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Michele Parrinello

Publications and source records attributed to Michele Parrinello.

49 records · Page 3Linked to original sources
PubMed2003

First-principles molecular-dynamics simulations of a hydrated electron in normal and supercritical water.

A first principles study of a hydrated electron in water at ordinary and supercritical conditions is presented. In the first case, the electron cleaves a cavity in the hydrogen bond network in which six H2O molecules form the solvation shell. The electron distribution assumes an ellipsoidal shape, and the agreement of the computed and the experimental optical absorption seems to support this picture. At supercritical conditions, instead, the H-bond network is not continuous and allows us to predict that the electron localizes in preexisting cavities in a more isotropic way. Four water molecules form the solvation shell but the localization time shortens significantly.

Journal Article↗
PubMed2002

Pulling monatomic gold wires with single molecules: an Ab initio simulation.

Car-Parrinello molecular dynamics simulations demonstrate that pulling a single thiolate molecule anchored on a stepped gold surface does not preferentially break the sulfur-gold chemical bond. Instead, it is found that this process leads to the formation of a monoatomic gold nanowire, followed by breaking a gold-gold bond with a rupture force of about 1.2 nN. The simulations also indicate that previous single-molecule thiolate-gold and gold-gold rupture experiments both probe the same phenomenon, namely, the breaking of a gold-gold bond within a gold nanowire.

Journal Article↗
PubMed2002

Escaping free-energy minima.

We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the FES, allowing the efficient exploration and accurate determination of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.

Alanine↗
PubMed2002

Protonation state of the equatorial ligands and dynamics of the OH...O units in a cobaloxime biomimetic.

The protonation state of the dimethylglyoxime ligands in the B(12) coenzyme biomimetic [Co(CCl=CHCl)(dmgH)(2)(py)].CHCl(3) was investigated by using first-principles molecular dynamics. Our simulations at 173 and 300 K reveal that one of the oxime protons remains bonded to a nitroxyl group, while the proton of the second NO...H-ON unit is essentially shared with similar probability between the two oxygen atoms. This reconciles the results of the experimental determination (Jones, P. G.; Yang, L.; Steinborn, D. Acta Cryst. 1996, C52, 2399), showing all N-O distances as equivalent, with the commonly accepted rule that the protonation state of the dimethylglyoxime ligands can be identified by the different N-O distances. Further aspects of the dynamics of the OH...O units, in relation to the occurrence of weak CH...O intermolecular interactions, are analyzed.

Journal Article↗
PubMed2002

Ab-initio study of NMR chemical shifts of water under normal and supercritical conditions.

We present a theoretical investigation of the hydrogen nuclear magnetic resonance (NMR) chemical shift and the magnetic susceptibility of normal and supercritical water using a recently developed ab initio approach in the framework of density functional perturbation theory. The results are in very good agreement with experiment. The shifts can be used to determine whether the atomic configurations, taken from a first principles simulation, give a good description of the system on a microscopic scale. In particular, the hydrogen chemical shifts are very sensitive to the character of the hydrogen bond network, which plays a crucial role in the macroscopic properties of liquid water under normal and supercritical conditions.

Journal Article↗
PubMed2002

Electronic structure of wet DNA.

The electronic properties of a Z-DNA crystal synthesized in the laboratory are investigated by means of density-functional theory Car-Parrinello calculations. The electronic structure has a gap of only 1.28 eV. This separates a manifold of 12 occupied states which came from the pi guanine orbitals from the lowest empty states in which the electron is transferred to the Na+ from PO-4 groups and water molecules. We have evaluated the anisotropic optical conductivity. At low frequency the conductivity is dominated by the pi-->Na+ transitions. Our calculation demonstrates that the cost of introducing electron holes in wet DNA strands could be lower than previously anticipated.

Crystallization↗
PubMed2002

First-principles study of aqueous hydroxide solutions.

Car-Parrinello molecular dynamics simulations have been carried out for aqueous NaOH and KOH solutions under ambient conditions over a wide range of concentrations. From these simulations, we have observed a continuous change of the water structure with added hydroxide, characterized by a significant shift of the second peak of the OO radial distribution functions to shorter distances. At the highest concentration investigated, the normal tetrahedral coordination of pure water is completely missing, a result that is consistent with a recent neutron diffraction experiment. The added hydroxide also gives rise to some unique spectroscopic features, including a "free" O-H stretch, a broadening of the normal water OH stretching band, and a large blue shift of both the librational band and the low-frequency translation. These results are in good agreement with the experimental data. Finally, it was demonstrated that the structural and dynamical behavior is inextricably linked to the formation of compact hydroxide-water complexes.

Journal Article↗
PubMed2002

The nature and transport mechanism of hydrated hydroxide ions in aqueous solution.

Compared to other ions, protons (H(+)) and hydroxide ions (OH(-)) exhibit anomalously high mobilities in aqueous solutions. On a qualitative level, this behaviour has long been explained by 'structural diffusion' the continuous interconversion between hydration complexes driven by fluctuations in the solvation shell of the hydrated ions. Detailed investigations have led to a clear understanding of the proton transport mechanism at the molecular level. In contrast, hydroxide ion mobility in basic solutions has received far less attention, even though bases and base catalysis play important roles in many organic and biochemical reactions and in the chemical industry. The reason for this may be attributed to the century-old notion that a hydrated OH(-) can be regarded as a water molecule missing a proton, and that the transport mechanism of such a 'proton hole' can be inferred from that of an excess proton by simply reversing hydrogen bond polarities. However, recent studies have identified OH(-) hydration complexes that bear little structural similarity to proton hydration complexes. Here we report the solution structures and transport mechanisms of hydrated hydroxide, which we obtained from first-principles computer simulations that explicitly treat quantum and thermal fluctuations of all nuclei. We find that the transport mechanism, which differs significantly from the proton hole picture, involves an interplay between the previously identified hydration complexes and is strongly influenced by nuclear quantum effects.

Journal Article↗
PubMed2002

Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease.

The emergence of compensatory drug-resistant mutations in HIV-1 protease challenges the common view of the reaction mechanism of this enzyme. Here, we address this issue by performing classical and ab initio molecular dynamics simulations (MD) on a complex between the enzyme and a peptide substrate. The classical MD calculation reveals large-scale protein motions involving the flaps and the cantilever. These motions modulate the conformational properties of the substrate at the cleavage site. The ab initio calculations show in turn that substrate motion modulates the activation free energy barrier of the enzymatic reaction dramatically. Thus, the catalytic power of the enzyme does not arise from the presence of a pre-organized active site but from the protein mechanical fluctuations. The implications of this finding for the emergence of drug-resistance are discussed.

Binding Sites↗
PubMed2002

Anharmonic Raman spectra in high-pressure ice from ab initio simulations.

We calculate from ab initio molecular dynamics the Raman scattering of high-pressure ice. To this effect we apply a new method based on the Berry phase theory of polarization. Our results are in agreement with recent and difficult experiments and are compatible with a picture in which ice VII is a proton-disordered system and in ice X the hydrogen bond is symmetric.

Journal Article↗
PubMed2002

The role and perspective of ab initio molecular dynamics in the study of biological systems.

Ab initio molecular dynamics (MD) allows realistic simulations to be performed without adjustable parameters. In recent years, the technique has been used on an increasing number of applications to biochemical systems. Here we describe the principles on which ab initio MD is based. We focus on the most popular implementation, based on density functional theory and plane wave basis set. By a survey of recent applications, we show that despite the current limitations of size and time scale, ab initio MD (and hybrid ab initio MD/MM approaches) can play an important role for the modeling of biological systems. Finally, we provide a perspective for the advancement of methodological approaches which may further expand the scope of ab initio MD in biomolecular modeling.

Animals↗