Formation of a pre-reaction hydrogen-bonded complex and its significance in the potential energy surface of the OH + SO2→ HOSO2 reaction: A computational study

2017 ◽  
Vol 16 (05) ◽  
pp. 1750046 ◽  
Author(s):  
Vijay M. Miriyala ◽  
Priya Bhasi ◽  
Zanele P. Nhlabatsi ◽  
Sanyasi Sitha
Keyword(s):  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Computational Study ◽  
Stationary Points ◽  
Second Step ◽  
Computational Calculations ◽  
Reaction Complex ◽  
Hydrogen Bonded

Using computational calculations, we have revisited the potential energy surface (PES) of the reaction between OH and SO2, which is believed as the rate-limiting step in the atmospheric formation of H2SO4. In this work, we report for the first time the presence of a pre-reaction hydrogen-bonded complex between OH and SO2 in the reaction PES. Based on this finding, it has been shown that the reaction can be considered as a two-step process in which the first step is the formation of the pre-reaction complex and the second step is the transformation of this complex to the product. It was observed that due to the presence of this pre-reaction complex as a potential well in the reaction PES, the barrier height got increased by around two-fold for the second step. Based on this observation, it has been proposed that the kinetics of the reaction is going to be affected. Also based on the analysis of the geometries of this pre-reaction complex and the transition state, it has been argued that the step involving the transformation of this pre-reaction complex to the product via the transition state is going to be the slowest step as this transformation involves large structural changes of the stationary points involved.

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.

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>

The search for stationary points on a quantum mechanical/molecular mechanical potential-energy surface

2002 ◽  
Vol 107 (3) ◽  
pp. 147-153 ◽  
Author(s):  
Xavier Prat-Resina ◽  
Mireia Garcia-Viloca ◽  
Gerald Monard ◽  
Angels González-Lafont ◽  
José M. Lluch ◽  
...  
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Stationary Points ◽  
Quantum Mechanical

Conformational analysis of enantiomerization coupled to internal rotation in triptycyl-n-helicenes

2019 ◽  
Vol 21 (21) ◽  
pp. 11395-11404
Author(s):  
Abel Carreras ◽  
Luca Fuligni ◽  
Pere Alemany ◽  
Miquel Llunell ◽  
Josep Maria Bofill ◽  
...  
Keyword(s):  
Potential Energy ◽  
Conformational Analysis ◽  
Potential Energy Surface ◽  
Internal Rotation ◽  
Energy Surface ◽  
Computational Study ◽  
Reaction Coordinate

We present a computational study of a reduced potential energy surface (PES) to describe enantiomerization and internal rotation in three triptycyl-n-helicene molecules, centering the discussion on the issue of a proper reaction coordinate choice.

Potential energy surface stationary points and dynamics of the F−+ CH3I double inversion mechanism

2017 ◽  
Vol 19 (30) ◽  
pp. 20127-20136 ◽  
Author(s):  
Yong-Tao Ma ◽  
Xinyou Ma ◽  
Anyang Li ◽  
Hua Guo ◽  
Li Yang ◽  
...  
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Stationary Points ◽  
Direct Dynamics ◽  
Dynamics Simulations ◽  
Inversion Mechanism

Direct dynamics simulations were performed to study the SN2 double inversion mechanism SN2-DI, with retention of configuration, for the F−+ CH3I reaction.

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