An automated method to find transition states using chemical dynamics simulations

Abstract

A procedure to automatically find the transition states (TSs) of a molecular system (MS) is proposed. It has two components: high-energy chemical dynamics simulations (CDS), and an algorithm that analyzes the geometries along the trajectories to find reactive pathways. Two levels of electronic structure calculations are involved: a low level (LL) is used to integrate the trajectories and also to optimize the TSs, and a higher level (HL) is used to reoptimize the structures. The method has been tested in three MSs: formaldehyde, formic acid (FA), and vinyl cyanide (VC), using MOPAC2012 and Gaussian09 to run the LL and HL calculations, respectively. Both the efficacy and efficiency of the method are very good, with around 15 TS structures optimized every 10 trajectories, which gives a total of 7, 12, and 83 TSs for formaldehyde, FA, and VC, respectively. The use of CDS makes it a powerful tool to unveil possible nonstatistical behavior of the system under study.

A model of tetrahydrofuran low-temperature oxidation based on theoretically calculated rate constants

“…On the other hand, radical intermediate structures were then obtained by substraction of one H atom from several positions of the structure. Finally, we used the Transition State Search using Chemical Dynamics Simulations with the TSSCDS software [16,17] to obtain the transition state structures associated with the studied reactions. Intrinsic reaction coordinate (IRC) calculations were also carried out to confirm that the transition states linked the expected reactants, intermediates and products.…”

HCN elimination from vinyl cyanide: product energy partitioning, the role of hydrogen–deuterium exchange reactions and a new pathway

“…On the one hand, to re-compute the branching ratios of the different HCN/HNC elimination pathways, including the new HCN dissociation pathway (green line of Figure 1) found recently. 37 Secondly, to assess the importance of the H-and CN-migration channels, shown in the Supporting Information (SI). Therefore, two different sets of computations were performed.…”

“…The aim of this simulation is an assessment of the importance of H/D scrambling. For this reason, besides the HCN elimination channels of Figure 1, several H-and CN-migration channels 37 are also incorporated in the simulations. This set of calculations involves two approximations.…”

“…37 One of the test cases employed to study the efficiency and efficacy of the method was VCN, for which a total of 83 transition states were found using density function theory (DFT) calculations. Among all these transition states, many H 2 elimination pathways, as well as H-and CNmigration pathways were found.…”

“…Different HCN elimination pathways found in our previous work (3-center, 4-center and 5-center channels), 35 and the new pathway (green line) via the CCdiss transition state. 37 The numbers are relative energies in kcal/mol (including the zero-point vibrational energy) with respect to VCN, calculated at the CCSD(T)/6-311++G(3df,3pd)//CCSD/6-311+G(2d,2p) level of theory with the vibrational frequencies obtained using CCSD/6-311+G(2d,2p) numerical Hessians.…”