Formamide-based prebiotic chemistry

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Formamide-based prebiotic chemistry is a reconstruction of the beginnings of life on Earth, assuming that formamide could accumulate in sufficiently high amounts to serve as the building block and reaction medium for the synthesis of the first biogenic molecules. [1]

Contents

Formamide (NH2CHO), the simplest naturally occurring amide, contains all the elements (hydrogen, carbon, oxygen, and nitrogen), which are required for the synthesis of biomolecules, and is a ubiquitous molecule in the universe. [2] Formamide has been detected in galactic centers, [3] [4] star-forming regions of dense molecular clouds, [5] high-mass young stellar objects, [6] the interstellar medium, [7] comets, [8] [9] [10] and satellites. [11] In particular, dense clouds containing formamide, with sizes on the order of kiloparsecs, have been observed in the vicinity of the Solar System. [5]

Formamide forms under a variety of conditions, corresponding to both terrestrial environments and interstellar media: e.g., on high-energy particle irradiation of binary mixtures of ammonia (NH3) and carbon monoxide (CO), [12] or from the reaction between formic acid (HCOOH) with NH3. [13] It has been suggested that in hydrothermal pores formamide may accumulate in sufficiently high concentrations to enable synthesis of biogenic molecules. [14] Ab initio molecular dynamics simulations suggest that formamide could be a key intermediate of the Miller–Urey experiment as well. [15]

The combinatorial power of carbon is manifested in the composition of the molecular populations detected in circum- and interstellar media (see the Astrochemistry.net [16] web site). The number and the complexity of carbon-containing molecules are significantly higher than those of inorganic compounds, presumably all over the universe. One of the most abundant C-containing three-atoms molecule observed in space is hydrogen cyanide (HCN). [17] The chemistry of HCN has thus attracted attention in origin of life studies since the earliest times, and the laboratory synthesis of adenine from HCN under presumptive prebiotic conditions was reported as early as 1961. [18] The intrinsic limit of HCN stems from its high reactivity, which leads in turn, to instability and the difficulty associated with its concentration and accumulation in unreacted form. [19] The “Warm Little Pond” in which life is supposed to have started, as imagined by Charles Darwin [20] [21] and re-elaborated by Alexander Oparin, [22] had most likely to reach sufficiently high concentrations to start creating the next levels of complexity. Hence the necessity of a derivative of HCN that is sufficiently stable to survive for time periods extended enough to allow its concentration in the actual physico-chemical settings, but that is sufficiently reactive to originate new compounds in prebiotically plausible environments. [19] Ideally, this derivative should be able to undergo reactions in various directions, without prohibitively high energy barriers, thus allowing the production of different classes of potentially prebiotic compounds. Formamide fulfils all these requirements and, due to its significantly higher boiling point (210 °C), enables chemical synthesis in a much broader temperature range than water. [1] [23]

Prebiotic chemistry

Current living forms on Earth are essentially composed of four types of molecular entities: (i) nucleic acids, (ii) proteins, (iii) carbohydrates, and (iv) lipids. Nucleic acids (DNA and RNA) embody and express the genetic information and, together, constitute the genome and the apparatus for its expression (the genotype). Proteins, carbohydrates, and lipids form the structures, which harness and handle energy from the environment for organizing matter according to the instructions specified by the genotype, aiming to its conservation and transmission. The ensemble of proteins, carbohydrates, lipids and nucleic acids constitute the phenotype. Life is thus made of the interaction of metabolism and genetics, of the genotype with the phenotype. Both are built around the chemistry of the most common elements of the universe (hydrogen, oxygen, nitrogen, and carbon), important although ancillary roles being played by phosphorus and sulphur, and by other elements.

Given the overwhelming variety of the chemically conceivable molecules, the fact that in biological systems we observe only a small subset of organic molecules has raised questions how and which different reaction pathways could have plausibly lead to the synthesis of pre-biological molecules on the primordial Earth. These are the main objectives of prebiotic chemistry research.

Precursor of biogenic molecules

Figure 1. Relationship between formamide and other prebiotic feedstock molecules, such as HCN and ammonium formate(NH4 HCOO ). Figure1.tif
Figure 1. Relationship between formamide and other prebiotic feedstock molecules, such as HCN and ammonium formate(NH4 HCOO ).

Figure 1 summarizes the basic chemistry of formamide and its chemical connection with HCN and ammonium formate (NH4+HCOO−), considering selected examples of preparative and degradative reactions. [1]

The synthesis of purine from formamide was first reported in 1980. [24] A series of studies building on this observation was started 20 years later: the synthesis of a large panel of prebiotically relevant compounds (including purine, adenine, cytosine, and 4(3H)pyrimidinone) in good yields was reported in 2001. [25] These products were obtained by heating formamide in the presence of simple catalysts such as calcium carbonate (CaCO3), silica (SiO2), or alumina (Al2O3).

In addition to nucleobases, sugars, [26] carboxylic acids, [27] amino acids, [27] as well as heterogeneous compounds of various classes, [27] (including urea and carbodiimide) were also synthesized. The catalysts studied include, in addition to those mentioned, titanium oxides, [28] clays, [29] cosmic dust analogues, [30] phosphates, [31] iron sulphide minerals, [32] zirconium minerals, [33] borate minerals, [34] or numerous materials of meteoritic origin [26] [27] encompassing iron, stony-iron, chondrites, and achondrites meteorites.

Various energy sources, including thermal energy, [25] UV-radiation, [31] irradiation with high-energy (terawatt) laser pulses, [35] or slow protons [26] were tested. Mimics of different formamide-based prebiotic scenarios have been reconstructed and analyzed, including space-wise solar wind irradiation of meteorites, [26] dynamic chemical gardens, [36] and meteorites in aqueous environments. [37] It has been suggested that the stepwise decrease of the temperature of the prebiotic environment could induce a sequence of strongly non-equilibrium chemical events that led to the emergence of more and more complex species from formamide on the early Earth. [23] [38]

For each studied combination of catalyst/energy source/environment, formamide condensed into a variety of different prebiotically relevant compounds, each combination giving rise to a specific set of relatively complex molecules, usually encompassing several nucleobases, amino acids, and carboxylic acids. [1] The highest level of complexity was attained for the formamide/meteorite system, [27] using proton irradiation as the energy source, where the one-pot synthesis of four nucleosides (uridine, cytidine, adenosine, thymidine) was observed. [26] So far, no other one-carbon atom compound has shown the versatility of products that can be formed from formamide under plausible prebiotic conditions in a one-pot chemistry (see Figure 2). [39]

Figure 2. Main prebiotic building blocks that can be synthesized from formamide under plausible prebiotic conditions. Wikifig.tif
Figure 2. Main prebiotic building blocks that can be synthesized from formamide under plausible prebiotic conditions.

In addition to its dual function of substrate and solvent in one-pot syntheses affording prebiotic compounds as complex as nucleosides and long aliphatic chains, [37] it has been observed that formamide plays a role in the generation of molecules which are closer to the biological domain. In the presence of a phosphate source (e.g., phosphate minerals), formamide promotes the phosphorylation of nucleosides, leading to the formation of nucleotides, [40] [41] and strongly stimulates the non-enzymatic polymerization of 3’,5’ cyclic nucleotides, leading to the abiotic synthesis of RNA oligomers. [42] This is the reason why formamide is considered a plausible medium for prebiotic phosphorylation reactions also in the “discontinuous synthesis” scenario of the origin of life. [43] [44] As well as phosphorylation, formamide has been shown to be a competent medium for the production of amino acid derivatives from their simple aldehyde and nitrile precursors, demonstrating that water is not the only solvent that this process can occur in. [45] Most notably, formamide provides a medium for the prebiotic synthesis of cysteine derivatives, not considered previously considered plausible in strictly aqueous prebiotic environments.

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<span class="mw-page-title-main">Miller–Urey experiment</span> Experiment testing the origin of life

The Miller–Urey experiment, or Miller experiment, was an experiment in chemical synthesis carried out in 1952 that simulated the conditions thought at the time to be present in the atmosphere of the early, prebiotic Earth. It is seen as one of the first successful experiments demonstrating the synthesis of organic compounds from inorganic constituents in an origin of life scenario. The experiment used methane (CH4), ammonia (NH3), hydrogen (H2), in ratio 2:2:1, and water (H2O). Applying an electric arc (simulating lightning) resulted in the production of amino acids.

<span class="mw-page-title-main">Nucleotide</span> Biological molecules constituting nucleic acids

Nucleotides are organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver.

<span class="mw-page-title-main">Purine</span> Heterocyclic aromatic organic compound

Purine is a heterocyclic aromatic organic compound that consists of two rings fused together. It is water-soluble. Purine also gives its name to the wider class of molecules, purines, which include substituted purines and their tautomers. They are the most widely occurring nitrogen-containing heterocycles in nature.

Pyrimidine is an aromatic, heterocyclic, organic compound similar to pyridine. One of the three diazines, it has nitrogen atoms at positions 1 and 3 in the ring. The other diazines are pyrazine and pyridazine.

<span class="mw-page-title-main">RNA world</span> Hypothetical stage in the early evolutionary history of life on Earth

The RNA world is a hypothetical stage in the evolutionary history of life on Earth in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. The term also refers to the hypothesis that posits the existence of this stage. Alexander Rich first proposed the concept of the RNA world in 1962, and Walter Gilbert coined the term in 1986.

<span class="mw-page-title-main">Adenine</span> Chemical compound in DNA and RNA

Adenine is a purine nucleotide base. It is one of the nucleobases in the nucleic acids, DNA and RNA. The shape of adenine is complementary to either thymine in DNA or uracil in RNA. In cells adenine, as an independent molecule, is rare. It is almost always covalently bound to become a part of a larger biomolecule.

<span class="mw-page-title-main">Uracil</span> Chemical compound of RNA

Uracil is one of the four nucleotide bases in the nucleic acid RNA. The others are adenine (A), cytosine (C), and guanine (G). In RNA, uracil binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced by thymine (T). Uracil is a demethylated form of thymine.

<span class="mw-page-title-main">Thymine</span> Chemical compound of DNA

Thymine is one of the four nucleotide bases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known as 5-methyluracil, a pyrimidine nucleobase. In RNA, thymine is replaced by the nucleobase uracil. Thymine was first isolated in 1893 by Albrecht Kossel and Albert Neumann from calf thymus glands, hence its name.

<span class="mw-page-title-main">Nucleotide base</span> Nitrogen-containing biological compounds that form nucleosides

Nucleotide bases are nitrogen-containing biological compounds that form nucleosides, which, in turn, are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids. The ability of nucleobases to form base pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Five nucleobases—adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)—are called primary or canonical. They function as the fundamental units of the genetic code, with the bases A, G, C, and T being found in DNA while A, G, C, and U are found in RNA. Thymine and uracil are distinguished by merely the presence or absence of a methyl group on the fifth carbon (C5) of these heterocyclic six-membered rings. In addition, some viruses have aminoadenine (Z) instead of adenine. It differs in having an extra amine group, creating a more stable bond to thymine.

<span class="mw-page-title-main">Nucleoside</span> Any of several glycosylamines comprising a nucleobase and a sugar molecule

Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group. A nucleoside consists simply of a nucleobase and a five-carbon sugar whereas a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups. In a nucleoside, the anomeric carbon is linked through a glycosidic bond to the N9 of a purine or the N1 of a pyrimidine. Nucleotides are the molecular building blocks of DNA and RNA.

<span class="mw-page-title-main">Ribonucleotide</span> Nucleotide containing ribose as its pentose component

In biochemistry, a ribonucleotide is a nucleotide containing ribose as its pentose component. It is considered a molecular precursor of nucleic acids. Nucleotides are the basic building blocks of DNA and RNA. Ribonucleotides themselves are basic monomeric building blocks for RNA. Deoxyribonucleotides, formed by reducing ribonucleotides with the enzyme ribonucleotide reductase (RNR), are essential building blocks for DNA. There are several differences between DNA deoxyribonucleotides and RNA ribonucleotides. Successive nucleotides are linked together via phosphodiester bonds.

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<span class="mw-page-title-main">Formamide</span> CH3NO, simplest amide

Formamide is an amide derived from formic acid. It is a colorless liquid which is miscible with water and has an ammonia-like odor. It is chemical feedstock for the manufacture of sulfa drugs and other pharmaceuticals, herbicides and pesticides, and in the manufacture of hydrocyanic acid. It has been used as a softener for paper and fiber. It is a solvent for many ionic compounds. It has also been used as a solvent for resins and plasticizers. Some astrobiologists suggest that it may be an alternative to water as the main solvent in other forms of life.

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<span class="mw-page-title-main">Abiogenesis</span> Life arising from non-living matter

Abiogenesis is the natural process by which life arises from non-living matter, such as simple organic compounds. The prevailing scientific hypothesis is that the transition from non-living to living entities on Earth was not a single event, but a process of increasing complexity involving the formation of a habitable planet, the prebiotic synthesis of organic molecules, molecular self-replication, self-assembly, autocatalysis, and the emergence of cell membranes. The transition from non-life to life has never been observed experimentally, but many proposals have been made for different stages of the process.

<span class="mw-page-title-main">Diaminomaleonitrile</span> Chemical compound

Diaminomaleonitrile (DAMN) is an organic compound composed of two amino groups and two nitrile groups bonded to a central alkene unit. The systematic name reflects its relationship to maleic acid. DAMN form by oligomerization of hydrogen cyanide. It is the starting point for the synthesis of several classes of heterocyclic compounds. It has been considered as a possible organic chemical present in prebiotic conditions.

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  45. ↑ Green, N. J., Russell, D. A., Tanner, S. H., Sutherland, J. D. (2023). "Prebiotic Synthesis of N-Formylaminonitriles and Derivatives in Formamide". Journal of the American Chemical Society. 145 (19): 10533–10541. doi: 10.1021/jacs.2c13306 . PMC   10197134 . PMID   37146260.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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