Imidazolium-Catalyzed Synthesis of an Imidazolium Catalyst.

The chemistry of imidazolium-catalyzed imidazolium synthesis was studied as part of an effort to develop a plausible prebiotic synthesis of a small catalytic molecule capable of catalyzing its own synthesis. Specifically, we investigated the one-pot 1-ethyl-3-methylimidazolium acetate (EMIM-Ac) catalyzed synthesis of 1,3-dibutyl-4,5-difuryl-imidazolium acetate (DBDFIM-Ac) from furfural, n-butylamine, formaldehyde, and acetic acid at 80 °C. Liu et al. (2012) had previously demonstrated the first reaction of the synthetic process, the EMIM-Ac catalyzed benzoin condensation of furfural that yields furoin. Our early studies established the second reaction of the synthetic process, the multicomponent reaction of furoin, n-butylamine, formaldehyde, and acetic acid that yields the imidazolium salt, DBDFIM-Ac. Studies of the complete two-reaction process that uses furfural for the synthesis of DBDFIM-Ac showed that the highest yield of DBDFIM-Ac was obtained when the mole ratio of n-butylamine, formaldehyde, and acetic acid relative to furfural was respectively (0.5:0.25:0.25:1.0-furfural), or one-half of the stoichiometric ratio (1.0:0.5:0.5:1.0-furfural). A time course study of the process showed transient formation of furoin, the obligatory reaction intermediate. DBDFIM-Ac and the imidazolium side product, 1,3-dibutyl-4,5-trifuryl-imidazolium acetate (DBTFIM-Ac), were stable under the reaction conditions. Imidazolium products (DBDFIM and DBTFIM) and the furoin intermediate were not formed in control reactions (80 °C, 24 h) in which EMIM catalyst was either absent or replaced with an equal volume of acetonitrile or DMF. The imidazolium product, DBDFIM-Ac, was shown to catalyze the synthesis of structurally similar 1,3-dipentyl-4,5-difuryl-imidazolium acetate (DPDFIM-Ac) from furfural, n-pentylamine, formaldehyde, and acetic acid at 80 °C.

Synthesis of ß-Peptide Standards for Use in Model Prebiotic Reactions.

A one-pot method was developed for the preparation of a series of ß-alanine standards of moderate size (2 to ≥12 residues) for studies concerning the prebiotic origins of peptides. The one-pot synthesis involved two sequential reactions: (1) dry-down self-condensation of ß-alanine methyl ester, yielding ß-alanine peptide methyl ester oligomers, and (2) subsequent hydrolysis of ß-alanine peptide methyl ester oligomers, producing a series of ß-alanine peptide standards. These standards were then spiked into a model prebiotic product mixture to confirm by HPLC the formation of ß-alanine peptides under plausible reaction conditions. The simplicity of this approach suggests it can be used to prepare a variety of ß-peptide standards for investigating differences between α- and ß-peptides in the context of prebiotic chemistry.

Imidazolium Catalysts Formed by an Iterative Synthetic Process as a Model System for Chemical Evolution.

Processes exhibiting diversity and selection would have been necessary to promote chemical evolution on early Earth. In this work, a model process was developed using non-kinetic selection to synthesize and isolate small molecule imidazolium catalysts. These catalysts were purified by affinity chromatography and recycled back into the process, forming a product feedback loop. In dimethylformamide, the catalysts activated the coupling of formaldehyde to short chain sugars. This sugar mixture was reacted with aniline, acetic acid, and paraformaldehyde to generate new catalysts. Thus chemical diversity was produced through non-selective, multi-component synthesis. Applying sequential dilution-reaction-purification cycles it was demonstrated that this process can function independently of starting catalyst. Over three process cycles, the initiator catalyst is effectively diluted out as a new catalyst population emerges to take its place. This system offers an alternative viewpoint for chemical evolution via the generation of small molecule organocatalysts.

Sugar-driven prebiotic synthesis of ammonia from nitrite.

Reaction of 3-5 carbon sugars, glycolaldehyde, and alpha-ketoaldehydes with nitrite under mild anaerobic aqueous conditions yielded ammonia, an essential substrate for the synthesis of nitrogen-containing molecules during abiogenesis. Under the same conditions, ammonia synthesis was not driven by formaldehyde, glyoxylate, 2-deoxyribose, and glucose, a result indicating that the reduction process requires an organic reductant containing either an accessible alpha-hydroxycarbonyl group or an alpha-dicarbonyl group. Small amounts of aqueous Fe(+3) catalyzed the sugar-driven synthesis of ammonia. The glyceraldehyde concentration dependence of ammonia synthesis, and control studies of ammonia's reaction with glyceraldehyde, indicated that ammonia formation is accompanied by incorporation of part of the synthesized ammonia into sugar-derived organic products. The ability of sugars to drive the synthesis of ammonia is considered important to abiogenesis because it provides a way to generate photochemically unstable ammonia at sites of sugar-based origin-of-life processes from nitrite, a plausible prebiotic nitrogen species.

Stereoselective syntheses of pentose sugars under realistic prebiotic conditions.

Glycolaldehyde and DL-glyceraldehyde reacted in a water-buffered solution under mildly acidic conditions and in the presence of chiral dipeptide catalysts produced pentose sugars whose configuration is affected by the chirality of the catalyst. The chiral effect was found to vary between catalysts and to be largest for di-valine. Lyxose, arabinose, ribose and xylose are formed in different amounts, whose relative proportions do not change significantly with the varying of conditions. With LL-peptide catalysts, ribose was the only pentose sugar to have a significant D-enantiomeric excess (ee) (

Synthesis and base-pairing properties of pyrazine nucleic acids.

The diversity of backbone modifications in the study of primitive informational polymers is partly limited by the plausible formation of their prebiotic starting components. In this paper, we synthesize pyrazine nucleic acid, an acyclic polymer, with the nucleoside derivable from a prebiotic one-pot synthesis containing alanine amide and D-ribose. Pyrazine nucleic acid (PzNA) which has a backbone structurally similar to glycerol nucleic acid (GNA), contain pyrazine derived nucleosides as informational elements that may exhibit base pairing properties similar to the pyrimidines present in RNA.[1] We found that insertion of pyrazinone nucleotides into DNA oligonucleotide sequences is not well-tolerated, and that homogenous sequences of PzNA are unable to form duplexes with RNA or DNA. Reasons for our results may be attributed to the pyrazine-2-one moiety, which is purposed to be a thymine analog, but has a lower pKa (pKa ∼ 8.5) than thymine and uracil. Additionally, we discovered an "apparent" regioselective protection of pyrazine-2-one derivatives in the presence of a secondary hydroxyl group that proved crucial in the preparation of the pyrazine-2-one phosphoramidite. The regioselectivity observed is proposed to be of general interest in the context of heterocyclic chemistry. In the larger context of origins of life studies, it points to the importance of keto-enol preferences of the canonical nucleobases versus pyrazine heterocycles in functioning as recognition elements.

A reappraisal of the habitability of planets around M dwarf stars.

Stable, hydrogen-burning, M dwarf stars make up about 75% of all stars in the Galaxy. They are extremely long-lived, and because they are much smaller in mass than the Sun (between 0.5 and 0.08 M(Sun)), their temperature and stellar luminosity are low and peaked in the red. We have re-examined what is known at present about the potential for a terrestrial planet forming within, or migrating into, the classic liquid-surface-water habitable zone close to an M dwarf star. Observations of protoplanetary disks suggest that planet-building materials are common around M dwarfs, but N-body simulations differ in their estimations of the likelihood of potentially habitable, wet planets that reside within their habitable zones, which are only about one-fifth to 1/50th of the width of that for a G star. Particularly in light of the claimed detection of the planets with masses as small as 5.5 and 7.5 M(Earth) orbiting M stars, there seems no reason to exclude the possibility of terrestrial planets. Tidally locked synchronous rotation within the narrow habitable zone does not necessarily lead to atmospheric collapse, and active stellar flaring may not be as much of an evolutionarily disadvantageous factor as has previously been supposed. We conclude that M dwarf stars may indeed be viable hosts for planets on which the origin and evolution of life can occur. A number of planetary processes such as cessation of geothermal activity or thermal and nonthermal atmospheric loss processes may limit the duration of planetary habitability to periods far shorter than the extreme lifetime of the M dwarf star. Nevertheless, it makes sense to include M dwarf stars in programs that seek to find habitable worlds and evidence of life. This paper presents the summary conclusions of an interdisciplinary workshop (http://mstars.seti.org) sponsored by the NASA Astrobiology Institute and convened at the SETI Institute.

DetectTLC: Automated Reaction Mixture Screening Utilizing Quantitative Mass Spectrometry Image Features.

Full characterization of complex reaction mixtures is necessary to understand mechanisms, optimize yields, and elucidate secondary reaction pathways. Molecular-level information for species in such mixtures can be readily obtained by coupling mass spectrometry imaging (MSI) with thin layer chromatography (TLC) separations. User-guided investigation of imaging data for mixture components with known m/z values is generally straightforward; however, spot detection for unknowns is highly tedious, and limits the applicability of MSI in conjunction with TLC. To accelerate imaging data mining, we developed DetectTLC, an approach that automatically identifies m/z values exhibiting TLC spot-like regions in MS molecular images. Furthermore, DetectTLC can also spatially match m/z values for spots acquired during alternating high and low collision-energy scans, pairing product ions with precursors to enhance structural identification. As an example, DetectTLC is applied to the identification and structural confirmation of unknown, yet significant, products of abiotic pyrazinone and aminopyrazine nucleoside analog synthesis. Graphical Abstract ᅟ.

Bioenergetics and life's origins.

Bioenergetics is central to our understanding of living systems, yet has attracted relatively little attention in origins of life research. This article focuses on energy resources available to drive primitive metabolism and the synthesis of polymers that could be incorporated into molecular systems having properties associated with the living state. The compartmented systems are referred to as protocells, each different from all the rest and representing a kind of natural experiment. The origin of life was marked when a rare few protocells happened to have the ability to capture energy from the environment to initiate catalyzed heterotrophic growth directed by heritable genetic information in the polymers. This article examines potential sources of energy available to protocells, and mechanisms by which the energy could be used to drive polymer synthesis.

Sugar-driven prebiotic synthesis of 3,5(6)-dimethylpyrazin-2-one: a possible nucleobase of a primitive replication process.

Reaction of glyceraldehyde with alanine amide (or ammonia) under anaerobic aqueous conditions yielded 3,5(6)-dimethylpyrazin-2-one that is considered a possible complementary residue of a primitive replicating molecule that preceded RNA. Synthesis of the dimethylpyrazin-2-one isomers under mild aqueous conditions (65 degrees C, pH 5.5) from 100 mM glyceraldehyde and alanine amide (or ammonia) was complete in about 5 days. This synthesis using 25 mM glyceraldehyde and alanine amide gave a total pyrazinone yield of 9.3% consisting of 42% of the 3,5-dimethylprazin-2-one isomer and 58% of the 3,6-dimethylpyrazin-2-one isomer. The related synthesis of the dimethylpyrazin-2-one isomers from glyceraldehyde and ammonia was about 200-fold less efficient than the alanine amide reaction. This synthetic process is considered a reasonable model of origin-of-life chemistry because it uses plausible prebiotic substrates, and resembles modern biosynthesis by employing the energized carbon groups of sugars to drive the synthesis of small organic molecules. Possible sugar-driven pathways for the prebiotic synthesis of polymerizable 2-pyrazinone monomers are discussed.

The sugar model: autocatalytic activity of the triose-ammonia reaction.

Reaction of triose sugars with ammonia under anaerobic conditions yielded autocatalytic products. The autocatalytic behavior of the products was examined by measuring the effect of the crude triose-ammonia reaction product on the kinetics of a second identical triose-ammonia reaction. The reaction product showed autocatalytic activity by increasing both the rate of disappearance of triose and the rate of formation of pyruvaldehyde, the product of triose dehydration. This synthetic process is considered a reasonable model of origin-of-life chemistry because it uses plausible prebiotic substrates, and resembles modern biosynthesis by employing the energized carbon groups of sugars to drive the synthesis of autocatalytic molecules.

The peptide-catalyzed stereospecific synthesis of tetroses: a possible model for prebiotic molecular evolution.

Using a water-based prebiotic model of sugar synthesis involving glycolaldehyde self-condensation, we demonstrate that homochiral L-dipeptide catalysts lead to the stereospecific syntheses of tetroses. The asymmetric effect is largest for erythrose, which may reach a D-enantiomeric excess of >80% with L-Val-L-Val catalyst. Based on results obtained with various peptides, we propose a possible catalytic-reaction intermediate, consisting of an imidazolidinone ring formed between the two nitrogen atoms of the peptide catalyst and the C1 of one glycolaldehyde molecule. The study was motivated by the premise that exogenous material, such as the nonracemic amino acids found in meteorites, could have participated in the terrestrial evolution of molecular asymmetry by stereospecific catalysis. Because peptides might have formed readily on the early Earth, it is possible that their catalytic contribution was relevant in the prebiotic processes that preceded the onset of life.

Growth of organic microspherules in sugar-ammonia reactions.

Reaction of small sugars of less than four carbons with ammonia in water yielded organic microspherules generally less than ten microns in size. The time course of microspherule growth was examined for the D-erythrose-ammonia reaction that yielded microspherules attached to the glass walls of containers. Measurements were made of the elemental composition and infrared spectrum of the microspherule material. These viscose semi-solid microspherules are viewed as possible containers for prebiotic catalytic processes relevant to the origin of life.

Aqueous synthesis of peptide thioesters from amino acids and a thiol using 1,1'-carbonyldiimidazole.

A new method was developed for the synthesis of peptide thioesters from free amino acids and thiols in water. This one-pot simple method involves two steps: (1) activation in water of an amino acid presumably as its N-carboxyanhydride (NCA) using 1,1'-carbonyldiimidazole (CDI), and (2) subsequent condensation of the activated amino acid-NCA in the presence of a thiol. With this method citrulline peptide thioesters containing up to 10 amino acid residues were prepared in a single reaction. This aqueous synthetic method provides a simple way to prepare peptide thioesters for studies of peptide replication involving ligation of peptide thioesters on peptide templates. The relevance of peptide replication to the origin-of-life process is supported by previous studies showing that amino acid thioesters (peptide thioester precursors) can be synthesized under prebiotic conditions by reaction of small sugars with ammonia and a thiol.

Kinetics of organic transformations under mild aqueous conditions: implications for the origin of life and its metabolism.

The rates of thermal transformation of organic molecules containing carbon, hydrogen, and oxygen were systematically examined in order to identify the kinetic constraints that governed origin-of-life organic chemistry under mild aqueous conditions. Arrhenius plots of the kinetic data were used to estimate the reaction of half-lifes at 50 degrees C. This survey showed that hydrocarbons and organic substances containing a single oxygenated group were kinetically the most stable; whereas organic substances containing two oxygenated groups in which one group was an alpha- or beta-positioned carbonyl group were the most reactive. Compounds with an alpha- or beta-positioned carbonyl group (aldehyde or ketone) had rates of reaction that were up to 10(24)-times faster than rates of similar molecules lacking the carbonyl group. This survey of organic reactivity, together with estimates of the molecular containment properties of lipid vesicles and liquid spherules, indicates that an origins process in a small domain that used C,H,O-intermediates had to be catalytic and use the most reactive organic molecules to prevent escape of its reaction intermediates.

Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions.

The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies (deltaG) were estimated for four types of reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed (1) that generally when carbon-carbon bond cleavage involves groups from different functional group classes (i.e., carboxylic acids, carbonyl groups, alcohols, and hydrocarbons), the transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) that the energy of carbon-carbon bond transformation is primarily determined by the functional group class of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the shared electron-pair during cleavage, or that accepts the incipient shared electron-pair during synthesis). In contrast, the energy of hydrogen transfer between carbon groups is determined by the functional group class of both the hydrogen-donor group and the hydrogen-acceptor group. From these and other observations we concluded that the chemistry involved in the origin of metabolism (and to a lesser degree modern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readily dissipated in a few energetically favorable irreversible reactions; (2) the energy dominance of a few transformation half-reactions that determines whether carbon-carbon bond transformation (cleavage or synthesis) is energetically favorable (deltaG < -3.5 kcal/mol), reversible (deltaG between +/-3.5 kcal/mol), or unfavorable (deltaG > +3.5 kcal/mol); and (3) the dependence of carbon group transformation energy on the functional group class (i.e., oxidation state) of participating groups that in turn is contingent on prior reactions and precursors in the synthetic pathway.