Leonardo Baptista

Formation routes of interstellar glycine involving carboxylic acids: possible favoritism between gas and solid phase.

Despite the extensive search for glycine (NH₂CH₂COOH) and other amino acids in molecular clouds associated with star-forming regions, only upper limits have been derived from radio observations. Nevertheless, two of glycines precursors, formic acid and acetic acid, have been abundantly detected. Although both precursors may lead to glycine formation, the efficiency of reaction depends on their abundance and survival in the presence of a radiation field. These facts could promote some favoritism in the reaction pathways in the gas phase and solid phase (ice). Glycine and these two simplest carboxylic acids are found in many meteorites. Recently, glycine was also observed in cometary samples returned by the Stardust space probe. The goal of this work was to perform theoretical calculations for several interstellar reactions involving the simplest carboxylic acids as well as the carboxyl radical (COOH) in both gas and solid (ice) phase to understand which reactions could be the most favorable to produce glycine in interstellar regions fully illuminated by soft X-rays and UV, such as star-forming regions. The calculations were performed at four different levels for the gas phase (B3LYP/6-31G*, B3LYP/6-31++G**, MP2/6-31G*, and MP2/6-31++G**) and at MP2/6-31++G** level for the solid phase (ice). The current two-body reactions (thermochemical calculation) were combined with previous experimental data on the photodissociation of carboxylic acids to promote possible favoritism for glycine formation in the scenario involving formic and acetic acid in both gas and solid phase. Given that formic acid is destroyed more in the gas phase by soft X-rays than acetic acid is, we suggest that in the gas phase the most favorable reactions are acetic acid with NH or NH₂OH. Another possible reaction involves NH₂CH₂ and COOH, one of the most-produced radicals from the photodissociation of acetic acid. In the solid phase, we suggest that the reactions of formic acid with NH₂CH or NH₂CH₂OH are the most favorable from the thermochemical point of view.

Kinetics and thermodynamics of limonene ozonolysis.

Using density functional methods, the initial reaction steps of limonene ozonolysis have been investigated with a focus on primary ozonide formation and its decomposition to Criegee intermediates and carbonyl compounds. The ozonide formation is highly exothermic, and the decomposition channels have similar free energies of activation, ΔG(‡), indicating that there is no primary pathway for ozonide decomposition. Assuming that ozonide formation is the rate limiting step, the theoretical rate coefficient, k = 1.6 × 10(-16) molecule(-1) cm(3) s(-1), evaluated at the CCSD(T)/6-31G(d,p)//BHandHLYP/cc-pvdz level and 298.15 K for d-limonene is in good agreement with the experimental value, k(exp) = 3.3 × 10(-16) molecule(-1) cm(3) s(-1). The theoretical Arrhenius expression is also in good agreement with experimental results.

Theoretical Investigation on the Stability of Negatively Charged Formic Acid Clusters

Recent experimental results on negatively charged formic acid clusters generated by the impact of (252)Cf fission fragments on icy formic acid target are compared to quantum mechanical calculations. Structures for the clusters series, (HCOOH)nOH(-), where 2 < or = n < or = 4, are proposed based on ab initio electronic structure methods. The results show that cluster growth does not have a regular pattern of nucleation. A stability analysis was performed considering the commonly defined stability function. Temporal behavior of the clusters was evaluated by Born-Oppenheimer molecular dynamics to check the mechanism that provides cluster stability. The evaluated temporal profiles indicate the importance of hydrogen atom migration between the formic acid moieties in maintaining the stability of the structures and the water formation due to hydrogen abstraction by the hydroxyl approach.

Theoretical Investigation on the Stability of Ionic Formic Acid Clusters

Recent experimental results on positive charged formic acid clusters generated by the impact of (252)Cf fission fragments (FF) on icy formic acid target are examined in this paper by quantum mechanical calculations. Structures for the clusters series, (HCOOH)(n)H(+) and (HCOOH)(n)H(3)O(+), where 2 < or = n < or = 4, are proposed based on ab initio electronic structure methods. Results show that cluster growth does not present a regular pattern of nucleation. A stability analysis was performed considering the commonly defined stability function, where E is the total electronic energy plus the zero point vibrational energy correction, including the BSSE correction. The stability analysis leads to a picture that is compatible with experimental observations, indicating a decay of the stability with the increase of cluster mass. Temporal behavior of the clusters was evaluated by Born-Oppenheimer molecular dynamics to check the mechanism that provides cluster stability. The evaluated temporal profiles indicate the importance of hydrogen atom migration between the formic acid moieties to maintain the stability of the structures.

Carbonyl oxides reactions from geraniol-trans-(3,7-dimethylocta-2,6-dien-1-ol), 6-methyl-5-hepten-2-one, and 6-hydroxy-4-methyl-4-hexenal ozonolysis: kinetics and mechanisms.

A density functional theory (DFT) study of the mechanisms of carbonyl oxide reactions from geraniol-trans, 6-methyl-5-hepten-2-one, and 6-hydroxy-4-methyl-4-hexenal ozonolysis is presented. The geometries, energies, and harmonic vibrational frequencies of each stationary point were determined by B3LYP/6-31(d,p) and BH&HLYP/cc-pVDZ methods. According to the calculations, the ozonolysis reactions are initiated by the formation of van der Waals (VDW) complexes to yield primary ozonides, which rapidly open to carbonyl oxide compounds. These carbonyl oxide compounds react to form dioxanes and hydroperoxides. The hydroperoxides react by isomerization to form stable products. Glyoxal and methyl-glyoxal have been identified as the final product from geraniol-trans, 6-methyl-5-hepten-2-one, and 6-hydroxy-4-methyl-4-hexenal ozonolysis. Our results are in good agreement with the experimental studies.

The furan microsolvation blind challenge for quantum chemical methods: First steps

Herein we present the results of a blind challenge to quantum chemical methods in the calculation of dimerization preferences in the low temperature gas phase. The target of study was the first step of the microsolvation of furan, 2-methylfuran and 2,5-dimethylfuran with methanol. The dimers were investigated through IR spectroscopy of a supersonic jet expansion. From the measured bands, it was possible to identify a persistent hydrogen bonding OH-O motif in the predominant species. From the presence of another band, which can be attributed to an OH-π interaction, we were able to assert that the energy gap between the two types of dimers should be less than or close to 1 kJ/mol across the series. These values served as a first evaluation ruler for the 12 entries featured in the challenge. A tentative stricter evaluation of the challenge results is also carried out, combining theoretical and experimental results in order to define a smaller error bar. The process was carried out in a double-blind fashion, with both theory and experimental groups unaware of the results on the other side, with the exception of the 2,5-dimethylfuran system which was featured in an earlier publication.

Theoretical and experimental investigation for SO3 production in SO2-rich astrophysical environments

This work presents the results for the irradiation of pure SO2 sample that was condensed in a preevacuated chamber, from Laboratorio de Astroquimica e Astrobiologia (LASA/UNIVAP), at low temperature (12 K) and irradiated by ionizing photons which simulate Solar photons in the vacuum ultraviolet (VUV) and soft X-rays range. The infrared spectra of irradiated sample have presented the formation of SO3. Experimental formation cross section was determined. Theoretical investigations were performed at Second-order Moller- Plesset perturbation theory (MP2) level and indicate the most likely SO3 formation channels vary with the reaction supporting medium.

Solvation of barium atoms and singly charged cations in acetonitrile clusters

The size distributions of neutral and cationic Ba x (CH3CN) n (x = 0, +1; n ≤ 7) clusters, as produced by a standard laser vaporization-supersonic expansion pick-up source, were determined from molecular beam experiments. The size distribution for cations is in the range of n = 1-7, whereas only the n = 1 complex is observed for neutral clusters, and these two features are unaffected by the variables controlling the performance of the cluster source. The distinct behavior is compatible with the expected charge-dipole interactions in the ionic species, which are stronger than the dipole induced-dipole interactions at play in neutral clusters, and it is corroborated by the relative magnitude of the theoretical successive binding energies (SBEs) for the lowest-lying isomers of cationic and neutral clusters with n = 1-5, as computed at the density functional theory level. The theoretical results also allow for the rationalization of the bimodal Ba+(CH3CN)1-7 size distribution, featuring an apparent minimum at n = 3, in terms of chiefly 6s-5d σ hybridization of the Ba+ ions, which ultimately leads to a relatively small third SBE for the Ba+(CH3CN)3 complex, as compared to those for n = 1, 2, and 4. Additional Born-Oppenheimer molecular dynamics simulations on the Ba+(CH3CN)2-4 clusters suggest that all of the ligands are coordinated to the Ba+ ion and prevent considering completion of the first solvent shell as responsible for the bimodal size distribution.

Interaction of polyelectrolyte complex between sodium alginate and chitosan dimers with a single glyphosate molecule: A DFT and NBO study

The formation of a polyelectrolyte complex through dimers of alginate and chitosan in the presence of sodium cations (SA/CS), and its interaction with the glyphosate herbicide, has been investigated at the DFT level (B3LYP/6‒311+G(d,p)). The lowest energy structure for SA/CS presents one Na+ cation coordinated to both dimers and formation of two H-bonds involving COO- and NH3+. The coordination energy of Na+ contributes with about 40% of the total complex stabilization energy. LMOEDA method indicates important contribution of covalent nature to stabilization of SA/CS. This result is corroborated by NBO analysis which shows high contribution of lp(O)→σ*(NH) overlapping, with average energy of 30 kcal mol-1 for the formed H-bonds. Two water molecules neighboring the complex increases its stability and promotes an octahedral coordination arrangement around Na+. The glyphosate interacts with SA/CS coordinating to Na+ and bonding to the chitosan dimer by H-bond, in agreement to performed fluorescence microscopy measurements.

Theoretical study of the addition of OH radicals to trans-geraniol-(3,7-dimethylocta-2,6-dien-1-ol), 6-methyl-5-hepten-2-one, and 6-hydroxy-4-methyl-4-hexenal.

A combined density functional theory and transition state theory study of the gas-phase addition of OH to 3,7-dimethylocta-2,6-dien-1-ol (trans-geraniol), 6-methyl-5-hepten-2-one, and 6-hydroxy-4-methyl-4-hexenal is presented. In this study, all different possibilities for the addition of the OH radical to the C-C double bonds in trans-geraniol, 6-methyl-5-hepten-2-one, and 6-hydroxy-4-methyl-4-hexenal were considered. The geometries, energies, and harmonic vibrational frequencies at each stationary point were determined at the MPW1K/cc-pVDZ and BH&HLYP/cc-pVDZ levels. Global rate coefficients of 0.94 x 10(-10) and 3.1 x 10(-10) cm(3) molecule(-1) s(-1), 2.11 x 10(-11) and 7.53 x 10(-11) cm(3) molecule(-1) s(-1), and 2.70 x 10(-13), and 4.37 x 10(-12) cm(3) molecule(-1) s(-1) were calculated using data obtained at the BH&HLYP/cc-pVDZ and MPW1K/cc-pVDZ levels of theory. These coefficients correspond to the sum of the rate coefficients of the individual paths for trans-geraniol, 6-hydroxy-4-methyl-4-hexenal, and 6-methyl-5-hepten-2-one, when reacting with OH radicals. The calculated rate coefficients are in good agreement with the available experimental data.