Biomedical subjects

Marcella Iannuzzi

Publications and source records attributed to Marcella Iannuzzi.

7 recordsLinked to original sources

PubMed2006

Dissociation mechanism of acetic acid in water.

The reaction mechanism for acetic acid dissociation in aqueous solution has been investigated by combining the metadynamics method with transition path sampling (TPS). By using collective variables that describe not only the deprotonation of the acid but also the solvation state of the hydronium ion and its distance from the acetate, a reactive trajectory in which stable separated ions were produced was obtained. More transition trajectories were sampled by using the TPS technique, taking the metadynamics trajectory as the initial trajectory. Two different dissociation reaction pathways were determined, one driven by the breaking of an H-bond formed by the water molecule in contact with the hydroxyl and involving the formation of a metastable contact ion pair and the other characterized by a direct transfer of the proton to the solution through an unstable Zundel-ion-like intermediate.

Acetic Acid↗

PubMed2006

Proton transfer in imidazole-based molecular crystals.

Heterocycles' aggregates show rather good proton conductivity. In particular, condensed structures formed by imidazole rings that are held together by polymeric chains have attracted some interest as possible candidate materials for fuel cell membranes. However, the details of the proton diffusion process could not be resolved by means of experimental measurements because of the fast rearrangement of the structure after each proton exchange. In this work, we report in detail the results of ab initio molecular dynamics calculations, which were briefly presented in a previous Letter [M. Iannuzzi and M. Parrinello, Phys. Rev. Lett. 93, 025901 (2004)]. The conformational changes associated with the diffusion of protons in model crystalline structures containing chains of imidazole rings are described in the framework of an atomistic approach. In particular, the bonding pattern characterizing the structure of imidazole-2-ethylene-oxide doped by an excess proton is also studied through the calculation of the 1H NMR chemical shifts. The unresolved resonances appearing in the experimental spectra could be associated with specific structural features, in connection with the fluctuating hydrogen bonding. The analysis of the distortions that induce or are induced by the mobility of the protons offers some new hints for the engineering of new proton conducting materials.

Journal Article↗

PubMed2006

Ab initio molecular dynamics study of heterogeneous oxidation of graphite by means of gas-phase nitric acid.

The interaction between gas-phase nitric acid and the graphite surface is taken as a simple model of interactions occurring at the surface of atmospheric soot particles. In particular, we study the heterogeneous processes that lead to the dissociation of the nitric acid and the production of nitrous acid. The atomistic details of the reaction mechanisms are reproduced by use of the new metadynamics method. The binding interactions of the HNO3 molecule and its fragments with the graphite surface are calculated, and the role of the surface in catalyzing the reaction is taken into account. From the reactive trajectory generated by the metadynamics, it is seen that the path goes through several different intermediate states. We analyze in detail the electronic structures and spin density distributions of the relevant products and report on the mechanisms and the main features of the transition regions relative to all the activated processes observed.

Journal Article↗

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↗

PubMed2004

Azulene-to-naphthalene rearrangement: the Car-Parrinello metadynamics method explores various reaction mechanisms.

We studied the thermal intramolecular and radical rearrangement of azulene to naphthalene by employing a novel metadynamics method based on Car-Parrinello molecular dynamics. We demonstrate that relatively short simulations can provide us with several possible reaction mechanisms for the rearrangement. We show that different choices of the collective coordinates can steer the reaction along different pathways, thus offering the possibility of choosing the most probable mechanism. We consider herein three intramolecular mechanisms and two radical pathways. We found the norcaradiene pathway to be the preferable intramolecular mechanism, whereas the spiran mechanism is the favored radical route. We obtained high activation energies for all the intramolecular pathways (81.5-98.6 kcal mol(-1)), whereas the radical routes have activation energies of 24-39 kcal mol(-1). The calculations have also resulted in elementary steps and intermediates not yet considered. A few attractive features of the metadynamics method in studying chemical reactions are pointed out.

Journal Article↗

PubMed2004

Influence of DNA structure on the reactivity of the guanine radical cation.

Oxidative damage of DNA via radical cation formation is a common cause of mutagenesis, cancer and of the physiological changes associated with aging. By using state-of-the-art ab initio molecular dynamics simulations, we study the mechanism that guides the first steps of this process. In the mechanism proposed here, guanine, which among the bases has the lowest oxidation potential, and the phosphate backbone play a crucial role. We found that the rate limiting step is the water protolysis. We illuminate the role of the local environment in considerably lowering the barrier. Of particular relevance in this respect is the role of the phosphate backbone.

Cytosine↗

PubMed2003

Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics.

The possibility of observing chemical reactions in ab initio molecular dynamics runs is severely hindered by the short simulation time accessible. We propose a new method for accelerating the reaction process, based on the ideas of the extended Lagrangian and coarse-grained non-Markovian metadynamics. We demonstrate that by this method it is possible to simulate reactions involving complex atomic rearrangements and very large energy barriers in runs of a few picoseconds.

Journal Article↗