Integrating Machine Learning in the Coarse-Grained Molecular Simulation of Polymers.

Machine learning (ML) is having an increasing impact on the physical sciences, engineering, and technology and its integration into molecular simulation frameworks holds great potential to expand their scope of applicability to complex materials and facilitate fundamental knowledge and reliable property predictions, contributing to the development of efficient materials design routes. The application of ML in materials informatics in general, and polymer informatics in particular, has led to interesting results, however great untapped potential lies in the integration of ML techniques into the multiscale molecular simulation methods for the study of macromolecular systems, specifically in the context of Coarse Grained (CG) simulations. In this Perspective, we aim at presenting the pioneering recent research efforts in this direction and discussing how these new ML-based techniques can contribute to critical aspects of the development of multiscale molecular simulation methods for bulk complex chemical systems, especially polymers. Prerequisites for the implementation of such ML-integrated methods and open challenges that need to be met toward the development of general systematic ML-based coarse graining schemes for polymers are discussed.

Molecular Simulations and Mechanistic Analysis of the Effect of CO2 Sorption on Thermodynamics, Structure, and Local Dynamics of Molten Atactic Polystyrene.

A simulation strategy encompassing different scales was applied to the systematic study of the effects of CO2 uptake on the properties of atactic polystyrene (aPS) melts. The analysis accounted for the influence of temperature between 450 and 550 K, polymer molecular weights (M w) between 2100 and 31000 g/mol, and CO2 pressures up to 20 MPa on the volumetric, swelling, structural, and dynamic properties of the polymer as well as on the CO2 solubility and diffusivity by performing molecular dynamics (MD) simulations of the system in a fully atomistic representation. A hierarchical scheme was used for the generation of the higher M w polymer systems, which consisted of equilibration at a coarse-grained level of representation through efficient connectivity-altering Monte Carlo simulations, and reverse-mapping back to the atomistic representation, obtaining the configurations used for subsequent MD simulations. Sorption isotherms and associated swelling effects were determined by using an iterative procedure that incorporated a series of MD simulations in the NPT ensemble and the Widom test particle insertion method, while CO2 diffusion coefficients were extracted from long MD runs in the NVE ensemble. Solubility and diffusivity compared favorably with experimental results and with predictions of the Sanchez-Lacombe equation of state, which was reparametrized to capture the M w dependence of polymer properties with greater accuracy. Structural features of the polymer matrix were correctly reproduced by the simulations, and the effects of gas concentration and M w on structure and local dynamics were thoroughly investigated. In the presence of CO2, a significant acceleration of the segmental dynamics of the polymer occurred, more pronouncedly at low M w. The speed-up effect caused by the swelling agent was not limited to the chain ends but affected the whole chain in a similar fashion.

Molecular Modeling Investigations of Sorption and Diffusion of Small Molecules in Glassy Polymers.

With a wide range of applications, from energy and environmental engineering, such as in gas separations and water purification, to biomedical engineering and packaging, glassy polymeric materials remain in the core of novel membrane and state-of the art barrier technologies. This review focuses on molecular simulation methodologies implemented for the study of sorption and diffusion of small molecules in dense glassy polymeric systems. Basic concepts are introduced and systematic methods for the generation of realistic polymer configurations are briefly presented. Challenges related to the long length and time scale phenomena that govern the permeation process in the glassy polymer matrix are described and molecular simulation approaches developed to address the multiscale problem at hand are discussed.

Thermophysical properties of imidazolium tricyanomethanide ionic liquids: experiments and molecular simulation.

The low-viscous tricyanomethanide ([TCM](-))-based ionic liquids (ILs) are gaining increasing interest as attractive fluids for a variety of industrial applications. The thermophysical properties (density, viscosity, surface tension, electrical conductivity and self-diffusion coefficient) of the 1-alkyl-3-methylimidazolium tricyanomethanide [Cnmim][TCM] (n = 2, 4 and 6-8) IL series were experimentally measured over the temperature range from 288 to 363 K. Moreover, a classical force field optimized for the imidazolium-based [TCM](-) ILs was used to calculate their thermodynamic, structural and transport properties (density, surface tension, self-diffusion coefficients, viscosity) in the temperature range from 300 to 366 K. The predictions were directly compared against the experimental measurements. The effects of anion and alkyl chain length on the structure and thermophysical properties have been evaluated. In cyano-based ILs, the density decreases with increasing molar mass, in contrast to the behavior of the fluorinated anions, being in agreement with the literature. The contribution per -CH2- group to the increase of the viscosity presents the following sequence: [PF6](-) > [BF4](-) > [Tf2N](-) > [DCA](-) > [TCB](-) > [TCM](-). [TCM](-)-based ILs show lower viscosity than dicyanamide ([DCA](-))- and tetracyanoborate ([TCB](-))-based ILs, while the latter two exhibit a crossover which depends both on temperature and the alkyl chain length of the cation. The surface tension of the investigated ILs decreases with increasing alkyl chain length. [C2mim][TCM] shows an outlier behavior compared to other members of the homologous series. The surface enthalpies and surface entropies for all the studied systems have been calculated based on the experimentally determined surface tensions. The relationship between molar conductivity and viscosity was analyzed using the Walden rule. The experimentally determined self-diffusion coefficients of the cations are in good agreement with the molecular simulation predictions, in which a decrease of the self-diffusion of the cations with increasing alkyl chain length is observed with a simultaneous increase in viscosity and for the longer alkyl lengths the anion becomes more mobile than the cation.

Molecular simulations of imidazolium-based tricyanomethanide ionic liquids using an optimized classical force field.

Imidazolium-based ionic liquids (ILs) incorporating the tricyanomethanide ([TCM(-)]) anion are studied using an optimized classical force field. These ILs are very promising candidates for use in a wide range of cutting-edge technologies and, to our knowledge, it is the first time that this IL family is subject to a molecular simulation study with the use of a classical atomistic force field. The [C4mim(+)][TCM(-)] ionic liquid at 298.15 K and at atmospheric pressure was used as the basis for force field optimization which primarily involved the determination of the Lennard-Jones parameters of [TCM(-)] and the implementation of three quantum mechanical schemes for the calculation of the partial charge distribution and the identification of the appropriate scaling factor for the reduction of the total ionic charge. The optimized force field was validated by performing simulations of the 1-alkyl-3-methylimidazolium tricyanomethanide ([Cnmim(+)][TCM(-)], n = 2, 4, 6, and 8) IL family at various temperatures. The results for density, self-diffusivity and viscosity are in very good agreement with the available experimental data for all ILs verifying that the force field reliably reproduces the behaviour of the imidazolium-based [TCM(-)] IL family in a wide temperature range. Furthermore, a detailed analysis of the microscopic structure and the complex dynamic behaviour of the ILs under study was performed.

Elucidation of the binding mechanism of renin using a wide array of computational techniques and biological assays.

We investigate the binding mechanism in renin complexes, involving three drugs (remikiren, zankiren and enalkiren) and one lead compound, which was selected after screening the ZINC database. For this purpose, we used ab initio methods (the effective fragment potential, the variational perturbation theory, the energy decomposition analysis, the atoms-in-molecules), docking, molecular dynamics, and the MM-PBSA method. A biological assay for the lead compound has been performed to validate the theoretical findings. Importantly, binding free energy calculations for the three drug complexes are within 3 kcal/mol of the experimental values, thus further justifying our computational protocol, which has been validated through previous studies on 11 drug-protein systems. The main elements of the discovered mechanism are: (i) minor changes are induced to renin upon drug binding, (ii) the three drugs form an extensive network of hydrogen bonds with renin, whilst the lead compound presented diminished interactions, (iii) ligand binding in all complexes is driven by favorable van der Waals interactions and the nonpolar contribution to solvation, while the lead compound is associated with diminished van der Waals interactions compared to the drug-bound forms of renin, and (iv) the environment (H2O/Na(+)) has a small effect on the renin-remikiren interaction.

Coarse graining using pretabulated potentials: liquid benzene.

The large length and time scales involved in polymer simulation render the atomistic representation of polymer systems a computationally expensive and unnecessarily detailed procedure. We present a novel coarse-graining method for the description of nonbonded interactions between moieties composing the monomeric units of polymers, phenyl rings in particular. The method is based on the determination of the interactions between pairs of moieties from precalculated and tabulated values of the energy between the moieties in their atomistic representation. Validation of the method is performed by carrying out coarse-grained and fully atomistic simulations of a benzene liquid, where structural and thermodynamic properties at various state points are compared. The effects of the coarse grained model assumptions and of the energy table dimension and discretization are investigated. Results are also presented for the reverse mapping from the coarse grained to the fully atomistic representation.