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, Campus Champion and Education Allocation
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 search the literature for proposed structures of copper nitrous oxide reductase enzyme intermediates and use these structures as geometrical inputs for calculating X-ray emission (XES) spectra. 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 Gordon cluster. The student will also calculate 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. The PI has experimental XES data for these model complexes, which the student will then compare to the predicted spectra. The initial stages of the project are anticipated to take 12 weeks, with the possibility for extension of an additional quarter and summer. By the end of the 12 weeks, the student will have completed calculations of at least four complexes, analysis and written a report of the results with the aim of punishing the results. The student will also be expected to present findings at our local undergraduate research conference at the end of March.
Computational Resources	The student will use the Gordon 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	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 determine target species for initial studies, to be approved by the PI before commencing work. 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	Semester
Start Date	01/02/2018
End Date	03/24/2018