The influence of simulation conditions in molecular dynamics investigations of model β-sheet peptides

The influence of simulation methods, cutoff based and particle mesh Ewald (PME) on the accuracy by which experimentally derived nuclear Overhauser effect (NOE) data are reproduced, has been investigated using 500-ns-long molecular dynamics simulations on a model -sheet peptide in explicit solvent. The structural and conformational features under the different conditions were evaluated in terms of flexibility, secondary structure content, hydrogen-bonding pattern and percent of native contacts as a function of time. It was found that the different simulation methods strongly influence the dynamics of the peptide, confirming previous observations based on ideal peptide models simulated for much shorter times. Moreover, the results of our simulations prove once more that it is necessary to reach extremely long time scales to obtain enough statistics to accurately reproduce experimental NOE restraints even in the case of the PME method, despite its tendency to the stabilization of conformations which are structurally closely related to the ones derived through experiment. Possible implications regarding the stabilization and folding mechanisms, together with their relationship to the experimental study of peptide models, are discussed.     

Spot overlapping in two-dimensional polyacrylamide gel electrophoresis separations: a statistical study of complex protein maps

A statistical approach able to extract the information contained in a two-dimenisional polyacrylamide gel electrophoresis (2-D PAGE) separation is here reported. The method is based on the quantitative theory of peak overlapping, a procedure previously developed by the authors and here extended to 2-D separations. The whole map is divided into many strips in order to obtain 1-D separations on which the statistic procedure is applied: the developed algorithms, on the basis of spot experimental data (intensity and spatial coordinates) permit to estimate the intrinsic number of components and to single out the specific order present in spot positions. The procedure was validated on computer-simulated maps. Its applicability to real samples was tested on maps obtained from literature sources. The following important information on protein mixtures can be extracted: (i) the number of proteins can be accurately estimated, on the basis of the spatial coordinates and intensities of spots detected in the 2-D PAGE map; (ii) the model describing distribution of interdistance between adjacent spots can be identified in both the separation dimensions; (iii) the presence of repeated interdistances in spot positions in the maps can be easily singled out: these regularities suggest specific protein modifications.     

Synthesis of 4,5-dihydro-2,4-benzoxazepin-3( 1H)ones and 1,3,4,5-tetrahydro-2,4-benzoxazepines

o- Aminomethylbeiizyl alcohols (X) easily cyclize with phosgene in an aqueous alkaline medium to form 4,5-dihydro-2,4-benzoxazepin-3(1H)ones (IV) and with aldehydes in acidic conditions to yield 1,3,4,5-tetrahydro-2,4-benzoxazepines (V). The characteristics and chemical behaviour of these new heterocyclic ring systems are reported.     

Novel heteroaromatic-based multi-branched dyes with enhanced two-photon absorption activity

The first examples of heterocycle-based multi-branched dyes with efficient two-photon absorption (TPA) activity are reported; the novel chromophores exhibit large TPA cross sections (as high as 1600 x 10(-50) cm4 s photon(-1) molecule(-1), measured with 150 fs laser pulses at 800 nm); a strong cooperative enhancement in the branched systems with respect to the one-dimensional sub-units is found.     

The Art of Rearranging

Equimeasurable rearrangements of real-valued functions of one or more real variables are surveyed. We outline the development of a relevant theory over the years and some applications to mathematical analysis, calculus of variations and partial differential equations.     

A Journey from Thermally Tunable Synthesis to Spectroscopy of Phenylmethanimine in Gas Phase and Solution

Phenylmethanimine is an aromatic imine with a twofold relevance in chemistry: organic synthesis and astrochemistry. To tackle both aspects, a multidisciplinary strategy has been exploited and a new, easily accessible synthetic approach to generate stable imine-intermediates in the gas phase and in solution has been introduced. The combination of this formation pathway, based on the thermal decomposition of hydrobenzamide, with a state-of-the-art computational characterization of phenylmethanimine laid the foundation for its first laboratory observation by means of rotational electric resonance spectroscopy. Both E and Z isomers have been accurately characterized, thus providing a reliable basis to guide future astronomical observations. A further characterization has been carried out by nuclear magnetic resonance spectroscopy, showing the feasibility of this synthetic approach in solution. The temperature dependence as well as possible mechanisms of the thermolysis process have been examined.