On the benefits of acquiring peptide fragment ions at high measured mass accuracy

The advantages and disadvantages of acquiring tandem mass spectra by collision-induced dissociation (CID) of peptides in linear ion trap Fourier-transform hybrid instruments are described. These instruments offer the possibility to transfer fragment ions from the linear ion trap to the FT-based analyzer for analysis with both high resolution and high mass accuracy. In addition, performing CID during the transfer of ions from the linear ion trap (LTQ) to the FT analyzer is also possible in instruments containing an additional collision cell (i.e., the "C-trap" in the LTQ-Orbitrap), resulting in tandem mass spectra over the full m/z range and not limited by the ejection q value of the LTQ. Our results show that these scan modes have lower duty cycles than tandem mass spectra acquired in the LTQ with nominal mass resolution, and typically result in fewer peptide identifications during data-dependent analysis of complex samples. However, the higher measured mass accuracy and resolution provides more specificity and hence provides a lower false positive ratio for the same number of true positives during database search of peptide tandem mass spectra. In addition, the search for modified and unexpected peptides is greatly facilitated with this data acquisition mode. It is therefore concluded that acquisition of tandem mass spectral data with high measured mass accuracy and resolution is a competitive alternative to "classical" data acquisition strategies, especially in situations of complex searches from large databases, searches for modified peptides, or for peptides resulting from unspecific cleavages.     

Xanthene-Based Nitric Oxide-Responsive Nanosensor for Photoacoustic Imaging in the SWIR Window

Shortwave infrared (SWIR) dyes are characterized by their ability to absorb light from 900 to 1400 nm, which is ideal for deep tissue imaging owing to minimized light scattering and interference from endogenous pigments. An approach to access such molecules is to tune the photophysical properties of known near-infrared dyes. Herein, we report the development of a series of easily accessible (three steps) SWIR xanthene dyes based on a dibenzazepine donor conjugated to thiophene ( SCR-1 ), thienothiophene ( SCR-2 ), or bithiophene ( SCR-3 ). We leverage the fact that SCR-1 undergoes a bathochromic shift when aggregated for in vivo studies by developing a ratiometric nanoparticle for NO ( rNP-NO ), which we employed to successfully visualize pathological levels of nitric oxide in a drug-induced liver injury model via deep tissue SWIR photoacoustic (PA) imaging. Our work demonstrates how easily this dye series can be utilized as a component in nanosensor designs for imaging studies.     

Towards a consistent mechanism of emulsion polymerization—new experimental details

The application of atypical experimental methods such as conductivity measurements, optical microscopy, and nonstirred polymerizations to investigations of the ‘classical’ batch ab initio emulsion polymerization of styrene revealed astonishing facts. The most important result is the discovery of spontaneous emulsification leading to monomer droplets even in the quiescent styrene in water system. These monomer droplets with a size between a few and some hundreds of nanometers, which are formed by spontaneous emulsification as soon as styrene and water are brought into contact, have a strong influence on the particle nucleation, the particle morphology, and the swelling of the particles. Experimental results confirm that micelles of low-molecular-weight surfactants are not a major locus of particle nucleation. Brownian dynamics simulations show that the capture of matter by the particles strongly depends on the polymer volume fraction and the size of the captured species (primary free radicals, oligomers, single monomer molecules, or clusters).     

Studies toward the total synthesis of axinellamine and massadine

Intramolecular Diels-Alder reactions of several N-O linked 4-vinylimidazole dimers provide the expected adduct in moderate to good yield as a single, all trans stereoisomer, along with smaller amounts of the inverse electron demand adduct. Oxidative rearrangement of the cycloadducts occurs on treatment with Davis' reagent, providing a single spiro imidazolone in good yield and with excellent levels of stereocontrol albeit epimeric at the spiro center found in axinellamine and massadine.     

Density functional theory study of triphenyl phosphite: molecular flexibility and weak intermolecular hydrogen bonding

The high conformational flexibility of triphenyl phosphite (TPP) is investigated by density functional theory (DFT) calculations. First, through a scan of the molecular potential energy surface, we bring to light a new stable conformation of an isolated molecule, not yet encountered in the crystal states of TPP. Different relevant conformations of the TPP monomer in the gas state are further presented and discussed in terms of molecular structure, relative energy, and dipole moments. Second, we considered dimer and trimer of TPP starting from their structural topology within the hexagonal crystal, which is characterized by the existence of molecular rods. It is shown that weak C-H...O intermolecular hydrogen bonds in TPP cannot definitely be excluded, and finally this point is discussed in the scope of the glacial state problem.     

Combined theoretical and experimental analysis of the bonding in the heterobimetallic cubane-type Mo(3)NiS(4) and Mo(3)CuS(4) core clusters

X-ray structural data for the cubane-type clusters [Mo3CuS4(dmpe)3Cl4](+) and Mo3NiS4(dmpe)3Cl4 (dmpe = 1,2-bis(dimethylphosphino)ethane) with 16 metal electrons have been compared with optimized structural parameters calculated using "ab initio" methodologies. Compound Mo3NiS4(dmpe)3Cl4 crystallizes in the cubic noncentrosymmetric space group P213 with a Mo-Ni distance of 2.647 Angstrom, that is 0.2 Angstrom shorter than the Mo-Cu bond length in the isoelectronic copper cluster. The best agreement between theory and experiments has been obtained using the B3P86 method. In order to validate the B3P86 results, accurate infrared and Raman spectra have been acquired and the vibrational modes associated to the cubane-type Mo3M'S4 (M' = Cu or Ni) unit have been assigned theoretically. The electronic changes taking place when incorporating the M' into the Mo3S4 unit have been analyzed from a theoretical and experimental perspective. The bond dissociation energies between M'-Cl and Mo3S4 fragments show that formation of [Mo3CuS4(dmpe)3Cl4](+) is 135 kcal/mol energetically less favorable than the Ni incorporation. The more robust nature of the Mo3NiS4 fragment has been confirmed by mass spectrometry. The X-ray photoelectron spectroscopy (XPS) spectra of the trimetallic and tetrametallic complexes have been measured and the obtained binding energies compared with the computed electronic populations based on topological approaches of the electron localization function (ELF). The energies and shapes of the Cu 2p and Ni 2p lines indicate formal oxidation states of Cu(I) and Ni(II). However, the reductive addition of nickel into [Mo3S4(dmpe)3Cl3](+) causes a small decrease in the Mo 3d binding energies. This fact prevents an unambiguous assignment of an oxidation state in a conventional way, a circumstance that has been analyzed through the covariance of the electronic populations associated to the C(M') core and V(Mo3Ni) and V(S(2)') valence basins where Mo3NiS4 is a particularly electronically delocalized chemical entity.     

Use of a partial-filling technique in affinity capillary electrophoresis for determining binding constants of ligands to receptors

This work evaluates the concept of a partial-filling technique in affinity capillary electrophoresis (ACE) using two model systems: vancomycin from Streptomyces orientalis and carbonic anhydrase B (CAB, EC 4.2.1.1). In this technique the capillary is first partially-filled with ligand followed by a sample of receptor and non-interacting standard and electrophoresed. Analysis of the change in the mobility ratio, M, of the receptor, relative to the non-interacting standard, as a function of the concentration of the ligand, yields a value for the binding constant. These values agree well with those estimated using other binding and ACE techniques. Data demonstrating the quantitative potential of this method is presented.     

Biocompatibility Study of Electrospun Nanocomposite Membranes Based on Chitosan/Polyvinyl Alcohol/Oxidized Carbon Nano-Onions

In recent decades, the number of patients requiring biocompatible and resistant implants that differ from conventional alternatives dramatically increased. Among the most promising are the nanocomposites of biopolymers and nanomaterials, which pretend to combine the biocompatibility of biopolymers with the resistance of nanomaterials. However, few studies have focused on the in vivo study of the biocompatibility of these materials. The electrospinning process is a technique that produces continuous fibers through the action of an electric field imposed on a polymer solution. However, to date, there are no reports of chitosan (CS) and polyvinyl alcohol (PVA) electrospinning with carbon nano-onions (CNO) for in vivo implantations, which could generate a resistant and biocompatible material. In this work, we describe the synthesis by the electrospinning method of four different nanofibrous membranes of chitosan (CS)/(PVA)/oxidized carbon nano-onions (ox-CNO) and the subdermal implantations after 90 days in Wistar rats. The results of the morphology studies demonstrated that the electrospun nanofibers were continuous with narrow diameters (between 102.1 nm ± 12.9 nm and 147.8 nm ± 29.4 nm). The CS amount added was critical for the diameters used and the successful electrospinning procedure, while the ox-CNO amount did not affect the process. The crystallinity index was increased with the ox-CNO introduction (from 0.85% to 12.5%), demonstrating the reinforcing effect of the nanomaterial. Thermal degradation analysis also exhibited reinforcement effects according to the DSC and TGA analysis, with the higher ox-CNO content. The biocompatibility of the nanofibers was comparable with the porcine collagen, as evidenced by the subdermal implantations in biological models. In summary, all the nanofibers were reabsorbed without a severe immune response, indicating the usefulness of the electrospun nanocomposites in biomedical applications.     

Superelectrophilic Activation of N‐Substituted Isatins: Implications for Polymer Synthesis,a Theoretical Study

The stability and reactivity of mono‐ and multi‐protonatred N‐substituted isatin derivatives were studied at PBE0/aug‐cc‐pvtz//PBE0/6‐31+G** level of theory in triflic acid (TFSA) solution. Calculations showed that the monocationic intermediates are the principal reactive species in the reaction of hydroxyalkylation of isatin derivatives in TFSA media. Electron‐withdrawing substituents on the nitrogen atom increase the reactivity of isatin‐containing electrophiles towards aromatic hydrocarbons, in accordance with their expected electronic influence. Steric factors also play an important role in the reactivity of isatin‐containing electrophiles, especially in the second reaction step, due to their more sterically hindered reactive center.

     

A neural network based model for urban noise prediction

Noise is a global problem. In 1972 the World Health Organization (WHO) classified noise as a pollutant. Since then, most industrialized countries have enacted laws and local regulations to prevent and reduce acoustic environmental pollution. A further aim is to alert people to the dangers of this type of pollution. In this context, urban planners need to have tools that allow them to evaluate the degree of acoustic pollution. Scientists in many countries have modeled urban noise, using a wide range of approaches, but their results have not been as good as expected. This paper describes a model developed for the prediction of environmental urban noise using Soft Computing techniques, namely Artificial Neural Networks (ANN). The model is based on the analysis of variables regarded as influential by experts in the field and was applied to data collected on different types of streets. The results were compared to those obtained with other models. The study found that the ANN system was able to predict urban noise with greater accuracy, and thus, was an improvement over those models. The principal component analysis (PCA) was also used to try to simplify the model. Although there was a slight decline in the accuracy of the results, the values obtained were also quite acceptable.