Simone Raugei - Publications

Affiliations: 
Pacific Northwest National Laboratory, Richland, WA, United States 
 Washington State University, Pullman, WA, United States 

46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Johnson SI, Baer MD, Raugei S. Protonation of Serine in Gas and Condensed and Microsolvated States in Aqueous Solution. The Journal of Physical Chemistry. A. 126: 44-52. PMID 34941278 DOI: 10.1021/acs.jpca.1c08795  0.626
2021 Guy JE, Cai Y, Baer MD, Whittle E, Chai J, Yu XH, Lindqvist Y, Raugei S, Shanklin J. Regioselectivity mechanism of the Thunbergia alata Δ6-16:0-acyl carrier protein desaturase. Plant Physiology. PMID 34893899 DOI: 10.1093/plphys/kiab577  0.637
2021 Patwardhan A, Sarangi R, Ginovska B, Raugei S, Ragsdale SW. Nickel-Sulfonate Mode of Substrate Binding for Forward and Reverse Reactions of Methyl-SCoM Reductase Suggest a Radical Mechanism Involving Long-Range Electron Transfer. Journal of the American Chemical Society. PMID 33761259 DOI: 10.1021/jacs.1c01086  0.728
2021 Huang Q, Tokmina-Lukaszewska M, Johnson LE, Kallas H, Ginovska B, Peters JW, Seefeldt LC, Bothner B, Raugei S. Mechanical coupling in the nitrogenase complex. Plos Computational Biology. 17: e1008719. PMID 33661889 DOI: 10.1371/journal.pcbi.1008719  0.732
2021 Baer MD, Shanklin J, Raugei S. Atomistic insight on structure and dynamics of spinach acyl carrier protein with substrate length. Biophysical Journal. PMID 33631202 DOI: 10.1016/j.bpj.2020.12.036  0.644
2020 Fantuzzi F, Nascimento MAC, Ginovska B, Bullock RM, Raugei S. Splitting of multiple hydrogen molecules by bioinspired diniobium metal complexes: a DFT study. Dalton Transactions (Cambridge, England : 2003). 50: 840-849. PMID 33237062 DOI: 10.1039/d0dt03411h  0.73
2019 Artz JH, Zadvornyy OA, Mulder DW, Keable SM, Cohen AE, Ratzloff MW, Williams SG, Ginovska B, Kumar N, Song J, McPhillips SE, Davidson C, Lyubimov AY, Pence N, Schut GJ, ... ... Raugei S, et al. Tuning catalytic bias of hydrogen gas producing hydrogenases. Journal of the American Chemical Society. PMID 31816235 DOI: 10.1021/jacs.9b08756  0.738
2019 Johnson LE, Ginovska B, Fenton AW, Raugei S. Chokepoints in Mechanical Coupling Associated with Allosteric Proteins: The Pyruvate Kinase Example. Biophysical Journal. PMID 31010662 DOI: 10.1016/J.Bpj.2019.03.026  0.709
2018 Keable SM, Zadvornyy OA, Johnson LE, Ginovska B, Rasmussen AJ, Danyal K, Eilers BJ, Prussia GA, LeVan AX, Raugei S, Seefeldt LC, Peters JW. Structural characterization of the P intermediate state of the P-cluster of nitrogenase. The Journal of Biological Chemistry. PMID 29720402 DOI: 10.1074/Jbc.Ra118.002435  0.715
2016 Reback ML, Ginovska B, Buchko GW, Dutta A, Priyadarshani N, Kier BL, Helm ML, Raugei S, Shaw WJ. Investigating the role of chain and linker length on the catalytic activity of an H production catalyst containing a β-hairpin peptide. Journal of Coordination Chemistry. 69: 1730-1747. PMID 33093711 DOI: 10.1080/00958972.2016.1188924  0.727
2016 Cardenas AJ, Ginovska B, Kumar N, Hou J, Raugei S, Helm ML, Appel AM, Bullock RM, O'Hagan M. Controlling Proton Delivery through Catalyst Structural Dynamics. Angewandte Chemie (International Ed. in English). PMID 27677094 DOI: 10.1002/Anie.201607460  0.736
2016 Wongnate T, Sliwa D, Ginovska B, Smith D, Wolf MW, Lehnert N, Raugei S, Ragsdale SW. The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase. Science (New York, N.Y.). 352: 953-8. PMID 27199421 DOI: 10.1126/Science.Aaf0616  0.713
2016 Cornish AJ, Ginovska B, Thelen A, Da Silva JC, Soares TA, Raugei S, Dupuis M, Shaw WJ, Hegg EL. Single Amino Acid Modifications Reveal Additional Controls on the Proton Pathway of [FeFe]-Hydrogenase. Biochemistry. PMID 27186945 DOI: 10.1021/Acs.Biochem.5B01044  0.747
2016 Dutta A, Ginovska B, Raugei S, Roberts JA, Shaw WJ. Optimizing conditions for utilization of an H2 oxidation catalyst with outer coordination sphere functionalities. Dalton Transactions (Cambridge, England : 2003). PMID 26905754 DOI: 10.1039/C6Dt00280C  0.725
2015 Raugei S, Helm ML, Hammes-Schiffer S, Appel AM, O'Hagan M, Wiedner ES, Bullock RM. Experimental and Computational Mechanistic Studies Guiding the Rational Design of Molecular Electrocatalysts for Production and Oxidation of Hydrogen. Inorganic Chemistry. PMID 26653114 DOI: 10.1021/Acs.Inorgchem.5B02262  0.328
2015 Zhang C, Raugei S, Eisenberg B, Carloni P. Molecular Dynamics in Physiological Solutions: Force Fields, Alkali Metal Ions, and Ionic Strength. Journal of Chemical Theory and Computation. 6: 2167-75. PMID 26615943 DOI: 10.1021/ct9006579  0.443
2015 Ho MH, O'Hagan M, Dupuis M, DuBois DL, Bullock RM, Shaw WJ, Raugei S. Water-assisted proton delivery and removal in bio-inspired hydrogen production catalysts. Dalton Transactions (Cambridge, England : 2003). 44: 10969-79. PMID 25999141 DOI: 10.1039/C5Dt00782H  0.599
2015 Raugei S, DuBois DL, Rousseau R, Chen S, Ho MH, Bullock RM, Dupuis M. Toward molecular catalysts by computer. Accounts of Chemical Research. 48: 248-55. PMID 25574854 DOI: 10.1021/Ar500342G  0.57
2014 Smith DM, Raugei S, Squier TC. Modulation of active site electronic structure by the protein matrix to control [NiFe] hydrogenase reactivity. Physical Chemistry Chemical Physics : Pccp. 16: 24026-33. PMID 25285653 DOI: 10.1039/c4cp03518f  0.308
2014 Li J, Rossetti G, Dreyer J, Raugei S, Ippoliti E, Lüscher B, Carloni P. Molecular simulation-based structural prediction of protein complexes in mass spectrometry: the human insulin dimer. Plos Computational Biology. 10: e1003838. PMID 25210764 DOI: 10.1371/Journal.Pcbi.1003838  0.477
2014 Das P, Ho MH, O'Hagan M, Shaw WJ, Bullock RM, Raugei S, Helm ML. Controlling proton movement: electrocatalytic oxidation of hydrogen by a nickel(II) complex containing proton relays in the second and outer coordination spheres. Dalton Transactions (Cambridge, England : 2003). 43: 2744-54. PMID 24306451 DOI: 10.1039/C3Dt53074D  0.58
2014 Quy VC, Carnevale V, Manganaro L, Lusic M, Rossetti G, Leone V, Fenollar-Ferrer C, Raugei S, Del Sal G, Giacca M, Carloni P. HIV-1 integrase binding to its cellular partners: a perspective from computational biology. Current Pharmaceutical Design. 20: 3412-21. PMID 24001231 DOI: 10.2174/13816128113199990631  0.669
2014 Ginovska-Pangovska B, Ho MH, Linehan JC, Cheng Y, Dupuis M, Raugei S, Shaw WJ. Molecular dynamics study of the proposed proton transport pathways in [FeFe]-hydrogenase. Biochimica Et Biophysica Acta. 1837: 131-8. PMID 23981729 DOI: 10.1016/J.Bbabio.2013.08.004  0.591
2013 Ho MH, Raugei S, Rousseau R, Dupuis M, Bullock RM. Evaluation of the Role of Water in the H2 Bond Formation by Ni(II)-Based Electrocatalysts. Journal of Chemical Theory and Computation. 9: 3505-14. PMID 26584107 DOI: 10.1021/Ct400396S  0.568
2013 Stewart MP, Ho MH, Wiese S, Lindstrom ML, Thogerson CE, Raugei S, Bullock RM, Helm ML. High catalytic rates for hydrogen production using nickel electrocatalysts with seven-membered cyclic diphosphine ligands containing one pendant amine. Journal of the American Chemical Society. 135: 6033-46. PMID 23384205 DOI: 10.1021/Ja400181A  0.576
2013 Reback ML, Ginovska-Pangovska B, Ho MH, Jain A, Squier TC, Raugei S, Roberts JA, Shaw WJ. The role of a dipeptide outer-coordination sphere on H2-production catalysts: influence on catalytic rates and electron transfer. Chemistry (Weinheim An Der Bergstrasse, Germany). 19: 1928-41. PMID 23233438 DOI: 10.1002/Chem.201202849  0.594
2012 O'Hagan M, Ho MH, Yang JY, Appel AM, Rakowski DuBois M, Raugei S, Shaw WJ, DuBois DL, Bullock RM. Proton delivery and removal in [Ni(P(R)2N(R')2)2]2+ hydrogen production and oxidation catalysts. Journal of the American Chemical Society. 134: 19409-24. PMID 23072436 DOI: 10.1021/Ja307413X  0.593
2012 Marchese R, Grandori R, Carloni P, Raugei S. A computational model for protein ionization by electrospray based on gas-phase basicity. Journal of the American Society For Mass Spectrometry. 23: 1903-10. PMID 22993040 DOI: 10.1007/S13361-012-0449-0  0.473
2012 Yusuff OK, Babalola JO, Bussi G, Raugei S. Role of the subunit interactions in the conformational transitions in adult human hemoglobin: an explicit solvent molecular dynamics study. The Journal of Physical Chemistry. B. 116: 11004-9. PMID 22838506 DOI: 10.1021/Jp3022908  0.574
2012 Raugei S, Chen S, Ho MH, Ginovska-Pangovska B, Rousseau RJ, Dupuis M, DuBois DL, Bullock RM. The role of pendant amines in the breaking and forming of molecular hydrogen catalyzed by nickel complexes. Chemistry (Weinheim An Der Bergstrasse, Germany). 18: 6493-506. PMID 22532421 DOI: 10.1002/Chem.201103346  0.573
2012 Fenollar-Ferrer C, Anselmi C, Carnevale V, Raugei S, Carloni P. Insights on the acetylated NF-κB transcription factor complex with DNA from molecular dynamics simulations. Proteins. 80: 1560-8. PMID 22419549 DOI: 10.1002/Prot.24047  0.679
2011 O'Hagan M, Shaw WJ, Raugei S, Chen S, Yang JY, Kilgore UJ, DuBois DL, Bullock RM. Moving protons with pendant amines: proton mobility in a nickel catalyst for oxidation of hydrogen. Journal of the American Chemical Society. 133: 14301-12. PMID 21595478 DOI: 10.1021/Ja201838X  0.341
2010 Marchese R, Grandori R, Carloni P, Raugei S. On the zwitterionic nature of gas-phase peptides and protein ions. Plos Computational Biology. 6: e1000775. PMID 20463874 DOI: 10.1371/Journal.Pcbi.1000775  0.485
2010 Muñoz-López FJ, Raugei S, De la Rosa MA, Díaz-Quintana AJ, Carloni P. Changes in non-core regions stabilise plastocyanin from the thermophilic cyanobacterium Phormidium laminosum. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 15: 329-38. PMID 19915878 DOI: 10.1007/S00775-009-0605-6  0.49
2007 Dal Peraro M, Ruggerone P, Raugei S, Gervasio FL, Carloni P. Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. Current Opinion in Structural Biology. 17: 149-56. PMID 17419051 DOI: 10.1016/J.Sbi.2007.03.018  0.669
2007 Sulpizi M, Raugei S, VandeVondele J, Carloni P, Sprik M. Calculation of redox properties: understanding short- and long-range effects in rubredoxin. The Journal of Physical Chemistry. B. 111: 3969-76. PMID 17388622 DOI: 10.1021/Jp067387Y  0.653
2007 Miani A, Raugei S, Carloni P, Helfand MS. Structure and Raman spectrum of clavulanic acid in aqueous solution. Journal of Physical Chemistry B. 111: 2621-2630. PMID 17302447 DOI: 10.1021/Jp066135U  0.434
2007 Ivanov I, Chen B, Raugei S, Klein ML. Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonation. The Journal of Physical Chemistry. B. 110: 6365-71. PMID 16553455 DOI: 10.1021/Jp056750I  0.661
2007 Budrìa JG, Raugei S, Cavallo L. Structure and bonding in monomeric iron(III) complexes with terminal oxo and hydroxo ligands. Inorganic Chemistry. 45: 1732-8. PMID 16471987 DOI: 10.1021/ic051372h  0.477
2006 Carnevale V, Raugei S, Micheletti C, Carloni P. Convergent dynamics in the protease enzymatic superfamily. Journal of the American Chemical Society. 128: 9766-9772. PMID 16866533 DOI: 10.1021/Ja060896T  0.702
2006 Bucher D, Raugei S, Guidoni L, Dal Peraro M, Rothlisberger U, Carloni P, Klein ML. Polarization effects and charge transfer in the KcsA potassium channel. Biophysical Chemistry. 124: 292-301. PMID 16737771 DOI: 10.1016/J.Bpc.2006.04.008  0.7
2006 Raugei S, Carloni P. Structure and function of vanadium haloperoxidases Journal of Physical Chemistry B. 110: 3747-3758. PMID 16494433 DOI: 10.1021/Jp054901B  0.518
2005 Dal Peraro M, Raugei S, Carloni P, Klein ML. Solute-solvent charge transfer in aqueous solution. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 6: 1715-8. PMID 16080223 DOI: 10.1002/Cphc.200500039  0.71
2005 Raugei S, Klein ML. On the quantum nature of an excess proton in liquid hydrogen fluoride. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 5: 1569-76. PMID 15535556 DOI: 10.1002/CPHC.200400198  0.515
2004 Raugei S, Cascella M, Carloni P. A proficient enzyme: Insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations Journal of the American Chemical Society. 126: 15730-15737. PMID 15571395 DOI: 10.1021/Ja0455143  0.491
2004 Raugei S, Klein ML. Nuclear quantum effects and hydrogen bonding in liquids. Journal of the American Chemical Society. 125: 8992-3. PMID 15369337 DOI: 10.1021/JA0351995  0.496
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