Two-photon absorption of Zn(II) octupolar molecules

In this work we present an investigation of the non-linear optical (NLO) properties of two octupolar chromophores: [Zn(4,4'-bis(dibutylaminostyryl)-[2,2']-bipyridine)(3)](2+) and [Zn(4,4'-bis((E)-2-(N-(TEG)pyrrol-2-yl)vinyl)-[2,2']-bipyridine)(3)](2+) with Zn(ii) as the coordination center, using two-photon emission technique (TPE) in fs-pulse temporal regime. Compared to the free ligands, our results do not show a net increase in the two-photon absorption (TPA) cross-section for the octupolar complexes, once normalized to the ligand unit. This is in partial disagreement with a previous theoretical study investigating the first molecule where a significant increase of the TPA cross-section was predicted (X. J. Liu, et al., J. Chem. Phys., 2004, 120, 11 493).     

Synthetic molecular motors and mechanical machines

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.     

Fullerenes against COVID-19: Repurposing C60 and C70 to Clog the Active Site of SARS-CoV-2 Protease

The persistency of COVID-19 in the world and the continuous rise of its variants demand new treatments to complement vaccines. Computational chemistry can assist in the identification of moieties able to lead to new drugs to fight the disease. Fullerenes and carbon nanomaterials can interact with proteins and are considered promising antiviral agents. Here, we propose the possibility to repurpose fullerenes to clog the active site of the SARS-CoV-2 protease, M^pro. Through the use of docking, molecular dynamics, and energy decomposition techniques, it is shown that C₆₀ has a substantial binding energy to the main protease of the SARS-CoV-2 virus, M^pro, higher than masitinib, a known inhibitor of the protein. Furthermore, we suggest the use of C₇₀ as an innovative scaffold for the inhibition of SARS-CoV-2 M^pro. At odds with masitinib, both C₆₀ and C₇₀ interact more strongly with SARS-CoV-2 M^pro when different protonation states of the catalytic dyad are considered. The binding of fullerenes to M^pro is due to shape complementarity, i.e., vdW interactions, and is aspecific. As such, it is not sensitive to mutations that can eliminate or invert the charges of the amino acids composing the binding pocket. Fullerenic cages should therefore be more effective against the SARS-CoV-2 virus than the available inhibitors such as masinitib, where the electrostatic term plays a crucial role in the binding.     

DiTe2: Calculating the diffusion tensor for flexible molecules

We report on an extended hydrodynamic modeling of the friction tensorial properties of flexible molecules including all types of natural, Z-Matrix like, internal coordinates. We implement the new methodology by extending and updating the software DiTe [Barone et al. J. Comput. Chem. 30, 2 (2009)]. DiTe (DIffusion TEnsor) implements a hydrodynamic modeling of the generalized translational, rotational, and configurational friction and diffusion tensors of flexible molecules in which flexibility is described in terms of dihedral angles. The new tool, DiTe2, has been renewed to include also stretching and bending types of internal mobility. Furthermore, DiTe2 is able to calculate the friction and diffusion tensors along collective (or reaction) coordinates defined as linear combinations of the internal natural ones. A number of tests are reported to show the new features of DiTe2. As leitmotiv for the tests, the calmodulin protein is taken into consideration, described both at all-atom and coarse-grained levels. © 2018 Wiley Periodicals, Inc.     

Nanostructured TiO x film on Si substrate: room temperature formation of TiSi x nanoclusters

We present a morphologic and spectroscopic study of cluster-assembled TiO _x films deposited by supersonic cluster beam source on clean silicon substrates. Data show the formation of nanometer—thick and uniform titanium silicides film at room temperature (RT). Formation of such thick TiSi _x film goes beyond the classical interfacial limit set by the Ti/Si diffusion barrier. The enhancement of Si diffusion through the TiO _x film is explained as a direct consequence of the porous film structure. Upon ultra high vacuum annealing beyond 600 °C, TiSi₂ is formed and the oxygen present in the film is completely desorbed. The morphology of the nanostructured silicides is very stable for thermal treatments in the RT—1000 °C range, with a slight cluster size increase, resulting in a film roughness an order of magnitude smaller than other TiO _x /Si and Ti/Si films in the same temperature range. The present results might have a broad impact in the development of new and simple TiSi synthesis methods that favour their integration into nanodevices.     

Quantitative analysis of charge-carrier trapping in organic thin-film transistors from transfer characteristics

A dynamic method for quantifying the amount and mechanism of trapping in organic field effect transistors (OFETs) is proposed. It exploits transfer characteristics acquired upon application of a triangular waveform gate sweep V _G. The analysis of the transfer characteristics at the turning point V _G=−V _max between forward and backward gate sweeps, viz. around the maximum gate voltage V _max applied, provides a differential slope Δm which depends exclusively on trapping. Upon a systematic change of V _max it is possible to extract the initial threshold voltage, equivalent to one of the observables of conventional stress measurements, and assess the mechanism of trapping via the functional dependence on the current. The analysis of the differential logarithmic derivative at the turning point yields the parameters of trapping, as the exponent β and the time scale of trapping τ. In the case of an ultra-thin pentacene OFET we extract β=1 and τ=10²–10³ s, in agreement with an exponential distribution of traps. The analysis of the hysteresis parameter Δm is completely general and explores time scales much shorter than those involved in bias stress measurements, thus avoiding irreversible damage to the device.     

Self-organization of rotaxane thin films into spatially correlated nanostructures: morphological and structural aspects

The self-organization of rotaxane thin films into spatially correlated nanostructures is shown to occur upon a thermal stimulus. The mechanism of formation of nanostructures and their organization has been investigated using atomic force microscopy, bright field transmission electron microscopy, selected area electron diffraction, and molecular mechanics simulations. The evolution of the nanostructures follows a complex pathway, where a rotaxane thin film first dewets from the substrate to form nanosized droplets. Droplets coalesce by ripening, generating spatially correlated motifs. In a later stage, the larger droplets change shape, nucleate, and coalesce to yield crystallites that grow into larger crystals by incorporating the surrounding droplets. The results show the following: (i) the nanostructures represent a metastable state of a crystallization process; (ii) spatial correlations emerge during ripening, but they are destroyed as stable nuclei are formed and crystallization proceeds to completion; iii) crystallization, either on graphite or amorphous carbon films, leads to a precise basal plane, viz. (010), which has minimum surface energy. The inherent degrees of freedom permitted in the rotaxane architecture favors the re-organization and nucleation of the film in the solid state. Low-energy trajectories leading to crystallites with stable surfaces and minimum energy contact plane are found to occur via concerted, small amplitude, internal motions without disruption of packing and intermolecular contacts.     

Interactions in single wall carbon nanotubes/pyrene/porphyrin nanohybrids

This work provides an in-depth look at a range of physicochemical aspects of (i) single wall carbon nanotubes (SWNT), (ii) pyrene derivatives (pyrene(+)), (iii) porphyrin derivatives (ZnP(8)()(-)() and H(2)()P(8)()(-)()), (iv) poly(sodium 4-styrenesulfonate), and (v) their combinations. Implicit in their supramolecular combinations is the hierarchical integration of SWNT (as electron acceptors), together with ZnP(8)()(-)() or H(2)()P(8)()(-)() (as electron donors), in an aqueous environment mediated through pyrene(+). This supramolecular approach yields novel electron donor-acceptor nanohybrids (SWNT/pyrene(+)/ZnP(8)()(-)() or SWNT/pyrene(+)/H(2)()P(8)()(-)()). In particular, we report on electrochemical and photophysical investigations that as a whole suggest sizeable and appreciable interactions between the individual components. The key step to form SWNT/pyrene(+)()/ZnP(8)()(-)() or SWNT/pyrene(+)()/H(2)()P(8)()(-)() hybrids is pi-pi interactions between SWNT and pyrene(+), for which we have developed for the first time a sensitive marker. The marker is the monomeric pyrene fluorescence, which although quenched is (i) only present in SWNT/pyrene(+) and (ii) completely lacking in just pyrene(+). Electrostatic interactions help to immobilize ZnP(8)()(-)() or H(2)()P(8)()(-)() onto SWNT/pyrene(+) to yield the final electron donor-acceptor nanohybrids. A series of photochemical experiments confirm that long-lived radical ion pairs are formed as a product of a rapid excited-state deactivation of ZnP(8)()(-)() or H(2)()P(8)()(-)(). This formation is fully rationalized on the basis of the properties of the individual moieties. Additional modeling shows that the data are likely to be relevant to the SWNTs present in the sample, which possess wider diameters.     

Adsorption of fumaramide [2]rotaxane and its components on a solid substrate: a coverage-dependent study

The coverage-dependent adsorption on Au(111) of a fumaramide [2]rotaxane and its components, a benzylic amide macrocycle and a fumaramide thread, is studied using high-resolution electron energy loss spectroscopy (HREELS). Up to monolayer coverage, the relative intensity of out-of-plane to in-plane phenyl ring vibrational modes indicates that the macrocycle adopts an orientation with the phenyl rings largely parallel to the surface. The formation of a chemisorption bond is evidenced by the presence of a Au-O stretching vibration. In contrast, the thread shows no evidence of chemisorption or a preferential orientation. The introduction of the thread into the macrocycle partly disrupts the film order so that the resulting chemisorbed rotaxane shows intermediate behavior with a preferential orientation up to 0.5 ML coverage. A decrease in film order and the absence of a preferred molecular orientation is observed for all three molecules at multilayer coverages. The spectral differences are addressed by molecular dynamics simulations in terms of the mobility of the phenyls of the three molecules on Au(111).