Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes

2004 ◽  
Vol 120 (17) ◽  
pp. 8039-8052 ◽  
Author(s):  
Li Xie ◽  
Haiyan Liu ◽  
Weitao Yang
Keyword(s):  
Chemical Reactions ◽  
Minimum Energy ◽  
Elastic Band ◽  
Band Method ◽  
Minimum Energy Paths

scholarly journals Effects of Aluminum on Hydrogen Solubility and Diffusion in Deformed Fe-Mn Alloys

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
C. Hüter ◽  
S. Dang ◽  
X. Zhang ◽  
A. Glensk ◽  
R. Spatschek
Keyword(s):  
Ab Initio ◽  
Equilibrium Model ◽  
Hydrogen Diffusion ◽  
Local Equilibrium ◽  
Minimum Energy ◽  
Trap Site ◽  
Elastic Band ◽  
Band Method ◽  
Minimum Energy Paths ◽  
And Diffusion

We discuss hydrogen diffusion and solubility in aluminum alloyed Fe-Mn alloys. The systems of interest are subjected to tetragonal and isotropic deformations. Based onab initiomodelling, we calculate solution energies and then employ Oriani’s theory which reflects the influence of Al alloying via trap site diffusion. This local equilibrium model is complemented by qualitative considerations of Einstein diffusion. Therefore, we apply the climbing image nudged elastic band method to compute the minimum energy paths and energy barriers for hydrogen diffusion. Both for diffusivity and solubility of hydrogen, we find that the influence of the substitutional Al atom has both local chemical and nonlocal volumetric contributions.

A climbing image nudged elastic band method for finding saddle points and minimum energy paths

2000 ◽  
Vol 113 (22) ◽  
pp. 9901-9904 ◽  
Author(s):  
Graeme Henkelman ◽  
Blas P. Uberuaga ◽  
Hannes Jónsson
Keyword(s):  
Minimum Energy ◽  
Saddle Points ◽  
Elastic Band ◽  
Band Method ◽  
Minimum Energy Paths

scholarly journals Ab Initio Investigation of Helium Mobility in La2Zr2O7 Pyrochlore

Crystals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 667
Author(s):  
Yanxia Lu ◽  
Qing Peng ◽  
Chenguang Liu
Keyword(s):  
Nuclear Waste ◽  
Density Functional ◽  
Minimum Energy ◽  
Elastic Band ◽  
Waste Forms ◽  
Band Method ◽  
And Migration ◽  
High Level ◽  
Migration Pathways ◽  
Nuclear Waste Forms

The α-decay of incorporated actinides continuously produces helium, resulting in helium accumulation and causing security concerns for nuclear waste forms. The helium mobility is a key issue affecting the accumulation and kinetics of helium. The energy barriers and migration pathways of helium in a potential high-level nuclear waste forms, La2Zr2O7 pyrochlore, have been investigated in this work using the climbing image nudged elastic band method with density functional theory. The minimum energy pathway for helium to migrate in La2Zr2O7 is identified as via La–La interstitial sites with a barrier of 0.46 eV. This work may offer a theoretical foundation for further prospective studies of nuclear waste forms.

Nudged elastic band method and density functional theory calculation for finding a local minimum energy pathway of p-benzoquinone and phenol fragmentation in mass spectrometry

2017 ◽  
Vol 23 (1) ◽  
pp. 40-44 ◽  
Author(s):  
Natsuhiko Sugimura ◽  
Yoko Igarashi ◽  
Reiko Aoyama ◽  
Toshimichi Shibue
Keyword(s):  
Mass Spectrometry ◽  
Energy Barrier ◽  
Minimum Energy ◽  
Minimum Energy Path ◽  
Intermediate Structure ◽  
Elastic Band ◽  
Final State ◽  
Fragmentation Pathways ◽  
Reaction Coordinates ◽  
Band Method

Analysis of the fragmentation pathways of molecules in mass spectrometry gives a fundamental insight into gas-phase ion chemistry. However, the conventional intrinsic reaction coordinates method requires knowledge of the transition states of ion structures in the fragmentation pathways. Herein, we use the nudged elastic band method, using only the initial and final state ion structures in the fragmentation pathways, and report the advantages and limitations of the method. We found a minimum energy path of p-benzoquinone ion fragmentation with two saddle points and one intermediate structure. The primary energy barrier, which corresponded to the cleavage of the C–C bond adjacent to the CO group, was calculated to be 1.50 eV. An additional energy barrier, which corresponded to the cleavage of the CO group, was calculated to be 0.68 eV. We also found an energy barrier of 3.00 eV, which was the rate determining step of the keto-enol tautomerization in CO elimination from the molecular ion of phenol. The nudged elastic band method allowed the determination of a minimum energy path using only the initial and final state ion structures in the fragmentation pathways, and it provided faster than the conventional intrinsic reaction coordinates method. In addition, this method was found to be effective in the analysis of the charge structures of the molecules during the fragmentation in mass spectrometry.

Utility of the Nudged Elastic Band Method in Identifying the Minimum Energy Path of an Elementary Organometallic Reaction Step

2016 ◽  
Vol 35 (11) ◽  
pp. 1861-1865 ◽  
Author(s):  
Kate E. McPherson ◽  
Libero J. Bartolotti ◽  
Andrew T. Morehead ◽  
Andrew L. Sargent
Keyword(s):  
Minimum Energy ◽  
Minimum Energy Path ◽  
Reaction Step ◽  
Elastic Band ◽  
Band Method

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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