Automated methods to discover reaction mechanisms

Over the last few years we have been involved in the development of automated methods to discover complex reaction mechanisms. The methods are based on the use of accelerated dynamics simulations and Graph Theory. The procedure, termed tsscds, has been applied to different systems and a computer program is available: tsscds-2018.

The cobalt-catalyzed hydroformylation of ethylene has been studied with our procedure, explaining not only the major mechanism, but also side  reactions like hydrogenation. (Chem. Sci. 2017, 8, 3843)


The method has been also employed to elucidate the different HCN and HNC elimination channels from methyl cyanoformate (MCF). The simulated vibrational energy distributions agree very well with those measured experimentally, as can be observed below. MCF was postulated as a possible source of HCN/HNC in the inter-stellar medium (ApJ, 2017, 849,15).


The potential energy surface of protonated uracil has been explored using our automated method, resulting in the finding of 1398 stationary points and 751 reactive channels. The KMC/RRKM product abundances show that the major fragmentation channels are isocyanic acid and ammonia losses, in good agreement with experiments. The third predominant channel is water loss according to both theory and experiments (PCCP, 2016, 18, 14980). 

 Energy transfer models in gas-surface collisions

An energy transfer model has been developed for gas-surface collisions (see equation below). The model relies on simple gas-phase scattering models. When energy transfer is analyzed in the limit of high incident energies, the following results are found:

a) The percent of energy transfer to vibration (and rotation) of light diatomic projectiles decreases as the projectile’s mass increases, while this transfer is almost independent of the mass for heavier projectiles.

b) For small projectiles (less than 10 atoms), transfer to vibration increases as a function of the projectile’s size.

c) However, for larger projectiles, the percent transfer to vibration is nearly constant, a result that can be attributed to a mass effect and also to the fact that only a reduced subset of “effective” vibrational dof is being activated in the collisions

You can consult the full details of this study here: JPC C2014118, 2609