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

Purine Chemistry in the Early RNA World at the Origins of Life: From RNA and Nucleobases Lesions to Current Key Metabolic Routes

In early life, RNA probably played the central role and, in the corresponding RNA world, the main produced amino acids and small peptides had to react continuously with RNA, ribonucleos(t)ides and nucleobases, especially with purines. A RNA-peptide world and key metabolic pathways have emerged from the corresponding chemical modifications such as the translation process performed by the ribosome. Some interesting reactions of the purine bicycle and of the corresponding ribonucleos(t)ides are performed under plausible prebiotic conditions and described RNA chemical lesions are reviewed with the prospect to highlight their connection with some major steps of the purine and histidine biosynthetic pathways that are, in an intriguingly way, related through two key metabolites, adenosine 5'-triphosphate and the imidazole ribonucleotide 5-aminoimidazole-4-carboxamide ribonucleotide. Ring-opening reactions of purines stand out as efficient accesses to imidazole ribonucleotides and to formamidopyrimidine (Fapy) ribonucleotides suggesting that biosynthetic pathway' first steps have emerged from RNA and ribonucleos(t)ide damages. Also, are summarized the works on the formation and catalytic properties, under plausible prebiotic conditions, of N6-derivatives of the purine base adenine as potential surrogates of histidine in catalysis accordingly to their structural relationship.

Origin of the RNA World in Cold Hadean Geothermal Fields Enriched in Zinc and Potassium: Abiogenesis as a Positive Fallout from the Moon-Forming Impact?

The ubiquitous, evolutionarily oldest RNAs and proteins exclusively use rather rare zinc as transition metal cofactor and potassium as alkali metal cofactor, which implies their abundance in the habitats of the first organisms. Intriguingly, lunar rocks contain a hundred times less zinc and ten times less potassium than the Earth's crust; the Moon is also depleted in other moderately volatile elements (MVEs). Current theories of impact formation of the Moon attribute this depletion to the MVEs still being in a gaseous state when the hot post-impact disk contracted and separated from the nascent Moon. The MVEs then fell out onto juvenile Earth's protocrust; zinc, as the most volatile metal, precipitated last, just after potassium. According to our calculations, the top layer of the protocrust must have contained up to 1019 kg of metallic zinc, a powerful reductant. The venting of hot geothermal fluids through this MVE-fallout layer, rich in metallic zinc and radioactive potassium, both capable of reducing carbon dioxide and dinitrogen, must have yielded a plethora of organic molecules released with the geothermal vapor. In the pools of vapor condensate, the RNA-like molecules may have emerged through a pre-Darwinian selection for low-volatile, associative, mineral-affine, radiation-resistant, nitrogen-rich, and polymerizable molecules.

On the Origin of Information Dynamics in Early Life

We hypothesize that predictable variations in environmental conditions caused by night/day cycles created opportunities and hazards that initiated information dynamics central to life's origin. Increased daytime temperatures accelerated key chemical reactions but also caused the separation of double-stranded polynucleotides, leading to hydrolysis, particularly of single-stranded RNA. Daytime solar UV radiation promoted the synthesis of organic molecules but caused broad damage to protocell macromolecules. We hypothesize that inter-related simultaneous adaptations to these hazards produced molecular dynamics necessary to store and use information. Self-replicating RNA heritably reduced the hydrolysis of single strands after separation during warmer daytime periods by promoting sequences that formed hairpin loops, generating precursors to transfer RNA (tRNA), and initiating tRNA-directed evolutionary dynamics. Protocell survival during daytime promoted sequences in self-replicating RNA within protocells that formed RNA-peptide hybrids capable of scavenging UV-induced free radicals or catalyzing melanin synthesis from tyrosine. The RNA-peptide hybrids are precursors to ribosomes and the triplet codes for RNA-directed protein synthesis. The protective effects of melanin production persist as melanosomes are found throughout the tree of life. Similarly, adaptations mitigating UV damage led to the replacement of Na+ by K+ as the dominant mobile cytoplasmic cation to promote diel vertical migration and selected for homochirality. We conclude that information dynamics emerged in early life through adaptations to predictably fluctuating opportunities and hazards during night/day cycles, and its legacy remains observable in extant life.

Recent advances in the synthesis, reaction, and bio-evaluation potential of purines as precursor pharmacophores in chemical reactions: a review

Purines are nitrogenous heterocyclic compounds characterized by the presence of two fused rings: pyrimidine and imidazole. Their significance is underscored by their widespread occurrence in natural products as the metabolic processes of all living organisms heavily rely on purines and their synthetic derivatives. Furthermore, purines exhibit considerable bioactivity, highlighting their importance in biological systems. Given their unique structural characteristics and ability to yield a diverse array of bioactive molecules, purines have attracted substantial attention from researchers. This review illustrates the recent methods for the synthesis of purines from diaminomaleonitrile, urea derivatives, imidazole, and pyrimidine derivatives reported from 2019 to 2024. Additionally, it elucidates the various chemical modifications applied to the purine nucleus, including benzoylation, alkylation, halogenation, amination, selenylation, thiolation, condensation, diazotization, coupling reactions, and other miscellaneous reactions. Moreover, this review discusses several biological evaluations, including the mechanisms of action of purine derivatives as anticancer, antimicrobial, anti-inflammatory, antiviral, antioxidant, and anti-Alzheimer agents. This review aims to assist researchers in synthetic organic and medicinal chemistry toward the development and enhancement of novel methodologies for the synthesis of new purine molecules while supporting biologists in the identification of new targets for bio-evaluation.

Selection of Early Life Codons by Ultraviolet Light

How life developed in its earliest stages is a central but notoriously difficult question in science. The earliest lifeforms likely used a reduced set of codon sequences that were progressively completed over time, driven by chemical, physical, and combinatorial constraints. However, despite its importance for prebiotic chemistry, UV radiation has not been considered a selection pressure for the evolution of early codon sequences. In this proof-of-principle study, we quantified the UV susceptibility of large pools of DNA protogenomes and tested the timing of evolutionary incorporation of codon sequences using a Monte Carlo method utilizing sequence-context-dependent damage rates previously determined by high throughput sequencing experiments. We traced the UV-radiation selection pressure on early protogenomes comprising a limited number of codon sequences to late protogenomes with access to all codons. The modeling showed that in just minutes under early sunlight, the choice of the first codons determined whether most of the protogenomes remained intact or became damaged entirely. The results correlated with earlier chemical models of the evolution of the genetic code. Our results show how UV could have played a crucial role in the evolution of the early genetic code for a DNA-based genome and provide the concept for future RNA-based studies.

Do-Nothing Prebiotic Chemistry: Chemical Kinetics as a Window into Prebiotic Plausibility

ConspectusOrigin of Life research is a fast growing field of study with each year bringing new breakthroughs. Recent discoveries include novel syntheses of life's building blocks, mechanisms of activation and interaction between molecules, and newly identified environments that provide promising conditions for these syntheses and mechanisms. Even with these new findings, firmly grounded in rigorous laboratory experiments, researchers often find themselves uncertain about how to apply them. How can a bridge be built between the laboratory and the geochemical environment? A critical question to ask when seeking to apply new results in origins is: how can this chemistry occur without direct intervention from a chemist? We believe the first step toward answering this question lies in the determination of rate constants and the construction of chemical networks to describe prebiotic chemistry in geochemical environments.So far, our group has measured several rate constants relevant to different prebiotic reaction networks, starting with the synthetic pathways of the cyanosulfidic network. The reactions we explore often involve ultraviolet light-driven photochemistry, facilitated by our StarLab setup that accurately simulates the spectrum of the young Sun and other stars. Our latest work investigates environments with active photochemistry in the absence of cyanide. In this study, we measure the effective rate constant for the production of formate from the reduction of carbon species using sulfite within the context of early Martian waters. The underlying goal of the work done in our group is to predict the likelihood that certain geological conditions will result in a specific set of chemical products. These predictions can be combined with those we have made for the necessary astrophysical conditions in certain origins of life scenarios on extrasolar planets.In the near future we expect that a sufficient number of rate constants will be measured, by our group and others, to allow for aspects of prebiotic chemistry to be predicted using chemical kinetics models. Once these models have been benchmarked against experimental data, our next step will be applying them to natural environments that better mimic the conditions thought to have been present at the onset of life. Following this, we can test these models by comparing their predictions to additional experiments. After refinement, these models will be able to provide guidance on the optimal conditions for conducting laboratory experiments, while helping to minimize and characterize any interference from a chemist.This approach can provide valuable insights into what is possible within geochemical environments, where all chemistry is by necessity do-nothing chemistry.

Groundwater-Driven Evolution of Prebiotic Alkaline Lake Environments

Alkaline lakes are thought to have facilitated prebiotic synthesis reactions on the early Earth because their modern analogs accumulate vital chemical feedstocks such as phosphate through the evaporation of dilute groundwaters. Yet, the conditions required for some building block synthesis reactions are distinct from others, and these conditions are generally incompatible with those permissible for nascent cellular function. However, because current scenarios for prebiotic synthesis have not taken account of the physical processes that drive the chemical evolution of alkaline lakes, the potential for the co-occurrence of both prebiotic synthesis and the origins and early evolution of life in prebiotic alkaline lake environments remains poorly constrained. Here, we investigate the dynamics of active, prebiotically relevant alkaline lakes using near-surface geophysics, aqueous geochemistry, and hydrogeologic modeling. Due to their small size, representative range of chemistry, and contrasting evaporation behavior, the investigated, neighboring Last Chance and Goodenough Lakes in British Columbia, Canada offer a uniquely tractable environment for investigating the dynamics of alkaline lake behavior. The results show that the required, extreme phosphate enrichments in alkaline lake waters demand geomorphologically-driven vulnerability to evaporation, while the resultant contrast between evaporated brines and inflowing groundwaters yields Rayleigh-Taylor instabilities and vigorous surface-subsurface cycling and mixing of lake and groundwaters. These results provide a quantitative basis to reconcile conflicting prebiotic requirements of UV light, salinity, metal concentration, and pH in alkaline lake environments. The complex physical and chemical processing inherent to prebiotic alkaline lake environments thus may have not only facilitated prebiotic reaction networks, but also provided habitable environments for the earliest evolution of life.

Wet-dry cycles cause nucleic acid monomers to polymerize into long chains

The key first step in the oligomerization of monomers is to find an initiator, which is usually done by thermolysis or photolysis. We present a markedly different approach that initiates acid-catalyzed polymerization at the surface of water films or water droplets, which is the reactive phase during a wet-dry cycle in freshwater hot springs associated with subaerial volcanic landmasses. We apply this method to the oligomerization of different nucleic acids, a topic relevant to how it might be possible to go from simple nucleic acid monomers to long-chain polymers, a key step in forming the building blocks of life. It has long been known that dehydration at elevated temperatures can drive the synthesis of ester and peptide bonds, but this reaction has typically been carried out by incubating dry monomers at elevated temperatures. We report that single or multiple cycles of wetting and drying link mononucleotides by forming phosphodiester bonds. Mass spectrometric analysis reveals uridine monophosphate oligomers up to 53 nucleotides, with an abundance of 35 and 43 nt in length. Long-chain oligomers are also observed for thymidine monophosphate, adenosine monophosphate, and deoxyadenosine monophosphate after exposure to a few wet-dry cycles. Nanopore sequencing confirms that long linear chains are formed. Enzyme digestion shows that the linkage is the phosphodiester bond, which is further confirmed by 31P NMR and Fourier transform infrared spectroscopy. This suggests that nucleic acid oligomers were likely to be present on early Earth in a steady state of synthesis and hydrolysis.

Solvothermal Polymerization of Diaminomaleonitrile Reveals Optimal Green Solvents for the Production of C=N-Based Polymers

Solvothermal polymerization (STP) of diaminomaleonitrile (DAMN) was evaluated using a wide variety of solvents and in the temperature range from 80 to 170 °C. The highest yields, almost quantitative, were achieved with protic n-alcohols such as n-pentanol or n-hexanol at 130 and 150 °C, respectively. The kinetic behavior was studied by gravimetry and the DAMN consumption was monitored by UV-vis spectroscopy and HPLC. GC-MS identified byproducts of the DAMN hydrolysis and oxidation reactions, which were significantly reduced when n-pentanol or n-hexanol were used with respect to hydrothermal conditions. This led to an exploration of compositional changes and microstructural variations by FTIR and NMR spectroscopy and simultaneous thermal analysis. n-Hexanol appears to be an ideal eco-friendly solvent for the DAMN self-STP. The results presented here are not only of interest for the design of polymeric materials based on C=N structures but also show remarkable implications for prebiotic chemistry.

Deep-Ultraviolet Photoexcitation of Aqueous Urea Forms Carbamic Acid/Carbamate in Less Than One Picosecond

Urea is believed to have been essential to the synthesis of prebiotic nucleotides and thereby the RNA or DNA of the first lifeforms. Models suggesting that life began in wet-dry cycles around shallow aquatic ponds imply that reactants such as urea were exposed to deep ultraviolet irradiation from the young sun. Detrimental photodissociation of urea induced by deep UV excitation potentially challenges these models. We here follow the primary deep ultraviolet photochemistry of aqueous urea. The data show that urea is barely excited at 200 nm due to weak ultraviolet absorption. The likelihood of photodissociation is further reduced by strong intra-molecular coupling of the CN and CO stretch vibrations accompanied by an efficient dissipation of the excitation energy to the surrounding water molecules mitigated by urea-water hydrogen bonds. We find that 54±5 % of the excited urea molecules dissociate. Reactions between the photoproducts and surrounding solvent molecules form carbamic acid or the carbamate anions within 0.6 ps. The molecules that do not dissociate return to the electronic ground state in 2 ps. Interestingly, the photodissociation processes of urea in the aqueous phase is different from earlier reported reactions observed following the VUV photolysis of urea in noble gas matrices and highlight the potential influence of water on the prebiotic photochemistry.

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.

Base-pairing of uracil and 2,6-diaminopurine: from cocrystals to photoreactivity

We show that the non-canonical nucleobase 2,6-diaminopurine (D) spontaneously base pairs with uracil (U) in water and the solid state without the need to be attached to the ribose-phosphate backbone. Depending on the reaction conditions, D and U assemble in thermodynamically stable hydrated and anhydrated D-U base-paired cocrystals. Under UV irradiation, an aqueous solution of D-U base-pair undergoes photochemical degradation, while a pure aqueous solution of U does not. Our simulations suggest that D may trigger the U photodimerization and show that complementary base-pairing modifies the photochemical properties of nucleobases, which might have implications for prebiotic chemistry.

Photodissociation of leucine-enkephalin protonated peptide: an experimental and theoretical perspective

Understanding the competing processes that govern far ultraviolet photodissociation (FUV-PD) of biopolymers such as proteins is a challenge. Here, we report a combined experimental and theoretical investigation of FUV-PD of protonated leucine-enkephalin pentapeptide ([YGGFL + H]+) in the gas-phase. Time-dependent density functional theory (TD-DFT) calculations in combination with experiments and previous results for amino acids and shorter peptides help in rationalizing the evolution of the excited states. The results confirm that fragmentation of [YGGFL + H]+ results mainly from vibrationally excited species in the ground electronic state, populated after internal conversion. We also propose fragmentation mechanisms for specific photo-fragments such as tyrosine side chain loss (with an extra hydrogen) or hydrogen loss. In general, we observe the same mechanisms as for smaller peptides or protonated Tyr and Phe, that are not quenched by the presence of other amino acids. Nevertheless, we also found some differences, as for H loss, in part due to the fact that the charge is solvated by the peptide chain and not only by the COOH terminal group.

UV Transmission in Prebiotic Environments on Early Earth

Ultraviolet (UV) light is likely to have played important roles in surficial origins of life scenarios, potentially as a productive source of energy and molecular activation, as a selective means to remove unwanted side products, or as a destructive mechanism resulting in loss of molecules/biomolecules over time. The transmission of UV light through prebiotic waters depends upon the chemical constituents of such waters, but constraints on this transmission are limited. Here, we experimentally measure the molar decadic extinction coefficients for a number of small molecules used in various prebiotic synthetic schemes. We find that many small feedstock molecules absorb most at short (∼200 nm) wavelengths, with decreasing UV absorption at longer wavelengths. For comparison, we also measured the nucleobase adenine and found that adenine absorbs significantly more than the simpler molecules often invoked in prebiotic synthesis. Our results enable the calculation of UV photon penetration under varying chemical scenarios and allow further constraints on plausibility and self-consistency of such scenarios. While the precise path that prebiotic chemistry took remains elusive, improved understanding of the UV environment in prebiotically plausible waters can help constrain both the chemistry and the environmental conditions that may allow such chemistry to occur.

A Surface Hydrothermal Source of Nitriles and Isonitriles

Giant impacts can generate transient hydrogen-rich atmospheres, reducing atmospheric carbon. The reduced carbon will form hazes that rain out onto the surface and can become incorporated into the crust. Once heated, a large fraction of the carbon is converted into graphite. The result is that local regions of the Hadean crust were plausibly saturated with graphite. We explore the consequences of such a crust for a prebiotic surface hydrothermal vent scenario. We model a surface vent fed by nitrogen-rich volcanic gas from high-temperature magmas passing through graphite-saturated crust. We consider this occurring at pressures of 1-1000bar and temperatures of 1500-1700 ∘C. The equilibrium with graphite purifies the leftover gas, resulting in substantial quantities of nitriles (0.1% HCN and 1ppm HC3N) and isonitriles (0.01% HNC) relevant for prebiotic chemistry. We use these results to predict gas-phase concentrations of methyl isocyanide of ∼1 ppm. Methyl isocyanide can participate in the non-enzymatic activation and ligation of the monomeric building blocks of life, and surface or shallow hydrothermal environments provide its only known equilibrium geochemical source.

Photoinduced charge separation and DNA self-repair depend on sequence directionality and stacking pattern

Charge separation is one of the most common consequences of the absorption of UV light by DNA. Recently, it has been shown that this process can enable efficient self-repair of cyclobutane pyrimidine dimers (CPDs) in specific short DNA oligomers such as the GAT[double bond, length as m-dash]T sequence. The mechanism was characterized as sequential electron transfer through the nucleobase stack which is controlled by the redox potentials of nucleobases and their sequence. Here, we demonstrate that the inverse sequence T[double bond, length as m-dash]TAG promotes self-repair with higher quantum yields (0.58 ± 0.23%) than GAT[double bond, length as m-dash]T (0.44 ± 0.18%) in a comparative study involving UV-irradiation experiments. After extended exposure to UV irradiation, a photostationary equilibrium between self-repair and damage formation is reached at 33 ± 13% for GAT[double bond, length as m-dash]T and at 40 ± 16% for T[double bond, length as m-dash]TAG, which corresponds to the maximum total yield of self-repair. Molecular dynamics and quantum mechanics/molecular mechanics (QM/MM) simulations allowed us to assign this disparity to better stacking overlap between the G and A bases, which lowers the energies of the key A-˙G+˙ charge transfer state in the dominant conformers of the T[double bond, length as m-dash]TAG tetramer. These conformational differences also hinder alternative photorelaxation pathways of the T[double bond, length as m-dash]TAG tetranucleotide, which otherwise compete with the sequential electron transfer mechanism responsible for CPD self-repair. Overall, we demonstrate that photoinduced electron transfer is strongly dependent on conformation and the availability of alternative photodeactivation mechanisms. This knowledge can be used in the identification and prediction of canonical and modified DNA sequences exhibiting efficient electron transfer. It also further contributes to our understanding of DNA self-repair and its potential role in the photochemical selection of the most photostable sequences on the early Earth.

Radical Reactions in Organic Synthesis: Exploring in-, on-, and with-Water Methods

Radical reactions in water or aqueous media are important for organic synthesis, realizing high-yielding processes under non-toxic and environmentally friendly conditions. This overview includes (i) a general introduction to organic chemistry in water and aqueous media, (ii) synthetic approaches in, on, and with water as well as in heterogeneous phases, (iii) reactions of carbon-centered radicals with water (or deuterium oxide) activated through coordination with various Lewis acids, (iv) photocatalysis in water and aqueous media, and (v) synthetic applications bioinspired by naturally occurring processes. A wide range of chemical processes and synthetic strategies under different experimental conditions have been reviewed that lead to important functional group translocation and transformation reactions, leading to the preparation of complex molecules. These results reveal how water as a solvent/medium/reagent in radical chemistry has matured over the last two decades, with further discoveries anticipated in the near future.

Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It

Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.

The Nature of the Spark Is a Pivotal Element in the Design of a Miller-Urey Experiment

Miller and Urey applied electric sparks to a reducive mixture of CH4, NH3, and water to obtain a complex organic mixture including biomolecules. In this study, we examined the impact of temperature, initial pressure, ammonia concentration, and the spark generator on the chemical profile of a Miller-Urey-type prebiotic broth. We analyzed the broth composition using Gas Chromatography combined with Mass Spectroscopy (GC/MS). The results point towards strong compositional changes with the nature of the spark. Ammonia exhibited catalytic properties even with non-nitrogen-containing compounds. A more elevated temperature led to a higher variety of substances. We conclude that to reproduce such a broth as well as possible, all the studied parameters need to be tightly controlled, the most difficult and important being spark generation.

Impact of M Dwarfs Ultraviolet Radiation on Prebiotic Chemistry: The Case of Adenine

To date, several exoplanets have been found to orbit within the habitable zone of main sequence M stars (M dwarfs). These stars exhibit different levels of chromospheric activity that produces ultraviolet (UV) radiation. UV may be harmful to life, but it can also trigger reactions of prebiotic importance on the surface of a potentially habitable planet (PHP). We created a code to obtain the adenine yield for a known adenine synthesis route from diaminomaleonitrile (DAMN). We used computational methods to calculate the reaction coefficient rates (photolysis rate J and rate constant K) for the intermediate molecules DAMN, diaminofumaronitrile (DAFN), and 4-aminoimidazole-5-carbonitrile (AICN) of the adenine synthesis route. We used stellar UV sources and a mercury lamp to compare the theoretical results with experiments performed with lamps. The surface UV flux of planets in the habitable zone of two active M dwarfs (Proxima Centauri and AD Leonis) and the prebiotic Earth was calculated using the photochemical model ATMOS, considering a CO₂-N₂-H₂O atmosphere. We obtained UV absorption coefficients for DAMN and DAFN and thermodynamic parameters that are useful for prebiotic chemistry studies. According to our results, experiments using UV lamps may underestimate the photolysis production of molecules of prebiotic importance. Our results indicate that photolysis reactions are fast with a yield of 50% of AICN in 10 s for the young Sun and ∼1 h for Proxima Centauri b. Planets around active M dwarfs may provide the most favorable environment for UV-mediated production of compounds relevant to the origins of life. The kinetic reaction AICN + HCN  adenine is the bottleneck of the pathway with reaction rates <10^-22 L/(mol·s).

Prebiotic Synthesis of N-Formylaminonitriles and Derivatives in Formamide

Amino acids and their derivatives were probably instrumental in the transition of prebiotic chemistry to early biology. Accordingly, amino acid formation under prebiotic conditions has been intensively investigated. Unsurprisingly, most of these studies have taken place with water as the solvent. Herein, we describe an investigation into the formation and subsequent reactions of aminonitriles and their formylated derivatives in formamide. We find that N-formylaminonitriles form readily from aldehydes and cyanide in formamide, even in the absence of added ammonia, suggesting a potentially prebiotic source of amino acid derivatives. Alkaline processing of N-formylaminonitriles proceeds with hydration at the nitrile group faster than deformylation, protecting aminonitrile derivatives from reversion of the Strecker condensation equilibrium during hydration/hydrolysis and furnishing mixtures of N-formylated and unformylated amino acid derivatives. Furthermore, the facile synthesis of N-formyldehydroalanine nitrile is observed in formamide from glycolaldehyde and cyanide without intervention. Dehydroalanine derivatives have been proposed as important compounds for prebiotic peptide synthesis, and we demonstrate both a synthesis suggesting that they are potentially plausible components of a prebiotic inventory, and reactions showing their utility as abiotic precursors to a range of compounds of prebiological interest.

Reflections on the Origin and Early Evolution of the Genetic Code

Examination of the genetic code (GeCo) reveals that amino acids coded by (A/U) codons display a large functional spectrum and bind RNA whereas, except for Arg, those coded by (G/C) codons do not. From a stereochemical viewpoint, the clear preference for (A/U)-rich codons to be located at the GeCo half blocks suggests they were specifically determined. Conversely, the overall lower affinity of cognate amino acids for their (G/C)-rich anticodons points to their late arrival to the GeCo. It is proposed that i) initially the code was composed of the eight (A/U) codons; ii) these codons were duplicated when G/C nucleotides were added to their wobble positions, and three new codons with G/C in their first position were incorporated; and iii) a combination of A/U and G/C nucleotides progressively generated the remaining codons.

Prebiotic Synthesis of ATP: A Terrestrial Volcanism-Dependent Pathway

Adenosine triphosphate (ATP) is a multifunctional small molecule, necessary for all modern Earth life, which must be a component of the last universal common ancestor (LUCA). However, the relatively complex structure of ATP causes doubts about its accessibility on prebiotic Earth. In this paper, based on previous studies on the synthesis of ATP components, a plausible prebiotic pathway yielding this key molecule is constructed, which relies on terrestrial volcanism to provide the required materials and suitable conditions.

Advancing mechanochemical synthesis by combining milling with different energy sources

Owing to its efficiency and unique reactivity, mechanochemical processing of bulk solids has developed into a powerful tool for the synthesis and transformation of various classes of materials. Nevertheless, mechanochemistry is primarily based on simple techniques, such as milling in comminution devices. Recently, mechanochemical reactivity has started being combined with other energy sources commonly used in solution-based chemistry. Milling under controlled temperature, light irradiation, sound agitation or electrical impulses in newly developed experimental setups has led to reactions not achievable by conventional mechanochemical processing. This Perspective describes these unique reactivities and the advances in equipment tailored to synthetic mechanochemistry. These techniques - thermo-mechanochemistry, sono-mechanochemistry, electro-mechanochemistry and photo-mechanochemistry - represent a notable advance in modern mechanochemistry and herald a new level of solid-state reactivity: mechanochemistry 2.0.

A Physicochemical Consideration of Prebiotic Microenvironments for Self-Assembly and Prebiotic Chemistry

The origin of life on Earth required myriads of chemical and physical processes. These include the formation of the planet and its geological structures, the formation of the first primitive chemicals, reaction, and assembly of these primitive chemicals to form more complex or functional products and assemblies, and finally the formation of the first cells (or protocells) on early Earth, which eventually evolved into modern cells. Each of these processes presumably occurred within specific prebiotic reaction environments, which could have been diverse in physical and chemical properties. While there are resources that describe prebiotically plausible environments or nutrient availability, here, we attempt to aggregate the literature for the various physicochemical properties of different prebiotic reaction microenvironments on early Earth. We introduce a handful of properties that can be quantified through physical or chemical techniques. The values for these physicochemical properties, if they are known, are then presented for each reaction environment, giving the reader a sense of the environmental variability of such properties. Such a resource may be useful for prebiotic chemists to understand the range of conditions in each reaction environment, or to select the medium most applicable for their targeted reaction of interest for exploratory studies.

A Facile Route for the Formation of Complex Nitrogen-Containing Prebiotic Molecules in the Interstellar Medium

Prebiotic molecules have often been identified in the interstellar medium and meteorite samples. However, we still have only a fragmentary knowledge of the mechanism of the evolutionary process of these prebiotic molecules. With the aid of state-of-the-art vacuum ultraviolet (VUV)-infrared (IR) spectroscopy and ab initio calculations, we reveal a new pathway leading to the formation of the biorelevant molecules carrying amine groups or peptide bonds via the single-photon ionization induced Michael/cyclization reaction of acrylonitrile (AN)-alcohol heterodimer complexes in the gas phase. In the reactions, not only N-H nitrilium cations with H⁺-N≡C-R Lewis structure but also cyclic amine cations with a peptide bond can be formed when the AN reacts with alcohols of increasing molecular size (such as ethanol, propanol, or butanol). This study suggests the possibility of unsaturated nitriles being reduced by ionized alcohols in space, which can further drive sequential Michael addition/cyclization reactions to form more complex biorelevant molecules.

Sources of Nitrogen-, Sulfur-, and Phosphorus-Containing Feedstocks for Prebiotic Chemistry in the Planetary Environment

Biochemistry on Earth makes use of the key elements carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur (or CHONPS). Chemically accessible molecules containing these key elements would presumably have been necessary for prebiotic chemistry and the origins of life on Earth. For example, feedstock molecules including fixed nitrogen (e.g., ammonia, nitrite, nitrate), accessible forms of phosphorus (e.g., phosphate, phosphite, etc.), and sources of sulfur (e.g., sulfide, sulfite) may have been necessary for the origins of life, given the biochemistry seen in Earth life today. This review describes potential sources of nitrogen-, sulfur-, and phosphorus-containing molecules in the context of planetary environments. For the early Earth, such considerations may be able to aid in the understanding of our own origins. Additionally, as we learn more about potential environments on other planets (for example, with upcoming next-generation telescope observations or new missions to explore other bodies in our Solar System), evaluating potential sources for elements necessary for life (as we know it) can help constrain the potential habitability of these worlds.

Electronic Structure Effects Related to the Origin of the Remarkable Near-Infrared Absorption of Blastochloris viridis' Light Harvesting 1-Reaction Center Complex

Various photosynthetic organisms have evolved to absorb light in different regions of the visible light spectrum, thus adapting to the various lighting conditions available on Earth. While most of these autotrophic organisms absorb wavelengths around the 700-800 nm region, some are capable of red-shifted absorptions above this range, but none as remarkably as Blastochloris viridis whose main absorption is observed at 1015 nm, approximately 220 nm (0.34 eV) lower in energy than their main constituent pigments, BChl-b, whose main absorption is observed at 795 nm. The structure of its light harvesting 1-reaction center was recently elucidated by cryo-EM; however, the electronic structure details behind this red-shifted absorption remain unattended. We used hybrid quantum mechanics/molecular mechanics (QM/MM) calculations to optimize one of the active centers and performed classical molecular dynamics (MD) simulations to sample conformations beyond the optimized structure. We did excited state calculations with the time-dependent density functional theory method at the CAM-B3LYP/cc-pVDZ level of theory. We reproduced the near IR absorption by sequentially modifying the number of components involved in our systems using representative structures from the calculated MD ensemble. Natural transition orbital analysis reveals the participation of the BChl-b fragments to the main transition in the native structure and the structures obtained from the QM/MM and MD simulations. H-bonding pigment-protein interactions play a role on the conformation stabilization and orientation; however, the bacteriochlorin ring conformations and the exciton delocalization are the most relevant factors to explain the red-shifting phenomenon.

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'.

On the Origin of Sugar Handedness: Facts, Hypotheses and Missing Links-A Review

By paraphrasing one of Kipling's most amazing short stories (How the Leopard Got His Spots), this article could be entitled "How Sugars Became Homochiral". Obviously, we have no answer to this still unsolved mystery, and this perspective simply brings recent models, experiments and hypotheses into the homochiral homogeneity of sugars on earth. We shall revisit the past and current understanding of sugar chirality in the context of prebiotic chemistry, with attention to recent developments and insights. Different scenarios and pathways will be discussed, from the widely known formose-type processes to less familiar ones, often viewed as unorthodox chemical routes. In particular, problems associated with the spontaneous generation of enantiomeric imbalances and the transfer of chirality will be tackled. As carbohydrates are essential components of all cellular systems, astrochemical and terrestrial observations suggest that saccharides originated from environmentally available feedstocks. Such substances would have been capable of sustaining autotrophic and heterotrophic mechanisms integrating nutrients, metabolism and the genome after compartmentalization. Recent findings likewise indicate that sugars' enantiomeric bias may have emerged by a transfer of chirality mechanisms, rather than by deracemization of sugar backbones, yet providing an evolutionary advantage that fueled the cellular machinery.

Orange-Light-Induced Photochemistry Gated by pH and Confined Environments

We introduce a new photochemically active compound, i.e., pyridinepyrene (PyPy), entailing a pH-active moiety that effects a significant halochromic shift into orange-light (λ = 590 nm) activatable photoreactivity while concomitantly exerting control over its reaction pathways. With blue light (λ = 450 nm) in neutral to basic pH, a [2 + 2] photocycloaddition can be triggered to form a cyclobutene ring in a reversible fashion. If the pH is decreased to acidic conditions, resulting in a halochromic absorption shift, photocycloaddition on the small-molecule level is blocked due to repulsive interactions and exclusive trans-cis isomerization is observed. Through implementation of PyPy into the confined environment of a single-chain nanoparticle (SCNP) design, one can overcome the repulsive forces and exploit the halochromic shift for orange light (λ = 590 nm)-induced cycloaddition and formation of macromolecular three-dimensional (3D) architectures.

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 F e C N 6 4 - . 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., e a q - 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.

Methods to identify and characterize iron-sulfur oligopeptides in water

Iron-sulfur clusters are ubiquitous cofactors that mediate central biological processes. However, despite their long history, these metallocofactors remain challenging to investigate when coordinated to small (≤ six amino acids) oligopeptides in aqueous solution. In addition to being often unstable in vitro, iron-sulfur clusters can be found in a wide variety of forms with varied characteristics, which makes it difficult to easily discern what is in solution. This difficulty is compounded by the dynamics of iron-sulfur peptides, which frequently coordinate multiple types of clusters simultaneously. To aid investigations of such complex samples, a summary of data from multiple techniques used to characterize both iron-sulfur proteins and peptides is provided. Although not all spectroscopic techniques are equally insightful, it is possible to use several, readily available methods to gain insight into the complex composition of aqueous solutions of iron-sulfur peptides.

Prebiotic photoredox synthesis from carbon dioxide and sulfite

Carbon dioxide (CO2) is the major carbonaceous component of many planetary atmospheres, which includes the Earth throughout its history. Carbon fixation chemistry-which reduces CO2 to organics, utilizing hydrogen as the stoichiometric reductant-usually requires high pressures and temperatures, and the yields of products of potential use to nascent biology are low. Here we demonstrate an efficient ultraviolet photoredox chemistry between CO2 and sulfite that generates organics and sulfate. The chemistry is initiated by electron photodetachment from sulfite to give sulfite radicals and hydrated electrons, which reduce CO2 to its radical anion. A network of reactions that generates citrate, malate, succinate and tartrate by irradiation of glycolate in the presence of sulfite was also revealed. The simplicity of this carboxysulfitic chemistry and the widespread occurrence and abundance of its feedstocks suggest that it could have readily taken place on the surfaces of rocky planets. The availability of the carboxylate products on early Earth could have driven the development of central carbon metabolism before the advent of biological CO2 fixation.

Carbamoyl phosphate and its substitutes for the uracil synthesis in origins of life scenarios

The first step of pyrimidine synthesis along the orotate pathway is studied to test the hypothesis of geochemical continuity of protometabolic pathways at the origins of life. Carbamoyl phosphate (CP) is the first high-energy building block that intervenes in the in vivo synthesis of the uracil ring of UMP. Thus, the likelihood of its occurrence in prebiotic conditions is investigated herein. The evolution of carbamoyl phosphate in water and in ammonia aqueous solutions without enzymes was characterised using ATR-IR, ³¹P and ¹³C spectroscopies. Carbamoyl phosphate initially appears stable in water at ambient conditions before transforming to cyanate and carbamate/hydrogenocarbonate species within a matter of hours. Cyanate, less labile than CP, remains a potential carbamoylating agent. In the presence of ammonia, CP decomposition occurs more rapidly and generates urea. We conclude that CP is not a likely prebiotic reagent by itself. Alternatively, cyanate and urea may be more promising substitutes for CP, because they are both “energy-rich” (high free enthalpy molecules in aqueous solutions) and kinetically inert regarding hydrolysis. Energy-rich inorganic molecules such as trimetaphosphate or phosphoramidates were also explored for their suitability as sources of carbamoyl phosphate. Although these species did not generate CP or other carbamoylating agents, they exhibited energy transduction, specifically the formation of high-energy P–N bonds. Future efforts should aim to evaluate the role of carbamoylating agents in aspartate carbamoylation, which is the following reaction in the orotate pathway.

Prebiotic Photochemical Coproduction of Purine Ribo- and Deoxyribonucleosides

The hypothesis that life on Earth may have started with a heterogeneous nucleic acid genetic system including both RNA and DNA has attracted broad interest. The recent finding that two RNA subunits (cytidine, C, and uridine, U) and two DNA subunits (deoxyadenosine, dA, and deoxyinosine, dI) can be coproduced in the same reaction network, compatible with a consistent geological scenario, supports this theory. However, a prebiotically plausible synthesis of the missing units (purine ribonucleosides and pyrimidine deoxyribonucleosides) in a unified reaction network remains elusive. Herein, we disclose a strictly stereoselective and furanosyl-selective synthesis of purine ribonucleosides (adenosine, A, and inosine, I) and purine deoxynucleosides (dA and dI), alongside one another, via a key photochemical reaction of thioanhydroadenosine with sulfite in alkaline solution (pH 8–10). Mechanistic studies suggest an unexpected recombination of sulfite and nucleoside alkyl radicals underpins the formation of the ribo C2′–O bond. The coproduction of A, I, dA, and dI from a common intermediate, and under conditions likely to have prevailed in at least some primordial locales, is suggestive of the potential coexistence of RNA and DNA building blocks at the dawn of life.

Water-Air Interfaces as Environments to Address the Water Paradox in Prebiotic Chemistry: A Physical Chemistry Perspective

The asymmetric water-air interface provides a dynamic aqueous environment with properties that are often very different than bulk aqueous or gaseous phases and promotes reactions that are thermodynamically, kinetically, or otherwise unfavorable in bulk water. Prebiotic chemistry faces a key challenge: water is necessary for life yet reduces the efficiency of many biomolecular synthesis reactions. This perspective considers water-air interfaces as auspicious reaction environments for abiotic synthesis. We discuss recent evidence that (1) water-air interfaces promote condensation reactions including peptide synthesis, phosphorylation, and oligomerization; (2) photochemistry at water-air interfaces may have been a significant source of prebiotic molecular complexity, given the lack of oxygen and increased availability of near-ultraviolet radiation on early Earth; and (3) water-air interfaces can promote spontaneous reduction and oxidation reactions, potentially providing protometabolic pathways. Life likely began within a relatively short time frame, and water-air interfaces offer promising environments for simultaneous and efficient biomolecule production.