Dynamic Organic Reaction Networks,
Transition metals and sulfides and Origins of Life
Abiotic organic synthesis relevant to Earth’s Crust and possible the origins of life
Research Support: NASA Exobiology and NASA Astrobiology
BACKGROUND: The hypothetical path from the initial abiotic world to Earth’s first biology has been described (in purely general terms) as passing through several key stages (e.g. de Duve, 1991). In de Duve's world, such a path starts with proto-metabolism (with an emphasis on abiotic nucleotide synthesis), leads into RNA replication (the nascent stages of “RNA world”), and eventually achieves encapsulation (the first membrane). The development of RNA dependent peptide synthesis, followed by the final development of translation, yields the “pre”-biotic system poised to initiate biological metabolism and herald in Earth’s first life (de Duve, 1991). Although, over the past three decades there has been substantial progress made in research covering many of these path segments, for example in the area of RNA catalysis, and high yield cytidine mono phosphate, there remains considerable uncertainty regarding how organic chemistry intrinsic to a primitive terrestrial planet segued into the initiation of the RNA world. While clever chemists continue to solve the "total synthesis" problems for discrete biomolecules, we take a very different approach of studying dynamic organic reaction networks and seek to identify interesting reaction pathways that might have had utility for the origin of life.
WHAT WE DO and WHY WE DO IT: We focus on the prebiotic story. As a starting point, It appears a requisite that for life to emerge anywhere on the primitive Earth, it had to be in an environment capable of sustained and re-generative organic synthesis, where potentially reactive organic compounds would be present. As a counter example, if a given environment solely promoted the conversion of CO2 and H2 to saturated hydrocarbons (predominantly n-alkanes, e.g. through Fischer Tropsch synthesis), we would consider this a potentially useless environment for emergent life. What we look for is environments that promote molecular growth, initially through catalyzed carbonyl insertion reactions (e.g. Cody et al. 2000, 2001, and 2004) and simultaneously allowing for partial oxidation reactions to re-generate organic reactivity either through the formation of olefinic moieties and keto groups. These potentially reactive products are capable of forward reaction towards more complexity but, of course, are subject to degradation reactions (in some cases to even more reactive molecules - e.g. alpha-keto acids).
What becomes immediately apparent that what we are seeking is an environment that sustains a "Dynamic Organic Reaction Network" (DORN?). This is not an immediately obvious environment to search for, even as the requirements appear necessary to an ultimately emergent system. So... what we do is first work on establishing the topology of the small molecular reaction network through many experimental studies, we look for connective pathways- NOT "A ONE POT SYNTHESIS". We do not worry about yield, only pathway connectedness. Our approach is simply to establish what pathways operate and those that do not - always focusing on pathways that might have proto-biological significance.
A (simple) Example: Extant biochemical pathways to aspartic acid rely on reductive amination of oxaloacetate to aspartic acid. Oxaloacetate is completely unstable under prebiotic conditions (i.e. sans protein enzymes) and this reaction will not occur. Note: the reductive amination of pyruvate to alanine does go nicely- pyruvate is not nearly as reactive as oxaloacetate. What one finds in the small molecule reaction network is that amination of fumarate is facile and the most logical route to aspartate. System shunts around oxaloacetate.
A more complex Example: Extant biochemical pathways to isocitric acid either move (in the oxidative sense) from citric acid - past aconitic acid - to isocitric or (in the reductive sense- R-TCA) from alpha ketoglutarate through oxalo succinate to isocitrate. We have tried with no success to show that the oxidative pathway can occur "pre-biotically" (sans protein catalysts)- hydration of aconitic acid always yields 100 % citric acid and aconitate is extremely unstable (see Cody et al. 2001 and references therein). The reductive pathway is challenged (GRAND CHALLENGE) by finding a catalytic path from succinic acid to alpha ketoglutarate then CO2 addition (like pyruvate to form oxalacetate) to yield oxalosuccinate. Shohei Ohara and Vijay S. working in my lab found clever and simple "prebiotic routes to both alphaketoqlutarate and isocitrate that are simple, yet not used by extant biochemistry (NEED TO PUBLISH THIS!!!!). This chemistry works surprisingly well- but requires a reactive (and lossy) chemical system.
We similarly find simple routes to pyrimidines (NOT ribosylated!) and can imagine a similar simple route to basic purine nucleobases (not yet realized- working on it). Neither route strictly emulates extant biochemistry, but are closer at a pathway level then other pathways (e.g. HCN condensation).
I am more convinced then ever that this chemical approach provides a view into plausible pathways to moderate chemical complexity- what I do not yet know is how to drive the system towards maximum complexity. This is what I am focusing on now- please stay tuned.
This is really quite fertile area of research- perhaps not so much that one can build a career on it, but lots of chemistry to explore- So off we go!
How we got started: Initially we set out to establish, experimentally, whether transition metal catalyzed reactions in the presence of water could provide potentially useful protometabolic chemistry. Our early efforts focused on primitive carbon fixation pathways. We found that the all but one of the transition metal sulfides studied thus far promote reactions that mimic the key intermediate steps of the critical enzyme complex acetyl-CoA synthase operating at the core of the anabolic metabolism of acetogens and methanogens (Cody et al. 2004). The most significant thing that metal sulfides do is catalyze well carbonyl insertion at specific locations in certain reactive molecules and do not promote continuous carbon chain growth (almost a "cancer" to the chemistry- wastes CO2 and H2). The metal sulfides also catalyze other reactions (see Cody et al. 2004) and in one case, NiS, also promote a partial oxidation that primes the system for a second carbonyl insertion (see Cody et al. 2001). We have moved further into transition metal ion catalysis following hunch of Harold Morowitz and have not been disappointed.
Figure (Right): The yield of decanoic acid from nonane thiol and formic acid under high pressure (200 Mpa) moderate temperature (250 °C) in the presence of a range of transition metal sulfides. Note that maximum yield in the presence of NiS (millerite) is on the order of a 30 % yield based on the starting amount of nonane thiol. note that the turn over frequencies for these catalysts rival that of industrial catalysts, e.g. Cobalt metal. See Cody et al. (2004) GCA.
We further showed that metal sulfide catalysis can promote a series of hydrocarboxylation reactions that highlight a potential reaction pathway leading up from propene to hydroaconitic acid; i.e. an abiotic carbon fixation pathway that ends within two electrons and one water molecule away from citric acid (Cody et al. GCA, 2001). This we believe is the initiation point of the "small molecule" reaction network and the key to developing a robust Dynamic Organic Reaction Network.
Figure (Right): The principal hydrothermal decomposition pathways (a and b) of citric acid. In the presence of a transition metal sulfide (NiS) catalyst and a reduced CO2 bearing fluid, we have identified a plausible pathway (the b’ pathway above) for the formation of citric acid that follows a route that differs completely from extant metabolic pathways (akin to reversing the a pathway) (see Cody et al. 2001 GCA).
Really, the b' pathway is the natural abiotic pathway into intermediary metabolism- simple compounds simple chemistry- robust!
For my part I am focusing on this route. There are of course others- HCN is really popular right now- I get that HCN is great if you can generate it and sustain it- that is really the game I think.
The potential of such such a pathway is compelling as it is well known that under hydrothermal reactions citric acid can be a good source for pyruvic acid and possibly oxalacetic acid (although this compound has never been observed due to its extreme thermal instability). Pyruvic acid is a very useful prebiotic product, for example, in the presence of NH4+ a simple reductive amination reaction provides a ready source of alanine (e.g. Brandes et al. 1999).
Figure (Right): Another view of the potential prebiotic pathway based on our current hydrothermal abiotic reactions. Whereas this complete cycle has not been completed as a “one-pot” reaction, each step has been demonstrated experimentally. Exploring the pathways moving off this small molecule network is under study and points to a wide range of amino acids, pyrimidines, and possibly purines (not yet realized). I have not yet found a good way of render this.
Update: I am way beyond this right now- but this points you in the direction I am going.
It is fun to do!
Where Are We Going: we are exploring potential hydrothermal prebiotic pathways towards pyrimidine and purine synthesis, starting from various branch points in our previously defined dynamic reaction network. We are also attempting to derive experiments that might identify environmental constraints that could sustain a truly dynamic organic reaction network.