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François Gygi

Publications and source records attributed to François Gygi.

10 recordsLinked to original sources
PubMed2006

A unified electrostatic and cavitation model for first-principles molecular dynamics in solution.

The electrostatic continuum solvent model developed by [Fattebert and Gygi J. Comput. Chem. 23, 662 (2002); Int. J. Quantum Chem. 93, 139 (2003)] is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.

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PubMed2005

Growth of carbon nanotubes on metal nanoparticles: a microscopic mechanism from ab initio molecular dynamics simulations.

We report on ab initio molecular dynamics simulations of the early stages of single-walled carbon nanotube (SWCNT) growth on metal nanoparticles. Our results show that a sp2 bonded cap is formed on an iron catalyst, following the diffusion of C atoms from hydrocarbon precursors on the nanoparticle surface. The weak adhesion between the cap and iron enables the graphene sheet to "float" on the curved surface, as additional C atoms covalently bonded to the catalyst "hold" the tube walls. Hence the SWCNT grows capped. At the nanoscale, we did not observe any tendency of C atoms to penetrate inside the catalyst, consistent with total energy calculations showing that alloying of Fe and C is very unlikely for 1 nm particles. Root growth was observed on Fe but not on Au, consistent with experiment.

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PubMed2004

Early chemistry in hot and dense nitromethane: molecular dynamics simulations.

We report density functional molecular dynamic simulations to determine the early chemical events of hot (T=3000 K) and dense (rho=1.97 g/cm(3), V/V(0)=0.68) nitromethane (CH(3)NO(2)). The first step in the decomposition process is an intermolecular proton abstraction mechanism that leads to the formation of CH(3)NO(2)H(+) and the aci ion H(2)CNO(2) (-). This event is also confirmed to occur in a fast annealing simulation to a final temperature of 4000 K at rho=2.20 g/cm(3). An intramolecular hydrogen transfer that transforms nitromethane into the aci acid form, CH(2)NO(2)H, accompanies this event. To our knowledge, this is the first confirmation of chemical reactivity with bond selectivity for an energetic material near the Chapman-Jouget state of the fully reacted material. We also report the decomposition mechanism followed up to the formation of H(2)O as the first stable product. We note that similarities in the global features of reactants, intermediates, and products of the reacting fluid seem to indicate a threshold for similar chemistry in the range of high densities and temperatures reported herein.

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PubMed2004

Self-healing of CdSe nanocrystals: first-principles calculations.

Ab initio calculations of the structural, electronic, and optical properties of CdSe nanoparticles are presented. The atomic structures of the clusters are relaxed both in vacuum and in the presence of surfactant ligands. In both cases, we predict significant geometrical rearrangements of the nanoparticle surface while the wurtzite core is maintained. These reconstructions lead to the opening of an optical gap without the aid of passivating ligands, thus "self-healing" the surface electronic structure. Our calculations also predict the existence of a midgap state responsible for recently observed subband emission.

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PubMed2004

A first principles simulation of rigid water.

We present the results of Car-Parrinello (CP) simulations of water at ambient conditions and under pressure, using a rigid molecule approximation. Throughout our calculations, water molecules were maintained at a fixed intramolecular geometry corresponding to the average structure obtained in fully unconstrained simulations. This allows us to use larger time steps than those adopted in ordinary CP simulations of water, and thus to access longer time scales. In the absence of chemical reactions or dissociation effects, these calculations open the way to ab initio simulations of aqueous solutions that require time scales substantially longer than presently feasible (e.g., simulations of hydrophobic solvation). Our results show that structural properties and diffusion coefficients obtained with a rigid model are in better agreement with experiment than those determined with fully flexible simulations. Possible reasons responsible for this improved agreement are discussed.

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PubMed2004

Towards an assessment of the accuracy of density functional theory for first principles simulations of water.

A series of Car-Parrinello (CP) molecular dynamics simulations of water are presented, aimed at assessing the accuracy of density functional theory in describing the structural and dynamical properties of water at ambient conditions. We found negligible differences in structural properties obtained using the Perdew-Burke-Ernzerhof or the Becke-Lee-Yang-Parr exchange and correlation energy functionals; we also found that size effects, although not fully negligible when using 32 molecule cells, are rather small. In addition, we identified a wide range of values of the fictitious electronic mass (micro) entering the CP Lagrangian for which the electronic ground state is accurately described, yielding trajectories and average properties that are independent of the value chosen. However, care must be exercised not to carry out simulations outside this range, where structural properties may artificially depend on micro. In the case of an accurate description of the electronic ground state, and in the absence of proton quantum effects, we obtained an oxygen-oxygen correlation function that is overstructured compared to experiment, and a diffusion coefficient which is approximately ten times smaller.

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PubMed2003

Structure and bonding of dense liquid oxygen from first principles simulations.

Using first principles simulations we have investigated the structural and bonding properties of dense fluid oxygen up to 180 GPa. We have found that band gap closure occurs in the molecular liquid, with a "slow" transition from a semiconducting to a poor metallic state occurring over a wide pressure range. At approximately 80 GPa, molecular dissociation is observed in the metallic fluid. Spin fluctuations play a key role in determining the electronic structure of the low pressure fluid, while they are suppressed at high pressure.

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PubMed2003

Melting of lithium hydride under pressure.

We have computed the melting line of lithium hydride up to 200 GPa using the two-phase simulation technique coupled with first-principles molecular dynamics. Our predicted melting temperature at high pressures varies slowly with compression, ranging from 2000 to 2450 K at 50-200 GPa pressures. The compressed fluid close to the melting line retains the ionic character of the low pressure molten state, while at higher temperatures dynamical hydrogen clustering processes are observed, which are accompanied by changes in the electronic structure.

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PubMed2002

Density functional theory for efficient ab initio molecular dynamics simulations in solution.

We present a density functional for first-principles molecular dynamics simulations that includes the electrostatic effects of a continuous dielectric medium. It allows for numerical simulations of molecules in solution in a model polar solvent. We propose a smooth dielectric model function to model solvation into water and demonstrate its good numerical properties for total energy calculations and constant energy molecular dynamics.

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