Prediction of thermodynamic properties of fluid mixtures by molecular dynamics simulations: methane-ethane

Chemical library design, QSAR modeling and molecular dynamics simulations of naturally occurring coumarins as dual inhibitors of MAO-B and AChE

Coumarins are a highly privileged scaffold in medicinal chemistry. It is present in many natural products and is reported to display various pharmacological properties. A large plethora of compounds based on the coumarin ring system have been synthesized and were found to possess biological activities such as anticonvulsant, antiviral, anti-inflammatory, antibacterial, antioxidant as well as neuroprotective properties. Despite the wide activity spectrum of coumarins, its naturally occurring derivatives are yet to be investigated in detail. In the current study, a chemical library was created to assemble all chemical information related to naturally occurring coumarins from the literature. Additionally, a multi-stage virtual screening combining QSAR modeling, molecular docking, and ADMET prediction was conducted against monoamine oxidase B and acetylcholinesterase, two relevant targets known for their neuroprotective properties and 'disease-modifying' potential in Parkinson's and Alzheimer's disease. Our findings revealed ten coumarin derivatives that may act as dual-target drugs against MAO-B and AChE. Two coumarin candidates were selected from the molecular docking study: CDB0738 and CDB0046 displayed favorable interactions for both proteins as well as suitable ADMET profiles. The stability of the selected coumarins was assessed through 100 ns molecular dynamics simulations which revealed promising stability through key molecular interactions for CDB0738 to act as dual inhibitor of MAO-B and AChE. However, experimental studies are necessary to evaluate the bioactivity of the proposed candidate. The current results may generate an increasing interest in bioprospecting naturally occurring coumarins as potential candidates against relevant macromolecular targets by encouraging virtual screening studies against our chemical library.Communicated by Ramaswamy H. Sarma.

Cutting-edge molecular modelling to unveil new microscopic insights into the guest-controlled flexibility of metal-organic frameworks

Metal-organic frameworks are a class of porous solids that exhibit intriguing flexibility under stimuli, leading often to reversible giant structural changes upon guest adsorption. DUT-49(Cu) and MIL-53(Cr) are fascinating flexible MOFs owing to their guest-induced breathing and negative gas adsorption behaviors respectively. Molecular simulation is one of the most relevant tools to examine these phenomena at the atomistic scale and gain a unique understanding of the physics behind them. Although molecular dynamics and Monte Carlo simulations are widely used in the field of porous materials, these methods hardly consider the structural deformation of a soft material upon guest adsorption. In this work, a cutting-edge osmotic molecular dynamics approach is developed to consider simultaneously the fluid adsorption process and material flexibility. We demonstrate that this newly developed computational strategy offers a unique opportunity to gain unprecedented molecular insights into the flexibility of this class of materials.

Interpretation of the pressure-induced Raman frequency shift of the ν1 stretching bands of CH4 and N2 within CH4-CO2, N2-CO2 and CH4-N2 binary mixtures

The relationships between the frequency shift of the ν₁ stretching bands of CH₄ and N₂ with pressure (or density) and composition have been previously provided in the literature as reliable parameters for accurate empirical barometers and densimeters for the direct determination of the pressure or density of gas mixtures. However, the latter results still remain a pure description of the experimental data without any interpretation of the physical mechanisms hidden behind the variation trend of the observed peak position. The present paper is devoted to interpreting the origin of the pressure-induced vibrational frequency shifts of the ν₁ stretching bands of CH₄ and N₂ within CH₄-CO₂, N₂-CO₂ and CH₄-N₂ binary mixtures at the molecular level. Two different theoretical models (i.e., the Lennard-Jones 6-12 potential approximation - LJ, and the generalized perturbed hard-sphere fluid - PHF) are used to intuitively and qualitatively assess the variation trend as well as the magnitude of the frequency shift of the CH₄ and N₂ν₁ bands for an in-depth understanding. Thereby, the contribution of the attractive and repulsive solvation-mean forces to the variation of the Raman frequency shift as a function of pressure and composition is assessed. A predictive model of the variation trend of the frequency shift of the CH₄ν₁ band as a function of pressure (up to 3000 bars), density and composition within CH₄-N₂ and CH₄-CO₂ binary mixtures is then provided.

Thermodynamic Analysis of n-Hexane-Ethanol Binary Mixtures Using the Kirkwood-Buff Theory

A complete thermodynamic analysis of mixtures consisting of molecules with complex chemical constitution can be rather demanding. The Kirkwood-Buff theory of solutions allows the estimation of thermodynamic properties, which cannot be directly extracted from atomistic simulations, such as the Gibbs energy of mixing (Δ_mix G). In this work, we perform molecular dynamics simulations of n-hexane-ethanol binary mixtures in the liquid state under two temperature-pressure conditions and at various mole fractions. On the basis of the recently published methodology of Galata [ Fluid Phase Equilib. 2018 , 470 , 25 - 37 ] , we first calculate the Kirkwood-Buff integrals in the isothermal-isobaric ( NpT) ensemble, identifying how system size affects their estimation. We then extract the activity coefficients, excess Gibbs energy, excess enthalpy, and excess entropy for the n-hexane-ethanol binary mixtures we simulate. We employ two approaches for quantifying composition fluctuations: one based on counting molecular centers of mass and a second one based on counting molecular segments. Results from the two approaches are practically indistinguishable. We compare our results against predictions of vapor-liquid equilibria obtained in a previous simulation work using the same force field, as well as with experimental data, and find very good agreement. In addition, we develop a simple methodology to identify the hydrogen bonds between ethanol molecules and analyze their effects on mixing properties.

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.

Physical Absorption of Green House Gases in Amines: The Influence of Functionality, Structure, and Cross-Interactions

Monte Carlo simulations were performed in the isothermal-isobaric ensemble (NPT) to calculate the Henry constants of methane (CH₄), nitrous oxide (N₂O), and carbon dioxide (CO₂) in pure H₂O, amines, and alkanolamines using the classical Lorentz-Berthelot combining rules (L-B). The Henry constants of N₂O and CO₂ in water are highly overestimated and motivated us to propose a new set of unlike interactions. Contrarily, the Henry constant of N₂O in MEA is underestimated by around 40%, and again, a new reoptimized cross unlike parameter is able to reproduce the constant to within 10%. An analysis is given of the relationship between the physical absorption of these gases and the chemical structure or functionality of 12 molecules including amines and alkanolamines using the anisotropic united atom intermolecular potential (AUA4). Finally, the solubility of N₂O in an aqueous solution of monoethanolamine (MEA) at 30% (wt) was also studied. A Henry constant within 7% of the experimental value was found by using the reoptimized parameters along with L-B to account for the MEA + H₂O unlike interactions. This very good agreement without additional adjustments for the MEA + H₂O system may be attributed to the good excess properties predictions found in previous works for the binary mixture (MEA + H₂O). However, further work, including additional alkanolamines in aqueous solutions at several concentrations, is required to verify this particular point.

Classical force field for hydrofluorocarbon molecular simulations. Application to the study of gas solubility in poly(vinylidene fluoride)

A classical all-atoms force field for molecular simulations of hydrofluorocarbons (HFCs) has been developed. Lennard-Jones force centers plus point charges are used to represent dispersion-repulsion and electrostatic interactions. Parametrization of this force field has been performed iteratively using three target properties of pentafluorobutane: the quantum energy of an isolated molecule, the dielectric constant in the liquid phase, and the compressed liquid density. The accuracy and transferability of this new force field has been demonstrated through the simulation of different thermophysical properties of several fluorinated compounds, showing significant improvements compared to existing models. This new force field has been applied to study solubilities of several gases in poly(vinylidene fluoride) (PVDF) above the melting temperature of this polymer. The solubility of CH4, CO2, H2S, H2, N2, O2, and H2O at infinite dilution has been computed using test particle insertions in the course of a NpT hybrid Monte Carlo simulation. For CH4, CO2, and their mixtures, some calculations beyond the Henry regime have also been performed using hybrid Monte Carlo simulations in the osmotic ensemble, allowing both swelling and solubility determination. An ideal mixing behavior is observed, with identical solubility coefficients in the mixtures and in pure gas systems.

Modeling adsorption properties on the basis of microscopic, molecular, and structural descriptors for nonpolar adsorbents

We propose a method for analytically predicting single-component adsorption isotherms from molecular, microscopic and structural descriptors of the adsorbate-adsorbent system and concepts of statistical thermodynamics. Expressions for Henry's constant and the heat of adsorption at zero coverage are derived. These functions depend on the pore size, pore shape, chemical composition, and density of the adsorbent material. They quantify the strength of the solid-fluid interaction, which governs the low-pressure part of the adsorption isotherm. For intermediate and high pressures, the fluid-fluid interactions must also be taken into account. Both solid-fluid and fluid-fluid interactions are combined within the framework of the Ruthven statistical model (RSM). The RSM thus constructs theoretical adsorption isotherms that are entirely based on microscopic molecular and structural descriptors. The theoretical results that we obtained are compared with experimental data for the adsorption of pure CO2 and CH4 on all-silica zeolites. The developed methodology allows for the estimation of the optimum properties of a nonpolar adsorbent for the adsorption of CO2 in cyclic adsorption processes.

On the isobaric thermal expansivity of liquids

The temperature and pressure dependence of isobaric thermal expansivity, α(p), in liquids is discussed in this paper. Reported literature data allow general trends in this property that are consistent with experimental evidence to be established. Thus, a negative pressure dependence is to be expected except around the critical point. On the other hand, α(p) exhibits broad regions of negative and positive temperature dependence in the (T, p) plane depending on the nature of the particular liquid. These trends are rationalized here in terms of various molecular-based equations of state. The analysis of the Lennard-Jones, hard sphere square well and restricted primitive model equations allows understanding the differences in the α(p) behavior between liquids of diverse chemical nature (polar, nonpolar, and ionic): broader regions of negative temperature and positive pressure dependencies are obtained for liquids characterized by larger ranges of the interparticle potential. Also, using the statistical associating fluid theory (SAFT) allowed the behavior of more complex systems (basically, those potentially involving chain and association effects) to be described. The effect of chain length is rather simple: increasing it is apparently equivalent to raise the interaction range. By contrast, association presents a quite complex effect on α(p), which comes from a balance between the dispersive and associative parts of the interaction potential. Thus, if SAFT parameters are adjusted to obtain low association ability, α(p) is affected by each mechanism at clearly separate regions, one at low temperature, due to association, and the other to dispersive forces, which has its origin in fluctuations related with vapor-liquid transition.

Surface tension and vapor-liquid phase coexistence of confined square-well fluid

Phase equilibria of a square-well fluid in planar slit pores with varying slit width are investigated by applying the grand-canonical transition-matrix Monte Carlo (GC-TMMC) with the histogram-reweighting method. The wall-fluid interaction strength was varied from repulsive to attractive such that it is greater than the fluid-fluid interaction strength. The nature of the phase coexistence envelope is in agreement with that given in literature. The surface tension of the vapor-liquid interface is calculated via molecular dynamics simulations. GC-TMMC with finite size scaling is also used to calculate the surface tension. The results from molecular dynamics and GC-TMMC methods are in very good mutual agreement. The vapor-liquid surface tension, under confinement, was found to be lower than the bulk surface tension. However, with the increase of the slit width the surface tension increases. For the case of a square-well fluid in an attractive planar slit pore, the vapor-liquid surface tension exhibits a maximum with respect to wall-fluid interaction energy. We also report estimates of critical properties of confined fluids via the rectilinear diameter approach.

An advanced Gibbs-Duhem integration method: Theory and applications

The conventional Gibbs-Duhem integration method is very convenient for the prediction of phase equilibria of both pure components and mixtures. However, it turns out to be inefficient. The method requires a number of lengthy simulations to predict the state conditions at which phase coexistence occurs. This number is not known from the outset of the numerical integration process. Furthermore, the molecular configurations generated during the simulations are merely used to predict the coexistence condition and not the liquid- and vapor-phase densities and mole fractions at coexistence. In this publication, an advanced Gibbs-Duhem integration method is presented that overcomes above-mentioned disadvantage and inefficiency. The advanced method is a combination of Gibbs-Duhem integration and multiple-histogram reweighting. Application of multiple-histogram reweighting enables the substitution of the unknown number of simulations by a fixed and predetermined number. The advanced method has a retroactive nature; a current simulation improves the predictions of previously computed coexistence points as well. The advanced Gibbs-Duhem integration method has been applied for the prediction of vapor-liquid equilibria of a number of binary mixtures. The method turned out to be very convenient, much faster than the conventional method, and provided smooth simulation results. As the employed force fields perfectly predict pure-component vapor-liquid equilibria, the binary simulations were very well suitable for testing the performance of different sets of combining rules. Employing Lorentz-Hudson-McCoubrey combining rules for interactions between unlike molecules, as opposed to Lorentz-Berthelot combining rules for all interactions, considerably improved the agreement between experimental and simulated data.