NCSI: Computational Analysis of Copper Intermediates in Reduction of Nitrous Oxide

Status	Completed
Mentor Name	S. Chantal E. Stieber
Mentor's XSEDE Affiliation	Research Allocation, Education Allocation and Campus Champion
Mentor Has Been in XSEDE Community	3-4 years
Project Title	Computational Analysis of Copper Intermediates in Reduction of Nitrous Oxide
Summary	An intern will conduct quantum mechanical calculations of copper enzyme intermediates and calculate X-ray emission spectra. These calculated spectra will be compared with calculated spectra of model complexes to determine whether different coordination modes of nitrous oxide and reduced species can be distinguished by XES to identify enzyme intermediates.
Job Description	The intern will continue to calculate X-ray emission (XES) spectra for proposed structures of copper nitrous oxide reductase enzyme intermediates. The XES spectra will be calculated using the ORCA program, which is a free software for computational chemistry that the PI has installed on the Comet cluster and will be analyzed to determine orbital contributions to spectra. The project is anticipated to take an additional summer to complete. By the end of the project, the student will have completed all calculations, analysis and written a report of the results with the aim of also publishing the results of enzyme intermediate calculations. The student will also be expected to present findings at a scientific meeting. Progress report: In the previous quarter, the student searched the literature for proposed intermediates to calculate and has determined a series of complexes for study. The student also calculated XES spectra for model complexes that have been crystallographically characterized, to predict whether different bonding modes of nitrogen and oxygen containing small molecules can be distinguished by XES. These have been compared to the predicted spectra and a manuscript has been submitted for publication. The student was also selected to participate in the ACS COMP division undergraduate workshop at the New Orleans ACS meeting and will be presenting these results.
Computational Resources	The student will use the Comet cluster with Oasis storage to conduct quantum mechanical calculations that necessitate the use of parallel processing. The program the student will use is already installed on the cluster and has been actively used by the PI, the research group, and the educational allocations. For the complexes of interest, typically one node is sufficient, however up to 24 processors greatly improve the speed.
Contribution to Community
Position Type	Intern
Training Plan	This is a continuation of the previous quarter/semester worth of work by the student. The student should have a familiarity with searching the chemical literature, conducting and analyzing quantum mechanical calculations using the ORCA program, and writing up results. The student is expected to work independently to continue DFT calculations and write up results for publication. The goal is to give an advanced student the chance to further become an independent scientist by working within a relatively well established framework to help design the project and see the project through from start to finish. The student will need access to a computer, but all software for computations and data analysis is free.
Student Prerequisites/Conditions/Qualifications
Duration	Summer
Start Date	05/01/2018
End Date	08/18/2018