Formamide reaction network in gas phase and solution via a unified theoretical approach: Toward a reconciliation of different prebiotic scenarios

Abstract

Increasing experimental and theoretical evidence points to formamide as a possible hub in the complex network of prebiotic chemical reactions leading from simple precursors like H2, H2O, N2, NH3, CO, and CO2 to key biological molecules like proteins, nucleic acids, and sugars. We present an in-depth computational study of the formation and decomposition reaction channels of formamide by means of ab initio molecular dynamics. To this aim we introduce a new theoretical method combining the metadynamics sampling scheme with a general purpose topological formulation of collective variables able to track a wide range of different reaction mechanisms. Our approach is flexible enough to discover multiple pathways and intermediates starting from minimal insight on the systems, and it allows passing in a seamless way from reactions in gas phase to reactions in liquid phase, with the solvent active role fully taken into account. We obtain crucial new insight into the interplay of the different formamide reaction channels and into environment effects on pathways and barriers. In particular, our results indicate a similar stability of formamide and hydrogen cyanide in solution as well as their relatively facile interconversion, thus reconciling experiments and theory and, possibly, two different and competing prebiotic scenarios. Moreover, although not explicitly sought, formic acid/ammonium formate is produced as an important formamide decomposition byproduct in solution.

Keywords: ab initio molecular dynamics; chemical reactions; formamide; free energy landscapes; prebiotic scenarios.

Fig. 1.

Construction principle of topological path collective variables. The connectivity patterns of reactants and products are represented by tables having individual, nonhydrogen atoms on rows and atomic species (the set of all atoms of a given element) on columns. Arrows indicate changes of coordination numbers; however, all other matrix elements are free to change as well thanks to the flexibility of path collective variables (see text).

Fig. 2.

Free energy landscape for interconversion of formamide (region A) and CO $+$ NH₃ (region B) in the gas phase. Representative atomic configurations of free energy minima and transition states are shown as insets.

Fig. 3.

Free energy landscape for reactions in aqueous solution between formamide (region A), CO $+$ NH₃ (region B), and HCOOH $+$ NH₃ (region C). Representative atomic configurations are shown as insets.

Fig. 4.

Examples of unbiased trajectories observed within committor analysis and representative structures of transition states for reactions among formamide, CO $+$ NH₃, and HCOOH $+$ NH₃.

Fig. 5.

Free energy landscape for reactions in aqueous solution between formamide (region A), OHCHNH (region B), and HCN (region C). Representative atomic configurations are shown as insets.

Fig. 6.

Examples of unbiased trajectories observed within committor analysis and representative structures of transition states for reactions between OHCHNH and HCN. The orange contour indicates atoms belonging to the reacting OHCHNH molecule.

Fig. S1.

Comparison of free energy landscapes at T = 300 K computed using (A) a smaller (30 water molecules) or (B) a larger (62 water molecules) simulation box for transitions between formamide (region A), CO + NH₃ (region B), and HCOOH + NH₃ (region C).

Fig. S2.

Comparison of free energy landscapes at T = 300 K computed using (A) a smaller (30 water molecules) or (B) a larger (62 water molecules) simulation box for transitions between formamide (region A), OHCHNH (region B), and HCN + H₂O (region C). (C) Free energy landscape at T = 400K (including 30 water molecules).

Fig. S3.

Gas-phase free energy landscape at T = 300 K for the reaction between formamide (region A) and CO + NH₃ (region B). The topological path collective variables are defined starting from six different patterns of coordination, as sampled from a reactive trajectory in the simulation reported in Fig. 2. Representative committor analysis trajectories are shown as colored lines superimposed to the free energy landscape.

Fig. S4.

Gas-phase free energy landscape at T = 300 K (A) for the reaction between formamide (region A) and OHCHNH (region B) and (B) for the reaction between another OHCHNH isomer (region B′) and HCN + H₂O (region C). The topological path collective variables are defined starting from two different patterns of coordination in the first case (regions A and C) and from five different patterns in the second case (between regions B′ and C, sampled from a reactive trajectory obtained with the same setup as in A).

Fig. S5.

Gas-phase free energy landscape at T = 400 K (A) for the reaction between formamide (region A) and OHCHNH (region B) and (B) for the reaction between another CHOHNH isomer (region B′) and HCN + H₂O (region C). To be compared with Fig. S4.