ProtonTransfer

Developed By Kelton Bassingthwaite

This is a command line tool that creates a novel proton indicator from a coordinate file (.xyz) to highlight proton movement in acid/base chemical reactions. It then appends the indicator to the data and creates a new coordinate file. This data is commonly used in complex organic chemistry and water wire studies.

Getting Started

Requirements:

• Python 3+
• numpy
• matplotlib

Install

First, create and activate a virtual environment.

python -m venv .venv
source .venv/bin/activate

Then, install dependencies.

pip install numpy matplotlib
pip install . -e

Tests

python -m unittest ./tests

Usage

The script reads in a .xyz file. Appends the aproximate position of the loose proton to each step. Then, if a graph is requested, plots the distance between the proton and (0, 0, 0). Finaly, a new .xyz file is written with the modified steps.

Arguments:

• -i file name
  • The path to and name of the data to be analyzed (without the .xyz extension)
• -g Boolean
  • Optional argument to display a graph of the Indicators distance from the origin

Examples:

c:\...\data>python ProtonTransfer.py -i filename -g True
c:\...\data>python ProtonTransfer.py -i filename

Citations:

• Formula to determine the position of Proton Indicator from:
  • Pezeshki, Soroosh, and Hai Lin. “Adaptive-Partitioning QM/MM for Molecular Dynamics Simulations: 4. Proton Hopping in Bulk Water.” https://pubs.acs.org/doi/abs/10.1021/ct501019y.

Other Readings

Presentation by Talachutla & Bhat at CU Denver's 2020 RaCAS conferance

These two projects were developed separately.

• Poster
• Video