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

Infrared Spectra of Small Radicals for Exoplanetary Spectroscopy: OH, NH, CN and CH: The State of Current Knowledge

In this study, we present a current state-of-the-art review of middle-to-near IR emission spectra of four simple astrophysically relevant molecular radicals-OH, NH, CN and CH. The spectra of these radicals were measured by means of time-resolved Fourier transform infrared spectroscopy in the 700-7500 cm^-1 spectral range and with 0.07-0.02 cm^-1 spectral resolution. The radicals were generated in a glow discharge of gaseous mixtures in a specially designed discharge cell. The spectra of short-lived radicals published here are of great importance, especially for the detailed knowledge and study of the composition of exoplanetary atmospheres in selected new planets. Today, with the help of the James Webb telescope and upcoming studies with the help of Plato and Ariel satellites, when the investigated spectral area is extended into the infrared spectral range, it means that detailed knowledge of the infrared spectra of not only stable molecules but also the spectra of short-lived radicals or ions, is indispensable. This paper follows a simple structure. Each radical is described in a separate chapter, starting with historical and actual theoretical background, continued by our experimental results and concluded by spectral line lists with assigned notation.

Photophysical Characterization of Isoguanine in a Prebiotic-Like Environment

It is intriguing how a mixture of organic molecules survived the prebiotic UV fluxes and evolved into the actual genetic building blocks. Scientists are trying to shed light on this issue by synthesizing nucleic acid monomers and their analogues under prebiotic Era-like conditions and by exploring their excited state dynamics. To further add to this important body of knowledge, this study discloses new insights into the photophysical properties of protonated isoguanine, an isomorph of guanine, using steady-state and femtosecond broadband transient absorption spectroscopies, and quantum mechanical calculations. Protonated isoguanine decays in ultrafast time scales following 292 nm excitation, consistently with the barrierless paths connecting the bright S₁ (ππ*) state with different internal conversion funnels. Complementary calculations for neutral isoguanine predict similar photophysical properties. These results demonstrate that protonated isoguanine can be considered photostable in contrast to protonated guanine, which exhibits 40-fold longer excited state lifetimes.

Pathways for the Formation of Formamide, a Prebiotic Biomonomer: Metal-Ions in Interstellar Gas-Phase Chemistry

The chemistry occurring in the interstellar medium (ISM) is an active area of contemporary research. New aspects of interstellar chemistry are getting unraveled regularly. In this context, the role of metal-ions in the chemistry occurring in the ISM is not well-studied so far. Herein, we highlight the role of metal-ions in interstellar chemistry. For this purpose, we choose the problem of gas-phase formamide formation in interstellar molecular clouds. Formamide is a key biomonomer and contains the simplest peptide [-(C═O)-NH-] linkage. With its two electronegative atoms ("O" and "N"), it provides an excellent platform to probe the role of the metal-ions. The metal-ions chosen are Na⁺, K⁺, Al⁺, Mg⁺, and Mg²⁺-all of them present in the ISM. The metal-ions are studied in three different forms as bare positively charged ions, as hydrated metal-ions co-ordinated with a molecule of water, and when the metal-ions are part of a neutral covalent molecule. With the aid of electronic structure calculations [CCSD(T) and DFT methods], we study different gas-phase pathways which result in the generation of interstellar formamide. Throughout our study, we find that metal-ions lower the barriers (with Mg⁺, Mg⁺⁺, and Al⁺ offering maximal stabilization of the transition states) and facilitate the reactions. The chemical factors influencing the reactions, how we consider the putative conditions in the ISM, the astrochemical implications of this study, and its connection with terrestrial prebiotic chemistry and refractory astrochemistry are subsequently presented. Based on our results, we also recommend the detection of two new closed-shell molecules, NH₂CH₂OH (aminomethanol) and CH₂NH₂⁺ (iminium ion), and two open-shell molecules, CONH₂ (carbamyl radical) and HCONH (an isomer of carbamyl radical), in the ISM.

Autocatalysis in Formose Reaction and Formation of RNA Nucleosides

Understanding of the abiotic formation of nucleosides under geochemical conditions is currently a major scientific challenge. In this study, free radical pathways for formation of RNA nucleosides with canonical nucleobases are proposed for the first time. The pathways proceed with relatively low energy barriers for the formation of ribose as well as all RNA nucleosides. The formose reaction proceeds either with or without Ca²⁺ and CaOH⁺ cations. An autocalytic cycle for the formation of both glycolaldehyde and glyceraldehyde is identified when Ca²⁺ or CaOH⁺ cations are involved in the reaction. The results suggest that Ca²⁺ cations are not involved in the formation of ribose from glyceraldehyde. In addition, these pathways lead to the formation of dihydroxyacetone and d-erythrose. Calculated results show that the glycosidic bond can be formed abiotically between the d-ribose and the nucleobase, where d-ribose forms a cyclic free radical that subsequently reacts with the neutral nucleobase. Involvement of proper nucleobase tautomer is important for the formation of RNA nucleosides. Our approaches provide a solution for the long-standing question of how the glycosidic bond is formed under the abiotic conditions with low energy barriers. The pathways for formation of the sugars without a catalyst are relevant to the formation of sugars in interstellar clouds. On the other hand, the autocalysis in the formose reaction followed by the formation of the nucleosides is appropriate for the abiotic synthesis taking place in the presence of water in the early Earth environment. The Ca²⁺ and CaOH⁺ cations appear to be the first nonenzymatic catalytic systems for formation of biomolecules.

Could Purines Be Formed from Cyanamide and Cyanoacetylene in a Prebiotic Earth Environment?

Knowledge of prebiotic nucleobase formation is important for understanding the origin of contemporary genetics. Observation of nucleobase precursor radicals in previous impact laser plasma simulations of the late heavy bombardment period (FerusProc. Natl. Acad. Sci. U.S.A.2015, 112, 657) points toward possible nucleobase formation through free-radical pathways. However, previously explored radical routes to nucleobase formation involve a large number of reaction steps, repetitive addition of precursors, and a number of chemical transformations. The possibility of competing side reactions under such conditions questions the feasibility of such pathways. In view of these shortcomings, the present work employs density functional theory to explore purine formation pathways through reaction of cyanamide and cyanoacetylene with radicals via a five-membered intermediate, 4-cyanoimidazole in the presence of ammonia. Our analysis reveals that the skeletal components of 4-cyanoimidazole can be solely obtained from cyanamide and cyanoacetylene via barrierless cyclization and a small number of reaction steps. In addition, the proposed mechanisms are characterized by a small number of precursors and low energy barriers and are thus likely feasible under extreme conditions on the prebiotic earth such as meteoritic impact during late heavy bombardment period. Overall, the present study underscores the importance of cyanamide and cyanoacetylene precursors in kinetically accessible routes to purine formation.

Thermal decomposition of syn- and anti-dihydropyrenes; functional group-dependent decomposition pathway

Syn and anti dihydropyrene (DHP) are excellent thermochromes, and therefore extensively studied for their thermochromic and photochromic properties, respectively. However, they suffer from thermal decomposition due to thermal instability. In this study, we thoroughly investigated pathways for the thermal decomposition of anti- and syn- dihydropyrenes through computational methods. The decomposition pathways include sigmatropic shift and hemolytic and heterolytic (cationic and anionic) cleavages. The decomposition pathway is influenced not only by the dihydropyrene (syn- or anti-) but also by the functional groups present. For anti-dihydropyrenes, sigmatropic shift is the most plausible pathways for CN and CHO internal groups. The cascade of sigmatropic shifts is followed by elimination to deliver substituted pyrenes. For CH₃- and H- dihydropyrenes, hemolytic cleavage of the internal groups is the most plausible pathway for decomposition to pyrenes. The pathway is changed to heterolytic cleavage when the internal groups on the dihydropyrenes are Cl^-, Br^-, and SMe^-. Comparison of the activation barriers for syn (30.18 kcal mol^-1) and anti (32.10 kcal mol^-1) dimethyldihydropyrenes for radical pathway reveal that decomposition of syn- DHP is more facile over anti-, which is consistent with the experimental observation. The decomposition pathway for syn-dihydropyrene is also hemolytic in cleavage when the internal groups are methyl and hydrogen. Syn-dihydropyrenes (symmetrical or unsymmetrical) bearing CN group do not follow sigmatropic shift, quite contrary to the anti-dihydropyrene. The lack of tendency of the syn-dihydropyrene for sigmatropic shift is rationalized on the planarity of the scaffold. The results of the theoretical study are consistent with the experimental observations. The results here help in understanding the behavior of substituents on the dihydropyrene scaffold, which will be useful in designing new molecules with improved thermal stabilities. Graphical abstract Functional group dependent decomposition pathways of dihydropyrenes.

Radical pathways for the formation of non-canonical nucleobases in prebiotic environments

Due to the inability of canonical nucleobases (adenine, uracil, guanine and cytosine) to spontaneously form ribonucleosides and base pairs in free form in solution, RNA is believed to be preceded by a primitive information polymer (preRNA). The preRNA is proposed to contain non-canonical, heterocyclic bases that possess the above-mentioned capabilities. An extensive search for such candidate heterocycles has recently revealed that barbituric acid (BA), melamine (MM) and 2,4,6-triaminopyrimidine (TAP) have the capability to spontaneously form ribonucleosides and supramolecular assemblies that are held by Watson–Crick type hydrogen-bonded base pairs involving BA, MM, TAP and cyanuric acid (CA) heterocycles. However, despite this evidence, the prebiotic formation pathways of these heterocycles have not been fully explored. Further, for these heterocycles to interact and assemble into informational polymers under prebiotic conditions, it is expected that they should have formed in the proximity of each other. In this context, the present work employs density functional theory to propose the associated radical based formation pathways starting from cyanamide. Our pathways suggest that cyanamide, its derivatives (malonic acid and urea) and malononitrile can form BA, MM, CA and TAP in the presence of ammonia and hydroxyl radicals. In addition to originating from a common precursor, similarities in the highest reaction barriers (13 to 20 kcal mol⁻¹) obtained for these pathways suggest that these heterocycles may likely form under similar conditions. Specifically, these pathways are relevant to high energy events such as meteoritic impact during the late heavy bombardment period on the early earth, which would have created conditions where radicals might have formed in reasonable concentrations. Overall, the present study emphasizes the importance of cyanamide in prebiotic heterocycle formation.

The study explores radical-assisted formations of the nucleobase components of primitive genetics from cyanamide and related precursors in impact events.

Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments

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.

High Energy Radical Chemistry Formation of HCN-rich Atmospheres on early Earth

Recent results in prebiotic chemistry implicate hydrogen cyanide (HCN) as the source of carbon and nitrogen for the synthesis of nucleotide, amino acid and lipid building blocks. HCN can be produced during impact events by reprocessing of carbonaceous and nitrogenous materials from both the impactor and the atmosphere; it can also be produced from these materials by electrical discharge. Here we investigate the effect of high energy events on a range of starting mixtures representative of various atmosphere-impactor volatile combinations. Using continuously scanning time–resolved spectrometry, we have detected ·CN radical and excited CO as the initially most abundant products. Cyano radicals and excited carbon monoxide molecules in particular are reactive, energy-rich species, but are resilient owing to favourable Franck–Condon factors. The subsequent reactions of these first formed excited species lead to the production of ground-state prebiotic building blocks, principally HCN.

State-of-the-Art Thermochemical and Kinetic Computations for Astrochemical Complex Organic Molecules: Formamide Formation in Cold Interstellar Clouds as a Case Study

We describe an integrated computational strategy aimed at providing reliable thermochemical and kinetic information on the formation processes of astrochemical complex organic molecules. The approach involves state-of-the-art quantum-mechanical computations, second-order vibrational perturbation theory, and kinetic models based on capture and transition state theory together with the master equation approach. Notably, tunneling, quantum reflection, and leading anharmonic contributions are accounted for in our model. Formamide has been selected as a case study in view of its interest as a precursor in the abiotic amino acid synthesis. After validation of the level of theory chosen for describing the potential energy surface, we have investigated several pathways of the OH + CH2NH and NH2 + H2CO reaction channels. Our results show that both reaction channels are essentially barrierless (in the sense that all relevant transition states lie below or only marginally above the reactants) and once tunneling is taken into the proper account indicate that the reaction can occur under the low temperature conditions of interstellar environments.

Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario

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.

Unified reaction pathways for the prebiotic formation of RNA and DNA nucleobases

The reaction pathways for the prebiotic formation of nucleobases are complex and lead to the formation of a mixture of products.

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.

Prebiotic synthesis of triazines from urea: a theoretical study of free radical routes to melamine, ammeline, ammelide and cyanuric acid

Prebiotic formation of triazines from urea was studied using density functional theory methods with the aim of understanding some of the neutral precursors that can lead to a mixture of triazines.