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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


  • Chambers G.M., S. Johnson, S. Raugei, and R.M. Bullock. 2019. "Anion control of tautomeric equilibria: Fe-H vs. N-H influenced by NH···F hydrogen bonding." Chemical Science 10, no. 5:1410-1418. PNNL-SA-135803. doi:10.1039/c8sc04239j


  • Peters J.W., D.N. Beratan, B.P. Bothner, R. Dyer, C. Harwood, Z.M. Heiden, and R. Hille, et al. 2018. "A new era for electron bifurcation." Current Opinion in Chemical Biology 47. PNNL-SA-138678. doi:10.1016/j.cbpa.2018.07.026
  • Seefeldt L.C., J.W. Peters, D.N. Beratan, B.P. Bothner, S.D. Minteer, S. Raugei, and B. Hoffman. 2018. "Control of electron transfer in nitrogenase." Current Opinion in Chemical Biology 47. PNNL-SA-138679. doi:10.1016/j.cbpa.2018.08.011


  • Bhattacharya P., Z.M. Heiden, E.S. Wiedner, S. Raugei, N.A. Piro, W.S. Kassel, and R.M. Bullock, et al. 2017. "Ammonia Oxidation by Abstraction of Three Hydrogen Atoms from a Mo-NH3 Complex." Journal of the American Chemical Society 139, no. 8:2916-2919. PNNL-SA-121628. doi:10.1021/jacs.7b00002
  • 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


  • Cardenas A.J., B. Ginovska-Pangovska, N. Kumar, J. Hou, S. Raugei, M.L. Helm, and A.M. Appel, et al. 2016. "Controlling Proton Delivery with Catalyst Structural Dynamics." Angewandte Chemie International Edition 55, no. 43:13509-13513. PNNL-SA-115082. doi:10.1002/anie.201607460
  • 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
  • Ho M., R.J. Rousseau, J.A. Roberts, E.S. Wiedner, M. Dupuis, D.L. DuBois, and R.M. Bullock, et al. 2015. "Ab Initio-Based Kinetic Modeling for the Design of Molecular Catalysts: the Case of H2 Production Electrocatalysts." ACS Catalysis 5, no. 9:5436-5452. PNNL-SA-110596. doi:10.1021/acscatal.5b01152


  • 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
  • Chen S., M. Ho, R.M. Bullock, D.L. DuBois, M. Dupuis, R.J. Rousseau, and S. Raugei. 2014. "Computing Free Energy Landscapes: Application to Ni-based Electrocatalysts with Pendant Amines for H2 Production and Oxidation." ACS Catalysis 4, no. 1:229-242. PNNL-SA-98868. doi:10.1021/cs401104w
  • Darmon J.M., S. Raugei, T.L. Liu, E.B. Hulley, C.J. Weiss, R.M. Bullock, and M.L. Helm. 2014. "Iron Complexes for the Electrocatalytic Oxidation of Hydrogen: Tuning Primary and Secondary Coordination Spheres." ACS Catalysis 4, no. 4:1246-1260. PNNL-SA-100586. doi:10.1021/cs500290w
  • Das P., M. Ho, M.J. O'Hagan, W.J. Shaw, R.M. Bullock, S. Raugei, and M.L. Helm. 2014. "Controlling Proton Movement: Electrocatalytic Oxidation of Hydrogen by a Nickel(II) Complex Containing Proton Relays in the Second and Outer Coordination Spheres." Dalton Transactions 43, no. 7:2744-2754. PNNL-SA-99116. doi:10.1039/c3dt53074d
  • 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


  • Franz J.A., M.J. O'Hagan, M. Ho, T.L. Liu, M.L. Helm, S. Lense, and D.L. DuBois, et al. 2013. "Conformational Dynamics and Proton Relay Positioning in Nickel Catalysts for Hydrogen Production and Oxidation." Organometallics 32, no. 23:7034-7042. PNNL-SA-97203. doi:10.1021/om400695w
  • Ho M., S. Chen, R.J. Rousseau, M. Dupuis, R.M. Bullock, and S. Raugei. 2013. "Bio-Inspired Molecular Catalysts for Hydrogen Oxidation and Hydrogen Production." In Application of Molecular Modeling to Challenges in Clean Energy. ACS Symposium Series, edited by G Fitzgerald and N Govind. 89-111. Washington, District Of Columbia:American Chemical Society. PNNL-SA-92715.
  • Ho M., S. Raugei, R.J. Rousseau, M. Dupuis, and R.M. Bullock. 2013. "Evaluation of the Role of Water in the H2 Bond Formation by Ni(II)-based Electrocatalysts." Journal of Chemical Theory and Computation 9, no. 8:3505-3514. PNNL-SA-95935. doi:10.1021/ct400396s
  • 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
  • Stewart M.P., M. Ho, S. Wiese, M.L. Lindstrom, C.E. Thogerson, S. Raugei, and R.M. Bullock, et al. 2013. "High Catalytic Rates for Hydrogen Production Using Nickel Electrocatalysts with Seven-Membered Diphosphine Ligands Containing One Pendent Amine." Journal of the American Chemical Society 135, no. 16:6033-6046. PNNL-SA-92846. doi:10.1021/ja400181a


  • 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
  • O'Hagan M.J., M. Ho, J.Y. Yang, A.M. Appel, M. Rakowski DuBois, S. Raugei, and W.J. Shaw, et al. 2012. "Proton Delivery and Removal in [Ni(PR2NR'2)2]2+ Hydrogen Production and Oxidation Catalysts." Journal of the American Chemical Society 134, no. 47:19409-19424. PNNL-SA-88737. doi:10.1021/ja307413x
  • Raugei S., S. Chen, M. Ho, B. Ginovska-Pangovska, R.J. Rousseau, M. Dupuis, and D.L. DuBois, et al. 2012. "The Role of Pendant Amines in the Breaking and Forming of Molecular Hydrogen Catalyzed by Nickel Complexes." Chemistry - A European Journal 18, no. 21:6493-6506. PNNL-SA-83517. doi:10.1002/chem.201103346
  • Wiedner E.S., J.Y. Yang, S. Chen, S. Raugei, W.G. Dougherty, W.S. Kassel, and M.L. Helm, et al. 2012. "Stabilization of Nickel Complexes with Ni0···H-N Bonding Interactions Using Sterically Demanding Cyclic Diphosphine Ligands." Organometallics 31, no. 1:144-156. PNNL-SA-81603. doi:10.1021/om200709z


  • Dupuis M., S. Chen, S. Raugei, D.L. DuBois, and R.M. Bullock. 2011. "Comment on 'New Insights in the Electrocatalytic Proton Reduction and Hydrogen Oxidation by Bioinspired Catalysts: A DFT Investigation'." Journal of Physical Chemistry A 115, no. 18:4861-4865. PNNL-SA-76591. doi:10.1021/jp111479z
  • 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
  • O'Hagan M.J., W.J. Shaw, S. Raugei, S. Chen, J.Y. Yang, U.J. Kilgore, and D.L. DuBois, et al. 2011. "Moving Protons with Pendant Amines: Proton Mobility in a Nickel Catalyst for Oxidation of Hydrogen." Journal of the American Chemical Society 133, no. 36:14301-14312. PNNL-SA-77814. doi:10.1021/ja201838x


  • Chen S., S. Raugei, R.J. Rousseau, M. Dupuis, and R.M. Bullock. 2010. "Homogeneous Ni catalysts for H2 Oxidation and Production: An Assessment of Theoretical Methods, from Density Functional Theory to Post Hartree-Fock Correlated Wave-Function Theory." Journal of Physical Chemistry A 114, no. 48:12716-12724. PNNL-SA-73995. doi:10.1021/jp106800n

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