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Fundamental and Computational Sciences Directorate

Staff information

Simone Raugei

Computational Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K1-83
Richland, WA 99352

PNNL Publications


  • Khadka N., R.D. Milton, S. Shaw, D. Lukoyanov, D.R. Dean, S.D. Minteer, and S. Raugei, et al. 2017. "Mechanism of Nitrogenase H-2 Formation by Metal-Hydride Protonation Probed by Mediated Electrocatalysis and H/D Isotope Effects." Journal of the American Chemical Society 139, no. 38:13518-13524. PNNL-SA-128474. doi:10.1021/jacs.7b07311
  • Lukoyanov D., N. Khadka, D.R. Dean, S. Raugei, L.C. Seefeldt, and B. Hoffman. 2017. "Photoinduced Reductive Elimination of H2 from the Nitrogenase Dihydride (Janus) State Involves a FeMo-cofactor-H2 Intermediate." Inorganic Chemistry 56, no. 4:2233-2240. PNNL-SA-123286. doi:10.1021/acs.inorgchem.6b02899


  • Cornish A.J., B. Ginovska-Pangovska, A. Thelen, J.C. Da Silva, T.A. Soares, S. Raugei, and M. Dupuis, et al. 2016. "Single Amino Acid Modifications Reveal Additional Controls on the Proton Pathway of [FeFe]-hydrogenase." Biochemistry 55, no. 22:3165-3173. PNNL-SA-111944. doi:10.1021/acs.biochem.5b01044
  • Danyal K., S. Shaw, T.R. Page, S.S. Duval, M. Horitani, A.R. Marts, and D. Lukoyanov, et al. 2016. "Negative cooperativity in the nitrogenase Fe protein electron delivery cycle." Proceedings of the National Academy of Sciences of the United States of America 113, no. 40:E5783-E5791. PNNL-SA-111505. doi:10.1073/pnas.1613089113
  • Dutta A., B. Ginovska-Pangovska, S. Raugei, J.A. Roberts, and W.J. Shaw. 2016. "Optimizing Conditions for Utilization of an H2 Oxidation Catalyst with Outer Coordination Sphere Functionalities." Dalton Transactions 45, no. 24:9786-9793. PNNL-SA-107665. doi:10.1039/C6DT00280C
  • Ginovska-Pangovska B., S. Raugei, and W.J. Shaw. 2016. "Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics." In Methods in Enzymology: Computational Approaches for Studying Enzyme Mechanism Part B, edited by GA Voth. 73-101. Cambridge, Massachusetts:Academic Press. PNNL-SA-114509. doi:10.1016/bs.mie.2016.05.044
  • Pegis M.L., B.A. McKeown, N. Kumar, K. Lang, D.J. Wasylenko, P. Zhang, and S. Raugei, et al. 2016. "Homogenous Electrocatalytic Oxiygen Reduction Rates Correlate with Reaction Overpotential in Acidic Organic Solutions." ACS Central Science 2, no. 11:850-856. PNNL-SA-117180. doi:10.1021/acscentsci.6b00261
  • Priyadarshani N., A. Dutta, B. Ginovska-Pangovska, G.W. Buchko, M.J. O'Hagan, S. Raugei, and W.J. Shaw. 2016. "Achieving Reversible H2/H+ Interconversion at Room Temperature with Enzyme-Inspired Molecular Complexes: A Mechanistic Study." ACS Catalysis 6, no. 9:6037-6049. PNNL-SA-115312. doi:10.1021/acscatal.6b01433
  • Reback M.L., B. Ginovska-Pangovska, G.W. Buchko, A. Dutta, N. Priyadarshani, B.L. Kier, and M.L. Helm, et al. 2016. "Investigating the role of chain and linker length on the catalytic activity of an H2 production catalyst containing a b-hairpin peptide." Journal of Coordination Chemistry 69, no. 11-13:1730-1747. PNNL-SA-116292. doi:10.1080/00958972.2016.1188924
  • Wongnate T., D. Sliwa, B. Ginovska-Pangovska, D.M. Smith, M.W. Wolf, N. Lehnert, and S. Raugei. 2016. "The Radical Mechanism of Biological Methane Synthesis by Methyl-Coenzyme M Reductase." Science 352, no. 6288:953-958. PNNL-SA-114957. doi:10.1126/science.aaf0616


  • Danyal K., A.J. Rasmussen, S.M. Keable, B.S. Inglet, S. Shaw, O. Zadvornyy, and S.S. Duval, et al. 2015. "Fe Protein-Independent Substrate Reduction by Nitrogenase MoFe Protein Variants." Biochemistry 54, no. 15:2456-2462. PNNL-SA-108124. doi:10.1021/acs.biochem.5b00140


  • Blacquiere J.M., M.L. Pegis, S. Raugei, W. Kaminsky, A. Forget, S. Cook, and T. Taguchi, et al. 2014. "Synthesis and Reactivity of Tripodal Complexes Containing Pendant Bases." Inorganic Chemistry 53, no. 17:9242-9253. PNNL-SA-102914. doi:10.1021/ic5013389
  • Ginovska-Pangovska B., M. Ho, J.C. Linehan, Y. Cheng, M. Dupuis, S. Raugei, and W.J. Shaw. 2014. "Molecular Dynamics Study of the Proposed Proton Transport Pathways in [FeFe]-Hydrogenase." Biochimica et Biophysica Acta--Bioenergetics 1837, no. 1:131-138. PNNL-SA-94298. doi:10.1016/j.bbabio.2013.08.004
  • Kumar N., D.M. Camaioni, M. Dupuis, S. Raugei, and A.M. Appel. 2014. "Mechanistic Insights into Hydride Transfer for Catalytic Hydrogenation of CO2 with Cobalt Complexes." Dalton Transactions 43, no. 31:11803-11806. PNNL-SA-101141. doi:10.1039/c4dt01551g
  • Reback M.L., G.W. Buchko, B.L. Kier, B. Ginovska-Pangovska, Y. Xiong, S. Lense, and J. Hou, et al. 2014. "Enzyme Design From the Bottom Up: An Active Nickel Electrocatalyst with a Structured Peptide Outer Coordination Sphere." Chemistry - A European Journal 20, no. 6:1510-1514. PNNL-SA-96857. doi:10.1002/chem.201303976
  • Smith D.M., K. Danyal, S. Raugei, and L.C. Seefeldt. 2014. "Substrate Channel in Nitrogenase Revealed by a Molecular Dynamics Approach." Biochemistry 53, no. 14:2278-2285. PNNL-SA-98485. doi:10.1021/bi401313j
  • Smith D.M., S. Raugei, and T.C. Squier. 2014. "Modulation of Active Site Electronic Structure by the Protein Matrix to Control [NiFe] Hydrogenase Reactivity." Physical Chemistry Chemical Physics. PCCP 16, no. 43:24026-24033. PNNL-SA-103780. doi:10.1039/c4cp03518f


  • Reback M.L., B. Ginovska-Pangovska, M. Ho, A. Jain, T.C. Squier, S. Raugei, and J.A. Roberts, et al. 2013. "The Role of a Dipeptide Outer-Coordination Sphere on H2 -Production Catalysts: Influence on Catalytic Rates and Electron Transfer." Chemistry - A European Journal 19, no. 6:1928-1941. PNNL-SA-89749. doi:10.1002/chem.201202849


  • Lense S., M. Ho, S. Chen, A. Jain, S. Raugei, J.C. Linehan, and J.A. Roberts, et al. 2012. "Incorporating Amino Acid Esters into Catalysts for Hydrogen Oxidation: Steric and Electronic Effects and the Role of Water as a Base." Organometallics 31, no. 19:6719-6731. PNNL-SA-87812. doi:10.1021/om300409y
  • Matson B.D., C.T. Carver, A.L. Von Ruden, J.Y. Yang, S. Raugei, and J.M. Mayer. 2012. "Distant protonated pyridine groups in water-soluble iron porphyrin electrocatalysts promote selective oxygen reduction to water." Chemical Communications 48, no. 90:11100-11102. PNNL-SA-89163. doi:10.1039/c2cc35576k


  • Jain A., S. Lense, J.C. Linehan, S. Raugei, H.M. Cho, D.L. DuBois, and W.J. Shaw. 2011. "Incorporating Peptides in the Outer Coordination Sphere of Bio-inspired Electrocatalysts for Hydrogen Production." Inorganic Chemistry 50, no. 9:4073-4085. PNNL-SA-75284. doi:10.1021/ic1025872

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