Biomedical subjects

Nicola Marzari

Publications and source records attributed to Nicola Marzari.

15 recordsLinked to original sources

PubMed2006

Effect of counterions on the interactions of charged oligothiophenes.

The functionality of conjugated polymer systems often relies on oxidations or reductions, in most cases mediated by the presence of counterions. The effect that the common counterion hexafluorophosphate (PF6-) has on the intermolecular interactions between charged oligothiophenes is investigated here using ab initio quantum chemistry methods. Counterions are explicitly included in the simulations of oxidized oligothiophenes and in the dimerization process. Our calculations provide quantitative and qualitative insight into the intermolecular interactions in oligothiophene-counterion systems and show that the intermolecular pi-stacking of oligothiophenes is not adversely affected by the presence of counterions and that in fact oligothiophene dimerization is further stabilized by their presence.

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PubMed2006

Dynamical structure, bonding, and thermodynamics of the superionic sublattice in alpha-AgI.

We characterize the superionic phase transition and the lattice and electronic structures of the archetypal type-I superionic conductor alpha-AgI using extensive first-principles molecular dynamics calculations. We find that superionicity is signaled by a phase transition of the silver ions alone. In the superionic phase, the first silver shell surrounding an iodine displays a distinct dynamical structure that would escape a time-averaged characterization, and we capture this structure in a set of ordering rules. The electronic structure demonstrates a unique chemical signature of the weakest-bound silver in the first shell, which in turn is most likely to diffuse. Silver diffusion decreases upon melting, pointing to an unusual entropic contribution to the stability of the superionic phase.

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PubMed2006

Cycloaddition functionalizations to preserve or control the conductance of carbon nanotubes.

We identify a class of covalent functionalizations that preserve or control the conductance of single-walled metallic carbon nanotubes. [2+1] cycloadditions can induce bond cleaving between adjacent sidewall carbons, recovering in the process the sp;{2} hybridization and the ideal conductance of the pristine tubes. This is radically at variance with the damage permanently induced by other common ligands, where a single covalent bond is formed with a sidewall carbon. Chirality, curvature, and chemistry determine bond cleaving, and in turn the electrical transport properties of a functionalized tube. A well-defined range of diameters can be found for which certain addends exhibit a bistable state, where the opening or closing of the sidewall bond, accompanied by a switch in the conductance, could be directed with chemical, optical, or thermal means.

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PubMed2006

Density functional theory in transition-metal chemistry: a self-consistent Hubbard U approach.

Transition-metal centers are the active sites for a broad variety of biological and inorganic chemical reactions. Notwithstanding this central importance, density-functional theory calculations based on generalized-gradient approximations often fail to describe energetics, multiplet structures, reaction barriers, and geometries around the active sites. We suggest here an alternative approach, derived from the Hubbard U correction to solid-state problems, that provides an excellent agreement with correlated-electron quantum chemistry calculations in test cases that range from the ground state of Fe2 and Fe2- to the addition elimination of molecular hydrogen on FeO+. The Hubbard U is determined with a novel self-consistent procedure based on a linear-response approach.

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PubMed2006

Realistic quantitative descriptions of electron transfer reactions: diabatic free-energy surfaces from first-principles molecular dynamics.

A general approach to calculate the diabatic surfaces for electron-transfer reactions is presented, based on first-principles molecular dynamics of the active centers and their surrounding medium. The excitation energy corresponding to the transfer of an electron at any given ionic configuration (the Marcus energy gap) is accurately assessed within ground-state density-functional theory via a novel penalty functional for oxidation-reduction reactions that appropriately acts on the electronic degrees of freedom alone. The self-interaction error intrinsic to common exchange-correlation functionals is also corrected by the same penalty functional. The diabatic free-energy surfaces are then constructed from umbrella sampling on large ensembles of configurations. As a paradigmatic case study, the self-exchange reaction between ferrous and ferric ions in water is studied in detail.

Electron Transport↗

PubMed2006

Stacking of oligo- and polythiophene cations in solution: surface tension and dielectric saturation.

The stacking of positively charged (or doped) terthiophene oligomers and quaterthiophene polymers in solution is investigated applying a recently developed unified electrostatic and cavitation model for first-principles calculations in a continuum solvent. The thermodynamic and structural patterns of the dimerization are explored in different solvents, and the distinctive roles of polarity and surface tension are characterized and analyzed. Interestingly, we discover a saturation in the stabilization effect of the dielectric screening that takes place at rather small values of epsilon(0). Moreover, we address the interactions in trimers of terthiophene cations, with the aim of generalizing the results obtained for the dimers to the case of higher-order stacks and nanoaggregates.

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PubMed2006

Ab initio studies of layering behavior of liquid sodium surfaces and interfaces.

We have studied the liquid surface of sodium with extensive ab initio molecular dynamics simulations based on ensemble density-functional theory. We find clear evidence of layering in the direction perpendicular to the surface that persists to temperatures more than 100 K above the melting point. We also observe clear Friedel oscillations in the electronic density response to the presence of a surface, but their direct effect on atomic layering is ruled out. A careful finite-size effect analysis accompanies our results, showing that liquid slabs 20-25 A thick capture the essential details of the surface structure. We conclude that geometrical confinement is the common cause for layer formation, which is similar to what happens at a liquid-solid interface: at a free liquid surface, the rapid decay of the electronic density from the bulk liquid value to zero in the vapor forms a hard wall against which the atoms pack. Finally, we predict x-ray reflectivities from ab initio molecular dynamics data that include some of the large surface-normal wave vector-transfer regions that, for alkali metals, are not accessible to experiments.

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PubMed2006

Static dielectric properties of carbon nanotubes from first principles.

We characterize the response of isolated single-wall (SWNT) and multiwall (MWNT) carbon nanotubes and nanotube bundles to static electric fields using first-principles calculations and density-functional theory. The longitudinal polarizability of SWNTs scales as the inverse square of the band gap, while in MWNTs and bundles it is given by the sum of the polarizabilities of the constituent tubes. The transverse polarizability of SWNTs is insensitive to band gaps and chiralities and is proportional to the square of the effective radius; in MWNTs, the outer layers dominate the response. The transverse response is intermediate between metallic and insulating, and a simple electrostatic model based on a scale-invariance relation captures accurately the first-principles results. The dielectric response of nonchiral SWNTs in both directions remains linear up to very high values of applied field.

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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

Dielectric response of periodic systems from quantum Monte Carlo calculations.

We present a novel approach that allows us to calculate the dielectric response of periodic systems in the quantum Monte Carlo formalism. We employ a many-body generalization for the electric-enthalpy functional, where the coupling with the field is expressed via the Berry-phase formulation for the macroscopic polarization. A self-consistent local Hamiltonian then determines the ground-state wave function, allowing for accurate diffusion quantum Monte Carlo calculations where the polarization's fixed point is estimated from the average on an iterative sequence, sampled via forward walking. This approach has been validated for the case of an isolated hydrogen atom and then applied to a periodic system, to calculate the dielectric susceptibility of molecular-hydrogen chains. The results found are in excellent agreement with the best estimates obtained from the extrapolation of quantum-chemistry calculations.

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PubMed2005

Band structure and quantum conductance of nanostructures from maximally localized Wannier functions: the case of functionalized carbon nanotubes.

We have combined large-scale, tau-point electronic-structure calculations with the maximally localized Wannier functions approach to calculate efficiently the band structure and the quantum conductance of complex systems containing thousands of atoms while maintaining full first-principles accuracy. We have applied this approach to study covalent functionalizations in metallic single-walled carbon nanotubes. We find that the band structure around the Fermi energy is much less dependent on the chemical nature of the ligands than on the sp(3) functionalization pattern disrupting the conjugation network. Common aryl functionalizations are more stable when paired with saturating hydrogens; even when paired, they still act as strong scattering centers that degrade the ballistic conductance of the nanotubes already at low degrees of coverage.

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PubMed2005

Static and dynamical properties of heavy water at ambient conditions from first-principles molecular dynamics.

The static and dynamical properties of heavy water have been studied at ambient conditions with extensive Car-Parrinello molecular-dynamics simulations in the canonical ensemble, with temperatures ranging between 325 and 400 K. Density-functional theory, paired with a modern exchange-correlation functional (Perdew-Burke-Ernzerhof), provides an excellent agreement for the structural properties and binding energy of the water monomer and dimer. On the other hand, the structural and dynamical properties of the bulk liquid show a clear enhancement of the local structure compared to experimental results; a distinctive transition to liquidlike diffusion occurs in the simulations only at the elevated temperature of 400 K. Extensive runs of up to 50 ps are needed to obtain well-converged thermal averages; the use of ultrasoft or norm-conserving pseudopotentials and the larger plane-wave sets associated with the latter choice had, as expected, only negligible effects on the final result. Finite-size effects in the liquid state are found to be mostly negligible for systems as small as 32 molecules per unit cell.

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PubMed2005

Electronic-enthalpy functional for finite systems under pressure.

We introduce the notion of electronic enthalpy for first-principles structural and dynamical calculations of finite systems under pressure. An external pressure field is allowed to act directly on the electronic structure of the system studied via the ground-state minimization of the functional E+PV(q), where V(q) is the quantum volume enclosed by a charge isosurface. The Hellmann-Feynman theorem applies, and assures that the ionic equations of motion follow an isoenthalpic dynamics. No pressurizing medium is explicitly required, while coatings of environmental ions or ligands can be introduced if chemically relevant. We apply this novel approach to the study of group-IV nanoparticles during a shock wave, highlighting the significant differences in the plastic or elastic response of the diamond cage under load, and their potential use as novel nanostructured impact-absorbing materials.

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PubMed2005

pi-Stacking in thiophene oligomers as the driving force for electroactive materials and devices.

The pi-stacking between aromatic oligomers has been extensively studied for many years, although the notion of exploiting this phenomenon as the driving force for molecular actuation has only recently emerged. In this work we examine with MP2 and Car-Parrinello ab initio calculations the actuation properties of a novel class of thiophene-based materials introduced by Swager et al. (Adv. Mater. 2002, 14, 368; J. Am. Chem. Soc. 2003, 125, 1142). The chemical ingredients of the assembly, calix[4]arenes and oligothiophenes, are screened separately to characterize the actuation mechanisms and design optimal architectures. In particular, ab initio methods are used to study pi-stacking in mixed-valence oligothiophene dimers, revealing strong interactions that can be turned on and off as a function of the electrochemical potential. We show how these interactions could be harnessed to achieve molecular actuation and investigate the response of an active unit in real time with first-principles molecular dynamics simulations.

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PubMed2002

A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP.

We used classical molecular mechanics (MM) simulations and quantum mechanical (QM) structural relaxations to examine the active site of myosin when bound to ATP. Two conformations of myosin have been determined by x-ray crystallography. In one, there is no direct interaction between switch 2 and the nucleotide (open state). In the other (closed state), the universally conserved switch 2 glycine forms a hydrogen bond with a gamma-phosphate oxygen. MM simulations indicate that the two states are thermodynamically stable and allow us to investigate the extent to which the P-loop, switch 1, and switch 2 are involved in hydrolysis. We find that the open structure has a higher affinity for ATP than the closed structure, and that ATP is distorted toward a transition state by interactions with the protein. We also examine how the structure of the binding site changes with either MgATP or CaATP as the nucleotide in myosin in the open conformer. Our analyses suggest that higher CaATPase rates occur because the leaving phosphate (P(i)) group is more weakly bound and dissociation occurs faster. Finally, we validate the use of a particular formulation of a QM methodology (Car-Parrinello) to further refine the structures of the active site.

Adenosine Triphosphate↗