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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]

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]

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]

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]

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 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]

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]

The front cover artwork is provided by Judit Šponer (Institute of Biophysics, Czech Academy of Sciences). The image shows that polymerization of H‐form 3',5' cyclic guanosine monophosphate (GMP) exhibits an oscillatory behavior when studying the reaction on longer time scales (of several days). Domains of the material, differing in the level of hydration, interlock like pieces of a puzzle, resulting in a complex chemical system working far from equilibrium. Read the full text of the Article at 10.1002/syst.202000011. [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]

Template-free nonenzymatic polymerization of 3′,5′ cyclic nucleotides is an emerging topic of the origin of life research. In the last ten years, a number of papers have been published addressing various aspects of this process. These works evoked a vivid discussion among scientists working in the field of prebiotic chemistry. The aim of the current review is to answer the most frequently raised questions related to the detection and characterization of oligomeric products as well as to the geological context of this chemistry. [ABSTRACT FROM AUTHOR]

Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously emerging in the ensembles of molecules composing prebiotic pools, initiates subsequent evolution of increasingly complex and innovative chemical information. On the conservation side, it is a posteriori observed that numerous biological processes are based on prebiotically promptly made compounds, as proposed by the concept of Chemomimesis. Molecular Darwinian evolution and Chemomimesis are principles acting in balanced cooperation in the frame of Systems Chemistry. The one-pot synthesis of nucleosides in radical chemistry conditions is possibly a telling example of the operation of these principles. Other indications of similar cases of molecular evolution can be found among biogenic processes. [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]

Piano stool ruthenium complexes of the composition [Ru(II)(η6-arene)(en)Cl]+/2+ (en = ethylenediamine) represent an emerging class of cisplatin-analogue anticancer drug candidates. In this study, we use computational quantum chemistry to characterize the structure, stability and reactivity of these compounds. All these structures were optimized at DFT(B3LYP)/6-31G(d) level and their single point properties were determined by the MP2/6-31++G(2df,2pd) method. Thermodynamic parameters and rate constants were determined for the aquation process, as a replacement of the initial chloro ligand by water and subsequent exchange reaction of aqua ligand by nucleobases. The computations were carried out at several levels of DFT and ab initio theories (B3LYP, MP2 and CCSD) utilizing a range of bases sets (from 6-31G(d) to aug-cc-pVQZ). Excellent agreement with experimental results for aquation process was obtained at the CCSD level and reasonable match was achieved also with the B3LYP/6-31++G(2df,2pd) method. This level was used also for nucleobase-water exchange reaction where a smaller rate constant for guanine exchange was found in comparison with adenine. Although adenine follows a simple replacement mechanism, guanine complex passes by a two-step mechanism. At first, Ru-O6(G) adduct is formed, which is transformed through a chelate TS2 to the Ru-N7(G) final complex. In case of guanine, the exchange reaction is more favorable thermodynamically (releasing in total by about 8 kcal/mol) but according to our results, the rate constant for guanine substitution is slightly smaller than the analogous constant in adenine case when reaction course from local minimum is considered. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [ABSTRACT FROM AUTHOR]

X-ray, phylogenetic and quantum chemical analysis of molecular interactions and conservation patterns of cis Watson–Crick (W.C.) A/G base-pairs in 16 S rRNA, 23 S rRNA and other molecules was carried out. In these base-pairs, the A and G nucleotides interact with their W.C. edges with glycosidic bonds oriented cis relative to each other. The base-pair is stabilised by two hydrogen bonds, the C1′–C1′ distance is enlarged and the G(N2) amino group is left unpaired. Quantum chemical calculations show that, in the absence of other interactions, the unpaired amino group is substantially non-planar due to its partial sp3 pyramidalization, while the whole base-pair is internally propeller twisted and very flexible. The unique molecular properties of the cis W.C. A/G base-pairs make them distinct from other base-pairs. They occur mostly at the ends of canonical helices, where they serve as interfaces between the helix and other motifs. The cis W.C. A/G base-pairs play crucial roles in natural RNA structures with salient sequence conservation patterns. The key contribution to conservation is provided by the unpaired G(N2) amino group that is involved in a wide range of tertiary and neighbor contacts in the crystal structures. Many of them are oriented out of the plane of the guanine base and utilize the partial sp3 pyramidalization of the G(N2). There is a lack of A/G to G/A covariation, which, except for the G(N2) position, would be entirely isosteric. On the contrary, there is a rather frequent occurrence of G/A to G/U covariation, as the G/U wobble base-pair has an unpaired amino group in the same position as the cis W.C. G/A base-pair. The cis W.C. A/G base-pairs are not conserved when there is no tertiary or neighbor interaction. Obtaining the proper picture of the interactions and phylogenetic patterns of the cis W.C. A/G base-pairs requires a detailed analysis of the relation between the molecular structures and the energetics of interactions at a level of single H-bonds and contacts. [Copyright &y& Elsevier]

Chemical environments of young planets are assumed to be significantly influenced by impacts of bodies lingering after the dissolution of the protoplanetary disk. We explore the chemical consequences of impacts of these bodies under reducing planetary atmospheres dominated by carbon monoxide, methane, and molecular nitrogen. Impacts were simulated by using a terawatt high-power laser system. Our experimental results show that one-pot impact-plasma-initiated synthesis of all the RNA canonical nucleobases and the simplest amino acid glycine is possible in this type of atmosphere in the presence of montmorillonite. This one-pot synthesis begins with de novo formation of hydrogen cyanide (HCN) and proceeds through intermediates such as cyanoacetylene and urea. [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]

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]

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 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 coincidence of the Late Heavy Bombardment (LHB) period and the emergence of terrestrial life about 4 billion years ago suggest that extraterrestrial impacts could contribute to the synthesis of the building blocks of the first life-giving molecules. We simulated the high-energy synthesis of nucleobases from formamide during the impact of an extraterrestrial body. A high-power laser has been used to induce the dielectric breakdown of the plasma produced by the impact. The results demonstrate that the initial dissociation of the formamide molecule could produce a large amount of highly reactive CN and NH radicals, which could further react with formamide to produce adenine, guanine, cytosine, and uracil. Based on GC-MS, high-resolution FTIR spectroscopic results, as well as theoretical calculations, we present a comprehensive mechanistic model, which accounts for all steps taking place in the studied impact chemistry. Our findings thus demonstrate that extraterrestrial impacts, which were one order of magnitude more abundant during the LHB period than before and after, could not only destroy the existing ancient life forms, but could also contribute to the creation of biogenic molecules. [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]

The formation of nucleobases fromformamide during a high-energydensity event, i.e., the impact of an extraterrestrial body into theplanetary atmosphere, was studied by irradiation of formamide iceand liquid samples with a high-power laser in the presence of potentialcatalysts. FTIR spectroscopy, time-resolved emission spectroscopy,and GC-MS were subsequently used to monitor the dissociation of thismolecule into stable molecular fragments (HCN, H2O, HNCO,H2, CO, and NH3) and unstable species (HNC,•CN, and •NH). The kinetic and thermodynamic modelsof the high-energy density event molecular dynamics have been suggestedtogether with the reaction routes leading from the dissociation productsto the nucleobases. In addition, using theoretical calculations, wepropose a simple new reaction pathway for the formation of both pyrimidineand purine nucleobases involving •CN radical chemistry. [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]

The highly ordered supramolecular architecture present in the monomer crystals provides ideal steric conditions for the formation of intermolecular phosphodiester linkages between the cyclic nucleotide units. Cover Feature: Acid-Catalyzed RNA-Oligomerization from 3',5'-cGMP (Chem. Eur. J. 70/2021) Keywords: cGMP; nonenzymatic polymerization; nucleotides; prebiotic chemistry EN cGMP nonenzymatic polymerization nucleotides prebiotic chemistry 17506 17506 1 12/22/21 20211215 NES 211215 B Heat, protons and a dry crystalline material b are the three prerequisites for oligonucleotide synthesis from acid-form 3',5'-cyclic guanosine monophosphate monomers. [Extracted from the article]

The formamide-based synthesis of nucleic acids is considered as a nonaqueous scenario for the emergence of biomolecules from inorganic matter. In the current study, we scrutinized the chemical composition of formamide ices mixed with an FeNi meteorite material treated with laser-induced dielectric breakdown plasma created in nitrogen buffer gas. These experiments aimed to capture the first steps of those chemical transformations that may lead to the formation of nucleobases during the impact of an extraterrestrial icy body containing formamide on an early Earth atmosphere. High-resolution FT-IR spectroscopy combined with quantum chemical calculations was used to analyze the volatile fraction of the products formed during such an event. We have found that the spectrum of the evaporated formamide ices is dominated by the spectral signatures of the dimeric form of formamide. Upon exposure to laser sparks, new well-defined bands appear in the spectrum centered at ∼820, ∼ 995, and ∼ 1650 cm-1. On the basis of quantum chemical calculations, these bands can be assigned to the absorptions of 2-amino-2-hydroxy-acetonitrile and to 2-amino-2-hydroxy-malononitrile, which are formed in a direct reaction between formamide and CN• radicals upon the high-energy impact event. We also show that there is an exergonic reaction route via these intermediates leading to diaminomaleonitrile, which is generally considered to play a key role in the synthesis of nucleobases. [ABSTRACT FROM AUTHOR]

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]

RNA molecules are stabilized by a wide range of noncanonical interactions that are not present in DNA. Among them, the recently classified base--phosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomal crystal structures are involved in BPh interactions. BPh interactions are highly conserved and provide major constraints on RNA sequence evolution. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects. The reference computations are compared with DFT-D and DFT-D3 approaches, the SAPT method, and the molecular mechanics force field. The computations, besides providing the basic benchmark for the BPh interactions, allow some refinements of the original classification, including identification of some potential doubly bonded BPh patterns. The reference computations are followed by analysis of some larger RNA fragments that consider the context of the BPh interactions. The computations demonstrate the complexity of interaction patterns utilizing the BPh interactions in real RNA structures. The BPh interactions are often involved in intricate interaction networks. We studied BPh interactions of protonated adenine that can contribute to catalysis of hairpin ribozyme, the key BPh interaction in the S-turn motif of the sarcin--ricin loop, which may predetermine the S-turn topology and complex BPh patterns from the glmS riboswitch. Finally, the structural stability of BPh interactions in explicit solvent molecular dynamics simulations is assessed. The simulations well preserve key BPh interactions and allow dissection of structurally/functionally important water-meditated BPh bridges, which could not be considered in earlier bioinformatics classification of BPh interactions. [ABSTRACT FROM AUTHOR]

Examines the nature of stacking interactions between incalators. Isolation of intercalators properties; Failure to reveal energy minimum for potential energy curve; Determination on the atomic charges of nucleic acid bases.

To celebrate International Women′s Day on March 8th 2016, Chemistry – A European Journal is publishing a special issue dedicated to women around the world currently working in chemical research. The cover picture shows the frontispieces of the Concept, Review, and Minireview articles published in this issue, highlighting the broad range of chemistry that is currently being carried out by female researchers. In the top row from left to right: S. Harutyunyan et al. (page 3558 ff.), J. Sponer et al. (page 3572 ff.), and M. Brimble et al. (page 3622 ff.). In the middle row from left to right: M. Resmini et al. (page 3612 ff.), the logo for International Women′s Day 2016 (http://www. internationalwomensday.com/), and Y. Xie and J. Xie (page 3588 ff.). In the bottom row from left to right: I. Beletskaya and P. Sazonov (page 3644 ff.), T. Gaich and M. Pfaffenbach (page 3600 ff.), and A. Lattanzi and S. Meninno (page 3632 ff.). [ABSTRACT FROM AUTHOR]

Oligonucleotides In their Full Paper on page 3596 ff., J. E. Šponer et al. report on the results of molecular dynamics (MD) simulations used to investigate whether tetraloop ‐ like overhang geometries might give rise to ribozyme ‐ like activity in short Watson – Crick complementary oligoG/oligoC sequences. Their results demonstrate that the studied tetraloop ‐ like overhang geometries are able to stabilize the 2′ ‐ and 3′ ‐ OH groups of the acceptor ribose in the vicinity of the phosphate of the donor strand for several tens to hundreds of nanoseconds, which is entirely sufficient for the required transphosphorylation reactions to proceed. [ABSTRACT FROM AUTHOR]