Gaussian Process Regression for Minimum Energy Path Optimization and Transition State Search

2019 ◽  
Vol 123 (44) ◽  
pp. 9600-9611 ◽  
Author(s):  
Alexander Denzel ◽  
Bernard Haasdonk ◽  
Johannes Kästner
Keyword(s):  
Transition State ◽  
Gaussian Process ◽  
Minimum Energy ◽  
Gaussian Process Regression ◽  
Path Optimization ◽  
Minimum Energy Path ◽  
Transition State Search

BrHgO• + C2H4 and BrHgO• + HCHO in Atmospheric Oxidation of Mercury: Determining Rate Constants of Reactions with Pre-Reactive Complexes and a Bifurcation

2019 ◽  
Author(s):  
Khoa T. Lam ◽  
Curtis J. Wilhelmsen ◽  
Theodore Dibble
Keyword(s):  
Hydrogen Atom ◽  
Quantum Chemistry ◽  
Transition State ◽  
Rate Constant ◽  
Rate Constants ◽  
Minimum Energy ◽  
Atmospheric Oxidation ◽  
Minimum Energy Path ◽  
Oh Radical ◽  
Hydrogen Atoms

Models suggest BrHgONO to be the major Hg(II) species formed in the global oxidation of Hg(0), and BrHgONO undergoes rapid photolysis to produce the thermally stable radical BrHgO•. We previously used quantum chemistry to demonstrate that BrHgO• can, like OH radical, readily can abstract hydrogen atoms from sp<sup>3</sup>-hybridized carbon atoms as well as add to NO and NO<sub>2</sub>. In the present work, we reveal that BrHgO• can also add to C<sub>2</sub>H<sub>4</sub> to form BrHgOCH<sub>2</sub>CH<sub>2</sub>•, although this addition appears to proceed with a lower rate constant than the analogous addition of •OH to C<sub>2</sub>H<sub>4</sub>. Additionally, BrHgO• can readily react with HCHO in two different ways: either by addition to the carbon or by abstraction of a hydrogen atom. The minimum energy path for the BrHgO• + HCHO reaction bifurcates, forming two pre-reactive complexes, each of which passes over a separate transition state to form a different product.

scholarly journals Nudged Elastic Band Calculations Accelerated with Gaussian Process Regression Based on Inverse Inter-Atomic Distances

2019 ◽  
Author(s):  
Olli-Pekka Koistinen ◽  
Vilhjálmur Ásgeirsson ◽  
Aki Vehtari ◽  
Hannes Jónsson
Keyword(s):  
Gaussian Process ◽  
Minimum Energy ◽  
Gaussian Process Regression ◽  
Dissociative Adsorption ◽  
Elastic Band ◽  
Data Set ◽  
Relaxation Phase ◽  
Atomic Force ◽  
Band Method ◽  
The Difference

Calculations of minimum energy paths for atomic rearrangements using the nudged elastic band method can be accelerated with Gaussian process regression to reduce the number of energy and atomic force evaluations needed for convergence. Problems can arise, however, when configurations with large forces due to short distance between atoms are included in the data set. Here, a significant improvement to the Gaussian process regression approach is obtained by basing the difference measure between two atomic configurations in the covariance function on the inverted inter-atomic distances and by adding a new early stopping criterion for the path relaxation phase. This greatly improves the performance of the method in two applications where the original formulation does not work well: a dissociative adsorption of an H<sub>2</sub> molecule on a Cu(110) Surface and a diffusion hop of an H<sub>2</sub>O molecule on an ice Ih(0001) surface. Also, the revised method works better in the previously analyzed benchmark application to rearrangement transitions of a heptamer island on a surface, requiring fewer energy and force evaluations for convergence to the minimum energy path.

PHYSISORPTION TO CHEMISORPTION TRANSFORMATION OF A H2 MOLECULE ON B-DOPED FULLERENE C59B

2011 ◽  
Vol 10 (06) ◽  
pp. 839-847 ◽  
Author(s):  
CHUANJIN TIAN ◽  
WENYAN ZHAO ◽  
ZHIGANG WANG ◽  
MINGXING JIN
Keyword(s):  
Transition State ◽  
Energy Barrier ◽  
Minimum Energy ◽  
Transformation Process ◽  
Minimum Energy Path ◽  
First Principle ◽  
Adsorption State ◽  
First Principle Calculations ◽  
Dynamics Stability ◽  
H2 Molecule

By first principle calculations we have explored the minimum energy path of H2 molecule dissociating on the C59B which is a system as stable as C60 . Our results show that the transformation process from physisorption state (also called nondissociation adsorption state) to the chemisorption state of the H2 molecule on the C59B surface should cross a transition state. However, the energy barrier of this reaction is very low. Therefore, the dynamics stability of the physisorption state is not high.

BrHgO• + C2H4 and BrHgO• + HCHO in Atmospheric Oxidation of Mercury: Determining Rate Constants of Reactions with Pre-Reactive Complexes and a Bifurcation

2019 ◽  
Author(s):  
Khoa T. Lam ◽  
Curtis J. Wilhelmsen ◽  
Theodore Dibble
Keyword(s):  
Hydrogen Atom ◽  
Quantum Chemistry ◽  
Transition State ◽  
Rate Constant ◽  
Rate Constants ◽  
Minimum Energy ◽  
Atmospheric Oxidation ◽  
Minimum Energy Path ◽  
Oh Radical ◽  
Hydrogen Atoms

Models suggest BrHgONO to be the major Hg(II) species formed in the global oxidation of Hg(0), and BrHgONO undergoes rapid photolysis to produce the thermally stable radical BrHgO•. We previously used quantum chemistry to demonstrate that BrHgO• can, like OH radical, readily can abstract hydrogen atoms from sp<sup>3</sup>-hybridized carbon atoms as well as add to NO and NO<sub>2</sub>. In the present work, we reveal that BrHgO• can also add to C<sub>2</sub>H<sub>4</sub> to form BrHgOCH<sub>2</sub>CH<sub>2</sub>•, although this addition appears to proceed with a lower rate constant than the analogous addition of •OH to C<sub>2</sub>H<sub>4</sub>. Additionally, BrHgO• can readily react with HCHO in two different ways: either by addition to the carbon or by abstraction of a hydrogen atom. The minimum energy path for the BrHgO• + HCHO reaction bifurcates, forming two pre-reactive complexes, each of which passes over a separate transition state to form a different product.

scholarly journals Nudged Elastic Band Calculations Accelerated with Gaussian Process Regression Based on Inverse Inter-Atomic Distances

2019 ◽  
Author(s):  
Olli-Pekka Koistinen ◽  
Vilhjálmur Ásgeirsson ◽  
Aki Vehtari ◽  
Hannes Jónsson
Keyword(s):  
Gaussian Process ◽  
Minimum Energy ◽  
Gaussian Process Regression ◽  
Dissociative Adsorption ◽  
Elastic Band ◽  
Data Set ◽  
Relaxation Phase ◽  
Atomic Force ◽  
Band Method ◽  
The Difference

Calculations of minimum energy paths for atomic rearrangements using the nudged elastic band method can be accelerated with Gaussian process regression to reduce the number of energy and atomic force evaluations needed for convergence. Problems can arise, however, when configurations with large forces due to short distance between atoms are included in the data set. Here, a significant improvement to the Gaussian process regression approach is obtained by basing the difference measure between two atomic configurations in the covariance function on the inverted inter-atomic distances and by adding a new early stopping criterion for the path relaxation phase. This greatly improves the performance of the method in two applications where the original formulation does not work well: a dissociative adsorption of an H<sub>2</sub> molecule on a Cu(110) Surface and a diffusion hop of an H<sub>2</sub>O molecule on an ice Ih(0001) surface. Also, the revised method works better in the previously analyzed benchmark application to rearrangement transitions of a heptamer island on a surface, requiring fewer energy and force evaluations for convergence to the minimum energy path.

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