1. J. Campeggio, W. Giurlani, M. Pagliai, M. Innocenti, C. Fontanesi, R. Chelli*   Insights into the rate-determining step of the ethanol electrooxidation reaction on the Pd(111) surface through ab initio molecular dynamics simulations
   J. Phys. Chem. C 2023, 127, 21075


2. G. M. Romano, M. Savastano, C. Bazzicalupi, R. Chelli, V. Lippolis, A. Bencini   Inorganic anion recognition in aqueous solution by coupling nearby highly hydrophilic and hydrophobic moieties in a macrocyclic receptor
   Dalton Trans. 2023, 52, 6457


3. V. Volkov, R. Chelli, C. C. Perry   Cu(Proline)2 complex: a model of bio-copper structural ambivalence
   Molecules 2022, 27, 5846


4. J. Campeggio, V. Volkov, M. Innocenti, W. Giurlani, C. Fontanesi, M. Zerbetto, M. Pagliai, A. Lavacchi, R. Chelli   Ethanol electro-oxidation reaction on the Pd(111) surface in alkaline media: insights from quantum and molecular mechanics
   Phys. Chem. Chem. Phys. 2022, 24, 12569-12579


5. A. de Oliveira Cavalcante, R. Chelli   Polarizability relaxation in water/ethanol mixtures
   J. Mol. Liq. 2021, 332, 115839


6. M. Innocenti, A. Giaccherini, R. Chelli, S. Martinuzzi, W. Giurlani, M. Passaponti, A. Lavacchi, C. Fontanesi   Modelling of the elementary steps involved in the Aluminum electrochemical deposition from ionic liquid based solution: the BMImCl/AlCl₃ system
   J. Electrochem. Soc. 2020, 167, 013525


7. V. V. Volkov, R. Chelli, R. Righini, C. C. Perry   Indigo chromophores and pigments: structure and dynamics
   Dyes and Pigments 2020, 172, 107761


8. F. Nuti, C. Gellini, M. Larregola, L. Squillantini, R. Chelli, P. R. Salvi, O. Lequin, G. Pietraperzia, A. M. Papini   A photochromic azobenzene peptidomimetic of a beta-turn model peptide structure as a conformational switch
   Front. Chem. 2019, 7, 180


9. M. Pagliai, G. Funghi, D. Vassetti, P. Procacci, R. Chelli, G. Cardini   Imidazole in aqueous solution: hydrogen bond interactions and structural reorganization with concentration
   J. Phys. Chem. B 2019, 123, 4055-4064


10. L. Briccolani-Bandini, A. Brandi, G. Cardini, R. Chelli, F. M. Cordero, C. Gellini, M. Pagliai   Computational investigation of the selective cleavage of diastereotopic cyclopropane bonds in 5-spirocyclopropane isoxazolidines rearrangement
    J. Org. Chem. 2019, 84, 6757-6764


11. E. Giovannelli, C. Gellini, G. Pietraperzia, G. Cardini, P. Procacci, M. Pagliai, V. Volkov, R. Chelli   Correspondence between light-absorption spectrum and nonequilibrium work distribution as a mean to access free energy differences between electronic states
    J. Chem. Phys. 2018, 149, 084101


12. G. La Penna, R. Chelli   Structural insights into the Osteopontin-Aptamer complex by molecular dynamics simulations
    Front. Chem. 2018, 6, 2


13. E. Giovannelli, M. Cioni, P. Procacci, G. Cardini, M. Pagliai, V. Volkov, R. Chelli   Binding free energies of host-guest systems by nonequilibrium alchemical simulations with constrained dynamics: Illustrative calculations and numerical validation
    J. Chem. Theory Comput. 2017, 13, 5887-5899


14. E. Giovannelli, P. Procacci, G. Cardini, M. Pagliai, V. Volkov, R. Chelli   Binding free energies of host-guest systems by nonequilibrium alchemical simulations with constrained dynamics: Theoretical framework
    J. Chem. Theory Comput. 2017, 13, 5874-5886


15. C. Caratelli, R. Cammi, R. Chelli, M. Pagliai, G. Cardini, V. Schettino   Insights on the realgar crystal under pressure from XP-PCM and periodic model calculations
    J. Phys. Chem. A 2017, 121, 8825-8834


16. L. Moroni, M. Pagliai, R. Chelli, G. Pietraperzia, P. R. Salvi, C. Gellini   Photochemical reactivity of 1,6-Methano[10]annulene
    J. Phys. Chem. A 2017, 121, 4412-4421


17. P. Procacci, R. Chelli   Statistical mechanics of ligand-receptor noncovalent association, revisited: Binding site and standard state volumes in modern alchemical theories
    J. Chem. Theory Comput. 2017, 13, 1924-1933


18. E. Giovannelli, G. Cardini, V. Volkov, R. Chelli   Nonequilibrium work theorems applied to transitions between configurational domains
    J. Stat. Mech.-Theory Exp. 2016, 123204


19. V. Volkov, R. Chelli   Resolving capacity of infrared-visible sum frequency generation microscopy to address discrete structural realizations of a protein at interface
    J. Raman Spectrosc. 2016, 47, 828-838


20. F. Nerattini, R. Chelli, P. Procacci   II. Dissociation free energies in drug-receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands
    Phys. Chem. Chem. Phys. 2016, 18, 15005-15018


21. E. Giovannelli, G. Cardini, R. Chelli   Elastic barrier dynamical freezing in free energy calculations: a way to speed up nonequilibrium molecular dynamics simulations by orders of magnitude
    J. Chem. Theory Comput. 2016, 12, 1029-1039


22. E. Giovannelli, G. Cardini, R. Chelli   Simulations in generalized ensembles through noninstantaneous switches
    Phys. Rev. E 2015, 92, 043310


23. R. Chelli, G. Cardini, E. Giovannelli, G. F. Signorini, P. Procacci   Implementations of nonequilibrium methods for free energy calculations: forthcoming developments of the ORAC molecular dynamics simulation code
    VIRT&L-COMM 2015, 7, 7


24. E. Giovannelli, G. Cardini, C. Gellini, G. Pietraperzia, R. Chelli   Computing free energy differences of configurational basins
    J. Chem. Theory Comput. 2015, 11, 3561-3571


25. V. Volkov, R. Chelli   Polarization entanglement of sum-frequency photons: A tool to probe the Markovian limit
    Phys. Rev. A 2015, 91, 063831


26. R. Chelli, G. Pietraperzia, A. Bencini, C. Giorgi, V. Lippolis, P. R. Salvi, C. Gellini   A fluorescent receptor for halide recognition: clues for the design of anion chemosensors
    Phys. Chem. Chem. Phys. 2015, 17, 10813-10822


27. E. Giovannelli, G. Cardini, C. Gellini, G. Pietraperzia, R. Chelli   Annealed importance sampling with constant cooling rate
    J. Chem. Phys. 2015, 142, 074102


28. R. Chelli   About a world where second law of thermodynamics can be violated
    J. Theor. Comput. Sci. 2014, 1, e107


29. E. Giovannelli, C. Gellini, G. Pietraperzia, G. Cardini, R. Chelli   Nonequilibrium candidate Monte Carlo simulations with configurational freezing schemes
    J. Chem. Theory Comput. 2014,10, 4273-4283


30. G. F. Signorini, E. Giovannelli, Y. G. Spill, M. Nilges, R. Chelli   Convective replica-exchange in ergodic regimes
    J. Chem. Theory Comput. 2014, 10, 953-958


31. E. Giovannelli, C. Gellini, G. Pietraperzia, G. Cardini, R. Chelli   Combining path-breaking with bidirectional nonequilibrium simulations to improve efficiency in free energy calculations
    J. Chem. Phys. 2014, 140, 064104


32. R. Chelli   Journal of Theoretical and Computational Science: Open Access, A bridge to link knowledge from chemistry, physics, biology and more
    J. Theor. Comput. Sci. 2013, 1, e102


33. P. Nicolini, D. Frezzato, C. Gellini, M. Bizzarri, R. Chelli   Toward quantitative estimates of binding affinities for protein-ligand systems involving large inhibitor compounds: a steered molecular dynamics simulation route
    J. Comput. Chem. 2013, 34, 1561-1576


34. S. Puccioni, C. Bazzicalupi, A. Bencini, C. Giorgi, B. Valtancoli, G. De Filippo, V. Lippolis, P. R. Salvi, G. Pietraperzia, R. Chelli, C. Gellini   Tuning the emission properties of fluorescent ligands by changing pH: the unusual case of an acridine-containing polyamine macrocycle
    J. Phys. Chem. A 2013, 117, 3798-3808


35. R. Chelli, C. Gellini, G. Pietraperzia, E. Giovannelli, G. Cardini   Path-breaking schemes for nonequilibrium free energy calculations
    J. Chem. Phys. 2013, 138, 214109


36. R. Chelli   Local sampling in steered Monte Carlo simulations decreases dissipation and enhances free energy estimates via nonequilibrium work theorems
    J. Chem. Theory Comput. 2012, 8, 4040-4052


37. A. Paarmann, M. Lima, R. Chelli, R. Righini, D. Miller   Excitonic effects in the 2DIR spectra of liquid formamide
    Research in Optical Sciences, 2012, paper IW3D.2, OSA Technical Digest (Optical Society of America)


38. R. Chelli, G. F. Signorini   Serial generalized ensemble simulations of biomolecules with self-consistent determination of weights
    J. Chem. Theory Comput. 2012, 8, 830-842   Erratum: J. Chem. Theory Comput. 2012, 8, 2552-2552


39. A. Paarmann, M. Lima, R. Chelli, V. V. Volkov, R. Righini, R. J. D. Miller   Excitonic effects in two-dimensional vibrational spectra of liquid formamide
    Phys. Chem. Chem. Phys. 2011, 13, 11351-11358


40. V. V. Volkov, R. Chelli, F. Muniz-Miranda, R. Righini   Structural properties of a membrane associated anchor dipeptide
    J. Phys. Chem. B 2011, 115, 5294-5303


41. P. Nicolini, D. Frezzato, R. Chelli   Exploiting configurational freezing in nonequilibrium Monte Carlo simulations
    J. Chem. Theory Comput. 2011, 7, 582-593


42. R. Chelli   Optimal weights in serial generalized-ensemble simulations
    J. Chem. Theory Comput. 2010, 6, 1935-1950


43. P. Nicolini, P. Procacci, R. Chelli   Hummer and Szabo-like potential of mean force estimator for bidirectional nonequilibrium pulling experiments/simulations
    J. Phys. Chem. B 2010, 114, 9546-9554


44. S. Marsili, G. F. Signorini, R. Chelli, M. Marchi, P. Procacci   ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level
    J. Comput. Chem. 2010, 31, 1106-1116


45. P. Nicolini, R. Chelli   Improving fast-switching free energy estimates by dynamical freezing
    Phys. Rev. E 2009,  80, 041124


46. M. Lima, R. Chelli, V. V. Volkov, R. Righini   Two-dimensional infrared spectroscopy of a structured liquid: Neat formamide
    J. Chem. Phys. 2009, 130, 204518


47. R. Chelli, P. Procacci   A potential of mean force estimator based on nonequilibrium work exponential averages
    Phys. Chem. Chem. Phys. 2009, 11, 1152-1158


48. R. Chelli   Nonequilibrium work relations for systems subject to mechanical and thermal changes
    J. Chem. Phys. 2009, 130, 054102


49. V. Bambagioni, D. Bani, A. Bencini, T. Biver, M. Cantore, R. Chelli, L. Cinci, P. Failli, L. Ghezzi, C. Giorgi, S. Nappini, F. Secco, M. R. Tiné, B. Valtancoli, M. Venturini   Polyamine-polycarboxylate metal complexes with different biological effectiveness as nitric oxide scavengers. Clues for drug design
    J. Med. Chem. 2008, 51, 3250-3260


50. S. Marsili, R. Chelli, V. Schettino, P. Procacci   Thermodynamics of stacking interactions in proteins
    Phys. Chem. Chem. Phys. 2008, 10, 2673-2685


51. R. Chelli, V. V. Volkov, R. Righini   Retrieval of spectral and dynamic properties from two-dimensional infrared pump-probe experiments
    J. Comput. Chem. 2008, 29, 1507-1516


52. C. P. Calderon, R. Chelli   Approximating nonequilibrium processes using a collection of surrogate diffusion models
    J. Chem. Phys. 2008, 128, 145103


53. R. Chelli, S. Marsili, P. Procacci   Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimators
    Phys. Rev. E 2008, 77, 031104


54. G. Nannucci, L. Moroni, C. Gellini, R. Chelli, P. R. Salvi, V. Schettino, G. Dellepiane   Fluorescence emissions and torsional conformations in pi-conjugated chains of PolyDCHD-HS
    J. Phys. Chem. C 2007, 111, 17485-17492


55. V. V. Volkov, R. Chelli, W. Zhuang, F. Nuti, Y. Takaoka, A. M. Papini, S. Mukamel, R. Righini   Electrostatic interactions in phospholipid membranes revealed by coherent 2D IR spectroscopy
    Proc. Natl. Acad. Sci. USA 2007, 104, 15323-15327


56. J.-P. Piquemal, R. Chelli, P. Procacci, N. Gresh   Key role of the polarization anisotropy of water in modeling classical polarizable force fields
    J. Phys. Chem. A 2007, 111, 8170-8176


57. R. Chelli, S. Marsili, A. Barducci, P. Procacci   Numerical verification of the generalized Crooks nonequilibrium work theorem for non-Hamiltonian molecular dynamics simulations
    J. Chem. Phys. 2007, 127, 034110


58. D. Racko, R. Chelli, G. Cardini, S. Califano, J. Bartos   Free volume from molecular dynamics simulations and its relationships to the positron annihilation lifetime spectroscopy
    Theor. Chem. Acc. 2007, 118, 443-448


59. R. Chelli, S. Marsili, A. Barducci, P. Procacci   Generalization of the Jarzynski and Crooks nonequilibrium work theorems in molecular dynamics simulations
    Phys. Rev. E 2007, 75, 050101


60. V. Schettino, R. Chelli, S. Marsili, A. Barducci, C. Faralli, M. Pagliai, P. Procacci, G. Cardini   Problems in molecular dynamics of condensed phases
    Theor. Chem. Acc. 2007, 117, 1105-1120


61. R. Chelli, S. Marsili, A. Barducci, P. Procacci   Recovering the Crooks equation for dynamical systems in the isothermal-isobaric ensemble: A strategy based on the equations of motion
    J. Chem. Phys. 2007, 126, 044502


62. P. Procacci, S. Marsili, A. Barducci, G. F. Signorini, R. Chelli   Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostat
    J. Chem. Phys. 2006, 125, 164101


63. S. Marsili, A. Barducci, R. Chelli, P. Procacci, V. Schettino   Self-healing Umbrella Sampling: a non equilibrium approach for quantitative free energy calculations
    J. Phys. Chem. B 2006, 110, 14011-14013


64. V. V. Volkov, F. Nuti, Y. Takaoka, R. Chelli, A.M. Papini, R. Righini   Hydration and hydrogen bonding of carbonyls in dimyristoyl-phosphatidylcholine bilayer
    J. Am. Chem. Soc. 2006, 128, 9466-9471


65. R. Chelli, P. Procacci   Comment on  "From subtle to substantial: role of metal ions on pi-pi interactions"
    J. Phys. Chem. B 2006, 110, 10204-10205


66. A. Barducci, R. Chelli, P. Procacci, V. Schettino, F. L. Gervasio, M. Parrinello   Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding
    J. Am. Chem. Soc. 2006, 128, 2705-2710


67. V. V. Volkov, R. Chelli, R. Righini   Domain formation in lipid bilayers probed by two-dimensional infrared spectroscopy
    J. Phys. Chem. B 2006, 110, 1499-1501


68. R. Chelli, A. Barducci, L. Bellucci, V. Schettino, P. Procacci   Behavior of polarizable models in presence of strong electric fields. I. Origin of nonlinear effects in water-point charge systems
    J. Chem. Phys. 2005, 123, 194109


69. M. Paolantoni, R. Chelli, M. Ricci, P. Foggi   The ultrafast dynamics of liquid 1-octanol measured by femtosecond optical Kerr effect
    Proceedings of the "XI TRVS International Conference": Time Resolved Vibrational Spectroscopy. p. 211-216, 2005


70. A. Magro, D. Frezzato, A. Polimeno, G. J. Moro, R. Chelli, R. Righini   Dynamics of liquid benzene: A cage analysis
    J. Chem. Phys. 2005, 123, 124511


71. R. Chelli, R. Righini, S. Califano   Structure of liquid formic acid investigated by first principle and classical molecular dynamics simulations
    J. Phys. Chem. B 2005, 109, 17006-17013


72. R. Chelli, V. Schettino, P. Procacci   Comparing polarizable force fields to ab initio calculations reveals nonclassical effects in condensed phases
    J. Chem. Phys. 2005, 122, 234107


73. A. Barducci, R. Chelli, P. Procacci, V. Schettino   Misfolding pathways of the prion protein probed by molecular dynamics simulations
    Biophys. J. 2005, 88, 1334-1343


74. R. Chelli, M. Pagliai, P. Procacci, G. Cardini, V. Schettino   Polarization response of water and methanol investigated by a polarizable force field and density functional theory calculations: Implications for charge transfer
    J. Chem. Phys. 2005, 122, 074504


75. D. Racko, R. Chelli, G. Cardini, J. Bartos, S. Califano   Insights into positron annihilation lifetime spectroscopy by molecular dynamics simulations. Free-volume calculations for liquid and glassy glycerol
    Eur. Phys. J. D 2005, 32, 289-297


76. R. Chelli, P. Procacci   Comment to  "Calculation of the dipole moment for polypeptides using the generalized Born-electronegativity equalization method: results in vacuum and continuum-dielectric solvent"
    J. Phys. Chem. B 2004, 108, 16995-16997


77. G. Pietraperzia, R. Chelli, M. Becucci, A. Riganelli, M. Alberti, A. Laganà   Molecular mechanics and dynamics calculations to bridge molecular structure information and spectroscopic measurements on complexes of aromatic compounds
    Lect. Notes Comput. Sc. 2004, 3044, 374-382


78. G. F. Signorini, R. Chelli, P. Procacci, V. Schettino   Energetic fitness of histidine protonation states in PDB structures
    J. Phys. Chem. B 2004, 108, 12252-12257


79. M. Becucci, G. Pietraperzia, M. Pasquini,  G. Piani, A. Zoppi, R. Chelli, E. Castellucci, W. Demtroeder   A study on the anisole-water complex by molecular beam-electronic spectroscopy and molecular mechanics calculations
    J. Chem. Phys. 2004, 120, 5601-5607


80. A. S. Gemechu, L. J. H. Hoffmann, S. Marquardt, C. G. Eisenhardt, H. Baumgartel, R. Chelli, G. Cardini, S. Califano   The absorption spectrum of anisole and the anisole/CO₂ 1:1-cluster. The influence of intermolecular interaction on intramolecular vibrations
    Z. Phys. Chem. 2004, 218, 123-153


81. R. Chelli, F. L. Gervasio, P. Procacci, V. Schettino   Inter-residue and solvent-residue interactions in proteins: a statistical study on experimental structures
    PROTEINS 2004, 55, 139-151


82. R. Chelli, G. Cardini, P. Procacci, R. Righini, S. Califano   Dynamics and structure of liquid and supercooled liquid m-toluidine investigated by molecular dynamics simulations
    Proceedings of the "XII UPS Conference": Recent Advances in Ultrafast Spectroscopy. p. 57-67, 2003


83. R. Chelli, G. Cardini, P. Procacci, R. Righini, S. Califano   Dynamical and structural correlation in supercooled liquids: a molecular dynamics investigation of m-toluidine
    J. Chem. Phys. 2003, 119, 357-363


84. R. Chelli, P. Procacci   Comment on "Classical polarizable force fields parametrized from ab initio calculations" [J. Chem. Phys. 117, 1416 (2002)]
    J. Chem. Phys. 2003, 118, 1571-1572


85. R. Chelli, P. Procacci   A transferable polarizable electrostatic force field for molecular mechanics based on the chemical potential equalization principle
    J. Chem. Phys. 2002, 117, 9175-9189


86. F. L. Gervasio, R. Chelli, P. Procacci, V. Schettino   The nature of intermolecular interactions between aromatic amino acid residues
    PROTEINS 2002, 48, 117-125


87. R. Chelli, F. L. Gervasio, P. Procacci, V. Schettino   Stacking and T-shape competition in aromatic-aromatic amino acid interactions
    J. Am. Chem. Soc. 2002, 124, 6133-6143


88. R. Chelli, G. Cardini, P. Procacci, R. Righini, S. Califano   Molecular dynamics of glass-forming liquids: structure and dynamics of liquid metatoluidine
    J. Chem. Phys. 2002, 116, 6205-6215


89. F. L. Gervasio, R. Chelli, P. Procacci, V. Schettino   Is the T-shaped toluene dimer a stable intermolecular complex?
    J. Phys. Chem. A 2002, 106, 2945-2948


90. R. Chelli, R. Righini, S. Califano, P. Procacci   Towards a polarizable force field for molecular liquids
    J. Mol. Liq. 2002, sp. issue 96-97, 87-100


91. C. G. Eisenhardt, A. S. Gemechu, H. Baumgartel, R. Chelli, G. Cardini, S. Califano   Excited state photoelectron spectroscopy of anisole
    Phys. Chem. Chem. Phys. 2001, 3, 5358-5368


92. F. L. Gervasio, R. Chelli, M. Marchi, P. Procacci, V. Schettino   Determination of the potential of mean force of aromatic amino acid complexes in various solvents using molecular dynamics simulations: the case of the tryptophan-histidine pair
    J. Phys. Chem. B 2001, 105, 7835-7846


93. R. Chelli, G. Cardini, M. Ricci, P. Bartolini, R. Righini, S. Califano   The fast dynamics of benzene in the liquid phase. Part II. A molecular dynamics simulation
    Phys. Chem. Chem. Phys. 2001, 3, 2803-2810


94. M. Ricci, P. Bartolini, R. Chelli, G. Cardini, S. Califano, R. Righini   The fast dynamics of benzene in the liquid phase. Part I. Optical Kerr effect experimental investigation
    Phys. Chem. Chem. Phys. 2001, 3, 2795-2802


95. R. Chelli, G. Cardini, P. Procacci, R. Righini, S. Califano, A. Albrecht   Simulated structure, dynamics, and vibrational spectra of liquid benzene
    J. Chem. Phys. 2000, 113, 6851-6863


96. R. Chelli, F. L. Gervasio, C. Gellini, P. Procacci, G. Cardini, V. Schettino   Conformational distribution of gas-phase glycerol
    J. Phys. Chem. A 2000, 104, 11220-11222


97. R. Chelli, F. L. Gervasio, C. Gellini, P. Procacci, G. Cardini, V. Schettino   Density functional calculation of structural and vibrational properties of glycerol
    J. Phys. Chem. A 2000, 104, 5351-5357


98. R. Chelli, P. Procacci, R. Righini, S. Califano   Electrical response in chemical potential equalization schemes
    J. Chem. Phys. 1999, 111, 8569-8575


99. R. Chelli, S. Ciabatti, G. Cardini, R. Righini, P. Procacci   Calculation of optical spectra in liquid methanol using molecular dynamics and the chemical potential equalization method
    J. Chem. Phys. 1999, 111, 4218-4229   Erratum: J. Chem. Phys. 2000, 112, 5515-5515


100. R. Chelli, P. Procacci, G. Cardini, S. Califano   Glycerol condensed phases Part II. A molecular dynamics study of the conformational structure and hydrogen bonding
     Phys. Chem. Chem. Phys. 1999, 1, 879-885


101. R. Chelli, P. Procacci, G. Cardini, R. G. Della Valle, S. Califano   Glycerol condensed phases Part I. A molecular dynamics study
     Phys. Chem. Chem. Phys. 1999, 1, 871-877


102. R. Chelli, G. Cardini, S. Califano   Calculation of elastic coherent neutron scattering spectra from molecular dynamics data: the NaCN plastic crystal
     Chem. Phys. Lett. 1997, 274, 335-340


103. R. Chelli, G. Cardini, S. Califano   A molecular dynamics study of translation-rotation coupling in the NaCN plastic crystal
     J. Chem. Phys. 1997, 107, 8041-8050


104. PhD Thesis (2000): Numerical experiments: methods and applications


105. Degree Thesis (1996): Structure and rotational dynamics of the sodium cyanide crystal in the plastic phase