Formose Reaction Research Articles

The Effects of Iron on In Silico Simulated Abiotic Reaction Networks.

Iron is one of the most abundant elements in the Universe and Earth's surfaces, and undergoes a redox change of approximately 0.77 mV in changing between its +2 and +3 states. Many contemporary terrestrial organisms are deeply connected to inorganic geochemistry via exploitation of this redox change, and iron redox reactions and catalysis are known to cause significant changes in the course of complex abiotic reactions. These observations point to the question of whether iron may have steered prebiotic chemistry during the emergence of life. Using kinetically naive in silico reaction modeling we explored the potential effects of iron ions on complex reaction networks of prebiotic interest, namely the formose reaction, the complexifying degradation reaction of pyruvic acid in water, glucose degradation, and the Maillard reaction. We find that iron ions produce significant changes in the connectivity of various known diversity-generating reaction networks of proposed prebiotic significance, generally significantly diversifying novel molecular products by ~20%, but also adding the potential for kinetic effects that could allow iron to steer prebiotic chemistry in marked ways.

Preliminary Free Energy Map of Prebiotic Compounds Formed from CO2, H2 and H2S.

What kinds of CHOS compounds might be formed in a prebiotic milieu by reducing CO2 in the presence of H2 and H2S? How might the presence of sulfur influence the chemical composition of the mixture? We explore these questions by using first-principles quantum chemistry to calculate the free energies of CHOS compounds in aqueous solution, by first generating a thermodynamic map of one- and two-carbon species. We find that while thiols are thermodynamically favored, thioesters, thioacids, and thiones are less favorable than their non-sulfur counterparts. We then focus on the key role played by mercaptoacetaldehyde in sulfur analogs of the autocatalytic formose reaction, whereby the thiol group introduces asymmetry and potential thermodynamic selectivity of some compounds over others.

Fully Automated Generation of Prebiotically Relevant Reaction Networks from Optimized Nanoreactor Simulations.

The nanoreactor approach first introduced by the group of Martı́nez [Wang et al. Nat. Chem. 2014, 6, 1044-1048] has recently attracted much attention because of its ability to accelerate the discovery of reaction pathways. Here, we provide a comprehensive study of various simulation parameters and present an alternative implementation for the reactivity-enhancing spherical constraint function, as well as for the detection of reaction events. In this context, a fully automated postsimulation evaluation procedure based on RDKit and NetworkX analysis is introduced. The chemical and physical robustness of the procedure is examined by investigating the reactivity of selected homogeneous systems. The optimized procedure is applied at the GFN2-xTB level of theory to a system composed of HCN molecules and argon atoms, acting as a buffer, yielding prebiotically plausible primary and secondary precursors for the synthesis of RNA. Furthermore, the formose reaction network is explored leading to numerous sugar precursors. The discovered compounds reflect experimental findings; however, new synthetic routes and a large collection of exotic, highly reactive molecules are observed, highlighting the predictive power of the nanoreactor approach for unraveling the reactive manifold.

Toward abiotic sugar synthesis from CO2 electrolysis

Toward abiotic sugar synthesis from CO2 electrolysis

Development of a kinetic model and figures of merit for formaldehyde carboligations catalyzed by formolase enzymes.

There is an increasing interest in the upgrading of inexpensive and abundant C1 feedstocks to higher carbon products. Linear carbon ligation routes are of particular interest due to their simplicity and potential for high carbon efficiencies. The formolase (FLS) enzyme was computationally designed to catalyze the formose reaction, where formaldehyde molecules are coupled to produce a mixture of C2 (glycolaldehyde) and C3 (dihydroxyacetone) molecules. Recent protein engineering efforts have resulted in the introduction of several FLS variants with altered catalytic properties. As is often the case with enzymes catalyzing reactions with complex and/or nonnatural trajectories, there are no mechanistic kinetic models that fully describe the activity of the FLS enzyme. FLS variants are typically evaluated by fitting rate data to empirical rate laws, with some variation of the kcat /KM ratio used to report and rank performances. The apparent parameters estimated in this manner are unlikely to capture the full catalytic performance of these enzymes. In this study, we derive a mechanistic rate law describing FLS activity as well as theory-based figures of merit to rank FLS performance under relevant conditions. We proceed to fit the rate equation to initial rate data obtained from several FLS mutants, and use the figures of merit to compare the mutations. This study provides a theoretical framework for comparing FLS enzymes which will be essential as novel carbon ligation pathways are devised and implemented.

Do Soluble Phosphates Direct the Formose Reaction towards Pentose Sugars?

The formose reaction has been a leading hypothesis for the prebiotic synthesis of sugars such as ribose for many decades but tends to produce complex mixtures of sugars and often tars. Channeling the formose reaction towards the synthesis of biologically useful sugars such as ribose has been a holy grail of origins-of-life research. Here, we tested the hypothesis that a simple, prebiotically plausible phosphorylating agent, acetyl phosphate, could direct the formose reaction towards ribose through phosphorylation of intermediates in a manner resembling gluconeogenesis and the pentose phosphate pathway. We did indeed find that addition of acetyl phosphate to a developing formose reaction stabilized pentoses, including ribose, such that after 5 h of reaction about 10-fold more ribose remained compared with control runs. But mechanistic analyses using liquid chromatography-mass spectrometry showed that, far from being directed towards ribose by phosphorylation, the formose reaction was halted by the precipitation of Ca2+ ions as phosphate minerals such as apatite and hydroxyapatite. Adding orthophosphate had the same effect. Phosphorylated sugars were only detected below the limit of quantification when adding acetyl phosphate. Nonetheless, our findings are not strictly negative. The sensitivity of the formose reaction to geochemically reasonable conditions, combined with the apparent stability of ribose under these conditions, serves as a valuable constraint on possible pathways of sugar synthesis at the origin of life.

Monte Carlo simulation of sugar synthesis on icy dust particles intermittently irradiated by UV in a protoplanetary disk

Context. While synthesis of organic molecules in molecular clouds or protoplanetary disks is complex, observations of interstellar grains, analyses of carbonaceous chondrites, and UV photochemistry experiments are rapidly developing and are providing constraints on and clues to the complex organic molecule synthesis in space. This motivates us to construct a theoretical synthesis model. Aims. We developed a new code to simulate global reaction sequences of organic molecules and apply it to sugar synthesis by intermittent UV irradiation on the surface of icy particles in a protoplanetary disk. Here we show the first results of our new simulation. Methods. We applied a Monte Carlo method to select reaction sequences from all possible reactions, using the graph-theoretic matrix model for chemical reactions and modeling reactions on the icy particles during UV irradiation. Results. We obtain results consistent with the organic molecules in carbonaceous chondrites and obtained by experiments, albeit through a different pathway from the conventional formose reactions previously suggested. During UV irradiation, loosely bonded O-rich large molecules are continuously created and destroyed. After UV irradiation is turned off, the ribose abundance rapidly increases through the decomposition of the large molecules via breakage of O−O bonds and replacements of C−OH by C−H to reach O/C = 1 for sugars. The sugar abundance is regulated mostly by the total atomic ratio H/O of starting materials, but not by their specific molecular forms. Deoxyribose is simultaneously synthesized, and most of the molecules end up in complexes with C-rich molecules.

Possible Ribose Synthesis in Carbonaceous Planetesimals.

The origin of life might be sparked by the polymerization of the first RNA molecules in Darwinian ponds during wet-dry cycles. The key life-building block ribose was found in carbonaceous chondrites. Its exogenous delivery onto the Hadean Earth could be a crucial step toward the emergence of the RNA world. Here, we investigate the formation of ribose through a simplified version of the formose reaction inside carbonaceous chondrite parent bodies. Following up on our previous studies regarding nucleobases with the same coupled physico-chemical model, we calculate the abundance of ribose within planetesimals of different sizes and heating histories. We perform laboratory experiments using catalysts present in carbonaceous chondrites to infer the yield of ribose among all pentoses (5Cs) forming during the formose reaction. These laboratory yields are used to tune our theoretical model that can only predict the total abundance of 5Cs. We found that the calculated abundances of ribose were similar to the ones measured in carbonaceous chondrites. We discuss the possibilities of chemical decomposition and preservation of ribose and derived constraints on time and location in planetesimals. In conclusion, the aqueous formose reaction might produce most of the ribose in carbonaceous chondrites. Together with our previous studies on nucleobases, we found that life-building blocks of the RNA world could be synthesized inside parent bodies and later delivered onto the early Earth.

Gas-phase identification of (Z)-1,2-ethenediol, a key prebiotic intermediate in the formose reaction.

Prebiotic sugars are thought to be formed on primitive Earth by the formose reaction. However, their formation is not fully understood and it is plausible that key intermediates could have formed in extraterrestrial environments and subsequently delivered on early Earth by cometary bodies. 1,2-Ethenediol, the enol form of glycolaldehyde, represents a highly reactive intermediate of the formose reaction and is likely detectable in the interstellar medium. Here, we report the identification and first characterization of (Z)-1,2-ethenediol by means of rotational spectroscopy. The title compound has been produced in the gas phase by flash vacuum pyrolysis of bis-exo-5-norbornene-2,3-diol at 750 °C, through a retro-Diels-Alder reaction. The spectral analysis was guided by high-level quantum-chemical calculations, which predicted spectroscopic parameters in very good agreement with the experiment. Our study provides accurate spectral data to be used for searches of (Z)-1,2-ethenediol in the interstellar space.

Increasing in the Selectivity of Formose Reaction for Glyceraldehyde Production in the Presence of Fumed Silica and Montmorillonite Catalysts

In the present paper, the Formose reaction is investigated to produce polyols in the presence of two different catalysts at different pHs. The Formose reaction mechanism is the same as aldol condensation, which occurs in alkaline media and is accelerated by the presence of a heterogeneous catalysis. The products observed in the reaction medium are ethylene glycol, and glyceraldehyde. The present study shows that in the presence of fumed silica catalyst, increasing the pH from 7.6 to 9.3 reduces the production of ethylene glycol; however, it increases the conversion of ethylene glycol to glyceraldehyde. As a result, the amount of ethylene glycol in the reaction mixture decreases compared with neutral pHs. Nevertheless, the selectivity of the reaction to the production of glyceraldehyde increases. The same result can be observed when using montmorillonite as another heterogeneous catalyst. The difference is that the montmorillonite catalyst has less ability to accelerate the reaction than fumed silica. Also, at pH around 9 and above, practically no product is observed in the reaction medium.

Identification of Glycolaldehyde Enol (HOHC═CHOH) in Interstellar Analogue Ices.

Glycolaldehyde is considered the entry point in the aqueous prebiotic formose (Butlerow) reaction although it mainly exists in its unreactive hydrated form in aqueous solution. The characterization of the more reactive nucleophilic enol form under interstellar conditions has remained elusive to date. Here we report on the identification of glycolaldehyde enol (1,2-ethenediol, HOHC═CHOH) in low temperature methanol-bearing ices at temperatures as low as 5 K. Exploiting isotope labeling and isomer-selective photoionization coupled with reflectron time-of-flight mass spectrometry, our results unravel distinct reaction pathways to 1,2-ethenediol, thus demonstrating the kinetic stability, availability for prebiotic sugar formation, and potential detectability in deep space.

Prebiotic Pathway from Ribose to RNA Formation.

At the focus of abiotic chemical reactions is the synthesis of ribose. No satisfactory explanation was provided as to the missing link between the prebiotic synthesis of ribose and prebiotic RNA (preRNA). Hydrogen cyanide (HCN) is assumed to have been the principal precursor in the prebiotic formation of aldopentoses in the formose reaction and in the synthesis of ribose. Ribose as the best fitting aldopentose became the exclusive sugar component of RNA. The elevated yield of ribose synthesis at higher temperatures and its protection from decomposition could have driven the polymerization of the ribose-phosphate backbone and the coupling of nucleobases to the backbone. RNA could have come into being without the involvement of nucleotide precursors. The first nucleoside monophosphate is likely to have appeared upon the hydrolysis of preRNA contributed by the presence of reactive 2′-OH moieties in the preRNA chain. As a result of phosphorylation, nucleoside monophosphates became nucleoside triphosphates, substrates for the selective synthesis of genRNA.

Autocatalysis in Formose Reaction and Formation of RNA Nucleosides.

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

Chemical dynamics simulations of collision induced dissociation of deprotonated glycolaldehyde

First step of formose or Butlerov reaction involves C–C bond formation between two formaldehyde molecules resulting in glycolaldehyde. This reaction happens under basic conditions in solution. A tandem mass spectrometry investigation of dissociation of deprotonated glycolaldehyde in the gas phase, to study the formose reaction in a retro-synthetic point of view, has been reported. In the present work, we have carried out electronic structure theory calculations and quasi-classical direct chemical dynamics simulations to model the gas phase dissociation of the conjugate base of glycolaldehyde. The dynamics simulations were performed on-the-fly using the hybrid density functional B3LYP theory with the 6-31+G∗ basis set under collision induced dissociation (CID) conditions. Trajectories were launched with two different deprotonated forms of glycolaldehyde for a range of collision energies mimicking experiments. Reverse formose reaction was observed primarily from the slightly higher energy isomer via a non-statistical pathway. Intramolecular hydrogen transfer was ubiquitous in the trajectories. Simulation results were compared with experiments and detailed atomic level dissociation mechanisms are presented.

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.

Mineral-mediated carbohydrate synthesis by mechanical forces in a primordial geochemical setting

The formation of carbohydrates represents an essential step to provide building blocks and a source of chemical energy in several models for the emergence of life. Formaldehyde, glycolaldehyde and a basic catalyst are the initial components forming a variety of sugar molecules in the cascade-type multi-step formose reaction. While numerous side reactions and even deterioration can be observed in aqueous media, selective prebiotic sugar formation is feasible in solid-state, mechanochemical reactions and might have occurred in early geochemistry. However, the precise role of different basic catalysts and the influence of the atmospheric conditions in the solid-state formose reaction remain unknown. Here we show, that in a primordial scenario the mechanochemical formose reaction is capable to form monosaccharides with a broad variety of mineral classes as catalysts with only minute amounts of side products such as lactic acid or methanol, independent of the atmospheric conditions. The results give insight into recent findings of formose sugars on meteorites and offer a water-free and robust pathway for monosaccharides independent of the external conditions both for the early Earth or an extra-terrestrial setting.

Cometary Glycolaldehyde as a Source of pre-RNA Molecules.

Over 200 molecules have been detected in multiple extraterrestrial environments, including glycolaldehyde (C2(H2O)2, GLA), a two-carbon sugar precursor that has been detected in regions of the interstellar medium. Its recent in situ detection on the nucleus of comet 67P/Churyumov-Gerasimenko and through remote observations in the comae of others provides tantalizing evidence that it is common on most (if not all) comets. Impact experiments conducted at the Experimental Impact Laboratory at NASA's Johnson Space Center have shown that samples of GLA and GLA mixed with montmorillonite clays can survive impact delivery in the pressure range of 4.5 to 25 GPa. Extrapolated to amounts of GLA observed on individual comets and assuming a monotonic impact rate in the first billion years of Solar System history, these experimental results show that up to 1023 kg of cometary GLA could have survived impact delivery, with substantial amounts of threose, erythrose, glycolic acid, and ethylene glycol also produced or delivered. Importantly, independent of the profile of the impact flux in the early Solar System, comet delivery of GLA would have provided (and may continue to provide) a reservoir of starting material for the formose reaction (to form ribose) and the Strecker reaction (to form amino acids). Thus, comets may have been important delivery vehicles for starting molecules necessary for life as we know it.

Plausibility of the Formose Reaction in Alkaline Hydrothermal Vent Environments.

Prebiotic processes required a reliable source of free energy and complex chemical mixtures that may have included sugars. The formose reaction is a potential source of those sugars. At moderate to elevated temperature and pH ranges, these sugars rapidly decay. Here it is shown that CaCO3-based chemical gardens catalyze the formose reaction to produce glucose, ribose, and other monosaccharides. These thin inorganic membranes are explored as analogs of hydrothermal vent materials-a possible place for the origin of life-and similarly exposed to very steep pH gradients. Supported by simulations of a simple reaction-diffusion model, this study shows that such gradients allow for the dynamic accumulation of sugars in specific layers of the thin membrane, effectively protecting formose sugar yields. Therefore, the formose reaction may be a plausible prebiotic reaction in alkaline hydrothermal vent environments, possibly setting the stage for an RNA world.

The Messy Alkaline Formose Reaction and Its Link to Metabolism.

Sugars are essential for the formation of genetic elements such as RNA and as an energy/food source. Thus, the formose reaction, which autocatalytically generates a multitude of sugars from formaldehyde, has been viewed as a potentially important prebiotic source of biomolecules at the origins of life. When analyzing our formose solutions we find that many of the chemical species are simple carboxylic acids, including α-hydroxy acids, associated with metabolism. In this work we posit that the study of the formose reaction, under alkaline conditions and moderate hydrothermal temperatures, should not be solely focused on sugars for genetic materials, but should focus on the origins of metabolism (via metabolic molecules) as well.

Meteorites contain extraterrestrial ribose

Astrobiologists have long thought that the building blocks of life may have arrived on Earth via meteorites. They now may have proof of that idea. For the first time, scientists have discovered complex, biologically essential sugars in two meteorite samples (Proc. Natl. Acad. Sci. U.S.A. 2019, DOI: 10.1073/pnas.1907169116). The researchers analyzed sugars from three chondrites, or primarily rocky meteorites, and found detectable levels of ribose in two of the samples. They analyzed the carbon isotopes of their samples and found that the sugars were enriched in carbon-13, indicating that they originated extraterrestrially. It’s unclear why these two meteorites preserved sugars and the third did not, says Tohoku University geochemist Yoshihiro Furukawa, who led the study. One potential pathway for the formation of extraterrestrial sugars is the formose reaction, which creates complex sugars from simple precursors like formaldehyde. The researchers showed that a formose-like reaction carried out in the laboratory produced