Safranin-O dye in the ground state. A study by density functional theory, Raman, SERS and infrared spectroscopy.

The analysis of ground state structural and vibrational properties of Safranin-O is presented. The experimental results, obtained by FTIR, Raman and SERS spectroscopy, are discussed in comparison to the results of DFT calculations carried out at the B3LYP/6-311+G(d,p) level of theory. The calculated spectra reproduce quite satisfactorily the experimental data. The calculated Safranin-O equilibrium structure and the assignment of the vibrational spectra are reported as well. From the changes between Raman and SERS spectra a model is presented for the interaction of Safranin-O with silver nanoparticles.

Binding energy determination in a π-stacked aromatic cluster: the anisole dimer.

The binding energies of the neutral and positively charged anisole dimer have been determined in molecular beam-laser spectroscopy experiments. This is the first report on the direct experimental determination of the binding energy for an aromatic cluster in π stacked configuration. The anisole dimer is formed by two anisole molecules superimposed in a planar arrangement and it has been proposed as a model system in which the π-stacking interaction, among other intermolecular forces, plays a relevant role. Its binding energy has been determined thanks to both velocity mapping ion/electron imaging experiments and previous spectroscopic information. The binding energy amounts to 3926(250) cm(-1) in the ground state and 4144(250) cm(-1) in the S2 (first spectroscopically accessible) electronic excited state; its value for the positively charged dimer ion increases to 6147(250) cm(-1). These values are quite higher with respect to the results of previous DFT calculations.

The gas phase anisole dimer: a combined high-resolution spectroscopy and computational study of a stacked molecular system.

The gas phase structures of anisole dimer in the ground and first singlet electronic excited states have been characterized by a combined experimental and computational study. The dimer, formed in a molecular beam, has been studied by resonance-enhanced multiphoton ionization and high-resolution laser-induced fluorescence techniques. The assignment of the rotational fine structure of the S(1) <-- S(0) electronic transition origin has provided important structural information on the parallel orientation of aromatic rings of anisole moieties. By comparison with the DFT/TD-DFT computational results, it has been possible to infer the detailed equilibrium structure of the complex. The analysis of the equilibrium structure and interaction energy confirms that the anisole dimer is stabilized by dispersive interaction in the gas phase. This is, to the best of our knowledge, the first detailed work (reporting both theoretical and high-resolution experimental data) on an isolated cluster in the pi-stacking configuration.

A new compact instrument for Raman, laser-induced breakdown, and laser-induced fluorescence spectroscopy of works of art and their constituent materials.

A small, potentially transportable prototype instrument capable of carrying out Raman, laser-induced breakdown (LIB), and laser-induced fluorescence (LIF) spectroscopy using a single pulsed laser source was developed for the analysis of cultural heritage objects. The purpose of this instrumentation is to perform fast and reliable analysis of surfaces with minimum damage to an object. For this purpose, a compact (51 x 203 x 76 mm) nanosecond Q-switched neodymium doped yttrium aluminum garnet laser (8 ns, 20 Hz, 0.01-115 mJ/pulse) was used as an irradiation source. The use of a nanosecond-gated detector sensitive between 180 and 900 nm allows the acquisition of elemental emissions in LIB spectroscopy and can also be employed for both LIF and time-resolved Raman spectroscopy. In this work, attention is focused on the description of the instrument and its optical components, and two examples of applications for the analysis of pigments and binding media used in works of art are presented.

Analysis of natural and artificial ultramarine blue pigments using laser induced breakdown and pulsed Raman spectroscopy, statistical analysis and light microscopy.

Pulsed laser induced breakdown spectroscopy (LIBS) and Raman spectroscopy were performed using a novel laboratory setup employing the same Nd:YAG laser emission at 532 nm for the analysis of five commercially available pigments collectively known as "ultramarine blue", a sodium silicate material of either mineral origin or an artificially produced glass. LIBS and Raman spectroscopy have provided information regarding the elemental and molecular composition of the samples; additionally, an analytical protocol for the differentiation between natural (lapis lazuli) and artificial ultramarine blue pigments is proposed. In particular LIBS analysis has allowed the discrimination between pigments on the basis of peaks ascribed to calcium. The presence of calcite in the natural blue pigments has been confirmed following Raman spectroscopy in specific areas of the samples, and micro-Raman and optical microscopy have further corroborated the presence of calcite inclusions in the samples of natural origin. Finally multivariate analysis of Laser induced breakdown spectra using principal component analysis (PCA) further enhanced the differentiation between natural and artificial ultramarine blue pigments.

A study on the anisole-water complex by molecular beam-electronic spectroscopy and molecular mechanics calculations.

An experimental and theoretical study is made on the anisole-water complex. It is the first van der Waals complex studied by high resolution electronic spectroscopy in which the water is seen acting as an acid. Vibronically and rotationally resolved electronic spectroscopy experiments and molecular mechanics calculations are used to elucidate the structure of the complex in the ground and first electronic excited state. Some internal dynamics in the system is revealed by high resolution spectroscopy.

Differential activity and structure of highly similar peroxidases. Spectroscopic, crystallographic, and enzymatic analyses of lignifying Arabidopsis thaliana peroxidase A2 and horseradish peroxidase A2.

Anionic Arabidopsis thaliana peroxidase ATP A2 was expressed in Escherichia coli and used as a model for the 95% identical commercially available horseradish peroxidase HRP A2. The crystal structure of ATP A2 at 1.45 A resolution at 100 K showed a water molecule only 2.1 A from heme iron [Ostergaard, L., et al. (2000) Plant Mol. Biol. 44, 231-243], whereas spectroscopic studies of HRP A2 in solution at room temperature [Feis, A., et al. (1998) J. Raman Spectrosc. 29, 933-938] showed five-coordinated heme iron, which is common in peroxidases. Presented here, the X-ray crystallographic, single-crystal, and solution resonance Raman studies at room temperature confirmed that the sixth coordination position of heme iron of ATP A2 is essentially vacant. Furthermore, electronic absorption and resonance Raman spectroscopy showed that the heme environments of recombinant ATP A2 and glycosylated plant HRP A2 are indistinguishable at neutral and alkaline pH, from room temperature to 12 K, and are highly flexible compared with other plant peroxidases. Ostergaard et al. (2000) also demonstrated that ATP A2 expression and lignin formation coincide in Arabidopsis tissues, and docking of lignin precursors into the substrate binding site of ATP A2 predicted that coniferyl and p-coumaryl alcohols were good substrates. In contrast, the additional methoxy group of the sinapyl moiety gave rise to steric hindrance, not only in A2 type peroxidases but also in all peroxidases. We confirm these predictions for ATP A2, HRP A2, and HRP C. The specific activity of ATP A2 was lower than that of HRP A2 (pH 4-8), although a steady-state study at pH 5 demonstrated very little difference in their rate constants for reaction with H2O2 (k1 = 1.0 microM(-1) x s(-1). The oxidation of coniferyl alcohol, ferulic, p-coumaric, and sinapic acids by HRP A2, and ATP A2, however, gave modest but significantly different k3 rate constants of 8.7 +/- 0.3, 4.0 +/- 0.2, 0.70 +/- 0.03, and 0.04 +/- 0.2 microM(-1) x s(-1) for HRP A2, respectively, and 4.6 +/- 0.2, 2.3 +/- 0.1, 0.25 +/- 0.01, and 0.01 +/- 0.004 microM(-1) x s(-1) for ATP A2, respectively. The structural origin of the differential reactivity is discussed in relation to glycosylation and amino acid substitutions. The results are of general importance to the use of homologous models and structure determination at low temperatures.

Peroxidase-benzhydroxamic acid complexes: spectroscopic evidence that a Fe-H2O distance of 2.6 A can correspond to hexa-coordinate high-spin heme.

Resonance Raman (RR) spectra have been obtained for single-crystal horseradish peroxidase isozyme C complexed with benzhydroxamic acid (BHA). The data are compared with those obtained in solution by both RR and electronic absorption spectroscopies at room and low (12-80 K) temperatures. Moreover, the analysis has been extended to Coprinus cinereus peroxidase complexed with BHA. The results obtained for the two complexes are very similar and are consistent with the presence of an aqua six-coordinate high-spin heme. Therefore it can be concluded that despite the rather long Fe-H2O distance of 2.6-2.7 A found by X-ray crystallography in both complexes, the distal water molecule can still coordinate to the heme iron.

Accuracy of remote sensing of water temperature by Raman spectroscopy.

We present an experimental study of the Raman spectrum of pure and synthetic seawater with respect to its salinity and temperature dependence. Experiments made in the laboratory with both cw and pulsed excitation yield information on the limits and applicability of the technique in actual experiments in the field. We have also performed an experimental analysis to determine the presence of stimulated Raman scattering and its influence on the temperature dependence of the spectrum.