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Reactive molecular dynamics: from small molecules in gas phase to enzymatic reactions

Brickel, Sebastian. Reactive molecular dynamics: from small molecules in gas phase to enzymatic reactions. 2019, Doctoral Thesis, University of Basel, Faculty of Science.

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Official URL: http://edoc.unibas.ch/diss/DissB_13450

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Abstract

In this thesis, a comprehensive range of applications for the reactive molecular dynamics method
Multi-Surface Adiabatic Reactive Molecular Dynamics (MS-ARMD) will be presented. My research
investigates molecules calculated in gas phase as well as simulations in solution and in solvated enzymes.
The motivation for each simulations will be highlighted, the parametrization of the energy functions
explained and comparisons with other reactive Molecular Dynamics (MD) methods will be made.
Reactive molecular dynamics simulations allow the study of experimentally non amenable time- and
length scales, providing essential insights into the mechanistic details of reactions. Knowledge drawn
from such simulations allow i.a. the refinement of computational models and synthetic pathways, and
finding new applications. The power of MS-ARMD lies in the calculation of converged reaction rates
since thousands of individual trajectories can be run. This allows for the generation of statistically
significant ensemble sizes for analysis such as quantitative characterization of final state distributions.
This is usually not possible for conventional mixed quantum mechanics/classical mechanics (QM/MM)
molecular dynamics or full ab initio molecular dynamics simulations due to the computational cost of
the quantum calculations.
Simulations in condensed phase allow for direct comparison with experiments, which are often performed in (aqueous) solution or in the presence of a biologically relevant enzyme. Furthermore, those
simulations provide additional insight into the mechanism of reactions with chemical and biochemical
interest, beyond experimental findings. It was shown that MS-ARMD force fields (FF) parametrized
in gas phase can be applied directly, without further modifications, to condensed phase simulations.
This allows for quantitatively fitted FF to be used for simulations in solution and enzymes which is an
additional advantage of MS-ARMD in comparison to other reactive molecular dynamics methods.
Advisors:Meuwly, Markus and Lilienfeld, O. Anatole <<von>>
Faculties and Departments:05 Faculty of Science > Departement Chemie > Chemie > Physikalische Chemie (Meuwly)
UniBasel Contributors:Meuwly, Markus
Item Type:Thesis
Thesis Subtype:Doctoral Thesis
Thesis no:13450
Thesis status:Complete
Bibsysno:Link to catalogue
Number of Pages:1 Online-Ressource (ix, 131 Seiten)
Language:English
Identification Number:
Last Modified:14 Dec 2019 05:30
Deposited On:13 Dec 2019 11:36

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