Pietro Ballone

Structure and spin in small iron clusters

Abstract Density functional calculations have been performed for iron clusters with up to seven atoms. The electron-ion interaction is treated by a pseudopotential, and the large effect of core electrons on the spin configuration by modifying the exchange-correlation function. The scheme allows us to perform molecular dynamics (MD, Car-Parrinello) simulations and to explore the potential energy surface of the cluster without symmetry or other constraints. The most stable structures have magnetic moments ≈3 μ B per atom and are generally compact. We discuss the structural trends, particularly the similarities with the close-packed structures found in clusters where the atoms interact with a pairwise Lennard-Jones potential.

ZERO TEMPERATURE PHASES OF THE ELECTRON GAS

The stability of different phases of the three-dimensional nonrelativistic electron gas is analyzed using stochastic methods. With decreasing density, we observe a {ital continuous} transition from the paramagnetic to the ferromagnetic fluid, with an intermediate stability range (20{plus_minus}5{le}r{sub s}{le}40{plus_minus}5 ) for the {ital partially} spin-polarized liquid. The freezing transition into a ferromagnetic Wigner crystal occurs at r{sub s}=65{plus_minus}10 . We discuss the relative stability of different magnetic structures in the solid phase. {copyright} {ital 1999} {ital The American Physical Society}

Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems

This study deals with a novel molecular simulation technique, named adiabatic bias molecular dynamics (MD), which provides a simple and reasonably inexpensive route to generate MD trajectories joining points in conformational space separated by activation barriers. Because of the judicious way the biasing potential is updated during the MD runs, the technique allows with some additional effort the computation of the free energy change experienced during the trajectory. The adiabatic bias method has been applied to a nontrivial problem: The unfolding of an atomistic model of lysozyme. Here, the radius of gyration (Rg) was used as a convenient reaction coordinate. For changes in Rg between 19.7 and 28 A, we observe a net loss of the native tertiary structure of lysozyme. At the same time, secondary structure elements such as α-helices are retained although some of the original order is diminished. The calculated free energy profile for the unfolding transition shows a monotonous increase with Rg and depends...

Ion Association in [bmim][PF6]/Naphthalene Mixtures: An Experimental and Computational Study

Mixtures of room temperature ionic liquids (IL) with neutral organic molecules provide a valuable testing ground to investigate the interplay of the ionic and molecular-dipolar state in dense Coulomb systems at near ambient conditions. In the present study, the viscosity eta and the ionic conductivity sigma of 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6])/naphthalene mixtures at T = 80 degrees C have been measured at 10 stoichiometries spanning the composition range from pure naphthalene to pure [bmim][PF6]. The viscosity grows nearly monotonically with increasing IL mole fraction ( x), whereas the conductivity per ion displays a clear peak at x approximately 15%. The origin of this maximum has been investigated using molecular dynamics simulations based on a classical force field. Snapshots of the simulated samples show that the conductivity maximum is due to the gradual transition in the IL component from an ionic state at high x to a dipolar fluid made of neutral ion pairs at low x. At concentrations x < 0.20 the ion pairs condense into molecular-thin filaments bound by dipolar forces and extending in between nanometric droplets of IL. These results are confirmed and complemented by the computation of dynamic and transport properties in [bmim][PF6]/naphthalene mixtures at low IL concentration.

A DENSITY FUNCTIONAL STUDY OF IRON-PORPHYRIN COMPLEXES

Abstract Equilibrium structures for oxygen and carbon monoxide complexes of iron porphyrin (FeP), computed with Car-Parrinello molecular dynamics, are in agreement with experimental data of heme models. In addition, we provide information on binding energies and spin-structure relationships, helping to understand the chemistry of the heme prosthetic group.

STRUCTURE AND DYNAMICS OF PROTONATED MG2SIO4 : AN AB-INITIO MOLECULAR DYNAMICS STUDY

Abstract We studied structural and dynamical properties of H+ absorbed in Mg2SiO4 by ab-initio molecular dynamics. We first calculated the T = 0 equation of state of pure forsterite as a function of pressure, and we determined the relative stabilities of the olivine, p-spinel, and spinel polymorphs. The results show that the ab-initio model successfully reproduces the known structural properties of the system. In the protonated phases, in agreement with experimental evidence, our computations show that H+ is absorbed preferentially in the β-spinel phase. The most stable absorption site is located close to the O1 atom, which is coordinated by five Mg2+ cations and not directly bound to Si. In addition to this stable absorption site, the computation reveals othe|r low-energy positions, forming an extended network of hydrogen bonds, that could play an important role in the diffusion of H+ in β-spinel. We analyze the dependence of structure and dynamics of the pure and protonated phases as a function of temperature and pressure.

A dielectric continuum molecular dynamics method

We introduce a novel method to simulate hydrated macromolecules with a dielectric continuum representation of the surrounding solvent. In our approach, the interaction between the solvent and the molecular degrees of freedom is described by means of a polarization density free energy functional which is minimum at electrostatic equilibrium. After a pseudospectral expansion of the polarization and a discretization of the functional, we construct the equations of motion for the system based on a Car–Parrinello technique. In the limit of the adiabatic evolution of the polarization field variables, our method provides the solution of the dielectric continuum problem “on the fly,” while the molecular coordinates are propagated. In this first study, we show how our dielectric continuum molecular dynamics method can be successfully applied to hydrated biomolecules, with low cost compared to free energy simulations with explicit solvent. To our knowledge, this is the first time that stable and conservative molecu...

Computational study of room-temperature ionic liquids interacting with a POPC phospholipid bilayer.

Molecular dynamics simulations based on an empirical force field have been carried out to investigate the properties of a zwitter-ionic phospholipid (POPC) bilayer in contact with a water solution of [bmim][Cl], [bmim][PF(6)] and [bmim][Tf(2)N] at concentration c = 0.5 M. The results reveal important and specific interactions of cations and anions with the bilayer. The [bmim](+) cation, in particular, shows a clear tendency to be incorporated tail-first into the bilayer. [Cl](-) remains in solution, [PF(6)](-) forms a thin layer on the lipid surface, and [bmim][Tf(2)N] precipitates out of the solution, giving rise to an ionic droplet deposited on the lipid surface. The simulation results provide a microscopic basis to interpret the available experimental observations.

Density functional and Monte Carlo studies of sulfur. I. Structure and bonding in Sn rings and chains (n=2–18)

Density functional calculations have been performed for ring isomers of sulfur with up to 18 atoms, and for chains with up to ten atoms. There are many isomers of both types, and the calculations predict the existence of new forms. Larger rings and chains are very flexible, with numerous local energy minima. Apart from a small, but consistent overestimate in the bond lengths, the results reproduce experimental structures where known. Calculations are also performed on the energy surfaces of S8 rings, on the interaction between a pair of such rings, and the reaction between one S8 ring and the triplet diradical S8 chain. The results for potential energies, vibrational frequencies, and reaction mechanisms in sulfur rings and chains provide essential ingredients for Monte Carlo simulations of the liquid–liquid phase transition. The results of these simulations will be presented in Part II.

Squeezing lubrication films: Layering transition for curved solid surfaces with long-range elasticity

The properties of an atomic lubricant confined between two approaching solids are investigated by a model that accounts for the curvature and elastic properties of the solid surfaces. Well defined atomic layers develop in the lubricant film when the width of the film is of the order of a few atomic diameters. An external squeezing-pressure induces discontinuous, thermally activated changes in the number n of lubricant layers. The precise mechanism for these layering transitions depends on n, and on the lubricant-surface pinning barriers. Thus, in the absence of sliding, unpinned or weakly pinned incommensurate lubricant layers give rise to fast and complete layering transitions. Strongly pinned incommensurate and commensurate layers give rise to sluggish and incomplete transformations, resulting in trapped islands. In particular, for commensurate layers it is often not possible to squeeze out the last few lubricant layers. However, lateral sliding of the two solid surfaces breaks down the pinned structures, greatly enhancing the rate of the layering transitions. In the case of sliding, an important parameter is the barrier for sliding one lubricant layer with respect to the others. When this barrier is larger than the lubricant-surface pinning barrier, the lubricant film tends to move like a rigid body with respect to the solid surface. In the opposite case, slip events may occur both within the lubricant film and at the lubricant–solid interface, making the squeeze-out process much more complex. In some of the simulations we observe an intermediate phase, forming immediately before the layering transition. This transient structure has a lower 2D density than the initial phase, and allows the system to release elastic energy, which is the driving force for the phase transformation.