Pamela Rubio-Pereda

Density functional theory study of the organic functionalization of hydrogenated silicene

Silicene, the silicon analogous of graphene, is a newly synthesized two-dimensional nanomaterial, with unique features and promising potential applications. In this paper we present density functional theory calculations of the organic functionalization of hydrogenated silicene with acetylene, ethylene, and styrene. The results are compared with previous works of the adsorption on H-Si[111]. For styrene, binding energies for the intermediate and final states as well as the energy barrier for hydrogen abstraction are rather similar for the two systems. On the other hand, results for acetylene and ethylene are surprisingly different in H-silicene: the abstraction barrier is much smaller in H-silicene than in H-Si[111]. These differences can be understood by the different electrostatic potentials due to the presence of the H atoms at the bottom of the silicene bilayer that allows the delocalization of the spin density at the reaction intermediate state.

Albumin (BSA) Adsorption over Graphene in Aqueous Environment: Influence of Orientation, Adsorption Protocol, and Solvent Treatment.

We report 150 ns explicit solvent MD simulations of the adsorption on graphene of albumin (BSA) in two orientations and using two different adsorption protocols, i.e., free and forced adsorption. Our results show that free adsorption occurs with little structural rearrangements. Even taking adsorption to an extreme, by forcing it with a 5 nN downward force applied during the initial 20 ns, we show that along a particular orientation BSA is able to preserve the structural properties of the majority of its binding sites. Furthermore, in all the cases considered in this work, the ibuprofen binding site has shown a strong resilience to structural changes. Finally, we compare these results with implicit solvent simulations and find that the latter predicts an extreme protein unfolding upon adsorption. The origin of this discrepancy is attributed to a poor description of the water entropic forces at interfaces in the implicit solvent methods.

Van der Waals molecular interactions in the organic functionalization of graphane, silicane, and germanane with alkene and alkyne molecules: a DFT-D2 study

Density functional theory with the addition of a semi-empirical dispersion potential was applied to the conventional Kohn–Sham energy to study the adsorption of alkene and alkyne molecules on hydrogen-terminated two-dimensional group IV systems (graphane, silicane, and germanane) by means of a radical-initiated reaction. In particular, we investigated the interactions of acetylene, ethylene, and styrene with those surfaces. Although we had studied these systems previously, we included van der Waals interactions in all of the cases examined in the present work. These forces, which are noncovalent interactions, can heavily influence different processes in molecular chemistry, such as the adsorption of organic molecules on semiconductor surfaces. This unified approach allowed us to perform a comparative study of the relative reactivities of the various organic molecule/surface systems. The results showed that the degree of covalency of the surface, the lattice size, and the partial charge distribution (caused by differences in electronegativity) are all key elements that determine the reactivity between the molecules and the surfaces tested in this work. The covalent nature of graphane gives rise to energetically favorable intermediate states, while the opposite polarities of the charge distributions of silicane and germanane with the organic molecules favor subsequent steps of the radical-initiated reaction. Finally, the lattice size is a factor that has important consequences due to steric effects present in the systems and the possibility of chain reaction continuation. The results obtained in this work show that careful selection of the substrate is very important. Calculated energy barriers, heats of adsorption, and optimized atomic structures show that the silicane system offers the best reactivity in organic functionalization.

Reactivity of phosphorene with a 3d element trioxide (CrO3) considering van der Waals molecular interactions: a DFT-D2 study

First-principle calculations are performed to investigate the interaction between clean black phosphorene and the CrO3 molecule which is known to be a powerful oxidizer and a suspected carcinogen. Van der Waals forces are included in all calculations through empirical corrections. Energetics studies are first done to determine the structural stability. Then charge density, Löwdin population analysis and electronic states are evaluated. Results show that the CrO3 molecule, with an acceptor electron character, is chemisorbed on the phosphorene surface inducing minimal geometrical distortions, however, after adsorption, a partial charge gradient is produced between the P atoms located at the phosphorene upper and lower planes. Furthermore, variations on the CrO3 concentration causes different interaction strengths. At high concentrations of adsorbed CrO3 molecules, the interaction with the surface becomes stronger due to an increased steric effect between neighboring molecules. Nevertheless, this effect along with the geometrical distortions produced on the phosphorene structure, due to the large number of molecules adsorbed, leads to a decrement on the adsorption energy. It is expected that the reported results may render phosphorene as a promising material for application as a gas sensor.

Albumin (BSA) adsorption onto graphite stepped surfaces

Nanomaterials are good candidates for the design of novel components with biomedical applications. For example, nano-patterned substrates may be used to immobilize protein molecules in order to integrate them in biosensing units. Here, we perform long MD simulations (up to 200 ns) using an explicit solvent and physiological ion concentrations to characterize the adsorption of bovine serum albumin (BSA) onto a nano-patterned graphite substrate. We have studied the effect of the orientation and step size on the protein adsorption and final conformation. Our results show that the protein is stable, with small changes in the protein secondary structure that are confined to the contact area and reveal the influence of nano-structuring on the spontaneous adsorption, protein-surface binding energies, and protein mobility. Although van der Waals (vdW) interactions play a dominant role, our simulations reveal the important role played by the hydrophobic lipid-binding sites of the BSA molecule in the adsorption process. The complex structure of these sites, that incorporate residues with different hydrophobic character, and their flexibility are crucial to understand the influence of the ion concentration and protein orientation in the different steps of the adsorption process. Our study provides useful information for the molecular engineering of components that require the immobilization of biomolecules and the preservation of their biological activity.