Algorithm for accurate similarity measurements of peptide mass fingerprints and its application

We present a simple algorithm which allows accurate estimates of the similarity between peptide fingerprint mass spectra from matrix assisted laser desorption/ionization (MALDI) spectrometers. The algorithm, which is a combination of mass correlation and intensity rank correlation, was used to cluster similar spectra and to generate consensus spectra from a data store of more than 100,000 spectra. The resulting first spectra library of 1248 unambiguously identified different protein digests was used to search for missed cleavage patterns that have not been reported so far and to shed light on some peptide ionization characteristics. The findings of this study could be directly implemented in peptide mass fingerprint search algorithms to decrease the false positive error rate to <0.25%. Furthermore, the results contribute to the understanding of the peptide ionization process in MALDI experiments.     

Tailoring the interface using thiophene small molecules in TiO(2)/P3HT hybrid solar cells

In this paper we focus on the effect of carboxylated thiophene small molecules as interface modifiers in TiO(2)/P3HT hybrid solar cells. Our results show that small differences in the chemical structure of these molecules, for example, the presence of the -CH(2)- group in the 2-thiopheneacetic acid (TAA), can greatly increase the TiO(2) surface wettability, improving the TiO(2)/polymer contact. This effect is important to enhance exciton splitting and charge separation.     

Phase diagram of trivalent and pentavalent patchy particles

We compute the equilibrium phase diagram of two simple models for patchy particles with three and five patches in a very broad range of pressure and temperature. The phase diagram presents low-density crystal structures which compete with the fluid phase. The phase diagram of the five-patch model shows re-entrant melting, in analogy with the previously studied four-patch case, a metastable gas-liquid critical point and a stable, high-density liquid. The three-patch model shows a stable gas-liquid critical point and, in the region of temperatures where equilibration is numerically feasible, a stable liquid phase, suggesting the possibility that in this small valence model the liquid retains its thermodynamic stability down to the vanishing range limit.     

Nanostructured diamine-fullerene derivatives: computational density functional theory study and experimental evidence for their formation via gas-phase functionalization

Nanostructure derivatives of fullerene C(60) are used in emerging applications of composite matrices, including protective and decorative coating, superadsorbent material, thin films, and lightweight high-strength fiber-reinforced materials, etc. In this study, quantum chemical calculations and experimental studies were performed to analyze the derivatives of diamine-fullerene prepared by the gas-phase solvent-free functionalization technique. In particular, the aliphatic 1,8-diamino-octane and the aromatic 1,5-diaminonaphthalene, which are diamines volatile in vacuum, were studied. We addressed two alternative mechanisms of the amination reaction via polyaddition and cross-linking of C(60) with diamines, using the pure GGA BLYP, PW91, and PBE functionals; further validation calculations were performed using the semiempirical dispersion GGA B97-D functional which contains parameters that have been specially adjusted by a more realistic view on dispersion contributions. In addition, we looked for experimental evidence for the covalent functionalization by using laser desorption/ionization time-of-flight mass spectrometry, thermogravimetric analysis, and atomic force microscopy.     

A multifaceted approach to hydrogen storage

The widespread adoption of hydrogen as an energy carrier could bring significant benefits, but only if a number of currently intractable problems can be overcome. Not the least of these is the problem of storage, particularly when aimed at use onboard light-vehicles. The aim of this overview is to look in depth at a number of areas linked by the recently concluded HYDROGEN research network, representing an intentionally multi-faceted selection with the goal of advancing the field on a number of fronts simultaneously. For the general reader we provide a concise outline of the main approaches to storing hydrogen before moving on to detailed reviews of recent research in the solid chemical storage of hydrogen, and so provide an entry point for the interested reader on these diverse topics. The subjects covered include: the mechanisms of Ti catalysis in alanates; the kinetics of the borohydrides and the resulting limitations; novel transition metal catalysts for use with complex hydrides; less common borohydrides; protic-hydridic stores; metal ammines and novel approaches to nano-confined metal hydrides.     

Ferroxidase Activity in Eukaryotic Ferritin is Controlled by Accessory‐Iron‐Binding Sites in the Catalytic Cavity

Ferritins are iron‐storage nanocage proteins that catalyze the oxidation of Fe²⁺ to Fe³⁺ at ferroxidase sites. By a combination of structural and spectroscopic techniques, Asp140, together with previously identified Glu57 and Glu136, is demonstrated to be an essential residue to promote the iron oxidation at the ferroxidase site. However, the presence of these three carboxylate moieties in close proximity to the catalytic centers is not essential to achieve binding of the Fe²⁺ substrate to the diferric ferroxidase sites with the same coordination geometries as in the wild‐type cages.     

Axial dispersion in a liquid fluidized bed of particles akin to immobilized enzymes

The axial dispersion of a liquid fluidized bed of controlled pore silica (CPS) particles has been determined by the pulse tracer method. The CPS used was the same as for enzyme immobilization, having an average diameter of 0.436 mm and mean pore size of 37.5 nm. The fluidization liquid is α-amylase liquefied manioc starch, 30% w/v, 45°C pH=4.5. Nominal bed porosities tested were 0.7 and 0.8. The results show that the axial dispersion coefficient increases with greater superficial liquid velocities. Various available correlations tested disagree with each other to a large extent and are unable to represent collected experimental data.     

How Does Diet Influence Our Lives? Evaluating the Relationship between Isotopic Signatures and Mortality Patterns in Italian Roman Imperial and Medieval Periods

The present research investigates the relationship between dietary habits and mortality patterns in the Roman Imperial and Medieval periods. The reconstructions of population dynamics and subsistence strategies provide a fascinating source of information for understanding our history. This is particularly true given that the changes in social, economic, political, and religious aspects related to the transition from the Roman period to the Middle Ages have been widely discussed. We analyzed the isotopic and mortality patterns of 616 individuals from 18 archeological sites (the Medieval Latium sites of Colonna, Santa Severa, Allumiere, Cencelle, and 14 Medieval and Imperial funerary contexts from Rome) to compile a survivorship analysis. A semi-parametric approach was applied, suggesting variations in mortality patterns between sexes in the Roman period. Nitrogen isotopic signatures influenced mortality in both periods, showing a quadratic and a linear effect for Roman Imperial and Medieval populations, respectively. No influence of carbon isotopic signatures has been detected for Roman Imperial populations. Conversely, increased mortality risk for rising carbon isotopic values was observed in Medieval samples.     

Molecularly Imprinted Polymers Combined with Electrochemical Sensors for Food Contaminants Analysis

Detection of relevant contaminants using screening approaches is a key issue to ensure food safety and respect for the regulatory limits established. Electrochemical sensors present several advantages such as rapidity; ease of use; possibility of on-site analysis and low cost. The lack of selectivity for electrochemical sensors working in complex samples as food may be overcome by coupling them with molecularly imprinted polymers (MIPs). MIPs are synthetic materials that mimic biological receptors and are produced by the polymerization of functional monomers in presence of a target analyte. This paper critically reviews and discusses the recent progress in MIP-based electrochemical sensors for food safety. A brief introduction on MIPs and electrochemical sensors is given; followed by a discussion of the recent achievements for various MIPs-based electrochemical sensors for food contaminants analysis. Both electropolymerization and chemical synthesis of MIP-based electrochemical sensing are discussed as well as the relevant applications of MIPs used in sample preparation and then coupled to electrochemical analysis. Future perspectives and challenges have been eventually given.     

Determination of thickness, dielectric constant of thiol films, and kinetics of adsorption using surface plasmon resonance

This paper describes the formation of a self-assembled monolayer of 11-mercaptoundecanoic acid (MUA) under different concentrations on a gold sensor disk, monitoring in situ and in real time using surface plasmon resonance spectroscopy (SPR). The film thickness and dielectric constant were determined for a fully formed monolayer using one-color approach SPR. The kinetic studies of the film formation in ethanol solution indicated that the self-assembled monolayer is formed in a two-step adsorption process. In this sense, this unpublished route was applied on the basis of a model where many molecules are adsorbed at an initial step and then can be desorbed and/or rearranged to form a perfect monolayer.