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 H 2 , H 2 O, N 2 , NH 3 , CO, and CO 2 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.chemical reactions | free energy landscapes | ab initio molecular dynamics | formamide | prebiotic scenarios V ery different environments have been suggested as possible cradles for the emergence of biomolecules, including a primordial liquid soup (1), rarified gaseous interstellar clouds (2, 3), liquid-solid interfaces at hydrothermal conditions (4), and the extreme case of impact sites of meteorites and comets (5). Biochemically relevant reactions can be fueled by a range of different energy sources, and a large number of possible chemical reactions and reaction paths are suggested to have played an important role in the process leading simple molecules to form small organic molecules and, from them, biological monomers and polymers.Among such small organic molecules, formamide is assuming an ever more central role in prebiotic chemistry research, as recently shown in experiments mimicking some of those origins of life scenarios, such as laser sparks (6), UV light (7), proton irradiation (8), or shock waves (as in meteorite impacts) (9). The main reason for such strong interest in formamide, besides its ubiquitousness in the solar system, is its chemical flexibility: it can be formed from (or, conversely, dissociated into) different molecular species that represent fundamental building blocks, including H 2 , H 2 O, NH 3 , CO, HCN, HNCO, and HCOOH (10, 11). The barriers for these different processes lie in a relatively narrow range, providing many synthetic directions. Additionally, as has been also showed experimentally and computationally, for...

Formation of nucleobases in a Miller–Urey reducing atmosphere

“…the formation barrier increases from 57 kcal/mol at 650 K to 96 kcal/mol at 4500 K. At both temperatures, the barriers are thus comparable with those for the formation of formamide, a situation already observed in aqueous solution (48). Once formed, the collision of HCOOH with ammonia yields formamide and water ( Fig.…”

“…To help interpret the reactions in the shock wave plasma (4500 K) and electric discharge (650 K) experiments, further ab initio molecular-dynamics simulations combined with enhanced sampling were performed (48). We remark that our simulations proceed without introducing any information about the possible reaction pathway.…”

“…Formamide, in particular, was continuously produced and fueled the formation of more complex organic molecules up to the simplest amino acid, glycine. Subsequently, a theoretical study on formamide synthesis and dissociation chemistry pointed to the importance of HCN, NH 3 , CO, and H 2 O in its reaction network (48).…”

Navigating at Will on the Water Phase Diagram

“…Yet the CVs available to describe phase transitions are specifically designed for a given type of structural transformation [17][18][19], while no general CV scheme has been proven successful for a wide class of problems, in particular those involving amorphous systems. Recently, distance metrics developed for condensed matter [7,20,21,[23][24][25] have been proven to be successful in classifying structures in molecular or extended systems based on their atomic environment and/or interatomic network. Here we show that by combining enhanced sampling techniques with a novel CV based on a general metric we are able to define in an efficient way the topological space of transformations among liquid, amorphous, and crystalline forms of water.…”

Novel Enhanced Sampling Strategies for Transitions Between Ordered and Disordered Structures

“…However, the CVs suitable to this task are often designed for specific classes of structural transformations (Lechner and Dellago 2008;Martoňák et al 2003;Giberti et al 2015;Haji-Akbari and Debenedetti 2015): no general CV scheme was proved successful for a wide class of different problems, in particular those involving disordered systems. Recently, on the other hand, several distance metrics have been developed with the aim of distinguishing and classifying structures of molecular or extended systems, based on atomic environment and/or interatomic networks (Valle and Oganov 2010;Gallet and Pietrucci 2013;Pietrucci and Martoňák 2015;Pietrucci and Saitta 2015;Zhu et al 2016;De et al 2016;Piaggi and Parrinello 2017;Martelli et al 2018;Barthel et al 2018). In this context, an important question is whether a given metric is able, besides classifying locally stable structures, to also track dynamical transitions in a continuous and accurate way.…”