Prebiotic synthesis of simple sugars by an interstellar formose reaction

The Origin of RNA and the Formose-Ribose-RNA Pathway

Prebiotic pre-Darwinian reactions continued throughout biochemical or Darwinian evolution. Early chemical processes could have occurred on Earth between 4.5 and 3.6 billion years ago when cellular life was about to come into being. Pre-Darwinian evolution assumes the development of hereditary elements but does not regard them as self-organizing processes. The presence of biochemical self-organization after the pre-Darwinian evolution did not justify distinguishing between different types of evolution. From the many possible solutions, evolution selected from among those stable reactions that led to catalytic networks, and under gradually changing external conditions produced a reproducible, yet constantly evolving and adaptable, living system. Major abiotic factors included sunlight, precipitation, air, minerals, soil and the Earth's atmosphere, hydrosphere and lithosphere. Abiotic sources of chemicals contributed to the formation of prebiotic RNA, the development of genetic RNA, the RNA World and the initial life forms on Earth and the transition of genRNA to the DNA Empire, and eventually to the multitude of life forms today. The transition from the RNA World to the DNA Empire generated new processes such as oxygenic photosynthesis and the hierarchical arrangement of processes involved in the transfer of genetic information. The objective of this work is to unite earlier work dealing with the formose, the origin and synthesis of ribose and RNA reactions that were published as a series of independent reactions. These reactions are now regarded as the first metabolic pathway.

Metal-Organic Frameworks as Formose Reaction Catalysts with Enhanced Selectivity

The formose reaction is an autocatalytic series of aldol condensations that allows one to obtain monosaccharides from formaldehyde. The formose reaction suffers from a lack of selectivity, which hinders practical applications at the industrial level. Over the years, many attempts have been made to overcome this selectivity issue, with modest results. Heterogeneous porous catalysts with acid-base properties, such as Metal-Organic Frameworks (MOFs), can offer advantages compared to homogeneous strong bases (e.g., calcium hydroxide) for increasing the selectivity of this important reaction. For the very first time, four different Zeolite Imidazolate Frameworks are presented in this work as catalysts for the formose reaction in liquid phase, and their catalytic performances were compared with those of the typical homogeneous catalyst (i.e., calcium hydroxide). The heterogeneous nature of the catalysis, the possible contribution of leached metal or linkers to the solution, and the stability of the materials were investigated. The porous structure of these solids and their mild basicity make them suitable for obtaining enhanced selectivity at 30% formaldehyde conversion. Most of the MOFs tested showed low structural stability under reaction conditions, thereby indicating the need to search for new MOF families with higher robustness. However, this important result opens the path for future research on porous heterogeneous basic catalysts for the formose reaction.

Sugars in space: a quantum chemical study on the barrierless formation of dihydroxyacetone in the interstellar medium

Among many theories on the life’s origins, the regions between star systems in a galaxy are hypothesized to provide prebiotic material on Earth. Simple sugars, including glycolaldehyde, are confirmed to exist in interstellar medium (ISM) and can be intermediates in the formose reaction to form dihydroxyacetone (DHA). In the studied segment of the formose reaction, hydroxy carbene is sequentially added to formaldehyde, forming glycolaldehyde (hydroxyacetaldehyde) after the first addition and glycerone in the second addition. The proposed theoretical mechanism was validated through quantum chemical calculations. An exothermic and exergonic pathway favourable in ISM conditions was found, giving a possible explanation for glycerone formation. The products in question participate in biological processes like energy production, the phosphorylated form of glycerone (DHA-P) participates in glycolysis, and energy storage while glycerone is the source of the glycerine backbone in lipids. The studied reaction is a segment of the formose reaction and further polymerization can lead to pentose and hexose, which participate in the formation of RNA and DNA. Hence, this research explores the exogenous production and delivery of prebiotic material to Earth, building up to the conditions allowing the formation of rudimentary lifeforms.

Electron-induced origins of prebiotic building blocks of sugars: mechanism of self-reactions of a methanol anion dimer

Reactions of methanol dimers in interstellar medium driven by low energy irradiation may lead to prebiotic precursors.

Formose Reaction Controlled by a Copolymer of N,N-Dimethylacrylamide and 4-Vinylphenylboronic Acid

The formose reaction is an oligomerization of formaldehyde under basic conditions, which produces a complicated mixture of monosaccharides and sugar alcohols. Selective formation of useful monosaccharides by the formose reaction has been an important challenge. In this study, we have investigated the formose reaction controlled by N,N-dimethylacrylamide/4-vinylphenylboronic acid copolymer (pDMA/VBA) and phenylboronic acid (PBA) because boronic acid compounds form esters with polyols, e.g., monosaccharides and sugar alcohols. We obtained time⁻conversion data in the presence of these boronic acid compounds, and characterized the products by liquid chromatography-mass spectroscopy and NMR measurements. pDMA/VBA and PBA decelerated the formose reaction because of the formation of boronic acid esters with products. It is noteworthy that the formose reaction in the presence of pDMA/VBA and PBA formed favorably six- and seven-carbon branched monosaccharides and sugar alcohols.

Phosphoribosyl Pyrophosphate: A Molecular Vestige of the Origin of Life on Minerals

In this contribution, we report the formation under prebiotic conditions of phosphoribosyl pyrophosphate (PRPP) as a molecular precursor in the one-pot synthesis of a canonical nucleotide, namely adenosine monophosphate (AMP) from its building blocks (KH₂ PO₄ or P_i , adenine, and d-ribose), on a fumed silica surface. The on-the-rocks approach has been successfully applied to the simultaneous phosphorylation and glycosylation of ribose. The one-pot formation mechanism of AMP involves a two-step pathway via an activated intermediate, namely PRPP, obtained by multiple ribose phosphorylations upon mild thermal activation.

Photosynthesis and photo-stability of nucleic acids in prebiotic extraterrestrial environments

Laboratory experiments have shown that the UV photo-irradiation of low-temperature ices of astrophysical interest leads to the formation of organic molecules, including molecules important for biology such as amino acids, quinones, and amphiphiles. When pyrimidine is introduced into these ices, the products of irradiation include the nucleobases uracil, cytosine, and thymine, the informational sub-units of DNA and RNA, as well as some of their isomers. The formation of these compounds, which has been studied both experimentally and theoretically, requires a succession of additions of OH, NH₂, and CH₃groups to pyrimidine. Results show that H₂O ice plays key roles in the formation of the nucleobases, as an oxidant, as a matrix in which reactions can take place, and as a catalyst that assists proton abstraction from intermediate compounds. As H₂O is also the most abundant icy component in most cold astrophysical environments, it probably plays the same roles in space in the formation of biologically relevant compounds. Results also show that although the formation of uracil and cytosine from pyrimidine in ices is fairly straightforward, the formation of thymine is not. This is mostly due to the fact that methylation is a limiting step for its formation, particularly in H₂O-rich ices, where methylation must compete with oxidation. The relative inefficiency of the abiotic formation of thymine to that of uracil and cytosine, together with the fact that thymine has not been detected in meteorites, are not inconsistent with the RNA world hypothesis. Indeed, a lack of abiotically produced thymine delivered to the early Earth may have forced the choice for an RNA world, in which only uracil and cytosine are needed, but not thymine.

Formation of complex organic molecules in methanol and methanol-carbon monoxide ices exposed to ionizing radiation--a combined FTIR and reflectron time-of-flight mass spectrometry study

The radiation induced chemical processing of methanol and methanol-carbon monoxide ices at 5.5 K exposed to ionizing radiation in the form of energetic electrons and subsequent temperature programmed desorption is reported in this study. The endogenous formation of complex organic molecules was monitored online and in situ via infrared spectroscopy in the solid state and post irradiation with temperature programmed desorption (TPD) using highly sensitive reflectron time-of-flight (ReTOF) mass spectrometry coupled with single photoionization at 10.49 eV. Infrared spectroscopic analysis of the processed ice systems resulted in the identification of simple molecules including the hydroxymethyl radical (CH2OH), formyl radical (HCO), methane (CH4), formaldehyde (H2CO), carbon dioxide (CO2), ethylene glycol (HOCH2CH2OH), glycolaldehyde (HOCH2CHO), methyl formate (HCOOCH3), and ketene (H2CCO). In addition, ReTOF mass spectrometry of subliming molecules following temperature programmed desorption definitely identified several closed shell C/H/O bearing organics including ketene (H2CCO), acetaldehyde (CH3COH), ethanol (C2H5OH), dimethyl ether (CH3OCH3), glyoxal (HCOCOH), glycolaldehyde (HOCH2CHO), ethene-1,2-diol (HOCHCHOH), ethylene glycol (HOCH2CH2OH), methoxy methanol (CH3OCH2OH) and glycerol (CH2OHCHOHCH2OH) in the processed ice systems. Additionally, an abundant amount of molecules yet to be specifically identified were observed sublimating from the irradiated ices including isomers with the formula C3H(x=4,6,8)O, C4H(x=8,10)O, C3H(x=4,6,8)O2, C4H(x=6,8)O2, C3H(x=4,6)O3, C4H8O3, C4H(x=4,6,8)O4, C5H(x=6,8)O4 and C5H(x=6,8)O5. The last group of molecules containing four to five oxygen atoms observed sublimating from the processed ice samples include an astrobiologically important class of sugars relevant to RNA, phospholipids and energy storage. Experiments are currently being designed to elucidate their chemical structure. In addition, several reaction pathways were identified in the irradiated ices of mixed isotopes based upon the results of both in situ FTIR analysis and TPD ReTOF gas phase analysis. In general, the results of this study provide crucial information on the formation of a variety of classes of organics including alcohols, ketones, aldehydes, esters, ethers, and sugars within the bulk ices upon exposure to ionizing radiation that are relevant to the molecular clouds within the interstellar medium.