Characterization of phospho-olivines as materials for Li-ion cell cathodes

Solid State Reaction was employed to prepare phospho-olivines LiMPO₄ (where M=Fe, Co) as pure phase and LiNiPO₄ in presence of foreign phases, as cathodic materials for lithiumions batteries. The relationship between structural, morphological and electrochemical properties were investigated in the case of LiFePO₄. Structural investigation has been carried out by means of X-ray powder diffraction (XRPD) and Rietveld refinement. The influence on the morphology of annealing temperature, different flowing gas mixture and addition of ascorbic acid during the synthesis, has been analysed via scanning electron microscopy. The electrochemical cycling performances on LiFePO₄ showed to be positively affected by the modifications of the experimental conditions. Cyclic voltammetry showed a good reversibility during insertion-extraction mechanism, in particular in presence of additives. LiCoPO₄ and LiNiPO₄ are interesting as high voltage cathode materials for Li-ion batteries and have been taken into account, but their electrochemical operating conditions are still to be optimised. In the case of LiNiPO₄ it is very difficult to obtain, by solid state synthesis, suitable purity powders, having a grain size small enough to exploit it usefully as cathodic material for Li-ion cells. Paper presented at the 8th EuroConference on Ionics, Carvoeiro, Algarve, Portugal, Sept. 16 – 22, 2000.     

Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site

A recent 13C NMR experiment (Smith et al. Nature Struct. Biol. 1996, 3, 946-950) on the Asp 25-Asp25' dyad in pepstatin A/HIV-1 protease measured two separate resonance lines, which were interpreted as being a singly protonated dyad. We address this issue by performing ab initio molecular dynamics calculations on models for this site accompanied by calculations of 13C NMR chemical shifts and isotopic shifts. We find that already on the picosecond time-scale the model proposed by Smith et al. is not stable and evolves toward a different monoprotonated form whose NMR pattern differs from the experimental one. We suggest, instead, a different protonation state in which both aspartic groups are protonated. Despite the symmetric protonation state, the calculated 13C NMR properties are in good agreement with the experiment. We rationalize this result using a simple valence bond model, which explains the chemical inequality of the two C sites. The model calculations, together with our calculations on the complex, allow also the rationalization of 13C NMR properties on other HIV-1 PR/inhibitor complexes. Both putative binding of the substrate to the free enzyme, which has the dyad singly protonated (Piana, S.; Carloni, P. Proteins: Struct., Funct., Genet. 2000, 39, 26-36), and pepstatin A binding to the diprotonated form are consistent with the inverse solvent isotope effect on the onset of inhibition of pepsin by pepstatin and the kinetic iso-mechanism proposed for aspartic proteases (Cho, T.-K.; Rebholz, K.; Northrop, D.B. Biochemistry 1994, 33, 9637-9642).     

A finite-element-based coarse-grained model for global protein vibration

Meccanica - Protein mechanical vibrations play a pivotal role in biological activity. In particular, low-frequency (terahertz) modes are related to protein conformational changes, which represent...     

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

The accurate characterization of the structure and dynamics of proteins in disordered states is a difficult problem at the frontier of structural biology whose solution promises to further our understanding of protein folding and intrinsically disordered proteins. Molecular dynamics (MD) simulations have added considerably to our understanding of folded proteins, but the accuracy with which the force fields used in such simulations can describe disordered proteins is unclear. In this work, using a modern force field, we performed a 200 μs unrestrained MD simulation of the acid-unfolded state of an experimentally well-characterized protein, ACBP, to explore the extent to which state-of-the-art simulation can describe the structural and dynamical features of a disordered protein. By comparing the simulation results with the results of NMR experiments, we demonstrate that the simulation successfully captures important aspects of both the local and global structure. Our simulation was ~2 orders of magnitude longer than those in previous studies of unfolded proteins, a length sufficient to observe repeated formation and breaking of helical structure, which we found to occur on a multimicrosecond time scale. We observed one structural feature that formed but did not break during the simulation, highlighting the difficulty in sampling disordered states. Overall, however, our simulation results are in reasonable agreement with the experimental data, demonstrating that MD simulations can already be useful in describing disordered proteins. Finally, our direct calculation of certain NMR observables from the simulation provides new insight into the general relationship between structural features of disordered proteins and experimental NMR relaxation properties.     

The nature of the adsorption of nucleobases on the gold [111] surface

Biochip technology is based on the immobilization of biological macromolecules on the surface of electronic devices. The biochemical properties of the immobilized molecules can be influenced to a large extent by the interaction with the inorganic surface. The interaction of DNA with the surface of gold, a metal commonly used in biochip technologies, is sequence dependent as the four nucleobases, adenine, thymine, cytosine, and guanine, interact to a different extent with the gold surface. The nature of nucleobase adsorption on the gold [111] surface has been investigated by performing density functional theory and post-Hartree-Fock calculations. It turns out that the interaction is dominated by dispersion forces and an appreciable degree of chemisorption is observed for adenine only. A set of Lennard-Jones parameters that describe the interaction was derived from the post-Hartree-Fock calculations. Classical molecular dynamics simulations of nucleobase monolayers based on these parameters are in remarkable agreement with the experiment and show that the interaction of the nucleobases with the gold surface is strongly modulated by base-base interactions and reaches a maximum when a full monolayer is formed.     

Microbiological control and antibacterial action of a propolis-containing mouthwash and control of dental plaque in humans

Propolis is a bee product with several biological properties. This study aimed at investigating a propolis-containing mouthwash, its organoleptic properties, microbial contamination and its antibacterial action in vitro. This mouthwash was assessed in vivo to control dental plaque in humans. The presence of microorganisms was analyzed and the minimum inhibitory concentration against Streptococcus mutans was determined. A comparative study was done in vivo using propolis, chlorhexidine, and propolis plus chlorhexidine in lower concentrations for 14 days. Dental plaque was analyzed by the Patient Hygiene Performance (PHP) index. The odontological product was yellow, cloudy, free of microbial contamination, and exerted an inhibitory action in vitro. Individuals who used a propolis-containing mouthwash for 14 consecutive days in combination or not to chlorhexidine showed a similar PHP index to chlorhexidine alone. The product exerted an antibacterial action in vitro and in vivo, exhibiting a positive action in the control of dental plaque.     

A bias-exchange approach to protein folding

By suitably extending a recent approach [Bussi, G.; et al. J. Am. Chem. Soc. 2006, 128, 13435] we introduce a powerful methodology that allows the parallel reconstruction of the free energy of a system in a virtually unlimited number of variables. Multiple metadynamics simulations of the same system at the same temperature are performed, biasing each replica with a time-dependent potential constructed in a different set of collective variables. Exchanges between the bias potentials in the different variables are periodically allowed according to a replica exchange scheme. Due to the efficaciously multidimensional nature of the bias the method allows exploring complex free energy landscapes with high efficiency. The usefulness of the method is demonstrated by performing an atomistic simulation in explicit solvent of the folding of a Triptophane cage miniprotein. It is shown that the folding free energy landscape can be fully characterized starting from an extended conformation with use of only 40 ns of simulation on 8 replicas.     

The use of the linear sampling method for obtaining super-resolution effects in Born approximation

A two-step reconstruction scheme is introduced to solve fixed frequency inverse scattering problems in Born approximation conditions. The aim of the approach is to achieve super-resolution effects by constraining the inversion method to exploit some a priori knowledge on the scatterer. Therefore, the first step is to apply the linear sampling method to the far-field data in order to obtain an estimate of the support of the inhomogeneity. The second step is to apply the projected Landweber method to the linearized scattering equation in order to obtain super-resolution effects via out-of-band extrapolation. The effectiveness of the approach, which has a rather wide applicability power, is tested in the case of a two-dimensional problem for some scatterers of simple geometry.     

Assisted desolvation as a key kinetic step for crystal growth

The crystallization of materials from a supersaturated solution is a fundamental chemical process. Although several very successful models that provide a qualitative understanding of the crystal growth process exist, in most cases the atomistic detail of crystal growth is not fully understood. In this work, molecular dynamics simulations of the morphologically most important surfaces of barite in contact with a supersaturated solution have been performed. The simulations show that an ordered and tightly bound layer of water molecules is present on the crystal surface. The approach of an ion to the surface requires desolvation of both the surface and the ion itself leading to an activated process that is rate limiting for two-dimensional nucleation to occur. However, desolvation on specific surfaces can be assisted by anions adsorbed on the crystal surface. This hypothesis, corroborated by crystallization and scanning electron microscopy studies, allows the rationalization of the morphology of barite crystals grown at different supersaturations.