Miguel Jorge

1-Octanol/water partition coefficients of n-Alkanes from molecular simulations of absolute solvation free energies

The 1-octanol/water partition coefficient is an important thermodynamic variable usually employed to understand and quantify the partitioning of solutes between aqueous and organic phases. It finds widespread use in many empirical correlations to evaluate the environmental fate of pollutants as well as in the design of pharmaceuticals. The experimental evaluation of 1-octanol/water partition coefficients is an expensive and time-consuming procedure, and thus, theoretical estimation methods are needed, particularly when a physical sample of the solute may not yet be available, such as in pharmaceutical screening. 1-Octanol/water partition coefficients can be obtained from Gibbs free energies of solvation of the solute in both the aqueous and the octanol phases. The accurate evaluation of free energy differences remains today a challenging problem in computational chemistry. In order to study the absolute solvation Gibbs free energies in 1-octanol, a solvent that can mimic many properties of important biological systems, free energy calculations for n-alkanes in the range C1-C8 were performed using molecular simulation techniques, following the thermodynamic integration approach. In the first part of this paper, we test different force fields by evaluating their performance in reproducing pure 1-octanol properties. It is concluded that all-atom force fields can provide good accuracy but at the cost of a higher computational time compared to that of the united-atom force fields. Recent versions of united-atom force fields, such as Gromos and TraPPE, provide satisfactory results and are, thus, useful alternatives to the more expensive all-atom models. In the second part of the paper, the Gibbs free energy of solvation in 1-octanol is calculated for several n-alkanes using three force fields to describe the solutes, namely Gromos, TraPPE, and OPLS-AA. Generally, the results obtained are in excellent agreement with the available experimental data and are of similar accuracy to commonly used QSPR models. Moreover, we have estimated the Gibbs free energy of hydration for the different compounds with the three force fields, reaching average deviations from experimental data of less than 0.2 kcal/mol for the case of the Gromos force field. Finally, we systematically compare different strategies to obtain the 1-octanol/water partition coefficient from the simulations. It is shown that a fully predictive method combining the Gromos force field in the aqueous phase and the OPLS-AA/TraPPE force field for the organic phase can give excellent predictions for n-alkanes up to C8 with an absolute average deviation of 0.1 log P units to the experimental data.

Molecular dynamics simulation of self-assembly of n-Decyltrimethylammonium Bromide micelles

In this paper, a molecular dynamics simulation of surfactant self-assembly using realistic atomistic models is presented. The simulations are long enough to enable the observation of several processes leading to equilibrium, such as monomer addition and detachment, micelle dissolution, and micelle fusion. The self-assembly of DeTAB surfactants takes place in three stages: fast aggregation of monomers to form small disordered oligomers; ripening process by which larger aggregates grow at the expense of smaller ones; slower stage involving collisions between large micelles. The first two stages were described well by a simple kinetic model with a size-independent rate constant estimated from the self-diffusion coefficient and collision radius of an isolated monomer. The average cluster size, area per headgroup, degree of counterion dissociation, and critical micelle concentration estimated from the simulation are in reasonable agreement with experimental values. An all-atom and united-atom surfactant model were compared, and the results were seen to be almost independent of the choice of model. DeTAB micelles are spheroidal, with a hydrophobic core composed of tail atoms surrounded by a hydrophilic corona of head atoms. A Stern layer composed of bromide counterions was also identified. Water molecules solvate the counterions and the head atoms, penetrating into the micelle up to the location of the atom connecting the head to the aliphatic tail, in agreement with recent experimental observations.

Salting-in with a Salting-out Agent: Explaining the Cation Specific Effects on the Aqueous Solubility of Amino Acids

Although the understanding of ion specific effects on the aqueous solubilities of biomolecules is crucial for the development of many areas of biochemistry and life sciences, a consensual and well-supported molecular picture of the phenomena has not yet been established. Mostly, the influence of cations and the nature of the molecular interactions responsible for the reversal of the Hofmeister trend in aqueous solutions of amino acids and proteins are still defectively understood. Aiming at contributing to the understanding of the molecular-level mechanisms governing the cation specific effects on the aqueous solubilities of biocompounds, experimental solubility measurements and classical molecular dynamics simulations were performed for aqueous solutions of three amino acids (alanine, valine, and isoleucine), in the presence of a series of inorganic salts. The evidence gathered suggests that the mechanism by which salting-in inducing cations operate in aqueous solutions of amino acids is different from that of anions, and allows for a novel and consistent molecular description of the effect of the cation on the solubility based on specific interactions of the cations with the negatively charged moieties of the biomolecules.

Molecular Dynamics Simulation Studies of the Interactions between Ionic Liquids and Amino Acids in Aqueous Solution

Although the understanding of the influence of ionic liquids (ILs) on the solubility behavior of biomolecules in aqueous solutions is relevant for the design and optimization of novel biotechnological processes, the underlying molecular-level mechanisms are not yet consensual or clearly elucidated. In order to contribute to the understanding of the molecular interactions established between amino acids and ILs in aqueous media, classical molecular dynamics (MD) simulations were performed for aqueous solutions of five amino acids with different structural characteristics (glycine, alanine, valine, isoleucine, and glutamic acid) in the presence of 1-butyl-3-methylimidazolium bis(trifluoromethyl)sulfonyl imide. The results from MD simulations enable to relate the properties of the amino acids, namely their hydrophobicity, to the type and strength of their interactions with ILs in aqueous solutions and provide an explanation for the direction and magnitude of the solubility phenomena observed in [IL + amino acid + water] systems by a mechanism governed by a balance between competitive interactions of the IL cation, IL anion, and water with the amino acids.

Water adsorption by activated carbons in relation to their microporous structure

The present paper examines the adsorption of water by microporous carbons in the absence of specific interactions. The modelling of water adsorption for 293 and 310 K, using variable pore size distributions (PSD), shows that the type V isotherms follow the Dubinin-Astakhov (DA) equation and fulfill the requirement for temperature invariance. Furthermore, the parameters of the DA equation can be related in a simple way to structural properties of the model carbons. For a number of well-characterized carbons, the type V isotherms generated by combining model isotherms with the corresponding PSDs are in good agreement with the limiting isotherms at 293 and 310 K derived on the basis of a recent development of Dubinins theory. This approach will provide the basis for further studies including specific interactions.

Modeling Adsorption in Metal–Organic Frameworks with Open Metal Sites: Propane/Propylene Separations

We present a new approach for modeling adsorption in metal-organic frameworks (MOFs) with unsaturated metal centers and apply it to the challenging propane/propylene separation in copper(II) benzene-1,3,5-tricarboxylate (CuBTC). We obtain information about the specific interactions between olefins and the open metal sites of the MOF using quantum mechanical density functional theory. A proper consideration of all the relevant contributions to the adsorption energy enables us to extract the component that is due to specific attractive interactions between the π-orbitals of the alkene and the coordinatively unsaturated metal. This component is fitted using a combination of a Morse potential and a power law function and is then included into classical grand canonical Monte Carlo simulations of adsorption. Using this modified potential model, together with a standard Lennard-Jones model, we are able to predict the adsorption of not only propane (where no specific interactions are present), but also of propylene (where specific interactions are dominant). Binary adsorption isotherms for this mixture are in reasonable agreement with ideal adsorbed solution theory predictions. We compare our approach with previous attempts to predict adsorption in MOFs with open metal sites and suggest possible future routes for improving our model.

Molecular simulation of phase coexistence in adsorption in porous solids

In this work a recently proposed method, the gauge-cell Gibbs ensemble Monte Carlo, is extended to deal with polar substances. The behaviour of water, a hydrogen bonding, weakly adsorbing fluid, is compared with that of methane, a strongly adsorbing, non-polar fluid, in the vicinity of the phase transition. The mechanisms of condensation for the two species are seen to be significantly different in nature. A systematic study of the effect of the pore width on the phase equilibrium of water is also performed. Our results show that the narrowing of the pore shifts the equilibrium transition pressure to lower values and reduces the extent of vapour metastability, but exerts little influence on the stability of the liquid phase.

The generalized identification of truly interfacial molecules (ITIM) algorithm for nonplanar interfaces

We present a generalized version of the ITIM algorithm for the identification of interfacial molecules, which is able to treat arbitrarily shaped interfaces. The algorithm exploits the similarities between the concept of probe sphere used in ITIM and the circumsphere criterion used in the α-shapes approach, and can be regarded either as a reference-frame independent version of the former, or as an extended version of the latter that includes the atomic excluded volume. The new algorithm is applied to compute the intrinsic orientational order parameters of water around a dodecylphosphocholine and a cholic acid micelle in aqueous environment, and to the identification of solvent-reachable sites in four model structures for soot. The additional algorithm introduced for the calculation of intrinsic density profiles in arbitrary geometries proved to be extremely useful also for planar interfaces, as it allows to solve the paradox of smeared intrinsic profiles far from the interface.

What does an ionic liquid surface really look like? Unprecedented details from molecular simulations

We present the first intrinsic analysis of the surface of the [bmim][PF(6)] room-temperature ionic liquid. Our detailed analysis reveals unprecedented details about the structure of the interface by providing the relative prevalence of different molecular orientations. These results suggest that experimental data should be reinterpreted considering a distribution of molecular arrangements.

Computational approaches to study adsorption in MOFs with unsaturated metal sites

Metal-organic frameworks (MOFs) with coordinatively unsaturated sites (CUS) offer interesting possibilities for tuning the affinity of these materials towards certain adsorbates, potentially increasing their selectivity and storage capacity. From a modelling point of view, however, they pose a significant challenge due to the inability of conventional force-fields for dealing with these specific interactions. In this paper, we review recent developments in the application of quantum-mechanical (QM) methods and classical molecular simulations to understand and predict adsorption in MOFs with CUS. We find that hybrid approaches that incorporate QM-based information into classical models are able to provide dramatically improved adsorption predictions relative to conventional force-fields, while yielding a realistic description of the adsorption mechanism in these materials.