UV photostability of three 2-aminoazoles with key roles in prebiotic chemistry on the early earth

Prebiotic synthesis of dihydrouridine by photoreduction of uridine in formamide

In this report, we show that a very common modification (especially in tRNA), dihydrouridine, was efficiently produced by photoreduction of the canonical pyrimidine ribonucleoside, uridine in formamide. Formamide not only acts as a solvent in this reaction, but also as the reductant. The other three components of the canonical alphabet (C, A, G) remained intact under the same conditions, suggesting that dihydrouridine might have coexisted with all four canonical RNA nucleosides (C, U, A, G) at the dawn of life.

Heat flows enrich prebiotic building blocks and enhance their reactivity

The emergence of biopolymer building blocks is a crucial step during the origins of life1-6. However, all known formation pathways rely on rare pure feedstocks and demand successive purification and mixing steps to suppress unwanted side reactions and enable high product yields. Here we show that heat flows through thin, crack-like geo-compartments could have provided a widely available yet selective mechanism that separates more than 50 prebiotically relevant building blocks from complex mixtures of amino acids, nucleobases, nucleotides, polyphosphates and 2-aminoazoles. Using measured thermophoretic properties7,8, we numerically model and experimentally prove the advantageous effect of geological networks of interconnected cracks9,10 that purify the previously mixed compounds, boosting their concentration ratios by up to three orders of magnitude. The importance for prebiotic chemistry is shown by the dimerization of glycine11,12, in which the selective purification of trimetaphosphate (TMP)13,14 increased reaction yields by five orders of magnitude. The observed effect is robust under various crack sizes, pH values, solvents and temperatures. Our results demonstrate how geologically driven non-equilibria could have explored highly parallelized reaction conditions to foster prebiotic chemistry.

Enhancing Prebiotic Phosphorylation and Modulating the Regioselectivity of Nucleosides with Diamidophosphate†

Among the many prebiotic phosphorylation chemistries investigated, diamidophosphate (DAP) has shown promising potential for nucleoside phosphorylation. Herein, we show that DAP's phosphorylation capability is enhanced significantly (up to 90%) in wet-dry cycles by a range of prebiotically plausible pHs (6-10) and temperatures (up to 80 °C) in the presence of additives such as formamide, cyanamide, urea, guanidine, 2-aminoimidazole, and hydantoin. For ribonucleosides, the main products are the 2',3'-cyclic phosphates along with the corresponding 2'- and 3'-phosphates, while deoxyribonucleosides form 5'- and 3'-phosphates, the ratios of which are affected by cycles and the presence and nature of the additives. A simple change of temperature to 80 °C with additives leads to higher conversion yields (≈80-90%) with an increased level of 5'-phosphorylation (≈40-49%). This demonstration of enhancing and controlling the regioselectivity of DAP-mediated phosphorylation by a range of additives and conditions potentiates transitioning to the search for more efficient catalysts, enabling regiospecific phosphorylations and oligonucleotide formation in the same milieu and setting.

Photochemistry of 2-thiooxazole: a plausible prebiotic precursor to RNA nucleotides

Potentially prebiotic chemical reactions leading to RNA nucleotides involve periods of UV irradiation, which are necessary to promote selectivity and destroy biologially irrelevant side products. Nevertheless, UV light has only been applied to promote specific stages of prebiotic reactions and its effect on complete prebiotic reaction sequences has not been extensively studied. Here, we report on an experimental and computational investigation of the photostability of 2-thiooxazole (2-TO), a potential precursor of pyrimidine and 8-oxopurine nucleotides on early Earth. Our UV-irradiation experiments resulted in rapid decomposition of 2-TO into unidentified small molecule photoproducts. We further clarify the underlying photochemistry by means of accurate ab initio calculations and surface hopping molecular dynamics simulations. Overall, the computational results show efficient rupture of the aromatic ring upon the photoexcitation of 2-TO via breaking of the C-O bond. Consequently, the initial stage of the divergent prebiotic synthesis of pyrimidine and 8-oxopurine nucleotides would require periodic shielding from UV light either with sun screening chromophores or through a planetary scenario that would protect 2-TO until it is transformed into a more stable intermediate compound, e.g. oxazolidinone thione.

Protometabolism as out-of-equilibrium chemistry

It is common to compare life with machines. Both consume fuel and release waste to run. In biology, the engine that drives the living system is referred to as metabolism. However, attempts at deciphering the origins of metabolism do not focus on this energetic relationship that sustains life but rather concentrate on nonenzymatic reactions that produce all the intermediates of an extant metabolic pathway. Such an approach is akin to studying the molecules produced from the burning of coal instead of deciphering how the released energy drives the movement of pistons and ultimately the train when investigating the mechanisms behind locomotion. Theories that do explicitly invoke geological chemical gradients to drive metabolism most frequently feature hydrothermal vent conditions, but hydrothermal vents are not the only regions of the early Earth that could have provided the fuel necessary to sustain the Earth's first (proto)cells. Here, we give examples of prior reports on protometabolism and highlight how more recent investigations of out-of-equilibrium systems may point to alternative scenarios more consistent with the majority of prebiotic chemistry data accumulated thus far. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.

Structure, Spectra and Photochemistry of 2-Amino-4-Methylthiazole: FTIR Matrix Isolation and Theoretical Studies

The structure, tautomerization pathways, vibrational spectra, and photochemistry of 2-amino-4-methylthiazole (AMT) molecule were studied by matrix isolation FTIR spectroscopy and DFT calculations undertaken at the B3LYP/6-311++G(3df,3pd) level of theory. The most stable tautomer with the five-membered ring stabilized by two double C=C and C=N bonds, was detected in argon matrices after deposition. When the AMT/Ar matrices were exposed to 265 nm selective irradiation, three main photoproducts, N-(1-sulfanylprop-1-en-2-yl)carbodiimide (fp1), N-(1-thioxopropan-2-yl)carbodiimide (fp2) and N-(2-methylthiiran-2-yl)carbodiimide (fp3), were photoproduced by a cleavage of the CS–CN bond together with hydrogen atom migration. The minor photoreaction caused by the cleavage of the CS–CC bond and followed by hydrogen migration formed 2-methyl-1H-azirene-1-carbimidothioic acid (fp15). We have also found that cleavage of the CS–CN bond followed by disruption of the N–C bond produced cyanamide (fp11) and the C(CH3)=CH–S biradical that transformed into 2-methylthiirene (fp12) and further photoreactions produced 1-propyne-1-thiole (fp13) or methylthioketene (fp14). Cleavage of the CS–CC bond followed by disruption of the N–C bond produced propyne (fp22) and the S–C(NH₂)=N biradical that transformed into 3-aminethiazirene (fp23); further photoreactions produced N-sulfanylcarbodiimide (fp25). As a result of these transformations, several molecular complexes were identified as photoproducts besides new molecules in the AMT photolysis process.

UV Transmission in Natural Waters on Prebiotic Earth

Ultraviolet (UV) light plays a key role in surficial theories of the origin of life, and numerous studies have focused on constraining the atmospheric transmission of UV radiation on early Earth. However, the UV transmission of the natural waters in which origins-of-life chemistry (prebiotic chemistry) is postulated to have occurred is poorly constrained. In this work, we combine laboratory and literature-derived absorption spectra of potential aqueous-phase prebiotic UV absorbers with literature estimates of their concentrations on early Earth to constrain the prebiotic UV environment in marine and terrestrial natural waters, and we consider the implications for prebiotic chemistry. We find that prebiotic freshwaters were largely transparent in the UV, contrary to assumptions in some models of prebiotic chemistry. Some waters, such as high-salinity waters like carbonate lakes, may be deficient in shortwave (≤220 nm) UV flux. More dramatically, ferrous waters can be strongly UV-shielded, particularly if the Fe²⁺ forms highly UV-absorbent species such as FeCN64-. Such waters may be compelling venues for UV-averse origin-of-life scenarios but are unfavorable for some UV-dependent prebiotic chemistries. UV light can trigger photochemistry even if attenuated through photochemical transformations of the absorber (e.g., eaq- production from halide irradiation), which may have both constructive and destructive effects for prebiotic syntheses. Prebiotic chemistries that invoke waters that contain such absorbers must self-consistently account for the chemical effects of these transformations. The speciation and abundance of Fe²⁺ in natural waters on early Earth is a major uncertainty and should be prioritized for further investigation, as it played a major role in UV transmission in prebiotic natural waters.

Computational Analysis of a Prebiotic Amino Acid Synthesis with Reference to Extant Codon-Amino Acid Relationships

Novel density functional theory calculations are presented regarding a mechanism for prebiotic amino acid synthesis from alpha-keto acids that was suggested to happen via catalysis by dinucleotide species. Our results were analysed with comparison to the original hypothesis (Copley et al., PNAS, 2005, 102, 4442–4447). It was shown that the keto acid–dinucleotide hypothesis for possible prebiotic amino acid synthesis was plausible based on an initial computational analysis, and details of the structures for the intermediates and transition states showed that there was wide scope for interactions between the keto acid and dinucleotide moieties that could affect the free energy profiles and lead to the required proto-metabolic selectivity.

Timescales for Prebiotic Photochemistry Under Realistic Surface Ultraviolet Conditions

Ultraviolet (UV) light has long been invoked as a source of energy for prebiotic chemical synthesis, but experimental support does not involve sources of UV light that look like the young Sun. Here we experimentally investigate whether the UV flux available on the surface of early Earth, given a favorable atmosphere, can facilitate a variety of prebiotic chemical syntheses. We construct a solar simulator for the UV light of the faint young Sun on the surface of early Earth, called StarLab. We then attempt a series of reactions testing different aspects of a prebiotic chemical scenario involving hydrogen cyanide (HCN), sulfites, and sulfides under the UV light of StarLab, including hypophosphite oxidation by UV light and hydrogen sulfide, photoreduction of HCN with bisulfite, the photoanomerization of α-thiocytidine, the production of a chemical precursor of a potentially prebiotic activating agent (nitroprusside), the photoreduction of thioanhydrouridine and thioanhydroadenosine, and the oxidation of ethanol (EtOH) by photochemically generated hydroxyl radicals. We compare the output of StarLab to the light of the faint young Sun to constrain the timescales over which these reactions would occur on the surface of early Earth. We predict that hypophosphite oxidation, HCN reduction, and photoproduction of nitroprusside would all operate on the surface of early Earth in a matter of days to weeks. The photoanomerization of α-thiocytidine would take months to complete, and the production of oxidation products from hydroxyl radicals would take years. The photoreduction of thioanhydrouridine with hydrogen sulfide did not succeed even after a long period of irradiation, providing a lower limit on the timescale of several years. The photoreduction of thioanhydroadenosine with bisulfite produced 2'-deoxyriboadenosine (dA) on the timescale of days. This suggests the plausibility of the photoproduction of purine deoxyribonucleotides, such as the photoproduction of simple sugars, proceeds more efficiently in the presence of bisulfite.

A cyanosulfidic origin of the Krebs cycle

The centrality of the Krebs cycle in metabolism has long been interpreted as evidence of its antiquity, and consequently, questions regarding its provenance, and whether it initially functioned as a cycle or not, have received much attention. The present report shows that prebiotic oxidation of α-hydroxy carboxylates can be achieved by UV photolysis of a simple geochemical species (HS^-), which leads to α-oxo carboxylates that feature in the Krebs cycle and glyoxylate shunt. Further reaction of these products leads to almost all intermediates of the Krebs cycle proper, succinate semialdehyde bypass, and glyoxylate shunt. Fumarate, the missing Krebs cycle component, and the required α-hydroxy carboxylates can be provided by a highly related hydrogen cyanide chemistry, which also provides precursors for amino acids, nucleotides, and phospholipids.

Illuminating Life's Origins: UV Photochemistry in Abiotic Synthesis of Biomolecules

Solar radiation is the principal source of energy available to Earth and has unmatched potential for the synthesis of organic material from primordial molecular building blocks. As well as providing the energy for photochemical synthesis of (proto)biomolecules of interest in origins of life-related research, light has also been found to often provide remarkable selectivity in these processes, for molecules that function in extant biology and against those that do not. As such, light is heavily implicated as an environmental input on the nascent Earth that was important for the emergence of complex yet selective chemical systems underpinning life. Reactivity and selectivity in photochemical prebiotic synthesis are discussed, as are their implications for origins of life scenarios and their plausibility, and the future directions of this research.

Ultrafast excited-state dynamics of promising nucleobase ancestor 2,4,6-triaminopyrimidine

The ultrafast excited-state dynamics of 2,4,6-triaminopyrimidine - thought to be a promising candidate for a proto-RNA nucleobase - have been investigated via static multireference quantum-chemical calculations and mixed-quantum-classical/trajectory surface-hopping dynamics with a focus on the lowest-lying electronic states of the singlet manifold and with a view towards understanding the UV(C)/UV(B) photostability of the molecule. Ultrafast internal conversion channels have been identified that connect the lowest-lying ππ* electronically-excited state of 2,4,6-triaminopyrimidine with the ground electronic state, and non-radiative decay has been observed to take place on the picosecond timescale via a ππ* out-of-plane NH2 ("oop-NH2") minimum-energy crossing point. The short excited-state lifetime is competitive with the excited-state lifetimes of the canonical pyrimidine nucleobases, affirming the promise of 2,4,6-triaminopyrimidine as an ancestor. Evidence for energy-dependent excited-state dynamics is presented, and the open question of intersystem crossing is discussed speculatively.

Shielding from UV Photodamage: Implications for Surficial Origins of Life Chemistry on the Early Earth

UV light has been invoked as a source of energy for driving prebiotic chemistry, but such high energy photons are also known to cause damage to biomolecules and their precursors. One potential mechanism for increasing the lifetime of UV-photounstable molecules is to invoke a protection or shielding mechanism. UV shielding could either occur by the molecule in question itself (self-shielding) or by the presence of other UV-absorbing molecules. We investigate and illustrate these two shielding mechanisms as means of increasing the lifetime of 2-aminooxazole (AO), a prebiotic precursor molecule moderately susceptible to UV photodamage, with an expected half-life of 7 h on the surface of the early Earth. AO can be protected by being present in high concentrations, such that it self-shields. AO can similarly be protected by the presence of UV-absorbing nucleosides; the degree of protection depends on the concentration and identity of the nucleoside. The purine nucleosides (A, G, and I) confer more protection than the pyrimidines (C and U). We find that 0.1 mM purine ribonucleosides affords AO about the same protection as 1 mM AO self-shielding, corresponding to a lifetime enhancement of 2-3×. This suggests that only a modest yield of nucleosides can potentially allow for protection of UV photounstable molecules, and therefore this could be a plausible mechanism for protecting sensitive molecules while prebiotic synthesis is occurring simultaneously. Our findings suggest that both synthetic and degradative reactions can proceed at the same time, given various degrees of shielding.

Ultrafast nonradiative deactivation of photoexcited 8-oxo-hypoxanthine: a nonadiabatic molecular dynamics study

In the scientific endeavor to understand the chemical origins of life, the photochemistry of the smallest life building blocks, nucleobases, has been a constant object of focus and intense research. Here, we report the results of the first theoretical study on the photo-properties of an 8-oxo-hypoxanthine molecule, the chromophore of 8-oxo-inosine, which is relevant to the recently proposed, prebiotically plausible synthetic routes to the formation of purine- and pyrimidine-nucleotides. With ab initio and semi-empirical OM2/MRCI quantum-chemistry calculations, we predict a strong photostability of the 8-oxo-hypoxanthine system and see the origin of this effect in ultrafast nonradiative relaxation through puckering of the 6-membered heterocyclic ring.

Photoredox chemistry in the synthesis of 2-aminoazoles implicated in prebiotic nucleic acid synthesis

Prebiotically plausible ferrocyanide-ferricyanide photoredox cycling oxidatively converts thiourea to cyanamide, whilst HCN is reductively homologated to intermediates which either react directly with the cyanamide giving 2-aminoazoles, or have the potential to do so upon loss of HCN from the system. Thiourea itself is produced by heating ammonium thiocyanate, a product of the reaction of HCN and hydrogen sulfide under UV irradiation.

Potentially Prebiotic Activation Chemistry Compatible with Nonenzymatic RNA Copying

The nonenzymatic replication of ribonucleic acid (RNA) may have enabled the propagation of genetic information during the origin of life. RNA copying can be initiated in the laboratory with chemically activated nucleotides, but continued copying requires a source of chemical energy for in situ nucleotide activation. Recent work has illuminated a potentially prebiotic cyanosulfidic chemistry that activates nucleotides, but its application to nonenzymatic RNA copying had not been demonstrated. Here, we report a novel pathway that activates RNA nucleotides in a manner compatible with template-directed nonenzymatic copying. We show that this pathway, which we refer to as bridge-forming activation, selectively yields the reactive imidazolium-bridged dinucleotide intermediate required for copying. Our results will enable more realistic simulations of RNA propagation based on continuous in situ nucleotide activation.

A continuous reaction network that produces RNA precursors

Continuous reaction networks, which do not rely on purification or timely additions of reagents, serve as models for chemical evolution and have been demonstrated for compounds thought to have played important roles for the origins of life such as amino acids, hydroxy acids, and sugars. Step-by-step chemical protocols for ribonucleotide synthesis are known, but demonstrating their synthesis in the context of continuous reaction networks remains a major challenge. Herein, compounds proposed to be important for prebiotic RNA synthesis, including glycolaldehyde, cyanamide, 2-aminooxazole, and 2-aminoimidazole, are generated from a continuous reaction network, starting from an aqueous mixture of NaCl, NH4Cl, phosphate, and HCN as the only carbon source. No well-timed addition of any other reagents is required. The reaction network is driven by a combination of γ radiolysis and dry-down. γ Radiolysis results in a complex mixture of organics, including the glycolaldehyde-derived glyceronitrile and cyanamide. This mixture is then dried down, generating free glycolaldehyde that then reacts with cyanamide/NH3 to furnish a combination of 2-aminooxazole and 2-aminoimidazole. This continuous reaction network models how precursors for generating RNA and other classes of compounds may arise spontaneously from a complex mixture that originates from simple reagents.

pH-Dependent Adsorption of Peptides on Montmorillonite for Resisting UV Irradiation

Ultraviolet (UV) irradiation is considered an energy source for the prebiotic chemical synthesis of life's building blocks. However, it also results in photodegradation of biology-related organic compounds on early Earth. Thus, it is important to find a process to protect these compounds from decomposition by UV irradiation. Herein, pH effects on both the adsorption of peptides on montmorillonite (MMT) and the abilities of peptides to resist UV irradiation due to this adsorption were systematically studied. We found that montmorillonite (MMT) can adsorb peptides effectively under acidic conditions, while MMT-adsorbed peptides can be released under basic conditions. Peptide adsorption is positively correlated with the length of the peptide chains. MMT's adsorption of peptides and MMT-adsorbed peptide desorption are both rapid-equilibrium, and it takes less than 30 min to reach the equilibrium in both cases. Furthermore, compared to free peptides, MMT-adsorbed peptides under acidic conditions are well protected from UV degradation even after prolonged irradiation. These results indicate amino acid/peptides are able to concentrate from aqueous solution by MMT adsorption under low-pH conditions (concentration step). The MMT-adsorbed peptides survive under UV irradiation among other unprotected species (storage step). Then, the MMT-adsorbed peptides can be released to the aqueous solution if the environment becomes more basic (releasing step), and these free peptides are ready for polymerization to polypeptides. Hence, a plausible prebiotic concentration-storage-release cycle of amino acids/peptides for further polypeptide synthesis is established.