M. Albertí

Atom-bond pairwise additive representation for cation-benzene potential energy surfaces: An ab initio validation study.

The achievement of extensive and meaningful molecular dynamics simulations requires both the detailed knowledge of the basic features of the intermolecular interaction and the representation of the involved potential energy surface in a simple, natural and analytical form. This double request stimulated us to extend to ion-molecule systems a semiempirical method previously introduced for the description of weakly interacting atom-molecule aggregates and formulated in terms of atomic species-molecular bond interaction additivity. The method is here applied to the investigation of the prototypical M(+)-C6H6 systems (M = Li, Na, K, Rb and Cs) and some of its predictions are tested against accurate ab initio calculations. Such calculations have been performed by employing the MP2 method and large basis sets, privileging the description of the metal atoms. The agreement between potential energy scans semiempirically obtained and ab initio results is good for all the investigated geometries, thus showing that the adopted representation is in general able to reproduce all the main features of the potential energy surface for these systems. The role of the various noncovalent interaction components, as a function of the geometry and of the intermolecular distance in the M(+)-C6H6 complexes, is also investigated for a more detailed assessment of the results of the semiempirical method.

Tetrahedral ordering in water: Raman profiles and their temperature dependence.

The supramolecular organization of liquid water is discussed in connection with both the spectral profile of the OH stretching Raman signal measured in pure water and the distribution of tetrahedral order computed by molecular dynamics simulations. Both curves show common features and a similar temperature dependence never pointed out before. Energetic information extracted from the Raman profiles using a recently proposed integration method is also discussed. Overall results confirm that thermally induced structural variations of water in the interval of temperature ranging from 10 to 75 degrees C involve a change of the local tetrahedral order associated with a redistribution energy of 1.6-1.7 kcal/mol.

A generalized formulation of ion-π electron interactions: role of the nonelectrostatic component and probe of the potential parameter transferability.

The intermolecular potentials for hexafluorobenzene (HFBz) and 1,3,5-trifluorobenzene (TFBz) interacting with alkali (M(+); M = Li, Na, K, Rb, Cs) and halogen (X(-); X = F, Cl, Br, I) ions are provided as a combination of electrostatic and nonelectrostatic terms. The ion-HFBz and ion-TFBz electrostatic components are formulated as a sum of Coulombic potentials associated with the interactions between the ion charge and point charges on the molecular frame, whose distributions are consistent with the permanent quadrupole moment of HFBz and TFBz, respectively. The corresponding nonelectrostatic components are represented as a sum of effective potential functions, each one having a specific physical meaning, related to ion-molecular bond pair interactions. In the present paper, we test the transferability of the ion-bond potential parameters. Moreover, the powerfulness of the model is analyzed by comparing predicted binding energies and equilibrium geometries for the family of M(+)-HFBz, X(-)-HFBz, M(+)-TFBz, and X(-)-TFBz systems with available ab initio results.

Rare gas-benzene-rare gas interactions: structural properties and dynamic behavior.

In the present work, some static and dynamic properties of trimers containing one benzene molecule and two rare gas atoms are investigated. These trimers can be formed in two different configurations, one in which the two rare gas atoms are placed in opposite sides of the benzene plane, (1|1), and the other in which the two atoms are placed on the same side, (2|0). The (1|1) configuration is more stable than the (2|0), and both minima are connected by small energy barriers. Accordingly, molecular dynamics simulations show frequent (2|0) <--> (1|1) interconversions, even at low temperatures. The time spent in each configuration has been related to the abundance of isomers. It has been found that at temperatures just below the dissociation, when interconversions are quite frequent, the relative abundance of (2|0) is always higher than that of (1|1), independently of the nature of the two rare gases.

Cation−π-Anion Interaction in Alkali Ion−Benzene−Halogen Ion Clusters†

The present investigation on some ternary M(+)-benzene-X(-) aggregates follows previous studies concerning the binary, M(+)-benzene (M = Li, Na, K, Rb, Cs) and X(-)-benzene (X = F, Cl, Br, I), systems. A semimepirical model describing the intermolecular potential energy, formulated as a combination of few leading effective components, is here extended and applied to investigate more complex systems. The balancing of size repulsion with induction and dispersion attraction is described as a combination of ion-bond interactions and an electrostatic component, rationalized on the basis of the benzene quadrupole moment, is also included. For M(+)-benzene-X(-) aggregates, the simultaneous presence of a cation and an anion close to the pi system originates a strong Coulombic attraction and nonadditivity effects of the induction energy, which are carefully considered and explicitly included to obtain a proper analytical functional representation of the ternary compound. The proposed semiempirical methodology, providing the whole potential energy surface in a convenient analytical form, is useful to predict the main features of stable and unstable configurations, saddle points, and energy barriers, allowing for investigation of their influence on molecular dynamics simulations.

A study to improve the van der Waals component of the interaction in water clusters

A portable model potential, representing the intermolecular interaction of water as a combination of a few effective components given in terms of the polarizability and dipole moment values of the molecular partners, is here proposed as a building block of the force field of water clusters in molecular dynamics simulations. In this spirit, here, we discuss the key properties of the model potential and its application to water dimers, trimers and tetramers with the purpose of extrapolating the results to very large clusters mimicking the liquid phase. The suitability of the model potential for dynamics investigations is checked by comparing on one hand the value of the second virial coefficient calculated for the gaseous dimer with experimental data measured over a wide range of temperature (273–3000 K) and, on the other hand, the calculated radial distribution functions and density with those obtained from experiments performed using liquid water.

A Model Potential for Acetonitrile: from Small Clusters to Liquid

A portable model potential, representing the intermolecular interaction of acetonitrile with itself and with ions, is proposed. Such model, formulated as a combination of a few effective components, given in terms of the polarizability and dipole moment values of the molecular partners, is here adopted as a building block of the force field of acetonitrile clusters in molecular dynamics simulations. Its reliability is tested by comparing the predicted features for both small ionic and neutral clusters containing acetonitrile with ab initio results and experimental information. Its application to molecular dynamics simulations of liquid acetonitrile and of the solvated Li(+), Na(+), K(+), and I(-), performed at several values of the temperature, discloses an ample and interesting phenomenology, described in an internally consistent way. Such model will be useful to assess the effect of intermolecular interactions on the dynamics of acetonitrile processes occurring in various environments of applied relevance, with emphasis on the dye-sensitized solar cell framework.

Benzene-hydrogen bond (C6H6-HX) interactions: the influence of the X nature on their strength and anisotropy.

The intermolecular potential energy of the C6H6-SH2 and C6H6-NH3 dimers is formulated as combination of independent electrostatic and nonelectrostatic contributions. The relevant parameters of the nonelectrostatic terms, derived from molecular polarizability components, have been proved to be useful to describe in a consistent way both size repulsion and dispersion attraction forces. The representation adopted for the electrostatic contribution asymptotically reproduces the dipole quadrupole interaction. To test the validity of the proposed potential formulation, the features of the most stable configurations of the systems predicted have been compared with the available ab initio and experimental data. Moreover, the strength of the C6H6-HX interaction has been analyzed comparing the obtained results with the corresponding ones for the C6H6-H2O and C6H6-CH4 systems, investigated previously with the same methodology. Information on the relative orientation dependence of the partners, arising from the anisotropy of the intermolecular interaction, evaluated at different intermolecular distances, has been also obtained. Such information is crucial to evaluate sterodynamics effects in bimolecular collisions.

An innovative synergistic grid approach to the computational study of protein aggregation mechanisms

Thanks to the advances in grid technologies, we are able to propose here an evolution of our molecular simulator that, when moving to larger systems, instead of reducing the granularity of the dynamical treatment (as is often done in molecular dynamics studies of such systems) exploits the extra power of the grid approach to the end of preserving the detailed nature of theatomistic formulation of the interaction. Key steps of such evolution are: (1) the assemblage of the interaction based on a composition of the ab initio intramolecular data and a portable parameterization of the intermolecular potential linking ab initio evaluation of intramolecular potentials and the partitioning of molecular polarizability; (2) the exploitation of an efficient coordinated porting and running of molecular dynamics codes on the European grid distributed computing infrastructure. As a prototype case study, the N-methylacetamide dimer in vacuo has been considered and the formation of possible conformers is analyzed.

Competitive role of CH4-CH4 and CH-π interactions in C6H6-(CH4)n aggregates: the transition from dimer to cluster features.

The intermolecular methane-methane and benzene (Bz)-methane interactions formulated in this paper are suitable to investigate systems of increasing complexity. The proposed CH(4)-CH(4) and Bz-CH(4) potential energy functions are indeed applied to study some macroscopic properties of methane and important features of both small Bz-(CH(4))(n) (n > 1-10) clusters and Bz surrounded by several CH(4) molecules. Relevant parameters of the interaction, derived from molecular polarizability components, have been proved to be useful to describe in a consistent way both size repulsion and dispersion attraction forces. The proposed potential model also allows one to isolate the role of the different intermolecular energy contributions. The spatial distribution of the CH(4) molecules in the clusters is investigated by means of molecular dynamics simulations under various conditions, even when methane phase transition from liquid to gas is likely to occur. In addition, several properties, such as radial distribution functions, density values, and mean diffusion coefficients, are analyzed in detail.