Exploration of the (ethanol)4 -water heteropentamers potential energy surface by simulated annealing and Ab initio molecular dynamics

2010 ◽  
Vol 111 (12) ◽  
pp. 3080-3096 ◽  
Author(s):  
Sol M. Mejía ◽  
Juan F. Orrego ◽  
Juan F. Espinal ◽  
Patricio Fuentealba ◽  
Fanor Mondragón
Keyword(s):  
Molecular Dynamics ◽  
Simulated Annealing ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Ab Initio Molecular Dynamics

scholarly journals 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 ◽  
Active Learning ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Ab Initio Molecular Dynamics ◽  
Dynamics Simulations

Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires ab initio 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 training dataset size of approximately 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. These tools are then used to automatically predict a reaction mechanism that is in agreement with the experimentally-reported product distribution. In addition, thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a very minor role in the reaction. Furthermore, a transfer-learning strategy effectively allowed to upgrade the potential energy surface to higher levels of theory (def2-TZVPD basis set and double hybrid functional) using less than 10% additional calculations. Since these methods capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for entropic intermediates. This overall approach is broadly applicable and opens the door to the study of dynamical effects in larger, previously-intractable reactive systems.

CONSTRUCTION OF A GLOBAL POTENTIAL ENERGY SURFACE FROM NOVEL AB INITIO MOLECULAR DYNAMICS FOR THE O(3P) + C3H3 REACTION

2005 ◽  
Vol 04 (01) ◽  
pp. 163-173 ◽  
Author(s):  
SEUNG C. PARK ◽  
BASTIAAN J. BRAAMS ◽  
JOEL M. BOWMAN
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Radical Reaction ◽  
Ab Initio Molecular Dynamics ◽  
Stationary Points ◽  
Permutational Symmetry ◽  
Diffusion Monte Carlo Method

We present a global potential energy surface (PES) for the 2 A state of the O (3 P ) + C 3 H 3 radical reaction. The global PES is constructed mainly using direct ab initio molecular dynamics and further sampling is done using the Diffusion Monte Carlo method. The potential is fully invariant with respect to permutational symmetry of like atoms. Special techniques, based on invariant theory of finite groups, have been used to develop basis functions for fitting that display this symmetry. The resultant potential energy surface shows multiple reaction paths with six different product channels. The products of the reactions are CO + C 2 H 3 radicals H + C 3 H 2 O radicals (with two isomers, propynal and propa-1,2-dien-1-one) and OH + C 3 H 2 radicals (with three isomers, vinylidenecarbene, propargylene and cyclopropenylidene). Energies of the PES are in excellent agreement with ab initio energies for each stationary point, the reactants and the products. Most stationary points are fitted at the sub Kcal/mol level. The global potential surface represents all the stationary points and six different product channels correctly. Preliminary dynamics calculations show abstraction and insertion mechanisms for the OH + vinylidenecarbene channel and the H + propynal channel, respectively.

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.

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>

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
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