Supercomputing Center for University and Research

Rome, Italy

Supercomputing Center for University and Research

Rome, Italy
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Aschi M.,University of L'Aquila | Fontana A.,University of Chieti Pescara | Di Meo E.M.,University of Chieti Pescara | Zazza C.,Supercomputing Center for University and Research | Amadei A.,University of Rome Tor Vergata
Journal of Physical Chemistry B | Year: 2010

characterization of quantum states in complex molecular systems is a rather complicated task because of the necessity of maintaining the pure quantum definition of a state interacting with a configurationally complex molecular environment. Unfortunately, many of the "observables" that are of interest for a chemist, typically dealing with "complex objects", belong to the above class and their theoretical modeling may represent a hard task. In this respect, we have developed a new theoretical methodology, "perturbed matrix method", essentially based on the perturbation theory whose main aim is the characterization of the quantum states of a predefined portion of a complex molecular system, e.g., a solute, classically interacting with the environment, e.g., the solvent. This method has been used in this study to systematically characterize, for the first time and in conjunction with experimental observations, the intrinsic nature of pyrene whose vibrational and electronic states are highly sensitive to the nature of molecular environment. More precisely, pyrene shows a strong alteration of spectral intensities upon modification of polarity of the solvent. This property has been extensively used in many experimental studies and has been intepreted in the present study by characterizing pyrene electronic states as fluctuating states strictly connected to the polarity and the fluctuations of the surrounding medium. A correct theoretical modeling has been also obtained and commented for the vertical transitions in different media and also for the vibronic structure for the first transition in water. © 2010 American Chemical Society.


Zazza C.,Supercomputing Center for University and Research | Sanna N.,Supercomputing Center for University and Research | Tatoli S.,Supercomputing Center for University and Research | Tatoli S.,University of Rome La Sapienza | And 2 more authors.
International Journal of Quantum Chemistry | Year: 2010

Quadratic configuration interaction procedure with single and double electronic excitations (QCISD) has been used, for the first time, to calculate the electronic structure of the Compound I (CpdI), which represents a key intermediate in the catalytic cycle of Horseradish Peroxidase (HRP) enzyme. The QCISD method is applied to lowest quasi-isoenergetic doublet and quartet spin multiplicity and results compared with density functional theory (DFT/B3LYP) data. This investigation shows that, at present, QCISD is more accurate than DFT-based approach in discriminating between the two lowest magnetic states of CpdI complex in. HRP enzyme. Such a result opens the possibility of theoretically addressing the reaction mechanism, leading to CpdI complex in HRP using a correlated wavefunction based approach. © 2009 Wiley Periodicals, Inc.


Zazza C.,Supercomputing Center for University and Research | Palma A.,CNR Institute of Nanostructured Materials | Amadei A.,University of Rome Tor Vergata | Sanna N.,Supercomputing Center for University and Research | And 3 more authors.
Faraday Discussions | Year: 2010

In this study the question as to whether and to what extent horseradish peroxidase (HRP) enzyme structural flexibility affects the free energy barrier for the formation of the key intermediate compound 0 (Cpd0) is addressed by the use of a combined application of molecular dynamics simulations and perturbed matrix method calculations. Results are intriguing and indicate that, within the simulated conditions, free energy profiles are substantially affected by structural fluctuations of the whole surrounding biological environment (i.e. HRP enzyme and solvent). In this respect our results show that the combined effect of enzyme and solvent provides a substantial lowering of the free energy barrier to the formation of Cpd0, with respect to both gas-phase and QM/MM results carried out at a comparable level of theory. A careful inspection of such observations and their general implications in currently employed methodological approaches to the modelling of enzyme reactions, is also discussed. © 2010 The Royal Society of Chemistry.


Zazza C.,Supercomputing Center for University and Research | Mancini G.,Supercomputing Center for University and Research | Mancini G.,University of Tuscia | Amadei A.,University of Rome Tor Vergata | And 2 more authors.
Physical Chemistry Chemical Physics | Year: 2010

Irreversible redox-induced relaxation processes occurring in a synthetic thread for rotaxane-based molecular devices are investigated; the results show that such a system in solution allows chemists to efficiently realize a nanosecond timescale/electrochemically-driven "conformational shaping" through simple control of non-covalent interactions. © the Owner Societies.


Zazza C.,Supercomputing Center for University and Research | Sanna N.,Supercomputing Center for University and Research | Rutigliano M.,CNR Institute of Inorganic Methodologies and Plasmas | Cacciatore M.,CNR Institute of Inorganic Methodologies and Plasmas | Palma A.,CNR Institute of Nanostructured Materials
Computational and Theoretical Chemistry | Year: 2011

The interaction of methane with an aluminium-free zeolite (ZSM-5) porous substrate has been investigated by means of DFT and DFT-D calculations. We observe no charge transfer between host-guest species and, most interestingly, the energetic balance appears to be reasonably linked to the volume size of individual internal cavities. In fact, the gaseous-molecule is loosely bound only in larger 10MR pores while, inside the narrow 6MR ring, on because of the proximity of individual electronic clouds, the chemical interaction is repulsive. From a comparison with DFT approach it is evident that dispersion energies are crucial for a correct energetics and that long range forces drive the adsorption processes. Similar results are obtained for other small species, like hydrogen (atom and molecule) and CH3 radical species, considered in our current, although not exhaustive, investigation as products of hypothetical methane dissociative adsorptions. © 2011 Elsevier B.V.


Zazza C.,Supercomputing Center for University and Research | Zazza C.,Normal School of Pisa | Olsen J.M.,University of Southern Denmark | Kongsted J.,University of Southern Denmark
Computational and Theoretical Chemistry | Year: 2011

We address the role played by a different subset of nanosolvation patterns on the lowest π-π * and n-π * solvatochromic shifts of uracil in water at 298K. To this end, a computational investigation which compares perturbed electronic properties based on correlated electronic wavefunctions - computed either at the DFT or CCSD level of theory - in conjunction with two nanoseconds time-scale classical trajectories is presented. The simulations are based on the use of either an implicit or an explicit description of polarization. The predicted π-π * solvatochromic shifts based on these two simulations are very similar but slightly underestimate the experimental values. This finding reinforce the idea that for a proper estimation of the π-π * transition local interactions beyond those of purely electrostatic origin are mandatory. On the other hand, the n-π * excitation is seen to increase its shift upon inclusion of explicit polarization, thereby bringing the predicted shift in closer agreement with experimental data. © 2011 Elsevier B.V..


Mancini G.,Supercomputing Center for University and Research | Zazza C.,Supercomputing Center for University and Research | Aschi M.,University of L'Aquila | Sanna N.,Supercomputing Center for University and Research
Physical Chemistry Chemical Physics | Year: 2011

A reduced form of a synthetic hydrogen-assembled molecular shuttle for nano-technological applications has been investigated by molecular dynamics simulations and density functional theory calculations. It is composed by a benzylic amide macrocycle mechanically locked onto a thread in acetonitrile solution. Classical sampling indicates, in agreement with experimental findings, that in equilibrium condition at 298 K the macrocycle and the naphthalimide radical anion moiety within the thread strongly interact forming four strong OCN-H-OCNR hydrogen bonds. Simulations also revealed that the geometry of the supramolecular assembly reversibly oscillates between unfolded and folded conformations, with the latter characterized by an electrostatic hook involving the succinamide end group and the macrocycle itself. Finally, the simulated UV-Vis absorption spectra for free and complexed reduced naphthalimide quantitatively confirm that the transient spectroscopic change experimentally used as a probe for monitoring the translational motion of the macrocycle, from succinamide to naphthalimide stations, accompanying the selective electrochemical reduction. © the Owner Societies.


PubMed | Supercomputing Center for University and Research
Type: Journal Article | Journal: Physical chemistry chemical physics : PCCP | Year: 2010

The UV-Vis absorption spectra of the protocatechuic acid, a potential new drug for the treatment of cancerous tumors and central nervous diseases, is for the first time fully reproduced in water solution at room temperature; these results open up the routes to integrated experimental/simulated studies in order to identify characteristic spectroscopic features of such a molecule and its derivatives within different hosting receptors in nature.


Zazza C.,Normal School of Pisa | Mancini G.,Supercomputing Center for University and Research | Brancato G.,Normal School of Pisa | Sanna N.,Supercomputing Center for University and Research | Barone V.,Normal School of Pisa
Computational and Theoretical Chemistry | Year: 2012

The oxidized form of a fully synthetic rotaxane - composed by a benzylic amide macrocycle (bam) mechanically locked onto a thread - in acetonitrile dilute solution has been investigated by classical molecular dynamics (MD) simulations and density functional theory (DFT) computations. On the basis of experimental observations, we performed MD simulations considering such a supramolecular assembly for nano-technological applications in a conformation showing the bam in electrostatic interaction with the succinamide (succ) station. At room temperature and equilibrium conditions the MD trajectory reveals that, the bam macrocycle coordinates the succ moiety by means of a cooperative hydrogen bonding network composed by four strong OCNH...OCNR contacts. In turn, DFT-predicted 1H NMR chemical shifts for methylene protons of the free and complexed succ in solution result in excellent agreement with the upfield shift of 1.2ppm detected in laboratory, thus reinforcing the experimental scenario put forward in absence of any external perturbation. Also, we realize that the intrinsic flexibility of the investigated rotaxane allows the presence of folded conformations clearly exhibiting the naphthalimide end-group in interaction, through π-π interactions, with complementary aromatic moieties located within the locked macrocycle itself. © 2012 Elsevier B.V.

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