Acetylene as an essential building block for prebiotic formation of pyrimidine bases on Titan

Prebiotic building blocks for the formation of biomolecules are important in understanding the abiotic origin of biomolecules. However, there is a limited choice of the building blocks as precursors for the biomolecules. Acetylene (HCCH) is found in Titan's atmosphere and is an abiotic-precursor of pyrimidine bases. HCCH reacts with urea to form both cytosine and uracil. The mechanisms for the formation of both cytosine and uracil were studied by density functional theory at B3LYP/6-311G(d,p) level. Ethynyl radicals (˙CCH) are relevant for the chemistry of Titan's atmosphere therefore both HCCH and ˙CCH were evaluated as carbon sources. The pathways, for both HCCH and ˙CCH, lead to intermediates with an unsaturated-group that facilitate the formation of the six-membered ring of the pyrimidine bases. The predicted structures for cytosine and uracil were compared with labeled cytosine and uracil that were formed from the reaction of DCCD with urea. The results suggest that cytosine is formed from HCCH while uracil is formed from ˙CCH. The mechanisms are energetically feasible and there is no conclusive evidence for the preferred pathway (HCCH or ˙CCH). The pathways were further extended for the formation of both uric acid and 8-oxoguanine from HCCH and urea, and demonstrate the utility of HCCH as a carbon source for diverse biomolecules. Biuret is identified as a precursor for the pyridimine bases, and it unifies the free radical pathways for the pyrimidine bases with those of triazines. The pathways are appropriate for the reducing atmosphere that creates both radicals and electrons due to ionizing radiation on Titan. The mechanisms are feasible for the extraterrestrial formation of the pyrimidine bases.status: publishe

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.status: publishe

Free radical pathways for the prebiotic formation of xanthine and isoguanine from formamide

Free radical pathways for the synthesis of xanthine and isoguanine from formamide were studied using density functional theory (B3LYP/6-311G(d,p)). The proposed mechanisms are complex and appropriate for the non-aqueous scenario of prebiotic reactions. Formation of the carbonyl bond in the nucleobases proceeds through enol-keto tautomerization since the direct formation of the CO bond is a highly endothermic step. The mechanisms show 2-amino-imidazole as a precursor for nucleobases and polyazaporphyrin. The proposed mechanisms contribute to a further understanding of the origin of biomolecules. © 2014 Elsevier B.V. All rights reserved.status: publishe

Structural evolution and bonding of phosphorus-doped silicon clusters SinPm-/0/+ with n=1-10, m=1, 2

© 2017 Elsevier B.V. The geometrical evolution, electronic structure and thermodynamic stability of a series of singly-doped SinP and doubly-doped SinP2 silicon clusters with n = 1–10, in the neutral, cationic and anionic states were systematically investigated using DFT computations. The global minimum structures were identified using different search approaches. The isoelectronic structures including the neutral SinP, the cation Sin−1P2+ and the anion Sin+1− exhibit a similar shape. Structural evolution of doubly P-doped SinP2 was found to adopt a substitution mechanism rather than a caption pathway. Dissociation energies for various channels of SinP2 clusters point out that the fragmentations generating P2 atoms plus the corresponding Sin host is the most preferred process. The closed-shell species Si4P−, Si3P2, Si7P− and Si6P2 are found to have high thermodynamic stability with large binding energies and second-order difference energies. Their enhanced stability can be rationalized in terms of the Jellium shell model. The aromatic character was probed using the ring current maps of electron densities. The planar SiP2, Si2P− and Si3P− clusters feature an aromatic character, whereas only the five-membered plane of the bipyramid-like structures involving Si6P− and Si5P2 are locally aromatic.status: publishe

Reaction Routes for Experimentally Observed Intermediates in the Prebiotic Formation of Nucleobases under High-Temperature Conditions

The prebiotic synthesis of nucleobases is of particular interest, given the experimental evidence that indicated formation of the nucleobases under abiotic conditions on the Early Earth under high-temperature conditions. Biomolecules have been formed under meteoritic impact scenarios that lead to high temperature and the generation of high energy. Free radical pathways for the formation of biomolecules are appropriate under these conditions. Density functional theory computations were used to study the free radical routes for the formation of nucleobases at the UB3LYP/6-311G(d,p) level. We have found that both 5-aminoimidazole-4-carboxamide (AICA) and 5-(formylamino)imidazole-4-carboxamide (fAICA) are formed first from formamide then the nucleobases are formed. Calculated results show the radical reaction routes of AICA as a precursor for guanine. Both hypoxanthine and xanthine are formed from radical pathways of fAICA. In addition, generation of imino-AICA and imino-fAICA has been shown for the first time to be needed for the production of adenine, purine, and isoguanine. Formation of hypoxanthine and adenine/purine from fAICA and imino-fAICA, respectively, is consistent with experiments performed nearly seven decades ago.status: publishe

Design of Liquid Crystal Materials Based on Palmitate, Oleate, and Linoleate Derivatives for Optoelectronic Applications

Herein, liquid crystalline derivatives based on palmitate, oleate, and linoleate moieties with azomethine cores were synthesized, and their physical, chemical, optical, and photophysical properties were investigated in detail. The mesomorphic activity of these materials was examined through polarized optical microscopy (POM) and differential scanning calorimetry (DSC). The observed results revealed that the stability of the thermal mesophase depends on the terminal polar as well as on the fatty long-chain substituents. Purely smectogenic phases were detected in all three terminal side chains. A eutectic composition with a low melting temperature and a broad smectic A range was found by constructing a binary phase diagram and addressing it in terms of the mesomorphic temperature range. The energy bandgap of the palmitate-based derivative (Ia) was determined as 3.95 eV and slightly increased to 4.01 eV and 4.05 eV for the oleate (Ib) and linoleate (Ic) derivatives, respectively. The optical constants (n, κ, εr, and εi) were extracted from the fitting of measured spectroscopic ellipsometer data. The steady-state spectra of these samples exhibited a broad emission in the range 400–580 nm, which was found to be blue shifted to 462 nm for both Ib and Ic derivatives. The average fluorescence decay lifetime of the Ia derivative was found to be 598 ps, which became faster for the Ib and Ic derivatives and slower for the sample with a chloride end polar group

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 <b>7a</b> and <b>1a</b>), uracil (main route, routes <b>7b</b> and <b>1b</b>), and thymine (main route and route <b>26a</b>), 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

Reaction Routes for Experimentally Observed Intermediates in the Prebiotic Formation of Nucleobases under High-Temperature Conditions

The prebiotic synthesis of nucleobases is of particular interest, given the experimental evidence that indicated formation of the nucleobases under abiotic conditions on the Early Earth under high-temperature conditions. Biomolecules have been formed under meteoritic impact scenarios that lead to high temperature and the generation of high energy. Free radical pathways for the formation of biomolecules are appropriate under these conditions. Density functional theory computations were used to study the free radical routes for the formation of nucleobases at the UB3LYP/6-311G­(d,p) level. We have found that both 5-aminoimidazole-4-carboxamide (AICA) and 5-(formylamino)­imidazole-4-carboxamide (fAICA) are formed first from formamide then the nucleobases are formed. Calculated results show the radical reaction routes of AICA as a precursor for guanine. Both hypoxanthine and xanthine are formed from radical pathways of fAICA. In addition, generation of imino-AICA and imino-fAICA has been shown for the first time to be needed for the production of adenine, purine, and isoguanine. Formation of hypoxanthine and adenine/purine from fAICA and imino-fAICA, respectively, is consistent with experiments performed nearly seven decades ago