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Table of contents
Abstract
Acknowledgements
1 Introduction
1.1 Prebiotic Context
1.2 Mineral Surfaces and Confined Water
1.3 The Electric Field
2 Theoretical Background
2.1 Ab Initio Molecular Dynamics
2.1.1 Molecular Dynamics
2.1.2 Density Functional Theory
2.1.3 CarParrinello
Molecular Dynamics
2.1.4 Applying an Electric Field via The Modern Theory of Polarisation
2.2 Accessing the Electric field
2.2.1 Application to a model surface
2.3 Enhanced Sampling Techniques
2.3.1 Parametrisation of the Free Energy Landscape
2.3.2 Metadynamics
2.3.3 Umbrella Sampling
3 The Electric Field at the Surface of MgO
3.1 Introduction and Context
3.2 Static Results on Bare MgO
3.2.1 MgO(001)
3.2.2 MgO(111) and MgO(015)
3.3 One monolayer of H2O on MgO(001)
3.4 Dynamic Results on the MgO/water Interface at 300K
3.4.1 Surfaceassisted
proton transfer
3.5 Mimicking the Surface Electric Field
3.5.1 Description and implementation
3.5.2 Tests and Remarks
3.5.3 Results
3.6 Conclusion
4 Surface Effects on a Prebiotic Reaction
4.1 Introduction and Context
4.2 Preliminary Study of the Configuration Space
4.3 Simulation Procedure
4.4 Temperature and Electric Field Effects
4.5 Effect of the Mineral Surface
4.6 Further Analysis
4.6.1 Entropic vs Enthalpic Contributions
4.6.2 Transition States and Isomers
4.7 Conclusion
5 Conclusions and Perspectives
Appendices
A Simulation Details
A.1 Computational Details
A.1.1 AIMD with Quantum Espresso
A.1.2 Metadynamics and Umbrella Sampling with the Plumed Plugin
A.2 System Descriptions
Bibliography
