Planetary organic chemistry and the origins of biomolecules

Abstract

Organic chemistry on a planetary scale is likely to have transformed carbon dioxide and reduced carbon species delivered to an accreting Earth. According to various models for the origin of life on Earth, biological molecules that jump-started Darwinian evolution arose via this planetary chemistry. The grandest of these models assumes that ribonucleic acid (RNA) arose prebiotically, together with components for compartments that held it and a primitive metabolism that nourished it. Unfortunately, it has been challenging to identify possible prebiotic chemistry that might have created RNA. Organic molecules, given energy, have a well-known propensity to form multiple products, sometimes referred to collectively as "tar" or "tholin." These mixtures appear to be unsuited to support Darwinian processes, and certainly have never been observed to spontaneously yield a homochiral genetic polymer. To date, proposed solutions to this challenge either involve too much direct human intervention to satisfy many in the community, or generate molecules that are unreactive "dead ends" under standard conditions of temperature and pressure. Carbohydrates, organic species having carbon, hydrogen, and oxygen atoms in a ratio of 1:2:1 and an aldehyde or ketone group, conspicuously embody this challenge. They are components of RNA and their reactivity can support both interesting spontaneous chemistry as part of a "carbohydrate world," but they also easily form mixtures, polymers and tars. We describe here the latest thoughts on how on this challenge, focusing on how it might be resolved using minerals containing borate, silicate, and molybdate, inter alia.

Figure 1.

Lewis structures of chemical bonds for dihydrogen (H₂), water (H₂O) and formaldehyde (H₂C=O, or CH₂O, or HCHO).

Figure 2.

Nucleophilic centers have an unshared pair of electrons that can form a new bond, or can get one (via resonance, for example). Electrophilic centers have a vacant orbital (or can get one via resonance, for example) that can accept an unshared pair of electrons from a nucleophilic center to form a new bond. In a resonance form a pair of electrons moves between adjacent atoms (electrons are dynamic entities), creating a new representation for the same molecule. The resulting resonance forms are joined by a double headed arrow to indicate equivalence.

Figure 3.

Reaction of the nucleophilic center on the oxygen of water with an electrophilic center, H⁺. The movement of a pair of electrons in the reaction is illustrated using a curved arrow. The result is H₃O⁺, the hydronium ion.

Figure 4.

Reaction of the nucleophilic center on the oxygen of water with an electrophilic center, the carbon atom of formaldehyde forms the hydrate of formaldehyde. The movement of a pair of electrons in the reaction is illustrated using a curved arrow.

Figure 5.

The Strecker synthesis of glycine, an amino acid. Reaction of the nucleophilic centers on the nitrogen of ammonia, the carbon of the cyanide anion and the oxygen of water with electrophilic centers on formaldehyde and key intermediates. The movements of pairs of electrons in the reactions are illustrated using curved arrows.

Figure 6.

Strecker synthesis of alanine starting from acetaldehyde.

Figure 7.

HCN yields adenine via the Oró-Orgel synthesis.

Figure 8.

The Eschenmoser synthesis of ribose-2,4-diphosphate from a proposed starting material derived from HCN.

Figure 9.

Two reaction types create formose. Top. In an enolization reaction, a base (here, hydroxide) removes a proton (H+) from a carbon adjacent to a C=O unit to give an enediol. The enediol can then react as a nucleophile in an aldol addition reaction. Bottom. In an aldol addition reaction, an enediol reacts as a nucleophile to form a new bond to the C of a C=O unit (the electrophilic center). If the carbonyl species is formaldehyde, R“=R”'=H.

Figure 10.

This figure shows the complexity that is possible simply by repeating the two reactions shown in Figure 9. It shows the structures of organic molecules made of only carbon atoms (C), hydrogen atoms (H), and oxygen atoms (O) in a ratio of 1:2:1. The compounds are ordered by size, with compounds containing two and three carbon atoms (C2 and C3, respectively) at the top, and compounds containing four, five, six, seven and eight carbon atoms (C4, C5, C6, C7, and C8) ordered in rows below. The arrows show reactions that interconvert these compounds. The heavy black arrows show the addition of formaldehyde (HCHO) to a species in the row above; this converts that species to a new species with one more carbon atom. The open arrows show reactions that interconvert species having the same number of carbon atoms. Red arrows show reactions that fragment a larger molecule to give two smaller molecules, where the bond that is broken in the fragmentation is red. Blue compounds are dead-end compounds that accumulate in the reaction. A chemist must intervene to prevent this mixture from evolving further to give still more complexity.

Figure 11.

Carbohydrates with 5 carbons (pentoses or pentuloses, penta=5). Pentoses have a HC=O group in their open form; pentuloses have a C=O unit flanked by two carbons All have the formula C₅H₁₀O₅. All can exist in both open and cyclic forms, as the C of the C=O unit is an electrophile and can react with the O of an –OH group as a nucleophile to form a ring. In many cases, more than one cyclic form is possible. Different pentoses differ in how their atoms are arranged in space. We represent these 3D orientations on a 2D sheet of paper by drawing thicker bonds (which are forwards) and placing the H and OH groups up or down. Cyclic pyranose forms (with six atoms in the ring) are not shown.

Figure 12.

The NMR structure of the borate-ribose complex, with boron complexing adjacent 1,2-hydroxyl groups.

Figure 13.

Borate-guided prebiotic path to form carbohydrates from formaldehyde. Compounds in green are known to be prebiotic. Compounds in blue cannot enolize. Dihydroxyacetone is shown in brown.

Figure 14.

Binding of borate to the 3,4-diol unit of erythrulose should direct enolization to give the 1,2-enediolate, as this removes the H⁺ from the carbon the farthest from the negative charge on boron.

Figure 15.

The Bilik reaction uses molybdate minerals to catalyze the stereospecific isomerization of carbohydrates such as the branched pentoses to give linear pentuloses such as ribulose at neutral pH under mild conditions.