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I'm currently working on building a simulator for the early earth to examine the spontaneous occurrence of food generated autocatalytic sets. No one in my group is a chemist, so the bottle neck for the project is implementing some sort of realistic chemistry in our model.

We are considering using the software outlined in this paper: http://arxiv.org/abs/1304.1356

This will allow us to create a reaction network from an initial set, based on a set of general rules. The paper demonstrates well how the formose reactions are executed, which we intend to include. What other reaction groups would it be important to include? Our initial set of molecules would be comprised of the food molecules for each set of reaction rules included, we don't intend to start from H,O,N,C for example, so fundamental chemical rules should not be too crucial, as they should be generalised into the major reaction groups we will use.

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  • $\begingroup$ The idea is questionable at best. Too much work to do. $\endgroup$ – permeakra Jul 23 '13 at 21:14
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For the reactions look up Stanley Miller's experiment. The experiment used water (H2O), methane (CH4), ammonia (NH3), and hydrogen (H2). I think you should start with that.

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The formose reaction is one of the proposed pathways that carbohydrates could form. Two equivalents of formaldehyde ($\ce{CH2O}$) react to form glycoaldehyde ($\ce{HOCH2CHO}$), which reacts with further equivalents of formaledehyde or gycloaldehyde in aldol condensations to produce the 3-, 4-, 5-, and 6-carbon sugars.

$$\ce{CH2O + CH2O -> HOCH2CHO}$$ $$\ce{CH2O + HOCH2CHO -> HOCH2CH(OH)CHO}$$ $$\ce{HOCH2CHO + HOCH2CHO -> HOCH2CH(OH)CH(OH)CHO}$$

Formaldehyde can be produced from hydrogen and carbon monoxide or dioxide, themselves the products of steam reforming of methane and the water-gas shift reaction.

Steam-reformation: $$\ce{CH4 + H2O <=> CO + 3H2}$$ Water-gas shift: $$\ce{CO + H2O <=> CO2 + H2}$$ Fomaldehyde synthesis: $$\ce{H2 + CO <=> H2CO}$$

Once you have the sugars, the carbonyl group and the alcohols give you the option to bring all of organic chemistry to bear and convert the sugars into anything you want through substitutions, additions, eliminations, and redox. Consider the Chichibabin pyridine synthesis, which can operate with as simple molecules as acetaldehyde ($\ce{CH3CHO}$), formaldehyde, and ammonia:

$$\ce{H2CO + CH3CHO <=> H2C=CHCHO + H2O}$$ $$\ce{H2C=CHCHO + CH3CHO + NH3 + 1/2 O2 <=> C5H5N + 3H2O}$$

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