Entropy and enthalpy calculations from perturbation and integration thermodynamics methods using molecular dynamics simulations: applications to the calculation of hydration and association thermodynamic properties

Toward a Better Understanding of the Poly(glycerol sebacate)-Water Interface

Molecular simulations were conducted to provide a better description of the poly(glycerol sebacate) (PGS)-water interface. The density and the glass-transition temperature as well as their dependencies on the degree of esterification were examined in close connection with the available experimental data. The work of adhesion and water contact angle were calculated as a function of the degree of esterification. A direct correlation was established between the strength of the hydrogen bond network in the interfacial region and the change in the water contact angle with respect to the degree of esterification. The interfacial region was described by local density profiles and orientations of the water molecules.

Importance of the Electrostatic Correlations in Surface Tension of Hydrated Reline Deep Eutectic Solvent from Combined Experiments and Molecular Dynamics Simulations

In this study, the surface tension and the structure of hydrated reline are investigated by using diverse methods. Initially, the surface tension displays a nonlinear pattern as water content increases, decreasing until reaching 45 wt %, then gradually matching that of pure water. This fluctuation is associated with strong electrostatic correlations present in pure reline, which decrease as more water is added. Changes in surface tension reflect a shift from charge layering in pure reline to an increased interfacial hydrogen bonding as the water content rises. This shift causes the segregation of urea molecules into the bulk phase and a gradual anchoring of water molecules to the air-reline interface. An interesting observation is the antisurfactant effect, where heightened interfacial anchoring results in an unexpected increase in real contribution of surface tension. This, along with weakened electrostatic correlations beyond 45 wt % due to reinforced interfacial hydrogen bonding, contributes to the complex behavior of surface tension observed in this study.

A Consistent Thermodynamic Characterization of the Adsorption Process through the Calculation of Free Energy Contributions

We apply in this study different methodologies based on thermodynamic integration (TI), free energy perturbation (FEP), and potential of mean force (PMF) to address the challenging issue of the calculation of the free energy of adsorption. A model system composed of a solid substrate, an adsorbate, and solvent particles is specifically designed to reduce the dependence of our free energy results on the sampling of the phase space and the choice of the pathway. The reliability and efficiency of these alchemical free energy simulations are established through the closure of a thermodynamic cycle describing the adsorption process in solution and in a vacuum. We complete this study by the calculation of free energy contributions related to phenomena of desorption of solvent molecules and desolvation of the adsorbate upon adsorption. This calculation relies on the work of adhesion, the interfacial tension of the liquid-vapor of the solvent, and the free energy of solvation of the substrate. The different ways of calculating the free energy of adsorption are in excellent agreement and could complete experiments in the field of adsorption by giving quantitative data on the different energy contributions involved in the process.

Energetic and Structural Characterizations of the PET-Water Interface as a Key Step in Understanding Its Depolymerization

We report molecular simulations of the interaction between poly(ethylene terephthalate) (PET) surfaces and water molecules with a short-term goal to better evaluate the different energy contributions governing the enzymatic degradation of amorphous PET. After checking that the glass transition temperature, density, entanglement mass, and mechanical properties of an amorphous PET are well reproduced by our molecular model, we extend the study to the extraction of a monomer from the bulk surface in different environments, i.e., water, vacuum, dodecane, and ethylene glycol. We complete this energetic characterization by the calculation of the work of adhesion of PET surfaces with water and dodecane molecules and by the determination of the contact angle of water droplets. These calculations are compared with experiments and should help us to better understand the enzymatic degradation of PET from both the thermodynamic and molecular viewpoints.

Molecular interactions at the metal-liquid interfaces

We reported molecular simulations of the interactions among water, an epoxy prepolymer diglycidic ether of bisphenol A (DGEBA), and a hardener isophorone diamine (IPDA) on an aluminum surface. This work proposes a comprehensive thermodynamic characterization of the adhesion process from the calculation of different interfacial tensions. The cross-interactions between the atoms of the metal surface and different molecules are adjusted so as to reproduce the experimental work of adhesion. Water nanodroplets on the metal surface are then simulated to predict their contact angle. Liquid-vapor surface tensions of the epoxy prepolymer (DGEBA) and hardener (IPDA) and the solid-vapor surface tension of the aluminum surface are also calculated to provide the solid-liquid interfacial tension that remains very difficult to obtain from the mechanical definition.

Application of Molecular Dynamics Simulations in the Analysis of Cyclodextrin Complexes

Cyclodextrins (CDs) are highly respected for their ability to form inclusion complexes via host-guest noncovalent interactions and, thus, ensofance other molecular properties. Various molecular modeling methods have found their applications in the analysis of those complexes. However, as showed in this review, molecular dynamics (MD) simulations could provide the information unobtainable by any other means. It is therefore not surprising that published works on MD simulations used in this field have rapidly increased since the early 2010s. This review provides an overview of the successful applications of MD simulations in the studies on CD complexes. Information that is crucial for MD simulations, such as application of force fields, the length of the simulation, or solvent treatment method, are thoroughly discussed. Therefore, this work can serve as a guide to properly set up such calculations and analyze their results.

Understanding and Characterizing the Drug Sorption to PVC and PE Materials

Characterizing the sorption of drugs onto polyvinylchloride (PVC) and polyethylene (PE) materials in terms of thermodynamic adsorption properties and atomistic details (local arrangements, orientation, and diffusion) is fundamental for the development of alternative materials that would limit drug sorption phenomena and plasticizer release. Here, a combination of experiments and sophisticated calculations of potential of mean forces are carried out to investigate the sorption of paracetamol and diazepam to PE and PVC surfaces. The simulated Gibbs free energies of adsorption are in line with the experimental interpretations. The polymer-drug-water interface is then characterized at the molecular scale by an in-depth investigation of local properties such as density, orientation, and diffusion.

A Review on Combination of Ab Initio Molecular Dynamics and NMR Parameters Calculations

This review focuses on a combination of ab initio molecular dynamics (aiMD) and NMR parameters calculations using quantum mechanical methods. The advantages of such an approach in comparison to the commonly applied computations for the structures optimized at 0 K are presented. This article was designed as a convenient overview of the applied parameters such as the aiMD type, DFT functional, time step, or total simulation time, as well as examples of previously studied systems. From the analysis of the published works describing the applications of such combinations, it was concluded that including fast, small-amplitude motions through aiMD has a noticeable effect on the accuracy of NMR parameters calculations.

The pair distribution function in the planar gas-liquid interface: Application to the calculation of the surface tension

A Monte Carlo simulation is used to calculate the pair distribution function g⁽²⁾r₁,r₂ for a planar gas-liquid interface. Due to the cylindrical symmetry of the system, g⁽²⁾ can be stored as a three-dimensional array that can be readily manipulated and used to calculate the surface tension and the single atom density profile directly. The consistency and accuracy of our calculation of g⁽²⁾(r₁, r₂) is demonstrated by a calculation of the single atom density through the first Born-Green-Yvon equation. We show that the surface tension calculated directly from the pair distribution function and from other well-established routes is completely consistent. In the case of the gas-liquid interface for argon modeled with an explicit inclusion of the three-body forces, an accurate pair distribution can be used to estimate the long-range contribution to the three-body part of the surface tension. A detailed analysis of this correction, its dependence on the three-body cutoff, and its overall contribution to the surface tension are presented.

Thermodynamics of Supramolecular Associations with Macrocyclic Water-Soluble Hosts

The thermodynamic study of the complexation of the β-cyclodextrins and p-sulfonatocalix[n]arenes (CnS) with the 4-aminoazobenzene was reported and was carried out by molecular dynamics simulations. We determined the whole thermodynamic properties (K, Δr G°, Δr H°, and TΔr S°) using the potential of mean force (PMF) technique and more precisely the adaptive biasing force method. Depending on both the nature of the host molecule and the pH of the solution, the PMF profiles present different shapes and energy minima. Considering the complexity of these PMF profiles, we are also interested in the structural properties of these associations. Hence, we calculated hydrogen bonds, Lennard-Jones and electrostatic energies, the number of atoms of the guest molecule inserted inside the cagelike host molecule, and the number of water molecules expelled from the cavity.

Calculation of the interfacial tension of the graphene-water interaction by molecular simulations

We report the calculation of the solid-liquid interface tension of the graphene-water interaction by using molecular simulations. Local profiles of the interfacial tension are given through the mechanical and thermodynamic definitions. The dependence of the interfacial tension on the graphene area is investigated by applying both reaction field and Ewald summation techniques. The structure of the interfacial region close to the graphene sheet is analyzed through the profiles of the density and hydrogen bond number and the orientation of the water molecules. We complete this study by plotting the profiles of the components of the pressure tensor calculated by the Ewald summation and reaction field methods. We also investigate the case of a reaction field version consisting in applying a damped shifted force in the case of the calculation of the pressure components.

Importance of the tail corrections on surface tension of curved liquid-vapor interfaces

We report molecular simulations of the liquid-vapor cylindrical interface of methane. We apply the truncated Lennard-Jones potential and specific long-range corrections for the surface tension developed especially for cylindrical interfaces. We investigate the impact of the cutoff on the radial density profile, the intrinsic and long-range correction parts to the surface tension, and Tolman length. We also study the curvature dependence of the surface tension as a function of the cutoff used. In this work we shed light that both density and Tolman length are cutoff-dependent whereas the total surface tension is slightly curvature and cutoff dependent.

Test-area surface tension calculation of the graphene-methane interface: Fluctuations and commensurability

The surface tension (γ) of methane on a graphene monolayer is calculated by using the test-area approach. By using a united atom model to describe methane molecules, strong fluctuations of surface tension as a function of the surface area of the graphene are evidenced. In contrast with the liquid-vapor interfaces, the use of a larger cutoff does not fully erase the fluctuations in the surface tension. Counterintuitively, the description of methane and graphene from the Optimized Potentials for Liquid Simulations all-atom model and a flexible model, respectively, led to a lessening in the surface tension fluctuations. This result suggests that the origin of fluctuations in γ is due to a model-effect rather than size-effects. We show that the molecular origin of these fluctuations is the result of a commensurable organization between both graphene and methane. This commensurable structure can be avoided by describing methane and graphene from a flexible force field. Although differences in γ with respect to the model have been often reported, it is the first time that the model drastically affects the physics of a system.

Computer modelling of the surface tension of the gas–liquid and liquid–liquid interface

This review presents the state of the art in molecular simulations of interfacial systems and of the calculation of the surface tension from the underlying intermolecular potential.

How does the dehydration change the host-guest association under homogeneous and heterogeneous conditions?

In this study, the thermodynamic properties of association of some inorganic ions (ClO4(-) and SO4(2-)) with β-cyclodextrins (β-CD) in aqueous solution are determined under both free β-CD and surface confined β-CD conditions using atomistic simulations. The potential of mean force (PMF) is calculated as a function of the environment and the thermodynamic properties of association are deduced by integrating the free energy profiles. No inclusion complex between SO4(2-) and β-CD is detected. Nevertheless, the PMF curve obtained for gold-confined CD seems to evidence a small minimum at a larger separation distance that shows specific interactions such as hydrogen bonding outside the cavity. As concerns ClO4(-), our simulations reveal the formation of an inclusion complex with free β-CD in perfect agreement with the available experimental results. Nevertheless, we do not detect any formation of the host-guest inclusion complex under heterogeneous conditions. Finally, the differences observed as a function of the anions are interpreted through an atomistic description. The general trend of weaker complex stabilities with the increasing free energy of hydration of the anions is found in homogeneous systems.

Quantitative Predictions of the Interfacial Tensions of Liquid-Liquid Interfaces through Atomistic and Coarse Grained Models

We report molecular simulations of oil-water liquid-liquid interfaces by using atomistic and coarse grained (CG) MARTINI force fields. We also apply the electronic continuum (EC) model to the MARTINI force field for the calculation of the interfacial tension of oil/water-salt systems. In a first step, we propose to calculate the interfacial tensions using thermodynamic and mechanical definitions of hydrocarbon-water interfacial systems modified by the addition of salts and alcohol. We also establish here the order of magnitude of the long-range corrections to the interfacial tension in fluid-fluid interfaces. Whereas the atomistic models are able to reproduce quantitatively the interfacial tension and the coexisting densities of oil-water systems, the coarse-description shows some deviations in the prediction of the interfacial tensions. Nevertheless, the physical features of these liquid-liquid interfaces are well-captured by this CG description. The CG force field offers then a very challenging alternative that will require however a more developed calibration of the parameters on the basis of liquid-liquid properties.

Free energy calculations in electroactive self-assembled monolayers (SAMs): impact of the chain length on the redox reaction

The free energy approach is used to study the effect of the relative chain length of the two constituents of electroactive self-assembled monolayers (SAMs) on gold. In this study, the ferrocene groups are exposed to the electrolyte solution. This situation is achieved by using shorter diluent alkanethiol chains. To this end, the mixed monolayers formed by the self-assembly of 11-ferrocenylundecanethiol and butanethiol FcC(11)S/C(4)S and of 6-ferrocenylhexanethiol and butanethiol FcC(6)S/C(4)S onto a gold surface are studied. Calculation of enthalpy and entropy differences are also performed using molecular simulations. Additionally, the electrochemical signatures of these systems are determined to allow a direct comparison with our calculations. The thermodynamic properties are discussed in terms of enthalpy and entropy changes. Two effects account for the thermodynamic behavior. The first one involves the ion pairing between the ferrocenium group and the perchlorate anion. The second one concerns the desolvation of the first hydration shell of the anions. Finally, this work is also completed with a microscopic description associated with an energy characterization of these SAMs as a function of the surface coverage under conditions close to experiments.

Calculation of the absolute thermodynamic properties of association of host-guest systems from the intermolecular potential of mean force

The authors report calculations of the intermolecular potential of mean force (PMF) in the case of the host-guest interaction. The host-guest system is defined by a water soluble calixarene and a cation. With an organic cation such as the tetramethylammonium cation, the calixarene forms an insertion complex, whereas with the Lanthane cation, the supramolecular assembly is an outer-sphere complex. The authors apply a modified free energy perturbation method and the force constraint technique to establish the PMF profiles as a function of the separation distance between the host and guest. They use the PMF profile for the calculation of the absolute thermodynamic properties of association that they compare to the experimental values previously determined. They finish by giving some structural features of the insertion and outer-sphere complexes at the Gibbs free energy minimum.