scholarly journals Dynamical dimer method for the determination of transition states with ab initio molecular dynamics

2008 ◽  
Vol 128 (4) ◽  
pp. 044107 ◽  
Author(s):  
Alexander Poddey ◽  
Peter E. Blöchl
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Transition States ◽  
Ab Initio Molecular Dynamics

scholarly journals Determination of pKa Values via ab initio Molecular Dynamics and its Application to Transition Metal-Based Water Oxidation Catalysts

Inorganics ◽  
2019 ◽  
Vol 7 (6) ◽  
pp. 73 ◽  
Author(s):  
Mauro Schilling ◽  
Sandra Luber
Keyword(s):  
Molecular Dynamics ◽  
Reaction Mechanism ◽  
Transition Metal ◽  
Ab Initio ◽  
Water Oxidation ◽  
Ab Initio Molecular Dynamics ◽  
Oxidation Catalysts ◽  
Dynamics Simulations ◽  
Further Development

The p K a values are important for the in-depth elucidation of catalytic processes, the computational determination of which has been challenging. The first simulation protocols employing ab initio molecular dynamics simulations to calculate p K a values appeared almost two decades ago. Since then several slightly different methods have been proposed. We compare the performance of various evaluation methods in order to determine the most reliable protocol when it comes to simulate p K a values of transition metal-based complexes, such as the here investigated Ru-based water oxidation catalysts. The latter are of high interest for sustainable solar-light driven water splitting, and understanding of the underlying reaction mechanism is crucial for their further development.

Ab initio Molecular Dynamics for Determination of Structures of Alkali Metal Clusters and Their Temperatures Behavior; An Example of Li9+

1998 ◽  
Vol 63 (9) ◽  
pp. 1431-1446
Author(s):  
Vlasta Bonačič-Koutecký ◽  
Detlef Reichardt ◽  
Jiří Pittner ◽  
Piercarlo Fantucci ◽  
Jaroslav Koutecký
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Equations Of Motion ◽  
Dynamical Behavior ◽  
Iterative Solution ◽  
Excess Energy ◽  
Ab Initio Molecular Dynamics ◽  
Reverse Direction ◽  
Alkali Metal Clusters

It will be shown that an ab initio molecular dynamics procedure based on gradient corrected density functionals for exchange and correlation and using a Gaussian atomic basis (AIMD-GDF) implemented for parallel processing represents a suitable tool for detailed and accurate investigation of structural and dynamical properties of small systems. Gradients of the Born-Oppenheimer ground state energy, obtained by iterative solution of the Kohn-Sham equations, are used to calculate the forces acting on atoms at each instantaneous configuration along trajectories generated by solving classical equations of motion. Dynamics of different isomers of the Li9+ cluster have been investigated as a function of excess energy. It is shown that different isomers, even those similar in energy, can exhibit different structural and dynamical behavior. The analysis of the simulations leads to the conclusion that structures with a central atom, in particular the centered antiprism of Li9+ exhibit concerted mobility of the peripheral atoms at relatively low excess energy. In contrast, compact tetrahedral type structures show much more rigid behavior at low excess energy. However, the former ones need larger excess of internal energy to undergo isomerizations to geometrically different structures than the latter ones. At the time scale of our simulations we found that for the intermediate excess energies it is "easier" to carry the cluster in the basin of the lowest energy isomer than in the reverse direction. It has been found that the liquid-like behavior in small Li clusters becomes apparent at relatively high temperature in spite of large mobility of their atoms.

scholarly journals Ab initio molecular dynamics determination of competitive O2vs. N2 adsorption at open metal sites of M2(dobdc)

2016 ◽  
Vol 18 (16) ◽  
pp. 11528-11538 ◽  
Author(s):  
Marie V. Parkes ◽  
Jeffery A. Greathouse ◽  
David B. Hart ◽  
Dorina F. Sava Gallis ◽  
Tina M. Nenoff
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Gas Adsorption ◽  
Ab Initio Molecular Dynamics ◽  
N2 Adsorption ◽  
Open Metal Sites

AIMD simulations were used to examine competitive gas adsorption of O2 and N2 in the M2(dobdc) MOF series.

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Liqun Cao ◽  
Jinzhe Zeng ◽  
Mingyuan Xu ◽  
Chih-Hao Chin ◽  
Tong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Large Scale ◽  
Methane Combustion ◽  
Combustion Method ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Computational Time ◽  
Combustion Mechanism ◽  
Daily Lives

Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system.

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