Given the role of HCN as a reactant in RNA building block production (e.g. nucleobases, ribose, and 2-aminooxazole), we propose that an atmosphere rich in hydrogen cyanide (HCN) is a distinguishing feature of what we term biogenic worlds. These are worlds that can produce key biomolecules for the emergence of life in situ rather than requiring they be delivered, e.g., by meteorites. To attack the question of whether early Earth was biogenic, we develop a series of new capabilities including the calculation of missing/unknown HCN reaction rate coefficients, the simulation of HCN chemistry in planetary atmospheres, and the coupling of atmospheric HCN chemistry and rain-out to the production and evolution of RNA building blocks in warm little ponds (WLPs). We make a major leap in understanding the origin of RNA on a biogenic early Earth by building a comprehensive model that couples terrestrial geochemistry, radiative transfer, atmospheric photochemistry, lightning chemistry, and aqueous pond chemistry. We begin by developing an accurate and feasible method to calculate missing reaction rate coefficients related to HCN chemistry in planetary atmospheres. We use density functional theory simulations to solve the transition states for various reactions, and use the simulated energies and partition functions to calculate the corresponding rate coefficients using the principles of statistical mechanics. We initially explore and calculate rate coefficients for a total of 110 reactions present in reducing atmospheres dominated by N2, CH4, and H2, including 48 reactions that were previously unknown in the literature. Our rate coefficients are most commonly within a factor of two of experimental values, and generally always within an order of magnitude of these values. This accuracy is consistent with the typical uncertainties assigned in large-scale kinetic data evaluations. Next, we develop a consistent reduced atmospheric hybrid chemical network (CRAHCN) containing experimental values when available (32%) and our calculated rate coefficients otherwise (68%). To validate our chemistry, we couple CRAHCN to a 1D disequilibrium chemical kinetic model (ChemKM) to compute HCN production in the reducing atmosphere of Saturn's moon Titan. Our calculated atmospheric HCN profile agrees very well with the measurements performed by instruments aboard the Cassini spacecraft, suggesting our chemical network is accurate for modeling HCN production in reducing environments. We also perform sensitivity analyses on this chemistry and find HCN production and destruction on Titan can be understood in terms of only 19 dominant reactions. The process begins with UV photodissociation of N2 and CH4 in the upper atmosphere, and galactic cosmic ray dissociation of these species in the lower atmosphere. The dissociation radicals then proceed to react along four main channels to produce HCN. It is of particular excitement that one of these channels was newly discovered in this work. Moving forward to modeling early Earth, we expand upon CRAHCN by exploring and calculating rate coefficients related to HCN and H2CO chemistry in atmospheres with oxidizing conditions. We calculate the rate coefficients for 126 new reactions, including 45 reactions that were first discovered in this work. We find the accuracy of our method continues to produce most commonly factor of two agreement with respect to experimental values. Next, we develop the oxygen extension to CRAHCN (CRAHCN-O), containing a total of 259 reactions for computing HCN and H2CO production in atmospheres dominated by N2, CO2, H2, CH4, and H2O. Again, experimental rate coefficients are used when available (43%), and our calculated values are used otherwise (57%). We then build a comprehensive model with a unique coupling of early Earth geochemistry, radiative transfer, atmospheric UV and lightning chemistry, and aqueous chemistry in WLPs. We calculate self-consistent pressure-temperature profiles using a 1D radiative transfer code called petitRADTRANS, and couple these to CRAHCN-O and ChemKM to simulate HCN and H2CO production on early Earth. We model two epochs, at 4.4 and 4.0 billion years ago (bya), which differ in atmospheric composition, luminosity, UV intensity, radical production from lightning, and impact bombardment rate. The respective reducing and oxidizing atmospheric compositions of the 4.4 and 4.0 bya epochs are mainly driven by the balance of H2 impact degassing and CO2 outgassing from volcanoes. We then couple the rain-out of HCN with a comprehensive WLP model to compute the in situ production of RNA building blocks for each epoch. HCN pond concentrations are multiplied by experimental yields to calculate biomolecule production, and there are various biomolecule sinks present including UV photodissociation, hydrolysis and seepage. At 4.4 bya, we find that HCN rain-out leads to peak adenine production of 2.8μM (378 ppb) for maximum lightning conditions. These concentrations are comparable to the peak adenine concentrations delivered by carbon-rich meteorites (10.6μM); however, the concentrations from in situ production persist for > 100 million years in contrast to ~days for meteoritic concentrations. Guanine, cytosine, uracil and thymine concentrations from in situ production at this time peak in the 0.19–3.2μM range, and ribose and 2-aminooxazole peak in the nM range. We note that cytosine and thymine are not present in meteorites, suggesting this biogenic pathway may be one of the only plausible origins of these RNA and DNA building blocks. We find that the high mixing ratio of HCN near the surface of our 4.4 bya model is mainly driven by lightning chemistry rather than UV chemistry. Our results show that HCN production at the surface is linearly dependent on lightning flash density. This result supports a lightning-based Miller-Urey scenario for the origin of RNA building blocks. At 4.0 bya, HCN production and rain-out is 2–3 orders of magnitude less abundant than it is at 4.4 bya, leading to negligible concentrations of RNA building blocks in WLPs during this late oxidizing phase. Similar to HCN production in Titan's atmosphere, HCN production in early Earth's atmosphere is strongly correlated with CH4 content. Reducing (H2-dominant) conditions sustain CH4 levels at a roughly constant ppm-level over 100 million years, which is favourable for HCN production. In oxidizing conditions, CH4 is readily oxidized into CO2, leading to less HCN. These results suggest that early Earth was biogenic at 4.4 bya, and remained so for at least ~100 million years, but was over by 4.0 bya due to oxidation of the atmosphere. This thesis provides a firm theoretical foundation for an origin of RNA in WLPs on a biogenic early Earth within about 200 million years after the Moon-forming impact and the cooling of the magma ocean. / Thesis / Doctor of Philosophy (PhD)

Phosphorus is a key element for life. This work reviews the role of phosphorus in life. Theories on the origin of life are confounded by a lack of reactive phosphorus, and attempts to overcome the dearth of reactive phosphorus must employ unrealistic phosphorus compounds, energetic organic compounds, or unusual physical conditions.Meteoritic schreibersite provided an abundant source of reactive phosphorus for the early Earth. Water corrodes schreibersite to form a mixed valence series of phosphorus compounds. Schreibersite corrosion was studied by a variety of techniques, including NMR, MS, XRD, and EPR. Reduced phosphorus in schreibersite corrodes through release of phosphite radicals which react with other radicals to form the phosphorus compounds observed. These radicals are also capable of phosphorylating simple organic compounds to form P-C and P-O-C linkages.The meteoritic mass flux was calculated using the mass frequency distribution of several meteorite collections. Much of the meteoritic mass that falls to the Earth is composed of metallic material which supplies abundant reactive phosphorus. Meteorites are a comparatively poorer source of carbon. Craters concentrate both reduced phosphorus and organic compounds through geomorphologic processes.Phosphorus and sulfur biochemistry are intricately linked in metabolism. The cosmochemistry of sulfur was studied in depth using changing C/O ratios, sulfide formation kinetics, and gas diffusion. The results have implications for meteorites, studies of Jupiter, and of protoplanetary disks.

A brief introduction to the current state of research in the Origins of Life field is given in Part I of this work. Part II covers original research performed by the author and co-workers. Layered Double Hydroxide (LDH) systems are anion-exchanging clays that have the general formula M(II)xM(III)(OH)(2x+2)Y, where M(II) and M(III) are any divalent and trivalent metals, respectively. Y can be nearly any anion, although modern naturally occuring LDH systems incorporate carbonate (CO32-), chloride (Cl-), or sulfate (SO42-) anions. Intercalated cobalticyanide anion shows a small yet observable deviation from local Oh symmetry causing small differences between its oriented and non-oriented infrared spectra. Nitroprusside is shown to intercalate into 2:1 Mg:Al LDH with decomposition to form intercalated ferrocyanide and nitrosyl groups of an unidentified nature. The [Ru(CN)6]4- anion is shown to intercalate into layered double hydroxides in the same manner as other hexacyano anions, such as ferrocyanide and cobalticyanide, with its three-fold rotational axis perpendicular to the hydroxide sheets. The square-planar tetracyano-nickelate(II), -palladate(II), and platinate(II) anions were intercalated into both 2:1 and 3:1 Mg:Al layered double hydroxides (LDH). The basal spacings in the 2:1 hosts are approximately 11 Å, indicating that the anions are inclined approximately 75 degrees relative to the hydroxide layers, while in the 3:1 hosts the square-planar anions have enough space to lie more nearly parallel to the LDH cation layers, giving basal spacings of approximately 8 Å. It has been found that the LDH Mg2Al(OH)6Cl catalyzes the self-addition of cyanide, to give in a one-pot reaction at low concentrations an increased yield of diaminomaleonitrile and in addition, at higher ($0.1M) concentrations, a purple-pink material that adheres to the LDH. We are investigating whether this reaction also occurs with hydrotalcite itself, what is the minimum effective concentration of cyanide, and what can be learned about the products and how they compare with those reported at high HCN concentrations in the absence of catalyst.

The preparation of layered double hydroxides via co-precipitation of a divalent/trivalent metal solution against a base results in 1 mm LDH particles with a disorganized metal lattice. Research was performed to address these morphological issues using techniques such as Ostwald ripening and precipitation via aluminate. Another interesting issue in layered double hydroxide materials is the uptake and orientation of anions into the interlayer. Questions about iron cyanide interlayer anions have been posed. Fourier transform infared spectroscopy and powder x-ray diffraction have been used to investigate these topics. It was found that factors such as orientation, anion charge, and anion structure depended on the divalent/trivalent metal ratio of the hydroxide layer and reactivity time. The cyanide self-addition reaction is an important reaction of classical prebiotic chemistry. This reaction has been shown to give rise to amino acids, purines and pyrimidines. At cyanide concentrations similar to that expected on the early earth, hydrolysis to formamide rather than self-addition occurs. One theory to alleviate this side reaction is the use of minerals or clays that are thought to concentrate and catalyze prebiotics of interest. Layered double hydroxides have been studied as a catalyst for this reaction.

Certos ambientes subterrâneos da Terra possuem acumulados, naturalmente, compostos de radionuclídeos de longa vida, como 238U, 232Th 40K, próximo à presença de água líquida. O mesmo é esperado que aconteça em corpos planetários, no Sistema Solar, que possua quantidades apreciáveis de água. Nestes ambientes radioativos naturais, a radiólise da água produz espécies químicas e desequilíbrios químicos importantes para a vida. Apesar da proposta do decaimento radioativo como fonte alternativa de energia para sistemas vivos existir há mais de trinta anos, isto se mostrou realmente concreto após descoberta de um ecossistema peculiar cuja sobrevivência é dependente de espécies químicas produzidas por radiólise aquosa. Neste trabalho, avaliamos e quantificamos os desequilíbrios químicos gerados localmente pela radiólise aquosa e a possível contribuição destes para a emergência da vida, tendo como referência os estudos em ambientes de fontes hidrotermais alcalinas, consideradas promissores ambientes para esse evento. Também foram avaliados seus efeitos na habitabilidade de possíveis ambientes análogos na lua gelada Europa. Procuramos quantificar a diversidade química formada nessas condições e a associar aos desequilíbrios parâmetros termodinâmicos. As estimativas realizadas para ambientes radioativos na Terra primitiva apontaram para a similaridade entre o desequilíbrio causado por radiólise aquosa e o encontrado em fontes hidrotermais alcalinas. Confirmando e detalhando a análise preliminar que motivou o trabalho. Não obstante, considerando Europa, chegamos a valores de densidade de células do extremófilo Candidatus Desulforudis audaxviator que sobreviveriam em um conjunto de candidatos a análogos geológicos de possível ambiente radioativo na lua gelada. A partir deste estudo pudemos analisar o potencial para a emergência da vida e de protometabolismos nestes ambientes radioativos naturais na Terra primitiva, bem como levantar parâmetros mensuráveis para futuras missões espaciais que buscam vida ou habitabilidade em Europa. / Certain subterranean environments of the Earth has naturally accumulated compounds of longlived radionuclides, such as 238U, 232Th 40K, near the presence of liquid water. The same is estimated in wet planetary bodies in the Solar System. In these natural radioactive environments, water radiolysis produces chemical species and chemical disequilibria, which are important for life. Although the proposal of radioactive decay as an alternative source of energy for deep biospheres has existed for more than thirty years, this proved to be really feasible after the discovery of a peculiar ecosystem whose survivor is dependent on chemical species produced by water radiolysis. In this work, we evaluate and quantify the chemical disequilibria generated locally by water radiolysis and the possible contribution of these to the emergence of life, having as reference the studies alkaline hydrothermal vents, which is considered highly promising environment for this event. It is also evaluated their effects on the habitability of possible analogous environments on the Jupiter icy moon Europa. It was aimed to quantify the chemical diversity formed under these conditions and to calculate disequilibria using thermodynamic parameters. The estimates made for natural radioactive environments in early Earth pointed to the similarity between the disequilibrium caused by water radiolysis and those found in alkaline hydrothermal vents. What confirms and details the preliminary analysis that motivated this work. In addition, it was calculated values for cell density of the Candidatus Desulforudis audaxviator extremophile, that would survive in Europa comparable to the in situ analysis of some terrestrial radioactive environments, using a set of possible scenarios for possible local natural radioactive environments. From this study, we were able to analyze the potential for the emergence of life and protometabolisms in these natural radioactive environments in early Earth, as well as to provide measurable parameters for future space missions that seek for life or habitability in Europa.

Certos ambientes subterrâneos da Terra possuem acumulados, naturalmente, compostos de radionuclídeos de longa vida, como 238U, 232Th 40K, próximo à presença de água líquida. O mesmo é esperado que aconteça em corpos planetários, no Sistema Solar, que possua quantidades apreciáveis de água. Nestes ambientes radioativos naturais, a radiólise da água produz espécies químicas e desequilíbrios químicos importantes para a vida. Apesar da proposta do decaimento radioativo como fonte alternativa de energia para sistemas vivos existir há mais de trinta anos, isto se mostrou realmente concreto após descoberta de um ecossistema peculiar cuja sobrevivência é dependente de espécies químicas produzidas por radiólise aquosa. Neste trabalho, avaliamos e quantificamos os desequilíbrios químicos gerados localmente pela radiólise aquosa e a possível contribuição destes para a emergência da vida, tendo como referência os estudos em ambientes de fontes hidrotermais alcalinas, consideradas promissores ambientes para esse evento. Também foram avaliados seus efeitos na habitabilidade de possíveis ambientes análogos na lua gelada Europa. Procuramos quantificar a diversidade química formada nessas condições e a associar aos desequilíbrios parâmetros termodinâmicos. As estimativas realizadas para ambientes radioativos na Terra primitiva apontaram para a similaridade entre o desequilíbrio causado por radiólise aquosa e o encontrado em fontes hidrotermais alcalinas. Confirmando e detalhando a análise preliminar que motivou o trabalho. Não obstante, considerando Europa, chegamos a valores de densidade de células do extremófilo Candidatus Desulforudis audaxviator que sobreviveriam em um conjunto de candidatos a análogos geológicos de possível ambiente radioativo na lua gelada. A partir deste estudo pudemos analisar o potencial para a emergência da vida e de protometabolismos nestes ambientes radioativos naturais na Terra primitiva, bem como levantar parâmetros mensuráveis para futuras missões espaciais que buscam vida ou habitabilidade em Europa. / Certain subterranean environments of the Earth has naturally accumulated compounds of longlived radionuclides, such as 238U, 232Th 40K, near the presence of liquid water. The same is estimated in wet planetary bodies in the Solar System. In these natural radioactive environments, water radiolysis produces chemical species and chemical disequilibria, which are important for life. Although the proposal of radioactive decay as an alternative source of energy for deep biospheres has existed for more than thirty years, this proved to be really feasible after the discovery of a peculiar ecosystem whose survivor is dependent on chemical species produced by water radiolysis. In this work, we evaluate and quantify the chemical disequilibria generated locally by water radiolysis and the possible contribution of these to the emergence of life, having as reference the studies alkaline hydrothermal vents, which is considered highly promising environment for this event. It is also evaluated their effects on the habitability of possible analogous environments on the Jupiter icy moon Europa. It was aimed to quantify the chemical diversity formed under these conditions and to calculate disequilibria using thermodynamic parameters. The estimates made for natural radioactive environments in early Earth pointed to the similarity between the disequilibrium caused by water radiolysis and those found in alkaline hydrothermal vents. What confirms and details the preliminary analysis that motivated this work. In addition, it was calculated values for cell density of the Candidatus Desulforudis audaxviator extremophile, that would survive in Europa comparable to the in situ analysis of some terrestrial radioactive environments, using a set of possible scenarios for possible local natural radioactive environments. From this study, we were able to analyze the potential for the emergence of life and protometabolisms in these natural radioactive environments in early Earth, as well as to provide measurable parameters for future space missions that seek for life or habitability in Europa.

The Sutherland group recently demonstrated that from a mixture of oligoribonucleotide-2'- or 3'-phosphates the latter is chemoselectively acetylated. This is shown to mediate a template-directed ligation to give predominantly 3',5'-linked RNA that is acetylated at the ligation junction (acetyl-RNA). It was suggested that RNA emerged prebiotically via acetyl-RNA and also is proposed to have favourable genotypic properties due to greater propensity to form duplex structure. To study the properties of acetyl-RNA, their synthesis by solid-phase chemistry was required and described is the design of a 2'/3'-O-acetyl orthogonal protecting group strategy. Key to the orthogonal protecting group strategy is the use of (2-cyanoethoxy)carbonyl for the protection of the nucleobase exocyclic amines and a photolabile solid-phase linker group that allowed partial on-column deprotection. The synthesis of the 2'/3'-O-acetyl and 2'/3'-O-TBDMS phosphoramidites, in addition to preparation of a photolabile solid-phase support, are described. With the materials to hand the procedures for an automated synthesis of acetyl-RNA were optimised and several acetyl-RNA oligonucleotides were synthesised. The duplex stability of acetyl-RNA with up to four sites of 2'-O-acetylation were assessed by UV melting curve analysis. Remarkably, the acetyl groups caused a consistent decrease in Tm of between 3.0-3.2 °C. Thermodynamic parameters indicated a decrease in duplex stability that was consistent with a decrease in hydration of the minor groove resulting in a reduction of the stabilising hydrogen bonding network. The stability of a tetraloop was also found to decrease on acetylation. The acetylated- tetraloop it is able to form duplex at lower concentrations than the natural tetraloop. Additionally, it is more stable at high concentrations, indicating that acetyl-RNA favours duplex over other secondary structure. These properties are considered to give acetyl-RNA competitive advantage for their non-enzymatic replication. Aminoacylation of RNA is an important process in modern biology but the intermediacy of aminoacyl-adenylates is considered to be prebiotically implausible. A potentially prebiotic aminoacylation of nucleoside-3'-phosphates, selective for the 2'-hydroxyl, is presented. However, it was thought the aminoacylation yields could be improved and so a search for an alternative activator was conducted. Oligoribonucleotide-3'-phosphates were exposed to the aminoacylation conditions and selective aminoacylation at only the 2'-hydroxyl of the 3'-end was observed. In particular, the aminoacylation of a trimer lends support to Sutherland’s theory of a linked origin of RNA and coded peptide synthesis.

The 'RNA World' hypothesis states that RNA was the first living system on the primitive Earth, where it carried out dual genotypic and phenotypic functions. Therefore, RNA must have self-assembled by purely chemical means from small prebiotic feedstock molecules. A plausible demonstration of the synthesis of RNA with the natural [5'→3'] phosphodiester linkage, and its self-replication has not been achieved so far. Some have speculated a 'simpler' informational polymer preceded it, and biology based on this polymer subsequently 'invented' RNA. The structurally simpler L-α-threofuranosyl nucleic acid (TNA) has been proposed as a primordial ancestor to RNA. A study into the potential self-assembly of TNA nucleotides was carried out. It is shown that as a direct result of TNA's structural simplicity, its generational chemistry is more difficult than RNA. The tetrose aminooxazolines are unstable under the conditions of its formation. The tetrose anhydronucleosides efficiently incorporate phosphate to form activated tetrose cytidine-2',3'-cyclic phosphates, but with the wrong stereochemistry. Strong support for the 'RNA world' hypothesis came from a report in 2009 of the prebiotic synthesis of activated pyridimine ribonucleoside-2',3'-cyclic phosphates. Oligomerisation studies were carried out on these activated monomers with various catalysts, and NMR studies were carried out to determine the aspects of their reactivity. It was found that only short oligomers are formed. However, nucleoside-2',3'-cyclic phosphates were found to selectively hydrolyse to a 2:1 mixture of 3' and 2'-monophosphates, and this observation was considered as etiologically relevant. Nucleoside-2' and 3'-monophosphates cyclise back to nucleoside-2',3'-cyclic phosphates upon phosphate activation, and so cannot be considered as direct candidates for oligomerisation. A chemistry that selectively uses the nucleoside-3'-phosphate for the synthesis of RNA, and recycles the unwanted 2'-phosphate would be highly desirable. Thus, a regio- and chemoselective reaction that selectively acetylates monomer and oligomer nucleoside-3'-phosphates at the 2'-hydroxyl in water is presented. Nucleoside-2'-phosphates are shown to acetylate less efficiently, and show a greater propensity to recyclise back to nucleoside-2',3'-cyclic phosphates. Purine nucleotides were also found to acetylate better than pyrimidines. This potentially primordial protecting group chemistry approach towards the prebiotic synthesis of RNA is conceptually novel, and has the potential to give a natural [5'→3'] phosphodiester linkage isomer. It is considered as a major step towards solving the long-standing problem of non-enzymatic self-replication of RNA.

Life on Earth likely began as an RNA world, where cell-free or compartmentalized ribonucleic acid (RNA) molecules dominated as the replicating and evolving lifeforms prior to the emergence of DNA- and protein-based life. The focus of this thesis is on when and how this RNA world emerged. We use astrophysical and geophysical studies to constrain when the Earth was habitable, and biosignature studies to constrain when the Earth was inhabited. From this we obtain a time interval for the emergence of life. Considering all these constraints, we find that the Earth was habitable as early as 4.5 Ga, or as late as 3.9 Ga, depending on whether the early influx of asteroids inhibited life from emerging. The time that the Earth was inhabited is more precisely constrained to 3.7 Ga. This suggests life emerged within 800 Myr, and possibly in < 200 Myr. Between 4.5–3.7 Ga, the continental crust was slowly rising up from the global ocean, providing dry land on which warm little ponds could form. We develop the theory for the emergence of RNA polymers in these pond environments, whose wet-dry cycles promote polymerization. RNA is comprised of chains of nucleotides, and the latter is made up of ribose, phosphate, and a characteristic nucleobase. We numerically model the survival and evolution of nucleobases in warm little ponds from meteorite and interplanetary dust sources. The wet-dry cycles of our ponds are controlled by precipitation, evaporation, and seepage. The nucleobase sinks include photodissociation, seepage, and hydrolysis. Nucleobase and nucleotide seepage is efficient, therefore nucleotides and RNA molecules must have emerged rapidly (< a few years) in order to avoid falling through pores at the base of the pond. We find that meteorites, not interplanetary dust particles, are the dominant source of nucleobases used for RNA synthesis. Finally, under these conditions, we find that first RNA polymers likely emerged before 4.17 Ga. / Thesis / Master of Science (MSc)

Metabolism is a subset of chemistry that allows cells to defy thermodynamic equilibrium, a fundamental process that must have been in place from the very beginning of biology. Before evolution produced efficient catalysts in the form of complex protein machinery, short metal binding peptides might have preceded modern metalloproteins. Such prebiotic, metal-binding motifs have been hypothesized to have existed through analyses of extant protein sequences. However, it is unclear how metal-binding motifs might have evolved in the harsh prebiotic environment. Here, we show how certain environments, in particular seawater-like environments rich in divalent cations and especially Mg2+, support the survival of short peptides upon extreme temperatures as high as 150 °C. Moreover, while Mg2+ does not offer the same protection from UV light, peptides are protected from both heat and irradiation when bound to a metal ion. The results suggest that specific environments rich in metal ions may be better suited for the emergence of complex systems in the path toward life. Additionally, the conditional degradation of peptides depending on their ability of binding metals might have enabled a selection mechanism that would favor the survival of metal-binding motifs which resemble the motifs found in modern proteins. These short sequences could have acted as early, simple catalysts able to facilitate a restricted set of chemical reactions, which would shape the emergence and biology of the Last Universal Common Ancestor.