1. Computational Study Understanding Catalytic Hydrogen Oxidation/Reduction in Metal-Sulfur Proteins
Tyler Ewing
2017

2. Rubredoxin active site with iron metal center
Introduction
Problem
Platinum-based catalysts
Expensive, limited resource
Interest
Rubredoxin protein
Electron transport1
Active site of protein contains first-row transitional metal center
GOAL
Identify the portions of the metal-sulfur proteins that play a role in catalysis of molecular hydrogen
Determine which oxidation and multiplicity states of the metal-center (Fe, Ni) in the protein model demonstrates the strongest hydrogen binding potential
Rubredoxin active site with iron metal center
INCLUDE PURPOSE

3. Methodology Active Site (fragment) Example of additional fragment
Original model obtained from online protein database
Facio
Visualization, solvation, fragmentation
Fragment molecular orbital (FMO) theory6
GAMESS suite of programs
Computations
Geometry optimization, energy, etc.
Density Functional Theory (DFT)
Structures being tested
Fe(II), Fe(III), Ni(I), Ni(II)
High and low-spin state for each
Example of additional fragment

4. Blue Waters Supercomputer
Fragment molecular orbital (FMO) method scales well on multiple nodes
Each fragment energy calculated independently
Individual calculations combined in the end to predict protein properties
MPI
Optimize performance of GAMESS suite of programs for Blue Waters
Running jobs
Batch

5. Timeline Summer 2017 Fall 2017 Spring 2017
Preliminary FMO calculations and optimization of protein fragmentation scheme
Fall 2017
Production runs of the Fe-rubredoxin model
Spring 2017
Production runs of the Ni-rubredoxin model