Molecular Dynamics Investigations of Ozone on an Ab Initio Potential Energy Surface with the Utilization of Pattern-Recognition Neural Network for Accurate Determination of Product Formation

2011 ◽  
Vol 115 (40) ◽  
pp. 10862-10870 ◽  
Author(s):  
Hung M. Le ◽  
Thach S. Dinh ◽  
Hieu V. Le
Keyword(s):  
Neural Network ◽  
Molecular Dynamics ◽  
Pattern Recognition ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Accurate Determination ◽  
Product Formation

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>

Dynamics and kinetics of the Si(1D) + H2/D2 reactions on a new global ab initio potential energy surface

2021 ◽  
Vol 23 (10) ◽  
pp. 6141-6153
Author(s):  
Jianwei Cao ◽  
Yanan Wu ◽  
Haitao Ma ◽  
Zhitao Shen ◽  
Wensheng Bian
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Quantum Dynamics ◽  
Energy Surface ◽  
Molecular Dynamics Calculations ◽  
Ring Polymer ◽  
Ring Polymer Molecular Dynamics ◽  
Kinetics Of

Quantum dynamics and ring polymer molecular dynamics calculations reveal interesting dynamical and kinetic behaviors of an endothermic complex-forming reaction.

Ab initio determination of the CN–NH3 capture potential energy surface

1999 ◽  
Vol 241 (1) ◽  
pp. 29-42 ◽  
Author(s):  
Alexandre Faure ◽  
Claire Rist ◽  
Pierre Valiron
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface

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>

scholarly journals Rotational de-excitation of tricarbon monosulfide (C3S) in collision with (He): potential energy surface and rates

2020 ◽  
Vol 365 (12) ◽  
Author(s):  
E. Sahnoun ◽  
M. Ben Khalifa ◽  
F. Khadri ◽  
K. Hammami
Keyword(s):  
Potential Energy ◽  
Interstellar Medium ◽  
Potential Energy Surface ◽  
Cross Sections ◽  
Energy Surface ◽  
Accurate Determination ◽  
Carbon Chain ◽  
Basis Sets ◽  
Rate Coefficients

AbstractDespite that the tricarbon monosulfide (C3S) is among the first sulfur-containing carbon-chain molecules to be detected in the interstellar medium, no studies focused on the determination of its collisional rates. These rate coefficients are essential to estimate the abundance of C3S in the interstellar medium. Computations of the C3S($^{1}\Sigma^{+}$ Σ + 1 ) downward rate coefficients, induced by collision with He, are performed by averaging the integral cross sections at low temperature (below $25~\text{K}$ 25 K ). Calculations of the cross sections in the close-coupling quantum time independent formalism for $E_{c}\leq110~\text{cm}^{-1}$ E c ≤ 110 cm − 1 and $J\leq10$ J ≤ 10 are based on a new 2-D potential energy surface. This PES is obtained from the explicit correlated coupled cluster with a single, double and perturbative triple excitation [ccsd(t)-f12] ab initio approach and the aug-cc-pVTZ basis sets. The PES have a global minimum of $-55.69~\text{cm}^{-1}$ − 55.69 cm − 1 located at $R=6.25$ R = 6.25 bohr and $\theta=94^{\circ}$ θ = 94 ∘ , and a second minimum of $-36.95~\text{cm}^{-1}$ − 36.95 cm − 1 at $R=9.35$ R = 9.35 bohr and $\theta=0^{\circ}$ θ = 0 ∘ . A comparison of C3S rates with those of the isoelectronic molecule C3O was made. The results indicate a great temperature dependence of the rates for transitions of $\Delta J>2$ Δ J > 2 . We expect that the new collisional data will allow for accurate determination of the C3S abundance in several interstellar regions.

Interaction between Aromatic Residues. Molecular Dynamics and ab Initio Exploration of the Potential Energy Surface of the Tryptophan−Histidine Pair

2000 ◽  
Vol 104 (5) ◽  
pp. 1108-1114 ◽  
Author(s):  
Francesco Luigi Gervasio ◽  
Piero Procacci ◽  
Gianni Cardini ◽  
Antonio Guarna ◽  
Alessandro Giolitti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Aromatic Residues
Sign in / Sign up

Export Citation Format

Share Document