Fig. 7: Miller experiment simulation results for ANI-1xnr.
The reaction pathways discovered by ANI-1xnr in a Miller experiment simulation for the formation of glycine from small-molecule species (for example, NH3, CO, H2O, H2 and CH4). The green arrows denote reactions previously identified by Wang et al. or Saitta and Saija. The orange arrows denote reactions that have a similar reaction in Wang et al. or Saitta and Saija. The majority of reactions have been previously reported in the literature, confirming the validity of the ANI-1xnr mechanism. Three-dimensional snapshots extracted from the MD simulation trajectory are reported in Extended Data Fig. 6, further confirming that the reaction pathways are physically meaningful. Note that +H does not necessarily signify a free hydrogen atom, +H is short-hand for a proton donor, for example, NH4, NH3, CHO, CHNO, H3O or H2O. Likewise, −H does not necessarily signify dissociation of a hydrogen atom. −H is short-hand for a proton acceptor, for example, NH2, CO, CNO, H2O or OH. The boxes encapsulate the key intermediates, carbon dioxide (CO2) and methylene (CH2). The novel pathways to form these key intermediates are reported in Extended Data Fig. 7. The depiction of bond orders and radical species is based simply on chemical intuition, since ANI-1xnr does not provide explicit bonding, orbital or electronic information (for an alternative interpretation of this mechanism involving ionic species, see Extended Data Fig. 8).
