Biomedical subjects

M Parrinello

Publications and source records attributed to M Parrinello.

At least 37 records · Page 2Linked to original sources

PubMed2000

Solvation of radical cations in water--reactive or unreactive solvation?

The solvation and reaction of ethylene radical cation in aqueous solution has been studied with Car-Parrinello molecular dynamics simulations. All ab initio simulations were performed using a system of 56 water and one ethylene molecule. Using a favorable symmetrically solvated radical cation as the starting point of the simulation a fast addition of water (within 90 fs) to the radical cation is observed. The primary addition product is rapidly deprotonated (within 100 fs) to yield the ethanol-2-yl radical. A second simulation was initiated through vertical ionization of neutral hydrated ethylene, representing a significantly less favorable situation for the addition process. No addition of water can be observed in this second simulation over a time span of 1.7 ps. Taken together the two simulations are indicative of a rearrangement of the solvent shell which represents the major part of the overall reaction barrier. Under these circumstances, the reaction rate of an otherwise spontaneous reaction is limited by the intrinsic solvent relaxation time. This interpretation of the reactivity of hydrated radical cations reconciles previously conflicting experimental condensed phase and theoretical gas phase studies.

Journal Article↗

PubMed2000

Hydrogen bonding and dipole moment of water at supercritical conditions: a first-principles molecular dynamics study.

We present a first-principles molecular dynamics study of water near and above the critical point ( T = 647 K, rho = 0.32 g/cm(3)). We find that the systems undergo fast dynamics with continuous formation and breaking of H bonds. At low density, the system fragments mostly into trimers, dimers, and single molecules. At a higher density, more complex structures appear and an extended, albeit very dynamical, H-bond network can be identified. These structures have important consequences for the screening properties of the system. This offers a clue to understanding the peculiar chemical behavior of a supercritical system and allows thermodynamical tuning of its solvent properties.

Journal Article↗

PubMed2000

Ab initio simulation of phase transitions and dissociation of H2S at high pressure

By ab initio constant pressure molecular dynamics, we have identified the structure of phase V and phase VI of H2S at 35 and 65 GPa, respectively. The theoretical IR spectra of both phases are consistent with experimental findings and support our proposed structural models. We find that phase V is characterized by the presence of charged SH+3 and SH- species which are created and destroyed dynamically, whereas phase VI is no longer a molecular phase but consists of sheets of S with the majority of H intercalated between the layers. The stability of the two phases with respect to dissociation into elemental crystalline hydrogen and sulfur is discussed.

Journal Article↗

PubMed2000

Two-membered silicon rings on the dehydroxylated surface of silica

We present extensive modeling of the amorphous silica surface, aimed at connecting its structural and chemical features. beta-cristobalite surfaces are initially studied to model the hydroxylated surfaces. A model reconstruction of the (111) surface is used to define a path leading to the formation of two-membered silicon rings upon dehydroxylation. Subsequently, a realistic model of the amorphous dehydroxylated (dry) surface is produced, by full ab initio annealing of an initial model generated by classical simulation. The presence of surface two-membered silicon rings emerges naturally. A calculation of IR activity yields an associated peak doublet in agreement with experimental data.

Journal Article↗

PubMed2000

Ab initio molecular dynamics with a classical pressure reservoir: simulation of pressure-induced amorphization in a Si35H36 cluster

We present a new constant-pressure ab initio molecular dynamics method suitable for studying, e.g., pressure-induced structural transformations in finite nonperiodic systems such as clusters. We immerse an ab initio treated cluster into a model classical liquid, described by a soft-sphere potential, which acts as a pressure reservoir. The pressure is varied by tuning the parameter of the liquid potential. We apply the method to a Si35H36 cluster, which undergoes a pressure-induced amorphization at approximately 35 GPa, and remains in a disordered state even upon pressure release.

Journal Article↗

PubMed2000

A comparative study of galactose oxidase and active site analogs based on QM/MM Car-Parrinello simulations.

A parallel study of the radical copper enzyme galactose oxidase (GOase) and a low molecular weight analog of the active site was performed with dynamical density functional and mixed quantum-classical calculations. This combined approach enables a direct comparison of the properties of the biomimetic and the natural systems throughout the course of the catalytic reaction. In both cases, five essential forms of the catalytic cycle have been investigated: the resting state in its semi-reduced (catalytically inactive) and its oxidized (catalytically active) form, A(semi) and A(ox), respectively; a protonated intermediate B; the transition state for the rate-determining hydrogen abstraction step C, and its product D. For A and B the electronic properties of the biomimetic compound are qualitatively very similar to the ones of the natural target. However, in agreement with the experimentally observed difference in catalytic activity, the calculated activation energy for the hydrogen abstraction step is distinctly lower for GOase (16 kcal/mol) than for the mimetic compound (21 kcal/mol). The enzymatic transition state is stabilized by a delocalization of the unpaired spin density over the sulfur-modified equatorial tyrosine Tyr272, an effect that for geometric reasons is essentially absent in the biomimetic compound. Further differences between the mimic and its natural target concern the structure of the product of the abstraction step, which is characterized by a weakly coordinated aldehyde complex for the latter and a tightly bound linear complex for the former.

Binding Sites↗

PubMed2000

Harmonic and anharmonic dynamics of Fe-CO and Fe-O(2) in heme models.

We present density-functional molecular dynamics simulations of FeP(Im)(AB) heme models (AB = CO, O(2), Im = imidazole) as a way of sketching the dynamic motion of the axial ligands at room temperature. The FeP(Im)(CO) model is characterized by an essentially upright FeCO unit, undergoing small deviations with respect to its linear equilibrium structure (bending and tilting up to 10 degrees and 7 degrees, often occur). The motion of the carbon monoxide ligand is found to be quite complex and fast, its projection on the porphyrin plane sampling all the porphyrin quadrants in a short time ( approximately 0.5 ps). Simultaneously, the imidazole ligand rotates slowly around the Fe-N(epsilon) bond. In contrast to carbon monoxide, the oxygen ligand in FeP(Im)(O(2)) prefers a conformation where the projection of the O-O axis on the porphyrin plane bisects one of the porphyrin quadrants. A transition to other quadrants takes place through an O-O/Fe-N(p) overlapping conformation, within 4-6 ps. Further details of these mechanisms and their implications are discussed.

Carbon Monoxide↗

PubMed1999

Superionic and metallic states of water and ammonia at giant planet conditions.

The phase diagrams of water and ammonia were determined by constant pressure ab initio molecular dynamic simulations at pressures (30 to 300 gigapascal) and temperatures (300 to 7000 kelvin) of relevance for the middle ice layers of the giant planets Neptune and Uranus. Along the planetary isentrope water and ammonia behave as fully dissociated ionic, electronically insulating fluid phases, which turn metallic at temperatures exceeding 7000 kelvin for water and 5500 kelvin for ammonia. At lower temperatures, the phase diagrams of water and ammonia exhibit a superionic solid phase between the solid and the ionic liquid. These simulations improve our understanding of the properties of the middle ice layers of Neptune and Uranus.

Ammonia↗

PubMed1997

On the Quantum Nature of the Shared Proton in Hydrogen Bonds

The relative influence of thermal and quantum fluctuations on the proton transfer properties of the charged water complexes H5O2+ and H3O2- was investigated with the use of ab initio techniques. These small systems can be considered as prototypical representatives of strong and intermediate-strength hydrogen bonds. The shared proton in the strongly hydrogen bonded H5O2+ behaved in an essentially classical manner, whereas in the H3O2- low-barrier hydrogen bond, quantum zero-point motion played a crucial role even at room temperature. This behavior can be traced back to a small difference in the oxygen-oxygen separation and hence to the strength of the hydrogen bond.

Journal Article↗

PubMed1996