HOME People Articles Projects Positions Address Movies More

List of publications since 1993 2011   226. A. Magliano, M. Anselmi and A. Di Nola Molecular dynamics study of aggregation of amyloidogenic peptides in explicit water . Int. J. Quantum Chem. 2011 Accepted. 225. M. Anselmi, A. Di Nola and A. Amadei Kinetics of Carbon Monoxide migration and binding in solvated Neuroglobin as revealed by Molecular Dynamics Simulations and Quantum Mechanical Calculations. J. Phys. Chem. B 115(10) 2436-2446 (2011). 224. Thukral L., Daidone I. and Smith J.C Structured pathway across transition state for peptide folding revealed by molecular dynamics simulations. 2010, submitted. 223. Noé F., Doose S., Daidone I.,Lollmann 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 2010, in press 222. Neusius T., Daidone I., Sokolov I.M. and Smith J.C. Configurational Subdiffusion of Peptides: A Network Study. Phys. Rev. E (2010) in press.   221. I. Daidone, A. Di Nola and J. C. Smith Molecular origin of Gerstmann-Straussler-Scheinker syndrome: insight from computer simulation of an amyloidogenic prion peptide. Biophys. J. 100, 3000-3007 (2011). 220. Massimiliano Anselmi, Tommaso Eliseo, Laura Zanetti-Polzi, Maria Rosaria Fullone, Vincenzo Fogliano, Alfredo Di Nola, Maurizio Paci and Ingeborg Grgurina Structure of the lipodepsipeptide syringomycin E in phospholipids and sodium dodecylsulphate micelle: a circular dichroism and NMR spectroscopy combined with molecular dynamics study in octane. Biochim. Biophys. Acta-Biomembranes 1808(9),2102-2110 (2011). 219. Amadei A., Daidone I., Zanetti-Polzi L. and Aschi M. Modeling quantum vibrational excitations in condensed phase molecular systems. Theor. Chem. Acc. 2010, in press. 218.   M. Aschi, R. Zappacosta, P. De Maria, G. Siani, A. Fontana and A. Amadei. Entropy-energy balance in base catalyzed keto-enol interconversion: a joint theoretical and experimental investigation International Journal of Quantum Chemistry (submitted) 217. M. Anselmi, A. Di Nola and A. Amadei The effects of the L29F mutation on ligand migration kinetics in crystallized Myoglobin as revealed by Molecular Dynamics simulations.  Proteins: Structure, Function, and Bioinformatics 79, 867-879 (2011). 216. I. Daidone,  A.Magliano, A. Di Nola,  G. Mignogna, M.M Clarkson, A.R. Lizzi, A. Oratore, F. Mazza Structural investigation into the bovine Lactoferricin antimicrobial activity by Circular Dichroism and Molecular Dynamics simulations. Biometals 24(2) 259-268 (2011). 215. L. Zanetti-Polzi, I. Daidone, M. Anselmi, M. Aschi, G. Carchini, A. Di Nola and A. Amadei Analysis of infrared spectra of b-hairpin peptides as derived from molecular dynamics simulations. J. Phys. Chem B 115, 11872-11878 (2011).     2010   214. Zahran M., Daidone I., Smith J.C. and Imhof P. Mechanism of DNA recognition by EcoRV. J. Mol. Biol. , 401, 415-432 (2010). 213. Laura Zanetti-Polzi Molecular dynamics, quantum mechanics and statistical mechanics study of two Gramicidin S analogs and Syringomycin E. PhD Thesis 2010. 212. P. D'Angelo, S. Della Longa, A. Arcovito, M. Anselmi, A. Di Nola and G. Chillemi Dynamic investigation of protein metal active site: the interplay of XANES and molecular dynamics simulations. J. Am. Chem. Soc. 132(42), 14901-14909 (2010). 211. Romina Zappacosta, Monica Semeraro, Massimo Baroncini, Serena Silvi, Massimiliano Aschi, Alberto Credi and   Antonella Fontana Liposome Destabilization by a 2,7-Diazapyrenium Derivative Through Formation of Transient Pores in the Lipid Bilayer. Small, 6(8),  952-959 (2010). 210. Antonio Arcadi, Massimiliano Aschi, Marco Chiarini, Giovanni Ferrara and Fabio Marinelli Rhodium- and Palladium-Catalyzed Hydroarylation of Propargylic Amines with Arylboronic Acids. Advanced Synthesis & Catalysis, 352(2),  493-498 (2010). 209. G. Carchini Studio del folding di analoghi della Gramicidina S mediante simulazioni di dinamica molecolare. Thesis 2010. 208. A. Tarquini The effect of external electric fields on biological systems:theoretical-computational study. PhD Thesis 2010. 207. S. Marocchi Studio delle proprieta' spettroscopiche della Luciferina mediante l'uso di metodi quanto-meccanici e di dinamica molecolare. Thesis 2010. 206. Daidone I., Neuweiler H., Doose S., Sauer M. and Smith J.C. Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chain. PLoS Comput. Biol.  6(1), e1000645  (2010). 205. M. Aschi, A. Fontana, E. Di Meo, C.  Zazza and A. Amadei, Andrea Characterization of electronic properties in complex molecular systems: modeling of a micropolarity probe. J. Phys. Chem.B, 114 (5),  1915-1924 (2010). 204. A. Amadei, I. Daidone, A. Di Nola and M. Aschi Theoretical-computational modelling of infrared spectra in peptides and proteins: a new frontier for combined theoretical-experimental investigations. Curr Opin Struc Biol, 20, 1-7 (2010). 203. C. Zazza, A. Palma, A. Amadei, N. Sanna, S. Tatoli and M. Aschi  On the catalytic role of structural fluctuations in enzyme reactions: computational evidence on the formation of compound 0 in horseradish peroxidase.  Faraday Discussions 145/06 (2010). 202. I. Daidone, M. Aschi, L. Zanetti-Polzi, A. Di Nola and  A. Amadei On the origin of IR spectral changes upon protein folding. Chem. Phys. Lett. 488(4-6), 213-218 (2010). 201. A. Merlino; A. Vergara; F. Sica; M. Aschi, A. Amadei; A. Di Nola and L. Mazzarella Free Energy Profile for CO Binding to Separated Chains of Human and Trematomus Newnesi Hemoglobin: Insights from MD Simulations and Perturbed Matrix Method. J. Phys. Chem. B ,  114 (20),  7002-7008 (2010). 199. D. Mastrogiovanni, M. Anselmi, A. E. Miele, G. Boumis, F. Angelucci, A. Di Nola, M. Brunori and A. Belleli Combining crystallography and molecular dynamics: the case of Schistosoma mansoni phospholipid glutathione peroxidase. Proteins: Structure, Function, and Bioinformatics  78(2), 259-270 (2010). 2009   198. Thukral L., Smith J.C. and Daidone I. Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations. J. Am. Chem. Soc. 131, 18147-18152 (2009). 197. M. D'Abramo, M. Aschi and A. Amadei Charge transfer equilibria of aqueous single stranded DNA. Phys. Chem.Chem. Phys. 11, 10614-10618 (2009). 196. M. Aschi and A. Amadei Theoretical-computational modeling of quantum vibrational states of polyatomic systems in complex environment.. IJLSS, (2009) In print. 195. A. Tarquini, P.  Marracino, F. Apollonio, M. Liberti, G. d'Inzeo, A. Amadei and A. Di Nola Theoretical and computational characterization of the thermodynamic effects of external fields in dilute ionic solutions. IJLSS, Accepted (2009). 194. A. Amadei, M. D'Alessandro, M. D'Abramo and M. Aschi Theoretical characterization of electronic states in interacting chemical systems J. Chem. Phys. 130(8),  08410 (2009). 193. Simone Tatoli, Costantino Zazza, Nico Sanna, Amedeo Palma, Massimiliano Aschi The role of Arginine 38 in horseradish peroxidase enzyme revisited: A computational investigation. Biophys. Chem. 141, 87-93 (2009). 192. Costantino Zazza , Giordano Mancini, Nico Sanna and Massimiliano Aschi  Thermodynamic features and environmental effects in a two-states molecular device under strict electrochemical control. Theor Chem. Acc., 123, 383-390 (2009). 191 M. D'Abramo, R. Caminiti, A. Di Nola and A. Amadei What can we learn by comparing experimental and theoretical-computational X-ray scattering data? J. Mol. Liq. 144(1-2), 9-12 (2009). 190 L. Zanetti-Polzi, M. Anselmi, M. D'Alessandro, A. Amadei and A. Di Nola Structural, thermodynamic and kinetic properties of Gramicidin analogue GS6 studied by molecular dynamics simulations and statistical mechanics. Biopolymers 91(12),1154-1160 (2009). 189. M. D'Abramo, M. Aschi, A. Di Nola and A. Amadei The Kinetics of Carbon Monoxide migration and binding in solvated Myoglobin as revealed by Molecular Dynamics simulations. J. Phys. Chem. B 113, 16346-16353 (2009). 2008   188. Schulz R., Krishnan M., Daidone I. and Smith J.C. Instantaneous Normal Modes and the Protein Glass Transition. Biophys. J. 96, 476-484 (2008). 187. 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. 47, 9059-9062  (2008). 186. 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 100,  188103  (2008). 185. M. Pellegrino, F. Apollonio, M. Liberti, A. Amadei, A. Di Nola and G. D'Inzeo Molecular simulations of biochemical processes in presence of a MW signal. 2008 IEEE International Symposium on Antennas and Propagation and USNC/URSI National Radio Science Meeting, APSURSI, art. no. 4619666 (2008). 184.   Celenza G, Luzi C, Aschi M, Segatore B, Setacci D, Pellegrini C, Forcella C, Amicosante G, Perilli M Natural D240G Toho-1 mutant conferring resistance to ceftazidime: biochemical characterization of CTX-M-43 . J. Antimic. Therap. 62(5), 991-997 183.   Montanari R, Saccoccia F, Scotti E, Crestani M, Godio C, Gilardi F, Loiodice F, Fracchiolla G, Laghezza A, Tortorella P, Lavecchia A, Novellino E, Mazza F, Aschi M, Pochetti G Crystal Structure of the Peroxisome Proliferator-Activated Receptor gamma (PPAR gamma) Ligand Binding Domain Complexed with a Novel Partial Agonist: A New Region of the Hydrophobic Pocket Could Be Exploited for Drug Design. J. Med. Chem. 51(24), 7768-7776 (2008). 182. D. Narzi, I. Daidone, A. Amadei and A. Di Nola Protein folding pathways revealed by essential dynamics sampling. J.Chem. Theory Comput. 4(11), 1940-1948 (2008). 181. M. Anselmi, M. Brunori, B. Vallone and A. Di Nola Molecular dynamics simulation of the Neuroglobin crystal: comparison with the simulation in solution. Biophys. J. 95, 4157-4162 (2008). 180. C. Zazza, A. Amadei, N. Sanna and M. Aschi Can a synthetic thread act as an electrochemical switchable molecular device? Chem. Comm. 29,  3399-3401 (2008). 179. Francesca Apollonio, Andrea Amadei, Micaela Liberti, Massimiliano Aschi, Monica Pellegrino, Maira D'Alessandro, Marco D'Abramo, Alfredo Di Nola, Guglielmo d'Inzeo Mixed Quantum-Classical Methods for Molecular Simulations of Biochemical Reactions with Microwave Fields: the Case Study of Myoglobin. IEEE T  Microw. Theory  56(11), 2511-2519 (2008). 178. M. D'Abramo, A. Di Nola, M. Aschi and A. Amadei Theoretical characterization of temperature and density dependence of liquid water electronic excitation energy: Comparison with recent experimental data. J. Chem. Phys. 128, 021103 (2008). 177. M. Anselmi, A. Di Nola and A. Amadei The kinetics of ligand migration in crystallized Myoglobin as revealed by molecular dynamics simulations. Biophys. J. 94, 4277-4281 (2008). 176. F. Noe', I. Daidone, J. C. Smith, A. Di Nola and A. Amadei Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation J. Phys. Chem. B, 112(35), 11155-11163 (2008). 175. A. Amadei, M. Aschi and A. Di Nola Statistical mechanical modeling of chemical reactions in condensed phase systems. In Challenges and advances in Computational Chemistry and Physics, Vol. 6, Solvation Effects on Molecules and Biomolecules, 191-213 S. Canuto ed. Springer (2008). 174. Massimiliano Aschi, Maira D'Alessandro, Monica Pellegrino, Alfredo Di Nola, Marco D'Abramo and Andrea Amadei Intramolecular charge transfer in π-conjugated oligomers: a theoretical study on the effect of temperature and oxidation state. Theor. Chem. Acc. 119(5-6), 469-476 (2008). 173. C. Zazza, A. Amadei. A. Palma, N. Sanna, S. Tatoli and M. Aschi Theoretical modelling of enzyme reactions: the thermodynamics of formation of compound 0 in horseradish peroxidase. J. Phys. Chem. B 112, 3184-3192 (2008). 172. M. D'Alessandro, A. Di Lella, M. Aschi, A. Di Nola and A. Amadei Theoretical characterization of structural and energetical properties of water clusters, by means of a simple polarizable water Hamiltonian. J. Mol. Liq.142(1), 111-117 (2008). 2007   171. J.P. Ulmschneider_ , and M. B. Ulmschneider_ Folding simulation of the TM helix of Virus Protein U in an implicit membrane model. J. Chem. Theory Comput., 3 (6), 2335 -2346, (2007). 170. A. Bozzi, C. Coccia, A. Di Giulio, A. C. Rinaldi, A. Amadei, G. Mignogna, A. Bonamore, A. Fais and M. Aschi Folding propensity and biological activity of peptides: new insights from conformational properties of a novel peptide derived from vitreoscilla haemoglobin. Biopolymers 87, 85-92 (2007). 169. Isabella Daidone_ , Martin Ulmschneider_ , Alfredo Di Nola_ , Andrea Amadei _ and Jeremy C. Smith Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. Proc. Natl. Acad. Sci. U S A. 104, 15230-15235 (2007). 168. Marco D'Abramo Statistical mechanical modelling of complex molecular systems: thermodynamic and electronic properties. PhD Thesis (2007). 167. C. Leggio, M. Anselmi, A. Di Nola, L. Galantini, A. Jover, F. Meijide, N. V. Pavel, V. H. Soto Tellini and J. V. Tato Study on the structure of host-guest supramolecular polymers. Macromolecules 40(16), 5899-5906 (2007). 166. A. Amadei, M. D'Abramo, A. Di Nola, A. Arcadi, G. Cerichelli and M. Aschi Theoretical study of intramolecular charge transfer π-conjugated oligomers. Chem. Phys. Lett. 434(4-6), 194-199 (2007). 165. A. Amadei, M. D'Abramo, I. Daidone, M. D'Alessandro, A. Di Nola and M. Aschi Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the haem carbon monoxide binding-unbinding reaction in myoglobin. Theor. Chem. Acc. 117(5-6), 637-647 (2007). 164. M. B. Ulmschneider, J. P. Ulmschneider, M.S.P. Sanson and A. Di Nola A generalized Born implicit membrane representation compared to experimental insertion free energies. Biophys. J. 92, 2338-2349 (2007). 163. M. Anselmi, M. Aschi, A. Di Nola and A. Amadei Theoretical characterization of Carbon Monoxide vibrational spectrum in Sperm Whale Myoglobin distal pocket. Biophys. J. 92, 3442-3447 (2007). 162.   M. D'Abramo, M. Aschi, F. Marinelli, A. Di Nola and A. Amadei Theoretical prediction of thermodynamic equilibrium constants of chemical reactions in water. J. Mol. Struc.-Theochem. 811(1-3), 197-201 (2007). 161. Jakob P. Ulmschneider, Martin P. Ulmschneider and Alfredo Di Nola. Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane. Proteins: Structure, Function, and Bioinformatics 69(2), 297-308 (2007). 160. M. Anselmi, M. Brunori, B. Vallone and A. Di Nola Molecular dynamics simulation of deoxy and carboxy murine Neuroglobin in water. Biophys. J. 93, 434-441 (2007). 2006   159. D. Floeck, G. Rossetti, I. Daidone, A. Amadei and A. Di Nola Aggregation of small peptides studied by Molecular Dynamics simulations. Proteins: Structure, Function, and Bioinformatics 65(4), 914-921 (2006). 158. J. Ulmschneider, M. Ulmschneider and A. Di Nola Monte Carlo versus Molecular Dynamics for all-atom polypeptide folding simulations. J. Phys. Chem. B 110(33), 16733-16742 (2006). 157. Costantino Zazza, Andrea Amadei, Nico Sanna, Andrea Grandi, Giovanni Chillemi, Alfredo Di Nola, Marco D'Abramo and Massimiliano Aschi Theoretical modeling of the valence UV spectra of 1,2,3-triazine and uracil in solution. Phys. Chem. Chem. Phys. 8, 1385-1393 (2006). 156. M. D'Abramo, M. Aschi, A. Di Nola and A. Amadei On the importance of configurational sampling in theoretical calculation of electronic properties of complex molecular systems: acetone in water. Chem. Phys. Lett. 424(4-6), 289-294 (2006). 155. M. D'Abramo, M. C. Rinaldi, A. Bozzi, G. Mignogna, A. Di Nola, A. Amadei and M. Aschi Conformational behaviour of Temporin A and Temporin L in aqueous solution: a computational/experimental study. Biopolymers, 81(3), 215-224, (2006). 154. A. Amadei, M. D'Alessandro, M. Paci, A. Di Nola and M. Aschi On the Effect of a Point Mutation on the Reactivity of CuZn Superoxide Dismutase: A Theoretical Study. J. Phys. Chem. B 110(14),7538-7544 (2006). 153. D. Floeck, S. Colacino, G. Colombo and A. Di Nola Misfolding of the Amyloid beta-peptide: A Molecular Dynamics Study. Proteins: Structure, Function, and Bioinformatics 62, 183-192 (2006). 152. M.Aschi , M. D'Abramo, F. Ramondo, I. Daidone, M. D'Alessandro, A. Di Nola and A. Amadei Theoretical modeling of chemical reactions in complex environments: the intramolecular proton transfer in aqueous malonaldehyde. J. Phys. Org. Chem. 19, 518-530 (2006). 151. M. B. Ulmschneider, M. S. P. Sansom and A. Di Nola Evaluating tilt angles of trans-membrane helices: comparison of computational and NMR techniques. Biophys. J. 90 1650-1660 ( 2006) 2005   150. D. Floeck and A. Di Nola Molecular dynamics studies of protein and peptide misfolding. The FEBS Journal 272 370 (2005) 149. Cecilia Bossa Conformational fluctuations in proteins: a molecular dynamics based study. PhD Thesis (2005). 148. Isabella Daidone Folding, misfolding and aggregation of proteins and peptides: a molecular dynamics study. PhD Thesis (2005). 147. G. Brancato, A. Di Nola, V. Barone and A. Amadei A mean field approach for molecular simulations of fluid systems. J. Chem. Phys.122, 154109 (2005). 146. M. D'Alessandro, M. D'Abramo, M. Paci and A. Amadei . Theoretical Study of the Thermodynamics of a Solvated Peptide: Contryphan Vn Physica Scripta T118,  196,  (2005). 145. I. Daidone, M. D'Abramo, A. Di Nola and A. Amadei Theoretical characterization of a-helix and β-hairpin folding kinetics. J.Am.Chem.Soc. 127(42),   14825 - 14832  (2005). 144. C. Bossa, A. Amadei, I. Daidone, M. Anselmi, M. Brunori, B. Vallone and A. Di Nola. Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and cavities dynamics. Biophys. J. 89, 465-474 (2005). 143. M. D'Alessandro, F. Marinelli, M. D'Abramo, M. Aschi, A. Di Nola and A. Amadei . Ground and excited electronic state thermodynamics of aqueous carbon monoxide: a theoretical study. J. Chem. Phys. 122, 124507 (2005). 142. M. Aschi, C. Di Teodoro, A, Amadei, D. Roccatano, F. Malatesta and L. Ottaviano Conformational and electronic properties of a microperoxidase in aqueous solution: a computational study. ChemPhysChem 6(4), 681-689 (2005). 141. A. Amadei, F. Marinelli, M. D'Abramo, M. D'Alessandro, M. Anselmi, A. Di Nola and M. Aschi Theoretical modeling of vibro-electronic quantum states in complex molecular systems: solvated carbon monoxide, a test case. J. Chem. Phys. 122, 124506 (2005). 140. M. Aschi, M. D'Abramo, C. Di Teodoro, A. Di Nola and A. Amadei Theoretical characterization of liquid water electronic excitation. ChemPhysChem. 6(1), 53-58 (2005). 139. M. D'Abramo, M. Aschi, A. Di Nola, A. Amadei Calculation of the Optical Rotatory Dispersion of solvated alanine by means oF the Perturbed Matrix Method Chem. Phys. Lett. 402, 559-563 (2005). 138. Giorgio Colombo, Isabella Daidone, Ehud Gazit, Andrea Amadei, and Alfredo Di Nola Molecular dynamics simulation of the aggregation of the core recognition motif of the islet amyloid polypeptide in explicit water. Proteins: Structure, Function, and Bioinformatics 59(3) 519-527 (2005). 137. D. Roccatano, G. Sbardella, G. Amicosante, M. Aschi, C. Bossa, A. Di Nola and F. Mazza Dynamical Aspects of  TEM-1 β-Lactamase Probed by Molecular Dynamics. J. Comp.-Aided Molecular Design 19 329-340 (2005) . 136. M. Ulmschneider, M.S.P. Sanson and A. Di Nola Properties of Integral Membrane Protein Structures: Derivation of an Implicit Membrane Potential. Proteins: Structure, Function, and Bioinformatics 59(2) 252-265 (2005). 135. M. D'Abramo, M. D'Alessandro, A. Di Nola, D. Roccatano and A. Amadei Characterization of liquid behaviour by means of local density fluctuations. J. Mol. Liq. 117, 17-21 (2005). 134. I. Daidone, A. Amadei and A. Di Nola Thermodynamic and kinetic characterization of a β-hairpin peptide in solution: An extended phase space sampling by molecular dynamics simulations in explicit water. Proteins: Structure, Function, and Bioinformatics 59(3) 510-518 (2005). 2004   133. R. Spezia, C. Zazza, A. Palma, A. Amadei and M. Aschi A DFT study of the long-lying singlet excited states of the all-trans peridinin in vacuo J. Chem. Phys. A 108, 6763-6770 (2004). 132. D. Floeck, I. Daidone and A. Di Nola . A Molecular Dynamics Study of Acylphosphatase in aggregation promoting conditions: The Influence of TFE/water solvent. Biopolymers. 75, 491 - 496 (2004) . 131. V. M. Coiro , A. Di Nola, M. A. Vanoni, M. Aschi, A. Coda , B. Curti and D. Roccatano Molecular dynamics simulation of the interaction between the complex iron-sulfur flavoprotein glutamate synthase and its substrates. Protein Sci. 13, 2979 - 2991 (2004). 130. M. D'Alessandro, M. Aschi, M. Paci, A. Di Nola and A. Amadei Theoretical modeling of enzyme reactions chemistry: the electron transfer of the reduction mechanism in CuZn Superoxide Dismutase. J. Phys. Chem. B 108(41) 16255-16260 (2004). 129. A. Amadei, D'Alessandro and M. Aschi Statistical mechanical modeling of chemical reactions in complex systems: the reaction free energy surface. J. Phys. Chem.B 108(41), 16250-16254 (2004). 128. M. Daidone, D. Roccatano and S. Hayward . Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling J. Mol. Biol. 339(3) 515-525 (2004). 127. M. D'Alessandro, M. Paci and A. Amadei Characterization of the conformational behavior of peptide Contryphan Vn: a theoretical study. Biopolymers. 74(6), 448-456 (2004). 126. D. Roccatano, A. Di Nola and A. Amadei A theoretical model for folding/unfolding thermodynamics of single domain proteins based on the quasi-Gaussian entropy theory. J. Chem. Phys. 108(18), 5756-5762 (2004). 125. M. D'Abramo, M. D'Alessandro and A. Amadei On the use of the quasi Gaussian entropy theory in the study of simulated dilute solutions J. Chem. Phys. 120, 5526-5531 (2004). 124. C. Bossa, M. Anselmi, D. Roccatano, A. Amadei, B. Vallone, M. Brunori and A. Di Nola . Extended molecular dynamics simulation of the Carbon Monoxide migration in sperm whale Myoglobin Biophys. J. 86, 3855-3862 (2004). 123. M. Aschi, C. Zazza, R. Spezia, C. Bossa, A. Di Nola, M. Paci and A. Amadei Conformational fluctuations and electronic properties in Myoglobin. J. Comput. Chem. 7, 974-984 (2004). 122. I. Daidone, F. Simona, D. Roccatano, R. A. Broglia, G. Tiana, G. Colombo and A. Di Nola β-Hairpin conformation of fibrillogenic peptides: Structure and a-β transition mechanism revealed by molecular dynamics simulations. Proteins: Structure, Function, and Genetics. 57(1), 198- 204 (2004). 2003   121. D.O. Cicero, S. Melino, M. Orsale, G. Brancato, A. Amadei, F. Forlani, S. Pagani and M. Paci Structural rearrangements of the two domains of Azotobacter vinelandii rhodanese upon sulfane sulfur release: essential molecular dynamics, N NMR relaxation and deuterium exchange on the uniformly labeled protein. Int. J.Biol. Macromol., 33, 193- 201 (2003) . 120. R. Spezia Computational Studies of the Coupling between Molecular Dynamics and Electronic Properties in Complex Systems . PhD thesis (2003). 119. A. Amadei, M. D'Abramo, C. Zazza and M. Aschi Electronic properties of Formaldehyde in water: a theoretical study. Chem. Phys. Letters, 381, 187- 193 (2003) . 118. R. Spezia, C. Nicolas, A. Boutin and R. Vuilleumier Molecular dynamics simulations of a silver atom in water: evidence for a dipolar excitonic state. Phys. Rev. Lett. 91(20), 208304 (2003). 117. I. Daidone, A. Amadei, D. Roccatano and A. Di Nola Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c. Biophys. J. 85, 2865-2871 (2003). 116. R. Spezia, M. Aschi, A. Di Nola, M. Di Valentin, D. Carbonera and A. Amadei The effect of protein conformational flexibility on the electronic properties of a chromophore. Biophys. J. 84, 2805-2813 (2003). 115. G. Colombo, G.M. De Mori and D. Roccatano Interplay between hydrophobic cluster and loop propensity in β-hairpin formation:a molecular dynamics view. Protein Sci. 12(3), 538-50 (2003). 114. M. Fioroni, K. Burger, A. E. Mark and D. Roccatano The Influence of Trifluoromethyl Groups on the Miscibility of Fluorinated Alcohols with Water: A Molecular Dynamics Simulation Study of 1,1,1-Trifluoropropan-2-ol in Aqueous Solution. J. Phys. Chem. B, 107(20), 4855-4861 (2003). 113. M. E. F. Apol and A. Amadei Mixing Distributions within the Quasi-Gaussian Entropy Theory: Multistate Thermal Equations of State Valid for Large Temperature Ranges. J. Phys.Chem. B 107(6), 1410-1422 (2003). 112. M. F. Gerini, D. Roccatano, E. Baciocchi and A. Di Nola Molecular dynamics simulation of Lignine peroxidase in solution. Biophys. J. 84, 3883-3893 (2003). 111. J. N. Harvey and M. Aschi Modelling spin-forbidden reactions: recombination of carbon monoxide with iron tetracarbonyl. Faraday Discuss. 124 (2003). 110. D. Roccatano, I. Daidone, M.-A. Ceruso, C. Bossa and A. Di Nola Selective excitation of native fluctuations during thermal unfolding simulations: horse heart cytochrome c as a case study. Biophys. J. 84,1876-1883 (2003). 109. M.-A. Ceruso, A. Grottesi and A. Di Nola Dynamic effects of mutations within two loops of cytochrome c551 from Pseudomonas aeruginosa Proteins: Structure, Function, and Genetics 50, 222-229 (2003). 2002   108. M. D'Alessandro, M. D'Abramo, G. Brancato, A. Di Nola and A. Amadei Statistical mechanics and thermodynamics of simulated ionic solutions. J. Phys.Chem. B 106 (45) 11843-11848 ( 2002). 107. R. Spezia, M. Aschi A. Di Nola and A. Amadei Extension of the Perturbed Matrix Method: application to a water molecule. Chem. Phys. Lett. 365, 450-456 (2002). 106. D. Roccatano, G. Colombo, M. Fioroni and A. E. Mark The mechanism by which 2,2,2-trifluoroethanol/water mixtures tabilize secondary structure formation in peptides: A molecular dynamics study. Proc. Natl. Acad. Sci. U S A. 99(19) 12179-84 (2002). 105. M. D'Alessandro, A. Tenenbaum and A. Amadei Coherent Dynamics in a Butane Molecule. Phys. Rev. E 66 (2002). 104. M. Aschi, D. Roccatano, F. Mazza, A. Di Nola, C. Gallina, E. Gavuzzo, G. Pochetti, M. Pieper and H. Tschesche Computational study of the catalytic domain of human neutrophil collagenase. Specific role of the S-3 and S '(3) subsites in the interaction with a phosphonate inhibitor. J. Comp.-Aided Molecular Design 16(3), 213-225 (2002). 103. A. Merlino, L. Vitagliano, M.-A. Ceruso, A. Di Nola, and L. Mazzarella Global and Local Motions in Ribonuclease A: a Molecular Dynamics Study. Biopolymers 65(4), 274-283 (2002). 102. M. Aschi, F. Mazza and A. Di Nola Cation-π interactions between ammonium ion and aromatic rings: an energy decomposition study. J. Mol. Struct. THEOCHEM 587, 177-188 (2002). 101. M. D'Alessandro, A. Tenenbaum and A. Amadei Dynamical and statistical mechanical characterization of temperature coupling algorithms J. Phys. Chem. B 106, 5050-5057 (2002). 100. A. Amadei, M. Aschi, R. Spezia and A. Di Nola A first principles polarizable water model for molecular simulations: application to water dimer. J. Mol. Liq. 101, 181-198 (2002). 99. A. Amadei, M.E.F. Apol, G. Brancato and A. Di Nola Theoretical equations of state for temperature and electro-magnetic field dependence of fluid systems, based on the quasi-Gaussian entropy theory. J. Chem. Phys. 116 (11), 4437-4449 (2002). 98. M.E.F. Apol, A. Amadei and A. Di Nola Statistical mechanics and thermodynamics of magnetic and dielectric systems based on magnetization and polarization fluctuations: application of the quasi-Gaussian entropy theory. J. Chem. Phys. 116 (11), 4426-4436 (2002). 97. A. Grottesi, M.-A. Ceruso, A. Colosimo and A. Di Nola Molecular dynamics study of a hyperthermophilic and a mesophilic Rubredoxin. Proteins: Structure, Function, and Genetics 46 (3), 287-294 (2002). 96. G. Colombo, D. Roccatano, A. E. Mark Folding and Stability of the Three-Stranded beta-sheet Peptide Betanova: Insights from Molecular Dynamics Simulations. Proteins: Structure, Function, and Genetics 46, 380-392 (2002). 2001   95. M. Fioroni, K. Burger, A. E. Mark and D. Roccatano Model of 1,1,1,3,3,3-hexafluoro-propan-2-ol for molecular dynamics simulations. J. Phys. Chem. B 105, 10967-10975 (2001). 94. D. Roccatano, A. E. Mark, S. Hayward Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation. J. Mol. Biol. 310, 1039-1053 (2001). 93. M.Aschi, A.Largo Computational study of the thermal reaction rate between S+(4S) and acetylene. Chem. Phys. 256, 251, (2001). 92. A. Amadei, B. Iacono, S. Grego, G. Chillemi, E.M.F. Apol, E. Paci, M. Delfini and A. Di Nola On the use of  the quasi-Gaussian entropy theory in systems of polyatomic flexible molecules. J. Phys Chem., 105(9), 1834-1844 (2001). 91. M. Aschi, R. Spezia, A. Di Nola and A. Amadei A first-principle method to model perturbed electronic wavefunctions: the effect of an external homogeneous field. Chem. Phys. Lett. 344(3-4), 374-380 (2001). 2000   90. M. Fioroni, K. Bruger, A. E. Mark, D. Roccatano A new 2,2,2-trifluoroethanol model for molecular dynamics simulations. J. Phys. Chem. B, 104 (51), 12347-12354 (2000). 89. A. Amadei, G. Chillemi, M. Ceruso, A. Grottesi and A. Di Nola Molecular dynamics simulations with constrained roto-translational motions: theoretical basis and statistical mechanics consistency. J. Chem. Phys.,   112(1), 9-23 (2000). 88. M. Aschi, F. Grandinetti FBeNg+. Suitable cations for the lightest noble gases stable salts? Angewandte Chemie , 39, 1690, (2000). 87. M.Aschi, F.Grandinetti The ionisation potential of NF3. A G3 study. J. Mol. Structure (THEOCHEM), 497, 205, (2000). 86. M. Aschi, F. Grandinetti Spin-forbidden F+ transfer between 2NF+ and CO: a computational study on the detailed mechanistic aspects Int. J.Mass Spectrom., 201, 151, (2000). 85. M. Aschi, M. Attina', F. Cacace, A. Cartoni and F. Pepi Mass Spectrometric and Computational Study of Protonated Peroxynitric Acid. Int. J. Mass Spectrom., 195, 1, (2000). 84. P.R.P.de Moraes, H. V. Linnert, M.Aschi, J.M.Riveros Experimental and Theoretical Characterization of Long-Lived Triplet State CH3CH2S+ Cations. J. Am. Chem. Soc., 122, 10133, (2000). 83. M.Aschi, F.Grandinetti Unimolecular Loss of HF by Simple Inorganic Ions: a Dynamic Reaction Coordinate Study. Eur. J. Mass Spectr., 6, 31, (2000). 1999   82. M. F. E. Apol, A. Amadei, H. J. C. Berendsen and A. Di Nola Derivation of thermal equations of state for quantum systems using the quasi-Gaussian entropy theory. J. Chem .Phys.,  111(10), 4431-4441 (1999). 81. M. A. Ceruso, A. Grottesi and A. Di Nola Effects of core packing on the structure, function and dynamics of a four-helix-bundle protein ROP. Proteins: Structure, Function, and Genetics, 36(4), 436-446 (1999). 80. D. Roccatano, A. Amadei, A. Di Nola and H. J. C. Berendsen A Molecular dynamics study of the 41-56 beta-hairpin from Protein G B1 domain. Proteins Sci., 8(10),  2130-2143 (1999). 79. A. Amadei, M. E. F. Apol,  G. Chillemi, H.J. C. Berendsen and A. Di Nola Derivation of a general fluid equation of state based on the quasi-Gaussian entropy theory: application to the Lennard-Jones fluid. Molec. Phys. 96(10), 1469-1490 (1999). 78. M. Mangoni, D. Roccatano and A. Di Nola Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulations. Proteins: Structure, Function, and Genetics, 35(2), 153-162 (1999). 77. M-A. Ceruso, A. Amadei and A. Di Nola Mechanics and dynamics of B1 domain of protein G: role of packing and surface hydrophobic residues. Protein Sci., 8(1), 147-160 (1999). 76. A. Amadei, M.A. Ceruso and A. Di Nola On the convergence of the coordinates basis set obtained by the essential dynamics of proteins molecular dynamics simulations. Proteins: Structure, Function, and Genetics., 36 , 419-424 (1999). 75. A. Amadei, B.L. de Groot, M.A. Ceruso, M. Paci, A. Di Nola and H.J.C. Berendsen A  kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins: Structure, Function, and Genetics,. 35, 283-292 (1999). 74. J. N. Harvey, M. Aschi. Spin-Forbidden Dehydrogenation of methoxy cation: a statistical view. Physical Chemistry Chemical Physics, 1, 5555, (1999). 73. M. Diefenbach, M. Broenstrup, M. Aschi, D. Schroeder and H. Schwarz HCN-synthesis from methane and ammonia: mechanism of Pt+ mediated Carbon-Nitrogen coupling. J. Am.Chem. Soc., 121, 10614, (1999). 72. S. Barè, V.M. Coiro, A. Scaloni, A. Di Nola, M. Paci, A.L. Segre and A. Ballio Conformations in solution of the fuscopeptins, phytotoxic metabolites of Pseudomonas fuscovaginae. Eur. J. Biochem., 266, 484-492 (1999). 71. M. Aschi, F. Grandinetti Unimolecular decay of the thiomethoxy cation, CH3S+: A computational study on the detailed mechanistic aspects. J. Chem. Phys., 111, 6759-6768, (1999). 70. M. Aschi, J. N. Harvey Spin Isomerisation of p-Substituted Phenyl Cations. J. Chem. Soc. PerkinII 2, 1059 (1999). 69. M. Aschi, F. Grandinetti Carbonilation of Ammonia by Gaseous FCO+. A G2 and RRKM Study. Int. J. Mass Spectrom., 184, 89, (1999). 1998   68. M. Aschi, F. Grandinetti, V. Vinciguerra Mechanistic Aspects of F+ Transfer Reactions: a Model Study in the Gas Phase. Chemistry European Journal, 11, 2366, (1998). 67. M. Aschi, M. Attina', F. Cacace Evaluation of the Lifetime of Gaseous Ion Neutral Complexes. 2.The Rate of Isotopic Scrambling within Ethyl Ions as an Internal Clock. Chemistry European Journal, 4(8), 1535-1541 (1998). 66. M. Aschi, M. Attina', F. Cacace, G. D'Arcangelo Evaluation of the Lifetime of Gaseous Ion Neutral Complexes. 1.A Chemical Activation Study. J. Am. Chem. Soc., 120, 3982, (1998). 65. M. Aschi, M. Bronstrup, M. Diefenbach, J. N. Harvey, D. Schroeder, H. Schwarz A Gas Phase Model for the Pt+-catalyzed Coupling of Methane and Ammonia. Angew. Chem. Int. Ed. Engl., 37, 829, (1998). 64. D. Schroeder, J. N. Harvey, M. Aschi, H. Schwarz Experimental and Computational Study of Neutral Xenon Halides (XeX) in the Gas Phase for X=F, Cl, Br and I. J. Chem. Phys., 108 (20), 8446-8455, (1998). 63. J. N. Harvey, M. Aschi, H. Schwarz, W. Koch The Singlet and Triplet State of Phenyl Cation. A Hybrid Approach for Locating Minimum Energy Crossing Points between Non-interacting Potential Energy Surfaces. Theor. Chem. Acc. (Theor. Chim. Acta), 99, 95, (1998). 62. M. Aschi, J. N. Harvey, C. A. Schalley, D. Schroeder, H. Schwarz Reappraisal of the Spin Forbidden Unimolecular Chemistry of the Methoxy Cation. J. Chem. Soc. Chem. Commun., 531, (1998). 61. M. Aschi, M. Attina', F. Cacace, R. Cipollini, F. Pepi Gas Phase Positive and Negative Ion Chemistry of Methyl Hydroperoxide. Inorg. Chim. Acta, 275/276, 192, (1998). 60. M. Aschi, M. Attina', G. D'Arcangelo The Role of the Lifetime of Ion-Neutral Complexes in Gas Phase Electrophilic Aromatic Substitution. Chem. Phys. Lett., 283, 307, (1998). 59. A. Amadei  Theoretical models for fluid thermodynamics based on the  uasi-Gaussian entropy theory. PhD Thesis University of Groningen, (1998). 58. L. D. Creveld, A. Amadei, R. C. van Schaik, H. A. M. Pepermans, J. de Vlieg and H. J. C. Berendsen Identification of functional and unfolding movements of cutinase as obtained from molecular dynamics computer simulations. Proteins: Structure, Function, and Genetics,  33, 253-264 (1998). 57. B. L. de Groot, S. Hayward, D. M. F. van Aalten, A. Amadei and . J. C. Berendsen Domain motions in Bacteriophage T4 Lysozyme; a comparison between molecular dynamics and crystallographic data. Proteins: Structure, Function, and Genetics,  31,  116-127 (1998). 56. M. E. F. Apol, A. Amadei and H. J. C. Berendsen On the use of the quasi-Gaussian entropy theory in non-canonical ensembles. II. Density dependence of thermodynamic properties. J.Chem. Phys., 109, 3017-3027 (1998). 55. A. Amadei, M. E. F. Apol and H. J. C. Berendsen On the use of the quasi-Gaussian entropy theory in non-canonical ensembles. I. Temperature dependence of thermodynamic properties. J. Chem. Phys., 109(8), 3004-3016 (1998). 54. D. Roccatano, A. Amadei, M. E. F. Apol, A. Di Nola and H.J. C. Berendsen Application of the quasi-Gaussian entropy theory to molecular dynamics simulations of Lennard-Jones fluids. J. Chem Phys. 109, 6358-6363 (1998). 53. V. M. Coiro, A. Ballio, G. Veglia, A.L. Segre, M.  Paci and A. Di Nola Solution conformation of the Pseudomonas syringae MSU 16H phytotoxic lipodepsipeptide pseudomycin A by computer simulations using distance geometry and molecular dynamics from NMR data. Eur. J. Biochem.  257, 443-448 (1998). 52. M. Cirilli, V. M. Coiro, A. Di Nola and F. Mazza Relationship between conformation and geometry as evidenced by molecular dynamics simulation of Ca,a dialkylated glycines. Biopolymers, 46, 239-244 (1998). 51. A.  Di Nola and A. T.  Brünger Free energy calculations in globular proteins: methods to reduce errors. J. Comput. Chem. 18 (7), 1229-1240 (1998). 50. D. Roccatano, R. Bizzarri, G. Chillemi, N. Sanna and A. Di Nola Development of a parallel molecular dynamics code on SIMD computers: an algorithm for the use of pair list criterion. J. Comput. Chem. 18(7), 685-694 (1998). 49. D. Roccatano; H.J.C. Berendsen; P. D'Angelo Assessment of the validity of intermolecular potential models used in Molecular Dynamics simulations by extended x-ray absorption fine structure spectroscopy: A case study Sr2+ in methanol solution. J. Chem. Phys., 108(22), 9487-9497 (1998). 1997   48. D. M. F. van Aalten, D. A. Conn, B. L. de Groot, J. B. C. Findlay, H. J. C. Berendsen and A. Amadei Protein dynamics derived from clusters of crystal structures. Biophys. J.,  73,  2891-2896 (1997). 47. A. Amadei, M. E. F. Apol and H. J. C. Berendsen Extensions of the quasi-Gaussian entropy theory. J. Chem. Phys., 106, 1893-1912 (1997). 46. B. L. de Groot, D. M. F. van Aalten, R. M. Scheek, A. Amadei, G. Vriend and H. J. C. Berendsen Prediction of protein conformational freedom from distance constraints. Proteins: Structure, Function, and Genetics,   29,  240-251 (1997). 45. G. Chillemi, M. Falconi, A. Amadei, G. Zimatore, A. Desideri and  A. Di Nola The essential dynamics of Cu, Zn superoxide dismutase: suggestion of intersubunit  ommunication. Biophys. J.,  73,  1007-1018 (1997). 44. D. M. F. van Aalten, B. L. de Groot, H. J. C. Berendsen,  J. B. C. Findlay and A. Amadei A comparison of techniques for calculating protein essential dynamics. J. Comp. Chem.,  18,  169-181 (1997). 43. M. Aschi, F. Cacace, A. Troiani Probing Gaseous Ion-Molecule Complexes with Chiral Agents: the Reaction of Arenium Ions with R-(-)-s-Butylchloride. Angew. Chem. Int. Ed. Engl., 36, 83, (1997). 42. M. Aschi, F. Grandinetti Gaseous Protonated Nitrosamide. A G2 Computational Study on the Structure, Stability and Interconversion of the Protonated Isomers. Chem. Phys. Lett., 267, 98, (1997). 1996   41. P. D'Angelo; N.V. Pavel; D. Roccatano; H.F. Nolting Multielectron excitations at the L-edges of barium in aqueous solution. Phys. Rev. B ,  54, 12129-12138 (1996). 40. M.Aschi, B.Chiavarino, M. E. Crestoni, S. Fornarini Structure and Reactivity of Protonated Trifluoro Toluene in the Gas Phase. A Combined FT-ICR, Radiolytic and Ab Initio MO Study. J. Phys. Chem., 100, 19859, (1996). 39. M. Aschi, F. Cacace, G. de Petris, F. Pepi Gas Phase Proton Affinity of Nitric Acid and its Esters. A Mass Spectrometric and ab Initio Study on the Existence and the Relative Stability of Two Isomers of Protonated Ethyl Nitrate. J. Phys. Chem., 100, 16522, (1996). 38. M. Aschi, F.Grandinetti Protonated methyl nitrite. A theoretical investigation on the structure and stability of (MeO-NO)H+ and the proton affinity of RO-NO (R = H, Me) Chem. Phys. Lett., 258, 123, (1996). 37. M.  D'Alagni,  M.  Delfini,  A.  Di Nola,  M.  Eisenberg,  M.  Paci,  L. G.  Roda and G.  Veglia Conformational study of Met-enkephalin-Arg6-Phe7 in the presence of phosphatidylserine vesicles. Eur.  J.  Biochem. 240, 540-549 (1996). 36. P.  D'Angelo,  A.  Di Nola,  M.  Mangoni and V.  Pavel An extended x-ray absorption fine structure study by employing molecular dynamics simulations: bromine anion in methoanolic solution. J. Chem Phys. 104(5), 1779-90, (1996). 35. A. Di Nola and A. Amadei Simulazioni di dinamica molecolare: principi, applicazioni, prospettive e limiti. In Acta della 26ma scuola della societa' italiana di cristallografia. pp. 85-110. Perugia (1996). 34. B. L. de Groot, D. M. F. van Aalten, A. Amadei and H. J. C. Berendsen The consistency of large concerted motions in proteins in  molecular dynamics simulations.  Biophys. J.,  71, 1707-1713 (1996). 33. B. L. de Groot, A. Amadei, R. M. Scheek, N. A. J. van Nuland and  H. J. C. Berendsen An extended sampling of the configurational space of HPr E. coli. Proteins: Structure, Function, and Genetic,  26,  314-322 (1996). 32. B. L. de Groot, A. Amadei, D. M. F. van Aalten and H. J. C. Berendsen Towards an exhausive sampling of the configurational spaces of the two forms of the peptide hormone Guanylin. J. Biomolec. Struct. and Dyn.,  13,  741-751 (1996). 31. A. Amadei, D. Roccatano, M. E. F. Apol, H. J. C. Berendsen and  A. Di Nola Prediction of the liquid-vapor equilibrium pressure using the quasi-Gaussian entropy theory. J. Chem. Phys., 105, 7022-7025 (1996). 30. M. E. F. Apol, A. Amadei and H. J. C. Berendsen Derivation of a thermodynamic closure relation in the isothermal-isobaric ensemble using the quasi-Gaussian entropy theory. Chem. Phys. Lett., 256, 172-178 (1996). 29. M. E. F. Apol, A. Amadei and H. J. C. Berendsen Application of the quasi-Gaussian entropy theory to the calculation of thermodynamic properties of water and methane in the liquid and gas phase. J. Chem. Phys., 104, 6665-6678 (1996). 28. A. Amadei, M. E. F. Apol, A. Di Nola and H. J. C. Berendsen The quasi-Gaussian entropy theory: free energy calculations based on the potential energy distribution. J. Chem. Phys., 104(4), 1560-1574 (1996). 27. A. Amadei, A. B. M. Linssen, B. L. de Groot, D. M. F. van Aalten and H. J. C. Berendsen An efficient method for sampling the essential subspace of  proteins. Biomolec. Struct. and Dyn.,  13,  615-625 (1996). 26. D. M. F. van Aalten, A. Amadei, R. Bywater, J. B. C. Findlay,  H. J. C. Berendsen, C. Sander and P. F. W. Stouten A comparison of structural and dynamic properties of different simulation methods applied to SH3. Biophys. J.,  70,  684-692 (1996). 25. Amadei and B. Vallone Identification of a pattern in protein structure based on energetical and statistical considerations. Proteins: Structure, Function, and Genetics, 24,  35-50 (1996). 1995   24. M. F. van Aalten, J. B. C. Findlay, A. Amadei and H. J. C. Berendsen Essential dynamics of the cellular Retinol-binding protein: evidence for ligand induced conformational changes. Protein Eng.,  8,  1129-1136 (1995). 23. M. F. van Aalten, A. Amadei, A. B. M. Linssen, V. G. H. Eijsink, G. Vriend and H. J. C. Berendsen. The essential dynamics of Thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water. Proteins: Structure, Function, and Genetics,.  22, 45-54 (1995). 22. M. Scheek, N. A. J. van Nuland, B. L. de Groot and A. Amadei Structure from NMR and moelcular dynamics: distance  restraining inhibits motion in the essential subspace. J. Biomolec. NMR,  6, 106-111 (1995). 21. Amadei, A. B. M. Linssen, B. L. de Groot and H. J. C. Berendsen Essential degrees of freedom of proteins. In Modelling of biomolecular structures and mechanisms, A. Pullmann et al. (editors), Kluwer, Holland, 85-93 (1995). 20. A.  Ballio,  F.  Bossa,  A.  Di Nola,  C.  Manetti,  M.  Paci,  A.  Scaloni and A. L. Segre Solution conformation of the Pseudomonas syringae pv. syringae phytotoxic lipodepsipeptide syringopeptin 25-A. Two-dimensional NMR, distance geometry and molecular dynamics. Eur. J. Biochem.  234, 747-758, (1995). 19. P.  D'Angelo,  A.  Di Nola,  E.  Giglio,  M.  Mangoni and N. V.  Pavel EXAFS study of micelar aggregates of bile acid rubidium salts. J.  Phys.  Chem.  99, 5471-80,  (1995). 18. A.  Di Nola,  E.  Gavuzzo,  F.  Mazza and G.  Pochetti Internal β-turn hydration: crystallographic evidence and Molecular Dynamics simulation. J. Phys. Chem. 99, 9625-9631 (1995). 17. M.Aschi, M.Attina', F.Cacace Aromatic Substitution in the Complexes Formed upon Addition of Gaseous Arenium Ions to Proelectrophiles. A FT-ICR Study. Res. Chem. Int., 117, 12832, (1995). 16. M.Aschi, M.Attina', F.Cacace An Alternative Route to Electrophilic Substitution. J. Am. Chem. Soc., 117, 12832, (1995). 15. M.Aschi, M.Attina', F.Cacace The Crafts-Friedel Reaction: Aromatic Alkylation within the Complex Formed upon Addition of a Gaseous Arenium Ion to an Olefin. Angew. Chem. Int. Ed. Engl., 34, 1589, (1995). 14. F.Angelelli, M.Aschi, F.Cacace, F.Pepi, G.de Petris Gas Phase Reactivity of Hydroxylamine Toward Charged Electrophiles. A Mass Spectrometric and Computational Study of the Protonation and Methylation of NH2OH. J. Phys. Chem., 99, 6551, (1995). 1994   13. M.Aschi, M.Attina', F.Cacace, A.Ricci Experimental Study on the Mechanism of Gas Phase Aromatic Nitration by Protonated Methyl Nitrate. J. Am. Chem. Soc., 116, 9535, (1994). 12. M.Aschi, M.Attina', A.Ricci Trimethylsilylazide, an Efficient Trap for Gaseous Carbenium Ions. The azide-clock in the Gas Phase. Int. J. Mass Spectrom. Ion Processes, 139, 59, (1994). 11. M.Aschi, F.Cacace, F.Grandinetti, F.Pepi Gaseous Protonated Nitrosyl Fluoride. Experimental and Theoretical Characterization of Two Distingushable Isomers and Evaluation of The Barrier for Their Interconversion. J. Phys. Chem., 98, 2713, (1994). 10. M.Aschi, F.Grandinetti, F.Pepi The addition of NF2+ to H2O as a route to gaseous protonated F2NOH. Int. J.Mass Spectrom.Ion Processes, 130 , 117, (1994). 9. P.  D'Angelo,  A.  Di Nola,  A.  Filipponi,  N. V.  Pavel and D.  Roccatano An extended x-ray absorption fine structure study of aqueous solutions by employing molecular dynamics simulations. J.  Chem.  Phys.  100(2),  985-994,  (1994). 8. A.  Di Nola,  G.  Fabrizi,  D.  Lamba and A. L.  Segre Solution conformation of a pectic acid fragment by 1H NMR and molecular dynamics. Biopolymers, 34,  457-462 (1994). 7. A.  Ballio,  A.  Collina,  A.  Di Nola,  C.  Manetti,  M.  Paci and A. L.  Segre Determination of structure and conformation in solution of Syringotoxin,  a ipodepsipeptide from Pseudomonas Syringae pv. syringae by 2D NMR and molecular dynamics. Structural Chemistry,   5,  43-50 (1994). 6. A.  Di Nola,  D.  Roccatano,  H. J. C.  Berendsen Molecular dynamics simulation of the docking of substrates to proteins. Proteins: Structure, Function, and Genetics, 19, 174-182 (1994). 1993   5. G. Pagani Zecchini, M. Paglialunga Paradisi, I. Torrini, G. Lucente, E. Gavuzzo, F. Mazza, G. Pochetti, M. Paci, M. Sette and A. Di Nola, G.  Veglia,  S. Spisani and S. Traniello Synthesis, conformation, and activity of HCO-Met-delta Z Leu-Phe-OMe, an active analogue of chemotactic N-formyltripeptides. Biopolymers 33 (3), 437 (1993). 4. Amadei, A. B. M. Linssen and H. J. C. Berendsen Essential dynamics of proteins. Proteins: Structure, Function, and Genetics,  17, 412-425 (1993) 3. E. Brosio, M. Delfini, A. Di Nola, A. D'Ubaldo and C. Lintas 1H and 23Na NMR relaxation times studiy of pectin solutions and gels. Cell.  Mol.  Biol. ,   6, 583-588,  (1993). 2. E.  Brosio,  A.  Di Nola and B.  Verzegnassi NMR study of seed hydration: effect of pH and ionic strength on water uptake of soaked cowpeas. Cell.  Mol.  Biol. ,  39,  193-198,  (1993). 1. G.  Pagani Zecchini,  M.  Paglialunga Paradisi,  I.  Torrini,  G. Lucente,  E. Gavuzzo,  F. Mazza,  G.  Pochetti,  M.  Paci,  M.  Sette, A.  Di Nola, G.  Veglia,  S.Spisani and S. Traniello Synthesis,  conformation and activity of For-Met-DzLeu-Phe-OMe,  an active analog of chemotactic N-Formyltripeptides. Biopolymers, 33,  437-451 (1993).