Huyen Thi Nguyen

Radical Pathways for the Prebiotic Formation of Pyrimidine Bases from Formamide

The prebiotic formation of nucleobases, the building blocks of RNA/DNA, is of current interest. Highly reactive radical species present in the atmosphere under irradiation have been suggested to be involved in the prebiotic synthesis of nucleobases from formamide (FM). We studied several free radical reaction pathways for the synthesis of pyrimidine bases (cytosine, uracil, and thymine) from FM under cold conditions. These pathways are theoretically determined using density functional theory (DFT) computations to examine their kinetic and thermodynamic feasibilities. These free radical reaction pathways share some common reaction types such as H-rearrangement, (•)H/(•)OH/(•)NH2 radical loss, and intramolecular radical cyclization. The rate-determining steps in these pathways are characterized with low energy barriers. The energy barriers of the ring formation steps are in the range of 3-7 kcal/mol. Although DFT methods are known to significantly underestimate the barriers for addition of (•)H radical to neutral species, many of these reactions are highly exergonic with energy release of -15 to -52 kcal/mol and are thus favorable. Among the suggested pathways for formation of cytosine (main route, routes 7a and 1a), uracil (main route, routes 7b and 1b), and thymine (main route and route 26a), the main routes are in general thermodynamically more exergonic and more kinetically favored than other alternative routes with lower overall energy barriers. The reaction energies released following formation of cytosine, uracil, and thymine from FM via the main radical routes amount to -59, -81, and -104 kcal/mol, respectively. Increasing temperature induces unfavorable changes in both kinetic and thermodynamic aspects of the suggested routes. However, the main routes are still more favored than the alternative pathways at the temperature up to the boiling point of FM.

Effects of Sulfur-Deficient Defect and Water on Rearrangements of Formamide on Pyrite (100) Surface

The efficient formation of HCN/HNC from formamide (FM) combining the advantages of water-assistance, self-catalyzed reactions, and the mineral surfaces was investigated. Periodic density functional theory calculations with plane-wave pseudopotential basis sets were performed to study the interaction of FM with pyrite (100) ideal and defect surfaces. Effects of sulfur vacancy defect and water on tautomerization and rearrangement barriers of FM on the (100) surface were evaluated. Calculated results show that FM adsorbs more strongly on the defect surface than on the ideal surface, with the lowest adsorption energy on the defect surface being -22 kcal/mol. The energy barriers for rearrangements of FM on these two surfaces being close to each other suggests that the adsorptions on the surfaces have small effects on the energy barriers. The energy barriers for formimic acid isomer formations are 44.5 and 46.0 kcal/mol, and those of aminohydroxymethylene formations are 72.6 and 71.9 kcal/mol on the ideal and defect surfaces, respectively. A reduction of ∼30 kcal/mol in tautomerization energy barriers is observed in water-assisted process on the defect surface. Because this reduction is close to that of the gas-phase reactions, the catalytic effect is clearly due to the presence of water molecule instead of the interaction with the surface. In this case, the pyrite surfaces with the ability to accumulate reactive species only play the role of connecting bridges between the two steps of the proposed reaction mechanism: the water-assisted rearrangement and the self-catalyzed dehydration.

Structures, Thermochemical Properties, and Bonding of Mixed Alkaline-Earth-Metal Silicon Trimers Si3M(+/0/-) with M = Be, Mg, Ca.

The ground state geometries, electronic structures, and thermochemical properties of binary alkaline-earth-metal silicon clusters Si3M with M = Be, Mg, Ca in neutral, cationic, and anionic states were investigated using quantum chemical computations. Lowest-lying isomers of the clusters were determined on the basis of the composite G4 energies. Along with total atomization energies, thermochemical parameters were determined for the first time by means of the G4 and coupled-cluster theory with complete basis set CCSD(T)/CBS approaches. The most favored equilibrium formation sequences for Si3M clusters emerge as follows: all Si3M(+/0/-) clusters are formed by attaching the M atom into the corresponding cation, neutral and anion silicon trimer Si3(+/0/-), except for the Si3Mg(+) and Si3Ca(+) where the metal cations are bound to the neutral Si3. The resulting mixed tetramers exhibit geometrical and electronic features similar to those of the pure silicon tetramer Si4(+/0/-). Electron localization function (ELF) and ring current analyses point out that the σ-aromatic character of silicon tetramer remains unchanged upon substituting one Si atom by one alkaline-earth-metal atom.

Effects of Water Molecules on Rearrangements of Formamide on the Kaolinite Basal (001) Surface

The effects of kaolinite mineral surfaces on the unimolecular rearrangements of formamide (FM) were investigated using periodic density functional theory in conjunction with pseudopotential plane-wave approach. Surface hydroxyl groups covering the octahedral surface of kaolinite were found to play the role of catalysts in the transformations of FM. They induce a reduction of 31 kcal/mol on the energy barrier for formation of its isomer aminohydroxymethylene (AHM), which is close to the reduction amount calculated for water-catalyzed reactions. This suggests that the kaolinite octahedral surface exerts a catalytic effect similar to that of the water molecule. As the tetrahedral surface does not contain catalytic surface hydroxyl groups, only water-assisted FM transformation was therefore studied on this surface whose energy barrier amounts to ∼17 kcal/mol. The combined effect of both water and kaolinite on FM rearrangements via triple hydrogen transfer reactions does not significantly lower the energy barriers, as compared to those of double hydrogen transfer reactions. The triple hydrogen transfer energy barriers amount to ∼20 and ∼36 kcal/mol, and the double ones are ∼21 and ∼40 kcal/mol for formation of formimic acid and AHM isomers, respectively. However, the energies of the systems in water-catalyzed channels lie below the available energies of the original reactants, and thus these channels are more favored than the water-free ones. With its multiple functions as both a supporting plate-form and a catalyst for FM reactions, kaolinite can thus be regarded as an important natural catalyst for prebiotic synthesis.

Theoretical Study of Silicon Monoxide Reactions with Ammonia and Methane

High-accuracy calculations were performed to study the mechanisms of the reactions between the diatomic silicon monoxide (SiO) with NH3 and CH4. These reactions are relevant to the SiO-related astrochemistry and atmospheric chemistry as well as the activation of the N-H and C-H bonds by the SiO triple bond. Energetic data used in the construction of potential energy surfaces describing the SiO + NH3/CH4 reactions were obtained at the coupled-cluster theory with extrapolation to the complete basis set limit (CCSD(T)/CBS) using DFT/B3LYP/aug-cc-pVTZ optimized geometries. Standard heats of formation of a series of small Si-molecules were predicted. Insertion of SiO into the N-H bond is exothermic with a small energy barrier of ∼8 kcal/mol with respect to the SiO + NH3 reactants, whereas the C-H bond activation by SiO involves a higher energy barrier of 45 kcal/mol. Eight product channels are opened in the SiO + NH3 reaction including dehydrations giving HNSi/HSiN and dehydrogenations. These reactions are endothermic by 16-119 kcal/mol (calculated at 298.15 K) with the CCSD(T)/CBS energy barriers of 21-128 kcal/mol. The most stable set of products, HNSi + H2O, was also the product of the reaction pathway having lowest energy barrier of 21 kcal/mol. Ten product channels of the SiO + CH4 reaction including decarbonylation, dehydration, dehydrogenation, and formation of Si + CH3OH are endothermic by 19-118 kcal/mol with the energy barriers in the range of 71-126 kcal/mol. The formation of H2CSiO + H2O has the lowest energy barrier of 71 kcal/mol, whereas the most stable set of products, SiH4 + CO, is formed via a higher energy barrier of 90 kcal/mol. Accordingly, while SiO can break the N-H bond of ammonia without the assistance of other molecules, it is not able to break the C-H bond of methane.