Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: An automatic approach to explore multi-reaction mechanism for
  medium-sized bimolecular reactions via collision dynamics simulations and
  transition state searches   We develop a broadly-applicable computational method for the automatic
exploration of the bimolecular multi-reaction mechanism. The current
methodology mainly involves the high-energy Born-Oppenheimer molecular dynamics
(BOMD) simulation and the successive reaction pathway construction. Several
computational tricks are introduced, which include the selection of the
reactive regions based on the electronic-structure calculations and the
employment of the virtual collision-dynamics simulations with monitoring atomic
distance before BOMD. These prescreening steps largely reduce the number of
trajectories in the BOMD simulations and significantly save computational cost.
The hidden Markov model combined with modified atomic connectivity matrix is
taken for the detection of reaction events in each BOMD trajectory. Starting
from several geometries close to reaction events, the further intermediate
optimization and transition-state searches are conducted. The proposed method
allows us to build the complicated multi-reaction mechanism of medium-sized
bimolecular systems automatically. Here we examine the feasibility and
efficiency of the current method by its performance in searching the mechanisms
of two prototype reactions in environmental science, which are the penicillin G
anion + H2O and the penicillin G anion + OH radical reactions. The result
indicates that the proposed theoretical method is a powerful protocol for the
automatic searching of the bimolecular reaction mechanisms for medium-sized
compounds.

19
The categories of this paper are: eess
14
The categories of this paper are: math-ph
22
The categories of this paper are: chao-dyn
1
The categories of this paper are: cs
7
The categories of this paper are: hep-th
36
The categories of this paper are: cmp-lg
17
The categories of this paper are: q-fin
18
The categories of this paper are: econ
35
The categories of this paper are: mtrl-th
29
The categories of this paper are: funct-an
24
The categories of this paper are: dg-ga
34
The categories of this paper are: chem-ph
4
The categories of this paper are: cond-mat
27
The categories of this paper are: comp-gas
13
The categories of this paper are: quant-ph
28
The categories of this paper are: alg-geom