Toward an Understanding of the Pressure Effect on the Intramolecular Vibrational Frequencies of Sulfur Hexafluoride.

The structural and vibrational properties of the molecular units of sulfur hexafluoride crystal as a function of pressure have been studied by the Extreme Pressure Polarizable Continuum Model (XP-PCM) method. Within the XP-PCM model, single molecule calculations allow a consistent interpretation of the experimental measurements when considering the effect of pressure on both the molecular structure and the vibrational normal modes. This peculiar aspect of XP-PCM provides a detailed description of the electronic origin of normal modes variations with pressure, via the curvature of the potential energy surface and via the anharmonicity of the normal modes. When applied to the vibrational properties of the sulfur hexafluoride crystal, the XP-PCM method reveals a hitherto unknown interpretation of the effects of the pressure on the vibrational normal modes of the molecular units of this crystal.

Red lakes from Leonardo's Last Supper and other Old Master Paintings: Micro-Raman spectroscopy of anthraquinone pigments in paint cross-sections.

The analysis of red particles in paint cross-sections from Leonardo da Vinci's Last Supper, Masolino da Panicale's wall painting Beheading of St. John the Baptist in Castiglione Olona, Tintoretto's The Discovery of the Body of Saint Mark and Paolo Veronese's Supper in the House of Simon has been carried out with micro-Raman measurements. Subtracted shifted Raman spectroscopy methods have been employed to resolve the signals in the presence of fluorescence. Taking advantage of the vibrational assignments based on recent ab initio calculations of aluminum-complexes of anthraquinones, the approach allowed the discriminate between anthraquinone dyes and lakes based on kermesic and carminic acids present in the studied samples for the first time without heavy sample treatment.

Insights on the Realgar Crystal Under Pressure from XP-PCM and Periodic Model Calculations.

The spectroscopic properties of As4S4 with pressure have been computed by the quantum mechanical XP-PCM method and by density functional theory periodic calculations. The comparison has allowed the interpretation of the available experimental data. By comparison of the two methods and with experiments, we show that the XP-PCM method is able to reproduce the same behavior of the periodic calculations with much lower computational cost allowing to be adopted as a first choice computational tool for a qualitative interpretation of molecular crystals properties under pressure.

XP-PCM Calculations of High Pressure Structural and Vibrational Properties of P4S3.

The structure and the vibrational properties of the P4S3 crystal at high pressures are discussed by application of the XP-PCM method. The vibrational assignment has been clarified. The structure and the electron distribution changes as a function of pressure are analyzed. The pressure effect on the vibrational frequencies is satisfactorily reproduced and discussed in terms of confinement and structure relaxation contributions.

SERS, XPS, and DFT Study of Adenine Adsorption on Silver and Gold Surfaces.

The adsorption of adenine on silver and gold surfaces has been investigated combining density functional theory calculations with surface-enhanced Raman scattering and angle-resolved X-ray photoelectron spectroscopy measurements, obtaining useful insight into the orientation and interaction of the nucleobase with the metal surfaces.

Raman and computational study of solvation and chemisorption of thiazole in silver hydrosol.

A SERS investigation combined with ab initio computational analysis involving Car-Parrinello molecular dynamics simulations and Density Functional Theory approach allows fundamental information to be obtained on the behaviour of thiazole in silver aqueous suspension where solvation and chemisorption processes competitively occur.

Wavelet Transform for Spectroscopic Analysis: Application to Diols in Water.

Wavelet transform has been used to correlate spectroscopic and structural properties from trajectories obtained by ab initio molecular dynamics simulations. This method has been applied to hydrogen bond dynamics of glycols in heavy water solutions, showing how the stretching frequency of the intramolecular O-H bond changes with the intermolecular hydrogen-bond distance. The resulting wavelet spectrograms have been interpreted according to H-bond strength and stability.

Nanostructured Ag platforms as biosensors of nucleobase chains.

Nanostructured Ag platforms have been obtained by simple chemical procedure and characterized by AFM (atomic force microscopy) measurements, for use in biosensing by means of SERS (surface-enhanced Raman scattering) spectroscopy. The SERS efficiency of these substrates has been verified by microRaman measurements on small RNA chains with different nucleobase content, showing sensitivity near attomole level. It is our opinion that these metal substrates may be widely used as appropriate sensors for detecting biomolecules in many applications concerning medical diagnostics, pharmacological research and nanomaterials technology.

High-pressure reactivity of clathrate hydrates by two-photon dissociation of water.

It is shown that photoinduced reactions are observed at room temperature and pressure of few tenths of gigapascal in clathrate hydrates of CO and of model hydrocarbons under mild irradiation at 350 nm with power in the 50-610 mW range. The reactions are triggered by highly reactive OH radicals produced by two-photon excitation of the lowest electronic excited state of water having dissociative character. The formation of CO(2) is observed in all the reactions involving carbonaceous clathrate hydrates, and direct or indirect evidence for the formation of molecular hydrogen is obtained. The CO(2) produced in the reactions can be sequestered as a clathrate hydrate whose stability range seems to extend to room temperature at pressures of 0.5-0.6 GPa. Although the N(2) hydrate is stable up to 0.9 GPa under irradiation, a partial cleavage of the N-N triple bond is produced once the hydrate decomposes at 0.1 GPa.

Nitromethane decomposition under high static pressure.

The room-temperature pressure-induced reaction of nitromethane has been studied by means of infrared spectroscopy in conjunction with ab initio molecular dynamics simulations. The evolution of the IR spectrum during the reaction has been monitored at 32.2 and 35.5 GPa performing the measurements in a diamond anvil cell. The simulations allowed the characterization of the onset of the high-pressure reaction, showing that its mechanism has a complex bimolecular character and involves the formation of the aci-ion of nitromethane. The growth of a three-dimensional disordered polymer has been evidenced both in the experiments and in the simulations. On decompression of the sample, after the reaction, a continuous evolution of the product is observed with a decomposition into smaller molecules. This behavior has been confirmed by the simulations and represents an important novelty in the scene of the known high-pressure reactions of molecular systems. The major reaction product on decompression is N-methylformamide, the smallest molecule containing the peptide bond. The high-pressure reaction of crystalline nitromethane under irradiation at 458 nm was also experimentally studied. The reaction threshold pressure is significantly lowered by the electronic excitation through two-photon absorption, and methanol, not detected in the purely pressure-induced reaction, is formed. The presence of ammonium carbonate is also observed.

High-pressure reactivity of model hydrocarbons driven by near-UV photodissociation of water.

The ambient temperature photoinduced reactivity of mixtures containing water and some of the simplest model hydrocarbons has been studied in a diamond anvil cell below 1 GPa. The near-UV 350 nm emission of an Ar ion laser has been employed to photodissociate water molecules through two-photon absorption processes. The hydroxyl radicals generated through this process are able to trigger a chemical reaction in the mixtures containing ethane and acetylene, which are otherwise stable under the same P-T-hnu conditions, whereas the contribution of water has no effect or is very limited in the case of the ethylene and propene mixtures, respectively. The reaction evolution and the reaction products were characterized by using FTIR spectroscopy. The formation of fluorescent products limits or prevents, as in the case of acetylene, the characterization by Raman spectroscopy. Particularly relevant is the in situ efficient sequestration of the CO(2) formed during the reaction, through the formation of a clathrate hydrate, in the mixtures where water is largely in excess.

Crystalline indole at high pressure: chemical stability, electronic, and vibrational properties.

Vibrational and electronic spectra of crystalline indole were measured up to 25.5 GPa at room temperature in a diamond anvil cell. In particular, Fourier transform infrared (FTIR) spectra in the mid-infrared region and two-photon excitation profiles and fluorescence spectra in the region of the HOMO-LUMO transitions were obtained. The analysis of the FTIR spectra revealed a large red-shift of the N-H stretching mode with increasing pressure, indicating the strengthening of the H-bond between the NH group and the pi electron density of nearest neighbor molecules. The frequencies of four vibronic bands belonging to the (1)L(a) and (1)L(b) systems were obtained as a function of pressure. Comparison with literature data shows that the crystal acts as a highly polar environment with regard to the position of the (1)L(b) origin and of the fluorescence maximum, which are largely red-shifted with respect to the gas phase or to solutions in apolar solvents. A large, and increasing with pressure, frequency difference between the (1)L(b) origin and the blue edge of the fluorescence spectrum suggests that the emitting state is (1)L(a), that is known to be more stabilized than (1)L(b) by dipolar relaxation. Crystalline indole was found to be very stable with respect to pressure-induced reactivity. Only traces of a reaction product, containing saturated C-H bonds, are detected after a full compression-decompression cycle. In addition, differently from many unsaturated compounds at high pressure, irradiation with light matching a two-photon absorption for a HOMO-LUMO transition has no enhancing effect on reactivity. The chemical stability of indole at high pressure is ascribed to the crystal structure, where nearest neighbor molecules, formig H-bonds, are not in a favorable position to react, while reaction between equivalent molecules, for which a superposition of the pi electron clouds would be possible, is hindered by H-bonded molecules. Consistently, no excimer emission was observed except at the cell opening at the end of the compression-decompression run. Extremely limited chemical reactivity and excimer formation likely occur at crystal defects, evidencing the strict connection between the two phenomena.

Solvation dynamics and adsorption on Ag hydrosols of oxazole: a Raman and computational study.

The interactions between oxazole and water or silver nanoparticles in aqueous dispersions have been studied with a computational approach based on ab initio molecular dynamics simulations, with the Car-Parrinello method, and density functional calculations in combination with Raman and surface enhanced Raman scattering (SERS) experiments. The solvation dynamics of oxazole in water allowed for the characterization of the hydrogen bond between water and solute, which has been shown to occur essentially through the nitrogen atom of the heterocyclic molecule. To mimic the solvation process or the adsorption on silver and interpreting the corresponding Raman and SERS spectra in aqueous solution or in Ag hydrosols, density functional calculations have been carried out on model systems made up by oxazole bound to water molecules or to positively charged silver clusters. Also, the chemisorption on Ag nanoparticles is found to occur by means of the nitrogen atom of oxazole interacting with the metal substrate.

High-pressure photodissociation of water as a tool for hydrogen synthesis and fundamental chemistry.

High-pressure methods have been demonstrated to be efficient in providing new routes for the synthesis of materials of technological interest. In several molecular compounds, the drastic pressure conditions required for spontaneous transformations have been lowered to the kilobar range by photoactivation of the reactions. At these pressures, the syntheses are accessible to large-volume applications and are of interest to bioscience, space, and environmental chemistry. Here, we show that the short-lived hydroxyl radicals, produced in the photodissociation of water molecules by near-UV radiation at room temperature and pressures of a few tenths of a gigapascal (GPa), can be successfully used to trigger chemical reactions in mixtures of water with carbon monoxide or nitrogen. The detection of molecular hydrogen among the reaction products is of particular relevance. Besides the implications in fundamental chemistry, the mild pressure and irradiation conditions, the efficiency of the process, and the nature of the reactant and product molecules suggest applications in synthesis.

Anharmonic infrared and Raman spectra in Car-Parrinello molecular dynamics simulations.

The infrared and Raman spectra of naphthalene crystal with inclusion of anharmonic effects have been calculated by adopting the generalized variational density functional perturbation theory in the framework of Car-Parrinello molecular dynamics simulations. The computational approach has been generalized for cells of arbitrary shape. The intermolecular interactions have been analyzed with and without the van der Waals corrections, showing the importance of such interactions in the naphthalene crystal to reproduce the structural, dynamical, and spectroscopic properties.

Role of excited electronic states in the high-pressure amorphization of benzene.

High-pressure methods are increasingly used to produce new dense materials with unusual properties. Increasing efforts to understand the reaction mechanisms at the microscopic level, to set up and optimize synthetic approaches, are currently directed at carbon-based solids. A fundamental, but still unsolved, question concerns how the electronic excited states are involved in the high-pressure reactivity of molecular systems. Technical difficulties in such experiments include small sample dimensions and possible damage to the sample as a result of the absorption of intense laser fields. These experimental challenges make the direct characterization of the electronic properties as a function of pressure by linear and nonlinear optical spectroscopies up to several GPa a hard task. We report here the measurement of two-photon excitation spectra in a molecular crystal under pressure, up to 12 GPa in benzene, the archetypal aromatic system. Comparison between the pressure shift of the exciton line and the monomer fluorescence provides evidence for different compressibilities of the ground and first excited states. The formation of structural excimers occurs with increasing pressure involving molecules on equivalent crystal sites that are favorably arranged in a parallel configuration. These species represent the nucleation sites for the transformation of benzene into amorphous hydrogenated carbon. The present results provide a unified picture of the chemical reactivity of benzene at high pressure.

Thermodynamics of stacking interactions in proteins.

Using a database of 6166 experimental structures taken from the Protein Data Bank, we have studied pair interactions between planar residues (Phe, Tyr, His, Arg, Glu and Asp) in proteins, known as pi-pi interactions. On the basis of appropriate coordinates defining the mutual arrangement of two residues, we have calculated 2-D potentials of mean force aimed at determining the stability of the most probable structures for aromatic-aromatic, aromatic-cation and aromatic-anion bound pairs. Our analysis reveals the thermodynamic relevance and the ubiquity of stacked complexes in proteins.

Crystal structure of nitromethane up to the reaction threshold pressure.

Angle dispersion X-ray diffraction (AXDX) experiments on nitromethane single crystals and powder were performed at room temperature as a function of pressure up to 19.0 and 27.3 GPa, respectively, in a membrane diamond anvil cell (MDAC). The atomic positions were refined at 1.1, 3.2, 7.6, 11.0, and 15.0 GPa using the single-crystal data, while the equation of state (EOS) was extended up to 27.3 GPa, which is close to the nitromethane decomposition threshold pressure at room temperature in static conditions. The crystal structure was found to be orthorhombic, space group P2(1)2(1)2(1), with four molecules per unit cell, up to the highest pressure. In contrast, the molecular geometry undergoes an important change consisting of a gradual blocking of the methyl group libration about the C-N bond axis, starting just above the melting pressure and completed only between 7.6 and 11.0 GPa. Above this pressure, the orientation of the methyl group is quasi-eclipsed with respect to the NO bonds. This conformation allows the buildup of networks of strong intermolecular O...H-C interactions mainly in the bc and ac planes, stabilizing the crystal structure. This structural evolution determines important modifications in the IR and Raman spectra, occurring around 10 GPa. Present measurements of the Raman and IR vibrational spectra as a function of pressure at different temperatures evidence the existence of a kinetic barrier for this internal rearrangement.

Ab Initio Molecular Dynamics Study of Mg(2+) and Ca(2+) Ions in Liquid Methanol.

Ab initio Car-Parrinello molecular dynamics simulations have been performed in order to investigate the solvation properties of Mg(2+) and Ca(2+) in fully deuterated methanol solution to better understand polarization effects induced by the ions. Charge transfer and dipole moment calculations have been performed to give more detailed insight on the role of the electronic reorganization and its effect on the first solvation shell stability. The perturbation of the methanol H-bond network has been investigated.

Mechanism of the Ethylene Polymerization at Very High Pressure.

The reaction of ethylene in condensed phases under high pressure has been investigated by ab initio molecular dynamics. Both disordered and crystalline samples have been simulated, and some insights on the reaction mechanism have been obtained. System size effects have been investigated for the disordered samples. A polymerization reaction occurs by an ionic mechanism. In both the disordered and the crystal phases, the reaction products obtained (linear chains in the disordered systems and branched chains in the crystal) are in qualitative agreement with the experiments.