Product Ranking¶

Ranking the molecules based on the net flux over the molecular dynamics simulations is only as reliable as the simulations themselves. All reactive simulations use some kind of scheme to induce reactivity, and this means that reaction conditions like temperature and pressure will most likely be higher than the conditions in the target system. Letting a reaction under our extreme simulation conditions continue too long will most likely result in the degradation of viable products, combined with the formation of final products that would never be formed at the milder experimental conditions. To correct for the extreme conditions of the molecular dynamics simulations we assign stabilities to the molecules based on the reaction network.

Both a value for kinetic stability (cost) and thermodynamic stability are assigned, and ultimately the molecules are ordered based in the first place on cost, and in the second place on (thermodynamic) stability. The ranked stable products are saved in the files products.sdf and products.rkf.

Reaction Energies¶

As the first step in this procedure, we assign reaction energies to all reaction nodes in the network, based on the energies of the optimized molecules. These reaction energy values have the advantage that they are independent of the simulation conditions.

Product Cost¶

We perform a network search to assign a relative cost value to each molecule in the network. The cost \(c\) of the reactants is set to one. The cost \(c_p\) of any product/intermediate molecule \(p\) is then assigned in a breadth first search through the network.

\(c_p = \sum_r c_r + \left( 1 + e^{E_R/k_bT} \right)\)

Here \(R\) is the reaction that has molecule \(p\) as product, and results in the lowest possible cost \(c_p\). The molecules \(r\) are the reactants involved in reaction \(R\). The value \(E_R\) is the reaction energy of reaction \(R\). \(T\) is the ranking temperature, which is set to 300K by default. Selecting a higher temperature brings the contributions of different reactions closer together, resulting in relatively lower costs for molecules that are formed via reactions with high reaction energies.

Product Stability¶

In a similar manner, a thermodynamic relative product stability is assigned, with the stability of the initial reactants set to zero.

\(s_p = \sum_r s_r + E_R\)

Again, \(R\) is the reaction that has \(p\) as product and results in the lowest value of the cost \(c_p\).

Reaction Balance¶

Separate from the reaction network procedures, a set of stable products is extracted based on two different metrics. First, molecules with connectivities deviating vastly from the valences of the corresponding elements are discarded. Secondly, the molecular charges determined in the NetworkExtraction run are compared to the ‘formal’ molecular charges based on bond orders, and if the two values differ, the molecule is considered a radical, and discarded as a stable product.

For all stable products, an estimated balanced overall formation reaction is then determined by balancing the reaction of the initial reactants to this product. If it is not possible to balance the reaction, one of the other stable products is included as a co-product.

Example: ProductRanking from finished NetworkExtraction¶

Input:

MolecularDynamics Enabled=No
NetworkExtraction Enabled=No
ProductRanking Enabled=Yes ReactionNetwork=/some/path

ProductRanking%ReactionNetwork must be a previous Reactions Discovery result directory that has at least finished the network extraction.

ProductRanking
   DiscardIons Yes/No
   Enabled Yes/No
   ReactionNetwork string
   Temperature float
   WritePaths Yes/No
End

ProductRanking

Type: Block
Description: Options for ranking of the intermediates by stability

DiscardIons

Type: Bool
Default value: Yes
Description: Remove all ions from the final product list

Enabled

Type: Bool
Default value: Yes
GUI name: ProductRanking
Description: Whether to perform ranking of the reaction network.

ReactionNetwork

Type: String
Description: Directory containing a previous Reactions Discovery calculation with ‘NetworkExtraction%Enabled Yes’

Temperature

Type: Float
Default value: 298.0
Description: Temperature used to compute reaction rates from reaction energies of reactions in the reaction network.

WritePaths

Type: Bool
Default value: Yes
Description: Write full paths to the reaction network for each molecule.