Stacking of purines in water: the role of dipolar interactions in caffeine.

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.

Free electron laser-driven ultrafast rearrangement of the electronic structure in Ti.

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.

Reflectivity enhancement in titanium by ultrafast XUV irradiation.

The study of highly photo-excited matter at solid state density is an emerging field of research, which is benefitting the development of free-electron-laser (FEL) technology. We report an extreme ultraviolet (XUV) reflectivity experiment from a titanium (Ti) sample irradiated with ultrafast seeded FEL pulses at variable incident photon fluence and frequency. Using a Drude formalism we relate the observed increase in reflectivity as a function of the excitation fluence to an increase in the plasma frequency, which allows us to estimate the free electron density in the excited sample. The extreme simplicity of the experimental setup makes the present approach potentially a valuable complementary tool to determine the average ionization state of the excited sample, information of primary relevance for understanding the physics of matter under extreme conditions.

The single particle dynamics of iodine in the Sachs-Teller regime: an inelastic x-ray scattering study.

The high frequency dynamics of liquid iodine has been investigated by deep inelastic x-ray scattering at exchanged wave-vectors (q) ranging from 2.5 to 15 Å(-1). The experimental data have been analyzed in the frame of the Sachs-Teller theory of the molecular spectrum while accounting for final state corrections to the lineshape. The performed data analysis carries insights on physical quantities as relevant as the mean rototranslational kinetic energy and the mean square Laplacian of the intermolecular potential. In both cases the measured values are consistent with corresponding theoretical expectations.

Concentration-temperature dependencies of structural relaxation time in trehalose-water solutions by brillouin inelastic UV scattering.

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

Evidence for a crossover in the frequency dependence of the acoustic attenuation in vitreous silica.

We report measurements of the sound attenuation coefficient in vitreous silica, for sound waves of wavelength between 50 and 80 nm, performed with the new inelastic UV light scattering technique. These data indicate that in silica glass a crossover between a temperature-dependent (at low frequency) and a temperature-independent (at high frequency) acoustic attenuation mechanism occurs at Q approximately equal to 0.15 nm(-1). The absence of any signature in the static structure factor at this Q value suggests that the observed crossover should be associated with local elastic constant fluctuations.

Structural relaxation in liquid water by inelastic UV scattering.

Using the novel synchrotron radiation based inelastic ultraviolet scattering technique, the dynamic structure factor of normal and supercooled liquid water has been measured at a momentum transfer Q approximately equal to 0.1 nm(-1), in the temperature range 260-340 K. The structural (alpha) relaxation has been observed in the supercooled temperature region (T< or =273 K), where the inverse relaxation time matches the frequency of the probed sound modes. The T dependence of the relaxation time shows a diverging behavior with a critical temperature T approximately equal to 220 K. These results provide a unique experimental opportunity to frame the dynamics of water in the mode-coupling theory.

Inelastic ultraviolet scattering from high frequency acoustic modes in glasses.

The dynamic structure factor of vitreous silica and glycerol has been measured as a function of temperature and of the momentum transfer up to Q=0.105 nm(-1) using a novel experimental technique, the inelastic ultraviolet scattering. As in the case of Brillouin light scattering and ultrasonic measurements, the temperature dependence of the acoustic attenuation shows a plateau below the glass transition whose amplitude scales as Q2. Moreover, a slight temperature dependence of attenuation has been found in vitreous silica at about 130 K, which seems to be reminiscent of the peak measured at lower Qs. These two findings strongly support the idea that anharmonicity is responsible for sound attenuation at ultrasonic and hypersonic frequencies. Finally, we demonstrate that the attenuation mechanism should show a change of regime between 0.105 and 1 nm(-1).

X-ray micro-diffraction analysis of reconstructed bone at Zr prosthetic surface with sub-micrometre spatial resolution.

The purpose of the present investigation is to demonstrate the power of the x-ray micro-diffraction technique in biological studies. In particular the reported experiment concerns the study of the interface between a Zr prosthetic device implanted in a rat femur and the newly-formed bone, with a spatial resolution of 0.5 microm. The obtained results give interesting information on the Zr deformation and on the crystallographic phase, the grain size and the orientation of the new bone. Moreover the study reveals a marked difference in the structure of the reconstructed bone with respect to the native bone, which cannot be appreciated with other techniques.

Non-destructive determination of local strain with 100-nanometre spatial resolution

Structure sizes of approximately 180 nm are now standard in microelectronics, and state-of-the-art fabrication techniques can reduce these to just a few tens of nanometres. But at these length scales, the strain induced at interfaces can locally distort the crystal lattice, which may in turn affect device performance in an unpredictable way. A means of non-destructively characterizing such strain fields with high spatial resolution and sensitivity is therefore highly desirable. One approach is to use Raman spectroscopy, but this is limited by the intrinsic approximately 0.5-microm resolution limit of visible light probes. Techniques based on electron-beam diffraction can achieve the desired nanometre-scale resolution. But either they require complex sample preparation procedures (which may alter the original strain field) or they are sensitive to distortional (but not dilational) strain within only the top few tens of nanometres of the sample surface. X-rays, on the other hand, have a much greater penetration depth, but have not hitherto achieved strain analysis with sub-micrometre resolution. Here we describe a magnifying diffraction imaging procedure for X-rays which achieves a spatial resolution of 100nm in one dimension and a sensitivity of 10(-4) for relative lattice variations. We demonstrate the suitability of this procedure for strain analysis by measuring the strain depth profiles beneath oxidized lines on silicon crystals.

Soft-x-ray polarimeter with multilayer optics: complete analysis of the polarization state of light.

The design of a versatile high-precision eight-axis ultrahigh-vacuum-compatible polarimeter is presented. This multipurpose instrument can be used as a self-calibrating polarization detector for linearly and circularly polarized UV and soft-x-ray light. It can also be used for the characterization of reflection or transmission properties (reflectometer) or polarizing and phase-retarding properties (ellipsometer) of any optical element. The polarization properties of Mo/Si, Cr/C, Cr/Sc, and Ni/Ti multilayers used in this polarimeter as polarizers in transmission and as analyzers in reflection have been investigated theoretically and experimentally. In the soft-x-ray range, close to the p edges of Sc, Ti, and Cr, resonantly enhanced phase retardation of the transmission polarizers of as much as 18 degrees has been measured. With these newly developed optical elements the complete polarization analysis of soft-x-ray synchrotron radiation can be extended to the water-window range from 300 to 600 eV.

Submicrometre resolution phase-contrast radiography with the beam from an X-ray waveguide.

Experimental data with unprecedented submicrometre resolution obtained in a phase-contrast radiography experiment in a magnifying configuration are presented. The term 'phase contrast' here indicates that the phase retardation of coherent light in matter was utilized as the contrast mechanism. The coherent and divergent beam exiting an X-ray waveguide was used in a lensless configuration to magnify spatial variations in optical path length up to several hundred times. The defocused image of a nylon fibre was measured with a resolution of 0.14 micro m at the object. Sufficient contrast was found for exposure times of 0.1 s, i.e. in the regime for real-time studies.

Submicrometre beams from a hard X-ray waveguide at a third-generation synchrotron radiation source.

The use of an X-ray waveguide for scattering experiments at an undulator of a third-generation synchrotron radiation source is discussed. The performance with a perfect crystal monochromator, multilayer monochromator and focusing mirror is explored. A maximum flux of 8 x 109 photons s(-1) at lambda = 0.083 nm was obtained for a 0.15 (V) x 600 (H) micron(2) beam at the exit of the waveguide with a multilayer monochromator. The combination of an Si (111) monochromator and ellipsoidal mirror resulted in a flux of approximately 10(9) photons s(-1) but with a horizontal compression of the beam to approximately 30 micron. The use of the waveguide in diffraction experiments is addressed.

Characterization of sputtered nickel/carbon multilayers with soft-x-ray reflectivity measurements.

Several sputtered Ni/C multilayer mirrors with periods between 3.8 and 6.0 nm were investigated with the HASYLAB reflectometer to determine the peak reflectivity and the internal structure of the multilayers. The enhanced reflectivity in the Bragg maximum, especially below 284 eV (carbon K edge), is interesting for practical applications. For both materials (Ni and C), the optical constants were previously obtained from angular-dependent reflectivity measurements. The layer thicknesses, interface roughnesses, and mean thickness errors of multilayer mirrors are obtained from least-squares fits of theoretical reflectivity curves. A model is presented to describe the influence of interface roughness on other parameters obtained from the analysis. All Ni/C multilayers, with Ar as the sputter gas, were produced in the low-pressure triode-assisted sputtering facility of Sincrotrone Trieste.

Optical constants of float glass, nickel, and carbon from soft-x-ray reflectivity measurements.

Angular-dependent reflectivity was measured with a dynamic range of 5-6 orders of magnitude at ~20 different photon energies in the range from 40 to 800 eV with the HASYLAB reflectometer with synchrotron radiation. Several float-glass substrates and a number of sputtered Ni and C films were investigated to improve the accuracy. The optical constants were obtained from least-squares fits of theoretical reflectivity curves, taking into account the influence of film thicknesses and surface and interface roughnesses. All samples with Ni and C films were produced on float-glass substrates, with Ar as the sputter gas, in the low-pressure triode-assisted sputtering facility of the Sincrotrone Trieste.

A new human hemoglobin variant: Hb BARI (alpha 2 45 (CD3) His leads to Gln beta 2).

An alpha-chain variant hemoglobin was found in the hemolysate of a 21-year-old healthy male living in Bari (Puglia, Italy). Structural studies demonstrated a previously unreported amino acid substitution, alpha 2 45 (CD3) His leads to Gln beta 2, involving a distal heme contact. The new variant has been named Hb Bari. Its electrophoretic behavior was the same as for Hb A; it was stable to both isopropanol and heat denaturation and exhibited normal functional properties, with respect to whole blood and stripped hemolysate studies. The level of Hb Bari was about 20% in the observed carrier. No relative was available for further investigations.