Gianni Cardini

Hydrogen bond dynamics in liquid methanol

A Car–Parrinello molecular dynamics simulation has been performed on fully deuterated liquid methanol. The results are compared with the latest available experimental and theoretical data. It is shown that the liquid is aggregated in chains of hydrogen bonded molecules. The structure of the aggregates is characterized and it is found that the dynamics includes a fast and a slow regime. The weak H bond formed by the methyl group hydrogens and oxygen atom of surrounding molecules has been characterized. The importance of inductive effects is shown and discussed in terms of maximally localized Wannier function centers. Special attention is devoted to clarify how the molecular dipole moment depends on the number of H bonds formed by each molecule. The IR spectrum is computed and analyzed in terms of H-bond interactions. Insights on the short time dynamics and on the H-bond network are illustrated.

Structure and dynamics of carbon dioxide clusters: A molecular dynamics study

Molecular dynamics calculations have been used to explore the structure and dynamics of clusters of carbon dioxide, ranging in size up to 164 molecules. The most detailed calculations have been carried out around T=90 K with a view to interpreting the results of infrared data on clusters produced in a seeded argon beam. Under appropriate conditions, in addition to liquid‐like clusters, we have been able to produce clusters with the following structures: (i) an ordered solid—analogous to the bulk crystal, (ii) a bulk–solid core with liquid‐like outer layers, (iii) an amorphous solid, and (iv) an amorphous solid core with liquid‐like outer layers. We have calculated the dispersion of the infrared active intramolecular Q3 mode for these clusters using the transition‐dipole transition‐dipole interaction that is usually invoked to explain the infrared spectrum of the bulk crystal. The resulting spectrum for the Q3 mode of each type of cluster is quite distinct in appearance. This observation suggests that mole...

Glycerol condensed phases Part II.A molecular dynamics study of the conformational structure and hydrogen bonding

An analysis of the conformational properties and hydrogen bonding in the condensed phases of glycerol is reported using the same model as adopted in Part I (Phys. Chem. Chem. Phys., 1999, 1, 871). Structural properties of the liquid and glassy states are analyzed in relation to the molecular backbone conformation of the glycerol molecule. The effects of hydrogen bonding and of temperature on the conformational distribution are analyzed. The structural and dynamical properties of hydrogen bonding in glycerol are also investigated. The results are consistent with available experimental observations and clarify many important and interrelated aspects of the microscopic structure of liquid, glassy and crystalline phases of glycerol.

Calculation of optical spectra in liquid methanol using molecular dynamics and the chemical potential equalization method

We apply the chemical potential equalization (CPE) method to the calculation of the optical spectra in liquid methanol at 298 K and normal pressure. The configurations of the liquid are obtained by conventional molecular dynamics (MD) using a completely flexible all-atoms model. The infrared and Raman spectra are computed a posteriori using a CPE parametrization of methanol calibrated to reproduce the electronic properties of the isolated molecule evaluated with accurate ab initio calculations. The MD/CPE method reproduces correctly the optical spectra in the region of the intermolecular motions. The spectra are discussed and interpreted on the basis of hydrogen bonding structure and dynamics.

Glycerol condensed phases Part I. A molecular dynamics study

Using a model potential function we have performed a molecular dynamics simulation of several static and dynamical properties of glycerol in the crystal, glass and liquid phases. Comparison with available experimental data shows an excellent agreeent and proves the validity of the potential model used. For the calculation of the molar specific heat of the liquid and of the glass we have developed a theoretical approach which takes into account the contributions of the conformational structure energy and of the vibrational energy computed using the Bose–Einstein statistics.

Nitromethane decomposition under high static pressure.

The room-temperature pressure-induced reaction of nitromethane has been studied by means of infrared spectroscopy in conjunction with ab initio molecular dynamics simulations. The evolution of the IR spectrum during the reaction has been monitored at 32.2 and 35.5 GPa performing the measurements in a diamond anvil cell. The simulations allowed the characterization of the onset of the high-pressure reaction, showing that its mechanism has a complex bimolecular character and involves the formation of the aci-ion of nitromethane. The growth of a three-dimensional disordered polymer has been evidenced both in the experiments and in the simulations. On decompression of the sample, after the reaction, a continuous evolution of the product is observed with a decomposition into smaller molecules. This behavior has been confirmed by the simulations and represents an important novelty in the scene of the known high-pressure reactions of molecular systems. The major reaction product on decompression is N-methylformamide, the smallest molecule containing the peptide bond. The high-pressure reaction of crystalline nitromethane under irradiation at 458 nm was also experimentally studied. The reaction threshold pressure is significantly lowered by the electronic excitation through two-photon absorption, and methanol, not detected in the purely pressure-induced reaction, is formed. The presence of ammonium carbonate is also observed.

Simulated structure, dynamics, and vibrational spectra of liquid benzene

A classical molecular dynamics simulation of liquid benzene is performed, using a potential model which allows for full molecular flexibility. The short range intermolecular radial distribution function is on average reminiscent of the crystalline structure, although practically no preferential orientation can be found for the molecules in the first coordination shell. The average cage lifetime and its vibrational dynamics are obtained from appropriate time correlation functions. The intramolecular vibrations are investigated by calculating the vibrational density of states and the infrared and Raman spectra, achieving an excellent agreement with the experimental data. Finally, the dephasing of the ν1(A1g) ring breathing mode and of the ν6(E2g) in-plane bending mode is analyzed on the basis of the Kubo dephasing function. For ν1 mode the Kubo correlation time of 516 fs agrees with the experimental value, and is consistent with a relaxation mechanism involving the cage reorganization. In contrast, ν6 has a...

Characterization of a Langmuir-Blodgett monolayer using molecular dynamics calculations

Abstract Molecular dynamics calculations have been used to explore the structure and dynamics of a monolayer of long-chain molecules supported on a planar substrate. The simulation system consisted of a periodically replicated array of 90 flexible-chain molecules, each with 20 pseudo-atoms, interacting with each other via potentials appropriate to the liquid alkanes and with the substrate via a 9–3 potential. At room temperature and a surface density of 20.8 A 2 /chain, the system consists of highly ordered all-trans chains, with few conformational defects, canted at ≈40° with respect to the surface normal. Results are presented for the pseudo-atom density distribution of the film normal to the surface, the structure factor parallel to the surface, and the density of states for the low-frequency lattice vibrations. The effect of heating the system is also discussed.

On the vibrational assignment of fullerene C60

A recent density functional perturbation theory calculation of the vibrational frequencies of C60 is compared with the infrared spectrum of the crystal. The vibrational assignment of C60 is completed with the help of the calculation plus the available infrared, Raman, and inelastic neutron scattering spectra.

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.