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Nome: Andrea Amadei Data e luogo di nascita: 14 Gennaio 1966, Roma. Posizione attuale: Ricercatore (confermato) di Chimica Fisica (CHIM02) presso il Dipartimento di Chimica dell'Università di Roma "Tor Vergata". Studi: Dottorato di Ricerca (Ph.D.) in Chimica Fisica teorica (Università di Groningen, 1998), Laurea in Scienze Biologiche, indirizzo di Biologia Molecolare (Università di Roma "La Sapienza", 1990). Borse e contratti: Visiting Professor presso il Barcelona Supercomputer Center (BSC) (Prof. M. Orozco 2008) Post Dottorato presso l'Università di Roma "La Sapienza" Dipartimento di Chimica (Prof. A. Di Nola 1998-2000) Research Fellow e dottorando presso l'Università di Groningen (NL)-Dipartimento di Chimica Fisica Biologica (Prof. H.J.C. Berendsen 1992-1998) Attività didattica: a partire dal 2001 il Dr. Amadei ha svolto attività didattica insegnando Biofisica Molecolare (Università di Roma "Tor Vergata") e Meccanica e Dinamica Molecolare (Università di Roma "La Sapienza"). Attualmente il Dr. Amadei insegna Chimica Teorica per gli studenti di chimica dell'Università di Roma "Tor Vergata". Attività di ricerca: Il Dr. Amadei è autore di oltre 110 publicazioni (in massima parte articoli su importanti riviste scientifiche internazionali) che spesso hanno avuto un forte impatto scientifico. L'attività scientifica del Dr Amadei è dedicata allo studio teorico-computazionale dei sistemi molecolari complessi (dai liquidi alle macromolecole biologiche) finalizzato alla razionalizzazione e caratterizzazione dei processi classici e quantistici, coinvolgendo lo sviluppo di modelli teorici e metodi computazionali originali. Di seguito sono brevemente riassunti i principali risultati ottenuti dal Dr. Amadei, riportando specificamente i suoi contributi allo sviluppo di modelli e metodi per la chimica teorica e computazionale. 1) Dinamica Essenziale Il metodo della Dinamica Essenziale (ED) si basa su l'uso dell'analisi multivariata delle fluttuazioni posizionali atomiche ottenute dalle simulazioni di Dinamica Molecolare e fornisce un mezzo molto efficace per identificare i gradi di liberta' "essenziali" nelle macromolecole biologiche, ovvero quelle coordinate generalizzate interne responsabili delle transizioni conformazionali principali. Tale metodo ha fornito importanti informazioni sulle transizioni conformazionali biologicamente significative e recentemente ha reso possibile una modellizzazione quantitativa della termodinamica e cinetica di denaturazione-rinaturazione dei peptidi. 2) La teoria dell'entropia quasi-Gaussiana La teoria dell'entropia quasi-Gaussiana (QGE) e' essenzialmente una estensione della teoria delle fluttuazioni di Meccanica Statistica, in grado di fornire dei modelli rigorosi per la termodinamica dello stato condensato. Tale approccio teorico, basato sulla modellizzazione delle distribuzioni di probabilità per le fluttuazioni di proprietà meccaniche significative (per esempio l'energia), si e' dimostrato molto accurato ed efficiente per lo studio di una grande varietà di sistemi (in stato fluido-liquido e solido), fornendo uno strumento davvero potente, in combinazione con la Dinamica Molecolare, per ottenere le proprietà molari parziali in soluzione come per descrivere la termodinamica di proteine e peptidi. 3) Dinamica Molecolare in presenza di vincoli di roto-traslazione Nelle simulazioni di Dinamica Molecolare di macromolecole come per effettuare calcoli su molecole più semplici immerse in ambienti complessi, può essere importante simulare la molecola centrale (di solito il soluto) in presenza di vincoli (ideali) per le roto-traslazioni (ovvero le equazioni del moto sono definite sulla superficie di vincolo). Il Dr. Amadei ha sviluppato una tale procedura mostrando che se l'algoritmo e' correttamente implementato la traiettoria di Dinamica Molecolare ottenuta in presenza dei vincoli e' pienamente consistente dal punta di vista meccanico statistico. 4) Il Metodo della Matrice Perturbata} Il Metodo della Matrice Perturbata (PMM), basato su i principi primi della Meccanica Quantistica, e' una metodologia mista classico-quantistica finalizzata alla valutazione delle proprietà elettroniche di un centro quantistico immerso in un ambiente molecolare complesso. Ciò e' reso possibile attraverso la descrizione esplicita dell'accoppiamento tra i moti atomici e molecolari classici, ottenuti dalla Dinamica Molecolare, con le proprietà elettroniche di interesse per mezzo della matrice Hamiltoniana perturbata del sistema quantistico considerato. Attraverso la diagonalizzazione della matrice Hamiltoniana si possono ottenere tutte le proprietà quantistiche del sistema interagente in funzione del tempo (ovvero in funzione delle configurazioni fornite dalla traiettoria di Dinamica Molecolare). Tale metodologia teorica, usata con successo per riprodurre le eccitazioni elettroniche e vibrazionali di molecole in soluzione e cromofori in proteine, e' stata estesa per lo studio delle reazioni chimiche in sistemi complessi come le reazioni nei liquidi e in proteina

Name: Andrea Amadei Date and place of birth: 14th of January 1966, Rome Italy. Present position: senior Research Scientist (CHIM02-Physical Chemistry) at the Dep. of Chemistry of the University of Rome "Tor Vergata". Education: Ph.D in theoretical Physical Chemistry (1998 University of Groningen, NL), Degree in Molecular Biology (1992 University of Rome "La Sapienza"). Fellowships: Visiting Professor at the Barcelona Supercomputer Center (BSC) (Prof. M. Orozco 2008) Post Doctoral position at the University of Rome "La Sapienza"-Dept. of Chemistry (A. Di Nola 1998-2000) Research Fellow and Ph.D student at the University of Groningen (NL)-Dept. of Biophysical Chemistry (H.J.C. Berendsen 1992-1998). Teaching: Since 2001 Dr. Amadei has been involved in didactical activity teaching Molecular Biophysics (University of Rome "Tor Vergata) and Molecular Mechanics and Dynamics (University of Rome "La Sapienza"). Presently Dr. Amadei teaches Theoretical Chemistry for the Chemistry students of the University of Rome "Tor Vergata". Research activity: Dr. Amadei authored more than 110 publications (mostly articles published in top international scientific journals) which often had an important scientific impact. Dr. Amadei research activity has been devoted to the theoretical-computational study of complex atomic-molecular systems (ranging from liquids and solutions to biological macromolecules) aiming to rationalize and characterize both classical and quantum mechanical processes and involving the development of original theoretical models and computational methods. Below, a brief outline of Dr. Amadei main scientific achievements is given, specifically reporting his contributions to the development of models and methods to be used in theoretical and computational chemistry. 1) Essential Dynamics The Essential Dynamics (ED) method is based on the use of multivariate analysis for atomic positional fluctuations as obtained by Molecular Dynamics (MD) simulations, and provides a very powerful tool to identify the "essential" degrees of freedom in biomacromolecules, i.e. those generalized internal degrees of freedom responsible of the main conformational transitions. Such an approach is now widely used as a standard method in many molecular simulation programs including its extension for enhancing MD to sample large conformational changes. The combined use of MD simulations and ED method provided valuable information on functional protein conformational transitions and recently an efficient modelization of peptide folding-unfolding thermodynamics and kinetics. 2) The quasi-Gaussian entropy theory The quasi-Gaussian entropy (QGE) theory is essentially an extension of the statistical mechanical fluctuation theory, providing rigorous models for condensed phase thermodynamics. Such a theoretical approach, based on modeling the fluctuation distributions of relevant mechanical properties (e.g. the energy), proved to be very accurate and efficient for a wide range of systems (from fluid-liquid to solid) and it provided a very powerful tool to obtain, in combination with MD simulations, partial molar properties in solutions as well as to describe the thermodynamics of protein folding and solvated peptides. 3) Molecular Dynamics with roto-translational constraints In MD simulations of large and complex macromolecules as well as for calculations on simpler molecules embedded in a complex environment, it can be of interest to simulate the central molecule with roto-translational constraints (i.e. the equations of motions are defined within the corresponding constraints surface). Dr. Amadei developed such a procedure, showing that if the algorithm is properly made the corresponding constrained MD simulation is statistical mechanically fully consistent. 4) Perturbed Matrix Method The Perturbed Matrix Method (PMM), based on Quantum Mechanics first principles, is a mixed quantum-classical method aimed to obtain electronic properties of a "quantum center" embedded in a complex molecular environment. This is accomplished by evaluating the coupling between the classical atomic and molecular motions, as obtained by MD simulations, with the electronic properties of interest by means of constructing the perturbed Hamiltonian matrix of the quantum system. Hence, by diagonalization of such a matrix any perturbed quantum property is obtained as a function of time (i.e. as a function of the trajectory configuration). Such a theoretical method, which has been used to succesfully reproduce electronic and vibrational excitations of solvated molecules and chromophores in proteins, was extended for studying chemical reactions in complex systems, such as chemical reactions in liquids and biochemical reactions in proteins.

a:113:{i:0;a:14:{s:9:"citazione";s:156:"Biswas, A.D., Barone, V., Amadei, A., & Daidone, I. (2020). Length-scale dependence of protein hydration-shell density. PHYSICAL CHEMISTRY CHEMICAL PHYSICS.";s:4:"data";s:10:"2020-03-25";s:2:"id";s:20:"PUBBLICAZIONE_385256";s:6:"handle";s:11:"2108/243538";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";s:1345:"Here we present a computational approach based on molecular dynamics (MD) simulation to study the dependence of the protein hydration-shell density on the size of the protein molecule. The hydration-shell density of eighteen different proteins, differing in size, shape and function (eight of them are antifreeze proteins), is calculated. The results obtained show that an increase in the hydration-shell density, relative to that of the bulk, is observed (in the range of 4-14%) for all studied proteins and that this increment strongly correlates with the protein size. In particular, a decrease in the density increment is observed for decreasing protein size. A simple model is proposed in which the basic idea is to approximate the protein molecule as an effective ellipsoid and to partition the relevant parameters, i.e. the solvent-accessible volume and the corresponding solvent density, into two regions: inside and outside the effective protein ellipsoid. It is found that, within the model developed here, almost all of the hydration-density increase is located inside the protein ellipsoid, basically corresponding to pockets within, or at the surface of the protein molecule. The observed decrease in the density increment is caused by the protein size only and no difference is found between antifreeze and non-antifreeze proteins.";s:9:"metadata5";s:58:"Length-scale dependence of protein hydration-shell density";s:9:"metadata6";s:44:"Biswas, AD; Barone, V; Amadei, A; Daidone, I";s:9:"metadata7";s:18:"10.1039/c9cp06214a";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:1;a:14:{s:9:"citazione";s:235:"Vieira Pinto, S.M., Tasinato, N., Barone, V., Amadei, A., Zanetti-Polzi, L., & Daidone, I. (2020). Modeling amino-acid side chain infrared spectra: The case of carboxylic residues. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 22(5), 3008-3016.";s:4:"data";s:4:"2020";s:2:"id";s:20:"PUBBLICAZIONE_385258";s:6:"handle";s:11:"2108/243540";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:127:"Amino Acids; Aspartic Acid; Glutamic Acid; Proteins; Quantum Theory; Molecular Dynamics Simulation; Spectrophotometry, Infrared";s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";s:1547:"Infrared (IR) spectroscopy is commonly utilized for the investigation of protein structures and protein-mediated processes. While the amide I band provides information on protein secondary structures, amino acid side chains are used as IR probes for the investigation of protein reactions, such as proton pumping in rhodopsins. In this work, we calculate the IR spectra of the solvated aspartic acid, with both zwitterionic and protonated backbones, and of a capped form, i.e. mimicking the aspartic acid residue in proteins, by means of molecular dynamics (MD) simulations and the perturbed matrix method (PMM). This methodology has already proved its good modeling capabilities for the amide I mode and is here extended to the treatment of protein side chains. The computed side chain vibrational signal is in very good agreement with the experimental one, well reproducing both the peak frequency position and the bandwidth. In addition, the MD-PMM approach proposed here is able to reproduce the small frequency shift (5-10 cm-1) experimentally observed between the protonated and zwitterionic forms, showing that such a shift depends on the excitonic coupling between the modes localized on the side chain and on the backbone in the protonated form. The spectrum of the capped form, in which the amide I band is also calculated, agrees well with the corresponding experimental spectrum. The reliable calculation of the vibrational bands of carboxyl-containing side chains provides a useful tool for the interpretation of experimental spectra.";s:9:"metadata5";s:80:"Modeling amino-acid side chain infrared spectra: The case of carboxylic residues";s:9:"metadata6";s:81:"Vieira Pinto, SM; Tasinato, N; Barone, V; Amadei, A; Zanetti-Polzi, L; Daidone, I";s:9:"metadata7";s:18:"10.1039/c9cp04774c";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:2;a:14:{s:9:"citazione";s:152:"Amadei, A., & Aschi, M. (2019). Modelling vibrational relaxation in complex molecular systems. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 21(36), 20003-20017.";s:4:"data";s:4:"2019";s:2:"id";s:20:"PUBBLICAZIONE_385149";s:6:"handle";s:11:"2108/243436";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";N;s:9:"metadata5";s:61:"Modelling vibrational relaxation in complex molecular systems";s:9:"metadata6";s:19:"Amadei, A; Aschi, M";s:9:"metadata7";s:18:"10.1039/c9cp03379c";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:3;a:14:{s:9:"citazione";s:251:"D'Abramo, M., Del Galdo, S., & Amadei, A. (2019). Theoretical-computational modelling of the temperature dependence of the folding-unfolding thermodynamics and kinetics: The case of a trp-cage. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 21(41), 23162-23168.";s:4:"data";s:4:"2019";s:2:"id";s:20:"PUBBLICAZIONE_385139";s:6:"handle";s:11:"2108/243434";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:116:"Kinetics; Molecular Dynamics Simulation; Peptides; Models, Theoretical; Protein Folding; Temperature; Thermodynamics";s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";N;s:9:"metadata5";s:142:"Theoretical-computational modelling of the temperature dependence of the folding-unfolding thermodynamics and kinetics: The case of a trp-cage";s:9:"metadata6";s:36:"D'Abramo, M; Del Galdo, S; Amadei, A";s:9:"metadata7";s:18:"10.1039/c9cp03303c";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:4;a:14:{s:9:"citazione";s:183:"Del Galdo, S., Alba, J., Amadei, A., & D'Abramo, M. (2019). Evolutionary Modes in Protein Observable Space: The Case of Thioredoxins. JOURNAL OF MOLECULAR EVOLUTION, 87(4-6), 175-183.";s:4:"data";s:4:"2019";s:2:"id";s:20:"PUBBLICAZIONE_385219";s:6:"handle";s:11:"2108/243502";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:87:"Essential motions; Molecular dynamics; Protein dynamics; Protein evolution; Thioredoxin";s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";s:917:"In this article, we investigated the structural and dynamical evolutionary behaviour of a set of ten thioredoxin proteins as formed by three extant forms and seven resurrected ones in laboratory. Starting from the crystallographic structures, we performed all-atom molecular dynamics simulations and compare the trajectories in terms of structural and dynamical properties. Interestingly, the structural properties related to the protein density (i.e. the number of residues divided by the excluded molecular volume) well describe the protein evolutionary behaviour. Our results also suggest that the changes in sequence as occurred during the evolution have affected the protein essential motions, allowing us to discriminate between ancient and extant proteins in terms of their dynamical behaviour. Such results are yet more evident when the bacterial, archaeal and eukaryotic thioredoxins are separately analysed.";s:9:"metadata5";s:72:"Evolutionary Modes in Protein Observable Space: The Case of Thioredoxins";s:9:"metadata6";s:45:"Del Galdo, S; Alba, J; Amadei, A; D'Abramo, M";s:9:"metadata7";s:26:"10.1007/s00239-019-09894-4";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:5;a:14:{s:9:"citazione";s:279:"Zanetti-Polzi, L., Amadei, A., Djemili, R., Durot, S., Schoepff, L., Heitz, V., et al. (2019). Interpretation of Experimental Soret Bands of Porphyrins in Flexible Covalent Cages and in Their Related Ag(I) Fixed Complexes. JOURNAL OF PHYSICAL CHEMISTRY. C., 123(20), 13094-13103.";s:4:"data";s:4:"2019";s:2:"id";s:20:"PUBBLICAZIONE_385221";s:6:"handle";s:11:"2108/243504";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";N;s:9:"metadata5";s:126:"Interpretation of Experimental Soret Bands of Porphyrins in Flexible Covalent Cages and in Their Related Ag(I) Fixed Complexes";s:9:"metadata6";s:96:"Zanetti-Polzi, L; Amadei, A; Djemili, R; Durot, S; Schoepff, L; Heitz, V; Ventura, B; Daidone, I";s:9:"metadata7";s:24:"10.1021/acs.jpcc.9b00742";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:6;a:14:{s:9:"citazione";s:183:"Amadei, A., & Aschi, M. (2018). Theoretical-computational modeling of charge transfer and intersystem crossing reactions in complex chemical systems. RSC ADVANCES, 8(49), 27900-27918.";s:4:"data";s:4:"2018";s:2:"id";s:20:"PUBBLICAZIONE_385227";s:6:"handle";s:11:"2108/243510";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";N;s:9:"metadata5";s:116:"Theoretical-computational modeling of charge transfer and intersystem crossing reactions in complex chemical systems";s:9:"metadata6";s:19:"Amadei, A; Aschi, M";s:9:"metadata7";s:18:"10.1039/c8ra03900c";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:7;a:14:{s:9:"citazione";s:239:"Daidone, I., Amadei, A., Aschi, M., & Zanetti-Polzi, L. (2018). On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 192, 451-457.";s:4:"data";s:4:"2018";s:2:"id";s:20:"PUBBLICAZIONE_331474";s:6:"handle";s:11:"2108/198639";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:87:"Absorption spectrum; Molecular dynamics; Quantum chemistry; Riboflavin; Solvatochromism";s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";s:935:"We present here the calculation of the absorption spectrum of riboflavin in acetonitrile and dimethyl sulfoxide using a hybrid quantum/classical approach, namely the perturbed matrix method, based on quantum mechanical calculations and molecular dynamics simulations. The calculated spectra are compared to the absorption spectrum of riboflavin previously calculated in water and to the experimental spectra obtained in all three solvents. The experimentally observed variations in the absorption spectra upon change of the solvent environment are well reproduced by the calculated spectra. In addition, the nature of the excited states of riboflavin interacting with different solvents is investigated, showing that environment effects determine a recombination of the gas-phase electronic states and that such a recombination is strongly affected by the polarity of the solvent inducing significant changes in the absorption spectra.";s:9:"metadata5";s:90:"On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study";s:9:"metadata6";s:49:"Daidone, I; Amadei, A; Aschi, M; Zanetti-Polzi, L";s:9:"metadata7";s:25:"10.1016/j.saa.2017.11.031";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:8;a:14:{s:9:"citazione";s:197:"Daidone, I., Amadei, A., Del Galdo, S., & D’Abramo, M. (2018). Density discriminates between thermophilic and mesophilic proteins. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 36(12), 3265-3273.";s:4:"data";s:4:"2018";s:2:"id";s:20:"PUBBLICAZIONE_335045";s:6:"handle";s:11:"2108/201624";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";s:799:"Despite an intense interest and a remarkable number of studies on the subject, the relationships between thermostability and (primary, secondary and tertiary) structure of proteins are still not fully understood. Here, comparing the protein density - defined by the ratio between the residue number and protein excluded volume - for a set of thermophilic/mesophilic pairs, we provide evidence that this property is connected to the optimal growth temperature. In particular, our results indicate that thermophilic proteins have - in general - a lower density with respect to the mesophilic counterparts, being such a correlation more pronounced for optimal growth temperature differences greater than 40°C. The effect of the protein thermostability changes on the molecular shape is also presented.";s:9:"metadata5";s:66:"Density discriminates between thermophilic and mesophilic proteins";s:9:"metadata6";s:50:"Daidone, I; Amadei, A; Del Galdo, S; D’Abramo, M";s:9:"metadata7";s:29:"10.1080/07391102.2017.1385537";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:9;a:14:{s:9:"citazione";s:231:"Davis, C.M., Zanetti-Polzi, L., Gruebele, M., Amadei, A., Dyer, R.B., & Daidone, I. (2018). A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy. CHEMICAL SCIENCE, 9(48), 9002-9011.";s:4:"data";s:4:"2018";s:2:"id";s:20:"PUBBLICAZIONE_385223";s:6:"handle";s:11:"2108/243506";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";s:1540:"For small molecule reaction kinetics, computed reaction coordinates often mimic experimentally measured observables quite accurately. Although nowadays simulated and measured biomolecule kinetics can be compared on the same time scale, a gap between computed and experimental observables remains. Here we directly compared temperature-jump experiments and molecular dynamics simulations of protein folding dynamics using the same observable: the time-dependent infrared spectrum. We first measured the stability and folding kinetics of the fastest-folding β-protein, the GTT35 WW domain, using its structurally specific infrared spectrum. The relaxation dynamics of the peptide backbone, β-sheets, turn, and random coil were measured independently by probing the amide I' region at different frequencies. Next, the amide I' spectra along folding/unfolding molecular dynamics trajectories were simulated by accurate mixed quantum/classical calculations. The simulated time dependence and spectral amplitudes at the exact experimental probe frequencies provided relaxation and folding rates in agreement with experimental observations. The calculations validated by experiment yield direct structural evidence for a rate-limiting reaction step where an intermediate state with either the first or second hairpin is formed. We show how folding switches from a more homogeneous (apparent two-state) process at high temperature to a more heterogeneous process at low temperature, where different parts of the WW domain fold at different rates.";s:9:"metadata5";s:102:"A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy";s:9:"metadata6";s:73:"Davis, CM; Zanetti-Polzi, L; Gruebele, M; Amadei, A; Dyer, RB; Daidone, I";s:9:"metadata7";s:18:"10.1039/c8sc03786h";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:10;a:14:{s:9:"citazione";s:251:"Del Galdo, S., Mancini, G., Daidone, I., Zanetti Polzi, L., Amadei, A., & Barone, V. (2018). Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties. JOURNAL OF COMPUTATIONAL CHEMISTRY, 39(22), 1747-1756.";s:4:"data";s:4:"2018";s:2:"id";s:20:"PUBBLICAZIONE_385229";s:6:"handle";s:11:"2108/243512";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:233:"Perturbed Matrix Method; Tyrosine; force field refinement; molecular dynamics; semiclassical computational spectroscopy; Molecular Dynamics Simulation; Molecular Structure; Spectrophotometry, Ultraviolet; Tyrosine; Electrons; Protons";s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";s:1420:"The UV-vis spectrum of Tyrosine and its response to different backbone protonation states have been studied by applying the Perturbed Matrix Method (PMM) in conjunction with molecular dynamics (MD) simulations. Herein, we theoretically reproduce the UV-vis absorption spectrum of aqueous solution of Tyrosine in its zwitterionic, anionic and cationic forms, as well as of aqua-p-Cresol (i.e., the moiety that constitutes the side chain portion of Tyrosine). To achieve a better accuracy in the MD sampling, the Tyrosine Force Field (FF) parameters were derived de novo via quantum mechanical calculations. The UV-vis absorption spectra are computed considering the occurring electronic transitions in the vertical approximation for each of the chromophore configurations sampled by the classical MD simulations, thus including the effects of the chromophore semiclassical structural fluctuations. Finally, the explicit treatment of the perturbing effect of the embedding environment permits to fully model the inhomogeneous bandwidth of the electronic spectra. Comparison between our theoretical-computational results and experimental data shows that the used model captures the essential features of the spectroscopic process, thus allowing to perform further analysis on the strict relationship between the quantum properties of the chromophore and the different embedding environments. © 2018 Wiley Periodicals, Inc.";s:9:"metadata5";s:102:"Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties";s:9:"metadata6";s:76:"Del Galdo, S; Mancini, G; Daidone, I; Zanetti Polzi, L; Amadei, A; Barone, V";s:9:"metadata7";s:17:"10.1002/jcc.25351";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:11;a:14:{s:9:"citazione";s:270:"Zanetti-Polzi, L., Del Galdo, S., Daidone, I., D'Abramo, M., Barone, V., Aschi, M., et al. (2018). Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 20(37), 24369-24378.";s:4:"data";s:4:"2018";s:2:"id";s:20:"PUBBLICAZIONE_385225";s:6:"handle";s:11:"2108/243508";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";s:1461:"Some years ago we developed a theoretical-computational hybrid quantum/classical methodology, the Perturbed Matrix Method (PMM), to be used in conjunction with molecular dynamics simulations for the investigation of chemical processes in complex systems, that proved to be a valuable tool for the simulation of relevant experimental observables, e.g., spectroscopic signals, reduction potentials, kinetic constants. In typical PMM calculations the quantum sub-part of the system, the quantum centre, is embedded into an external perturbing field providing a perturbation operator explicitly calculated up to the dipolar terms. In this paper we further develop the PMM approach, beyond the dipolar terms in the perturbation operator expansion, by including explicitly the quadrupolar terms and/or by expanding the perturbation operator on each atom of the quantum centre. These different levels of the perturbation operator expansion, providing different levels of theory, have been tested by calculating three different spectroscopic observables: the spectral signal of liquid water and aqueous benzene due to the lowest energy electronic excitation and the infrared amide I band of aqueous trans-N-methylacetamide. All the systems tested show that, even though the previous PMM level of theory is already capable of reproducing the main features of the spectral signal, the higher levels of theory improve the quantitative reproduction of the spectral details.";s:9:"metadata5";s:112:"Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory";s:9:"metadata6";s:87:"Zanetti-Polzi, L; Del Galdo, S; Daidone, I; D'Abramo, M; Barone, V; Aschi, M; Amadei, A";s:9:"metadata7";s:18:"10.1039/C8CP04190C";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:12;a:14:{s:9:"citazione";s:248:"Carrillo-Parramon, O., Del Galdo, S., Aschi, M., Mancini, G., Amadei, A., & Barone, V. (2017). Flexible and Comprehensive Implementation of MD-PMM Approach in a General and Robust Code. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 13(11), 5506-5514.";s:4:"data";s:4:"2017";s:2:"id";s:20:"PUBBLICAZIONE_335043";s:6:"handle";s:11:"2108/201622";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";s:975:"The Perturbed Matrix Method (PMM) approach to be used in combination with Molecular Dynamics (MD) trajectories (MD-PMM) has been recoded from scratch, improved in several aspects, and implemented in the Gaussian suite of programs for allowing a user-friendly and yet flexible tool to estimate quantum chemistry observables in complex systems in condensed phases. Particular attention has been devoted to a description of rigid and flexible quantum centers together with powerful essential dynamics and clustering approaches. The default implementation is fully black-box and does not require any external action concerning both MD and PMM sections. At the same time, fine-tuning of different parameters and use of external data are allowed in all the steps of the procedure. Two specific systems (Tyrosine and Uridine) have been reinvestigated with the new version of the code in order to validate the implementation, check the performances, and illustrate some new features.";s:9:"metadata5";s:89:"Flexible and Comprehensive Implementation of MD-PMM Approach in a General and Robust Code";s:9:"metadata6";s:78:"Carrillo-Parramon, O; Del Galdo, S; Aschi, M; Mancini, G; Amadei, A; Barone, V";s:9:"metadata7";s:24:"10.1021/acs.jctc.7b00341";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:13;a:14:{s:9:"citazione";s:259:"Zanetti-Polzi, L., Aschi, M., Amadei, A., & Daidone, I. (2017). Alternative Electron- Transfer Channels Ensure Ultrafast Deactivation of Light-Induced Ex- cited States in Riboflavin Binding Protein. THE JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 8(14), 3321-3327.";s:4:"data";s:4:"2017";s:2:"id";s:20:"PUBBLICAZIONE_335039";s:6:"handle";s:11:"2108/201618";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";s:1061:"Flavoproteins, containing flavin chromophores, are enzymes capable of transferring electrons at very high speeds. The ultrafast photoinduced electron-transfer (ET) kinetics of riboflavin binding protein to the excited riboflavin was studied by femtosecond spectroscopy and found to occur within a few hundred femtoseconds [Zhong and Zewail, Proc. Natl. Acad. Sci. U.S.A.2001, 98, 11867–11872]. This ultrafast kinetics was attributed to the presence of two aromatic rings that could transfer the electron to riboflavin: the side chains of tryptophan 156 and tyrosine 75. However, the underlying ET mechanism remained unclear. Here, using a hybrid quantum mechanical–molecular dynamics approach, we perform ET dynamics simulations taking into account the motion of the protein and the solvent upon ET. This approach reveals that ET occurs via a major reaction channel involving tyrosine 75 (83%) and a minor one involving tryptophan 156 (17%). We also show that the protein environment is designed to ensure the fast quenching of the riboflavin excited state.";s:9:"metadata5";s:133:"Alternative Electron- Transfer Channels Ensure Ultrafast Deactivation of Light-Induced Ex- cited States in Riboflavin Binding Protein";s:9:"metadata6";s:49:"Zanetti-Polzi, L; Aschi, M; Amadei, A; Daidone, I";s:9:"metadata7";s:27:"10.1021/acs.jpclett.7b01575";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:14;a:14:{s:9:"citazione";s:174:"Zanetti-Polzi, L., Aschi, M., Daidone, I., & Amadei, A. (2017). Theoretical modeling of the absorption spectrum of aqueous riboflavin. CHEMICAL PHYSICS LETTERS, 669, 119-124.";s:4:"data";s:4:"2017";s:2:"id";s:20:"PUBBLICAZIONE_335037";s:6:"handle";s:11:"2108/201616";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";s:704:"In this study we report the modeling of the absorption spectrum of riboflavin in water using a hybrid quantum/classical mechanical approach, the MD-PMM methodology. By means of MD-PMM calculations, with which the effect of riboflavin internal motions and of solvent interactions on the spectroscopic properties can be explicitly taken into account, we obtain an absorption spectrum in very good agreement with the experimental spectrum. In particular, the calculated peak maxima show a consistent improvement with respect to previous computational approaches. Moreover, the calculations show that the interaction with the environment may cause a relevant recombination of the gas-phase electronic states.";s:9:"metadata5";s:69:"Theoretical modeling of the absorption spectrum of aqueous riboflavin";s:9:"metadata6";s:49:"Zanetti-Polzi, L; Aschi, M; Daidone, I; Amadei, A";s:9:"metadata7";s:28:"10.1016/j.cplett.2016.12.022";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:15;a:14:{s:9:"citazione";s:231:"Zanetti-Polzi, L., Davis, C.m., Gruebele, M., Dyer, R.b., Amadei, A., & Daidone, I. (2017). Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation. FEBS LETTERS, 591(20), 3265-3275.";s:4:"data";s:4:"2017";s:2:"id";s:20:"PUBBLICAZIONE_335041";s:6:"handle";s:11:"2108/201620";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:65:"fast-folding peptides; molecular dynamics simulations; β-hairpin";s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";s:802:"We present a calculation of the amide I' infrared (IR) spectra of the folded, unfolded, and intermediate states of the WW domain Fip35, a model system for β-sheet folding. Using an all-atom molecular dynamics simulation in which multiple folding and unfolding events take place we identify six conformational states and then apply perturbed matrix method quantum-mechanical calculations to determine their amide I' IR spectra. Our analysis focuses on two states previously identified as Fip35 folding intermediates and suggests that a three-stranded core similar to the folded state core is the main source of the spectroscopic differences between the two intermediates. In particular, we propose a hypothesis for why folding via one of these intermediates was not experimentally observed by IR T-jump";s:9:"metadata5";s:104:"Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation";s:9:"metadata6";s:73:"Zanetti-Polzi, L; Davis, Cm; Gruebele, M; Dyer, Rb; Amadei, A; Daidone, I";s:9:"metadata7";s:23:"10.1002/1873-3468.12836";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:16;a:14:{s:9:"citazione";s:250:"Aschi, M., Barone, V., Carlotti, B., Daidone, I., Elisei, F., & Amadei, A. (2016). Photoexcitation and relaxation kinetics of molecular systems in solution: towards a complete in silico model. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18(41), 28919-28931.";s:4:"data";s:4:"2016";s:2:"id";s:20:"PUBBLICAZIONE_385231";s:6:"handle";s:11:"2108/243514";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";s:1078:"In this study, we have modelled, through a theoretical-computational approach based on classical molecular dynamics simulations and quantum-chemical calculations, the complete relaxation process of a photo-excited ionic stilbene-like compound termed as DASPMI in solution. Starting from the absorption spectrum we have reconstructed the entire process of the excited-state relaxation involving the intramolecular charge-transfer and eventually leading to the charge-recombination regenerating the ground state. The results obtained, well reproducing the experimental time-resolved emission spectra and kinetic observables, show that the relaxation process is essentially driven by the internal conformational transitions of the chromophore with the solvent almost instantaneously relaxed for each chromophore conformation. This study represents the first attempt, carried out using our theoretical-computational approach, of modelling a complete experiment involving the overposition of relaxation kinetics ranging from hundreds of femtoseconds to nanoseconds on the time scale.";s:9:"metadata5";s:108:"Photoexcitation and relaxation kinetics of molecular systems in solution: towards a complete in silico model";s:9:"metadata6";s:66:"Aschi, M; Barone, V; Carlotti, B; Daidone, I; Elisei, F; Amadei, A";s:9:"metadata7";s:18:"10.1039/c6cp06167b";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:17;a:14:{s:9:"citazione";s:169:"Aschi, M., D'Abramo, M., & Amadei, A. (2016). Photoinduced electron transfer in a dichromophoric peptide: a numerical experiment. THEORETICAL CHEMISTRY ACCOUNTS, 135(5).";s:4:"data";s:4:"2016";s:2:"id";s:20:"PUBBLICAZIONE_385241";s:6:"handle";s:11:"2108/243524";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";N;s:9:"metadata5";s:82:"Photoinduced electron transfer in a dichromophoric peptide: a numerical experiment";s:9:"metadata6";s:32:"Aschi, M; D'Abramo, M; Amadei, A";s:9:"metadata7";s:25:"10.1007/s00214-016-1881-1";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:18;a:14:{s:9:"citazione";s:241:"Daidone, I., Zanetti-Polzi, L., Thukral, L., Alekozai, E.M., & Amadei, A. (2016). Theoretical-computational characterization of the temperature-dependent folding thermodynamics of a β-hairpin peptide. CHEMICAL PHYSICS LETTERS, 659, 247-251.";s:4:"data";s:4:"2016";s:2:"id";s:20:"PUBBLICAZIONE_385235";s:6:"handle";s:11:"2108/243518";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";N;s:9:"metadata5";s:118:"Theoretical-computational characterization of the temperature-dependent folding thermodynamics of a β-hairpin peptide";s:9:"metadata6";s:65:"Daidone, I; Zanetti-Polzi, L; Thukral, L; Alekozai, EM; Amadei, A";s:9:"metadata7";s:28:"10.1016/j.cplett.2016.07.041";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:19;a:14:{s:9:"citazione";s:195:"Del Galdo, S., & Amadei, A. (2016). The unfolding effects on the protein hydration shell and partial molar volume: A computational study. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18(40), 28175-28182.";s:4:"data";s:4:"2016";s:2:"id";s:20:"PUBBLICAZIONE_385233";s:6:"handle";s:11:"2108/243516";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:93:"Myoglobin; Pressure; Protein Conformation; Temperature; Protein Denaturation; Protein Folding";s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";s:781:"In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes. Moreover, by using both the native and unfolded protein partial molar volumes, we obtain the corresponding variations (unfolding partial molar volumes) to be compared with the available experimental estimates. We also reconstruct the temperature and pressure dependence of the unfolding partial molar volume of Myoglobin dissecting the structural and hydration effects involved in the process.";s:9:"metadata5";s:100:"The unfolding effects on the protein hydration shell and partial molar volume: A computational study";s:9:"metadata6";s:23:"Del Galdo, S; Amadei, A";s:9:"metadata7";s:18:"10.1039/c6cp05029h";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:20;a:14:{s:9:"citazione";s:234:"Del Galdo, S., Aschi, M., & Amadei, A. (2016). In silico characterization of bimolecular electron transfer reactions: The ferrocene–ferrocenium reaction as a test case. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 116(22), 1723-1730.";s:4:"data";s:4:"2016";s:2:"id";s:20:"PUBBLICAZIONE_385237";s:6:"handle";s:11:"2108/243520";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";N;s:9:"metadata5";s:122:"In silico characterization of bimolecular electron transfer reactions: The ferrocene–ferrocenium reaction as a test case";s:9:"metadata6";s:33:"Del Galdo, S; Aschi, M; Amadei, A";s:9:"metadata7";s:17:"10.1002/qua.25212";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:21;a:14:{s:9:"citazione";s:248:"Zanetti-Polzi, L., Corni, S., Daidone, I., & Amadei, A. (2016). Extending the essential dynamics analysis to investigate molecular properties: Application to the redox potential of proteins. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18(27), 18450-18459.";s:4:"data";s:4:"2016";s:2:"id";s:20:"PUBBLICAZIONE_385239";s:6:"handle";s:11:"2108/243522";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:135:"Azurin; Models, Molecular; Molecular Dynamics Simulation; Motion; Oxidation-Reduction; Physical Phenomena; Proteins; Static Electricity";s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";s:1447:"Here, a methodology is proposed to investigate the collective fluctuation modes of an arbitrary set of observables, maximally contributing to the fluctuation of another functionally relevant observable. The methodology, based on the analysis of fully classical molecular dynamics (MD) simulations, exploits the essential dynamics (ED) method, originally developed to analyse the collective motions in proteins. We apply this methodology to identify the residues that are more relevant for determining the reduction potential (E(0)) of a redox-active protein. To this aim, the fluctuation modes of the single-residue electrostatic potentials mostly contributing to the fluctuations of the total electrostatic potential (the main determinant of E(0)) are investigated for wild-type azurin and two of its mutants with a higher E(0). By comparing the results here obtained with a previous study on the same systems [Zanetti-Polzi et al., Org. Biomol. Chem., 2015, 13, 11003] we show that the proposed methodology is able to identify the key sites that determine E(0). This information can be used for a general deeper understanding of the molecular mechanisms on the basis of the redox properties of the proteins under investigation, as well as for the rational design of mutants with a higher or lower E(0). From the results of the present analysis we propose a new azurin mutant that, according to our calculations, shows a further increase of E(0).";s:9:"metadata5";s:125:"Extending the essential dynamics analysis to investigate molecular properties: Application to the redox potential of proteins";s:9:"metadata6";s:49:"Zanetti-Polzi, L; Corni, S; Daidone, I; Amadei, A";s:9:"metadata7";s:18:"10.1039/c6cp03394f";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:22;a:14:{s:9:"citazione";s:173:"Amadei, A., & Marracino, P. (2015). Theoretical-computational modelling of the electric field effects on protein unfolding thermodynamics. RSC ADVANCES, 5(117), 96551-96561.";s:4:"data";s:4:"2015";s:2:"id";s:20:"PUBBLICAZIONE_385245";s:6:"handle";s:11:"2108/243528";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";N;s:9:"metadata5";s:101:"Theoretical-computational modelling of the electric field effects on protein unfolding thermodynamics";s:9:"metadata6";s:23:"Amadei, A; Marracino, P";s:9:"metadata7";s:18:"10.1039/c5ra15605j";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:23;a:14:{s:9:"citazione";s:164:"D'Abramo, M., Aschi, M., & Amadei, A. (2015). Theoretical calculation of the pyrene emission properties in different solvents. CHEMICAL PHYSICS LETTERS, 639, 17-22.";s:4:"data";s:4:"2015";s:2:"id";s:20:"PUBBLICAZIONE_385247";s:6:"handle";s:11:"2108/243530";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";N;s:9:"metadata5";s:79:"Theoretical calculation of the pyrene emission properties in different solvents";s:9:"metadata6";s:32:"D'Abramo, M; Aschi, M; Amadei, A";s:9:"metadata7";s:28:"10.1016/j.cplett.2015.08.070";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:24;a:14:{s:9:"citazione";s:176:"D'Alessando, M., Amadei, A., Stener, M., & Aschi, M. (2015). Essential dynamics for the study of microstructures in liquids. JOURNAL OF COMPUTATIONAL CHEMISTRY, 36(6), 399-407.";s:4:"data";s:4:"2015";s:2:"id";s:20:"PUBBLICAZIONE_385254";s:6:"handle";s:11:"2108/243536";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:305:"clusters; computational spectroscopy; conformational sampling; essential dynamics; molecular dynamics; Hydrogen Bonding; Magnetic Resonance Spectroscopy; Molecular Conformation; Principal Component Analysis; Quantum Theory; Spectrophotometry, Infrared; Thermodynamics; Water; Molecular Dynamics Simulation";s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";s:1028:"Essential Dynamics (ED) is a powerful tool for analyzing molecular dynamics (MD) simulations and it is widely adopted for conformational analysis of large molecular systems such as, for example, proteins and nucleic acids. In this study, we extend the use of ED to the study of clusters of arbitrary size constituted by weakly interacting particles, for example, atomic clusters and supramolecular systems. The key feature of the method we present is the identification of the relevant atomic-molecular clusters to be analyzed by ED for extracting the information of interest. The application of this computational approach allows a straightforward and unbiased conformational study of the local microstructures in liquids, as emerged from semiclassical MD simulations. The good performance of the method is demonstrated by calculating typical observables of liquid water, that is, NMR, NEXAFS O1s, and IR spectra, known to be rather sensitive both to the presence and to the conformational features of hydrogen-bonded clusters.";s:9:"metadata5";s:62:"Essential dynamics for the study of microstructures in liquids";s:9:"metadata6";s:46:"D'Alessando, M; Amadei, A; Stener, M; Aschi, M";s:9:"metadata7";s:17:"10.1002/jcc.23814";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:25;a:14:{s:9:"citazione";s:209:"Daidone, I., Thukral, L., Smith, J.C., & Amadei, A. (2015). Monitoring the Folding Kinetics of a β-Hairpin by Time-Resolved IR Spectroscopy in Silico. THE JOURNAL OF PHYSICAL CHEMISTRY. B, 119(14), 4849-4856.";s:4:"data";s:4:"2015";s:2:"id";s:20:"PUBBLICAZIONE_385252";s:6:"handle";s:11:"2108/243534";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:206:"Amino Acid Sequence; Kinetics; Molecular Sequence Data; Peptides; Protein Structure, Secondary; Spectrophotometry, Infrared; Time Factors; Computer Simulation; Molecular Dynamics Simulation; Protein Folding";s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";s:1375:"Protein folding is one of the most fundamental problems in modern biochemistry. Time-resolved infrared (IR) spectroscopy in the amide I region is commonly used to monitor folding kinetics. However, associated atomic detail information on the folding mechanism requires simulations. In atomistic simulations structural order parameters are typically used to follow the folding process along the simulated trajectories. However, a rigorous test of the reliability of the mechanisms found in the simulations requires calculation of the time-dependent experimental observable, i.e., in the present case the IR signal in the amide I region. Here, we combine molecular dynamics simulation with a mixed quantum mechanics/molecular mechanics theoretical methodology, the Perturbed Matrix Method, in order to characterize the folding of a β-hairpin peptide, through modeling the time-dependence of the amide I IR signal. The kinetic and thermodynamic data (folding and unfolding rate constants, and equilibrium folded- and unfolded-state probabilities) obtained from the fit of the calculated signal are in good agreement with the available experimental data [Xu et al. J. Am. Chem. Soc. 2003, 125, 15388-15394]. To the best of our knowledge, this is the first report of the simulation of the time-resolved IR signal of a complex process occurring on a long (microsecond) time scale.";s:9:"metadata5";s:90:"Monitoring the Folding Kinetics of a β-Hairpin by Time-Resolved IR Spectroscopy in Silico";s:9:"metadata6";s:44:"Daidone, I; Thukral, L; Smith, JC; Amadei, A";s:9:"metadata7";s:24:"10.1021/acs.jpcb.5b01477";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:26;a:14:{s:9:"citazione";s:208:"Del Galdo, S., Marracino, P., D'Abramo, M., & Amadei, A. (2015). In silico characterization of protein partial molecular volumes and hydration shells. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17(46), 31270-31277.";s:4:"data";s:4:"2015";s:2:"id";s:20:"PUBBLICAZIONE_385243";s:6:"handle";s:11:"2108/243526";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:68:"Protein Conformation; Proteins; Water; Molecular Dynamics Simulation";s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";s:700:"In this paper we present a computational approach, based on NVT molecular dynamics trajectories, that allows the direct evaluation of the protein partial molecular volume. The results obtained for five different globular proteins demonstrate the accuracy of this computational procedure in reproducing protein partial molecular volumes, providing quantitative characterization of the hydration shell in terms of the protein excluded volume, hydration shell ellipsoidal volume and related solvent density. Remarkably, our data indicate for the hydration shell a ≈10% solvent density increase with respect to the liquid water bulk density, in excellent agreement with the available experimental data.";s:9:"metadata5";s:84:"In silico characterization of protein partial molecular volumes and hydration shells";s:9:"metadata6";s:50:"Del Galdo, S; Marracino, P; D'Abramo, M; Amadei, A";s:9:"metadata7";s:18:"10.1039/c5cp05891k";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:27;a:14:{s:9:"citazione";s:226:"Zanetti-Polzi, L., Bortolotti, C.A., Daidone, I., Aschi, M., Amadei, A., & Corni, S. (2015). A few key residues determine the high redox potential shift in azurin mutants. ORGANIC & BIOMOLECULAR CHEMISTRY, 13(45), 11003-11013.";s:4:"data";s:4:"2015";s:2:"id";s:20:"PUBBLICAZIONE_385249";s:6:"handle";s:11:"2108/243532";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:114:"Azurin; Molecular Dynamics Simulation; Oxidation-Reduction; Point Mutation; Pseudomonas aeruginosa; Quantum Theory";s:9:"metadata3";s:15:"Settore CHIM/02";s:9:"metadata4";s:1269:"The wide range of variability of the reduction potential (E(0)) of blue-copper proteins has been the subject of a large number of studies in the past several years. In particular, a series of azurin mutants have been recently rationally designed tuning E(0) over a very broad range (700 mV) without significantly altering the redox-active site [Marshall et al., Nature, 2009, 462, 113]. This clearly suggests that interactions outside the primary coordination sphere are relevant to determine E(0) in cupredoxins. However, the molecular determinants of the redox potential variability are still undisclosed. Here, by means of atomistic molecular dynamics simulations and hybrid quantum/classical calculations, the mechanisms that determine the E(0) shift of two azurin mutants with high potential shifts are unravelled. The reduction potentials of native azurin and of the mutants are calculated obtaining results in good agreement with the experiments. The analysis of the simulations reveals that only a small number of residues (including non-mutated ones) are relevant in determining the experimentally observed E(0) variation via site-specific, but diverse, mechanisms. These findings open the path to the rational design of new azurin mutants with different E(0).";s:9:"metadata5";s:77:"A few key residues determine the high redox potential shift in azurin mutants";s:9:"metadata6";s:75:"Zanetti-Polzi, L; Bortolotti, CA; Daidone, I; Aschi, M; Amadei, A; Corni, S";s:9:"metadata7";s:18:"10.1039/c5ob01819f";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:28;a:14:{s:9:"citazione";s:155:"Besker, N., Amadei, A., & D'Abramo, M. (2014). Molecular mechanisms of activation in CDK2. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32(12), 1929-1935.";s:4:"data";s:4:"2014";s:2:"id";s:20:"PUBBLICAZIONE_195655";s:6:"handle";s:10:"2108/93268";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:42:"Molecular mechanisms of activation in CDK2";s:9:"metadata6";s:33:"Besker, N; Amadei, A; D'Abramo, M";s:9:"metadata7";s:28:"10.1080/07391102.2013.844080";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:29;a:14:{s:9:"citazione";s:276:"D'Abramo, M., Aschi, M., & Amadei, A. (2014). Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: Explicit treatment of the vibronic transitions. THE JOURNAL OF CHEMICAL PHYSICS, 140(164104).";s:4:"data";s:4:"2014";s:2:"id";s:20:"PUBBLICAZIONE_195605";s:6:"handle";s:10:"2108/93249";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:183:"Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: Explicit treatment of the vibronic transitions";s:9:"metadata6";s:32:"D'Abramo, M; Aschi, M; Amadei, A";s:9:"metadata7";s:17:"10.1063/1.4871626";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:30;a:14:{s:9:"citazione";s:245:"Daidone, I., Amadei, A., Zaccanti, F., Borsari, M., & Bortolotti, C.A. (2014). How the Reorganization Free Energy Affects the Reduction Potential of Structurally Homologous Cytochromes. THE JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 5(9), 1534-1540.";s:4:"data";s:4:"2014";s:2:"id";s:20:"PUBBLICAZIONE_195621";s:6:"handle";s:10:"2108/93267";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:105:"How the Reorganization Free Energy Affects the Reduction Potential of Structurally Homologous Cytochromes";s:9:"metadata6";s:62:"Daidone, I; Amadei, A; Zaccanti, F; Borsari, M; Bortolotti, CA";s:9:"metadata7";s:17:"10.1021/jz5005208";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:31;a:14:{s:9:"citazione";s:268:"Daidone, I., Paltrinieri, L., Amadei, A., Battistuzzi, G., Sola, M., Borsari, M., et al. (2014). Unambiguous Assignment of Reduction Potentials in Diheme Cytochromes. JOURNAL OF PHYSICAL CHEMISTRY. B, MATERIALS, SURFACES, INTERFACES, & BIOPHYSICAL, 118(27), 7554-7560.";s:4:"data";s:4:"2014";s:2:"id";s:20:"PUBBLICAZIONE_195635";s:6:"handle";s:10:"2108/93251";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:68:"Unambiguous Assignment of Reduction Potentials in Diheme Cytochromes";s:9:"metadata6";s:90:"Daidone, I; Paltrinieri, L; Amadei, A; Battistuzzi, G; Sola, M; Borsari, M; Bortolotti, CA";s:9:"metadata7";s:17:"10.1021/jp506017a";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:32;a:14:{s:9:"citazione";s:256:"Piacente, G., Amadei, A., D'Abramo, M., Daidone, I., & Aschi, M. (2014). Theoretical-computational modeling of photo-induced charge separation spectrum and charge recombination kinetics in solution. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16(38), 20624-20638.";s:4:"data";s:4:"2014";s:2:"id";s:20:"PUBBLICAZIONE_195653";s:6:"handle";s:10:"2108/93250";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:125:"Theoretical-computational modeling of photo-induced charge separation spectrum and charge recombination kinetics in solution.";s:9:"metadata6";s:57:"Piacente, G; Amadei, A; D'Abramo, M; Daidone, I; Aschi, M";s:9:"metadata7";s:18:"10.1039/c4cp02422b";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:33;a:14:{s:9:"citazione";s:371:"Piacente, G., D'Aiuto, V., Aschi, M., Cerichelli, G., Chiarini, M., & Amadei, A. (2014). Inclusion of cybotactic effect in the theoretical modeling of absorption spectra of liquid-state systems with perturbed matrix method and molecular dynamics simulations: the UV-Vis absorption spectrum of para-nitroaniline as a case study. THEORETICAL CHEMISTRY ACCOUNTS, 133(5), 10.";s:4:"data";s:4:"2014";s:2:"id";s:20:"PUBBLICAZIONE_195604";s:6:"handle";s:10:"2108/93228";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:237:"Inclusion of cybotactic effect in the theoretical modeling of absorption spectra of liquid-state systems with perturbed matrix method and molecular dynamics simulations: the UV-Vis absorption spectrum of para-nitroaniline as a case study";s:9:"metadata6";s:72:"Piacente, G; D'Aiuto, V; Aschi, M; Cerichelli, G; Chiarini, M; Amadei, A";s:9:"metadata7";s:25:"10.1007/s00214-014-1478-5";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:34;a:14:{s:9:"citazione";s:299:"D'Alessandro, M., Aschi, M., Mazzuca, C., Palleschi, A., & Amadei, A. (2013). Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: the vertical transition approximation. THE JOURNAL OF CHEMICAL PHYSICS, 139, 114102.";s:4:"data";s:7:"2013-09";s:2:"id";s:20:"PUBBLICAZIONE_175661";s:6:"handle";s:10:"2108/85087";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:174:"Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: the vertical transition approximation";s:9:"metadata6";s:62:"D'Alessandro, M; Aschi, M; Mazzuca, C; Palleschi, A; Amadei, A";s:9:"metadata7";s:17:"10.1063/1.4821003";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:35;a:14:{s:9:"citazione";s:205:"Amadei, A., Daidone, I., & Bortolotti, C.A. (2013). A general statistical mechanical approach for modeling redox thermodynamics: the reaction and reorganization free energies. RSC ADVANCES, 3, 19657-19665.";s:4:"data";s:4:"2013";s:2:"id";s:20:"PUBBLICAZIONE_195603";s:6:"handle";s:10:"2108/93176";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:122:"A general statistical mechanical approach for modeling redox thermodynamics: the reaction and reorganization free energies";s:9:"metadata6";s:37:"Amadei, A; Daidone, I; Bortolotti, CA";s:9:"metadata7";s:18:"10.1039/C3RA42842G";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:36;a:14:{s:9:"citazione";s:204:"Cattenacci, G., Aschi, M., Graziano, G., & Amadei, A. (2013). A theoretical study on the spectral and electrochemical properties of Ferrocene in different solvents. INORGANICA CHIMICA ACTA, 407(1), 82-90.";s:4:"data";s:4:"2013";s:2:"id";s:20:"PUBBLICAZIONE_195665";s:6:"handle";s:10:"2108/93270";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:101:"A theoretical study on the spectral and electrochemical properties of Ferrocene in different solvents";s:9:"metadata6";s:47:"Cattenacci, G; Aschi, M; Graziano, G; Amadei, A";s:9:"metadata7";s:25:"10.1016/j.ica.2013.07.019";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:37;a:14:{s:9:"citazione";s:224:"D'Abramo, M., Castellazzi, C., Orozco, M., & Amadei, A. (2013). On the nature of DNA hyperchromic effect. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, 117(29), 8697-8704.";s:4:"data";s:4:"2013";s:2:"id";s:20:"PUBBLICAZIONE_159976";s:6:"handle";s:10:"2108/76144";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:40:"On the nature of DNA hyperchromic effect";s:9:"metadata6";s:55:"D'Abramo, M.; Castellazzi, C.L.; Orozco, M.; Amadei, A.";s:9:"metadata7";s:17:"10.1021/jp403369k";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:38;a:14:{s:9:"citazione";s:324:"D'Alessandro, M., Amadei, A., Daidone, I., Po, R., Alessi, A., & Aschi, M. (2013). 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. JOURNAL OF PHYSICAL CHEMISTRY. C, 117(27), 13785-13797.";s:4:"data";s:4:"2013";s:2:"id";s:20:"PUBBLICAZIONE_195663";s:6:"handle";s:10:"2108/93269";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:184:"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";s:9:"metadata6";s:66:"D'Alessandro, M; Amadei, A; Daidone, I; Po, R; Alessi, A; Aschi, M";s:9:"metadata7";s:17:"10.1021/jp401173s";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:39;a:14:{s:9:"citazione";s:287:"Marracino, P., Apollonio, F., Liberti, M., D'Inzeo, G., & Amadei, A. (2013). Effect of High Exogenous Electric Pulses on Protein Conformation: Myoglobin as a Case Study. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, 117(8), 2273-2279.";s:4:"data";s:4:"2013";s:2:"id";s:20:"PUBBLICAZIONE_159977";s:6:"handle";s:10:"2108/76141";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:91:"Effect of High Exogenous Electric Pulses on Protein Conformation: Myoglobin as a Case Study";s:9:"metadata6";s:61:"Marracino, P; Apollonio, F; Liberti, M; D'Inzeo, G; Amadei, A";s:9:"metadata7";s:17:"10.1021/jp309857b";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:40;a:14:{s:9:"citazione";s:283:"Zanetti-Polzi, L., Aschi, M., Amadei, A., & Daidone, I. (2013). Simulation of the Amide 1 Infrared Spectrum in Photoinduced Peptide Folding/Unfolding Transitions. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, 117(41), 12383-12390.";s:4:"data";s:4:"2013";s:2:"id";s:20:"PUBBLICAZIONE_195590";s:6:"handle";s:10:"2108/93169";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:97:"Simulation of the Amide 1 Infrared Spectrum in Photoinduced Peptide Folding/Unfolding Transitions";s:9:"metadata6";s:49:"Zanetti-Polzi, L; Aschi, M; Amadei, A; Daidone, I";s:9:"metadata7";s:17:"10.1021/jp406708p";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:41;a:14:{s:9:"citazione";s:255:"Zanetti-Polzi, L., Marracino, P., Aschi, M., Daidone, I., Fontana, A., Apollonio, F., et al. (2013). Modeling triplet flavin-indole electron transfer and interradical dipolar interaction: a perturbative approach. THEORETICAL CHEMISTRY ACCOUNTS, 132, 1393.";s:4:"data";s:4:"2013";s:2:"id";s:20:"PUBBLICAZIONE_195664";s:6:"handle";s:10:"2108/93287";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:110:"Modeling triplet flavin-indole electron transfer and interradical dipolar interaction: a perturbative approach";s:9:"metadata6";s:113:"Zanetti-Polzi, L; Marracino, P; Aschi, M; Daidone, I; Fontana, A; Apollonio, F; Liberti, M; D'Inzeo, G; Amadei, A";s:9:"metadata7";s:25:"10.1007/s00214-013-1393-1";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:42;a:14:{s:9:"citazione";s:179:"Amadei, A., Daidone, I., & Aschi, M. (2012). A general theoretical model for electron transfer reactions in complex systems. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14(4), 1360-1370.";s:4:"data";s:4:"2012";s:2:"id";s:20:"PUBBLICAZIONE_159884";s:6:"handle";s:10:"2108/76129";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:78:"A general theoretical model for electron transfer reactions in complex systems";s:9:"metadata6";s:31:"Amadei, A; Daidone, I; Aschi, M";s:9:"metadata7";s:18:"10.1039/c1cp22309g";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:43;a:14:{s:9:"citazione";s:244:"Anselmi, M., Marocchi, S., Aschi, M., & Amadei, A. (2012). Theoretical modeling of the spectroscopic absorption properties of luciferin and oxyluciferin: A critical comparison with recent experimental studies. CHEMICAL PHYSICS, 392(1), 205-214.";s:4:"data";s:4:"2012";s:2:"id";s:20:"PUBBLICAZIONE_159883";s:6:"handle";s:10:"2108/76143";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:149:"Theoretical modeling of the spectroscopic absorption properties of luciferin and oxyluciferin: A critical comparison with recent experimental studies";s:9:"metadata6";s:44:"Anselmi, M; Marocchi, S; Aschi, M; Amadei, A";s:9:"metadata7";s:30:"10.1016/j.chemphys.2011.11.021";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:44;a:14:{s:9:"citazione";s:258:"Aschi, M., Amadei, A., Pellegrino, A., Perin, N., & Po, R. (2012). Thermal and environmental effects on Oligothiophene low-energy singlet electronic excitations in dilute solution: a theoretical and experimental study. THEORETICAL CHEMISTRY ACCOUNTS, 131(3).";s:4:"data";s:4:"2012";s:2:"id";s:20:"PUBBLICAZIONE_159882";s:6:"handle";s:10:"2108/76140";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:150:"Thermal and environmental effects on Oligothiophene low-energy singlet electronic excitations in dilute solution: a theoretical and experimental study";s:9:"metadata6";s:51:"Aschi, M; Amadei, A; Pellegrino, A; Perin, N; Po, R";s:9:"metadata7";s:25:"10.1007/s00214-012-1177-z";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:45;a:14:{s:9:"citazione";s:253:"Bortolotti, C., Amadei, A., Aschi, M., Borsari, M., Corni, S., Sola, M., et al. (2012). The Reversible Opening of Water Channels in Cytochrome c Modulates the Heme Iron Reduction Potential. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134(33), 13670-13678.";s:4:"data";s:4:"2012";s:2:"id";s:20:"PUBBLICAZIONE_159880";s:6:"handle";s:10:"2108/76136";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:100:"The Reversible Opening of Water Channels in Cytochrome c Modulates the Heme Iron Reduction Potential";s:9:"metadata6";s:77:"Bortolotti, C; Amadei, A; Aschi, M; Borsari, M; Corni, S; Sola, M; Daidone, I";s:9:"metadata7";s:17:"10.1021/ja3030356";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:46;a:14:{s:9:"citazione";s:163:"Daidone, I., & Amadei, A. (2012). Essential dynamics: foundation and applications. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE, 2(5), 762-770.";s:4:"data";s:4:"2012";s:2:"id";s:20:"PUBBLICAZIONE_159879";s:6:"handle";s:10:"2108/76130";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:47:"Essential dynamics: foundation and applications";s:9:"metadata6";s:21:"Daidone, I; Amadei, A";s:9:"metadata7";s:17:"10.1002/wcms.1099";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:47;a:14:{s:9:"citazione";s:280:"Polzi, L., Daidone, I., & Amadei, A. (2012). A Theoretical reappraisal of polylysine in the investigation of secondary structure sensitivity of infrared spectra. JOURNAL OF PHYSICAL CHEMISTRY. 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