arXiv subjects

Paulo Siani

Publications and source records attributed to Paulo Siani.

6 recordsLinked to original sources

arXiv2026

Discovering structural, electronic and excitonic properties of bulk, nanostructured and doped C3N4 in diamond- and graphitic-like phases

In this systematic density functional theory study, we compare a standard gradient corrected functional (PBE) with a long-range hybrid functional (HSE06), with and without correction for the dispersion forces, relative to their ability to correctly reproduce structural and electronic properties of different bulk 3D C3N4 phases, encompassing diamond- and graphitic-like models. Corrugation is found to provide further stabilization to the layered structures with all methods. We observe that HSE06-D3 method provides results in good agreement with experimental data and with more sophisticated G0W0 calculations. Based on that, we exploited the method to investigate the nature of the bulk triplet excitons in these C3N4 structures to evaluate the S0-T1 energy difference, the self-trapping triplet exciton energy and the photoluminescence emission energy since this is a promising visible-light photocatalyst. Nanostructuring (0D and 2D) is another relevant aspect of these materials in practical applications; therefore, we have considered the effect of single- or multilayer exfoliation or space confinement in nanoparticles. Finally, we also discuss how the introduction of extrinsic dopants (e.g., S atoms) in the nanostructures modifies the atomic and electronic structure.

cond-mat.mtrl-sci↗

arXiv2022

Multi-scale modeling of folic acid-functionalized TiO$_{2}$ nanoparticles for active targeting of tumor cells

Strategies based on the active targeting of tumor cells are emerging as smart and efficient nanomedical procedures. Folic acid (FA) is a vitamin and a well-established tumor targeting agent because of its strong affinity for the folate receptor (FR), which is an overexpressed protein on the cell membranes of the tumor cells. FA can be successfully anchored to several nanocarriers, including inorganic nanoparticles (NPs) based on transition metal oxides. Among them, TiO$_{2}$ is extremely interesting because of its excellent photoabsorption and photocatalytic properties, which can be exploited in photodynamic therapy. However, it is not yet clear in which respects direct anchoring of FA to the NP or the use of spacers, based on polyethylene glycol (PEG) chains, are different and whether one approach is better than the other. In this work, we combine Quantum Mechanics (QM) and Classical Molecular Dynamics (MD) to design and optimize the FA functionalization on bare and PEGylated TiO$_{2}$ models and to study the dynamical behavior of the resulting nanoconjugates in pure water environment and in physiological conditions. We observe that they are chemically stable, even under the effect of increasing temperature (up to 500 K). Using the results from long MD simulations (100 ns) and from free energy calculations, we determine how the density of FA molecules on the TiO$_{2}$ NP and the presence of PEG spacers impact on the actual exposure of the ligands, especially by affecting the extent of FA-FA intermolecular interactions, which are detrimental for the targeting ability of FA towards the folate receptor. This analysis provides a solid and rational basis for experimentalists to define the optimal FA density and the more appropriate mode of anchoring to the carrier, according to the final purpose of the nanoconjugate.

cond-mat.mtrl-sci↗

arXiv2022

Molecular dynamics simulations of cRGD-conjugated PEGylated TiO$_2$ nanoparticles for targeted photodynamic therapy

The conjugation of high-affinity cRGD-containing peptides is a promising approach in nanomedicine to efficiently reduce off-targeting effects and enhance the cellular uptake by integrin-overexpressing tumor cells. Herein we utilize atomistic molecular dynamics simulations to evaluate key structural-functional parameters of these targeting ligands for an effective binding activity towards $α_Vβ_3$ integrins. An increasing number of cRGD ligands is conjugated to PEG chains grafted to highly curved TiO$_2$ nanoparticles to unveil the impact of cRGD density on the ligand's presentation, stability, and conformation in an explicit aqueous environment. We find that a low density leads to an optimal spatial presentation of cRGD ligands out of the "stealth" PEGylated layer around the nanosystem, favoring a straight upward orientation and spaced distribution of the targeting ligands in the bulk-water phase. On the contrary, high densities favor clustering and internalization of cRGD ligands in the inner region of the PEGylated layer, driven by a concerted mechanism of enhanced ligand-ligand interactions and reduced water accessibility over the ligand's molecular surface. These findings strongly suggest that the ligand density modulation is a key factor in the design of cRGD-targeting nanodevices to maximize their binding efficiency into over-expressed $α_Vβ_3$ integrin receptors.

cond-mat.soft↗

arXiv2021

Molecular Dynamics simulations of Doxorubicin in sphingomyelin-based lipid membranes

Doxorubicin (DOX) is one of the most efficient antitumor drugs employed in numerous cancer therapies. Its incorporation into lipid-based nanocarriers, such as liposomes, improves the drug targeting into tumor cells and reduces drug side effects. The carriers' lipid composition is expected to affect the interactions of DOX and its partitioning into liposomal membranes. To get a rational insight into this aspect and determine promising lipid compositions, we use numerical simulations, which provide unique information on DOX-membrane interactions at the atomic level of resolution. In particular, we combine classical molecular dynamics simulations and free energy calculations to elucidate the mechanism of penetration of a protonated Doxorubicin molecule (DOX+) into potential liposome membranes, here modeled as lipid bilayers based on mixtures of phosphatidylcholine (PC), sphingomyelin (SM) and cholesterol lipid molecules, of different compositions and lipid phases. Moreover, we analyze DOX+ partitioning into relevant regions of SM-based lipid bilayer systems using a combination of free energy methods. Our results show that DOX+ penetration and partitioning are facilitated into less tightly packed SM-based membranes and are dependent on lipid composition. This work paves the way to further investigations of optimal formulations for lipid-based carriers, such as those associated with pH-responsive membranes.

cond-mat.soft↗

arXiv2021

Parametrization of the Fe-Owater cross-interaction for a more accurate Fe3O4/water interface model and its application to a spherical Fe3O4 nanoparticle of realistic size

The accurate description of iron oxides/water interfaces requires reliable force field parameters that can be developed through the comparison with sophisticated quantum mechanical calculations. Here a set of CLASS2 force field parameters is optimized to describe the Fe-Owater cross interaction through comparison with hybrid density functional theory (HSE06) calculations of the potential energy function for a single water molecule adsorbed on the Fe3O4 (001) surface and with density functional tight binding (DFTB+U) molecular dynamics simulations for a water tri-layer on the same surface. The performance of the new parameters is assessed through the analysis of the number density profile of a water bulk (12 nm) sandwiched between two magnetite slabs of large surface area. Their transferability is tested for the water adsorption on the curved surface of a spherical Fe3O4 nanoparticle of realistic size (2.5 nm).

cond-mat.mtrl-sci↗

arXiv2020

Insight into the interface between Fe$_3$O$_4$(001) surface and water overlayers through multiscale molecular dynamics simulations

In this work we investigate the Fe$_3$O$_4$(001) surface/water interface by combining several theoretical approaches, ranging from a hybrid functional method (HSE06) to density-functional tight-binding (DFTB) to molecular mechanics (MM). First, we assess the accuracy of the DFTB method to reproduce correctly HSE06 results on structural details and energetics and available experimental data for the adsorption of isolated water, dimers, trimers, etc. up to a water monolayer. Secondly, we build two possible configurations of a second and a third overlayer and perform molecular dynamics simulations with DFTB, monitoring the water orientation, the H-bond network, and ordered water structures formation. To make our models more realistic, we then build a 12-nm thick water multilayer on top of the Fe$_3$O$_4$(001) surface slab model, which we investigate through MM molecular dynamics. The water layers structuring, revealed by the analysis of the atomic positions from a long MM-MD run for this large MM model, extends up to about 6-7 Å and nicely compares with that observed for a water trilayer model. However, MM and DFTB MD simulations show some discrepancy due to the poor description of the Fe--OH2 distance in MM that calls for further work in the parametrization of the model.

cond-mat.mtrl-sci↗