Search

The human telomeric G-quadruplex structural motif of DNA has come to be known as a new and stimulating target for anticancer drug discovery. Small molecules that interact with G-quadruplex structures in a selective way have gained impressive interest in recent years as they may serve as potential therapeutic agents. Here, we show how circular dichroism, UV resonance Raman and small angle X-ray scattering spectroscopies can be effectively combined to provide insights into structural and molecular aspects of the interaction between human telomeric quadruplexes and ligands. This study focuses on the ability of berberine and palmatine to bind with human telomeric quadruplexes and provides analysis of the conformational landscape visited by the relevant complexes upon thermal unfolding. With increasing temperature, both free and bound G-quadruplexes undergo melting through a multi-state process, populating different intermediate states. Despite the structural similarity of the two ligands, valuable distinctive features characterising their interaction with the G-quadruplex emerged from our multi-technique approach.

Background: SARS-CoV-2 is a RNA coronavirus responsible for the pandemic of the Severe Acute Respiratory Syndrome (COVID-19). RNA viruses are characterized by a high mutation rate, up to a million times higher than that of their hosts. Virus mutagenic capability depends upon several factors, including the fidelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Mutation rate drives viral evolution and genome variability, thereby enabling viruses to escape host immunity and to develop drug resistance., Methods: We analyzed 220 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 worldwide from December 2019 to mid-March 2020. SARS-CoV-2 reference genome was obtained from the GenBank database. Genomes alignment was performed using Clustal Omega. Mann-Whitney and Fisher-Exact tests were used to assess statistical significance., Results: We characterized 8 novel recurrent mutations of SARS-CoV-2, located at positions 1397, 2891, 14408, 17746, 17857, 18060, 23403 and 28881. Mutations in 2891, 3036, 14408, 23403 and 28881 positions are predominantly observed in Europe, whereas those located at positions 17746, 17857 and 18060 are exclusively present in North America. We noticed for the first time a silent mutation in RdRp gene in England (UK) on February 9th, 2020 while a different mutation in RdRp changing its amino acid composition emerged on February 20th, 2020 in Italy (Lombardy). Viruses with RdRp mutation have a median of 3 point mutations [range: 2-5], otherwise they have a median of 1 mutation [range: 0-3] (p value < 0.001)., Conclusions: These findings suggest that the virus is evolving and European, North American and Asian strains might coexist, each of them characterized by a different mutation pattern. The contribution of the mutated RdRp to this phenomenon needs to be investigated. To date, several drugs targeting RdRp enzymes are being employed for SARS-CoV-2 infection treatment. Some of them have a predicted binding moiety in a SARS-CoV-2 RdRp hydrophobic cleft, which is adjacent to the 14408 mutation we identified. Consequently, it is important to study and characterize SARS-CoV-2 RdRp mutation in order to assess possible drug-resistance viral phenotypes. It is also important to recognize whether the presence of some mutations might correlate with different SARS-CoV-2 mortality rates.

Laser-slicing at a diffraction-limited storage ring light source in the soft X-ray region is investigated with theoretical and numerical modelling. It turns out that the slicing efficiency is favoured by the ultra-low beam emittance, and that slicing can be implemented without interference to the standard multi-bunch operation. Spatial and spectral separation of the sub-picosecond radiation pulse from a hundreds of picosecond-long background is achieved by virtue of 1:1 imaging of the radiation source. The spectral separation is enhanced when the radiator is a transverse gradient undulator. The proposed configuration applied to the Elettra 2.0 six-bend achromatic lattice envisages total slicing efficiency as high as 10 -7 , one order of magnitude larger than the demonstrated state-of-the-art, at the expense of pulse durations as long as 0.4 ps FWHM and average laser power as high as ∼40 W.

The rapid development of extreme ultraviolet (EUV) and x-ray ultrafast coherent light sources such as free electron lasers (FELs) has triggered the extension of wave-mixing techniques to short wavelengths. This class of experiments, based on the interaction of matter with multiple light pulses through the N th order susceptibility, holds the promise of combining intrinsic ultrafast time resolution and background-free signal detection with nanometer spatial resolution and chemical specificity. A successful approach in this direction has been the combination of the unique characteristics of the seeded FEL FERMI with dedicated four-wave-mixing (FWM) setups, which leads to the demonstration of EUV-based transient grating (TG) spectroscopy. In this perspective paper, we discuss how the TG approach can be extended toward more general FWM spectroscopies by exploring the intrinsic multiparameter nature of nonlinear processes, which derives from the ability of controlling the properties of each field independently.

Advances in developing ultrafast coherent sources operating at extreme ultraviolet (EUV) and x-ray wavelengths allow the extension of nonlinear optical techniques to shorter wavelengths. Here, we describe EUV transient grating spectroscopy, in which two crossed femtosecond EUV pulses produce spatially periodic nanoscale excitations in the sample and their dynamics is probed via diffraction of a third time-delayed EUV pulse. The use of radiation with wavelengths down to 13.3 nm allowed us to produce transient gratings with periods as short as 28 nm and observe thermal and coherent phonon dynamics in crystalline silicon and amorphous silicon nitride. This approach allows measurements of thermal transport on the ~10-nm scale, where the two samples show different heat transport regimes, and can be applied to study other phenomena showing nontrivial behaviors at the nanoscale, such as structural relaxations in complex liquids and ultrafast magnetic dynamics.

A multi-technique approach, combining circular dichroism spectroscopy, ultraviolet resonance Raman spectroscopy and small angle scattering techniques, has been deployed to elucidate how the structural features of the human telomeric G-quadruplex d[A(GGGTTA)3GGG] (Tel22) change upon thermal unfolding. The system is studied both in the free form and when it is bound to Actinomycin D (ActD), an anticancer ligand with remarkable conformational flexibility. We find that at room temperature binding of Tel22 with ActD involves end-stacking upon the terminal G-tetrad. Structural evidence for drug-driven dimerization of a significant fraction of the G-quadruplexes is provided. When the temperature is raised, both free and bound Tel22 undergo melting through a multi-state process. We show that in the intermediate states of Tel22 the conformational equilibrium is shifted toward the (3+1) hybrid-type, while a parallel structure is promoted in the complex. The unfolded state of the free Tel22 is consistent with a self-avoiding random-coil conformation, whereas the high-temperature state of the complex is observed to assume a quite compact form. Such an unprecedented high-temperature arrangement is caused by the persistent interaction between Tel22 and ActD, which stabilizes compact conformations even in the presence of large thermal structural fluctuations.

We report an ab-initio study of a pump-probe experiment on the amino-acid glycine. We consider an UV pump followed by an X-ray probe tuned to carbon K-edge and study the vibronic structure of the core transition. The simulated experiment is feasible using existing free electron laser or high harmonic generation sources and thanks to the localization of the core orbitals posseses chemical selectivity. The present theory applies to other experimental schemes, including the use of a THz probe, available with present soft X-ray free electron lasers and/or high harmonic generation sources.

We hereby report on a set of transient optical reflectivity and transmissivity measurements performed on silicon nitride thin membranes excited by extreme ultraviolet (EUV) radiation from a free electron laser (FEL). Experimental data were acquired as a function of the membrane thickness, FEL fluence and probe polarization. The time dependence of the refractive index, retrieved using Jones matrix formalism, encodes the dynamics of electron and lattice excitation following the FEL interaction. The observed dynamics are interpreted in the framework of a two temperature model, which permits to extract the relevant time scales and magnitudes of the processes. We also found that in order to explain the experimental data thermo-optical effects and inter-band filling must be phenomenologically added to the model.

Nonlinear optical processes at soft x-ray wavelengths have remained largely unexplored due to the lack of available light sources with the requisite intensity and coherence. Here we report the observation of soft x-ray second harmonic generation near the carbon K edge (∼284  eV) in graphite thin films generated by high intensity, coherent soft x-ray pulses at the FERMI free electron laser. Our experimental results and accompanying first-principles theoretical analysis highlight the effect of resonant enhancement above the carbon K edge and show the technique to be interfacially sensitive in a centrosymmetric sample with second harmonic intensity arising primarily from the first atomic layer at the open surface. This technique and the associated theoretical framework demonstrate the ability to selectively probe interfaces, including those that are buried, with elemental specificity, providing a new tool for a range of scientific problems.

Time-resolved investigations have begun a new era of chemistry and physics, enabling the monitoring in real time of the dynamics of chemical reactions and matter. Induced transient optical absorption is a basic ultrafast electronic effect, originated by a partial depletion of the valence band, that can be triggered by exposing insulators and semiconductors to sub-picosecond extreme-ultraviolet pulses. Besides its scientific and fundamental implications, this process is very important as it is routinely applied in free-electron laser (FEL) facilities to achieve the temporal superposition between FEL and optical laser pulses with tens of femtoseconds accuracy. Here, a set of methodologies developed at the FERMI facility based on ultrafast effects in condensed materials and employed to effectively determine the FEL/laser cross correlation are presented.

High resolution metrology of beam profiles is presently a major challenge at X-ray free electron lasers. We demonstrate a characterization method based on beam imprints in poly (methyl methacrylate). By immersing the imprints formed at 47.8 eV into organic solvents, the regions exposed to the beam are removed similar to resist development in grayscale lithography. This allows for extending the sensitivity of the method by more than an order of magnitude compared to the established analysis of imprints created solely by ablation. Applying the Beer-Lambert law for absorption, the intensity distribution in a micron-sized focus can be reconstructed from one single shot with a high dynamic range, exceeding 10 3 . The procedure described here allows for beam characterization at free electron lasers revealing even faint beam tails, which are not accessible when using ablation imprint methods. We demonstrate the greatly extended dynamic range on developed imprints taken in focus of conventional Fresnel zone plates and spiral zone plates producing beams with a topological charge.

This review is focused on free-electron lasers (FELs) in the hard to soft x-ray regime. The aim is to provide newcomers to the area with insights into: the basic physics of FELs, the qualities of the radiation they produce, the challenges of transmitting that radiation to end users and the diversity of current scientific applications. Initial consideration is given to FEL theory in order to provide the foundation for discussion of FEL output properties and the technical challenges of short-wavelength FELs. This is followed by an overview of existing x-ray FEL facilities, future facilities and FEL frontiers. To provide a context for information in the above sections, a detailed comparison of the photon pulse characteristics of FEL sources with those of other sources of high brightness x-rays is made. A brief summary of FEL beamline design and photon diagnostics then precedes an overview of FEL scientific applications. Recent highlights are covered in sections on structural biology, atomic and molecular physics, photochemistry, non-linear spectroscopy, shock physics, solid density plasmas. A short industrial perspective is also included to emphasise potential in this area.

UV Raman and Brillouin light scattering (BLS) experiments have been used in this study to explore the complex phase change behavior occurring in pH-responsive polysaccharide hydrogels as a function of temperature. Due to the different physical quantities measured by the two techniques, the joint analysis of Raman and BLS spectra has provided an unprecedented large-scale characterization of the molecular rearrangements and of the different kinds of hydrophilic and hydrophobic interactions that cooperate to determine the phase transformation observed in these hydrogels during the heating of the gel. As the main result, the analysis of the Raman and BLS spectra showed the existence of a correlation between the local (molecular) and collective properties of the gels during the phase transformation undergone by the system, which is markedly triggered by pH. The joint set of experimental results suggests a model according to which the mechanism of pH dependence in the hydrogels under investigation is dominated by the interactions involving the hydrophobic parts of the polymer skeleton, whereas the solvation process observed under heating of the gels is driven by the progressive distancing of the polymer domains among them, as monitored by the Brillouin sound velocity.

Stimulated emission is a fundamental process in nature that deserves to be investigated and understood in the extreme ultra-violet (EUV) and x-ray regimes. Today, this is definitely possible through high energy density free electron laser (FEL) beams. In this context, we give evidence for soft-x-ray stimulated emission from a magnesium oxide solid target pumped by EUV FEL pulses formed in the regime of travelling-wave amplified spontaneous emission in backward geometry. Our results combine two effects separately reported in previous works: emission in a privileged direction and existence of a material-dependent threshold for the stimulated emission. We develop a novel theoretical framework, based on coupled rate and transport equations taking into account the solid-density plasma state of the target. Our model accounts for both observed mechanisms that are the privileged direction for the stimulated emission of the Mg L 2,3 characteristic emission and the pumping threshold.

Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based X-ray crystallography and cryo-electron microscopy have made major contributions in determining thousands of protein structures even from micro-sized crystals. They suffer from some limitations that have not been overcome, such as radiation damage, the natural inability to crystallize a number of proteins, and experimental conditions for structure determination that are incompatible with the physiological environment. Today, the ultra-short and ultra-bright pulses of X-ray free-electron lasers have made attainable the dream to determine protein structures before radiation damage starts to destroy the samples. However, the signal-to-noise ratio remains a great challenge to obtain usable diffraction patterns from a single protein molecule. With the perspective to overcome these challenges, we describe here a new methodology that has the potential to overcome the signal-to-noise-ratio and protein crystallization limits. Using a multidisciplinary approach, we propose to create ordered, two dimensional protein arrays with defined orientation attached on a self-assembled-monolayer. We develop a literature-based flexible toolbox capable of assembling different kinds of proteins on a functionalized surface and consider using a graphene cover layer that will allow performing experiments with proteins in physiological conditions.

Introduction: In light of the recent development of new soft materials, nanostructured self-assembled systems have attracted attention in a variety of technological fields of high social impact. Cyclodextrin nanosponges (CDNS) represent a new and highly versatile class of cross-linked cyclodextrin (CD)-based nanoporous polymers. Their intriguing properties, including safety, biodegradability, negligible toxicity, marked swelling behavior, superior inclusion capability with respect to native CD, are the bases for potential for applications in drug delivery, tissue engineering and regenerative medicine. Areas covered: We report on the state-of-art concerning a detailed characterization of structural and dynamical features of CDNS explored by the combined use of different and complementary techniques, such as Fourier transform infrared absorption in attenuated total reflectance geometry (FTIR-ATR) and Raman spectroscopies, and high resolution magic angle spinning (HR-MAS) NMR spectroscopy. The ambitious objective is to furnish an exhaustive survey of the role played by hydrophobic and hydrophilic groups within the cross-linked network, in dry and swollen states, in determining the macroscopic functional features of CDNS. Expert opinion: The reported results may significantly contribute in the rational design and optimization of new stimuli-responsive systems exhibiting tunable inclusion/release properties, adapted to the therapeutic demands of pathology.

The phenomenon of polymorphism is of great relevance in pharmaceutics, since different polymorphs have different physicochemical properties, e.g., solubility, hence, bioavailability. Coupling diffractometric and spectroscopic experiments with thermodynamic analysis and computational work opens to a methodological approach which provides information on both structure and dynamics in the solid as well as in solution. The present work reports on the conformational changes in crystalline iopamidol, which is characterized by atropisomerism, a phenomenon that influences both the solution properties and the distinct crystal phases. The conformation of iopamidol is discussed for three different crystal phases. In the anhydrous and monohydrate crystal forms, iopamidol molecules display a syn conformation of the long branches stemming out from the triiodobenzene ring, while in the pentahydrate phase the anti conformation is found. IR and Raman spectroscopic studies carried out on the three crystal forms, jointly with quantum chemical computations, revealed that the markedly different spectral features can be specifically attributed to the different molecular conformations. Our results on the conformational versatility of iopamidol in different crystalline phases, linking structural and spectroscopic evidence for the solution state and the solid forms, provide a definite protocol for grasping the signals that can be taken as conformational markers. This is the first step for understanding the crystallization mechanism occurring in supersaturated solution of iopamidol molecules.

Ethanol is an essential chemical reagent in DNA preparation as its use increases the yield of extraction. All methodologies for DNA isolation involve the use of ethanol in order to prevent DNA dissolution in water and to optimize the binding of DNA to chromatographic membranes. In this note, we show how the presence of ethanol traces in DNA aqueous solution affects ultraviolet Raman spectra, leading to possible misinterpretations. We report a simple method to remove the ethanol Raman features from the spectra, based on heating the DNA sample at 80 ℃, followed by a slow cooling procedure.

The development of free electron laser (FEL) sources has provided an unprecedented bridge between the scientific communities working with ultrafast lasers and extreme ultraviolet (XUV) and X-ray radiation. Indeed, in recent years an increasing number of FEL-based applications have exploited methods and concepts typical of advanced optical approaches. In this context, we recently used a seeded FEL to demonstrate a four-wave-mixing (FWM) process stimulated by coherent XUV radiation, namely the XUV transient grating (X-TG). We hereby report on X-TG measurements carried out on a sample of silicon nitride (Si 3 N 4 ). The recorded data bears evidence for two distinct signal decay mechanisms: one occurring on a sub-ps timescale and one following slower dynamics extending throughout and beyond the probed timescale range (100 ps). The latter is compatible with a slower relaxation (time decay > ns), that may be interpreted as the signature of thermal diffusion modes. From the peak intensity of the X-TG signal we could estimate a value of the effective third-order susceptibility which is substantially larger than that found in SiO 2 , so far the only sample with available X-TG data. Furthermore, the intensity of the time-coincidence peak shows a linear dependence on the intensity of the three input beams, indicating that the measurements were performed in the weak field regime. However, the timescale of the ultrafast relaxation exhibits a dependence on the intensity of the XUV radiation. We interpreted the observed behaviour as the generation of a population grating of free-electrons and holes that, on the sub-ps timescale, relaxes to generate lattice excitations. The background free detection inherent to the X-TG approach allowed the determination of FEL-induced electron dynamics with a sensitivity largely exceeding that of transient reflectivity and transmissivity measurements, usually employed for this purpose.

The focus of the present work is to shed light on possible modifications of the molecular properties of polysaccharide hydrogels induced by the establishment of specific non-covalent interactions during the loading of a guest compound inside the gel phase. With this aim, a case study of the encapsulation of caffeine (Caf) inside cyclodextrin-based hydrogels, namely, cyclodextrin nanosponges (NS), is systematically investigated here by using UV Raman scattering experiments. The UV Raman spectra of the hydrogels, analysed as a function of temperature, concentration of the guest molecule loaded in the gel phase and pH, prove particularly informative both on the structural rearrangements of the hydrophobic/hydrophilic groups of the polymeric network and on the breaking/formation of specific guest-matrix interactions. Analysis of the temperature dependence of dynamical parameters, i.e., the dephasing time associated with specific vibrational modes of the polymer backbone, enables the proposal of a molecular picture in which the loading of Caf in NS hydrogels tends to favour access of the water solvent to the more hydrophobic portions of the polymer matrix, which is in turn reflected in a marked increase in the solvation of the whole system. The achievements of this work appear of interest with respect to the design of new possible strategies for controlling the diffusion/release of bioactive molecules inside hydrogel networks, besides corroborating the potential of UV Raman scattering experiments to give new molecular insights into complex phenomena affecting hydrogel phases.

Free-electron lasers (FELs) currently represent a step forward on time-resolved investigations on any phase of matter through pump-probe methods involving FELs and laser beams. That class of experiments requires an accurate spatial and temporal superposition of pump and probe beams on the sample, which at present is still a critical procedure. More efficient approaches are demanded to quickly achieve the superposition and synchronization of the beams. Here, we present what we believe is a novel technique based on an integrated device allowing the simultaneous characterization and the fast spatial and temporal overlapping of the beams, reducing the alignment procedure from hours to minutes.

During the last few decades it has been ascertained that base stacking is one of the major contributions stabilizing nucleic acid conformations. However, the understanding of the nature of the interactions involved in the stacking process remains under debate and it is a subject of theoretical and experimental studies. Structural similarity between purine bases (guanine and adenine) in DNA and the caffeine molecule makes caffeine an excellent model for the purine bases. The present study clearly shows that dipolar interactions play a fundamental role in determining stacking of purine molecules in solution. In order to reach this achievement, polarized ultraviolet Raman resonant scattering experiments have been carried out on caffeine aqueous solutions as a function of concentration and temperature. The investigation pointed out at the aggregation and solvation properties, particularly at elevated temperatures. Kubo-Anderson theory was used as a framework to investigate the non-coincidence effect (NCE) occurring in the totally symmetric breathing modes of the purine rings, and in the bending modes of the methyl groups of caffeine. The NCE concentration dependence shows that caffeine aggregation at 80 °C occurs by planar stacking of the hydrophobic faces. The data clearly indicate that dipolar interactions determine the reorientational motion of the molecules in solution and are the driving force for the stacking of caffeine. In parallel, the observed dephasing times imply a change in caffeine interactions as a function of temperature and concentration. A decrease, at low water content, of the dephasing time for the ring breathing vibration mode indicates that self-association alters the solvation structure that is detectable at low concentration. These results are in agreement with simulation predictions and serve as an important validation of the models used in those calculations.

The fundamental question of how the reorganization of the hydrogen-bond (HB) network of water is influenced by the combination of nano-confinement and hydrophobic/hydrophilic solvation effects is addressed here using a spectroscopic study of water absorbed in a model, pH-sensitive polysaccharide hydrogel. The effects of temperature, hydration level and pH on the vibrational dynamics associated with the water molecules and the polymer skeleton are disentangled and analysed by a complementary and combined use of UV-Raman scattering and IR spectroscopy. The experimental data give evidence that the solvation effects in the hydrogel matrix are essentially dominated by the hydration of more hydrophobic parts of the polymer network, while the effect of pH on the HB reorganization of confined water molecules is found to be similar to that induced by cooling of the system. A tentative explanation of these results has been provided in terms of interplay between different kinds of interactions, i.e. hydrophobic vs. hydrophilic.

A vibrational study by means of UV-Raman and FTIR-ATR measurements has been performed on sulfobutyl ether β-cyclodextrin (SBE-β-CD)-water solutions, as a function of concentration and temperature, with the aim to provide a molecular-scale explanation of the enhanced performances as carrier agent exhibited by this modified macrocycle with respect to natural cyclodextrin. The attention has been mainly paid to the modifications induced on the vibrational band assigned to the O-H stretching intramolecular mode, in turn related to the dynamical rearrangement occurring in the hydrogen bonding (HB) network of water molecules. The results of our measurements clearly showed a characteristic "structure-breaker" effect on the tetrahedral HB arrangements induced on water molecules by increasing of both temperature and solute concentration, allowing us to also extract thermodynamic parameters. These results could be a key step for a clearer understanding of the connection between the dynamical properties of hydration water and the complexing ability of this cyclodextrin derivative.

The recent advent of free-electron laser (FEL) sources is driving the scientific community to extend table-top laser research to shorter wavelengths adding elemental selectivity and chemical state specificity. Both a compact setup (mini-TIMER) and a separate instrument (EIS-TIMER) dedicated to four-wave-mixing (FWM) experiments has been designed and constructed, to be operated as a branch of the Elastic and Inelastic Scattering beamline: EIS. The FWM experiments that are planned at EIS-TIMER are based on the transient grating approach, where two crossed FEL pulses create a controlled modulation of the sample excitations while a third time-delayed pulse is used to monitor the dynamics of the excited state. This manuscript describes such experimental facilities, showing the preliminary results of the commissioning of the EIS-TIMER beamline, and discusses original experimental strategies being developed to study the dynamics of matter at the fs-nm time-length scales. In the near future such experimental tools will allow more sophisticated FEL-based FWM applications, that also include the use of multiple and multi-color FEL pulses.

A new high-performance method for the free-electron laser (FEL) focused beam diagnosis has been successfully tested at the FERMI FEL in Trieste, Italy. The novel pixelated phosphor detector (PPD) consists of micrometric pixels produced by classical UV lithography and dry etching technique, fabricated on a silicon substrate, arranged in a hexagonal geometry and filled with suitable phosphors. It has been demonstrated that the overall resolution of the system has increased by reducing the diffusion of the light in the phosphors. Various types of PPD have been produced and tested, demonstrating a high resolution in the beam profile and the ability to measure the actual spot size shot-to-shot with an unprecedented resolution. For these reasons, the proposed detector could become a reference technique in the FEL diagnosis field.

High-energy density extreme ultraviolet radiation delivered by the FERMI seeded free-electron laser has been used to create an exotic nonequilibrium state of matter in a titanium sample characterized by a highly excited electron subsystem at temperatures in excess of 10 eV and a cold solid-density ion lattice. The obtained transient state has been investigated through ultrafast absorption spectroscopy across the Ti M2,3-edge revealing a drastic rearrangement of the sample electronic structure around the Fermi level occurring on a time scale of about 100 fs.

The molecular mechanism responsible for the thermosensitive behaviour exhibited by pH-responsive cyclodextrin-based hydrogels is explored here with the twofold aim of clarifying some basic aspects of H-bond interactions in hydrogel phases and contributing to a future engineering of cyclodextrin hydrogels for targeted delivery and release of bioactive agents. The degree of H-bond association of water molecules entrapped in the gel network and the extent of intermolecular interactions involving the hydrophobic/hydrophilic moieties of the polymer matrix are probed by UV Raman and IR experiments, in order to address the question of how these different and complementary aspects combine to determine the pH-dependent thermal activation exhibited by these hydrogels. Complementary vibrational spectroscopies are conveniently employed in this study with the aim of safely disentangling the spectral response arising from the two main components of the hydrogel systems, i.e. the polymer matrix and water solvent. The experimental evidence suggests that the dominant effects in the mechanism of solvation of cyclodextrin-based hydrogels are due to the changes occurring, upon increasing of temperature, in the hydrophobicity character of specific chemical moieties of the polymer, as triggered by pH variations. The achievements of this work corroborate the potentiality of the UV Raman scattering technique, in combination with more conventional IR experiments, to provide a "molecular view" of complex macroscopic phenomena exhibited in hydrogel phases.

The Diffraction and Projection Imaging (DiProI) beamline at FERMI, the Elettra free-electron laser (FEL), hosts a multi-purpose station that has been opened to users since the end of 2012. This paper describes the core capabilities of the station, designed to make use of the unique features of the FERMI-FEL for performing a wide range of static and dynamic scattering experiments. The various schemes for time-resolved experiments, employing both soft X-ray FEL and seed laser IR radiation are presented by using selected recent results. The ongoing upgrade is adding a reflection geometry setup for scattering experiments, expanding the application fields by providing both high lateral and depth resolution.

The Elastic and Inelastic Scattering (EIS) beamline at the free-electron laser FERMI is presented. It consists of two separate end-stations: EIS-TIMEX, dedicated to ultrafast time-resolved studies of matter under extreme and metastable conditions, and EIS-TIMER, dedicated to time-resolved spectroscopy of mesoscopic dynamics in condensed matter. The scientific objectives are discussed and the instrument layout illustrated, together with the results from first exemplifying experiments.

The formation of a hydration shell in acetamide aqueous solution has been investigated by means of UV Raman spectroscopy. The experimental results reveal the existence of two distinct regimes of water dynamics. At high acetamide concentration water molecules show a structural and dynamical behavior consistent with the so-called iceberg model. Upon increasing the amount of water we observe the formation of a hydration shell marked by fastening of hydrogen-bond dynamics. Such a behavior may help to shed light on the scientific debate on how water rearranges around the hydrophobic portions of solute molecules (iceberg vs. non-iceberg models).

A detailed experimental and theoretical vibrational analysis of hydrogels of β-cyclodextrin nanosponges (β-CDNS), obtained by polymerization of β-cyclodextrin (β-CD) with the cross-linking agent ethylenediaminetetraacetic acid (EDTA), is reported here. Thorough structural characterization is achieved by exploiting the complementary selection rules of FTIR-ATR and Raman spectroscopies and by supporting the spectral assignments by DFT calculations of the spectral profiles. The combined analysis of the FTIR-ATR spectra of the polymers hydrated with H2O and D2O allowed us to isolate the HOH bending of water molecules not involved in symmetrical, tetrahedral environments. The analysis of the HOH bending mode was carried out as a function of temperature, showing the existence of a supercooled state of the water molecules. The highest level of cooperativity of the hydrogen bond scheme was reached at a value of the β-CD/EDTA molar ratio n = 6. Finally, the connectivity pattern of "uncoupled" water molecules bound to the nanosponge backbone was found to be weakened by increasing T. The temperature above which the population of non-tetracoordinated water molecules becomes predominant turned out to be independent of the parameter n.

We report on the use of the UV Raman technique to monitor the oxidative damage of deoxynucleotide triphosphates (dATP, dGTP, dCTP and dTTP) and DNA (plasmid vector) solutions. Nucleotide and DNA aqueous solutions were exposed to hydrogen peroxide (H2O2) and iron containing carbon nanotubes (CNTs) to produce Fenton's reaction and induce oxidative damage. UV Raman spectroscopy is shown to be maximally efficient to reveal changes in the nitrogenous bases during the oxidative mechanisms occurring on these molecules. The analysis of Raman spectra, supported by numerical computations, revealed that the Fenton's reaction causes an oxidation of the nitrogenous bases in dATP, dGTP and dCTP solutions leading to the production of 2-hydroxyadenine, 8-hydroxyguanine and 5-hydroxycytosine. No thymine change was revealed in the dTTP solution under the same conditions. Compared to single nucleotide solutions, plasmid DNA oxidation has resulted in more radical damage that causes the breaking of the adenine and guanine aromatic rings. Our study demonstrates the advantage of using UV Raman spectroscopy for rapidly monitoring the oxidation changes in DNA aqueous solutions that can be assigned to specific nitrogenous bases.

The molecular dynamics of water and a polymer matrix is here explored in a paradigmatic model of a polysaccharide hydrogel, by the combined use of UV Raman scattering and infrared measurements. The case example of cyclodextrin nanosponges (CDNS)/hydrogel is chosen since the simultaneous presence in the structure of the polymer matrix of both hydrophilic and hydrophobic sites mimics the complexity of polysaccharide hydrogels. In this way, the contributions provided by the balance between the hydrophilicity/hydrophobicity and the grade of entanglement of the polymer hydrogel to lead to the formation of the gel phase are separately accounted and evaluated. As main results, we found that the hydrophobic CH groups inserted on the aromatic ring of CDNS experience a more pronounced dynamic perturbation with respect to the carbonyl groups due to the collision between the solvent and vibrating atoms of the polymer. The overall results provide a detailed molecular picture of the swelling phenomena occurring when a chemically cross-linked polymer contacts with water or biological fluids and exploits the potentiality of UV Raman spectroscopy to retrieve dynamic information besides their structural counterpart obtained by the classical analysis of the basic features of vibrational spectra.

In this Letter, we present a simple method to avoid the well-known spurious contributions in the Brillouin light scattering (BLS) spectrum arising from the finite aperture of collection optics. The method relies on the use of special spatial filters able to select the scattered light with arbitrary precision around a given value of the momentum transfer (Q). We demonstrate the effectiveness of such filters by analyzing the BLS spectra of a reference sample as a function of scattering angle. This practical and inexpensive method could be an extremely useful tool to fully exploit the potentiality of Brillouin acoustic spectroscopy, as it will easily allow for effective Q-variable experiments with unparalleled luminosity and resolution.

We report on the possibility of extracting fast dynamical relaxation times from homodyne transient grating measurements. We demonstrate the validity of our approach by experimental measurements on liquid acetonitrile and by comparison with literature. This approach would be of tremendous help in the case of free-electron-laser-based transient grating experiments due to the overcoming of technical difficulties, such as large-angle geometries.

X-ray free electron lasers (FEL) coupled with optical lasers have opened unprecedented opportunities for studying ultrafast dynamics in matter. The major challenge in pump-probe experiments using FEL and optical lasers is synchronizing the arrival time of the two pulses. Here we report a technique that benefits from the seeded-FEL scheme and uses the optical seed laser for nearly jitter-free pump-probe experiments. Timing jitter as small as 6 fs has been achieved and confirmed by measurements of FEL-induced transient reflectivity changes of Si3N4 using both collinear and non-collinear geometries. Planned improvements of the experimental set-up are expected to further reduce the timing jitter between the two pulses down to fs level.

We report on new opportunities for ultrafast science thanks to the use of two-colour extreme ultraviolet (XUV) pulses at the FERMI free electron laser (FEL) facility. The two pulses have been employed to carry out a pioneering FEL-pump/FEL-probe diffraction experiment using a Ti target and tuning the FEL pulses to the M(2/3)-edge in order to explore the dependence of the dielectric constant on the excitation fluence. The future impact that the use of such a two-colour FEL emission will have on the development of ultrafast wave-mixing methods in the XUV/soft X-ray range is addressed and discussed.

Glycine aqueous solutions have been studied as a function of temperature and concentration by means of UV Brillouin and Raman spectroscopes. Brillouin spectra provided information on the average relaxation time τα related to the mechanisms of hydrogen bonds (HBs) formation and breaking. The concentration-temperature behavior of τ has been compared to the vibrational dephasing lifetime of atoms involved in HBs, as derived by a lineshape analysis of Raman spectra. We point out how it is possible to trace the thermodynamic behavior of a selected HB from Raman data. In particular, our results confirm the predominant role played in the hydration process by the water molecules surrounding the hydrophobic groups and, furthermore, evidence how at low temperature the HB strength between these molecules is greater than those found in bulk water and between glycine and water molecules.

Raman spectra of acetic acid aqueous solutions in the 500-4000 cm(-1) range have been measured as a function of water concentration to investigate the hydration shell formation mechanism around the acetic acid molecules. A fitting procedure based on the Kubo-Anderson model has been applied to the spectra. This has allowed us to determine the average lifetime of the hydrogen bonds involving a given functional group, as well as their geometrical distribution as a function of water concentration. The comparison of our results with literature data has demonstrated that the fitting model is adequate to describe organic water mixtures. Finally, the role of water in the formation of the hydrophobic shell around the methyl group in diluted acetic acid water solutions has been discussed, evidencing how the methyl group hydrophobicity strongly influences the acetic acid behavior in aqueous solutions.

An inelastic UV scattering experiment has been carried out on acetic acid-water solutions as a function of temperature and concentration. The analysis of experimental data indicates the presence of a crossover temperature (T(c) approximately 325 +/- 10 K). Above T(c), the energy of hydrogen bonds responsible for water-acetic acid and acetic acid-acetic acid interactions is strongly reduced. This leads to a reduction in the average number of water molecule interacting with acetic acid, as well as to a lower number of acetic acid clusters. The latter behavior can be mainly ascribed to a temperature change in the activation energy of carboxylic groups of acetic acid. These results may be also relevant to better understand the folding mechanism in protein-water solutions.

A Brillouin scattering investigation has been carried out on trehalose-water solutions in a wide range of concentrations (0

We have developed a method to measure simultaneously the internal energy of bulk and the first layer atoms of a crystal. The internal energy of bulk and the surface atoms of lithium (110) have been evaluated from 22 K up to above the melting transition, applying the Debye model to the thermal broadening of the respective 1s photoemission lines. Our measurements clearly reveal two phase changes: the known liquid to solid transition and the surface melting, occurring 50 K below the bulk melting point.

An X-ray beam of 3 x 10(7) photons s(-1) with 2 x 10(8) relative energy resolution has been obtained at a third-generation synchrotron undulator X-ray source using the (13 13 13) Bragg reflection from a silicon perfect crystal. The production of these 25.70 keV X-rays with 450 +/- 50 mueV bandpass opens up new possibilities in X-ray optics and spectroscopies.