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Fabrication of ordered structures at the nanoscale limit poses a cornerstone challenge for modern technologies. In this work we show how naturally occurring moir\'e patterns in Ir(111)-supported graphene template the formation of 2D ordered arrays of substitutional boron species. A complementary experimental and theoretical approach provides a comprehensive description of the boron species distribution, bonding configurations, interfacial interaction with Ir(111) and the impact on graphene's electronic structure. Atomically-resolved scanning tunnelling microscopy images and density functional theory calculations reveal that boron preferably forms small aggregates of substitutional defects in geometrically low regions of the moir\'e superlattice of graphene, by inducing local bending of graphene towards the underlying Ir(111). Surprisingly, calculations reveal that the incorporation of electron deficient boron does not lead to an enhanced p-type doping, as the local rippling of the graphene layer prompts electron uptake from the iridium substrate that compensates the initial electron loss due to substitutional boron. Scanning tunnelling spectroscopy and angle-resolved photoemission spectroscopy measurements corroborate that the arrays of boron species do not modify the electronic structure of graphene near the Fermi level, hence preserving the slight p-type doping induced by Ir(111)., Comment: For Supplementary materials, see https://doi.org/10.1016/j.carbon.2022.09.087

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.

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 $\alpha_V\beta_3$ 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 $\alpha_V\beta_3$ integrin receptors.

Functionalized TiO2 nanoparticles with intense fluorescent dyes is a promising tool for several technological applications ranging from photochemistry, photocatalysis, photovoltaics, photodynamic therapy or bioimaging. Here, we present the case study of the Alizarin adsorption on TiO2 nanoparticles (NPs) of different shape and increasing size up to 2.2 nm (700 atoms), by means of density functional theory (DFT) calculations. We find that Alizarin can bind in three different ways, depending on the number and type of bonds between Alizarin and TiO2: "tridented", "bidented" and "chelated". Next, we investigate the optical properties of these systems by time-dependent density functional theory (TDDFT) calculations. Based on the absorption spectra and the Kohn-Sham orbitals analysis, we discovered that the mechanism of electron injection depends on the Alizarin binding mode to the TiO2 surface. While for bidented and chelated adsorption modes a direct charge transfer is observed, for the tridented one an indirect mechanism governs the charge transfer process following the excitation. Our results are in good agreement with existing experimental data and suggests that by tailoring the shape of the TiO2 NPs and, thus, determining the type of undercoordinated Ti atoms prevalently exposed at the surface, it is possible to control the predominant injection mechanism.

Saturation magnetization values close to the bulk have been reported for coated magnetite nanoparticles with organic acids. The mechanism of this effect is not yet understood. Here we show that a previously proposed rationalization in Nano Letters 12 (2021) 2499-2503 was based on electronic structure properties that are not consistent with several existing density functional theory studies. Our study is based on a wide set of Hubbard-corrected density functional tight binding (DTFB+U) and hybrid density functional theory (HSE06) calculations on Fe$_{3}$O$_{4}$ nanocubes of more than 400 atoms. We provide a new explanation for the spin ordering in coated nanoparticles, through the investigation of spin-flipping phenomena. In particular, we show that the spin-flip of d electrons at octahedral Fe$^{3+}$ sites, which is confirmed to be more favorable near the surface, especially where atomic reorganization can take place such as at corner sites, can be hampered by the presence of adsorbed organic acids because they do not only limit the surface reconstruction but also allow for additional ferromagnetic superexchange interaction between octahedral Fe sites as a consequence of the carboxylates bridging binding mode. The proof-of-concept of this mechanism is given by a simplified model of the Fe(III) tert-butoxide dimer.

Although the immobilization of oligonucleotides (nucleic acid) on mineral surfaces is at the basis of different biotechnological applications, an atomistic understanding of the interaction of the nucleic acid components with the titanium dioxide surfaces has not yet been achieved. Here, the adsorption of the phosphate anion, of the four DNA bases (adenine, guanine, thymine, and cytosine) and of some entire nucleotides and dinucleotides on the TiO 2 anatase (101) surface is studied through dispersion-corrected hybrid density functional theory (DFT) calculations. Several adsorption configurations are identified for the separated entities (phosphate anion or base) and then considered when studying the adsorption of the entire nucleotides. The analysis shows that both the phosphate anion and each base may anchor the nucleotides to the surface in a collaborative and synergistic adsorption mode. The tendency is that the nucleotides containing the guanine base present the strongest adsorption while those made up with the thymine base have the lowest adsorption energies. Nucleotides based on adenine and cytosine have a similar intermediate behavior. Finally, we investigated the adsorption of competing water molecules to understand whether in the presence of the aqueous solvent, the nucleotides would remain bonded to the surface or desorb.

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.

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).

Donor-modified TiO 2 nanoparticles are interesting hybrid systems shifting the absorption edge of this semiconductor from the ultra-violet to the visible or infrared light spectrum, which is a benefit for several applications ranging from photochemistry, photocatalysis, photovoltaics, or photodynamic therapy. Here, we investigate the absorption properties of two catechol-like molecules, i.e. dopamine and DOPAC ligands, when anchored to a spherical anatase TiO 2 nanoparticle of realistic size (2.2 nm), by means of time-dependent density functional theory calculations. By the differential absorbance spectra with the bare nanoparticle, we show how it is possible to determine the injection mechanism. Since new low-energy absorption peaks are observed, we infer a direct charge transfer injection, which, unexpectedly, does not involve the lowest energy conduction band states. We also find that the more perpendicular the molecular benzene ring is to the surface, the more intense is the absorption, which suggests aiming at high molecular packing in the synthesis. Through a comparative investigation with a flat TiO 2 surface model, we unravel both the curvature and coverage effects.

High-quality nitrogen-doped graphene on nickel is prepared by exploiting both the catalytic properties of nickel and the solubility of nitrogen atoms into its bulk. Following the standard chemical vapor deposition procedure, a previously nitrogen-doped nickel substrate is exposed to carbon-containing precursors so that nitrogen atoms, segregating to the surface, remain trapped in the growing graphene network. Morphological and chemical characterization by scanning tunneling microscopy and X-ray photoelectron spectroscopy demonstrates that the process yields a flat, wide, continuous nitrogen-doped graphene layer. Experimental results are combined with a thorough density functional theory investigation of possible structural models, to obtain a clear description at the atomic scale of the various configurations of the nitrogen atoms observed in the graphene mesh. This growth method is potentially scalable and suitable for the production of high-performance nano-devices with well-defined nitrogen centers, to be exploited as metal-free carbon-based catalysts in several applicative fields such as electrochemistry, energy storage, gas storage/sensing or wastewater treatment., Comment: 21 pages, including 4 figures, plus SI

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 {\AA} 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.

Iron oxide magnetic nanoparticles (NPs) are stimuli-responsive materials at the forefront of nanomedicine. Their realistic finite temperature simulations are a formidable challenge for first-principles methods. Here, we use density functional tight binding to open up the required time and length scales and obtain global minimum structures of Fe3O4 NPs of realistic size (1400 atoms, 2.5 nm) and of different shapes, which we then refine with hybrid density functional theory methods to accomplish proper electronic and magnetic properties, which have never been accurately described in simulations. On this basis, we develop a general empirical formula and prove its predictive power for the evaluation of the total magnetic moment of Fe3O4 NPs. By converting the total magnetic moment into the macroscopic saturation magnetization, we rationalize the experimentally observed dependence with shape. We also reveal interesting reconstruction mechanisms and unexpected patterns of charge ordering.

TiO2 nanoparticles (NPs) are attracting materials for biomedical applications, provided that they are coated with polymers to improve solubility, dispersion and biocompatibility. Conformation, coverage density and solvent effects largely influence their functionality and stability. In this work, we use atomistic molecular dynamics simulations to study polyethylene glycol (PEG) grafting to highly curved TiO2 NPs (2-3 nm) in different solvents. We compare the coating polymer conformations on NPs with those on (101) flat surfaces. In water, the transition from mushroom to brush conformation starts only at high density ({\sigma} = 2.25 chains/nm2). In dichloromethane (DCM), at low-medium coverage ({\sigma} < 1.35 chains/nm2), several interactions between the PEG chains backbone and undercoordinated Ti atoms are established, whereas at {\sigma} = 2.25 chains/nm2 the conformation clearly becomes brush-like. Finally, we demonstrate that these spherical brushes, when immersed in water, but not in DCM, follow the Daoud-Cotton (DC) classical scaling model for the polymer volume fraction dependence with the distance from the center of star-shaped systems.

Metal oxide nanoparticles (NPs) are regarded as good candidates for many technological applications, where their functional environment is often an aqueous solution. The correct description of metal oxide electronic structure is still a challenge for local and semilocal density functionals, whereas hybrid functional methods provide an improved description, and local atomic function based codes such as CRYSTAL17 outperform plane wave codes when it comes to hybrid functional calculations. However, the computational cost of hybrids are still prohibitive for systems of real sizes, in a real environment. Therefore, we here present and critically assess the accuracy of our electrostatic embedding quantum mechanical/molecular mechanical (QM/MM) coupling between CRYSTAL17 and AMBER16, and demonstrate some of its capabilities via the case study of TiO2 NPs in water. First, we produced new Lennard-Jones (LJ) parameters that improve the accuracy of water-water interactions in the B3LYP/TIP3P coupling. Then, we applied our QM/MM coupling methodology to describe the interaction of a 1 nm wide multilayer of water surrounding a spherical TiO2 nanoparticle (NP). Optimizing the QM/MM water water parameters was found to have little to no effect on the local NP properties, which provide insights into the range of influence that can be attributed to the LJ term in the QM/MM coupling. The effect of adding additional water in an MM fashion on the geometry optimized nanoparticle structure is small, but more evident effects are seen in its electronic properties. We also show that there is good transferability of existing QM/MM LJ parameters for organic molecules water interactions to our QM/MM implementation, even though these parameters were obtained with a different QM code and QM/MM implementation, but with the same functional.

Magnetite has attracted increasing attention in recent years due to its promising and diverse applications in biomedicine. Theoretical modelling can play an important role in understanding magnetite-based nanomaterials at the atomic scale for a deeper insight into the experimental observations. However, calculations based on density functional theory (DFT) are too costly for realistically large models of magnetite nanoparticles. Classical force field methods are very fast but lack of precision and of the description of electronic effects. Therefore, a cheap and efficient quantum mechanical simulation method with comparable accuracy than DFT is highly desired. Here, a less computational demanding DFT-based method, i.e. self-consistent charge density functional tight-binding (SCC-DFTB), is adopted to investigate magnetite bulk and low-index (001) surface with newly proposed parameters for Fe-O interactions. We report that SCC-DFTB with on-site Coulomb correction provides results in quantitatively comparable agreement with those obtained by DFT+U and hybrid functional methods. Therefore, SCC-DFTB is valued as an efficient and reliable method for the description magnetite. This assessment will promote SCC-DFTB computational studies on magnetite-based nanostructures that attract increasing attention for medical applications.

Computational modeling of titanium dioxide nanoparticles of realistic size is extremely relevant for the direct comparison with experiments but it is also a rather demanding task. We have recently worked on a multistep/scale procedure to obtain global optimized minimum structures for chemically stable spherical titania nanoparticles of increasing size, with diameter from 1.5 nm (~300 atoms) to 4.4 nm (~4000 atoms). We use first self-consistent-charge density functional tight-binding (SCC-DFTB) methodology to perform thermal annealing simulations to obtain globally optimized structures and then hybrid density functional theory (DFT) to refine them and to achieve high accuracy in the description of structural and electronic properties. This allows also to assess SCC-DFTB performance in comparison with DFT(B3LYP) results. As a further step, we investigate photoexcitation and photoemission processes involving electron/hole pair formation, separation, trapping and recombination in the nanosphere of medium size by hybrid DFT. Finally, we show how a recently defined new set of parameters for SCC-DFTB allows for a proper description of titania/water multilayers interface, which paves the way for modeling large realistic nanoparticles in aqueous environment.

TiO2 nanoparticles (NPs) are nowadays considered fundamental building blocks for many technological applications. Morphology is found to play a key role with spherical NPs presenting higher binding properties and chemical activity. From the experimental point of view, the characterization of these nano-objects is extremely complex, opening a large room for computational investigations. In this work, TiO2 spherical NPs of different size (from 300 to 4000 atoms) have been studied with a two-scale computational approach. Global optimization to obtain stable and equilibrated NSs was performed with a self-consistent charge density functional tight-binding (SCC-DFTB) simulated annealing process, causing a considerable atomic rearrangement within the nanospheres. Those SCC-DFTB relaxed structures have been then optimized at DFT(B3LYP) level of theory. We present a systematic and comparative SCC-DFTB vs DFT(B3LYP) study of the structural properties, with particular emphasis on the surface-to-bulk sites ratio, coordination distribution of surface sites and surface energy. From the electronic point of view, we compare HOMO-LUMO and Kohn-Sham gaps, total and projected density of states. Overall, the comparisons between DFTB and hybrid DFT show that DFTB provides a rather accurate geometrical and electronic description of these nanospheres of realistic size (up to a diameter of 4.4 nm) at an extremely reduced computational cost. This opens for new challenges in simulations of very large systems and more extended molecular dynamics.

Nanoparticles of very small size (below 10 nm) of TiO2 material are nowadays the functional building blocks of many developing technological applications. Nano is clearly different from bulk or extended systems as regards surface area, molecular binding properties, charge separation efficiency, electron/hole transport, photochemical conversion properties, etc. In this work, we investigate the life path of energy (excitons) and charge (electrons and holes) carriers in anatase TiO2 nanoparticles of different size (2-3 nm) and shape (faceted vs spherical), by means of a wide set of hybrid density functional theory calculations. The attention is focused on the exciton/charge carriers formation, separation, recombination, self-trapping processes, which are analyzed in terms of structural deformations, energy gain or cost, charge localization/delocalization and electronic transitions involved. The computational models are corroborated by an extensive comparison with available experimental data based on photoluminescence measurements, electron paramagnetic resonance and transient absorption spectroscopies. Peculiar differences are observed for spherical nanoparticles with respect to faceted ones because of the higher disorder and larger diversity of coordination sites present on the surface. For example, charge delocalization on several lattice sites is more competitive with self-trapping processes in faceted than in spherical nanoparticles. This relates to the fact that selective compression or elongation of Ti-O bonds play a key role in determining the effectiveness of trapping sites, with spherical nanoparticles being more flexible. Moreover, hydroxyl groups on surface five-fold coordinated Ti sites are also found to be good hole trapping sites.

Boron-doped graphene was reported to be the best non-metal doped graphene electrocatalyst for the oxygen reduction reaction (ORR) working at an onset potential of 0.035 V [JACS 136 (2014) 4394]. In the present DFT study, intermediates and transition structures along the possible reaction pathways are determined. Both Langmuir-Hinschelwood and Eley-Rideal mechanisms are discussed. Molecular oxygen binds the positively charged B atom and forms an open shell end-on dioxygen intermediate. The associative path is favoured with respect to the dissociative one. The free energy diagrams along the four-reduction steps are investigated with the methodology by N{\o}rskov and co. [JPC B 108 (2004) 17886] in both acidic and alkaline conditions. The pH effect on the stability of the intermediates of reduction is analyzed in terms of the Pourbaix diagram. At pH = 14 we compute an onset potential value for the electrochemical ORR of U = 0.05 V, which compares very well with the experimental value in alkaline conditions.

Tungsten trioxide (WO$_3$) is a paradigmatic electrochromic material, whose peculiar optical properties in the presence of oxygen vacancies or intercalated alkali atoms have been observed and investigated for a long time. In this paper we propose a rationalization of experiments based on first-principles calculations of optical and electrical properties of oxygen deficient (reduced) WO$_3$. Our approach is based on a parameter-free dielectric-dependent hybrid density functional methodology, used in combination with the charge transition levels formalism, for studying excitation mechanisms in the presence of defects. Our results indicate that oxygen vacancies lead to a different physics in $\gamma$-monoclinic WO$_3$, depending on the orientation of the W-O-W chain where the vacancy is created, thus evidencing strong anisotropic effects rooted in the peculiar structural properties of the original nondefective monoclinic cell. Different types of oxygen vacancies can hence be classified on the basis of the calculated ground state properties, electronic structure, and excitation/emission energies, giving a satisfactory explanation to a range of experimental observations made on oxygen deficient WO$_3$., Comment: Accepted for publication in J. Phys. Chem. C

We investigate the behavior of oxygen vacancies in three different metal-oxide semiconductors (rutile and anatase TiO2, monoclinic WO3, and tetragonal ZrO2) using a recently proposed hybrid density-functional method in which the fraction of exact exchange is material-dependent but obtained ab initio in a self-consistent scheme. In particular, we calculate charge-transition levels relative to the oxygen-vacancy defect and compare computed optical and thermal excitation/emission energies with the available experimental results, shedding light on the underlying excitation mechanisms and related materials properties. We find that this novel approach is able to reproduce not only ground-state properties and band structures of perfect bulk oxide materials, but also provides results consistent with the optical and electrical behavior observed in the corresponding substoichiometric defective systems., Comment: Accepted for publication in J. Chem. Phys

We investigate the long-standing problem of the hole localization at the Al impurity in quartz SiO$_2$, using a relatively recent DFT hybrid-functional method in which the exchange fraction is obtained \emph{ab initio}, based on an analogy with the static many-body COHSEX approximation to the electron self-energy. As the amount of the admixed exact exchange in hybrid functionals has been shown to be determinant for properly capturing the hole localization, this problem constitutes a prototypical benchmark for the accuracy of the method, allowing one to assess to what extent self-interaction effects are avoided. We obtain good results in terms of description of the charge localization and structural distortion around the Al center, improving with respect to the more popular B3LYP hybrid-functional approach. We also discuss the accuracy of computed hyperfine parameters, by comparison with previous calculations based on other self-interaction-free methods, as well as experimental values. We discuss and rationalize the limitations of our approach in computing defect-related excitation energies in low-dielectric-constant insulators., Comment: Accepted for publication in J. Chem. Phys. (Communications)

We investigate band gaps, equilibrium structures, and phase stabilities of several bulk polymorphs of wide-gap oxide semiconductors ZnO, TiO2,ZrO2, and WO3. We are particularly concerned with assessing the performance of hybrid functionals built with the fraction of Hartree-Fock exact exchange obtained from the computed electronic dielectric constant of the material. We provide comparison with more standard density-functional theory and GW methods. We finally analyze the chemical reduction of TiO2 into Ti2O3, involving a change in oxide stoichiometry. We show that the dielectric-dependent hybrid functional is generally good at reproducing both ground-state (lattice constants, phase stability sequences, and reaction energies) and excited-state (photoemission gaps) properties within a single, fully ab initio framework., Comment: Minor changes in the final published version