Ketene-ketenimine rearrangements in the gas phase and in polar media. 1,3-Migration intermediates and sequential transition states

[reaction: see text] Calculations of the activation barrier for the 1,3-shifts of substituents X in alpha-imidoylketenes 1 (HN=C(X)-CH=C=O), which interconverts them with alpha-oxoketenimines 3 (HN=C=CH-C(X)=O) via a four-membered cyclic transition state TS2 have been performed at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G* level. Substituents with accessible lone pairs have the lowest activation barriers for the 1,3-shift (halogens, OR, NR2). The corresponding activation barriers for the alpha-oxoketene-alpha-oxoketene rearrangement of 4 via TS5 are generally lower by 1-30 kJ/mol. A polar medium (acetonitrile, epsilon = 36.64) was simulated using the polarizable continuum (PCM) solvation model. The effect of the solvent field is a reduction of the activation barrier by an average of 12 kJ/mol. In the cases of 1,3-shifts of amino and dimethylamino groups, the stabilization of the transition state TS2 in a solvent field is so large that it becomes an intermediate, Int2, flanked by transition states (TS2' and TS2') that are due primarily to internal rotation of the amine functions, and secondarily to the 1,3-bonding interaction. In the case of the alpha-oxoketene-alpha-oxoketene rearrangement of 4, there is a corresponding intermediate Int5 for the 1,3-amine shift already in the gas phase.     

Synthesis of the C3-C19 segment of phorboxazole B

[reaction: see text]. Three segment-coupling Prins approaches to the C3-C19 segment of phorboxazole B have been developed. One successful strategy utilized a novel TMSBr-mediated cyclization that proceeded with complete axial selectivity. Displacement of bromide with cesium acetate provided the C13 hydroxyl stereocenter of 22. Additionally, treatment of alpha-acetoxy ether 20 with TFA enabled a more concise synthesis of the C3-C19 target 13 by allowing direct access to the equatorial alcohol.     

DNA polymerase-mediated DNA synthesis on a TNA template

TNA, or threose nucleic acid, is capable of Watson-Crick base pairing with DNA, RNA, and TNA; coupled with its chemical simplicity, this suggests that TNA is a possible progenitor of RNA. As an initial step toward developing the molecular tools necessary to investigate the functional capabilities of TNA by in vitro selection, we have screened a variety of DNA polymerases for activity on a TNA template. We report that despite having a repeating unit that is one atom shorter than that of DNA, several polymerases showed surprisingly good ability to copy limited stretches of TNA.     

1,1,3,3-Tetramethylguanidine-gallane, (Me2N)2CN(H).GaH3: an unusually strongly bound gallane adduct

The novel adduct 1,1,3,3-tetramethylguanidine-gallane, (Me2N)2CN(H).GaH3, has been prepared by the reaction of [(Me2N)2CNH2]+Cl- with LiGaH4 in Et2O solution. Its spectroscopic properties indicate a monomeric species with an unusually strong coordinate link between the imido function and GaH3, an inference confirmed by the crystal structure at 150 K which also reveals significant secondary interactions through non-classical N-H...H-Ga bridges. Despite the intrinsic strength of the Ga-N bond, however, vaporisation at ca. 310 K occurs with partial dissociation, and decomposition via more than one pathway proceeds at temperatures >330-350 K to give a variety of products, including the free base, Me2NH, H2, and a novel gallium-nitrogen compound composed of a Ga4N4 cubane-like core bridged on three edges by -N{C(NMe2)2}GaH2- units.     

Selectively detecting attomolar concentrations of proteins using gold lined nanopores in a nanopore blockade sensor

Disease diagnosis at earlier stages requires the development of ultrasensitive biosensors for detecting low-abundance biomarkers in complex biological fluids within a reasonable time frame. Here, we demonstrate the development of an ultrasensitive nanopore blockade biosensor that can rapidly diagnose a model protein biomarker, prostate-specific antigen (PSA) with high selectivity. The solid-state nanopores have gold located only along the length of the nanopore whilst the rest of the membrane is silicon nitride. The orthogonal use of materials allows nanopore arrays with a different surface chemistry inside the nanopore relative to the rest of the membrane to be fabricated. The importance of this differential surface chemistry is it can improve the detection limit of nanopore blockade sensors in quantitative analysis. Based on such functionalized nanopore devices, nanopore blockade sensors lower the limit of detection by an order of magnitude and enable ultrasensitive detection of PSA as low as 80 aM. The findings from this study open new opportunities for nanopore sensors in further developments including optical detection and ultralow detection limit biosensing at complex biological fluids.

Selective detection of attomolar proteins was achieved using gold lined nanopores in a nanopore blockade sensor.     

Structures of neat and hydrated 1-octanol from computer simulations

Molecular dynamics computer simulations of 1-octanol and its mixtures with water have been performed. The liquid is composed of regions enriched in either hydrocarbons or hydroxyl groups. In neat octanol, the hydroxyl groups form clusters of long, thin chains. Upon the addition of water, the clusters become longer and more spherical, forming a structure that can be described as consisting of "overlapping elongated inverse micelles". The structures of the mixtures obtained at different hydration levels are consistent with those of experimental diffraction studies of water/octanol mixtures and previous computer simulations of neat and water-saturated octanol. The saturation point of the model has been calculated using the cavity-bias particle insertion method. The solubility of water in octanol is slightly too low compared to experimental results, and suggestions for possible improvements to the force field are made.     

LC-mass spectrometry analysis of N- and C-terminal boundary sequences of polypeptide fragments by limited proteolysis

Limited proteolysis is an important and widely used method for analyzing the tertiary structure and determining the domain boundaries of proteins. Here we describe a novel method for determining the N- and C-terminal boundary amino acid sequences of products derived from limited proteolysis using semi-specific and/or non-specific enzymes, with mass spectrometry as the only analytical tool. The core of this method is founded on the recognition that cleavage of proteins with non-specific proteases is not random, but patterned. Based on this recognition, we have the ability to determine the sequence of each proteolytic fragment by extracting a common association between data sets containing multiple potential sequences derived from two or more different mass spectral molecular weight measurements. Proteolytic product sequences derived from specific and non-specific enzymes can be accurately determined without resorting to the conventional time-consuming and laborious methods of SDS-PAGE and N-terminal sequencing analysis. Because of the sensitivity of mass spectrometry, multiple transient proteolysis intermediates can also be identified and analyzed by this method, which allows the ability to monitor the progression of proteolysis and thereby gain insight into protein structures.     

DNA recognition interfaces: the influence of interfacial design on the efficiency and kinetics of hybridization

The effect of the surface chemistry of DNA recognition interfaces on DNA hybridization at a gold surface was investigated using both electrochemistry and the quartz crystal microbalance (QCM) technique. Different DNA recognition interfaces were prepared using a two-component self-assembled monolayer consisting of thiolated 20-mer probe single-stranded DNA (ss-DNA) containing either a 3'-mercaptopropyl or a 3'-mercaptohexyl linker group and an alcohol-terminated diluent layer with 2-, 6-, or 11-carbon length. The influence of the interfacial design on the hybridization efficiency, the affinity constant (Ka) describing hybridization, and the kinetics of hybridization was assessed. It was found that the further the DNA was above the surface defined by the diluent layer the higher the hybridization efficiency and Ka. The kinetics of DNA hybridization was assessed using both a QCM and an electrochemical approach to ascertain the influence of the interface on both the initial binding of target DNA to the surface and the formation of a complete duplex. These measurements showed that the length of the diluent layer has a large impact on the time taken to form a perfect duplex but no impact on the initial recognition of the target DNA by the immobilized probe DNA.     

Competing Effects of Chlorination on the Strength of Te⋅⋅⋅O Chalcogen Bonds Select the Structure of Mixed Supramolecular Macrocyclic Aggregates of Iso-Tellurazole N-Oxides

Chlorination of 3-methyl-5-phenyl-1,2-tellurazole-2-oxide yielded the λ⁴Te dichloro derivative. Its crystal structure demonstrates that the heterocycle retains its ability to autoassociate by chalcogen bonding (ChB) forming macrocyclic tetramers. The corresponding Te⋅⋅⋅O ChB distances are 2.062 Å, the shortest observed to date in aggregates of this type. DFT−D3 calculations indicate that while the halogenated molecule is stronger as a ChB donor it also is a weaker ChB acceptor; the overall effect is that the ChBs in the chlorinated homotetramer are not significantly stronger. However, partial halogenation or scrambling selectively yield the 2 : 2 heterotetramer with alternating λ⁴Te and λ²Te centers, which calculations identified as the thermodynamically preferred arrangement.