DNA Sensing Platforms: Novel Insights into Molecular Grafting Using Low Perturbative AFM Imaging.

By using AFM as a nanografting tool, we grafted micrometer-sized DNA platforms into inert alkanethiol SAMs. Tuning the grafting conditions (surface density of grafting lines and scan rate) allowed us to tailor the molecular density of the DNA platforms. Following the nanografting process, AFM was operated in the low perturbative Quantitative Imaging (QI) mode. The analysis of QI AFM images showed the coexistence of molecular domains of different heights, and thus different densities, within the grafted areas, which were not previously reported using contact AFM imaging. Thinner domains corresponded to low-density DNA regions characterized by loosely packed, randomly oriented DNA strands, while thicker domains corresponded to regions with more densely grafted DNA. Grafting with densely spaced and slow scans increased the size of the high-density domains, resulting in an overall increase in patch height. The structure of the grafted DNA was compared to self-assembled DNA, which was assessed through nanoshaving experiments. Exposing the DNA patches to the target sequence produced an increase in the patch height, indicating that hybridization was accomplished. The relative height increase of the DNA patches upon hybridization was higher in the case of lower density patches due to hybridization leading to a larger molecular reorganization. Low density DNA patches were therefore the most suitable for targeting oligonucleotide sequences.

Effective medium optical modelling of indium tin oxide nanocrystal films.

Doped semiconductor nanocrystal-based thin films are widely used for many applications, such as screens, electrochromic windows, light emitting diodes, and solar cells. Herein, we have employed spectroscopic ellipsometry to measure and model the complex dielectric response of indium tin oxide films fabricated by nanocrystal deposition and sintering. The films could be modelled as Bruggemann effective media, allowing estimation of the nanoscale interstitial porosity of the structure. The effective dielectric constants show the possibility of tuning the plasma frequency and the epsilon-near zero condition of the film.

Quantitative Ultrafast Electron-Temperature Dynamics in Photo-Excited Au Nanoparticles.

The femtosecond evolution of the electronic temperature of laser-excited gold nanoparticles is measured, by means of ultrafast time-resolved photoemission spectroscopy induced by extreme-ultraviolet radiation pulses. The temperature of the electron gas is deduced by recording and fitting high-resolution photo emission spectra around the Fermi edge of gold nanoparticles providing a direct, unambiguous picture of the ultrafast electron-gas dynamics. These results will be instrumental to the refinement of existing models of femtosecond processes in laterally-confined and bulk condensed-matter systems, and for understanding more deeply the role of hot electrons in technological applications.

Structural and Spectroscopic Properties of Benzoylpyridine-Based Hydrazones.

Photochromic hydrazones are attracting the attention in the field of photochromic systems especially due to their P-type character. To understand the structural features and their correlation with the spectroscopic data, UV-Vis, vibrational and ellipsometry spectroscopic techniques are employed with the support of density functional theory (DFT) calculations to three hydrazone derivatives based on benzoylpyridine. Interestingly, analysis of the structure shows the presence of two distinct rotamers around the pyridine ring with different energy and the well-defined conjugation path that changes due to E to Z isomerization especially in the hydrazone -C=N-NH part of the skeleton. IR and Raman spectra are analyzed, showing a higher selectivity in the Z form; moreover, the comparison with the normal modes proves the effect of the reaction on the backbone structure. The experimental results are in good agreement with the theoretical predictions, especially in the case of the Raman spectrum. The molecular polarization also changes from E to Z forms as predicted by DFT calculations. Spectroscopic ellipsometry on thin films of TOPAS doped with 10 %wt of the dimethylamino hydrazone derivative is used to prove such change at the molecular level. A modulation of the refractive index is observed, and it is correlated with the concentration of the active moiety and the calculated electronic polarizabilities.

Functionalizing gold with single strand DNA: novel insight into optical properties via combined spectroscopic ellipsometry and nanolithography measurements.

We have studied the self-assembly of 22-base oligonucleotides bound by a short alkyl thiol linker (C6-ssDNA) on flat Au films. The self-assembled monolayer (SAM) was modified by addition of a spacer (mercaptohexanol, MCH). Molecular depositions were monitored in situ by spectroscopic ellipsometry (SE). SAMs were characterized in a liquid environment by coupling SE (difference spectra method) with Atomic Force Microscope (AFM) measurements. We exploited the biofilm thickness obtained by AFM nanolithography and imaging to solve the refractive index/thickness correlation in optical measurements on ultrathin molecular layers. The combined SE/AFM analysis provided reliable estimates of the thickness and the refractive index of the biofilm in the NIR region (650-1300 nm) and revealed new aspects of DNA molecular organization: exposure to MCH leads to an increase of both film thickness and refractive index, which points to a reorganization of C6-ssDNA film. We show that the contribution of the thiol/Au interface has to be included in the optical model to obtain a more reliable determination of the refractive index of the biofilm in a liquid. The careful, correlative characterization of the mixed C6-ssDNA/MCH SAM represents a key step towards the optimization of a robust detection scheme based on helix-helix hybridization.

Morphological modulation of graphene-mediated hybridization in plasmonic systems.

We investigated the plasmonic response of a 2-dimensional ordered array of closely spaced (few-nm apart) Au nanoparticles covered by a large-area single-layer graphene sheet. The array consisted of coherently aligned nanoparticle chains, endowed with a characteristic uniaxial anisotropy. The joint effect of such a morphology and of the very small particle size and spacing led to a corresponding uniaxial wrinkling of graphene in the absence of detectable strain. The deposition of graphene redshifted the Au plasmon-resonance, strongly increased the optical absorption of the array and, most importantly, induced a marked optical anisotropy in the plasmonic response, absent in the pristine nanoparticle array. The experimental observations are accounted for by invoking a graphene-mediated resistive coupling between the Au nanoparticles, where the optical anisotropy arises from the wrinkling-induced anisotropic electron mobility in graphene at optical frequencies.

Spectroscopic ellipsometry meets AFM nanolithography: about hydration of bio-inert oligo(ethylene glycol)-terminated self assembled monolayers on gold.

For the first time, to our knowledge, spectroscopic ellipsometry (SE) has been combined with state-of-the-art AFM differential height measurements conducted after shaving nano-lithography of ultrathin, soft-matter films for thickness determination. We investigated self-assembled monolayers of SH-(CH2)11-EGn-OH molecules on gold, where EG is ethylene glycol units and n = 3 and 6, a prototypical non-fouling system. We performed SE measurements (245-1200 nm) focusing on the changes induced by the formation of the film (difference spectra). SE measurements, analysed by simple models, confirm the formation of the S-Au interface, transparency of the SAMs and provide a sharp picture of the ability of the EG functionality to protect the surface from unspecific adsorption of proteins. A quantitative assessment of the film thickness by SE was carried out ex situ, thanks to the optical contrast between the film and the ambient, and by AFM in liquid. The cross-check between SE and AFM height measurements combined with the comparison between in-liquid and ex situ SE measurements allowed obtaining non-perturbative information about the vertical density profile of the SAM. The in-liquid SE measurements indicate a refractive index matching between the aqueous medium and the outer part of the SAM, consistent with a disordered configuration of OEG and/or the penetration of water amid the OEG strands. A critical discussion provides a detailed insight into the subtle issues and pitfalls related to the thickness determination of soft-matter films to the monolayer limit.

Spectroscopic ellipsometry of self assembled monolayers: interface effects. The case of phenyl selenide SAMs on gold.

This work focuses on the quantitative application of spectroscopic ellipsometry to the study of optical properties and thickness of self assembled monolayers (SAMs) of phenyl selenide deposited from the liquid phase on gold. STM, XPS and cyclic voltammetry measurements provide additional chemical and morphological characterization of the SAMs. While routine ellipsometry analysis of SAMs often relies on the film-induced Î´Δ change in the Δ ellipsometric angle and discards SAM-substrate interface effects, the present data show a distinctive behaviour of the Î´Ψ data that we assign to interface effects, stronger than those previously found for densely packed alkanethiol SAMs. An inaccurate modelling of the variations in Ψ related to the nano-structured SAM-substrate interface leads to a large overestimation of the film thickness. A simple model, which takes into account an effective approximation for the interface layer between the film and the substrate, and the molecular optical absorptions, provides a good agreement between the data and a reliable thickness estimate of the SAM.

In-Operando Optical Spectroscopy of Field-Effect-Gated Al-Doped ZnO.

Transparent conductive oxides (TCO) have the unique characteristics of combining optical transparency with high electrical conductivity; such a property makes them uniquely alluring for applications in visible and infrared photonics. One of their most interesting features is the large sensitivity of their optical response to the doping level. We performed the active electrical manipulation of the dielectric properties of aluminum-doped ZnO (AZO), a TCO-based on Earth-abundant elements. We actively tuned the optical and electric performances of AZO films by means of an applied voltage in a parallel-plate capacitor configuration, with SrTiO3 as the dielectric, and monitored the effect of charge injection/depletion by means of in-operando spectroscopic ellipsometry. Calculations of the optical response of the gated system allowed us to extract the spatially resolved variations in the dielectric function of the TCO and infer the injected/depleted charge profile at the interface.

Biofunctionalization of Porous Titanium Oxide through Amino Acid Coupling for Biomaterial Design.

Porous transition metal oxides are widely studied as biocompatible materials for the development of prosthetic implants. Resurfacing the oxide to improve the antibacterial properties of the material is still an open issue, as infections remain a major cause of implant failure. We investigated the functionalization of porous titanium oxide obtained by anodic oxidation with amino acids (Leucine) as a first step to couple antimicrobial peptides to the oxide surface. We adopted a two-step molecular deposition process as follows: self-assembly of aminophosphonates to titanium oxide followed by covalent coupling of Fmoc-Leucine to aminophosphonates. Molecular deposition was investigated step-by-step by Atomic Force Microscopy (AFM) and X-ray Photoemission Spectroscopy (XPS). Since the inherent high roughness of porous titanium hampers the analysis of molecular orientation on the surface, we resorted to parallel experiments on flat titanium oxide thin films. AFM nanoshaving experiments on aminophosphonates deposited on flat TiO2 indicate the formation of an aminophosphonate monolayer while angle-resolved XPS analysis gives evidence of the formation of an oriented monolayer exposing the amine groups. The availability of the amine groups at the outer interface of the monolayer was confirmed on both flat and porous substrates by the following successful coupling with Fmoc-Leucine, as indicated by high-resolution XPS analysis.

Thermal Scanning-Probe Lithography for Broad-Band On-Demand Plasmonic Nanostructures on Transparent Substrates.

Thermal scanning-probe lithography (t-SPL) is a high-resolution nanolithography technique that enables the nanopatterning of thermosensitive materials by means of a heated silicon tip. It does not require alignment markers and gives the possibility to assess the morphology of the sample in a noninvasive way before, during, and after the patterning. In order to exploit t-SPL at its peak performances, the writing process requires applying an electric bias between the scanning hot tip and the sample, thereby restricting its application to conductive, optically opaque, substrates. In this work, we show a t-SPL-based method, enabling the noninvasive high-resolution nanolithography of photonic nanostructures onto optically transparent substrates across a broad-band visible and near-infrared spectral range. This was possible by intercalating an ultrathin transparent conductive oxide film between the dielectric substrate and the sacrificial patterning layer. This way, nanolithography performances comparable with those typically observed on conventional semiconductor substrates are achieved without significant changes of the optical response of the final sample. We validated this innovative nanolithography approach by engineering periodic arrays of plasmonic nanoantennas and showing the capability to tune their plasmonic response over a broad-band visible and near-infrared spectral range. The optical properties of the obtained systems make them promising candidates for the fabrication of hybrid plasmonic metasurfaces supported onto fragile low-dimensional materials, thus enabling a variety of applications in nanophotonics, sensing, and thermoplasmonics.

Local dielectric function of hBN-encapsulated WS2flakes grown by chemical vapor deposition.

Hexagonal boron nitride (hBN), sometimes referred to as white graphene, receives growing interest in the scientific community, especially when combined into van der Waals (vdW) homo- and heterostacks, in which novel and interesting phenomena may arise. hBN is also commonly used in combination with two-dimensional (2D) semiconducting transition metal dichalcogenides (TMDCs). The realization of hBN-encapsulated TMDC homo- and heterostacks can indeed offer opportunities to investigate and compare TMDC excitonic properties in various stacking configurations. In this work, we investigate the optical response at the micrometric scale of mono- and homo-bilayer WS2grown by chemical vapor deposition and encapsulated between two single layers of hBN. Imaging spectroscopic ellipsometry is exploited to extract the local dielectric functions across one single WS2flake and detect the evolution of excitonic spectral features from monolayer to bilayer regions. Exciton energies undergo a redshift by passing from hBN-encapsulated single layer to homo-bilayer WS2, as also confirmed by photoluminescence spectra. Our results can provide a reference for the study of the dielectric properties of more complex systems where hBN is combined with other 2D vdW materials into heterostructures and are stimulating towards the investigation of the optical response of other technologically-relevant heterostacks.

Doping-Dependent Optical Response of a Hybrid Transparent Conductive Oxide/Plasmonic Medium.

Understanding the interaction between plasmonic nanoparticles and transparent conductive oxides is instrumental to the development of next-generation photovoltaic, optoelectronic, and energy-efficient solid-state lighting devices. We investigated the optical response of hybrid media composed of gold nanoparticles deposited on aluminum-doped zinc oxide thin films with varying doping concentration by spectroscopic ellipsometry. The dielectric functions of bare AZO were addressed first, revealing doping-induced effects such as the band gap shift and the appearance of free carriers. In the hybrid media, a blue-shift of the localized surface plasmon resonance of Au NPs as a function of increasing Al doping of the substrate was observed, ascribed to the occurrence of a charge transfer between the two materials and the doping-dependent variation of the polarizability of the substrate.

A Two-Step Approach to Tune the Micro and Nanoscale Morphology of Porous Niobium Oxide to Promote Osteointegration.

We present a two-step surface modification process to tailor the micro and nano morphology of niobium oxide layers. Niobium was firstly anodized in spark regime in a Ca- and P-containing solution and subsequently treated by acid etching. The effects of anodizing time and applied potential on the surface morphology is investigated with SEM and AFM, complemented by XPS compositional analysis. Anodizing with a limiting potential of 250 V results in the fast growth of oxide layers with a homogeneous distribution of micro-sized pores. Cracks are, however, observed on 250 V grown layers. Limiting the anodizing potential to 200 V slows down the oxide growth, increasing the anodizing time needed to achieve a uniform pore coverage but produces fracture-free oxide layers. The surface nano morphology is further tuned by a subsequent acid etching process that leads to the formation of nano-sized pits on the anodically grown oxide surface. In vitro tests show that the etching-induced nanostructure effectively promotes cell adhesion and spreading onto the niobium oxide surface.

UPS, XPS, and NEXAFS study of self-assembly of standing 1,4-benzenedimethanethiol SAMs on gold.

We report a study of the self-assembly of 1,4-benzenedimethanethiol monolayers on gold formed in n-hexane solution held at 60 °C for 30 min and in dark conditions. The valence band characteristics, the thickness of the layer, and the orientation of the molecules were analyzed at a synchrotron using high resolution photoelectron spectroscopy and near edge X-ray adsorption spectroscopy. These measurements unambiguously attest the formation of a single layer with molecules arranged in the upright position and presenting a free -SH group at the outer interface. Near edge X-ray absorption fine structure (NEXAFS) measurements suggest that the molecular axis is oriented at 24° with respect to the surface normal. In addition, valence band features could be successfully associated to specific molecular orbital contributions thanks to the comparison with theoretically calculated density of states projected on the different molecular units.

Local Optical Properties in CVD-Grown Monolayer WS2 Flakes.

Excitons dominate the light absorption and re-emission spectra of monolayer transition-metal dichalcogenides (TMD). Microscopic investigations of the excitonic response in TMD almost invariably extract information from the radiative recombination step, which only constitutes one part of the picture. Here, by exploiting imaging spectroscopic ellipsometry (ISE), we investigate the spatial dependence of the dielectric function of chemical vapor deposition (CVD)-grown WS2 flakes with a microscopic lateral resolution, thus providing information about the spatially varying, exciton-induced light absorption in the monolayer WS2. Comparing the ISE results with imaging photoluminescence spectroscopy data, the presence of several correlated features was observed, along with the unexpected existence of a few uncorrelated characteristics. The latter demonstrates that the exciton-induced absorption and emission features are not always proportional at the microscopic scale. Microstructural modulations across the flakes, having a different influence on the absorption and re-emission of light, are deemed responsible for the effect.

Self-assembly of 1,4-benzenedimethanethiol self-assembled monolayers on gold.

A study of the self-assembly of 1,4-benzenedimethanethiol (BDMT; HS-CH(2)-(C(6)H(4))-CH(2)-SH) monolayers on gold is presented. Self-assembled monolayers (SAMs) are characterized by reflection-absorption infrared spectroscopy (RAIRS), X-ray photoelectron spectroscopy (XPS), and spectroscopic ellipsometry (SE) measurements. The ensemble of measurements consistently shows that well-organized BDMT SAMs, with "standing-up" molecules, can be obtained on high quality gold films with incubation in n-hexane provided that N(2)-degassed solutions are used and all preparation steps are performed at 60 degrees C in the absence of ambient light. SE data indicate that the optical interface properties of the BDMT-Au system are different from those of simple alkanethiol SAMs. A possible mechanism for the formation of the "standing-up" phase from the lying-down phase via a hydrogen exchange reaction involving chemisorbed lying-down and free dithiol molecules is discussed.

Morphological and Mechanical Characterization of DNA SAMs Combining Nanolithography with AFM and Optical Methods.

The morphological and mechanical properties of thiolated ssDNA films self-assembled at different ionic strength on flat gold surfaces have been investigated using Atomic Force Microscopy (AFM). AFM nanoshaving experiments, performed in hard tapping mode, allowed selectively removing molecules from micro-sized regions. To image the shaved areas, in addition to the soft contact mode, we explored the use of the Quantitative Imaging (QI) mode. QI is a less perturbative imaging mode that allows obtaining quantitative information on both sample topography and mechanical properties. AFM analysis showed that DNA SAMs assembled at high ionic strength are thicker and less deformable than films prepared at low ionic strength. In the case of thicker films, the difference between film and substrate Young's moduli could be assessed from the analysis of QI data. The AFM finding of thicker and denser films was confirmed by X-Ray Photoelectron Spectroscopy (XPS) and Spectroscopic Ellipsometry (SE) analysis. SE data allowed detecting the DNA UV absorption on dense monomolecular films. Moreover, feeding the SE analysis with the thickness data obtained by AFM, we could estimate the refractive index of dense DNA films.

High response photochromic films based on D-A diarylethenes and their application in holography.

A set of photochromic dithienylethenes bearing amino and nitro groups are synthesised and embedded at high concentrations in a polymer matrix (Cellulose Acetate Butyrate, CAB) to produce films showing a large reversible modulation of the complex refractive index in the Vis-NIR spectral range, thanks to an interesting combination of remarkable response at the molecular level and very high load capability in the chosen matrix. The photochromic derivatives are characterized in solution and in CAB films by means of electronic and vibrational spectroscopy, complemented by DFT calculations. Both the real and imaginary part of the refractive index are determined by spectroscopic ellipsometry. The modulation of the refractive index in the near infrared is in the range 0.02-0.04. These are very large values for such kinds of systems and they are due to a favourable combination of very large solubility of the derivatives in CAB and a high polarisability change. As for the change in transparency in the visible, contrast values larger than 103 are easily achieved. Based on such films, holograms are written and reconstructed with a very high fidelity and efficiency.

Observation of a Correlation Between Internal friction and Urbach Energy in Amorphous Oxides Thin Films.

We have investigated by spectroscopic ellipsometry (SE, 190-1700 nm) the optical properties of uniform, amorphous thin films of Ta2O5 and Nb2O5 as deposited and after annealing, and after so-called "doping" with Ti atoms which leads to mixed oxides. Ta2O5 and Ti:Ta2O5 are currently used as high-index components in Bragg reflectors for Gravitational Wave Detectors. Parallel to the optical investigation, we measured the mechanical energy dissipation of the same coatings, through the so-called "loss angle" ϕ = Q-1, which quantifies the energy loss in materials. By applying the well-known Cody-Lorentz model in the analysis of SE data we have been able to derive accurate information on the fundamental absorption edge through important parameters related to the electronic density of states, such as the optical gap (Eg) and the energy width of the exponential Urbach tail (the Urbach energy EU). We have found that EU is neatly reduced by suitable annealing as is also perceptible from direct inspection of SE data. Ti-doping also points to a minor decrease of EU. The reduction of EU parallels a lowering of the mechanical losses quantified by the loss angle ϕ. The correlation highlights that both the electronic states responsible of Urbach tail and the internal friction are sensitive to a self-correlation of defects on a medium-range scale, which is promoted by annealing and in our case, to a lesser extent, by doping. These observations may contribute to a better understanding of the relationship between structural and mechanical properties in amorphous oxides.