An Extended Group Additivity Method for Polycyclic Thermochemistry Estimation

Abstract

Automatic kinetic mechanism generation, virtual high‐throughput screening, and automatic transition state search are currently trending applications requiring exploration of a large molecule space. Large‐scale search requires fast and accurate estimation of molecules' properties of interest, such as thermochemistry. Existing approaches are not satisfactory for large polycyclic molecules: considering the number of molecules being screened, quantum chemistry (even cheap density functional theory methods) can be computationally expensive, and group additivity, though fast, is not sufficiently accurate. This paper provides a fast and moderately accurate alternative by proposing a polycyclic thermochemistry estimation method that extends the group additivity method with two additional algorithms: similarity match and bicyclic decomposition. It significantly reduces Hf(298 K) estimation error from over 60 kcal/mol (group additivity method) to around 5 kcal/mol, Cp(298 K) error from 9 to 1 cal/mol/K, and S(298 K) error from 70 to 7 cal/mol/K. This method also works well for heteroatomic polycyclics. A web application for estimating thermochemistry by this method is made available at http://rmg.mit.edu/molecule_search.

Self-Evolving Machine: A Continuously Improving Model for Molecular Thermochemistry

“…Because the ring strain of a polycyclic molecule is very sensitive to the configuration of the ring structure, polycyclic ring strain is often not additive, i.e., it does not equal the summation of the expected strain energies of individual rings. 21 Therefore, the convolutional neural network has to extract non-local geometry features to correctly predict the enthalpies of polycyclic species. This is possible with our architecture because we specify the number of rings of each size containing a given atom.…”

“…17,19,20 This problem manifests itself for strained structures and can cause significant errors for polycyclic molecules with fused rings. 21 Therefore, application of the additivity method is often restricted to simple chemical systems without the presence of polycyclic species.…”

“…Han et al developed two algorithms, similarity match and bicyclic decomposition, to ameliorate this problem. 21 Ring strain corrections of small cyclic structures were calculated using ab initio methods and organized into a functional group tree that can find similar matches for any new small cyclics in the similarity match approach. The bicyclic decomposition algorithm can estimate large polycyclic ring strain corrections by decomposing them into smaller ones and adding up the contributions from the fragments.…”

Modeling of aromatics formation in fuel-rich methane oxy-combustion with an automatically generated pressure-dependent mechanism

“…Furthermore, for predicting correct thermodynamic properties of PAH, estimation of polycyclic thermochemistry in RMG has been improved by two algorithms: similarity matching and bicyclic decomposition which extended the basic group additivity method. 50 When RMG encounters cyclic molecules, the thermodynamic properties are estimated by the revised group additivity method instead of the basic one assuming each atom-based group is independent. The error in estimated thermodynamic properties of multi-ring species relevant to PAH formation was reduced by an order of magnitude.…”

From benzene to naphthalene: direct measurement of reactions and intermediates of phenyl radicals and acetylene

“…8 For other species not in the Narayanaswamy library, RMG was used to estimate their thermochemical properties with the group additivity method, which has recently been improved and extended by similarity matching and bicyclic decomposition for predicting fused cyclics. 42 The abovementioned k(T,P) and thermochemical properties were used to construct a pressure-dependent kinetic mechanism for C 6 H 5 + C 2 H 2 . In addition to the main HACA routes, the mechanism includes side reactions that are important under our experimental conditions, such as addition of H atoms formed in HACA reactions to C 2 H 2 forming vinyl radicals.…”