Seeded-growth approach to fabrication of silver nanoparticle films on silicon for electrochemical ATR surface-enhanced IR absorption spectroscopy

Ag nanoparticle films (simplified as nanofilms hereafter) on Si for electrochemical ATR surface enhanced IR absorption spectroscopy (ATR-SEIRAS) have been successfully fabricated by using chemical deposition, which incorporates initial embedding of Ag seeds on the reflecting plane of an ATR Si prism and subsequent chemical plating of conductive and SEIRA-active Ag nanofilms. Two alternative methods for embedding initial Ag seeds have been developed: one is based on self-assembly of Ag colloids on an aminosilanized Si surface, whereas the other the reduction of Ag+ in a HF-containing solution. A modified silver-mirror reaction was employed for further growth of Ag seeds into Ag nanofilm electrodes with a theoretically average thickness of 40-50 nm. Both Ag seeds and as-deposited Ag nanofilms display island structure morphologies facilitating SEIRA, as revealed by AFM imaging. The cyclic voltammetric feature of the as-prepared Ag nanofilm electrodes is close to that of a polycrystalline bulk Ag electrode. With thiocyanate as a surface probe, enhancement factors of ca. 50-80 were estimated for the as-deposited Ag nanofilms as compared to a mechanically polished Ag electrode in the conventional IRAS after reasonable calibration of surface roughness factor, incident angles, surface coverage, and polarization states. As a preliminary example for extended application, the pyridine adsorption configuration at an as-deposited Ag electrode was re-examined by ATR-SEIRAS. The results revealed that pyridine molecules are bound via N end to the Ag electrode with its ring plane perpendicular or slightly tilted to the local surface without rotating its C2 axis about the surface normal, consistent with the conclusion drawn by SERS in the literature.     

Operon prediction based on SVM

The operon is a specific functional organization of genes found in bacterial genomes. Most genes within operons share common features. The support vector machine (SVM) approach is here used to predict operons at the genomic level. Four features were chosen as SVM input vectors: the intergenic distances, the number of common pathways, the number of conserved gene pairs and the mutual information of phylogenetic profiles. The analysis reveals that these common properties are indeed characteristic of the genes within operons and are different from that of non-operonic genes. Jackknife testing indicates that these input feature vectors, employed with RBF kernel SVM, achieve high accuracy. To validate the method, Escherichia coli K12 and Bacillus subtilis were taken as benchmark genomes of known operon structure, and the prediction results in both show that the SVM can detect operon genes in target genomes efficiently and offers a satisfactory balance between sensitivity and specificity.     

N- and P-channel transport behavior in thin film transistors based on tricyanovinyl-capped oligothiophenes

We report the structural and electrical characterization of thin films of organic semiconductor molecules consisting of an oligothiophene core capped with electron-withdrawing tricyanovinyl (TCV) groups. X-ray diffraction and atomic force microscopy of evaporated films of three different TCV-capped oligothiophenes showed that the films were highly crystalline. Electrical transport was measured in thin film transistors employing silver source and drain contacts and channel probes to correct for contact resistance. Three compounds exhibited n-channel (electron) conduction consistent with cyclic voltametry data that indicated they undergo facile reduction. Maximum electron mobilities were 0.02 cm2/V.s with an on/off current ratio of 10(6). A fourth end-capped molecule, TCV-6T-TCV, which had six thiophene rings, exhibited both p- and n-channel transport. Overall, these results confirm that substitution of oligothiophene cores with electron-withdrawing groups is a useful strategy to achieve electron-transporting materials.     

Progress of solid-phase microextraction coatings and coating techniques

Solid-phase microextraction (SPME) has been popular as an environmentally friendly sample pretreatment technique to extract a very wide range of analytes. This is partly owing to the development of SPME coatings. One of the key factors affecting the extraction performances, such as the sensitivity, selectivity, and reproducibility, is the properties of the coatings on SPME fibers. This paper classifies the materials used as SPME coatings and introduces some common preparation techniques of SPME coating in detail, such as sol-gel technique, electrochemical polymerization technique, particle direct pasting technique, restricted access matrix SPME technique, and molecularly imprinted SPME technique.     

Silicon hydride clusters Si5Hn (n = 3-12) and their anions: structures, thermochemistry, and electron affinities

The molecular structures, electron affinities, and dissociation energies of the Si(5)H(n)/Si(5)H(n)(-) (n = 3-12) species have been calculated by means of three density functional theory (DFT) methods. The basis set used in this work is of double-zeta plus polarization quality with additional diffuse s- and p-type functions, denoted DZP++. The geometries are fully optimized with each DFT method independently. Three different types of the neutral-anion energy separations presented in this work are the adiabatic electron affinity (EA(ad)), the vertical electron affinity (EA(vert)), and the vertical detachment energy (VDE). The first Si-H dissociation energies for neutral Si(5)H(n) and its anion have also been reported.     

Identification of radiation-induced cross-linking between thymine and tryptophan by electrospray ionization-mass spectrometry

Upon exposure to ionizing radiation, DNA undergoes a variety of modifications including the production of a covalent bond between the nucleobase thymine and aromatic amino acids. In this work, electrospray ionization-mass spectrometry(ESI-MS) was used to identify the gamma radiation-induced covalent cross-linking of model peptides (sequence YPPW and pYPPW) with the nucleobase thymine. Tandem electrospray ionization-mass spectrometry (ESI-MSn) was employed to investigate the cross-linking sites. The results showed that irrespective of whether tyrosine was phosphorylated or not, the nucleobase thymine was cross-linked with the tryptophan residue. Possible cross-linking mechanisms are proposed by investigating the related mass peaks.     

A molecular dynamics simulation study of peptide deformylase from Leptospira interrogans complex：Exploring the closing mechanism of the substrate pocket

To explore the closing mechanism of the substrate pocket,we perform a 16,000 ps molecular dynamics simulation separately on the ligand-free and actinonin-bound peptide deformylase from Leptospira interrogans.Our results show that the CD-loop, hydrophilic inhibitor and hydrophobic cluster are necessary for the formation of semi-open conformation,and Tyr71 plays an important role in mediating the movements of CD-loop.The average MD structure of the actinonin-bound LiPDF complex approaches to the crystal structure.These are consistent with experiment very well.     

Coupling a microchip with electrospray ionization quadrupole time-of-flight mass spectrometer for peptide separation and identification

The present study reports a simple method of coupling a glass microchip to an electrospray ionization (ESI) quadrupole time-of-flight mass spectrometer (QTOF-MS) for separation and identification of peptides. A sheath-flow electrospray interface was constructed based on attaching a short fused-silica capillary to the microchip. The dead volume at the interface was effectively reduced by wet etching an approximate flat-bottom capillary insertion channel coaxial to the end of separation microchannel and using a wire-controlled epoxy-blocking attachment method. The makeup liquid and neb gas were coaxially pumped through two stainless-steel tees to maintain a stable and efficient electrospray. The coupled microchip/ESI-QTOF-MS system was successfully used to carry out electrophoresis separation of peptides and ESI-QTOF-MS identification.     

金属纳米颗粒制备中的还原剂与修饰剂

金属纳米颗粒由于其独特的光学、电学、化学性质以及各种潜在的应用价值,受到不少研究人员的广泛关注。实现金属纳米粒子尺寸、形貌可控,改善粒子分散性和稳定性,提高产率及纯度已成为具有挑战性的研究课题,不断发展和完善金属纳米粒子的合成方法则显得尤为重要。本文总结了目前制备金属纳米材料的几种化学方法：化学试剂还原法、电化学还原法、辐射还原法等,分类介绍了化学试剂还原法中常用的无机、有机还原剂,以及含氮、磷、羧基、巯基小分子有机化合物以及高分子聚合物等修饰剂并重点总结了其还原和修饰机理。