On the aqueous origins of the condensation polymers of life

Water is essential for life as we know it, but it has paradoxically been considered inimical to the emergence of life. Proteins and nucleic acids have sustained evolution and life for billions of years, but both are condensation polymers, suggesting that their formation requires the elimination of water. This presents intrinsic challenges at the origins of life, including how condensation polymer synthesis can overcome the thermodynamic pressure of hydrolysis in water and how nucleophiles can kinetically outcompete water to yield condensation products. The answers to these questions lie in balancing thermodynamic activation and kinetic stability. For peptides, an effective strategy is to directly harness the energy trapped in prebiotic molecules, such as nitriles, and avoid the formation of fully hydrolysed monomers. In this Review, we discuss how chemical energy can be built into precursors, retained, and released selectively for polymer synthesis. Looking to the future, the outstanding goals include how nucleic acids can be synthesized, avoiding the formation of fully hydrolysed monomers and what caused information to flow from nucleic acids to proteins.

Prebiotic Synthesis of N-Formylaminonitriles and Derivatives in Formamide

Amino acids and their derivatives were probably instrumental in the transition of prebiotic chemistry to early biology. Accordingly, amino acid formation under prebiotic conditions has been intensively investigated. Unsurprisingly, most of these studies have taken place with water as the solvent. Herein, we describe an investigation into the formation and subsequent reactions of aminonitriles and their formylated derivatives in formamide. We find that N-formylaminonitriles form readily from aldehydes and cyanide in formamide, even in the absence of added ammonia, suggesting a potentially prebiotic source of amino acid derivatives. Alkaline processing of N-formylaminonitriles proceeds with hydration at the nitrile group faster than deformylation, protecting aminonitrile derivatives from reversion of the Strecker condensation equilibrium during hydration/hydrolysis and furnishing mixtures of N-formylated and unformylated amino acid derivatives. Furthermore, the facile synthesis of N-formyldehydroalanine nitrile is observed in formamide from glycolaldehyde and cyanide without intervention. Dehydroalanine derivatives have been proposed as important compounds for prebiotic peptide synthesis, and we demonstrate both a synthesis suggesting that they are potentially plausible components of a prebiotic inventory, and reactions showing their utility as abiotic precursors to a range of compounds of prebiological interest.

Selective Synthesis of Lysine Peptides and the Prebiotically Plausible Synthesis of Catalytically Active Diaminopropionic Acid Peptide Nitriles in Water

Why life encodes specific proteinogenic amino acids remains an unsolved problem, but a non-enzymatic synthesis that recapitulates biology's universal strategy of stepwise N-to-C terminal peptide growth may hold the key to this selection. Lysine is an important proteinogenic amino acid that, despite its essential structural, catalytic, and functional roles in biochemistry, has widely been assumed to be a late addition to the genetic code. Here, we demonstrate that lysine thioacids undergo coupling with aminonitriles in neutral water to afford peptides in near-quantitative yield, whereas non-proteinogenic lysine homologues, ornithine, and diaminobutyric acid cannot form peptides due to rapid and quantitative cyclization that irreversibly blocks peptide synthesis. We demonstrate for the first time that ornithine lactamization provides an absolute differentiation of lysine and ornithine during (non-enzymatic) N-to-C-terminal peptide ligation. We additionally demonstrate that the shortest lysine homologue, diaminopropionic acid, undergoes effective peptide ligation. This prompted us to discover a high-yielding prebiotically plausible synthesis of the diaminopropionic acid residue, by peptide nitrile modification, through the addition of ammonia to a dehydroalanine nitrile. With this synthesis in hand, we then discovered that the low basicity of diaminopropionyl residues promotes effective, biomimetic, imine catalysis in neutral water. Our results suggest diaminopropionic acid, synthesized by peptide nitrile modification, can replace or augment lysine residues during early evolution but that lysine's electronically isolated sidechain amine likely provides an evolutionary advantage for coupling and coding as a preformed monomer in monomer-by-monomer peptide translation.

Prebiotic synthesis of cysteine peptides that catalyze peptide ligation in neutral water

Peptide biosynthesis is performed by ribosomes and several other classes of enzymes, but a simple chemical synthesis may have created the first peptides at the origins of life. α-Aminonitriles-prebiotic α-amino acid precursors-are generally produced by Strecker reactions. However, cysteine's aminothiol is incompatible with nitriles. Consequently, cysteine nitrile is not stable, and cysteine has been proposed to be a product of evolution, not prebiotic chemistry. We now report a high-yielding, prebiotic synthesis of cysteine peptides. Our biomimetic pathway converts serine to cysteine by nitrile-activated dehydroalanine synthesis. We also demonstrate that N-acylcysteines catalyze peptide ligation, directly coupling kinetically stable-but energy-rich-α-amidonitriles to proteinogenic amines. This rare example of selective and efficient organocatalysis in water implicates cysteine as both catalyst and precursor in prebiotic peptide synthesis.

Synthetic connectivity, emergence, and self-regeneration in the network of prebiotic chemistry

The challenge of prebiotic chemistry is to trace the syntheses of life’s key building blocks from a handful of primordial substrates. Here we report a forward-synthesis algorithm that generates a full network of prebiotic chemical reactions accessible from these substrates under generally accepted conditions. This network contains both reported and previously unidentified routes to biotic targets, as well as plausible syntheses of abiotic molecules. It also exhibits three forms of nontrivial chemical emergence, as the molecules within the network can act as catalysts of downstream reaction types; form functional chemical systems, including self-regenerating cycles; and produce surfactants relevant to primitive forms of biological compartmentalization. To support these claims, computer-predicted, prebiotic syntheses of several biotic molecules as well as a multistep, self-regenerative cycle of iminodiacetic acid were validated by experiment.

Convergent and Biomimetic Enantioselective Total Synthesis of (-)-Communesin F

The first biomimetic enantioselective total synthesis of (-)-communesin F based on a late-stage heterodimerization and aminal exchange is described. Our synthesis features the expedient diazene-directed assembly of two advanced fragments to secure the congested C3a-C3a' linkage in three steps, followed by a highly efficient biogenetically inspired aminal reorganization to access the heptacyclic communesin core in only two additional steps. Enantioselective syntheses of the two fragments were developed, with highlights including the catalytic asymmetric halocyclization and diastereoselective oxyamination reactions of tryptamine derivatives, a stereoselective sulfinimine allylation, and an efficient cyclotryptamine-C3a-sulfamate synthesis by either a new silver-promoted nucleophilic amination or a rhodium-catalyzed C-H amination protocol. The versatile syntheses of the fragments, their stereocontrolled assembly, and the efficient aminal exchange as supported by in situ monitoring experiments, in addition to the final stage N1'-acylation of the communesin core, provide a highly convergent synthesis of (-)-communesin F.

The Origin of Life--Out of the Blue

Either to sustain autotrophy, or as a prelude to heterotrophy, organic synthesis from an environmentally available C1 feedstock molecule is crucial to the origin of life. Recent findings augment key literature results and suggest that hydrogen cyanide--"Blausäure"--was that feedstock.

Direct transformation of methyl imines to α-iminonitriles under mild and transition-metal-free conditions

A novel transformation of methyl imines into α-iminonitriles under mild and transition-metal-free conditions is described. Three C sp 3-H bonds are cleaved in a radical pathway at room temperature under air. Simple bromide salts are employed to assist this radical process (see scheme; FG=functional group, PIDA = iodobenzene diacetate, TMS = trimethylsilyl).

A possible prebiotic origin on volcanic islands of oligopyrrole-type photopigments and electron transfer cofactors

Tetrapyrroles are essential to basic biochemical processes such as electron transfer and photosynthesis. However, it is not known whether these evolutionary old molecules have a prebiotic origin. We have serendipitously obtained pyrroles, which are the corresponding monomers, in laboratory experiments that simulated the interaction of amino acid-containing seawater with molten lava. The thermal pyrrole formation from amino acids, which so far has only been reported for special cases, can be explained by the observation that the amino acids become metal bonded, for example in (CaCl2)3(Hala)2·6H2O (Hala=DL-alanine), when the seawater evaporates. At a few hundred degrees Celsius, sea salt crusts also release hydrochloric acid (HCl). On primordial volcanic islands, the volatile pyrroles and HCl must have condensed at cooler locations, for example, in rock pools. There, pyrrole oligomerization may have occurred. To study this possibility, we added formaldehyde and nitrite, two species for which plausible prebiotic sources are known, to 2,4-diethylpyrrole and HCl. We found that even at high dilution conjugated (oxidized) oligomers, including octaethylporphyrin and other cyclic and open-chain tetrapyrroles, were formed. All experiments were conducted under rigorously oxygen-free conditions. Our results suggest that primitive versions of present-day biological cofactors such as chlorophylls, bilins, and heme were spontaneously abiotically synthesized on primordial volcanic islands and thus may have been available to the first protocells.

Syntheses and properties of carboranylpyrroles

Synthetic routes to mono- and di-carboranylpyrroles (1-5) bearing the carborane groups linked either directly to the 3- and/or 4-positions of the pyrrole ring or via one or two methylene spacers are described. Several X-ray structures of key intermediates are presented and discussed. Carboranylpyrroles can be cyclotetramerized to afford carboranylporphyrins in low to moderate yields, depending on the number of carborane cages and their linkage to the pyrrole ring. The best yields of porphyrin were obtained with pyrrole 3, bearing a two carbon spacer between the carborane and pyrrole units. The electrochemical polymerization of pyrroles 2 and 3 gave functionalized conducting polymer films with increased overoxidation resistance and thermal stability compared with unsubstituted polypyrrole. Dicarboranylpyrrole 4 did not electropolymerize under a variety of experimental conditions, whereas pyrrole 5 formed only soluble oligomers.

Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective

"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.

Simple formation of an abiotic porphyrinogen in aqueous solution

Porphyrins have long been proposed as key ingredients in the emergence of life yet plausible routes for forming their essential pyrrole precursor have heretofore not been identified. Here we show that the anaerobic reaction of δ-aminolevulinic acid (ALA, 1-5 mM) with the β-ketoester methyl 4-methoxyacetoacetate (2-40 mM) in water (pH5-7) at 70-100°C for >6 h affords the porphyrinogen, which upon chemical oxidation gives the corresponding porphyrin in overall yield of up to 10%. The key intermediate is the α-methoxymethyl-substituted pyrrole, which undergoes tetramerization and macrocycle formation under kinetic control. The resulting type-I porphyrin bears four propionic acid and four carbomethoxy groups, is distinct from porphyrins (e.g., uroporphyrin or coproporphyrin) derivable from ALA alone via the extant universal biosynthetic path to tetrapyrroles, and is photoactive upon assembly into cationic micelles in aqueous solution. The simple self-organization of eight acyclic molecules into a tetrapyrrole macrocycle, from which a porphyrin is derived that is photoactive in lipid assemblies, augurs well for the spontaneous origin of catalysts and pigments essential for prebiotic metabolism and proto-photosynthesis.

B12: reminiscences and afterthoughts

This paper describes some of the chemistry of synthetic corrinoids and corphinoids carried out at the ETH (Swiss Federal Institute of Technology) after the completion of the non-enzymic synthesis of vitamin B12 and attempts to delineate the interplay between mechanistic hypotheses, model studies and the experimental research in B12 biosynthesis which had spurred this work. The afterthoughts deal with why and how the work on corrinoids eventually led to an experimental involvement in the problem of a chemical aetiology of the structure of natural nucleic acids.

Reactions of the HCN-tetramer with aldehydes

The HCN-tetramer, a 'classic' of the prebiotic chemistry of HCN, is shown to undergo a remarkable reaction with acetaldehyde in slightly basic or neutral aqueous solution at room temperature. The reaction consists in an aldolization-type C,C-bond formation, accompanied by a (presumably aldehyde-catalyzed) hydration of one of the two nitrile groups and the formation of two cyclic aminal-type groupings, each of the latter incorporating an additional molecule of the aldehyde. Should this so far unexplored type of chemistry of the HCN-tetramer prove to have some generality, the finding might add a new dimension to the potential etiological relevance of this HCN-oligomer.

Microwave Spectrum, Structure, and Quantum Chemical Studies of a Compound of Potential Astrochemical and Astrobiological Interest: Z-3-Amino-2-propenenitrile

Z-3-Amino-2-propenenitrile, H2NCH=CHCN, a compound of astrochemical and astrobiological interest, has been studied by Stark and Fourier transform microwave spectroscopy along with eight of its isotopologues; the synthesis of five of these are reported. The spectra of the ground vibrational state and of three vibrationally excited states belonging to the two lowest normal modes were assigned for the parent species, whereas the ground states were assigned for the isotopologues. The frequency of the lowest in-plane bending fundamental vibration was determined to be 152(20) cm(-1) and the frequency of the lowest out-of-plane fundamental mode was found to be 176(20) cm(-1) by relative intensity measurements. A delicate problem is whether this compound is planar or slightly nonplanar. It was found that the rotational constants of the nine species cannot be used to conclude definitely whether the molecule is planar or not. The experimental dipole moment is mu(a) = 16.45(12), mu(b) = 2.86(6), mu(c) = 0 (assumed), and mu(tot.) = 16.70(12) x 10(-30) C m [5.01(4) D]. The quadrupole coupling constants of the two nitrogen nuclei are chi(aa) = -1.4917(21) and chi(cc) = 1.5644(24) MHz for the nitrogen atom of the cyano group and chi(aa) = 1.7262(18) and chi(cc) = -4.0591(17) MHz for the nitrogen atom of the amino group. Extensive quantum-chemical calculations have been performed, and the results obtained from these calculations have been compared with the experimental values. The equilibrium structures of vinylamine, vinyl cyanide, and Z-3-amino-2-propenenitrile have been calculated. These calculations have established that the equilibrium structure of the title compound is definitely nonplanar. However, the MP2/VQZ energy difference between the planar and nonplanar forms is small, only -423 J/mol. Z-Amino-2-propenenitrile and E-3-amino-2-propenenitrile are formed simply by mixing ammonia and cyanoacetylene at room temperature. A plausible reaction path has been modeled. G3 calculations indicate that the enthalpy (298.15 K, 1 atm) of the transition state is about 130 kJ/mol higher than the sum of the enthalpies of the reactants ammonia and cyanoacetylene. This energy difference is comparatively high, which indicates that both E- and Z-3-aminopropenenitrile are not likely to be formed in the gas phase in cold interstellar clouds via a collision between ammonia and cyanoacetylene. An alternative reaction between protonated cyanoacetylene (H-C[triple bond]C-C[triple bond]NH+) and ammonia is predicted to have a much lower activation energy than the reaction between the neutral molecules. Although protonated E- and Z-3-aminopropenenitrile in principle may be formed this way, it is more likely that a collision between NH3 and H-C[triple bond]C-C[triple bond]NH+ leads to NH4+ and H-C[triple bond]C-C[triple bond]N.

Precursors of Biological Cofactors from Ultraviolet Irradiation of Circumstellar/Interstellar Ice Analogues

Biological cofactors include functionalized derivatives of cyclic tetrapyrrole structures that incorporate different metal ions. They build up structural partnerships with proteins, which play a crucial role in biochemical reactions. Porphyrin, chlorin, bacteriochlorin, and corrin are the basic structures of cofactors (heme, chlorophyll, bacteriochlorophyll, siroheme, F 430, and vitamin B12). Laboratory and theoretical work suggest that the molecular building blocks of proteins (alpha-amino acids) and nucleic acids (carbohydrates, purines, and pyrimidines) were generated under prebiotic conditions. On the other hand, experimental data on the prebiotic chemistry of cofactors are rare. We propose to search directly for the pathways of the formation of cofactors in the laboratory. Herein we report on the detection of N-heterocycles and amines in the room-temperature residue obtained after photo- and thermal processing of an interstellar ice analogue under high vacuum at 12 K. Among them, hexahydro-1,3,5-triazine and its derivatives, together with monopyrrolic molecules, are precursors of porphinoid cofactors. Hexahydropyrimidine was also detected. This is the first detection of these compounds in experiments simulating circumstellar/interstellar conditions. Except for 2-aminopyrrole and 2,4-diaminofuran, which were only found in 13C-labeled experiments, all the reported species were detected in both 12C- and 13C-labeled experiments, excluding contamination. The molecules reported here might be present in circumstellar/interstellar grains and cometary dust and could be detected by the Stardust and Rosetta missions.

Synthesis and structural characterization of mono- and bisfunctional o-carboranes

Functionalized o-carboranes are interesting ligands for transition metals. Reaction of LiC2B10H11 with Me2NCH2CH2Cl in toluene afforded 1-Me2NCH2CH2-1,2-C2B10H11 (1). Treatment of 1 with 1 equiv. of n-BuLi gave [(Me2NCH2CH2)C2B10H10]Li ([1]Li), which was a very useful synthon for the production of bisfunctional o-carboranes. Reaction of [1]Li with RCH2CH2Cl afforded 1-Me2NCH2CH2-2-RCH2CH2-1,2-C2B10H10 (R = Me2N (2), MeO (3)). 1 and 2 were also prepared from the reaction of Li2C2B10H10 with excess Me2NCH2CH2Cl. Treatment of [1]Li with excess MeI or allyl bromide gave the ionic salts, [1-Me3NCH2CH2-2-Me-1,2-C2B10H10][I] (4) and [1-Me2N(CH2=CHCH2)CH2CH2-2-(CH2=CHCH2)-1,2-C2B10H10][Br] (6), respectively. Interaction of [1]Li with 1 equiv. of allyl bromide afforded 1-Me2NCH2CH2-2-(CH2=CHCH2)-1,2-C2B10H10 (5). Treatment of [1]Li with excess dimethylfulvene afforded 1-Me2NCH2CH2-2-C5H5CMe2-1,2-C2B10H10 (7). Interaction of [1]Li with excess ethylene oxide afforded an unexpected product 1-HOCH2CH2-2-(CH2=CH)-1,2-C2B10H10 (8). 1 and 3 were conveniently converted into the corresponding deborated compounds, 7-Me2NHCH2CH2-7,8-C2B9H11 (9) and 7-Me2NHCH2CH2-8-MeOCH2CH2-7,8-C2B9H10 (10), respectively, in MeOH-MeOK solution. All of these compounds were characterized by various spectroscopic techniques and elemental analyses. The solid-state structures of 4 and 6-10 were confirmed by single-crystal X-ray analyses.

[Chemistry of alpha-aminonitriles. Aziridine-2-carbonitrile: photochemical formation from 2-aminopropenenitrile]

2-Aminopropenenitrile in solvents such as MeCN, MeOH, or H2O is photoisomerized by UV light to racemic aziridine-2-carbonitrile (rac-2); the larger part of the starting material, however, fragments to HCN and MeCN. The observed photocyclization constitutes a structural connection within an ensemble of C3H4N2 compounds considered to be potentially relevant to prebiotic chemistry.

A new method for assembling metabolic networks, with application to the Krebs citric acid cycle

To understand why a molecular network has a particular connectivity one can generate an ensemble of alternative networks, all of which meet the same performance criteria as the real network. We have generated alternatives to the Krebs cycle, allowing group transfers and B(12)-mediated shifts that were excluded in previous work. Our algorithm does not use a reaction list, but determines the reactants and products in generic reactions. It generates networks in order of increasing number of reaction steps. We find that alternatives to the Krebs cycle are very likely to be cycles. Many of the alternatives produce toxic or unstable compounds and use group transfer reactions, which have unfavorable consequences. Although alternatives are better than the Krebs cycle in some respects, the Krebs cycle has the most favorable combination of traits.