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

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

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

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

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