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Titanium dioxide (TiO2) shows significant potential as a self-cleaning material to inactivate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and prevent virus transmission. This study provides insights into the impact of UV-A light on the photocatalytic inactivation of adsorbed SARS-CoV-2 virus-like particles (VLPs) on a TiO2 surface at the molecular and atomic levels. X-ray photoelectron spectroscopy, combined with density functional theory calculations, reveals that spike proteins can adsorb on TiO2 predominantly via their amine and amide functional groups in their amino acids blocks. We employ atomic force microscopy and grazing-incidence small-angle X-ray scattering (GISAXS) to investigate the molecular-scale morphological changes during the inactivation of VLPs on TiO2 under light irradiation. Notably, in situ measurements reveal photoinduced morphological changes of VLPs, resulting in increased particle diameters. These results suggest that the denaturation of structural proteins induced by UV irradiation and oxidation of the virus structure through photocatalytic reactions can take place on the TiO2 surface. The in situ GISAXS measurements under an N-2 atmosphere reveal that the virus morphology remains intact under UV light. This provides evidence that the presence of both oxygen and UV light is necessary to initiate photocatalytic reactions on the surface and subsequently inactivate the adsorbed viruses. The chemical insights into the virus inactivation process obtained in this study contribute significantly to the development of solid materials for the inactivation of enveloped viruses.

Titanium dioxide nanotubes (TNT) have been extensively studied because of their unique properties, which make such systems ideal candidates for biomedical application, especially for the targeted release of drugs. However, knowledge about the properties of TiO2 nanotubes with typical dimensions of the order of the nanometer is limited, especially concerning the adsorption of molecules that can be potentially loaded in actual devices. In this work, we investigate, by means of simulations based on hybrid density functional theory, the adsorption of Vitamin C molecules on different nanotubes through a comparative analysis of the properties of different structures. We consider two different anatase TiO2 surfaces, the most stable (101) and the more reactive (001)A; we evaluate the role of the curvature, the thickness and of the diameter as well as of the rolling direction of the nanotube. Different orientations of the molecule with respect to the surface are studied in order to identify any trends in the adsorption mechanism. Our results show that there is no preferential functional group of the molecule interacting with the substrate, nor any definite spatial dependency, like a rolling orientation or the concavity of the nanotube. Instead, the adsorption is driven by geometrical factors only, i.e., the favorable matching of the position and the alignment of any functional groups with undercoordinated Ti atoms of the surface, through the interplay between chemical and hydrogen bonds. Differently from flat slabs, thicker nanotubes do not improve the stability of the adsorption, but rather develop weaker interactions, due to the enhanced curvature of the substrate layers.

In the field of nanomedicine, significant attention is directed toward near-infrared (NIR) light-responsive inorganic nanosystems, primarily for their applications in photodynamic therapy and fluorescence bioimaging. The crucial role of the NIR range lies in enabling optimal tissue penetration, which is essential for both irradiating and detecting nanoparticles deep within the human body. In this study, we employed density functional theory (DFT) and time-dependent DFT (TDDFT) calculations to explore the structural and electronic properties of cyanine-functionalized TiO2 spherical nanoparticles (NPs) with a realistic diameter of 2.2 nm. We revealed that different adsorption configurations of cyanine (VG20-C1) on the TiO2 NP surface exhibit distinct features in the optical spectra. These cyanine dyes, serving as bifunctional linkers with two carboxylic end groups, can adsorb in either a side-on mode (binding with both end groups) or an end-on mode (binding only one end group). In end-on adsorption structures, low-energy excitations are exclusive to dye-to-dye electronic transitions, while side-on structures exhibit electron charge transfer excitations from the dye to the TiO2 NP at low energy. This thorough analysis provides a rational foundation for designing cyanine-functionalized TiO2 nanosystems with optimal optical characteristics tailored for specific nanomedical applications such as photodynamic therapy or fluorescence bioimaging.

Experimental and theoretical studies have demonstrated that the use of single atom catalysts (SACs) for energy conversion processes is very promising. However, their stability under catalytic conditions is the main issue that hinders their commercial use. In this work, we report an oxygen evolution catalyst based on single nickel atoms stabilized in triazine-based carbon nitride (CN) and a detailed study of the evolution of the Ni centers under catalytic conditions. The nanostructured materials have been characterized by combining experimental techniques, such as X-ray diffraction, transmission electron microscopy, X-ray absorption and X-ray photoemission spectroscopy, with DFT theoretical calculations to determine the CN structure, the metal adsorption sites, the coordination of the Ni atoms, and the changes undergone under catalytic conditions. Electrochemical characterization showed a linear increase of the catalytic activity with Ni loading. The stability of the materials was studied by HR-TEM and XAS post-catalysis measurements and DFT simulations. Results indicated a partial chemical restructuring of the single Ni atoms under catalytic conditions with the formation of Ni-O-Ni moieties, stabilized in the CN cavities, which are the real catalytic species.

Nanoparticles' (NPs) permeation through cell membranes, whether it happens via passive or active transport, is an essential initial step for their cellular internalization. The NPs' surface coating impacts the way they translocate through the lipid bilayer and the spontaneity of the process. Understanding the molecular details of NPs' interaction with cell membranes allows the design of nanosystems with optimal characteristics for crossing the lipid bilayer: computer simulations are a powerful tool for this purpose. In this work, we have performed coarse-grained molecular dynamics simulations and free energy calculations on spherical titanium dioxide NPs conjugated with polymer chains of different chemical compositions. We have demonstrated that the hydrophobic/hydrophilic character of the chains, more than the nature of their terminal group, plays a crucial role in determining the NPs' interaction with the lipid bilayer and the thermodynamic spontaneity of NPs' translocation from water to the membrane. We envision that this computational work will be helpful to the experimental community in terms of the rational design of NPs for efficient cell membrane permeation.By coarse-grained molecular dynamics simulations, we have unveiled that nanoparticles coated with mixed hydrophobic/hydrophilic polymer chains spontaneously penetrate lipid membranes, unlike those covered with chains of hydrophilic character only.

Molecular dynamics simulation techniques have been in the spotlight of recent nanomedicine research, becoming an indispensable tool for unveiling complex molecular mechanisms that are sometimes unreachable by experimental methods. Here, we demonstrate how MD simulations can complement existing experimental knowledge or provide new mechanistic insights into relevant aspects of nanoscale devices designed for nanomedicine. Through some case studies - from how thermodynamic variables (e.g., pH and ionic strength) affect the protein corona formation onto organic-functionalized nanoparticles to the impact of lipid composition in the permeation process of anti-tumoral drugs in membranes - this work compilation illustrates how classical MD simulations can be helpful bridging the simulated microscopic behaviors to their corresponding macroscopic manifestation.

Molecular dynamics simulation techniques have been in the spotlight of recent nanomedicine research, becoming an indispensable tool for unveiling complex molecular mechanisms that are sometimes unreachable by experimental methods. Here, we demonstrate how MD simulations can complement existing experimental knowledge or provide new mechanistic insights into relevant aspects of nanoscale devices designed for nanomedicine. Through some case studies - from how thermodynamic variables (e.g., pH and ionic strength) affect the protein corona formation onto organic-functionalized nanoparticles to the impact of lipid composition in the permeation process of anti-tumoral drugs in membranes - this work compilation illustrates how classical MD simulations can be helpful bridging the simulated microscopic behaviors to their corresponding macroscopic manifestation.

The pertechnetate ion TcVIIO4- is a nuclear fission product whose major issue is the high mobility in the environment. Experimentally, it is well known that Fe3O4 can reduce TcVIIO4- to TcIV species and retain such products quickly and completely, but the exact nature of the redox process and products is not completely understood. Therefore, we investigated the chemistry of TcVIIO4- and TcIV species at the Fe3O4(001) surface through a hybrid DFT functional (HSE06) method. We studied a possible initiation step of the TcVII reduction process. The interaction of the TcVIIO4- ion with the magnetite surface leads to the formation of a reduced TcVI species without any change in the Tc coordination sphere through an electron transfer that is favored by the magnetite surfaces with a higher FeII content. Furthermore, we explored various model structures for the immobilized TcIV final products. TcIV can be incorporated into a subsurface octahedral site or adsorbed on the surface in the form of TcIVO2·xH2O chains. We propose and discuss three model structures for the adsorbed TcIVO2·2H2O chains in terms of relative energies and simulated EXAFS spectra. Our results suggest that the periodicity of the Fe3O4(001) surface matches that of the TcO2·2H2O chains. The EXAFS analysis suggests that, in experiments, TcO2·xH2O chains were probably not formed as an inner-shell adsorption complex with the Fe3O4(001) surface.

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, TiO2 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 TiO2 models and to study the dynamical behavior of the resulting nanoconjugates in a 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 TiO2 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.

Heterogeneous catalysis is an essential aspect for actual industrialization of chemical processes. Here a TiO2-based powder, typically used in photocatalysis, is exploited for the first time for visible-light-regulated Photoinduced Electron/Energy (PET)-reversible addition–fragmentation chain-transfer (RAFT). Titania is a non-toxic, low-cost, and heterogeneous catalyst that can offer several advantages in terms of sustainable polymerization and photocatalyst (PC) recovery. In this work, we aim not only at unraveling the mechanism of photopolymerization and the important interactions involved, but also at red-shifting the absorption region to achieve vis-light polymerization. The combination of the experimental investigation with Density Functional Theory (DFT) calculations provides new insights into the interactions between the chain transfer agents (CTAs) and the TiO2 surface, unveiling their pivotal role on the reaction rate and polymerization control. Moreover, to shift the polymerization under the less energetic blue light, high-surface area N-doped TiO2 nanoparticles are employed, avoiding the CTA degradation often observed with UV irradiation and increasing the overall sustainability of the process.

Doping magnetite surfaces with transition-metal atoms is a promising strategy to improve the catalytic performance toward the oxygen evolution reaction (OER), which governs the overall efficiency of water electrolysis and hydrogen production. In this work, we investigated the Fe3O4(001) surface as a support material for single-atom catalysts of the OER. First, we prepared and optimized models of inexpensive and abundant transition-metal atoms, such as Ti, Co, Ni, and Cu, trapped in various configurations on the Fe3O4(001) surface. Then, we studied their structural, electronic, and magnetic properties through HSE06 hybrid functional calculations. As a further step, we investigated the performance of these model electrocatalysts toward the OER, considering different possible mechanisms, in comparison with the pristine magnetite surface, on the basis of the computational hydrogen electrode model developed by Nørskov and co-workers. Cobalt-doped systems were found to be the most promising electrocatalytic systems among those considered in this work. Overpotential values (∼0.35 V) were in the range of those experimentally reported for mixed Co/Fe oxide (0.2-0.5 V).

Although graphitic-carbon nitride (gCN) is a highly investigated inorganic semiconductor, especially in the field of photocatalysis, it is still the object of many controversial discussions. The possibility to easily synthesize a homogeneous heterostructure through the condensation and the polymerization of simple molecules allows the growth of a variety of structures with different electronic and optical properties. With the aim of driving the development of the catalyst toward improved performances or newer applications, it is paramount to understand the optically-driven excitation process within each polymer. In this work, we focus on two models of melem-based gCN, i.e. the fully and the partially polymerized structures, and we perform a computational investigation, based on hybrid density functional theory calculations, of their optical properties in terms of vibrational and electronic excitations. First, we determine the normal modes of the ground state and we interpret the IR absorption spectrum. Then, we simulate the electronic excited state with an electron–hole pair model and we determine the exciton binding energy, the self-trapping energy and the photo-emission energy. We compare these numerical results with the experimental data available in literature and in addition we discuss the role of the different polymeric arrangements.

Fabrication of ordered structures at the nanoscale limit poses a cornerstone challenge for modern technologies. In this work we show how naturally occurring moiré 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 moiré 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).

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, TiO2 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 TiO2 models and to study the dynamical behavior of the resulting nanoconjugates in a 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 TiO2 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.

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 TiO2 anatase (1 0 1) 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.

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 Fe3O4 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 Fe3+ 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.

Inorganic nanoparticles (NPs) are gaining increasing attention in nanomedicine because of their stimuli responsiveness, which allows combining therapy with diagnosis. However, little information is known about their interaction with intracellular or plasma proteins when they are introduced in a biological environment. Here we present atomistic molecular dynamics (MD) simulations investigating the case study of dopamine-functionalized TiO2 nanoparticles and two proteins that are overexpressed in cancer cells, i.e. PARP1 and HSP90, since experiments proved them to be the main components of the corona in cell cultures. The mechanism and the nature of the interaction (electrostatic, van der Waals, H-bonds, etc.) is unravelled by defining the protein residues that are more frequently in contact with the NPs, the extent of contact surface area and the variations in the protein secondary structures, at different pH and ionic strength conditions of the solution where they are immersed to simulate a realistic biological environment. The effects of the NP surface functionalization and charge are also considered. Our MD results suggest that less acidic intracellular pH conditions in the presence of cytosolic ionic strength enhance PARP1 interaction with the nanoparticle, whereas the HSP90 contribution is partly weakened, providing a rational explanation to existing experimental observations.

The pertechnetate ion TcVIIO4− is a nuclear fission product whose major issue is the high mobility in the environment. Experimentally, it is well-known that Fe3O4 can reduce TcVIIO4− to TcIV species and retain such products quickly and completely, but the exact nature of the redox process and products is not completely understood. Therefore, we investigated the chemistry of TcVIIO4− and TcIV species at the Fe3O4(001) surface through a hybrid DFT functional (HSE06) method. We studied a possible initiation step of the TcVII reduction process. The interaction of the TcVIIO4− ion with magnetite surface leads to the formation of a reduced TcVI species without any change in the Tc coordination sphere, through an electron transfer that is favored by the magnetite surfaces with a higher FeII content. Furthermore, we explored various model structures for the immobilized TcIV final products. TcIV can be incorporated into a subsurface octahedral site or adsorbed on the surface in the form of TcIVO2·xH2O chains. We propose and discuss three model structures for the adsorbed TcIVO2·2H2O chains in terms of relative energies and simulated EXAFS spectra. Our results suggest that the periodicity of the Fe3O4(001) surface matches that of the TcO2·2H2O chains. The EXAFS analysis suggests that in experiments TcO2·xH2O chains were probably not formed as an inner-shell adsorption complex with the Fe3O4(001) surface.

Nonequilibrium molecular dynamics simulations were performed to study the electrokinetic properties of five mainstream TIPxP water models (namely, TIP3P-FB, TIP3Pm, TIP4P-FB, TIP4P-Ew, and TIP4P/2005) in NaCl aqueous solutions in the presence of a negatively charged TiO2 surface. The impact of solvent flexibility and system geometry on the electro-osmotic (EO) mobility and flow direction was systematically assessed and compared. We found that lack of water flexibility decelerates the forward EO flow of aqueous solutions at moderate (0.15 M) or high (0.30 M) NaCl concentrations, in some special cases to such an extent that EO flow reversal occurs. Zeta potential (ZP) values were then determined from the bulk EO mobilities using the Helmholtz-Smoluchowski formula. The straight comparison against available experimental data strongly suggests that water flexibility improves the ZP determination of NaCl solutions adjacent to a realistic TiO2 surface under neutral pH conditions.

Inorganic nanoparticles show promising properties that allow them to be efficiently used as drug carriers. The main limitation in this type of application is currently the drug loading capacity, which can be overcome with a proper functionalization of the nanoparticle surface. In this study, we present, for the first time, a computational approach based on metadynamics to estimate the binding free energy of the doxorubicin drug (DOX) to a functionalized TiO2 nanoparticle under different pH conditions. On a thermodynamic basis, we demonstrate the robustness of our approach to capture the overall mechanism behind the pH-triggered release of DOX due to environmental pH changes. Notably, binding free energy estimations align well with what is expected for a pH-sensitive drug delivery system. Based on our results, we envision the use of metadynamics as a promising computational tool for the rational design and in silico optimization of organic ligands with improved drug carrier properties.

Melem (2,6,10-triamino-s-heptazine) is the building block of melon, a carbon nitride (CN) polymer that is proven to produce H2from water under visible illumination. With the aim of bringing additional insight into the electronic structure of CN materials, we performed a spectroscopic characterization of gas-phase melem and of a melem-based self-assembled 2D H-bonded layer on Au(111) by means of ultraviolet and X-ray photoemission spectroscopy (UPS, XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. In parallel, we performed density functional theory (DFT) simulations of the same systems to unravel the molecular charge density redistribution caused by the in-plane H-bonds. Comparing the experimental results with the spectroscopic DFT simulations, we can correlate the induced charge accumulation on the Naminoatoms to the red-shift of the corresponding N 1s binding energy (BE) and of the Namino1s → LUMO+n transitions. Moreover, when introducing a supporting Au(111) surface in the computational simulations, we observe a molecule-substrate interaction that almost exclusively involves the out-of-plane molecular orbitals, leaving those engaged in the in-plane H-bonded network rather unperturbed.

We investigated the adsorption of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), the virus responsible for the current pandemic, on the surface of the model catalyst TiO2(101) using atomic force microscopy, transmission electron microscopy, fluorescence microscopy, and X-ray photoelectron spectroscopy, accompanied by density functional theory calculations. Three different methods were employed to inactivate the virus after it was loaded on the surface of TiO2(101): (i) ethanol, (ii) thermal, and (iii) UV treatments. Microscopic studies demonstrate that the denatured spike proteins and other proteins in the virus structure readsorb on the surface of TiO2 under thermal and UV treatments. The interaction of the virus with the surface of TiO2 was different for the thermally and UV treated samples compared to the sample inactivated via ethanol treatment. AFM and TEM results on the UV-treated sample suggested that the adsorbed viral particles undergo damage and photocatalytic oxidation at the surface of TiO2(101) which can affect the structural proteins of SARS-CoV-2 and denature the spike proteins in 30 min. The role of Pd nanoparticles (NPs) was investigated in the interaction between SARS-CoV-2 and TiO2(101). The presence of Pd NPs enhanced the adsorption of the virus due to the possible interaction of the spike protein with the NPs. This study is the first investigation of the interaction of SARS-CoV-2 with the surface of single crystalline TiO2(101) as a potential candidate for virus deactivation applications. Clarification of the interaction of the virus with the surface of semiconductor oxides will aid in obtaining a deeper understanding of the chemical processes involved in photoinactivation of microorganisms, which is important for the design of effective photocatalysts for air purification and self-cleaning materials.

Molecular dynamics simulation techniques have been in the spotlight of recent nanomedicine research, becoming an indispensable tool for unveiling complex molecular mechanisms that are sometimes unreachable by experimental methods. Here, I will exemplify how MD simulations can complement existing experimental knowledge or provide new mechanistic insights into relevant aspects of nanoscale devices designed for nanomedicine. Through some case studies - from how thermodynamic variables (e.g., pH and ionic strength) affect the protein corona formation onto organic-functionalized nanoparticles to the impact of lipid composition in the permeation process of anti-tumoral drugs in membranes - this presentation will address how classical MD simulations can be helpful bridging the simulated microscopic behavior to their corresponding macroscopic manifestation.

Inorganic nanoparticles are excellent tools to create smart bioinorganic nanodevices for drug delivery, targeting and imaging. To investigate these complex systems, we use multiscale approaches ranging from first-principles calculations to atomistic molecular dynamics simulations, metadynamics, umbrella sampling and machine learning.

Under near-ambient pressure conditions, carbon monoxide molecules intercalate underneath an epitaxial graphene monolayer grown on Ni(111), getting trapped into the confined region at the interface. On the basis of ab-initio density functional theory calculations, we provide here a full investigation of the intercalated CO pattern, highlighting the modifications induced on the graphene electronic structure. For a CO coverage as low as 0.14 monolayer (ML), the graphene layer is spatially decoupled from the metallic substrate, with a significant C 1s core level shift towards lower binding energies. The most relevant signature of the CO intercalation is a clear switching of the graphene doping state, which changes from n-type, when strongly interacting with the metal surface, to p-type. The shift of the Dirac cone linearly depends on the CO coverage, reaching about 0.9 eV for the saturation value of 0.57 ML. Theoretical predictions are compared with the results of scanning tunnelling microscopy, low-energy electron diffraction and photoemission spectroscopy experiments, which confirm the proposed scenario for the nearly saturated intercalated CO system. This result opens the way to the application of the graphene/Ni(111) interface as gas sensor to easily detect and quantify the presence of carbon monoxide.

The development of catalysts for the hydrogen evolution reaction is pivotal for the hydrogen economy. Thin iron films covered with monolayer graphene exhibit outstanding catalytic activity, surpassing even that of platinum, as demonstrated by a method based on evaluating the noise in the tunnelling current of electrochemical scanning tunnelling microscopy. Using this approach, we mapped with atomic-scale precision the electrochemical activity of the graphene–iron interface, and determined that single iron atoms trapped within carbon vacancies and curved graphene areas on step edges are exceptionally active. Density functional theory calculations confirmed the sequence of activity obtained experimentally. This work exemplifies the potential of electrochemical scanning tunnelling microscopy as the only technique able to determine both the atomic structure and relative catalytic performance of atomically well-defined sites in electrochemical operando conditions and provides a detailed rationale for the design of novel catalysts based on cheap and abundant metals such as iron. [Figure not available: see fulltext.].

The impact of iridium (Ir) doping on the oxygen vacancies, relative stability, crystallite size, surface area, and anatase-to-rutile transition of TiO2was comprehensively investigated in this study. Ir-doped TiO2(Ir-TiO2) was synthesized through a sol-gel technique, and the samples were annealed in the temperature range of 400-700 °C. Density functional theory calculations showed that the energy cost of an oxygen vacancy formation for Ir-TiO2was lower, as compared to that of the pristine TiO2, with the formation of Ir3+states in the band gap. Ir could provide more rutile nucleation sites and accelerate the rutile formation through the crystal strain relaxation. The entropy of mixing was reduced by the incorporation of Ir, which could induce the rutile formation with an increase in Gibbs free energy at temperatures below the normal phase transition temperature for pure TiO2. The rutile formation of Ir-TiO2could take place at a low annealing temperature (400 °C) compared to pristine TiO2(600 °C), indicating that the activation energy for phase transition could be decreased by incorporating Ir. XPS revealed the spin-orbit coupling of Ir 4f peaks, Ir 4f7/2(61.96 eV) and Ir 4f5/2(64.77 eV), due to the presence of Ir3+. Raman studies indicated the formation of charge-compensating oxygen vacancies and the presence of d states by Ir doping. It is concluded that the defects originated because the incorporation of Ir could facilitate rutile nucleation sites and thereby accelerate the phase transition through strain relaxation.

We report the study of two-dimensional graphitic carbon nitride (GCN) functionalized with copper single atoms as a catalyst for the reduction of CO2 (CO2RR). The correct GCN structure, as well as the adsorption sites and the coordination of the Cu atoms, was carefully determined by combining experimental techniques, such as X-ray diffraction, transmission electron microscopy, X-ray absorption, and X-ray photoemission spectroscopy, with DFT theoretical calculations. The CO2RR products in KHCO3 and phosphate buffer solutions were determined by rotating ring disk electrode measurements and confirmed by 1H-NMR and gas chromatography. Formate was the only liquid product obtained in bicarbonate solution, whereas only hydrogen was obtained in phosphate solution. Finally, we demonstrated that GCN is a promising substrate able to stabilize metal atoms, since the characterization of the Cu-GCN system after the electrochemical work did not show the aggregation of the copper atoms.

Polymeric graphitic carbon nitride (gCN) compounds are promising materials in photoacti-vated electrocatalysis thanks to their peculiar structure of periodically spaced voids exposing reactive pyridinic N atoms. These are excellent sites for the adsorption of isolated transition metal atoms or small clusters that can highly enhance the catalytic properties. However, several polymorphs of gCN can be obtained during synthesis, differing for their structural and electronic properties that ultimately drive their potential as catalysts. The accurate characterization of the obtained material is critical for the correct rationalization of the catalytic results; however, an unambiguous experimental identification of the actual polymer is challenging, especially without any reference spectroscopic features for the assignment. In this work, we optimized several models of melem-based gCN, taking into account different degrees of polymerization and arrangement of the monomers, and we present a thorough computational characterization of their simulated XRD, XPS, and NEXAFS spectroscopic properties, based on state-of-the-art density functional theory calculations. Through this detailed study, we could identify the peculiar fingerprints of each model and correlate them with its structural and/or electronic properties. Theoretical predictions were compared with the experimental data whenever they were available.

The accurate description of iron oxides/water interfaces requires reliable force field parameters that can be developed through 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 trilayer 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 water adsorption on the curved surface of a spherical Fe3O4 nanoparticle of realistic size (2.5 nm).

Iron oxide magnetic nanoparticles (NPs) are excellent systems in catalysis and in nanomedicine, where they are mostly immersed in aqueous media. Even though the NP solvation by water is expected to play an active role, the detailed structural insight at the nanostructure oxide/water interface is still missing. Here, based on our previous efforts to obtain accurate models of dehydrated Fe3O4 NPs and of their magnetic properties and through multiscale molecular dynamics simulations combining the density functional tight binding method and force field, we unravel the atomistic details of the short range (chemical) and long range (physical) interfacial effects when magnetite nanoparticles are immersed in water. The influence of the first hydration shell on the structural, electronic and magnetic properties of Fe3O4 NPs is revealed by high-level hybrid density functional calculations. Hydrated Fe3O4 NPs possess larger magnetic moment than dehydrated ones. This work bridges the large gap between experimental studies on solvated Fe3O4 NPs and theoretical investigations on flat Fe3O4 surfaces covered with water and paves the way for further study of Fe3O4 NPs in biological environments. This journal is

Single Atom Catalysts (SAC) in graphene have been recently gaining more and more attention. They are usually non-noble transition metal (TM) adatoms getting trapped at the carbon vacancies during the fabrication of the graphene layer, which then act as active centers for catalysis and adsorption. In this work we present a systematic and comparative investigation, by means of dispersion–corrected density functional theory (DFT) calculations, of Fe, Co, Ni, and Cu as possible SACs when they become trapped at graphene C vacancies. The stability of these TM atoms is further increased by introducing pyridinic nitrogen (N) atoms and transforming graphene into a giant porphyrin-like macrocyclic ligand. The structural, electronic and energetics properties of these systems, even under the effect of a metal substrate (weakly interacting Cu (111) or strongly interacting Ni (111)), are comparatively examined in great detail by means of crystal/ligand field theories and through ad-hoc energy decomposition analysis to highlight trends and peculiar behaviors. The position of the TM d-orbitals with respect to the Fermi level of the whole system is of considerable importance for designing prospective device applications in catalysis, electrocatalysis and sensors. To this purpose, we also examine how the reactivity of the SACs in graphene towards the hydrogen evolution reaction (HER) can be tuned with N-doping and with different substrates.

Gas sensors based on graphene are gaining more and more attention. The unique properties of the single-atom-thick, flexible, robust, and quanta-sensitive graphene make it an excellent candidate for sensors. However, its characteristics can be modified to suit specific applications by means of metal and nonmetal doping. In this systematic and detailed study, with the aid of density functional theory (DFT)-based simulations, we investigate the gas sensing capabilities of trapped transition-metal (TM) atoms at the graphene double vacancy (2VG). Eight different gas molecules, ranging from electron acceptors (Lewis acids) to donor species (Lewis bases), are investigated, namely, O2, NO2, NO, CO2, SO2, H2O, NH3, and CO. Four TM atoms Fe, Co, Ni, and Cu are considered as active sites for gas sensing. The effects of N-doping and the Ni(111) substrate are also examined. The performance of these systems in terms of stability, sensitivity, selectivity, and reusability is discussed for practical applications.

Inorganic nanoparticles are gaining increasing attention as drug carriers because they respond to external physical stimuli, allowing therapy to be combined with diagnosis. Their drawback is low drug loading capacity, which can be improved by proper and efficacious functionalization. In this computational study, we take TiO2 spherical nanoparticles as prototype photoresponsive inorganic nanoparticles and we fully decorate them with two different types of bifunctional ligands: TETTs and DOPACs, which present different surface anchoring groups (silanol or catechol) but the same drug tethering COOH group, although in different concentrations (3 vs. 1), thus causing different steric hindrances. Then, we put these two types of nanocarriers in bulk water and in the presence of several DOX molecules and let the systems evolve through molecular dynamics (MD) simulations, clearly observing drug loading on the nanocarriers. This comparative MD study allows the investigation of the loading mechanism, performance of a conformational analysis and establishment of the guiding interactions through an energy decomposition analysis. We learn that DOX mostly interacts with the functionalized NPs through electrostatics, as a consequence of the protonated amino group, although several H-bonds are also established both with the ligands and with the oxide surface. Different ligands induce a different electrostatic potential around the NP; therefore, those which lead to the formation of more negative hotspots (here TETTs) are found to favour DOX binding. The leading role of electrostatics can provide a rational explanation for a pH-dependent drug release mechanism that is often invoked for DOX when reaching diseased cells because under anomalous acidic conditions both the NP surface and the carboxylate groups of the ligands are expected to get protonated, which of course would weaken, if not totally quench, the interaction of the nanocarrier with protonated DOX.

Donor-modified TiO2 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, that is, dopamine and DOPAC ligands, when anchored to a spherical anatase TiO2 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 TiO2 surface model, we unravel both the curvature and coverage effects.

In this work, we present a quantum mechanical investigation, based on the self-consistent charge density functional tight-binding (SCC-DFTB) method, of the functionalization with silane-type ligands (TETT) of a spherical TiO2 nanoparticle of realistic size (2.2 nm containing 700 atoms) to create an efficient nanosystem for simultaneous photodynamic therapy and drug transport. We determine the mechanism of the TETT ligand anchoring and its stability under thermal treatment, through molecular dynamics simulations at 300 K. Then, we build a medium and a full coverage model (22 and 40 TETTs, respectively) and analyze the interaction among TETT ligands and between the ligands and the surface. Finally, on the fully covered nanoparticle, we succeed in localizing two minimum energy structures for an attached doxorubicin anticancer molecule (DOX) and provide the atomistic details for both the covalent and the non-covalent (electrostatic) types of interaction. A future development of this work will be the investigation of the loading capacity of this drug delivery system and of the pH effect of the surrounding aqueous environment.

An easy and cost-effective method is presented to functionalize graphene through thermally activated dimerization of 2,5-diaryltetrazoles. Consistently with the experimental spectroscopic results, theoretical calculations demonstrate that during the thermal treatment a dimerization process to tetrazine is energetically more favorable than covalent grafting. Since both the functionalization method by thermal activation and the use of tetrazoles have never been considered before to prepare graphene-based chemiresistors, this represents a promising approach to develop graphene-related sensing platforms. Five different 2,5-diaryltetrazoles have been tested here for the effective functionalization of low-defect graphene layers on silicon nitride. Based on these layers, an array of sensors has been prepared for testing upon ammonia exposure. The tests on the sensing performances clearly show sensitivity to ammonia, extending the current range of ammonia detection with a graphene-based chemiresistor down to the sub-ppm range, as results from a benchmarking with data available in the literature. Furthermore, all sensors perform better than bare graphene. Density functional theory (DFT) calculations, carried out on a model of the best performing layer of the array, provided the theoretical framework to rationalize the sensing mechanism and disclose a dual role played by the tetrazine molecules, (i) acting as ammonia concentrators and (ii) mediating the electron transfer between ammonia and graphene.

An easy and cost-effective method is presented to functionalize graphene through thermally activated dimerization of 2,5-diaryltetrazoles. Consistently with the experimental spectroscopic results, theoretical calculations demonstrate that during the thermal treatment a dimerization process to tetrazine is energetically more favorable than covalent grafting. Since both the functionalization method by thermal activation and the use of tetrazoles have never been considered before to prepare graphene-based chemiresistors, this represents a promising approach to develop graphene-related sensing platforms. Five different 2,5-diaryltetrazoles have been tested here for the effective functionalization of low-defect graphene layers on silicon nitride. Based on these layers, an array of sensors has been prepared for testing upon ammonia exposure. The tests on the sensing performances clearly show sensitivity to ammonia, extending the current range of ammonia detection with a graphene-based chemiresistor down to the sub-ppm range, as results from a benchmarking with data available in the literature. Furthermore, all sensors perform better than bare graphene. Density functional theory (DFT) calculations, carried out on a model of the best performing layer of the array, provided the theoretical framework to rationalize the sensing mechanism and disclose a dual role played by the tetrazine molecules, (i) acting as ammonia concentrators and (ii) mediating the electron transfer between ammonia and graphene.