Isabella Daidone

Research Interest

CV italiano

CV english







M. Davis C.M., Zanetti-Polzi L., Gruebele M., Amadei A., Dyer R.B.  and  Daidone I.*  A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy. Chem. Sci., 2018, DOI: 10.1039/C8SC03786H.


Del Galdo S., Mancini G., Daidone I., Zanetti-Polzi L. , Amadei A. and Barone V. Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties. J. Comput. Chem. 2018 39:1747-1756.


Daidone I., Amadei A., Aschi M. and Zanetti-Polzi L. On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study. Spectrochim. Acta A Mol. Biomol. Spectrosc. 2018, 192: 451-457.


Zanetti-Polzi L., Del Galdo S.,  Daidone I., D'Abramo M., Barone V.  Aschi A.  and  Amadei A. Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory. Phys. Chem. Chem. Phys., 2018, 20: 24369-24378.


Zanetti-Polzi L., Battistuzzi G.,  Borsari M., Pignataro M., Paltrinieri L.,  Daidone I.* and Bortolotti C.A.* Computational investigation of the electron transfer complex between neuroglobin and cytochrome c. Supramol. Chem. 2017, 29: 846-852.


Zanetti-Polzi L., Davis C. M.,Gruebele M., Dyer R. B., Amadei A. and Daidone I. Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation. FEBS Lett. 2017, 591: 3265-3275.


Zanetti-Polzi L., Aschi M., Amadei A. and Daidone I.* Alternative electron-transfer channels ensure ultrafast deactivation of light-induced excited states in riboflavin binding protein. J. Phys. Chem. Lett. 2017, 9: 3321-3327.


Paltrinieri L., Di Rocco G., Battistuzzi G., Borsari M., Sola M., Ranieri A., Zanetti-Polzi L., Daidone I.* and Bortolotti C. A. Computational evidence support the hypothesis of neuroglobin also acting as an electron transfer species. J. Biol. Inorg. Chem. 2 017, 22: 615-623.


Zanetti-Polzi L., Aschi M., Daidone I.* and Amadei A.* Theoretical modeling of the absorption spectrum of aqueous riboflavin. Chem. Phys. Lett. 2017, 669: 19-28.


Guzzo T., Mandaliti W., Nepravishta R., Aramini A., Bodo E., Daidone I., Allegretti M., Topai A. and Paci M. Conformational change in the mechanism of inclusion of ketoprofen in β-cyclodextrin: nmr spectroscopy, ab initio calculations, molecular dynamics simulations, and photoreactivity. J. Phys. Chem. B 2016, 120: 10668-10678.


Daidone I.*, Zanetti-Polzi L., Thukral L., Alekozai E.M. and Amadei A. Theoretical-computational characterization of the temperature-dependent folding thermodynamics of a β-hairpin peptide. Chem. Phys. Lett. 2016, 659: 247-251.  


Zanetti-Polzi L., Corni S., Daidone I. and Amadei A. Extending the essential dynamics analysis to investigate molecular properties: application to the redox potential of proteins. Phys. Chem. Chem. Phys. 2016, 18: 18450-18459.


Aschi M., Barone V., Carlotti B., Daidone I., Elisei F. and Amadei A. Photoexcitation and relaxation kinetics of molecular systems in solution: Towards a complete in silico model. Phys. Chem. Chem. Phys. 2016, 18: 28919-28931.


Zanetti-Polzi L., Bortolotti C.A., Daidone I., Aschi M., Amadei A. and Corni S. A few key residues determine the high redox potential shift in azurin mutants. Org. Biomol. Chem. 2015, 13: 11003-11013.


Thukral L., Schwarze S., Daidone I.* and Neuweiler H.*  b-structure within the denatured state of the helical protein domain BBL. J. Mol. Biol 2015, 427: 3166-3176.


Daidone I.*, Thukral L., Smith J.C. and Amadei A.  Monitoring the folding kinetics of a β-hairpin by time-resolved IR spectroscopy in silico. J. Phys. Chem. B 2015, 119: 4849-4856.


Zanetti-Polzi L., Daidone I., Bortolotti, C.A and Corni S.  Surface packing determines the redox potential shift of cytochrome c adsorbed on gold. J. Am. Chem. Soc. 2014, 136: 12929-12937.


Piacente G., Andrea A., D’Abramo M., Daidone I. and  Aschi M.  Theoretical-computational modeling of photo-induced charge separation spectrum and charge recombination kinetics in solution. Phys. Chem. Chem. Phys., 2014, 16: 20624-20638.


Daidone I., Paltrinieri L., Amadei A., Battistuzzi G., Sola, M., Borsari M. and Bortolotti C.A. Unambiguous assignment of reduction potentials in diheme cytochromes. J. Phys. Chem. B, 2014, 118: 7554-7560.


Daidone I., Amadei A., Zaccanti F., Borsari M. and Bortolotti C.A.  How the reorganization free energy affects the reduction potential of structurally homologous cytochromes. J. Phys. Chem. Lett., 2014, 5:1534-1540.


Zanetti-Polzi L., Marracino P., Aschi M., Daidone I., Fontana A., Apollonio F.,  Liberti M, D'Inzeo G. and Amadei A. Modeling triplet flavin-indole electron transfer and interradical dipolar interaction: a perturbative approach. Theor. Chem. Acc., 2013, 132: 1393.  


Amadei A., Daidone I. and Bortolotti C.A.  A general statistical mechanical approach for modeling redox thermodynamics: the reaction and reorganization free energies. RSC Adv. 2013, 3: 19657-19665.


Zanetti-Polzi L., Aschi M., Amadei A. and Daidone I.* Simulation of the amide i infrared spectrum in photoinduced peptide folding/unfolding transitions. J. Phys. Chem. B 2013, 117:12383-12390.


D'Alessandro M., Amadei A., Daidone I., Po R., Aessi A. and Aschi M.  Toward a realistic modeling of the photophysics of molecular building blocks for energy harvesting: the charge-transfer state in 4,7-dithien-2-yl-2,1,3-benzothiadiazole as a case study. J. Phys. Chem. C 2013, 117: 13785-13797.


Di Giampaolo A., Mazza F., Daidone I., Amicosante G., Perilli M. and Aschi M.  On the structural affinity of macromolecules with different biological properties: molecular dynamics simulations of a series of TEM-1 mutants. Biochem. Biophys. Res. Commun. 2013, 436: 666-671.


Di Giampaolo A., Cerichelli G., Chiarini M., Daidone I. and Aschi M. Structure and solvation properties of aqueous sulfobetaine micelles in the presence of organic spin probes: a Molecular Dynamics simulation study. Struct. Chem. 2013, 24: 945-953.


Daidone I.* , Aschi M., Patamia M., Bozzi A. and Petruzzelli R. Structural and dynamical properties of KTS-disintegrins: a comparison between Obtustatin and Lebestatin. Biopolymers 2013, 99: 47-54.  


Daidone I.* , Iacobucci C., McLain S.E. and Smith J.C.  Alteration of water structure by peptide clusters revealed by neutron scattering in the small angle region (below 1 Å-1). Biophys. J., 2012, 103:1518-1524.


Bortolotti C.A., Amadei A., Aschi M., Borsari M., Corni S., Sola M. and Daidone I.* The reversible opening of two water channels in cytochrome c modulates the redox potential. J. Am. Chem. Soc. 2012, 134:13670-13678.


Daidone I. and Amadei A.  Essential dynamics: foundation and applications.  WIREs Comput. Mol. Sci. 2012, 2:762-770.


Zanetti-Polzi L., Daidone I.* and Amadei A.*  A Theoretical reappraisal of polylysine in the investigation of secondary structure sensitivity of infrared spectra. J. Phys. Chem. B, 2012, 116: 3353-3360.


Amadei A., Daidone I. and Aschi M.  A general theoretical model for electron transfer reactions in complex systems. Phys. Chem. Chem. Phys. 2012, 14:1360-1370.


Zanetti-Polzi L., Daidone I., Anselmi M., Carchini G., Di Nola A. and Amadei A. Analysis of Infrared spectra of β-hairpin peptides as derived from molecular dynamics simulations. J. Phys. Chem. B 2011, 115:11872-11878.


Zanetti-Polzi L., Amadei A., Aschi M. and Daidone I.*  Insight into the IR-spectra/structure relationship in amyloid fibrils: a theoretical study on a prion peptide. J. Am. Chem. Soc. 2011, 133:11414-11417.


Thukral L., Daidone I.* and Smith J.C.*  Structured pathway across transition state for peptide folding revealed by molecular dynamics simulations. PLoS Comput. Biol. 2011, 7(9):e1002137.


Daidone I.*, Di Nola A.* and Smith J.C.  Molecular origin of Gerstmann-Strässler-Scheinker syndrome: insight from computer simulation of an amyloidogenic prion peptide. Biophys. J. 2011, 100:3000-3007.  Press/media release: UT Scientist Uncovers Trigger to Fatal Neurodegenerative Disease (


Noé F., Doose S., Daidone I., Löllmann M., Sauer M., Chodera J. and Smith J.C. Dynamical fingerprints: understanding biomolecular processes by combination of simulation and kinetic experiments. Proc. Natl. Acad. Sci. USA 2011, 108:4822-4827.


Neusius T., Daidone I., Sokolov I.M. and Smith J.C.  Configurational subdiffusion of peptides: A network study. Phys. Rev. E 2011, 83:021902.


Amadei A., Daidone I., Zanetti-Polzi L. and Aschi M.  Modeling quantum vibrational excitations in condensed phase molecular systems. Theor. Chem. Acc. 2011, 129:31-43.


Daidone I., Magliano A., Di Nola A., Mignogna G., Clarkson M.M., Lizzi A.R., Oratore A. and Mazza F. Structural investigation into the bovine Lactoferricin antimicrobial activity by circular dichroism and molecular dynamics simulations. Biometals 2011, 24:259-268.


Zahran M., Daidone I., Smith J.C. and Imhof P.  Mechanism of DNA recognition by EcoRV. J. Mol. Biol. 2010, 401:415-432.


Amadei A., Daidone I., Di Nola A. and Aschi M. Theoretical-computational modelling of infrared spectra in peptides and proteins: a new frontier for combined theoretical-experimental investigations. Curr. Opin. Struct. Biol. 2010, 20:155-161.


Daidone I.*, Aschi M., Zanetti-Polzi L., Di Nola A. and Amadei A.*  On the origin of IR spectral changes upon protein folding. Chem. Phys. Lett. 2010, 488:213-218.


Daidone I.*, Neuweiler H., Doose S., Sauer M. and Smith J.C.  Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains. PloS Comput. Biol. 2010, 6(1): e1000645.


Thukral L., Smith J.C.* and Daidone I.*  Common folding mechanism of a β-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations. J. Am. Chem. Soc. 2009, 131: 18147-18152.


Schulz R., Krishnan M., Daidone I. and Smith J.C.  Instantaneous normal modes and the protein glass transition. Biophys. J. 2009, 96: 476-484.


Narzi D., Daidone I.*, Amadei A. and Di Nola A.  Protein folding pathways revealed by essential dynamics sampling. J. Chem. Theor. Comput. 2008, 4:1940-1948.


McLain S.E., Soper A.K., Daidone I., Smith J.C. and Watts A.  Charge based interactions between peptides observed as the dominant force for association in aqueous solution. Angew. Chem. Int. Ed.  2008, 47: 9059-9062.


Noé F., Daidone I., Di Nola A., Smith J.C., Di Nola A. and Amadei A.  Solvent electrostriction driven peptide folding revealed by Quasi-Gaussian entropy theory and molecular dynamics simulation. J. Phys. Chem. B  2008, 112: 11155-11163.


Neusius T., Daidone I., Sokolov I.M. and Smith J.C.  Subdiffusion in peptides originates from fractal-like structure of configuration space. Phys. Rev. Lett. 2008, 100: 188103.


Daidone I., Ulmschneider M., Di Nola A., Amadei A. and Smith J.C.  Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. Proc. Natl. Acad. Sci. USA 2007, 104:15230-15235.  Press/media release: UT-ORNL Governor’s Chair Unlocks Secrets of Protein Folding (


Amadei A., D'Abramo M., Daidone I., D'Alessandro M., Di Nola A. and Aschi M. Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the haem carbon monoxide binding-unbinding reaction in myoglobin. Theor. Chem. Acc. 2007, 117:637-647.


Flöck D., Rossetti G., Amadei A. Daidone I., and Di Nola A.  Aggregation of small peptides studied by molecular dynamics simulations. Proteins 2006, 65:914-921.


Aschi M., D’Abramo M., Ramondo F., Daidone I., D’Alessandro M., Di Nola A. and Amadei A. Theoretical modeling of chemical reactions in complex environments: the intramolecular proton transfer in aqueous malonaldehyde for an intramolecular reaction: proton transfer in aqueous malonaldehyde. J. Phys. Org. Chem. 2006, 19:518-530.


Daidone I., Amadei A. and Di Nola A.  Theoretical characterization of α-helix and β-hairpin folding kinetics. J. Am. Chem. Soc. 2005, 127:14825-14832.


Bossa C., Amadei A., Daidone I., Anselmi M., Vallone B., Brunori M. and Di Nola A. Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and cavities dynamics. Biophys. J. 2005, 89:465-467.


Colombo G., Daidone I., Gazit E., Amadei A. and Di Nola A.  Molecular dynamics simulation of the aggregation of the core recognition motif of the islet amyloid polypeptide in explicit water. Proteins 2005, 59:519-527.


Daidone I., Amadei A. and Di Nola A.  Thermodynamic and kinetic characterization of a β-hairpin peptide in solution: an extended phase space sampling by molecular dynamics simulations in explicit water. Proteins 2005, 59:510-518.


Flöck D., Daidone I., and Di Nola A.  A Molecular Dynamics study of acylphosphatase in aggregation promoting conditions: the influence of TFE/water solvent. Biopolymers 2004, 75:491-496.


Daidone I., Simone F., Roccatano D., Broglia R.A., Tiana G., Colombo G. and Di Nola A. ß-hairpin conformation of fibrillogenic peptides: structure and α-β transition mechanism revealed by molecular dynamics simulations.  Proteins 2004, 339:515-525.


Daidone I., Roccatano D. and Hayward S.  Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling. J. Mol. Biol. 2004, 339:515-525.        


Daidone I., Amadei A., Roccatano D. and Di Nola A.  Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c. Biophys. J., 2003, 85:2865-2871.


Roccatano D., Daidone I., Ceruso M.A., Bossa C. and Di Nola A.  Selective excitation of  native fluctuations during thermal unfolding simulations: horse heart cythocrome c. Biophys J. 2003, 84:1876-1883.    


*Corresponding author

Isabella Daidone, thats me


Chemistry Department
University of L'Aquila
Via Vetoio (Coppito 1)
67010 L'Aquila