Theoretical Approaches to the Characterization of Water, Aqueous Interfaces, and Improved Sampling of Protein Conformational Changes

<p>Methods to advance the understanding of water and other aqueous systems are devel- oped. This work falls into three areas: The creation of better interaction potentials for water, improved methods for sampling configurational space, and the applications of these methods to understand systems of interest. Charge transfer has been shown by <em>ab initio</em> methods to be important in the water–water and water–ion interactions. A model for treating charge transfer in liquid water and aqueous systems is presented in this manuscript. The model is called Discrete Charge Transfer (DCT) and is based on the commonly-used TIP4P/2005 model, which represents the charge distribution of water molecules with three charge sites. Such models have been very successful in reproducing many of the physical properties of water. Charge transfer is introduced by transferring a small amount of charge, -0.02e, from the hydrogen bond acceptor to the hydrogen bond donor, as has been indicated by electronic structure calculations. We have parameterized both polarizable and non-polarizable potentials, optimized to include charge transfer. Methods to surmount the obstacles incurred by the introduction of charge transfer, which involve the amount of charge transfer at large distances and implementation into Molecular Dynamics simulation, is presented, along with our results assessing the importance of charge transfer in liquid water and aqueous systems. Also presented is a method for improving eciency of a sampling technique, Replica Exchange, by reducing the number of replicas. The improved method is called Replica Exchange with Driven Scaling (REDS2).</p>

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Chemistry

Year dc:date.available

2012

Author dc:creator

• Lee, Alexis J.

Contributors dc:contributor

• Steven W. Rick
• Chris Summa
• David Mobley

• Molecular Dynamics
• Charge transfer
• Water
• REDS2
• Physical Chemistry
• Theory and Algorithms

Repository record dc:identifier

https://scholarworks.uno.edu/td/1511

OAI identifier oai:identifier

oai:scholarworks.uno.edu:td-2545