What controls the melting properties of DNA-linked gold nanoparticle assemblies?

We report a series of experiments and a theoretical model designed to systematically define and evaluate the relative importance of nanoparticle, oligonucleotide, and environmental variables that contribute to the observed sharp melting transitions associated with DNA-linked nanoparticle structures. These variables include the size of the nanoparticles, the surface density of the oligonucleotides on the nanoparticles, the dielectric constant of the surrounding medium, target concentration, and the position of the nanoparticles with respect to one another within the aggregate. The experimental data may be understood in terms of a thermodynamic model that attributes the sharp melting to a cooperative mechanism that results from two key factors: the presence of multiple DNA linkers between each pair of nanoparticles and a decrease in the melting temperature as DNA strands melt due to a concomitant reduction in local salt concentration. The cooperative melting effect, originating from short-range duplex-to-duplex interactions, is independent of DNA base sequences studied and should be universal for any type of nanostructured probe that is heavily functionalized with oligonucleotides. Understanding the fundamental origins of the melting properties of DNA-linked nanoparticle aggregates (or monolayers) is of paramount importance because these properties directly impact one's ability to formulate high sensitivity and selectivity DNA detection systems and construct materials from these novel nanoparticle materials.     

Structure and stability of endohedral X@Si20H20 complexes (X = Li, Na, K, Be, Mg, Ca)

The structure and stability of endohedral X@Si₂₀H₂₀ complexes (X = Li^0/+, Na^0/+, K^0/+, Be^0/2+, Mg^0/2+, Ca^0/2+) have been studied at the B3LYP/6-31G* level of density functional theory. It is found that complexes with X = Na^0/+, K^0/+, Mg and Ca^0/2+ are energy minimum structures with X at the cage center in I_h symmetry, while those with X = Li^0/+, Be^0/2+, Mg²⁺ have off-centered structures with X towards one pentagon face in C_5v symmetry. Large electron or charge transfer between the Si₂₀H₂₀ cage and the encapsulated X has been observed.     

Determination of proanthocyanidins in fresh grapes and grape products using liquid chromatography with mass spectrometric detection

Fresh grapes and grape products, such as grape wine and grape juice, were analyzed for proanthocyanidins (PACs) using liquid chromatography with electrospray ionization mass spectrometric (MS) detection. PACs were successfully separated and analyzed on the basis of their protonated molecules, allowing the identification of PACs in different degrees of polymerization from monomers to oligomers (up to 7 units), and in various isomeric forms. Using reversed-phase high-performance liquid chromatography (HPLC) combined with MS detection, the PAC monomers, (+)-catechin (C), (-)-epicatechin (EC), (-)-catechin gallate (CG), and (-)-epicatechin gallate (ECG), were successfully quantified using selected ion monitoring (SIM) mode. Standard curves were fitted for each PAC ranging from 43.8 to 5600 ng/mL for C, from 42.2 to 5400 ng/mL for EC, from 36.7 to 4700 ng/mL for CG, and from 39.8 to 5100 ng/mL for ECG. Good linearity (r2>0.999) was achieved for each analyte. The accuracy and precision (RSD) were within 10% (n=8) at the limit of detection. This method allows direct quantification of monomeric PACs in fresh grapes and grape-derived products. Additionally, flow injection analysis (FIA) was applied to estimate the concentration levels of PAC oligomers by comparing their FIA-MS peak areas, which were well correlated (r2=0.936) to the total concentrations of PAC monomers.     

Reaction dynamics of Cl+CH3SH: rotational and vibrational distributions of HCl probed with time-resolved Fourier-transform spectroscopy

Rotationally resolved infrared emission spectra of HCl(v=1-3) in the reaction of Cl+CH3SH, initiated with radiation from a laser at 308 nm, are detected with a step-scan Fourier-transform spectrometer. Observed rotational temperature of HCl(v=1-3) decreases with duration of reaction due to collisional quenching; a short extrapolation to time zero based on data in the range 0.25-4.25 micros yields a nascent rotational temperature of 1150+/-80 K. The rotational energy averaged for HCl(v=1-3) is 8.2+/-0.9 kJ mol(-1), yielding a fraction of available energy going into rotation of HCl, fr=0.10+/-0.01, nearly identical to that of the reaction Cl+H(2)S. Observed temporal profiles of the vibrational population of HCl(v=1-3) are fitted with a kinetic model of formation and quenching of HCl(v=1-3) to yield a branching ratio (68+/-5):(25+/-4):(7+/-1) for formation of HCl(v=1):(v=2):(v=3) from the title reaction and its thermal rate coefficient k(2a)=(2.9+/-0.7)x10(-10) cm(3) molecule(-1) s(-1). Considering possible estimates of the vibrational population of HCl(v=0) based on various surprisal analyses, we report an average vibrational energy 36+/-6 kJ mol(-1) for HCl. The fraction of available energy going into vibration of HCl is f(v)=0.45+/-0.08, significantly greater than a value fv=0.33+/-0.06 determined previously for Cl+H2S. Reaction dynamics of Cl+H(2)S and Cl+CH3SH are compared; the adduct CH3S(Cl)H is likely more transitory than the adduct H(2)SCl.     

Stereoselektive Synthese einiger Amidester der (±)-erythro-2,3-Diphenylglutarsäure

Zusammenfassung Bei der Umsetzung von Methylphenylacetat mit Dialkylamiden der Zimtsäure in Gegenwart von NaNH₂ wurden Amidester der (±)-erythro-2,3-Diphenylglutarsäure hergestellt. Die Konfiguration der erhaltenen Verbindungen wurde durch Hydrolyse mit HCl (1:1) zu der entsprechenden Säure und im Falle der Umsetzung mit dem Zimtsäuredimethylamid durch eine mehrstufige Synthese aus demerythro-Säurenitril-ester festgestellt. Es wurden auch Bedingungen gefunden, unter welchen nur die Estergruppe hydrolysiert werden kann, wobei Mono-dimethylamid entsteht, das mit CH₂N₂ den Ausgangs-Amidester liefert.     

Reversible formation of DNA G-quadruplex hairpin dimers from stilbenediether conjugates

Rapid and reversible G-quadruplex hairpin dimer formation is observed for bis(oligonucleotide) conjugates possessing stilbenediether (Sd) linkers connecting two short poly(G) sequences.     

New 2D graphical representation of DNA sequences

We consider a 2D graphical representations of DNA sequences, which avoids loss of information associated with crossing and overlapping of the corresponding curve. We outline an approach, which is based on the construction of a three-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with DNA. The examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of different species illustrates the utility of the approach.     

Studies on the reactions of silyl enol ether with perfluoroorganic compounds1 III. Synthesis of perfluoroalkylated α, β-unsaturated aldehydes and their derivatives

Per- and poly-fluoroalkylated α, β-unsaturated alkenals were synthesized by the reaction of silyl enol ether of alkanals with per- and poly-fluoroalkyl iodide initiated by Na₂S₂O₄ conveniently in high yield. Their corresponding alkenol and 2,4-dinitrophenylhydrazone were also synthesized.     

The formation of a compact polymer film on a copper electrode from benzimidazole solution

The effects of the pretreatment of copper in benzimidazole solutions on the anodic reactions have been observed. The structures of the chemisorbed benzimidazole on copper were studied by using the infrared reflection-absorption technique and X-ray photoelectron spectroscopy. It was found that a compact film of benzimidazolato copper(I) was formed on the copper surface when copper was immersed in a stirred benzimidazole solution and cyclic voltammetry applied. This compact polymer film inhibited anodic oxidation effectively.     

Studies of the g factors and zero-field splitting for the trigonal Ti(2+)(Ga)-S(p) defect center in GaP crystal

The EPR g factors g(parallel), g(perpendicular) and zero-field splitting D suggested to be caused by a donor-acceptor nearest-neighbour pair defect [Ti(Ga)(2+)-Sp] in GaP:Ti(2+) co-doped with sulphur are calculated from the high-order perturbation formulas based on a two spin-orbit coupling parameter model for the EPR parameters of 3d(2) ion in trigonal symmetry. The calculated results are close to the observed values. The suggestion of [Ti(Ga)(2+)-Sp] pair defect in GaP:Ti co-doped with sulphur is also confirmed from this calculation.