scholarly journals The Time Evolution of the Trajectories After the Selectivity in a Symmetric Potential Energy Surface with a Post-transition-state Bifurcation

2021 ◽  
Vol 26 (6) ◽  
pp. 763-774
Author(s):  
Douglas Haigh ◽  
Matthaios Katsanikas ◽  
Makrina Agaoglou ◽  
Stephen Wiggins
Keyword(s):  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Time Evolution ◽  
Energy Surface ◽  
Symmetric Potential

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

Femtosecond Transition-State Dynamics of Dissociating OCS on the Excited1Σ+Potential Energy Surface†

1997 ◽  
Vol 101 (4) ◽  
pp. 694-704 ◽  
Author(s):  
Akiyoshi Hishikawa ◽  
Kyoko Ohde ◽  
Ryuji Itakura ◽  
Shilin Liu ◽  
Kaoru Yamanouchi ◽  
...  
Keyword(s):  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Energy Surface

scholarly journals Bifurcation of Dividing Surfaces Constructed from a Pitchfork Bifurcation of Periodic Orbits in a Symmetric Potential Energy Surface with a Post-Transition-State Bifurcation

2021 ◽  
Vol 31 (14) ◽  
Author(s):  
M. Katsanikas ◽  
M. Agaoglou ◽  
S. Wiggins
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Periodic Orbits ◽  
Lower Energy ◽  
Degrees Of Freedom ◽  
Energy Surface ◽  
Pitchfork Bifurcation ◽  
High Energy ◽  
Symmetric Potential ◽  
The Family

In this work, we analyze the bifurcation of dividing surfaces that occurs as a result of a pitchfork bifurcation of periodic orbits in a two degrees of freedom Hamiltonian System. The potential energy surface of the system that we consider has four critical points: two minima, a high energy saddle and a lower energy saddle separating two wells (minima). In this paper, we study the structure, the range, and the minimum and maximum extent of the periodic orbit dividing surfaces of the family of periodic orbits of the lower saddle as a function of the total energy.

scholarly journals Isomerization and Fragmentation Reactions on the [C2SH4] Potential Energy Surface. The Metastable Thione-S-Methylide Isomer

2020 ◽  
Author(s):  
Zoi Salta ◽  
Marc E. Segovia ◽  
Aline Katz ◽  
Nicola Tasinato ◽  
Vincenzo Barone ◽  
...  
Keyword(s):  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Density Functional ◽  
Energy Surface ◽  
Computational Study ◽  
Experimental Information ◽  
Reaction Scheme ◽  
Ring Closure ◽  
Complete Analysis

Thione S-methylide (TSM), the parent species of the thiocarbonyl ylide family, is a 1,3-dipolar, planar species on the [C2SH4] potential energy surface (PES), which has not shared the richness of studies dedicated to its isomers, the cyclic thiirane (THI), and the keto-enol pair vinyl thiol (VTH)/thioacetaldehyde (THA). While the conrotatory ring closure reaction toward THI was studied in the ‘90s, no complete analysis of the PES is available in the literature. In the present paper, we report a computational study of the reaction scheme linking all species on that PES. We employ several levels of calculation, ranging from density functional theory (DFT), through CCSD(T) based composite schemes, to CASSCF/CASPT2 multi-reference procedures, to find the best description of TSM, its isomers, and the transition states (TSs) ruling their interconversion. Fragmentation of TSM, THA and THI were investigated and compared to the available experimental information. We found that the B2PLYP-D3 functional, contrary to M06-2XD3 or B97X-D, describes well the geometry of both TSM and the transition state connecting it to THI. The reverse barrier, from THI to TSM, amounts to 52.2 kcal mol-1 (to be compared to 17.6 kcal mol-1 for the direct one), thus explaining why, in general, thiocarbonyl ylides cannot be prepared from thiiranes. Conversion of THI to VTH implies also a large barrier, explaining why the reaction has been observed only at high temperatures. The fragmentation of THI to S(3P) or S(1D) and ethylene was also explored, together with the decomposition to H2S plus acetylene. Open species, both in triplet and singlet states, were identified as intermediates in the fragmentations, and their energies were found to be lower than the transition state for the isomerization of THI to VTH, thus explaining the preference for fragmentation over isomerization at relatively low temperatures.

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

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