Mechanisms of proton transfer / Diane Elizabeth Sagnella.

Format:

Book

Manuscript

Microformat

Thesis/Dissertation

Author/Creator:

Sagnella, Diane Elizabeth.

Contributor:

Klein, Michael L., advisor.

University of Pennsylvania.

Language:

English

Subjects (All):

Penn dissertations--Chemistry.

Chemistry--Penn dissertations.

Local Subjects:

Penn dissertations--Chemistry.

Chemistry--Penn dissertations.

Physical Description:

xii, 161 pages : illustrations ; 29 cm

Production:

1996.

Summary:

Three studies of proton transfer have been performed. The first two presented are investigations of the effects of an excess proton in two model ion channels, gramicidin A (gA) and a poly-glycine analog of the gramicidin channel. In the first example, the effects of the hydronium ion ($\rm H\sb3O\sp+$) on the structure of gramicidin A and the linear chain of waters in that ion channel were studied using classical molecular dynamics. The average distance between the centers of mass of the channel waters, the dipole-dipole correlation functions of the channel waters, and the average distance of the backbone carbonyl oxygen atoms from the channel axis were calculated. These simulations indicated, among other things, the importance of the carbonyl groups of the channel backbone in the solvation of the excess proton. Furthermore, $\rm H\sb7O\sbsp{3}{+}$ and $\rm H\sb5O\sbsp{2}{+}$ complexes were observed for the first time in an ion channel. To further investigate the effects of these observations on proton transfer within ion channels Car-Parrinello ab initio molecular dynamics (CPMD) simulations of proton transfer within a poly-glycine analog of Gramicidin A were performed. Using CPMD several trajectories were run in the hope of elucidating a mechanism for proton transfer through ion channels. The simulations clearly demonstrated the importance of a priori carbonyl solvation in the transfer of the proton through the channel.

In third study, using an empirical valence bond (EVB) model, the differences in structure and dynamics of proton transfer in the $\rm H\sb5O\sbsp{2}{+}$ complex in bulk water with (second order Moller-Plesset perturbation theory, MP2) and without (Hartree-Fock theory, HF) the inclusion of electron correlation were investigated. Ab initio potential energy surfaces at both the HF and MP2 levels were calculated. These were then fit with an empirical potential so that classical molecular dynamics could be run. In addition, the previously calculated dependence of the charges on the position of the transferring proton was fit to an analytic form. Free-energy curves for proton transfer in both the gas and condensed phases were calculated. A comparison has also been made between the asymmetric stretch trajectories resulting from the two theories. The free-energy curves for the proton transfer are presented and discussed, and the structuring around the $\rm H\sb5O\sbsp{2}{+}$ complex has been examined.

Notes:

Supervisor: Michael L. Klein.

Thesis (Ph.D. in Chemistry) -- University of Pennsylvania, 1996.

Includes bibliographical references.

Local Notes:

University Microfilms order no.: 97-12994.

OCLC:

187469429