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Silicate glasses are ubiquitous on terrestrial planets wherever molten rock - generated by volcanism or impacts - is quenched by air or water. Hence, they provided ready and abundant reactive solid surfaces for prebiotic chemistry on the early Earth. Here, we show that rock glass composition determines basicity, which in turn modulates the outcome of prebiotic synthetic processes such as the polymerization of 3', 5' cyclic guanosine monophosphate. [ABSTRACT FROM AUTHOR]

For the emergence of life, the abiotic synthesis of RNA from its monomers is a central step. We found that in alkaline, drying conditions in bulk and at heated air‐water interfaces, 2′,3′‐cyclic nucleotides oligomerised without additional catalyst, forming up to 10‐mers within a day. The oligomerisation proceeded at a pH range of 7–12, at temperatures between 40–80 °C and was marginally enhanced by K+ ions. Among the canonical ribonucleotides, cGMP oligomerised most efficiently. Quantification was performed using HPLC coupled to ESI‐TOF by fitting the isotope distribution to the mass spectra. Our study suggests a oligomerisation mechanism where cGMP aids the incorporation of the relatively unreactive nucleotides C, A and U. The 2′,3′‐cyclic ribonucleotides are byproducts of prebiotic phosphorylation, nucleotide syntheses and RNA hydrolysis, indicating direct recycling pathways. The simple reaction condition offers a plausible entry point for RNA to the evolution of life on early Earth. [ABSTRACT FROM AUTHOR]

The assembly of ancient informational polymers from nucleotide precursors is the central challenge of life's origin on our planet. Among the possible solutions, dry polymerization of 3',5'‐cyclic guanosine monophosphate (3',5'‐cGMP) has been proposed as a candidate to create oligonucleotides of 15–20 units in length. However, the reported sensitivity of the reaction to the presence of cations raised questions of whether this chemistry could be relevant in a geological context. The experiments in this study show that the presence of cations is not restrictive as long as the reaction is conducted in an acidic environment, in contrast to previous reports that suggested optimal conditions at pH 9. [ABSTRACT FROM AUTHOR]

Previous studies on the polymerization of 3',5' cyclic guanosine monophosphate (cGMP) demonstrated the potential of the compound in the abiotic generation of the first oligonucleotide sequences on the early Earth. These experiments were conducted under idealized laboratory conditions, which logically raises the question whether the same chemistry could take place in the harsh environment present on our planet in its earliest days. In the current study, we focus on the mineralogical context of this chemistry and show that numerous, but not all, common minerals assumed to be present on the early Earth could host the polymerization of H‐form 3',5' cGMP. In particular, we have found that quartz varieties are especially suitable for this purpose, similar to andalusite, amphibole or micas. On the contrary, olivine, calcite, and serpentine‐group minerals interfere with the studied polymerization chemistry. Our results show that crystallization on mineral surfaces, which is mainly a diffusion controlled process, determines the ability of 3',5' cGMP to polymerize. The observation that numerous amorphous and crystalline SiO2 forms are compatible with the oligomerization chemistry suggests that the process could commonly occur in a wide range of primordial environments allowing for crystallization of the cyclic monomers from a dropping solution. [ABSTRACT FROM AUTHOR]

Polymerization of 3′,5′ cyclic guanosine monophosphate (3′,5′ cGMP) was previously reported to afford short RNA sequences from a plausible mildly activated prebiotic precursor in a non‐enzymatic and template‐free manner. In the current paper we analyze the reaction with PAGE as well as by infrared micro‐ and nanospectroscopy on time scales not considered before. We provide evidence that a preliminary oligomerization step in dry state allows for a continued synthesis of RNA oligomers even in the presence of subsequently added water. On a longer time scale, the oligomerization yield oscillates in an apparently chaotic fashion hinting at the importance of some non‐reversible phase‐separation processes on the experimentally observed outcome of the polymerization/degradation chemistries. The long‐lasting (hundreds of hours) intrinsic sustainability and resilience of the process gives a robust prebiotic potential to this unique oligomerization reaction, which could lead to the very first oligonucleotide sequences on the primordial Earth. [ABSTRACT FROM AUTHOR]

Formation and structural modification of oxygenated polycyclic aromatic hydrocarbons (oxyPAHs) by UV irradiation on minerals have recently been proposed as a possible channel of PAH transformation in astrochemical and prebiotic scenarios of possible relevance for the origin of life. Herein, it is demonstrated that high‐energy proton‐beam irradiation in the presence of various meteorites, including stony iron, achondrite, and chondrite types, promotes the conversion of two representative oxyPAH compounds, 1‐naphthol and 1,8‐dihydroxynaphthalene, to complex mixtures of oxygenated and oligomeric derivatives. The main identified products include polyhydroxy derivatives, isomeric dimers encompassing benzofuran and benzopyran scaffolds, and, notably, a range of quinones and perylene derivatives. Addition of urea, a prebiotically relevant chemical precursor, expanded the range of identified species to include, among others, quinone diimines. Proton‐beam irradiation of oxyPAH modulated by nitrogen‐containing compounds such as urea is proposed as a possible contributory mechanism for the formation and processing of insoluble organic matter in meteorites and in prebiotic processes. [ABSTRACT FROM AUTHOR]

Terrestrial volcanism has been one of the dominant geological forces shaping our planet since its earliest existence. Its associated phenomena, like atmospheric lightning and hydrothermal activity, provide a rich energy reservoir for chemical syntheses. Based on our laboratory simulations, we propose that on the early Earth volcanic activity inevitably led to a remarkable production of formic acid through various independent reaction channels. Large‐scale availability of atmospheric formic acid supports the idea of the high‐temperature accumulation of formamide in this primordial environment. [ABSTRACT FROM AUTHOR]

The abiotic phosphorylation of nucleosides is a major hurdle in origin‐of‐life studies. We suggest a plausible pathway for the synthesis of adenosine nucleotides from adenosine and NaH2PO4 under radiative conditions mimicking the solar wind in the presence of a meteorite of the aubrite‐type. Hydroxyapatite also performed as a mineral heterogeneous phosphorus source. Adenosine polyphosphate derivatives and inorganic polyphosphates were detected in the reaction mixture, highlighting the high reactivity of the system. Both the total yield of adenosine nucleotides and the conversion of adenosine increased upon performing the irradiation in the presence of formamide (NH2CHO) and aubrite. These experiments simulate conditions in space or on an early Earth fluxed by protons from the solar wind, potentially mimicking a plausible prebiotic phosphorylation scenario. [ABSTRACT FROM AUTHOR]

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]

In this work, we provide an answer to the question formulated by Albert Eschenmoser: "How would you envisage the bridge between potentially primordial geochemistry that had been disordered and one that gradually became self-organizing?" Analysis of the free-energy profiles of some of the key reactions leading to formation of nucleotides and their oligomers shows that, whereas the first part of the pathway, up to nucleotides, is energy-driven, in the second low-energy part entropic control in the form of structural compatibility becomes more important. We suggest that the birth of modern metabolism requires structural compatibility, which is enabled by the commensurability of the thermodynamics of the synthetic steps with the stabilizing effect of those intermolecular interactions that play a key role in dictating entropic control of these reactions. [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]

Recent studies illustrate that short oligonucleotide sequences can be easily produced from nucleotide precursors in a template-free non-enzymatic way under dehydrating conditions, i.e. using essentially dry materials. Here we report that 3’,5’ cyclic AMP may also serve as a substrate of the reaction, which proceeds under moderate conditions yet with a lower efficiency than the previously reported oligomerization of 3’,5’ cyclic GMP. Optimally the oligomerization requires (i) a temperature of 80°C, (ii) a neutral to alkaline environment and (iii) a time on the order of weeks. Differences in the yield and required reaction conditions of the oligomerizations utilizing 3’,5’ cGMP and cAMP are discussed in terms of the crystal structures of the compounds. Polymerization of 3’,5’ cyclic nucleotides, whose paramount relevance in a prebiotic chemistry context has been widely accepted for decades, supports the possibility that the origin of extant genetic materials might have followed a direct uninterrupted path since its very beginning, starting from non-elaborately pre-activated monomer compounds and simple reactions. [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]

50 years after the historical Miller-Urey experiment, the formamide-based scenario is perhaps the most powerful concurrent hypothesis for the origin of life on our planet besides the traditional HCN-based concept. The information accumulated during the last 15 years in this topic is astonishingly growing and nowadays the formamide-based model represents one of the most complete and coherent pathways leading from simple prebiotic precursors up to the first catalytically active RNA molecules. In this work, we overview the major events of this long pathway that have emerged from recent experimental and theoretical studies, mainly concentrating on the mechanistic, methodological, and structural aspects of this research. [ABSTRACT FROM AUTHOR]

The origin of the catalytic activity of ancient oligonucleotides is a largely unexplored field of contemporary science. In the current work we use molecular dynamics simulations to investigate the plausibility of tetraloop-like overhang geometries to initiate transphosphorylation reactions that lead to ligation and terminal cleavage in simple, Watson-Crick (WC) complementary oligoC/oligoG sequences observed experimentally. We show a series of examples of known tetraloop architectures, which can be adopted by the unpaired overhangs of short oligonucleotide sequences for a sufficiently long time to enable chemical reactions that lead to simple ribozyme-like catalytic activity. Thus, our computations demonstrate that the role of non-WC interactions at the emergence of the most ancient catalytic oligonucleotides could be more significant than ever believed. [ABSTRACT FROM AUTHOR]

The high-energy 3′,5′phosphodiester linkages conservedin 3′,5′ cyclic GMPs offer a genuine solution for monomeractivation required by the transphosphorylation reactions that couldlead to the emergence of the first simple oligonucleotide sequenceson the early Earth. In this work we provide an in-depth characterizationof the effect of the reaction conditions on the yield of the polymerizationreaction of 3′,5′ cyclic GMPs both in aqueous environmentas well as under dehydrating conditions. We show that the thresholdtemperature of the polymerization is about 30 °C lower underdehydrating conditions than in solution. In addition, we present aplausible exergonic reaction pathway for the polymerization reaction,which involves transient formation of anionic centers at the O3′positions of the participating riboses. We suggest that excess Na+cations inhibit the polymerization reaction because theyblock the anionic mechanism via neutralizing the negatively chargedO3′. Our experimental findings are compatible with a prebioticscenario, where gradual desiccation of the environment could inducepolymerization of 3′,5′ cyclic GMPs synthesized in liquid. [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]

The photoinduced isomerization of diaminomaleonitrile (DAMN) to diaminofumaronitrile (DAFN) was suggested to play a key role in the prebiotically plausible formation of purine nucleobases and nucleotides. In this work we analyze two competitive photoisomerization mechanisms on the basis of state-of-the-art quantum-chemical calculations. Even though it was suggested that this process might occur on the triplet potential-energy surface, our results indicate that the singlet reaction channel should not be disregarded either. In fact, the peaked topography of the S1/S0 conical intersection suggests that the deexcitation should most likely occur on a sub-picosecond timescale and the singlet photoisomerization mechanism might effectively compete even with a very efficient intersystem crossing. Such a scenario is further supported by the relatively small spin-orbit coupling of the S1 and T2 states in the Franck-Condon region, which does not indicate a very effective triplet bypass for this photoreaction. Therefore, we conclude that the triplet reaction channel in DAMN might not be as prominent as was previously thought. [ABSTRACT FROM AUTHOR]

3',5'-Cyclic GMP spontaneously nonenzymatically polymerizes in a base-catalyzed reaction affording G oligonucleotides. When reacted with fully or partially sequence-complementary RNA (oligo C), the abiotically generated oligo G RNA displays a typical ribozyme activity consisting of terminal ligation accompanied by cleavage of an internal phosphate site of the donor oligonucleotide stem upon attack of the acceptor 3' terminal OH. This reaction is dubbed Ligation following Intermolecular Cleavage (LIC). In a prebiotic perspective, the ability of oligo G polynucleotides to react with other sequences outlines a simple and possible evolutionary scenario based on the autocatalytic properties of RNA. [ABSTRACT FROM AUTHOR]

ABSTRACT Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last decades, base stacking has been extensively studied by experimental and theoretical methods. Advanced quantum-chemical calculations clarified that base stacking is a common interaction, which in the first approximation can be described as combination of the three most basic contributions to molecular interactions, namely, electrostatic interaction, London dispersion attraction and short-range repulsion. There is not any specific π-π energy term associated with the delocalized π electrons of the aromatic rings that cannot be described by the mentioned contributions. The base stacking can be rather reasonably approximated by simple molecular simulation methods based on well-calibrated common force fields although the force fields do not include nonadditivity of stacking, anisotropy of dispersion interactions, and some other effects. However, description of stacking association in condensed phase and understanding of the stacking role in biomolecules remain a difficult problem, as the net base stacking forces always act in a complex and context-specific environment. Moreover, the stacking forces are balanced with many other energy contributions. Differences in definition of stacking in experimental and theoretical studies are explained. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 978-988, 2013. [ABSTRACT FROM AUTHOR]

Highlights: [•] Applications of modern quantum chemical (QM) methods to nucleic acids are explained. [•] Prospect of large-scale QM calculations of nucleic acids is introduced. [•] Fundamental difference between modern QM and force field calculations is discussed. [•] Relation of QM and simulation studies to experiments is explained. [Copyright &y& Elsevier]

NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the 1H and 13C NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when 13C and 1H chemical shift data are combined. The approximate linear dependence of the C1′ shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects. [ABSTRACT FROM AUTHOR]

Synthesis of nucleobases in nonaqueous environments is an alternative way for the emergence of terrestrial life, which could solve the fundamental problem connected to the hydrolytic instability of nucleic acid components in an aqueous environment. In this contribution, we present a plausible reaction route for the prebiotic synthesis of nucleobases in formamide, which does not require participation of the formamide trimer and aminoimidazole-carbonitrile intermediates. The computed activation energy of the proposed pathway is noticeably higher than that of the HCN-based synthetic route, but it is still feasible under the experimental conditions of the Saladino synthesis. We show that, albeit both the pyrimidine and purine ring formation utilizes the undissociated form of formamide, the dehydration product of formamide, HCN, may also play a key role in the mechanism. The rate-determining step of the entire reaction path is the cyclization of the diaza-pentanimine precursor. The subsequent formation of the imidazole ring proceeds with a moderate activation energy. Our calculations thus demonstrate that the experimentally suggested reaction path without the involvement of aminoimidazole-carbonitrile intermediates is also a viable alternative for the nonaqueous synthesis of nucleobases. [ABSTRACT FROM AUTHOR]

In this feature article, we provide a side-by-side introduction for two research fields: quantum chemical calculations of molecular interaction in nucleic acids and RNA structural bioinformatics. Our main aim is to demonstrate that these research areas, while largely separated in contemporary literature, have substantial potential to complement each other that could significantly contribute to our understanding of the exciting world of nucleic acids. We identify research questions amenable to the combined application of modern ab initio methods and bioinformatics analysis of experimental structures while also assessing the limitations of these approaches. The ultimate aim is to attain valuable physicochemical insights regarding the nature of the fundamental molecular interactions and how they shape RNA structures, dynamics, function, and evolution. [ABSTRACT FROM AUTHOR]

Base pairs belonging to the cis Hoogsteen:sugar-edge (H:S) family play important structural roles in folded RNA molecules. Several of these are present in internal loops, where they are involved in interactions leading to planar dinucleotide platforms which stabilize higher order structures such as base triplets and quartets. We report results of analysis of 30 representative examples spanning 16 possible base pair combinations, with several of them showing multimodality of base pairing geometry. The geometries of 23 of these base pairs were modeled directly from coordinates extracted from RNA crystal structures. The other seven were predicted structures which were modeled on the basis of observed isosteric analogues. After appropriate satisfaction of residual valencies, these structures were relaxed using the B3LYP/6-31G(d,p) method and interaction energies were derived at the RIMP2/aug-cc-pVDZ level of theory. The geometries for each of the studied base pairs have been characterized in terms of the number and nature of H-bonds, rmsd values observed on optimization, base pair geometrical parameters, and sugar pucker analysis. In addition to its evaluation, the nature of intermolecular interaction in these complexes was also analyzed using Morokuma decomposition. The gas phase interaction energies range between −5.2 and −20.6 kcal/mol and, in contrast to the H:S trans base pairs, show enhanced relative importance of the electron correlation component, indicative of the greater role of dispersion energy in stabilization of these base pairs. The rich variety of hydrogen bonding pattern, involving the flexible sugar edge, appears to hold the key to several features of structural motifs, such as planarity and propensity to participate in triplets, observed in this family of base pairs. This work explores these aspects by integrating database analysis, and detailed base pairing geometry analysis at the atomistic level, with ab initio computation of interaction energies. The study, involving alternative classification of base pairs and triplets, provides insights into intrinsic properties of these base pairs and their possible structural and functional roles. [ABSTRACT FROM AUTHOR]