Ab Initio Molecular Dynamics Analysis Based on Reduced-Dimensionality Reaction Route Map

✍ Scribed by Takuro Tsutsumi

• Publisher: Springer
• Year: 2023
• Tongue: English
• Leaves: 123
• Series: Springer Theses
• Edition: 1
• Category: Library

✦ Synopsis

This thesis proposes useful tools, on-the-fly trajectory mapping method and Reaction Space Projector (ReSPer), to analyze chemical reaction mechanisms by combining the reaction route map and the ab initio molecular dynamics. The key concept for the proposed tools is the Cartesian distance between pairwise molecular structures, and a practical procedure to get the optimal distance is introduced. The on-the-fly trajectory mapping method tracks the distance function between reference structures and molecular structures along the trajectory. Although this method provides fruitful insight into dynamic reaction behaviors, the visualization of reaction routes into a low-dimensional space is still challenging because of the multi-dimensionality. ReSPer successfully constructs a low-dimensional reaction space defined by mathematically-selected principal coordinates representing mutual distance relationships in the full-dimensional space. ReSPer also enables us to project trajectories into the reaction space in the reduced dimension. In this thesis, these methods are applied to several reactions, including bifurcating and photochemical reactions, revealing dynamically-allowed reaction mechanisms. This thesis provides robust and versatile tools to elucidate dynamical reaction routes on the basis of the reduced-dimensionality reaction route map and will help control chemical reaction dynamics and select descriptors for machine learning. 

✦ Table of Contents

Supervisor’s Foreword
Acknowledgments
List of Published Articles
Contents
Abbreviations
1 General Introduction
1.1 How Chemical Reactions Occur?
1.2 Electronic Structure Theory
1.2.1 Born–Oppenheimer Approximation
1.2.2 Wave Function Theory
1.2.3 Density Functional Theory
1.3 Static Reaction Path Analysis
1.3.1 Intrinsic Reaction Coordinate
1.3.2 Global Reaction Route Mapping Strategy
1.4 Molecular Dynamics Simulation
1.4.1 On-The-Fly Molecular Dynamics
1.5 Analysis of Dynamics Effects Based on Static Reaction Path
1.6 Overview of this Thesis
References
2 Analysis of On-The-Fly Trajectory Based on Reaction Route Network
2.1 Introduction
2.2 On-The-Fly Trajectory Mapping Method
2.2.1 Linear Distance in Mass-Weighted Cartesian Coordinate
2.2.2 Nuclear Permutation-Inversion Isomer
2.2.3 On-The-Fly Trajectory Mapping Procedure
2.3 Results and Discussion
2.3.1 Global Reaction Route Network of Au5 Cluster
2.3.2 On-The-Fly Molecular Dynamics Simulation
2.3.3 Bifurcation Mechanisms: A Case of TS1-1d
2.3.4 Isomerization Reaction Mechanisms with Dynamics Effects
2.4 Conclusion
References
3 Visualization of Unique Reaction Route Map by Dimensionality Reduction Method
3.1 Introduction
3.2 Classical Multidimensional Scaling
3.3 Results and Discussion
3.3.1 Intramolecular Proton Transfer in Malonaldehyde
3.3.2 Collision Reaction of OH− + CH3F → [CH3OH···F]−
3.3.3 Global Reaction Route Network of Au5 Cluster
3.4 Conclusion
References
4 Projection of Dynamical Reaction Route onto Reduced-Dimensionality Reaction Space
4.1 Introduction
4.2 Out-of-Sample Extension of Classical Multidimensional Scaling
4.3 Results and Discussion
4.3.1 Collision Reaction of OH− + CH3F → [CH3OH···F]−
4.3.2 Global Reaction Route Map of Au5 Cluster
4.4 Conclusion
References
5 Theoretical Study of Excited-State Branching Reaction Mechanisms of α-Methyl-cis-Stilbene
5.1 Introduction
5.2 Computational Details
5.3 Results and Discussion
5.3.1 Geometries of Minima, TSs, and S1/S0-MECIs
5.3.2 Reaction Pathways in the S1 State
5.3.3 Excited-State On-The-Fly MD Simulations
5.4 Conclusion
References
6 Visualization of Multi-State Potential Energy Landscape: A Case Study on Photochemical Reaction of Stilbene
6.1 Introduction
6.2 Database of Molecular Structures in the S0 and S1 States
6.3 Results and Discussion
6.3.1 Ground-State Potential Energy Landscape
6.3.2 Excited-State Potential Energy Landscape
6.3.3 Multi-State Potential Energy Landscape
6.3.4 On-The-Fly Trajectory Analysis Based on Multi-State Landscape
6.3.5 Excited-State Reaction Route Maps of Stilbene Derivatives
6.4 Conclusion
References
7 General Conclusion
Appendix
Research Statement and Interests
Education
Employment Record
Major Honors and Awards