All Stories

  1. Mechanical coupling in the nitrogenase complex

    Article • PLoS Computational Biology, March 2021, PLOS

    Dr Simone Raugei

  2. HIV-1 Integrase Binding to its Cellular Partners: A Perspective from Computational Biology

    Article • Current Pharmaceutical Design, May 2014, Bentham Science Publishers

    Dr Simone Raugei

  3. Substrate Channel in Nitrogenase Revealed by a Molecular Dynamics Approach

    Article • Biochemistry, April 2014, American Chemical Society (ACS)

    Dr Simone Raugei

  4. Iron Complexes for the Electrocatalytic Oxidation of Hydrogen: Tuning Primary and Secondary Coordination Spheres

    Article • ACS Catalysis, March 2014, American Chemical Society (ACS)

    Dr Simone Raugei

  5. Enzyme Design from the Bottom Up: An Active Nickel Electrocatalyst with a Structured Peptide Outer Coordination Sphere

    Article • Chemistry - A European Journal, January 2014, Wiley

    Dr Simone Raugei

  6. Controlling proton movement: electrocatalytic oxidation of hydrogen by a nickel(ii) complex containing proton relays in the second and outer coordination spheres

    Article • Dalton Transactions, January 2014, Royal Society of Chemistry

    Dr Simone Raugei

  7. Mechanistic insights into hydride transfer for catalytic hydrogenation of CO2 with cobalt complexes

    Article • Dalton Transactions, January 2014, Royal Society of Chemistry

    Dr Simone Raugei

  8. Molecular dynamics study of the proposed proton transport pathways in [FeFe]-hydrogenase

    Article • Biochimica et Biophysica Acta (BBA) - Bioenergetics, January 2014, Elsevier

    Dr Simone Raugei

  9. Computing Free Energy Landscapes: Application to Ni-based Electrocatalysts with Pendant Amines for H2Production and Oxidation

    Article • ACS Catalysis, December 2013, American Chemical Society (ACS)

    Dr Simone Raugei

  10. Conformational Dynamics and Proton Relay Positioning in Nickel Catalysts for Hydrogen Production and Oxidation

    Article • Organometallics, November 2013, American Chemical Society (ACS)

    Dr Simone Raugei

  11. Hydrogen Production Using Nickel Electrocatalysts with Pendant Amines: Ligand Effects on Rates and Overpotentials

    Article • ACS Catalysis, October 2013, American Chemical Society (ACS)

    Dr Simone Raugei

  12. Evaluation of the Role of Water in the H2 Bond Formation by Ni(II)-Based Electrocatalysts

    Article • Journal of Chemical Theory and Computation, August 2013, American Chemical Society (ACS)

    Dr Simone Raugei

  13. High Catalytic Rates for Hydrogen Production Using Nickel Electrocatalysts with Seven-Membered Cyclic Diphosphine Ligands Containing One Pendant Amine

    Article • Journal of the American Chemical Society, February 2013, American Chemical Society (ACS)

    Dr Simone Raugei

  14. Cover Picture: The Role of a Dipeptide Outer‐Coordination Sphere on H2‐Production Catalysts: Influence on Catalytic Rates and Electron Transfer (Chem. Eur. J. 6/2013)

    Article • Chemistry - A European Journal, January 2013, Wiley

    Dr Simone Raugei

  15. Bio-Inspired Molecular Catalysts for Hydrogen Oxidation and Hydrogen Production

    Article • January 2013, American Chemical Society (ACS)

    Dr Simone Raugei

  16. The Role of a Dipeptide Outer‐Coordination Sphere on H2‐Production Catalysts: Influence on Catalytic Rates and Electron Transfer

    Article • Chemistry - A European Journal, December 2012, Wiley

    Dr Simone Raugei

  17. Proton Delivery and Removal in [Ni(PR2NR′2)2]2+ Hydrogen Production and Oxidation Catalysts

    Article • Journal of the American Chemical Society, November 2012, American Chemical Society (ACS)

    Dr Simone Raugei

  18. Incorporating Amino Acid Esters into Catalysts for Hydrogen Oxidation: Steric and Electronic Effects and the Role of Water as a Base

    Article • Organometallics, September 2012, American Chemical Society (ACS)

    Dr Simone Raugei

  19. A Computational Model for Protein Ionization by Electrospray Based on Gas-Phase Basicity

    Article • Journal of the American Society for Mass Spectrometry, September 2012, American Chemical Society (ACS)

    Dr Simone Raugei

  20. Role of the Subunit Interactions in the Conformational Transitions in Adult Human Hemoglobin: An Explicit Solvent Molecular Dynamics Study

    Article • The Journal of Physical Chemistry B, August 2012, American Chemical Society (ACS)

    Dr Simone Raugei

  21. Inside Cover: The Role of Pendant Amines in the Breaking and Forming of Molecular Hydrogen Catalyzed by Nickel Complexes (Chem. Eur. J. 21/2012)

    Article • Chemistry - A European Journal, May 2012, Wiley

    Dr Simone Raugei

  22. The Role of Pendant Amines in the Breaking and Forming of Molecular Hydrogen Catalyzed by Nickel Complexes

    Article • Chemistry - A European Journal, April 2012, Wiley

    Dr Simone Raugei

  23. Insights on the acetylated NF‐κB transcription factor complex with DNA from molecular dynamics simulations

    Article • Proteins Structure Function and Bioinformatics, March 2012, Wiley

    Dr Simone Raugei

  24. Distant protonated pyridine groups in water-soluble iron porphyrin electrocatalysts promote selective oxygen reduction to water

    Article • Chemical Communications, January 2012, Royal Society of Chemistry

    Dr Simone Raugei

  25. Stabilization of Nickel Complexes with Ni0···H–N Bonding Interactions Using Sterically Demanding Cyclic Diphosphine Ligands

    Article • Organometallics, December 2011, American Chemical Society (ACS)

    Dr Simone Raugei

  26. Comprehensive Thermodynamics of Nickel Hydride Bis(Diphosphine) Complexes: A Predictive Model through Computations

    Article • Organometallics, October 2011, American Chemical Society (ACS)

    Dr Simone Raugei

  27. Moving Protons with Pendant Amines: Proton Mobility in a Nickel Catalyst for Oxidation of Hydrogen

    Article • Journal of the American Chemical Society, June 2011, American Chemical Society (ACS)

    Dr Simone Raugei

  28. Comment on “New Insights in the Electrocatalytic Proton Reduction and Hydrogen Oxidation by Bioinspired Catalysts: A DFT Investigation”

    Article • The Journal of Physical Chemistry A, April 2011, American Chemical Society (ACS)

    Dr Simone Raugei

  29. Incorporating Peptides in the Outer-Coordination Sphere of Bioinspired Electrocatalysts for Hydrogen Production

    Article • Inorganic Chemistry, April 2011, American Chemical Society (ACS)

    Dr Simone Raugei

  30. 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

    Article • The Journal of Physical Chemistry A, November 2010, American Chemical Society (ACS)

    Dr Simone Raugei

  31. Molecular Dynamics in Physiological Solutions: Force Fields, Alkali Metal Ions, and Ionic Strength

    Article • Journal of Chemical Theory and Computation, June 2010, American Chemical Society (ACS)

    Dr Simone Raugei

  32. On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions

    Article • PLoS Computational Biology, May 2010, PLOS

    Dr Simone Raugei

  33. Hydrogen oxidation catalysis by a nickel diphosphine complex with pendant tert-butyl amines

    Article • Chemical Communications, January 2010, Royal Society of Chemistry

    Dr Simone Raugei

  34. On the Domain of Applicability of Currently used Force Fields for the Calculation of the Activity of Alkali Ions at Physiological Ionic Strength

    Article • Biophysical Journal, January 2010, Elsevier

    Dr Simone Raugei

  35. Changes in non-core regions stabilise plastocyanin from the thermophilic cyanobacterium Phormidium laminosum

    Article • JBIC Journal of Biological Inorganic Chemistry, November 2009, Springer Science + Business Media

    Dr Simone Raugei

  36. Ab Initio Raman Spectra of β-Lactamase Inhibitor Intermediates Bound to E166A SHV β-Lactamase

    Article • Journal of Chemical Theory and Computation, July 2009, American Chemical Society (ACS)

    Dr Simone Raugei

  37. Multi-scale modeling of HIV-1 proteins

    Article • Journal of Molecular Structure THEOCHEM, March 2009, Elsevier

    Dr Simone Raugei

  38. Large-Scale Motions and Electrostatic Properties of Furin and HIV-1 Protease

    Article • The Journal of Physical Chemistry A, November 2007, American Chemical Society (ACS)

    Dr Simone Raugei

  39. Investigating biological systems using first principles Car–Parrinello molecular dynamics simulations

    Article • Current Opinion in Structural Biology, April 2007, Elsevier

    Dr Simone Raugei

  40. Calculation of Redox Properties:  Understanding Short- and Long-Range Effects in Rubredoxin

    Article • The Journal of Physical Chemistry B, March 2007, American Chemical Society (ACS)

    Dr Simone Raugei

  41. The Potential Distribution Theorem and Models of Molecular Solutions. By Thomas L. Beck, Michael E. Paulaitis and Lawrence R. Pratt.

    Article • ChemPhysChem, March 2007, Wiley

    Dr Simone Raugei

  42. Structure and Raman Spectrum of Clavulanic Acid in Aqueous Solution

    Article • The Journal of Physical Chemistry B, February 2007, American Chemical Society (ACS)

    Dr Simone Raugei

  43. Mechanical Stabilization Effect of Water on a Membrane-like System

    Article • Journal of the American Chemical Society, February 2007, American Chemical Society (ACS)

    Dr Simone Raugei

  44. Triggering dynamics of the high-pressure benzene amorphization

    Article • Nature Materials, December 2006, Springer Science + Business Media

    Dr Simone Raugei

  45. Polarization effects and charge transfer in the KcsA potassium channel

    Article • Biophysical Chemistry, December 2006, Elsevier

    Dr Simone Raugei

  46. A novel parametrization scheme for classical and quantum mechanical simulations of large, floppy molecular systems

    Article • Chemical Physics Letters, August 2006, Elsevier

    Dr Simone Raugei

  47. Convergent Dynamics in the Protease Enzymatic Superfamily

    Article • Journal of the American Chemical Society, July 2006, American Chemical Society (ACS)

    Dr Simone Raugei

  48. DFT modeling of biological systems

    Article • physica status solidi (b), June 2006, Wiley

    Dr Simone Raugei

  49. Relative pKa Values from First-Principles Molecular Dynamics:  The Case of Histidine Deprotonation

    Article • The Journal of Physical Chemistry B, March 2006, American Chemical Society (ACS)

    Dr Simone Raugei

  50. Structure and Bonding in Monomeric Iron(III) Complexes with Terminal Oxo and Hydroxo Ligands

    Article • Inorganic Chemistry, January 2006, American Chemical Society (ACS)

    Dr Simone Raugei

  51. Structure and Function of Vanadium Haloperoxidases

    Article • The Journal of Physical Chemistry B, November 2005, American Chemical Society (ACS)

    Dr Simone Raugei

  52. Solute–Solvent Charge Transfer in Aqueous Solution

    Article • ChemPhysChem, September 2005, Wiley

    Dr Simone Raugei

  53. A Proficient Enzyme:  Insights on the Mechanism of Orotidine Monophosphate Decarboxylase from Computer Simulations

    Article • Journal of the American Chemical Society, November 2004, American Chemical Society (ACS)

    Dr Simone Raugei

  54. On the Quantum Nature of an Excess Proton in Liquid Hydrogen Fluoride

    Article • ChemPhysChem, October 2004, Wiley

    Dr Simone Raugei

  55. Formamide Hydrolysis Investigated by Multiple-Steering ab Initio Molecular Dynamics

    Article • The Journal of Physical Chemistry B, December 2003, American Chemical Society (ACS)

    Dr Simone Raugei

  56. Intramolecular solvation effects in the SN2 reaction Cl−+Cl(CH2)nCN

    Article • The Journal of Chemical Physics, November 2003, American Institute of Physics

    Dr Simone Raugei, Gianni Cardini

  57. Nuclear Quantum Effects and Hydrogen Bonding in Liquids

    Article • Journal of the American Chemical Society, July 2003, American Chemical Society (ACS)

    Dr Simone Raugei

  58. Car–Parrinello molecular dynamics on the SN2 reaction Cl−+CH3Br in water

    Article • Journal of Molecular Structure THEOCHEM, July 2003, Elsevier

    Dr Simone Raugei, Gianni Cardini

  59. Application of Density Functional Theory Based Car—Parrinello Simulations to the Study of Catalytic Processes

    Article • ChemInform, March 2003, Wiley

    Dr Simone Raugei

  60. Hydrocarbon Reactivity in the Superacid SbF5/HF:  an ab Initio Molecular Dynamics Study

    Article • The Journal of Physical Chemistry B, October 2002, American Chemical Society (ACS)

    Dr Simone Raugei

  61. Thermal effects on the Cl−+ClCH2CN reaction by Car-Parrinello molecular dynamics

    Article • The Journal of Chemical Physics, August 2002, American Institute of Physics

    Dr Simone Raugei, Gianni Cardini

  62. Structure of the strongly associated liquid antimony pentafluoride: An ab initio molecular dynamics study

    Article • The Journal of Chemical Physics, April 2002, American Institute of Physics

    Dr Simone Raugei

  63. An ab initio study of water molecules in the bromide ion solvation shell

    Article • The Journal of Chemical Physics, January 2002, American Institute of Physics

    Dr Simone Raugei

  64. Dynamics of Water Molecules in the Br- Solvation Shell:  An ab Initio Molecular Dynamics Study

    Article • Journal of the American Chemical Society, August 2001, American Chemical Society (ACS)

    Dr Simone Raugei

  65. Ab Initio Molecular Dynamics Investigation of the Formyl Cation in the Superacid SbF5/HF

    Article • The Journal of Physical Chemistry B, August 2001, American Chemical Society (ACS)

    Dr Simone Raugei

  66. Microsolvation effect on chemical reactivity: The case of the Cl−+CH3Br SN2 reaction

    Article • The Journal of Chemical Physics, March 2001, American Institute of Physics

    Dr Simone Raugei, Gianni Cardini

  67. Car–Parrinello molecular dynamics of the SN2 reaction Cl– + Cl2CH2

    Article • Physical Chemistry Chemical Physics, January 2001, Royal Society of Chemistry

    Dr Simone Raugei, Gianni Cardini

  68. Ab- initio molecular dynamics study of the SN2 reaction Cl- + ClCH2CN

    Article • Physical Chemistry Chemical Physics, January 2001, Royal Society of Chemistry

    Dr Simone Raugei, Gianni Cardini

  69. An ab initio molecular dynamics study of the SN2 reaction Cl−+CH3Br→CH3Cl+Br−

    Article • The Journal of Chemical Physics, December 1999, American Institute of Physics

    Dr Simone Raugei

  70. Pressure-Induced Frustration and Disorder in Mg ( OH ) 2 and Ca ( OH ) 2

    Article • Physical Review Letters, September 1999, American Physical Society (APS)

    Dr Simone Raugei

  71. Intermolecular interactions in the N2-N2 dimer

    Article • Molecular Physics, October 1998, Taylor & Francis

    Dr Simone Raugei

  72. Intermolecular interactions in the N2-N2dimer

    Article • Molecular Physics, October 1998, Taylor & Francis

    Dr Simone Raugei, Gianni Cardini

  73. A molecular dynamics simulation of the vibrational properties of the Ar1−x(N2)x crystal

    Article • The Journal of Chemical Physics, October 1998, American Institute of Physics

    Dr Simone Raugei, Gianni Cardini

  74. Orientational ordering in the mixed crystal Ar1−x(N2)x: A molecular dynamics study

    Article • The Journal of Chemical Physics, May 1997, American Institute of Physics

    Dr Simone Raugei