Dynamics of a monolayer of nitrogen physisorbed on graphite

The dynamics of a crystalline monolayer of molecular nitrogen physisorbed on the basal plane of graphite, which was assumed to be rigid, has been studied by means of lattice and molecular dynamics. The study focusses mainly on the registered solid in which the centres of mass adopt the √3 × √3 R30° structure, but some results are also reported for denser monlayers, including one where the centre-of-mass lattice is non-triangular. Harmonic dispersion curves are reported for two models of the N₂-N₂ interaction combined with Steele's representation of the molecule-surface interaction. The one-phonon density of states is given for one of the models. Molecular dynamics results for the same model at two temperatures, 5 and 17 K, are analysed in terms of the dynamical structure factor, and one-phonon approximation to it, and the out-of-plane motions are treated in a manner similar to the one-phonon approximation. In-plane and out-of-plane motions are largely decoupled in all cases studied, and the in-plane motions show evidence of marked anharmonicity. The out-of-plane motions appear to exhibit Fermi-Pasta-Ulam type recurrences, although this is not analysed in detail.     

Studies on the synthesis of heterocyclic compounds. X. Antimony derivatives for the preparation of macrocyclic tetraesters

Treatment of 2-chloro-1,3,2-benzodioxastibole with diacyl chlorides afforded cyclic tetraesters in yields depending on ring size. The exclusive formation of dimeric derivatives was obtained using this method. The products were characterized by analytical and spectroscopic (ir, nmr and ms) data.     

Metal-based antitumour drugs in the post genomic era

The discovery of new metal-based antitumour drugs, whether cisplatin derivatives or those based on other metals, has been largely based on cell viability assays (IC50 values) and compounds that bind to DNA. This approach has been applied for more than 30 years during which time very few new drugs have entered clinical use. In this article we discuss what the future holds for metal-based drugs, in particular anti-metastasis drugs, in these enlightened times of the post genomic era.     

A combined Raman, DFT and MD study of the solvation dynamics and the adsorption process of pyridine in silver hydrosols

The adsorption of pyridine onto silver colloids has been investigated by Raman spectroscopy experiments and by ab initio DFT and MP2 calculations. The solvation dynamics of the pyridine in water has been studied by a molecular dynamics simulation. The results are compared with the latest available experimental and theoretical data. It is found that the pyridine is essentially hydrogen bonded to one solvent molecule. Calculations based on pyridine-water and pyridine-Ag(+) complexes allow the reproduction of the experimentally observed Raman features and explain the adsorption process of the ligand in silver hydrosols.     

Quasistatic crack growth in finite elasticity with non-interpenetration

We present a variational model to study the quasistatic growth of brittle cracks in hyperelastic materials, in the framework of finite elasticity, taking into account the non-interpenetration condition.     

NMR studies of the Zn2+ interactions with rat and human beta-amyloid (1-28) peptides in water-micelle environment

Alzheimer's disease is a fatal neurodegenerative disorder involving the abnormal accumulation and deposition of peptides (amyloid-beta, Abeta) derived from the amyloid precursor protein. Here, we present the structure and the Zn2+ binding sites of human and rat Abeta(1-28) fragments in water/sodium dodecyl sulfate (SDS) micelles by using 1H NMR spectroscopy. The chemical shift variations measured after Zn2+ addition at T>310 K allowed us to assign the binding donor atoms in both rat and human zinc complexes. The Asp-1 amine, His-6 Ndelta, Glu-11 COO-, and His-13 Nepsilon of rat Abeta28 all enter the metal coordination sphere, while His-6 Ndelta, His-13, His-14 Nepsilon, Asp-1 amine, and/or Glu-11 COO- are all bound to Zn2+ in the case of human Abeta28. Finally, a comparison between the rat and human binding abilities was discussed.     

MMM-QSAR recognition of ribonucleases without alignment: comparison with an HMM model and isolation from Schizosaccharomyces pombe, prediction, and experimental assay of a new sequence

The study of type III RNases constitutes an important area in molecular biology. It is known that the pac1+ gene encodes a particular RNase III that shares low amino acid similarity with other genes despite having a double-stranded ribonuclease activity. Bioinformatics methods based on sequence alignment may fail when there is a low amino acidic identity percentage between a query sequence and others with similar functions (remote homologues) or a similar sequence is not recorded in the database. Quantitative structure-activity relationships (QSAR) applied to protein sequences may allow an alignment-independent prediction of protein function. These sequences of QSAR-like methods often use 1D sequence numerical parameters as the input to seek sequence-function relationships. However, previous 2D representation of sequences may uncover useful higher-order information. In the work described here we calculated for the first time the spectral moments of a Markov matrix (MMM) associated with a 2D-HP-map of a protein sequence. We used MMMs values to characterize numerically 81 sequences of type III RNases and 133 proteins of a control group. We subsequently developed one MMM-QSAR and one classic hidden Markov model (HMM) based on the same data. The MMM-QSAR showed a discrimination power of RNAses from other proteins of 97.35% without using alignment, which is a result as good as for the known HMM techniques. We also report for the first time the isolation of a new Pac1 protein (DQ647826) from Schizosaccharomyces pombe strain 428-4-1. The MMM-QSAR model predicts the new RNase III with the same accuracy as other classical alignment methods. Experimental assay of this protein confirms the predicted activity. The present results suggest that MMM-QSAR models may be used for protein function annotation avoiding sequence alignment with the same accuracy of classic HMM models.     

Structural features of the Cu(II) complex with the rat Abeta(1-28) fragment

The interaction between Cu(II) and the rat amyloid beta (1-28) fragment in micellar solutions at pH 7.5 was investigated by CD and NMR spectroscopy; the proton-copper distances were used in restrained molecular dynamics simulations to obtain a structural model of the Cu(II) complex.