Biomedical subjects

Giacomo Prampolini

Publications and source records attributed to Giacomo Prampolini.

4 recordsLinked to original sources

PubMed2006

Modeling a liquid crystal dynamics by atomistic simulation with an ab initio derived force field.

Atomistic molecular dynamics (MD) simulations of 4-n-pentyl 4'-cyano-biphenyl (5CB) have been performed, adopting a specific ab initio derived force field. Two state points in the nematic phase and three in the isotropic phase, as determined in a previous work, have been considered. At each state point, at least 10 ns have been produced, allowing us to accurately calculate single-molecule properties. In the isotropic phase, the values of the translational diffusion coefficient, and even more so the activation energy for the process, agree well with experimental data. Qualitatively, also the dynamic anisotropy of the nematic phase is correctly accounted for. Rotational diffusion coefficients, which describe spinning and tumbling motions, fall well within the range of experimental values. The reorientational dynamics of our model 5CB covers diverse time regimes. The longest one is strongly temperature dependent and characterized by a relaxation time in accord with experimental dielectric relaxation data. Shear viscosity and Landau-de Gennes relaxation times, typically collective variables, reproduce the experimental results very well in the isotropic phase. In the nematic phase, despite a large statistical uncertainty due to the extremely slow relaxation of the correlation functions involved, our simulation yields the correct relative order of the three experimental Miesowicz viscosities.

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PubMed2005

Density functional theory study of the conformational space of phenyl benzoate, a common fragment in many mesogenic molecules.

The complete conformational space of phenyl benzoate (three coupled rotors) has been studied by B3LYP density functional theory (DFT) at the 6-31+G* basis set level. The overall quality of the DFT results has been checked via Möller-Plesset second-order perturbation theory (MP2) calculations performed on a few significant molecular geometries. Contrary to the general belief, we have found that rotation around the C(=O)-O bond is not more restricted than rotation around the C(=O)-C bond. We have commented on the location and magnitude of the molecular dipole moment and their dependence on conformation. The energy data have been fitted through an expression containing a Fourier expansion plus a Lennard-Jones term, suitable to be used in computer simulations or to assist analysis of experimental data.

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PubMed2005

Atomistic simulation of a nematogen using a force field derived from quantum chemical calculations.

Bulk phase atomistic computer simulations of 4-n-pentyl-4'-cyanobiphenyl (5CB) were performed with a specific force field obtained from ab initio and DFT calculations. The intermolecular potential was previously derived through the fragmentation reconstruction method (FRM), developed in our group. The description of some intramolecular interactions, like the torsional potential between the phenyl rings and at the aryl-alkyl linkage, is achieved through accurate DFT studies. Lengthy ( approximately 40 ns) molecular dynamics (MD) simulations were then carried out at constant atmospheric pressure and different temperatures. The system was stable in the experimental crystalline structure up to 285 K, where the early stage of the melting process appears with the loss of positional order. At higher temperatures (between 290 and 305 K) a kinetically stable, orientationally ordered phase is obtained. This nematic phase was reached starting with three initial configurations, differing in their orientational order parameter. The calculated values of thermodynamic and structural properties of each phase were in fairly good agreement with the relevant experimental data.

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PubMed2004

Computer simulation of solid and liquid benzene with an atomistic interaction potential derived from ab initio calculations.

Molecular dynamics atomistic simulations of solid and liquid benzene have been performed, employing a model intermolecular potential derived from quantum mechanical calculations. The ab initio database includes approximately 200 geometries of the benzene dimer with interaction energies computed at the MP2 level of theory. The accuracy of the modeled force field results is satisfactory. The thermodynamic and structural properties, calculated in the condensed phases, are compared with experimental data and previous simulation results. Single particle and collective dynamical properties are also investigated through the calculation of translational and rotational diffusion coefficients, reorientational dynamics, and viscosities. The agreement of these data with experimental measurements confirms the reliability of the proposed force field.

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