Ana R. Garcia

The Infrared Spectrum of Solid L-Alanine : Influence of pH-Induced Structural Changes

The influence of the pH on the infrared spectrum of L-alanine has been analyzed by diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy. The amino acid was precipitated from aqueous solutions and dried at 36.5 degrees C, in order to stabilize cationic L-alanine or alaninium [CH3CH(NH3(+))COOH] at pH 1, the zwitterionic form [CH3CH(NH3(+))COO(-)] at pH 6, and anionic L-alanine or alaninate [CH3CH(NH2)COO(-)] at pH 13. New insight on the specific inter and intramolecular interactions in the different forms of L-alanine was reached by a novel methodological approach: an infrared technique not used before to analyze solid amino acid samples (DRIFTS), in combination with a detailed analysis based on spectral deconvolution. The frequency ranges of interest include the carbonyl/carboxyl stretching and amine deformation modes and the OH/NH stretching modes. It was shown that intermolecular hydrogen bonds between the NH3(+) and COO(-) groups are predominant in the zwitterionic form, whereas in cationic L-alanine, H bonds between the COOH groups are responsible for the formation of dimers. In anionic L-alanine, only strong electrostatic interactions between the COO(-) groups and Na(+) ions are proposed, evidencing the relevant role of the counterion.

Volumetric Properties and Spectroscopic Studies of Pyridine or Nicotine Solutions in Liquid Polyethylene Glycols

Densities and molar excess volumes of the solutions of pyridine or nicotine in liquid polyethylene glycol, PEG200 and PEG400, have been determined at several temperatures. The experimental molar excess volumes are negative, thus indicating strong attractive interactions between the components, as could be expected considering their highly polar nature and good hydrogen bond abilities. For the pyridine systems, this negativity is slightly increased as the temperature rises, while the opposite tendency is observed for the nicotine mixtures. When pyridine and nicotine solutions are compared, the former-particularly those with PEG400-exhibit substantially more negative molar excess volumes than the latter. The effect of the polymer chain length on the results for the nicotine solutions is almost negligible. However, this is not the case when pyridine is one of the components: a longer chain induced considerably higher compression on mixing. The Fourier-transform infrared analysis allowed interpretation of the negative experimental molar excess volumes in terms of specific inter- and intramolecular interactions.

Microplastics effects in Scrobicularia plana

One of the most common plastics in the marine environment is polystyrene (PS) that can be broken down to micro sized particles. Marine organisms are vulnerable to the exposure to microplastics. This study assesses the effects of PS microplastics in tissues of the clam Scrobicularia plana. Clams were exposed to 1mgL-1 (20μm) for 14days, followed by 7days of depuration. A qualitative analysis by infrared spectroscopy in diffuse reflectance mode period detected the presence of microplastics in clam tissues upon exposure, which were not eliminated after depuration. The effects of microplastics were assessed by a battery of biomarkers and results revealed that microplastics induce effects on antioxidant capacity, DNA damage, neurotoxicity and oxidative damage. S. plana is a significant target to assess the environmental risk of PS microplastics.

Phase behaviour of oleanolic acid, pure and mixed with stearic acid: Interactions and crystallinity.

The phase behaviour of pure oleanolic acid (OLA) and in mixtures with stearic acid (SA) was characterized by differential scanning calorimetry (DSC), X-ray powder diffraction (XRD), diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) and nuclear magnetic resonance (NMR). The crystalline OLA as received (OLA(ar)) becomes amorphous after being dissolved in chloroform and vacuum-dried at 50 degrees C (OLA(50)). Upon heating, both forms transform to the needle shape crystalline form (OLA(220)). Dimerization through H-bonding between COOH groups was detected both in OLA(ar) and OLA(220). Dimers are stronger in OLA(220), where H-bonding also involves the alcohol groups and plays a role in the crystalline organization. A eutectic type phase diagram was established for mixtures, with the eutectic composition close to pure SA. Mixtures rich in SA are miscible in the liquid and in the amorphous solid states, where the presence of SA-OLA co-dimers, formed through H-bonding between carboxyl groups, was detected. Miscibility and SA crystallinity decrease drastically with the OLA content.

Liquid Mixtures Involving Hydrogenated and Fluorinated Alcohols: Thermodynamics, Spectroscopy, and Simulation.

This article reports a combined thermodynamic, spectroscopic, and computational study on the interactions and structure of binary mixtures of hydrogenated and fluorinated substances that simultaneously interact through strong hydrogen bonding. Four binary mixtures of hydrogenated and fluorinated alcohols have been studied, namely, (ethanol + 2,2,2-trifluoroethanol (TFE)), (ethanol + 2,2,3,3,4,4,4-heptafluoro-1-butanol), (1-butanol (BuOH) + TFE), and (BuOH + 2,2,3,3,4,4,4-heptafluoro-1-butanol). Excess molar volumes and vibrational spectra of all four binary mixtures have been measured as a function of composition at 298 K, and molecular dynamics simulations have been performed. The systems display a complex behavior when compared with mixtures of hydrogenated alcohols and mixtures of alkanes and perfluoroalkanes. The combined analysis of the results from different approaches indicates that this results from a balance between preferential hydrogen bonding between the hydrogenated and fluorinated alcohols and the unfavorable dispersion forces between the hydrogenated and fluorinated chains. As the chain length increases, the contribution of dispersion increases and overcomes the contribution of H-bonds. In terms of the liquid structure, the simulations suggest the possibility of segregation between the hydrogenated and fluorinated segments, a hypothesis corroborated by the spectroscopic results. Furthermore, a quantitative analysis of the infrared spectra reveals that the presence of fluorinated groups induces conformational changes in the hydrogenated chains from the usually preferred all-trans to more globular arrangements involving gauche conformations. Conformational rearrangements at the CCOH dihedral angle upon mixing are also disclosed by the spectra.

Encapsulation of ruthenium nitrosylnitrate and DNA purines in nanostructured sol-gel silica matrices.

The interactions between DNA purines (guanine and adenine) and the ruthenium complex Ru(NO)(NO(3))(3) were studied within nanostructured silica matrices prepared by a two-step sol-gel process. By infrared analysis in diffuse reflectance mode, it was proved that encapsulation induces a profound modification on the complex, whereas guanine and adenine preserve their structural integrity. The complex undergoes nitrate ligand exchange and co-condenses with the silica oligomers, but the nitrosyl groups remain stable, which is an unusual behavior in Ru nitrosyl complexes. In turn, the doping molecules affect the sol-gel reactions and eventually the silica structure as it forms: the complex yields a microporous structure, and the purine bases are responsible for the creation of macropores due to hydrogen bonding with the silanol groups of the matrix. In a confined environment, the interactions are much stronger for the coencapsulated pair guanine complex. While adenine only establishes hydrogen bonds or van der Waals interactions with the complex, guanine bonds covalently to Ru by one N atom of the imidazole ring, which becomes strongly perturbed, resulting in a deformation of the complex geometry.

The reactivity of Z-2-hexene on Ru(001) studied by RAIRS

The adsorption at low temperature and the thermal decomposition of Z-2-hexene on the clean Ru(0 0 1) surface, under ultra-high-vacuum, were studied by reflection-absorption infrared spectroscopy (RAIRS). A comparison with the reactivity of other linear hexene isomers was made. It was proposed that, at 90 K, Z-2-hexene adsorbs non-dissociatively as a di-σ complex, in a mixture of conformations. Apparently, gauche conformers with the methyl group in C6 standing vertically are favored for increasing coverage, but forming a poorly ordered layer. For an exposure of 0.6 Langmuir (L), there is evidence of a second layer, physically adsorbed, eventually resulting in the condensation of a randomly oriented multilayer above 1 L. The multilayer desorbs between 100 and 110 K. Only one decomposition mechanism was identified, either by annealing the low temperature di-σ complex to T⩾110 K or by direct adsorption at higher temperatures. It consists on the dehydrogenation of the carbons anchored to the surface, with rehybridization to ∼sp2, yielding 2-hexyne di-σ/π complex, and concomitant C–C bond breaking in the adjacent positions, yielding methylidyne (Ru3CH) and ethyne (C2H2) di-σ/π complex. The latter is stable on Ru(0 0 1) up to at least 320 K, but, in the presence of co-adsorbed hydrogen, it may hydrogenate to ethylidyne (Ru3CCH3), at 125 K. At this temperature, the third decomposition fragment (–C3H7) dehydrogenates and remains adsorbed as propylidyne (Ru3CCH2CH3). Above 170 K, decomposition of propylidyne to ethylidyne and further to methylidyne occurs, leaving methylidyne and ethyne di-σ/π complex as the only RAIRS identifiable products at 320 K.

The chemical behaviour of 3-hexene on the Ru(0001) surface: a characterisation by RAIRS

Abstract The chemical nature of Z-3-hexene/Ru(0001) bond at different temperatures was studied by reflection-absorption infrared spectroscopy (RAIRS). At 92 K and for low exposures (0.05 L) the results indicate that Z-3-hexene adsorbs non-dissociatively as a di-σ complex. By annealing to 123 K, it dehydrogenates at the Cα carbons (C3 and C4, bonded to the surface), forming a hexyne di-σ/π complex in a mixture of rotational conformers. Upon thermal activation, this complex decomposes by breaking the Cα–Cβ (i.e., C2–C3 and C4–C5) bonds, yielding adsorbed ethylidyne. At 223 K, only this species and residual di-σ/π complex are present on the surface. A different decomposition path is proposed upon direct adsorption of Z-3-hexene at 223 K, since propylidyne appears to be formed on the surface, which implies breaking the C–C double bond with dehydrogenation. Since the behaviour of Z-3-hexene is identical to that of 3-hexyne, and rather different from 1-hexene, these results suggest that the decomposition of unsaturated hydrocarbons on clean Ru(0001) is determined by the position and not by the nature (double or triple bond) of the functionality.

Decomposition of 2-hexyne on clean Ru(0 0 1) studied by RAIRS

The decomposition of 2-hexyne on clean Ru(0 0 1), under ultra-high-vacuum, was studied by reflection–absorption infrared spectroscopy (RAIRS). The spectra obtained at 100 K are compatible with the formation of a non-dissociative di-r=p complex. Evidence was obtained for two decomposition paths. By annealing the low temperature complex above 110 K, the weakened C–C bonds adjacent to the anchoratoms (C 1–C2 and C3–C4 bonds) break, eventually yielding methylidyne (RuBC–H) and ethylidyne (RuBC–CH3), at 220 K. By direct adsorption of 2-hexyne at 130 K or higher temperatures, the C–C triple bond is the first to break, ethylidyne being the major surface species identified by RAIRS. These results are compared to those obtained for 1- and 3-hexyne isomers. 2003 Elsevier Science B.V. All rights reserved.

Interactions between DNA Purines and Ruthenium Ammine Complexes within Nanostructured Sol−Gel Silica Matrixes

The interactions between DNA purines (guanine and adenine) and three ruthenium ammine complexes (hexaammineruthenium(III) chloride, hexaammineruthenium(II) chloride, and ruthenium-red) were studied in a confined environment, within sol-gel silica matrixes. Two encapsulation methods were rehearsed (differing in temperature and condensation pH), in order to analyze the effects of the sol-gel processes on the purines and on the Ru complexes separately. The extent of decomposition of the Ru complexes, as well as the interactions established with the purine bases, proved to be determined by the coencapsulation method. Combined results by diffuse reflectance UV-vis and infrared spectroscopies showed that, when coencapsulation is carried out at 60 degrees C, specific H bonding interactions are established between the amine group of Ade and the ammine groups of the Ru complex or the hydroxo group of an early decomposition product. These are responsible for the important role of the purine in inhibiting the oxidation reactions of the Ru(II) and Ru(III) complexes. In contrast, Gua establishes preferential H bonds with the matrix (mainly due to the carbonyl group), leading to higher yields in the final oxidation products of the Ru complexes, namely, trimers and dimers. Direct covalent bonding of either purine to the metal was not observed.