Roberto Gaspari

Cu3-xP Nanocrystals as a Material Platform for Near-Infrared Plasmonics and Cation Exchange Reactions

Synthesis approaches to colloidal Cu3P nanocrystals (NCs) have been recently developed, and their optical absorption features in the near-infrared (NIR) have been interpreted as arising from a localized surface plasmon resonance (LSPR). Our pump–probe measurements on platelet-shaped Cu3-xP NCs corroborate the plasmonic character of this absorption. In accordance with studies on crystal structure analysis of Cu3P dating back to the 1970s, our density functional calculations indicate that this material is substoichiometric in copper, since the energy of formation of Cu vacancies in certain crystallographic sites is negative, that is, they are thermodynamically favored. Also, thermoelectric measurements point to a p-type behavior of the majority carriers from films of Cu3-xP NCs. It is likely that both the LSPR and the p-type character of our Cu3-xP NCs arise from the presence of a large number of Cu vacancies in such NCs. Motivated by the presence of Cu vacancies that facilitate the ion diffusion, we have additionally exploited Cu3-xP NCs as a starting material on which to probe cation exchange reactions. We demonstrate here that Cu3-xP NCs can be easily cation-exchanged to hexagonal wurtzite InP NCs, with preservation of the anion framework (the anion framework in Cu3-xP is very close to that of wurtzite InP). Intermediate steps in this reaction are represented by Cu3-xP/InP heterostructures, as a consequence of the fact that the exchange between Cu+ and In3+ ions starts from the peripheral corners of each NC and gradually evolves toward the center. The feasibility of this transformation makes Cu3-xP NCs an interesting material platform from which to access other metal phosphides by cation exchange.

Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations

Drug discovery is expensive and high-risk. Its main reasons of failure are lack of efficacy and toxicity of a drug candidate. Binding affinity for the biological target has been usually considered one of the most relevant figures of merit to judge a drug candidate along with bioavailability, selectivity and metabolic properties, which could depend on off-target interactions. Nevertheless, affinity does not always satisfactorily correlate with in vivo drug efficacy. It is indeed becoming increasingly evident that the time a drug spends in contact with its target (aka residence time) can be a more reliable figure of merit. Experimental kinetic measurements are operatively limited by the cost and the time needed to synthesize compounds to be tested, to express and purify the target, and to setup the assays. We present here a simple and efficient molecular-dynamics-based computational approach to prioritize compounds according to their residence time. We devised a multiple-replica scaled molecular dynamics protocol with suitably defined harmonic restraints to accelerate the unbinding events while preserving the native fold. Ligands are ranked according to the mean observed scaled unbinding time. The approach, trivially parallel and easily implementable, was validated against experimental information available on biological systems of pharmacological relevance.

Colloidal CuFeS2 Nanocrystals: Intermediate Fe d-Band Leads to High Photothermal Conversion Efficiency

We describe the colloidal hot-injection synthesis of phase-pure nanocrystals (NCs) of a highly abundant mineral, chalcopyrite (CuFeS2). Absorption bands centered at around 480 and 950 nm, spanning almost the entire visible and near-infrared regions, encompass their optical extinction characteristics. These peaks are ascribable to electronic transitions from the valence band (VB) to the empty intermediate band (IB), located in the fundamental gap and mainly composed of Fe 3d orbitals. Laser-irradiation (at 808 nm) of an aqueous suspension of CuFeS2 NCs exhibited significant heating, with a photothermal conversion efficiency of 49%. Such efficient heating is ascribable to the carrier relaxation within the broad IB band (owing to the indirect VB–IB gap), as corroborated by transient absorption measurements. The intense absorption and high photothermal transduction efficiency (PTE) of these NCs in the so-called biological window (650–900 nm) make them suitable for photothermal therapy as demonstrated by tumor cell annihilation upon laser irradiation. The otherwise harmless nature of these NCs in dark conditions was confirmed by in vitro toxicity tests on two different cell lines. The presence of the deep Fe levels constituting the IB is the origin of such enhanced PTE, which can be used to design other high performing NC photothermal agents.

Thermal Stability and Anisotropic Sublimation of Two-Dimensional Colloidal Bi2Te3 and Bi2Se3 Nanocrystals

The structural and compositional stabilities of two-dimensional (2D) Bi2Te3 and Bi2Se3 nanocrystals, produced by both colloidal synthesis and by liquid phase exfoliation, were studied by in situ transmission electron microscopy (TEM) during annealing at temperatures between 350 and 500 °C. The sublimation process induced by annealing is structurally and chemically anisotropic and takes place through the preferential dismantling of the prismatic {011̅0} type planes, and through the preferential sublimation of Te (or Se). The observed anisotropic sublimation is independent of the method of nanocrystal’s synthesis, their morphology, or the presence of surfactant molecules on the nanocrystals surface. A thickness-dependent depression in the sublimation point has been observed with nanocrystals thinner than about 15 nm. The Bi2Se3 nanocrystals were found to sublimate below 280 °C, while the Bi2Te3 ones sublimated at temperatures between 350 and 450 °C, depending on their thickness, under the vacuum conditions in the TEM column. Density functional theory calculations confirm that the sublimation of the prismatic {011̅0} facets is more energetically favorable. Within the level of modeling employed, the sublimation occurs at a rate about 700 times faster than the sublimation of the {0001} planes at the annealing temperatures used in this work. This supports the distinctly anisotropic mechanisms of both sublimation and growth of Bi2Te3 and Bi2Se3 nanocrystals, known to preferentially adopt a 2D morphology. The anisotropic sublimation behavior is in agreement with the intrinsic anisotropy in the surface free energy brought about by the crystal structure of Bi2Te3 or Bi2Se3.

Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η

Trans-lesion synthesis polymerases, like DNA Polymerase-η (Pol-η), are essential for cell survival. Pol-η bypasses ultraviolet-induced DNA damages via a two-metal-ion mechanism that assures DNA strand elongation, with formation of the leaving group pyrophosphate (PPi). Recent structural and kinetics studies have shown that Pol-η function depends on the highly flexible and conserved Arg61 and, intriguingly, on a transient third ion resolved at the catalytic site, as lately observed in other nucleic acid-processing metalloenzymes. How these conserved structural features facilitate DNA replication, however, is still poorly understood. Through extended molecular dynamics and free energy simulations, we unravel a highly cooperative and dynamic mechanism for DNA elongation and repair, which is here described by an equilibrium ensemble of structures that connect the reactants to the products in Pol-η catalysis. We reveal that specific conformations of Arg61 help facilitate the recruitment of the incoming base and favor the proper formation of a pre-reactive complex in Pol-η for efficient DNA editing. Also, we show that a third transient metal ion, which acts concertedly with Arg61, serves as an exit shuttle for the leaving PPi. Finally, we discuss how this effective and cooperative mechanism for DNA repair may be shared by other DNA-repairing polymerases.

Influence of the Ion Coordination Number on Cation Exchange Reactions with Copper Telluride Nanocrystals

Cu2–xTe nanocubes were used as starting seeds to access metal telluride nanocrystals by cation exchanges at room temperature. The coordination number of the entering cations was found to play an important role in dictating the reaction pathways. The exchanges with tetrahedrally coordinated cations (i.e., with coordination number 4), such as Cd2+ or Hg2+, yielded monocrystalline CdTe or HgTe nanocrystals with Cu2–xTe/CdTe or Cu2–xTe/HgTe Janus-like heterostructures as intermediates. The formation of Janus-like architectures was attributed to the high diffusion rate of the relatively small tetrahedrally coordinated cations, which could rapidly diffuse in the Cu2–xTe NCs and nucleate the CdTe (or HgTe) phase in a preferred region of the host structure. Also, with both Cd2+ and Hg2+ ions the exchange led to wurtzite CdTe and HgTe phases rather than the more stable zinc-blende ones, indicating that the anion framework of the starting Cu2–xTe particles could be more easily deformed to match the anion framework of the metastable wurtzite structures. As hexagonal HgTe had never been reported to date, this represents another case of metastable new phases that can only be accessed by cation exchange. On the other hand, the exchanges involving octahedrally coordinated ions (i.e., with coordination number 6), such as Pb2+ or Sn2+, yielded rock-salt polycrystalline PbTe or SnTe nanocrystals with Cu2–xTe@PbTe or Cu2–xTe@SnTe core@shell architectures at the early stages of the exchange process. In this case, the octahedrally coordinated ions are probably too large to diffuse easily through the Cu2–xTe structure: their limited diffusion rate restricts their initial reaction to the surface of the nanocrystals, where cation exchange is initiated unselectively, leading to core@shell architectures. Interestingly, these heterostructures were found to be metastable as they evolved to stable Janus-like architectures if annealed at 200 °C under vacuum.

Colloidal Monolayer β-In2Se3 Nanosheets with High Photoresponsivity

We report a low-temperature colloidal synthesis of single-layer, five-atom-thick, β-In2Se3 nanosheets with lateral sizes tunable from ∼300 to ∼900 nm, using short aminonitriles (dicyandiamide or cyanamide) as shape controlling agents. The phase and the monolayer nature of the nanosheets were ascertained by analyzing the intensity ratio between two diffraction peaks from two-dimensional slabs of the various phases, determined by diffraction simulations. These findings were further backed-up by comparing and fitting the experimental X-ray diffraction pattern with Debye formula simulated patterns and with side-view high-resolution transmission electron microscopy imaging and simulation. The β-In2Se3 nanosheets were found to be indirect band gap semiconductors (Eg = 1.55 eV), and single nanosheet photodetectors demonstrated high photoresponsivity and fast response times.

A theoretical investigation of the (0001) covellite surfaces

We report on the properties of the (0001) covellites surfaces, which we investigate by periodic slab density functional theory calculations. The absolute surface energies have been computed for all bulk terminations, showing that surfaces terminated by the flat CuS layer are associated with the lowest surface energy. Cleavage is predicted to occur across the [0001] interlayer Cu-S bond. The surfaces obtained by lowest energy cleavage are analyzed in terms of the atomic vertical relaxation, workfunction, and surface band structure. Our study predicts the presence of a shallow pz-derived surface state located 0.26 eV below the Fermi level, which is set to play an important role in the surface reactivity of covellite.

Pyramid-Shaped Wurtzite CdSe Nanocrystals with Inverted Polarity.

We report on pyramid-shaped wurtzite cadmium selenide (CdSe) nanocrystals (NCs), synthesized by hot injection in the presence of chloride ions as shape-directing agents, exhibiting reversed crystal polarity compared to former reports. Advanced transmission electron microscopy (TEM) techniques (image-corrected high-resolution TEM with exit wave reconstruction and probe-corrected high-angle annular dark field-scanning TEM) unequivocally indicate that the triangular base of the pyramids is the polar (0001̅) facet and their apex points toward the [0001] direction. Density functional theory calculations, based on a simple model of binding of Cl(-) ions to surface Cd atoms, support the experimentally evident higher thermodynamic stability of the (0001̅) facet over the (0001) one conferred by Cl(-) ions. The relative stability of the two polar facets of wurtzite CdSe is reversed compared to previous experimental and computational studies on Cd chalcogenide NCs, in which no Cl-based chemicals were deliberately used in the synthesis or no Cl(-) ions were considered in the binding models. Self-assembly of these pyramids in a peculiar clover-like geometry, triggered by the addition of oleic acid, suggests that the basal (polar) facet has a density and perhaps type of ligands significantly different from the other three facets, since the pyramids interact with each other exclusively via their lateral facets. A superstructure, however with no long-range order, is observed for clovers with their (0001̅) facets roughly facing each other. The CdSe pyramids were also exploited as seeds for CdS pods growth, and the peculiar shape of the derived branched nanostructures clearly arises from the inverted polarity of the seeds.

Charges Shift Protonation: Neutron Diffraction Reveals that Aniline and 2-Aminopyridine Become Protonated Upon Binding to Trypsin

Hydrogen atoms play a key role in protein-ligand recognition. They determine the quality of established H-bonding networks and define the protonation of bound ligands. Structural visualization of H atoms by X-ray crystallography is rarely possible. We used neutron diffraction to determine the positions of the hydrogen atoms in the ligands aniline and 2-aminopyridine bound to the archetypical serine protease trypsin. The resulting structures show the best resolution so far achieved for proteins larger than 100 residues and allow an accurate description of the protonation states and interactions with nearby water molecules. Despite its low pKa of 4.6 and a large distance of 3.6 Å to the charged Asp189 at the bottom of the S1 pocket, the amino group of aniline becomes protonated, whereas in 2-aminopyridine, the pyridine nitrogen picks up the proton although its amino group is 1.6 Å closer to Asp189. Therefore, apart from charge-charge distances, tautomer stability is decisive for the resulting binding poses, an aspect that is pivotal for predicting correct binding.