Biomedical subjects

Vincenzo Schettino

Publications and source records attributed to Vincenzo Schettino.

At least 19 recordsLinked to original sources

PubMed2006

Triggering dynamics of the high-pressure benzene amorphization.

Success in designing and tailoring solid-state reactions depends on the knowledge of the mechanisms regulating the reactivity at the microscopic level. In spite of several attempts to rationalize the reactivity of crystals, the question of the existence of a critical distance for a reaction to occur remains unsolved. In this framework, the role of lattice phonons, which continuously tune the relative distance and orientation of the molecules, is still not fully understood. Here, we show that at the onset of the transformation of crystalline benzene to an amorphous hydrogenated carbon the intermolecular C-C distance is always the same (about 2.6 A) once collective motions are taken into account, and it is independent of the pressure and temperature conditions. This conclusion is supported by first-principles molecular-dynamics simulations. This is a clear demonstration of the role of lattice phonons in driving the reactivity in the crystalline phase by fine-tuning of the nearest-neighbour distances. The knowledge of the critical C-C distance can be crucial in planning solid-state reactions at moderate pressure.

Journal Article↗

PubMed2006

Structure and dynamics of Br- ion in liquid methanol.

A Car-Parrinello molecular dynamics simulation has been performed on a solution of Br- in liquid methanol analyzing with particular attention charge transfer and polarization effects. The first solvation shell has been characterized in terms of H-bonds, and it has been found that the high polarization of the bromide gives rise to a stable solvent cage. The differences in the coordination number with the chloride can be ascribed to the ionic radius and to the stronger perturbations brought by the solvent to the bromide ion.

Journal Article↗

PubMed2006

Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations.

We propose a new approach for the umbrella sampling method in molecular dynamics simulations of complex systems. An accelerated sampling of the slow degrees of freedom is achieved by generating a single self-adaptive trajectory that tends to span uniformly the reaction coordinate using a time dependent bias potential derived from the preceding history of the system. To show the convergent behavior and the efficiency of the method, we present the free energy surface of alanine dipeptide in water as a function of the backbone dihedral angles.

Journal Article↗

PubMed2006

Solid-state phase transition induced by pressure in LiOH x H2O.

When the free energy surface of the lithium hydroxide monohydrate crystal was explored, the high-pressure solid-state phase transition was determined. The high-pressure phase has been obtained through ab initio Car-Parrinello molecular dynamics simulation in the isothermic-isobaric ensemble. The recent metadynamics method has been applied to overcome the high activation energy barriers typical of rare events, like solid-state phase transition at high pressures. In the LiOH x H2O system, there are two kinds of H bonds: water-water and hydroxyl-water. The effect of the pressure has been investigated, to give further insight into the high-pressure phase. The strengthening of the H bonds of the system produces modifications in the water and the hydroxyl ion dipole electronic environment. The infrared spectra of both phases have been calculated and compared with experiments, and the assignment of the external modes has been discussed.

Lithium Compounds↗

PubMed2006

Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding.

In the present study we have used molecular dynamics simulations to study the stability of the antiparallel beta-sheet in cellular mouse prion protein (PrP(C)) and in the D178N mutant. In particular, using the recently developed non-Markovian metadynamics method, we have evaluated the free energy as a function of a reaction coordinate related to the beta-sheet disruption/growth. We found that the antiparallel beta-sheet is significantly weaker in the pathogenic D178N mutant than in the wild-type PrP(C). The destabilization of PrP(C) beta-structure in the D178N mutant is correlated to the weakening of the hydrogen bonding network involving the mutated residue, Arg164 and Tyr128 side chains. This in turn indicates that such a network apparently provides a safety mechanism for the unzipping of the antiparallel beta-sheet in the PrP(C). We conclude that the antiparallel beta-sheet is likely to undergo disruption rather than growth under pathogenic conditions, in agreement with recent models of the misfolded monomer that assume a parallel beta-helix.

Animals↗

PubMed2006

Lithium hydroxide phase transition under high pressure: an ab initio molecular dynamics study.

The high-pressure phase transition in the deuterated lithium hydroxide crystalline state has been studied by Car-Parrinello molecular dynamics simulations, in the constant-pressure, constant-temperature ensemble. The recently developed metadynamics approach has been applied to encourage the system to transform into different phases in an affordable simulation time. A previously not completely characterized high-pressure phase has been obtained. The structural and spectroscopic properties have been studied and compared with the neutron scattering, infrared and Raman measurements. It has been found that the calculated structure differs slightly from the experimental hypothesis, and that the presence of strong hydrogen bonds is the source of the red shift and of the characteristic features of the OD-stretching bands in both IR and Raman spectra.

Journal Article↗

PubMed2005

Pressure-induced polymerization in solid ethylene.

Ethylene is the simplest organic molecule containing a double bond and is the starting monomeric unit in the synthesis of polyethylene, one of the most largely produced polymers. Here we report a high pressure infrared study of ethylene at room temperature. A polymerization reaction is observed when the crystalline phase I is compressed above 3.0 GPa. The reaction kinetics was investigated at two different pressures, 3.6 and 5.4 GPa. The recovered product was identified in both cases as polyethylene, but while a conformationally disordered and branched low-density polymer is obtained at the highest pressure, a high-density crystalline polymer is obtained at 3.6 GPa. A reaction mechanism was proposed on the basis of the kinetic data and the structural information.

Journal Article↗

PubMed2005

High-pressure reactivity of propene.

The phase diagram of propene has been investigated at high pressure by using the diamond anvil cell technique and Fourier transform infrared spectroscopy. The pressure conditions necessary to induce a spontaneous reaction of the sample have been found at different temperatures, allowing the stability boundary of propene to be drawn. The reaction is diffusion controlled and seems to occur only in the fluid phase, implying a slope inversion of the stability boundary at about 250 K. The product of the reaction is a mixture of linear oligomers independently of the P-T conditions. The activation volume and energy of the process have been obtained from the kinetic data. Also the activation of the reaction by laser absorption has been carefully studied. A high proton mobility has been identified as the likely reason that limits the lengthening of the chain up to six to eight monomeric units preventing the polymer formation.

Journal Article↗

PubMed2005

Behavior of polarizable models in presence of strong electric fields. I. Origin of nonlinear effects in water point-charge systems.

In the current opinion, the inclusion of polarization response in classical computer simulations is considered as one of the most important and urgent improvements to be implemented in modern empirical potential models. In this work we focus on the capability of polarizable models, based on the pairwise Coulomb interactions, to model systems where strong electric fields enter into play. As shown by Masia, Probst, and Rey (MPR) [in J. Chem. Phys. 121, 7362 (2004)], when a molecule interacts with point charges, polarizable models show underpolarization with respect to ab initio methods. We prove that this underpolarization, clearly related to nonlinear polarization effects, cannot be simply ascribed to the lack of hyperpolarization in the polarizable models, as suggested by MPR. Analysis of the electron-density rearrangement induced on a water molecule by a point charge reveals a twofold level of polarization response. One level involves intramolecular charge transfer on the whole molecular volume, with the related polarization exhibiting a seemingly linear behavior with the external electric field. The other nonlinear polarization level occurs only at strong electric fields and is found to be strictly correlated to the quantum-mechanical nature of the water molecule. The latter type of polarization has a local character, being limited to the space region of the water lone pairs.

Journal Article↗

PubMed2005

A combined Raman, DFT and MD study of the solvation dynamics and the adsorption process of pyridine in silver hydrosols.

The adsorption of pyridine onto silver colloids has been investigated by Raman spectroscopy experiments and by ab initio DFT and MP2 calculations. The solvation dynamics of the pyridine in water has been studied by a molecular dynamics simulation. The results are compared with the latest available experimental and theoretical data. It is found that the pyridine is essentially hydrogen bonded to one solvent molecule. Calculations based on pyridine-water and pyridine-Ag(+) complexes allow the reproduction of the experimentally observed Raman features and explain the adsorption process of the ligand in silver hydrosols.

Colloids↗

PubMed2005

Comparing polarizable force fields to ab initio calculations reveals nonclassical effects in condensed phases.

In a recent work [Giese and York J. Chem. Phys. 120, 9903 (2004)] showed that many-body force field models based solely on pairwise Coulomb screening cannot simultaneously reproduce both gas-phase and condensed-phase polarizability limits. In particular, polarizable force fields applied to bifurcated water chains have been demonstrated to be overpolarized with respect to ab initio methods. This behavior was ascribed to the neglect of coupling between many-body exchange and polarization. In the present article we reproduce those results using different ab initio levels of theory and a polarizable model based on the chemical-potential equalization principle. Moreover we show that, when hydrogen-bond (H-bond) forming systems are considered, an additional nonclassical effect, i.e., intermolecular charge transfer, must be taken into account. Such effect, contrarily to that of coupling between many-body exchange and polarization, makes classical polarizable force fields underpolarized. In the case of water at standard conditions, being H-bonded geometries much more probable than the bifurcated ones, intermolecular charge transfer is the dominant effect.

Journal Article↗

PubMed2005

Solvation dynamics of Li+ and Cl- ions in liquid methanol.

Car-Parrinello molecular dynamics simulations have been performed on Li(+) and Cl(-) in fully deuterated liquid methanol. The results have been compared with available experimental and theoretical data. It has been found that the lithium cation has a stable tetrahedral coordination, whereas the chloride anion presents an average coordination number of 3.56. The polarization effects induced by the ion on the solvent have been analyzed in terms of Wannier function centers. Particular attention has been devoted to the charge transfer, which is particularly important in these types of systems. Evidence for the stability of the lithium cation solvent cage also has been found in the vibrational spectra.

Chemistry, Physical↗

PubMed2005

Polarization response of water and methanol investigated by a polarizable force field and density functional theory calculations: implications for charge transfer.

Electronic polarization response in hydrogen-bond clusters and liquid configurations of water and methanol has been studied by density functional theory (DFT) and by a polarizable force field based on the chemical potential equalization (CPE) principle. It has been shown that an accurate CPE parametrization based on isolated molecular properties is not completely transferable to strongly interacting hydrogen-bond clusters with discrepancies between CPE and DFT overall dipole moments as large as 15%. This is due to the lack of intermolecular charge transfer in the standard CPE implementation. A CPE scheme for evaluating the amount of transferred charge has been developed. The charge transfer parameters are determined with the aid of accurate DFT calculations using only hydrogen-bond dimer configurations. The amount of transferred charge is found to be of the order of few hundredths of electrons, as already found in recent studies on hydrogen-bond systems. The parameters of the model are then used, without further adjustment, to different hydrogen-bond clustered forms of water and methanol (oligomer and liquid configurations). In agreement with different approaches proposed in literature for studying charge transfer effects, the transferred charge in hydrogen-bond dimers is found to decrease exponentially with the hydrogen-bond distance. When allowance is made for charge transfer according to the proposed scheme, the CPE dipole moments are found to reproduce satisfactorily the DFT data.

Journal Article↗

PubMed2004

Misfolding pathways of the prion protein probed by molecular dynamics simulations.

Although the cellular monomeric form of the benign prion protein is now well characterized, a model for the monomer of the misfolded conformation (PrP(Sc)) remains elusive. PrP(Sc) quickly aggregates into highly insoluble fibrils making experimental structural characterization very difficult. The tendency to aggregation of PrP(Sc) in aqueous solution implies that the monomer fold must be hydrophobic. Here, by using molecular dynamics simulations, we have studied the cellular mouse prion protein and its D178N pathogenic mutant immersed in a hydrophobic environment (solution of CCl4), to reveal conformational changes and/or local structural weaknesses of the prion protein fold in unfavorable structural and thermodynamic conditions. Simulations in water have been also performed. Although observing in general a rather limited conformation activity in the nanosecond timescale, we have detected a significant weakening of the antiparallel beta-sheet of the D178N mutant in CCl4 and to a less extent in water. No weakening is observed for the native prion protein. The increase of beta-structure in the monomer, recently claimed as evidence for misfolding to PrP(Sc), has been also observed in this study irrespective of the thermodynamic or structural conditions, showing that this behavior is very likely an intrinsic characteristic of the prion protein fold.

Animals↗

PubMed2004

High-pressure synthesis of crystalline polyethylene using optical catalysis.

Polymerization processes are probably the most relevant example of a chemical reaction activated by catalysts or radical initiators. Among polymers, polyethylene is by far the most common and largely produced. Here we present a high-pressure synthesis of high-density crystalline polyethylene by using only physical tools such as pressure and light. Low-density polyethylene is obtained by compressing ethylene at room temperature above 3 GPa in the ordered crystal phase, and a highly crystalline polymer is produced in the fluid phase at pressures lower than 1 GPa by using continuous-wave laser lines (lambda < or = 460 nm) as an optical catalyst. The photo-activation is based on a two-photon absorption process to pi* antibonding states, where the change in molecular geometry favours the polymeric chain formation. The high yield and crystallinity of the polymer recovered by the photoinduced reaction and the simplicity of the synthesis make this process appealing for large-scale applications.

Journal Article↗

PubMed2004

Inter-residue and solvent-residue interactions in proteins: a statistical study on experimental structures.

A large set of protein structures resolved by X-ray or NMR techniques has been extracted from the Protein Data Bank and analyzed using statistical methods. In particular, we investigate the interactions between side chains and the interactions between solvent and side chains, pointing out on the possibility of including the solvent as part of a knowledge-based potential. The solvent-residue contacts are accounted for on the basis of the Voronoi's polyhedron analysis. Our investigation confirms the importance of hydrophobic residues in determining the protein stability. We observe that in general hydrophobic-hydrophobic interactions and, more specifically, aromatic-aromatic contacts tend to be increasingly distally separated in the primary sequence of proteins, thus connecting distinct secondary structure elements. A simple relation expressing the dependence of the protein free energy by the number of residues is proposed. Such a relation includes both the residue-residue and the solvent-residue contributions. The former is dominant for large size proteins, whereas for small sizes (number of residues less than 100) the two terms are comparable. Gapless threading experiments show that the solvent-residue knowledge-based potential yields a significant contribution with respect to discriminating the native structure of proteins. Such contribution is important especially for proteins of small size and is similar to that given by the most favorable residue-residue knowledge-based potential referring to hydrophobic-hydrophobic interactions such as isoleucine-leucine. In general, the inclusion of the solvent-residue interaction produces a relevant increase of the free energy gap between the native structures and decoys.

Amino Acids↗

PubMed2004

High pressure reactivity of propene by first principles molecular dynamics calculations.

The reactivity of propene under high pressure has been investigated in the framework of Car-Parrinello molecular dynamics. Changes in structural and electronic properties due to pressure have been analyzed in systems with a density ranging from 0.855 to 2.151 g/cm(3). A ionic collective mechanism which leads to the formation of oligomers has been found by both spin restricted and spin polarized formalism. The maximally localized Wannier centers analysis has allowed us to characterize the addition scheme and to identify a Wannier center with a high spread value involved in the formation of the principal reaction products.

Journal Article↗

PubMed2002

The nature of intermolecular interactions between aromatic amino acid residues.

The nature of intermolecular interactions between aromatic amino acid residues has been investigated by a combination of molecular dynamics and ab initio methods. The potential energy surface of various interacting pairs, including tryptophan, phenilalanine, and tyrosine, was scanned for determining all the relevant local minima by a combined molecular dynamics and conjugate gradient methodology with the AMBER force field. For each of these minima, single-point correlated ab initio calculations of the binding energy were performed. The agreement between empirical force field and ab initio binding energies of the minimum energy structures is excellent. Aromatic-aromatic interactions can be rationalized on the basis of electrostatic and van der Waals interactions, whereas charge transfer or polarization phenomena are small for all intermolecular complexes and, particularly, for stacked structures. Proteins 2002;48:117-125.

Amino Acids, Aromatic↗