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Simulations of proton transfer processes using reactive force fields

Lammers, Sven. Simulations of proton transfer processes using reactive force fields. 2006, Doctoral Thesis, University of Basel, Faculty of Science.

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Official URL: http://edoc.unibas.ch/diss/DissB_7993

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Abstract

Within this thesis we presented the development of reactive force fields that are ca-
pable to describe the dynamics of proton and hydrogen atom transfer processes. The
presented implementation in CHARMM overcomes the limitation that bond break-
ing and formation cannot be investigated by conventional classical MD simulations.
Derived from high-level ab initio calculations this approach combines the accuracy of
such calculations with the speed of MD simulations. The high-quality force fields of
the prototype systems are comparable to high-level ab initio calculations in terms of
structure and energy barriers. The PESs of proton transfer reactions are extremely
sensitive with respect to the chemical environment. Nevertheless one is always able
to classify the PT under investigation into symmetric and asymmetric PES. We de-
veloped a series of parameter sets that are not only able to describe symmetric and
asymmetric correctly but also can accommodate to different locations of energetic
minima and barriers. The chosen three-dimensional potential energy functions have
shown to be quite flexible and transferable in characterizing PT reactions in quite
diverse chemical systems. The morphing transformation of MMPT force field param-
eter, starting from one of our prototype systems to develop a new force field for a new
molecular system which exhibits a similar topology in the PES along the proton reac-
tion coordinates, has been shown to be successfully applicable in various examples.
Energy scaling has been employed to investigate the effect on the proton transfer os-
cillation in NH+
4 · · ·NH3. New parameters through morphing have been developed
for protonated diglyme, as well as for double proton transfer in 2PY2HP and for as-
partic acid and water as model system for PT reactions in the active site of bacterial
ferredoxin I. We applied the MMPT force field to investigate the vibrational infrared
spectra of proton-bound species and explored the relationship of infrared spectra for
protonated water dimer and protonated diglyme. The results for protonated water
dimer compared well with other high-level calculations. Besides the further system-
atic development of the morphing approach one can also employ the force field in
combination with Feynman path integral methods. The MMPT force field could be a
viable alternative to lower level quantum mechanical methods because the accuracy
of the force field is only limited by the initial determination of the underlying PES for
the PT of interest.
Advisors:Meuwly, Markus
Committee Members:Huber, Hanspeter
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:7993
Thesis status:Complete
Number of Pages:113
Language:English
Identification Number:
Last Modified:22 Jan 2018 15:50
Deposited On:13 Feb 2009 16:11

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