Electron attachment to a hydrated DNA duplex: the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine

The minimal essential section of DNA helices, the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine dimer octahydrate, [dGpdC](2), has been constructed, fully optimized, and analyzed by using quantum chemical methods at the B3LYP/6-31+G(d,p) level of theory. Study of the electrons attached to [dGpdC](2) reveals that DNA double strands are capable of capturing low-energy electrons and forming electronically stable radical anions. The relatively large vertical electron affinity (VEA) predicted for [dGpdC](2) (0.38 eV) indicates that the cytosine bases are good electron captors in DNA double strands. The structure, charge distribution, and molecular orbital analysis for the fully optimized radical anion [dGpdC](2)(·-) suggest that the extra electron tends to be redistributed to one of the cytosine base moieties, in an electronically stable structure (with adiabatic electron affinity (AEA) 1.14 eV and vertical detachment energy (VDE) 2.20 eV). The structural features of the optimized radical anion [dGpdC](2)(·-) also suggest the probability of interstrand proton transfer. The interstrand proton transfer leads to a distonic radical anion [d(G-H)pdC:d(C+H)pdG](·-), which contains one deprotonated guanine anion and one protonated cytosine radical. This distonic radical anion is predicted to be more stable than [dGpdC](2)(·-). Therefore, experimental evidence for electron attachment to the DNA double helices should be related to [d(G-H)pdC:d(C+H)pdG](·-) complexes, for which the VDE might be as high as 2.7 eV (in dry conditions) to 3.3 eV (in fully hydrated conditions). Effects of the polarizable medium have been found to be important for increasing the electron capture ability of the dGpdC dimer. The ultimate AEA value for cytosine in DNA duplexes is predicted to be 2.03 eV in aqueous solution.     

Fluorescent Bioprobes: Structural Matching in the Docking Processes of Aggregation‐Induced Emission Fluorogens on DNA Surfaces

Whereas most conventional DNA probes are flat disklike aromatic molecules, we explored the possibility of developing quadruplex sensors with nonplanar conformations, in particular, the propeller‐shaped tetraphenylethene (TPE) salts with aggregation‐induced emission (AIE) characteristics. 1,1,2,2‐Tetrakis[4‐(2‐triethylammonioethoxy)phenyl]ethene tetrabromide (TPE‐ 1 ) was found to show a specific affinity to a particular quadruplex structure formed by a human telomeric DNA strand in the presence of K⁺ ions, as indicated by the enhanced and bathochromically shifted emission of the AIE fluorogen. Steady‐state and time‐resolved spectral analyses revealed that the specific binding stems from a structural matching between the AIE fluorogen and the DNA strand in the folding process. Computational modeling suggests that the AIE molecule docks on the grooves of the quadruplex surface with the aid of electrostatic attraction. The binding preference of TPE‐ 1 enables it to serve as a bioprobe for direct monitoring of cation‐driven conformational transitions between the quadruplexes of various conformations, a job unachievable by the traditional G‐quadruplex biosensors. Methyl thiazolyl tetrazolium (MTT) assays reveal that TPE‐ 1 is cytocompatible, posing no toxicity to living cells.     

Nanoscale Biomolecular Structures on Self‐Assembled Monolayers Generated from Modular Pegylated Disulfides

A solid‐phase synthetic strategy was developed that uses modular building blocks to prepare symmetric oligo(ethylene glycol)‐terminated disulfides with a variety of lengths and terminal functionalities. The modular disulfides, composed of alkyl amino groups linked by an amide group to oligoethylene chains were used to generate self‐assembled monolayers (SAMs), which were characterised to determine their applicability for biomolecular applications. X‐ray photoelectron spectroscopy (XPS) of the SAMs obtained from these molecules demonstrated improved stability towards displacement by 16‐hexadecanethiol, while surface plasmon resonance (SPR) analyses of SAMs prepared with the hydroxy‐terminated oligoethylene disulfide showed equal resistance to non‐specific protein adsorption in comparison to 11‐mercaptoundecyl tri(ethylene glycol). SAMs made from these adsorbates were amenable to nanoscale patterning by scanning near‐field photolithography (SNP), facilitating the fabrication of nanopatterned, protein‐functionalised surfaces. Such SAMs may be further developed for bionanotechnology applications such as the fabrication of nanoscale biological arrays and sensor devices.     

Synthesis, Characterization and Crystal Structures of Some Linked Metal Carbonyl Clusters Derived from Diethynyl-Substituted Silane and Disilane Ligands

The use of diethynylsilane, diethynyldisilane and diethynyldisiloxane in the synthesis of some linked metal carbonyl clusters is demonstrated. New dimeric η²-diyne complexes of cobalt [{Co₂(CO)₆}₂(η²-diyne)], ruthenium [{(μ-H)Ru₃(CO)₉}₂(μ₃-η²,η²-diyne)] and osmium [{(μ-CO)Os₃(CO)₉}₂(μ₃-η²-diyne)] {diyne=HC≡CSi(CH₃)₂C≡CH, HC≡CSi(CH₃)₂–Si(CH₃)₂C≡CH, HC≡CSi(CH₃)₂–O–Si(CH₃)₂C≡CH or HC≡CSi(Ph)₂C≡CH} have been prepared in good yields from the reaction of [Co₂(CO)₈], [Ru₃(CO)₁₂] and [Os₃(CO)₁₀(NCMe)₂] with half an equivalent of the appropriate diyne ligand, respectively. All the twelve compounds have been characterized by IR and ¹H NMR spectroscopies and mass spectrometry. The molecular structures of eight of them have been determined by X-ray crystallography. Structurally, each of the tetracobalt species displays two Co₂C₂ cores adopting the pseudo-tetrahedral geometry with the alkyne bond lying essentially perpendicular to the Co–Co vector. For the group 8 ruthenium and osmium analogues, the hexanuclear carbonyl clusters consist of two trinuclear metal cores with the μ₃-η²,η² bonding mode for the acetylene groups in the former case and μ₃-(η²-||) bonding mode in the latter one. Density functional theory was employed to study the electronic structures of these molecules in terms of the nature of the silyl or disilyl unit and its substituents.     

Quantitative analysis of closantel and rafoxanide in bovine and ovine muscles by high-performance liquid chromatography with fluorescence detection

An HPLC method with a fluorescence detector (HPLC-FLD) was described for the quantitative determination of closantel and rafoxanide in bovine and ovine muscles. A structural analog closely related to rafoxanide, viz., N-[4-(4-chlorophenoxy)phenyl]-2-hydroxy-3,5-diiodobenzamide, was synthesized as an internal standard. Bovine and ovine muscles were extracted with acetonitrile-acetone (60 + 40, v/v) followed by cleanup on mixed mode anionic exchange SPE cartridges. After evaporation and reconstitution with the mobile phase, the sample was analyzed by HPLC-FLD using internal standard calibration. The method was validated by using fortified bovine and ovine muscles at 15, 30, and 60 microg/kg. The accuracy and RSD were 70-110% and < or =10%, respectively.     

A facile chemical approach for preparing a SERS active silver substrate

This communication describes a new surface-enhanced Raman scattering (SERS) active silver substrate prepared by iodination of the evaporated silver foil. After iodination, the morphology of the silver substrate undergoes a self-evolution process in which it displays accordingly the UV-vis absorption shift as well as the AFM topological test. Rhodamine 6G (R6G) is used as the probe molecule to evaluate the enhancement efficiency of the silver substrate at different self-evolution time intervals. The SERS intensity of R6G increases up to ～29-fold and reaches a maximum after the substrate evolved for 24 h. This method is feasible for the production of an efficient SERS silver substrate.     

Comparison of different signal thresholds on data dependent sampling in orbitrap and LTQ mass spectrometry for the identification of peptides and proteins in complex mixtures

We evaluate the effect of ion-abundance threshold settings for data-dependent acquisition on a hybrid LTQ-Orbitrap mass spectrometer, analyzing features such as the total number of spectra collected, the signal to noise ratio of the full MS scans, the spectral quality of the tandem mass spectra acquired, and the number of peptides and proteins identified from a complex mixture. We find that increasing the threshold for data-dependent acquisition generally decreases the quantity but increases the quality of the spectra acquired. This is especially true when the threshold setting is set above the noise level of the full MS scan. We compare two distinct experimental configurations: one where full MS scans are acquired in the Orbitrap analyzer while tandem MS scans are acquired in the LTQ analyzer, and one where both full MS and tandem MS scans are acquired in the LTQ analyzer. We examine the number of spectra, peptides, and proteins identified under various threshold conditions, and we find that the optimal threshold setting is at or below the respective noise level of the instrument regardless of whether the full MS scan is performed in the Orbitrap or in the LTQ analyzer. When comparing the high-throughput identification performance of the two analyzers, we conclude that, used at optimal threshold levels, the LTQ and the Orbitrap identify similar numbers of peptides and proteins. The higher scan speed of the LTQ, which results in more spectra being collected, is roughly compensated by the higher mass accuracy of the Orbitrap, which results in improved database searching and peptide validation software performance.     

Structures and Properties of Nonchelated,d0 Alkyl Alkene Complexes of the Type [Cp2ZrMe(alkene)]+: Elusive Intermediates during Ziegler–Natta Polymerizations of Alkenes

Caught in the act : An alkyl alkene Zr^IV complex (see picture; Cp=C₅H₅) has been synthesized and characterized for the first time. The alkene bonding mode is highly asymmetric, and C2 is quite carbocationic. There is also evidence for rotation about the C1? C2 bond. This extremely unusual complex provides an exemplar of previously unknown intermediates in Ziegler–Natta and carbocationic polymerization reactions of alkenes.

     

Strong sums of projections in von Neumann factors

This paper presents necessary and sufficient conditions for a positive bounded operator on a separable Hilbert space to be the sum of a finite or infinite collection of projections (not necessarily mutually orthogonal), with the sum converging in the strong operator topology if the collection is infinite. A similar necessary condition is given when the operator and the projections are taken in a type II von Neumann factor, and the condition is proven to be also sufficient if the operator is “diagonalizable”. A simpler necessary and sufficient condition is given in the type III factor case.