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Besides delivering plausible prebiotic feedstock molecules and high-energy initiators, extraterrestrial impacts could also affect the process of abiogenesis by altering the early Earth's geological environment in which primitive life was conceived. We show that iron-rich smectites formed by reprocessing of basalts due to the residual post-impact heat could catalyze the synthesis and accumulation of important prebiotic building blocks such as nucleobases, amino acids and urea. [ABSTRACT FROM AUTHOR]

Synthesis of the first RNAs represents one of the cornerstones of the emergence of life. Recent studies demonstrated powerful scenarios of prebiotic synthesis of cyclic nucleotides in aqueous and formamide environments. This raised a question about their thermodynamic stability, a decisive factor determining their accumulation in a prebiotic pool. Here we performed ab initio molecular dynamics simulations at various temperatures in formamide and water to study the relative stabilities of the 2′,3′ and 3′,5′ isomers of cyclic nucleotides. The computations show that in an aqueous environment 2′,3′ cyclic nucleotides are more stable than their 3′,5′ counterparts at all temperatures up to the boiling point. In contrast, in formamide higher temperatures favor the accumulation of the 3′,5′ cyclic form, whereas below about 400 K the 2′,3′ cyclic form becomes more stable. The latter observation is consistent with a formamide-based origin scenario, suggesting that 3′,5′ cyclic nucleotides accumulated at higher temperatures subsequently allowed oligomerization reactions after fast cooling to lower temperatures. A statistical analysis of the geometrical parameters of the solutes indicates that thermodynamics of cyclic nucleotides in aqueous and formamide environments are dictated by the floppiness of the molecules rather than by the ring strain of the cyclic phosphodiester linkages. [ABSTRACT FROM AUTHOR]

The origin of life on Earth is one of the most fascinating questions of contemporary science. Extensive research in the past decades furnished diverse experimental proposals for the emergence of first informational polymers that could form the basis of the early terrestrial life. Side by side with the experiments, the fast development of modern computational chemistry methods during the last 20 years facilitated the use of in silico modelling tools to complement the experiments. Modern computations can provide unique atomic-level insights into the structural and electronic aspects as well as the energetics of key prebiotic chemical reactions. Many of these insights are not directly obtainable from the experimental techniques and the computations are thus becoming indispensable for proper interpretation of many experiments and for qualified predictions. This review illustrates the synergy between experiment and theory in the origin of life research focusing on the prebiotic synthesis of various nucleic acid building blocks and on the self-assembly of nucleotides leading to the first functional oligonucleotides. [ABSTRACT FROM AUTHOR]

4-Aminoimidazole-5-carbonitrile (AICN) was suggested as a prebiotically plausible precursor of purine nucleobases and nucleotides. Although it can be formed in a sequence of photoreactions, AICN is immune to further irradiation with UV-light. We present state-of-the-art multi-reference quantum-chemical calculations of potential energy surface cuts and conical intersection optimizations to explain the molecular mechanisms underlying the photostability of this compound. We have identified the N–H bond stretching and ring-puckering mechanisms that should be responsible for the photochemistry of AICN in the gas phase. We have further considered the photochemistry of AICN–water clusters, while including up to six explicit water molecules. The calculations reveal charge transfer to solvent followed by formation of an H3O+ cation, both of which occur on the 1πσ* hypersurface. Interestingly, a second proton transfer to an adjacent water molecule leads to a 1πσ*/S0 conical intersection. We suggest that this electron-driven proton relay might be characteristic of low-lying 1πσ* states in chromophore–water clusters. Owing to its nature, this mechanism might also be responsible for the photostability of analogous organic molecules in bulk water. [ABSTRACT FROM AUTHOR]

High-resolution FT-IR spectroscopy combined with quantum chemical calculations was used to study the chemistry of OCSdisproportionation over the reduced surface of isotopically labelled, nanocrystalline TiO2. Analysis of the isotopic composition of the product gases has revealed that the reaction involves solely OCS molecules from the gas-phase. Using quantum chemical calculations we propose a plausible mechanistic scenario, in which two reduced Ti3+ centres mediate the reaction of the adsorbed OCS molecules. [ABSTRACT FROM AUTHOR]

Quantum chemical calculations reveal that neither steric hindrance nor less polar solvent medium is able to reduce the otherwise high hydrolysis rate of arsenate-esters. These results question the stability of As-DNA not only in aqueous but also in non-aqueous environments. [ABSTRACT FROM AUTHOR]

High-resolution FT-IR spectroscopy combined with quantum chemical calculations was used to study the chemistry of OCS-disproportionation over the reduced surface of isotopically labelled, nanocrystalline TiO2. Analysis of the isotopic composition of the product gases has revealed that the reaction involves solely OCS molecules from the gas-phase. Using quantum chemical calculations we propose a plausible mechanistic scenario, in which two reduced Ti(3+) centres mediate the reaction of the adsorbed OCS molecules.

2-Aminooxazole is generally considered to play a central role in the origin of informational polymers. In the current contribution we use density functional calculations to investigate the detailed mechanism of 2-aminooxazole formation from the prebiotic soup according to the scenario suggested by M. W. Powner, B. Gerland and J. D. Sutherland, Nature, 2009, 459, 239-242. Parallel to the phosphate-catalyzed reaction pathway we also describe its water-assisted variant. Our calculations show that phosphate-catalysis is indispensable not only in the cyclization and the subsequent water-elimination steps, as previously suggested, but also in the very first reaction step leading to the formation of the carbinolamine intermediate. In addition, we suggest concurrent reaction channels for the cyclization and water-elimination reaction steps, both involving catalytic phosphate ions.

Knowledge of geometrical and physico-chemical properties of the sugar-phosphate backbone substantially contributes to the comprehension of the structural dynamics, function and evolution of nucleic acids. We provide a side by side overview of structural biology/bioinformatics, quantum chemical and molecular mechanical/simulation studies of the nucleic acids backbone. We highlight main features, advantages and limitations of these techniques, with a special emphasis given to their synergy. The present status of the research is then illustrated by selected examples which include classification of DNA and RNA backbone families, benchmark structure-energy quantum chemical calculations, parameterization of the dihedral space of simulation force fields, incorporation of arsenate into DNA, sugar-phosphate backbone self-cleavage in small RNA enzymes, and intricate geometries of the backbone in recurrent RNA building blocks. Although not apparent from the current literature showing limited overlaps between the QM, simulation and bioinformatics studies of the nucleic acids backbone, there in fact should be a major cooperative interaction between these three approaches in studies of the sugar-phosphate backbone.