the solution. Finally, in the presence of a large amount of SDS the more surface active surfactant molecules gradually replace the PEO monomer units at the interfacial positions, and squeezing out the PEO molecules from the surface in a monomer unit by monomer unit manner.