Interaction potential models for bulk ZnS, ZnS nanoparticle, and ZnS nanoparticle-PMMA from first-principles

Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning

Adsorption free energies of 32 small biomolecules (amino acids side chains, fragments of lipids, and sugar molecules) on 33 different nanomaterials, computed by the molecular dynamics - metadynamics methodology, have been analyzed using statistical machine learning approaches. Multiple unsupervised learning algorithms (principal component analysis, agglomerative clustering, and K-means) as well as supervised linear and nonlinear regression algorithms (linear regression, AdaBoost ensemble learning, artificial neural network) have been applied. As a result, a small set of biomolecules has been identified, knowledge of adsorption free energies of which to a specific nanomaterial can be used to predict, within the developed machine learning model, adsorption free energies of other biomolecules. Furthermore, the methodology of grouping of nanomaterials according to their interactions with biomolecules has been presented.

Biomolecular Adsorprion at ZnS Nanomaterials: A Molecular Dynamics Simulation Study of the Adsorption Preferences, Effects of the Surface Curvature and Coating

The understanding of interactions between nanomaterials and biological molecules is of primary importance for biomedical applications of nanomaterials, as well as for the evaluation of their possible toxic effects. Here, we carried out extensive molecular dynamics simulations of the adsorption properties of about 30 small molecules representing biomolecular fragments at ZnS surfaces in aqueous media. We computed adsorption free energies and potentials of mean force of amino acid side chain analogs, lipids, and sugar fragments to ZnS (110) crystal surface and to a spherical ZnS nanoparticle. Furthermore, we investigated the effect of poly-methylmethacrylate (PMMA) coating on the adsorption preferences of biomolecules to ZnS. We found that only a few anionic molecules: aspartic and glutamic acids side chains, as well as the anionic form of cysteine show significant binding to pristine ZnS surface, while other molecules show weak or no binding. Spherical ZnS nanoparticles show stronger binding of these molecules due to binding at the edges between different surface facets. Coating of ZnS by PMMA changes binding preferences drastically: the molecules that adsorb to a pristine ZnS surface do not adsorb on PMMA-coated surfaces, while some others, particularly hydrophobic or aromatic amino-acids, show high binding affinity due to binding to the coating. We investigate further the hydration properties of the ZnS surface and relate them to the binding preferences of biomolecules.

Computational approach to (ZnS)_{i} nanoclusters in ionic liquids

Unique and attractive properties have been predicted for II-VI-type semiconductor nanoclusters within the field of nanotechnology. However, the low reaction kinetics within the usual solvents gives only thermodynamic control during their production process, making the obtention of different metastable polymorphs extremely difficult. The use of ionic liquids as solvents has been proposed to overcome this problem. Identifying how these nanoclusters are solvated within ionic liquids is fundamental if this strategy is to be pursued. While computational chemistry tools are best suited for this task, the complexity and size of the system requires a careful design of the simulation protocol, which is put forward in this work. Taking as reference the (ZnS)_{12} nanocluster and the [EMIM][EtSO_{4}] ionic liquid, we characterize the interactions between the nanoparticle and first solvation shell by density functional theory calculations, considering most of the solvent implicitly. The DFT results are consistent through different theory levels showing a strong interaction between the Zn atoms of the nanocluster and the [EtSO_{4}^{-}] anion of the ionic liquid. A more realistic representation of the system is obtained by classical MD calculations, for which various classical force fields were considered and several atomic interactions parameterized. This new set of parameters correctly describes the interaction of different (ZnS) nanoclusters, supporting its transferability. The resulting MD simulation shows the formation of a structured ionic liquid solvation shell around the nanocluster with no exchange of ions for at least 5 ns, in agreement with the strong interactions observed in the density functional theory calculations.

Conceptual design of tetraazaporphyrin- and subtetraazaporphyrin-based functional nanocarbon materials: electronic structures, topologies, optical properties, and methane storage capacities

A large variety of conceptual three- and fourfold tetraazaporphyrin- and subtetraazaporphyrin-based functional 3D nanocage and nanobarrel structures have been proposed on the basis of in silico design. The designed structures differ in their sizes, topology, porosity, and conjugation properties. The stability of nanocages of Oh symmetry and nanobarrels of D4h symmetry was revealed on the basis of DFT and MD calculations, whereas their optical properties were assessed using a TDDFT approach and a long-range corrected LC-wPBE exchange-correlation functional. It was shown that the electronic structures and vertical excitation energies of the functional nanocage and nanobarrel structures could be easily tuned via their size, topology, and the presence of bridging sp(3) carbon atoms. TDDFT calculations suggest significantly lower excitation energies in fully conjugated nanocages and nanobarrels compared with systems with bridging sp(3) carbon fragments. Based on DFT and TDDFT calculations, the optical properties of the new materials can rival those of known quantum dots and are superior to those of monomeric phthalocyanines and their analogues. The methane gas adsorption properties of the new nanostructures and nanotubes generated by conversion from nanobarrels were studied using an MD simulation approach. The ability to store large quantities of methane (106-216 cm(3) (STP) cm(-3)) was observed in all cases with several compounds being close to or exceeding the DOE target of 180 cm(3) (STP) cm(-3) for material-based methane storage at a pressure of 3.5 MPa and room temperature.