Atomistic simulations of proton transport in the gas and condensed phases : spectroscopy, reaction kinetics and grotthuss mechanism

Xu, Zhen-Hao. Atomistic simulations of proton transport in the gas and condensed phases : spectroscopy, reaction kinetics and grotthuss mechanism. 2018, Doctoral Thesis, University of Basel, Faculty of Science.


Official URL: http://edoc.unibas.ch/diss/DissB_12759

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The empirical force field method of Molecular Mechanics with Proton Transfer (MMPT) follows concepts from a QM/MM scheme which treats the proton transfer (PT) process in its full dimensionality while improving on three important aspects of the problem: speed, accuracy, and versatility. Recent applications focused on the computation of infrared signatures for the shared proton between a donor and an acceptor atom. This was complemented and supported by recent experiments. Both conventional molecular dynamics and more advanced ring polymer molecular dynamics (RPMD) simulations were carried out to characterize the energetics, dynamics and spectroscopy of transferring protons in systems including formic acid dimer and protonated oxalate. The simulations were found reproducing infrared spectra in good agreement with experimental results.
Moreover, the primary kinetic isotope effects (KIEs) of intramolecular hydrogen transfer are determined in both classical molecular dynamics (MD) and quantum simulations with the MMPT force fields. For classical simulations, the parametric potential energy surfaces (PESs) were refined with zero point vibrational effects (ZPVEs) considered, which effectively leads to the reduction of reaction barrier heights for the corresponding systems such as malondialdehyde and acetylacetone. With ZPVE introduced, the effective barrier heights are different between the isotope unsubstituted and substituted systems. That led to the chemical contributions into the primary kinetic isotope effects. In addition to classical simulations, the nuclear quantum effects (NQEs) are explicitly included in the path integral simulations based on the same empirical potential surfaces. With the inclusion of NQEs, simulation results lead to the increase of KIE values at 250 K by a factor of 2.5~3.0 compared to those from classical MD simulations.
Rather than performing proton transfer within a priori defined reaction motif, in this thesis work, MMPT was extensively developed to be capable of delocalizing and treating diffusive proton transport in both gas and condensed phases. This became possible by combining the MMPT force field with multi-surface adiabatic reactive molecular dynamics (MS-ARMD), which leads to the new multi-state MMPT (MS-MMPT) method. In this method, a global potential energy for proton transports is built by mixing multiple potential energy surfaces, each of which corresponds to an oscillatory PT reaction. That enables, for instance, all hydrogen atoms in a water bulk with excess protons to equally participate into the transfer reactions within the force field framework. The integrated MS-MMPT method was applied to performing proton diffusion simulations for [H2O]nH+ clusters at the gas phase and bulk systems with the periodic boundary condition. Results were compared with both experiments and simulations using other established methods.
Advisors:Meuwly, Markus and Lilienfeld, 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:12759
Thesis status:Complete
Number of Pages:1 Online-Ressource (xii, 178 Seiten)
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edoc DOI:
Last Modified:11 Oct 2018 04:30
Deposited On:10 Oct 2018 12:08

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