Synthesis and structural characterisation as 12-helix of the hexamer of a beta-amino acid tethered to a pyrrolidin-2-one ring

Starting from (3S,4R,1'S)-3-amino-2-oxo-1-[1'-(4-methoxyphenylethyl)]pyrrolidine carboxylic acid (2), the first synthesis of a beta-foldamer containing pyrrolidin-2-one rings is described, whose 12-helix conformation is assigned by NMR analysis and confirmed by molecular dynamics (MD) simulations.     

A Click Chemistry Approach to Developing Molecularly Targeted DNA Scissors

Nucleic acid click chemistry was used to prepare a family of chemically modified triplex forming oligonucleotides (TFOs) for application as a new gene-targeted technology. Azide-bearing phenanthrene ligands—designed to promote triplex stability and copper binding—were ‘clicked’ to alkyne-modified parallel TFOs. Using this approach, a library of TFO hybrids was prepared and shown to effectively target purine-rich genetic elements in vitro. Several of the hybrids provide significant stabilisation toward melting in parallel triplexes (>20 °C) and DNA damage can be triggered upon copper binding in the presence of added reductant. Therefore, the TFO and ‘clicked’ ligands work synergistically to provide sequence-selectivity to the copper cutting unit which, in turn, confers high stabilisation to the DNA triplex. To extend the boundaries of this hybrid system further, a click chemistry-based di-copper binding ligand was developed to accommodate designer ancillary ligands such as DPQ and DPPZ. When this ligand was inserted into a TFO, a dramatic improvement in targeted oxidative cleavage is afforded.     

Computational DFT investigation of vicinal amide group anchimeric assistance in ether cleavage

Density functional theory (DFT) computations in solvent have been used to investigate the mechanism of anchimeric assistance (by a vicinal amide group) in the acid-induced ether cleavage. The calculations were carried out at the B3LYP/6-31G* level of theory via full geometry optimizations within the IEF-PCM continuum solvent model. Two different mechanisms have been investigated here that were previously hypothesized for the rate-determining step of this process: the first (mechanism A1) involves a protonated amide and an ethereal oxygen as the nucleophile, while the second (mechanism A2) involves protonation of the ethereal oxygen followed by a nucleophilic attack of the amide. Computations clearly show that the second (involving protonation of the less basic site) is the most favorite route and leads to the formation of an oxazolidinic intermediate that triggers ether hydrolysis. Results are produced that are in excellent agreement with the experiments, and a rationale for them is provided, which represents a general interpretative basis for similar anchimerically assisted processes, such as the ones characterizing the glycosidic activity of two very important classes of enzymes: beta-hexosaminidases and O-GlcNAcases.     

Issues of ligand accessibility and mobility in initial cell attachment

The influence of lateral ligand mobility on cell attachment and receptor clustering has previously been explored for membrane-anchored molecules involved in cell-cell adhesion. In this study, we considered instead a cell binding motif from the extracellular matrix. Even though the lateral mobility of extracellular matrix ligands in membranes does not occur in vivo, we believe it is of interest for cell engineering in vitro. As is the case for cell-cell adhesion molecules, lateral mobility of extracellular matrix ligands could influence cell attachment and, subsequently, cell behavior in cell culture. In this paper, the accessibility and functionality of extracellular matrix ligands presented at surfaces were evaluated for the conditions of laterally mobile versus non-mobile ligands by studying ligand-antibody binding events and early cell attachment as a function of ligand concentration. We compare the initial attachment of rat-derived adult hippocampal progenitor (AHP) cells on laterally mobile, supported phospholipid bilayer membranes to non-mobile, poly-L-lysine-grafted-poly(ethylene glycol) (PLL-g-PEG) polymer films functionalized with a range of laminin-derived IKVAV-containing peptide densities. To this end, synthesis of a new PLL-g-PEG/PEG-IKVAV polymer is described. The characterization of available IKVAV peptides on both surface presentations schemes was explored by studying the mass uptake of anti-IKVAV antibodies using a combination of the surface-sensitive techniques quartz crystal microbalance with dissipation monitoring, surface plasmon resonance spectroscopy, and optical waveguide lightmode spectroscopy. IKVAV-containing peptides presented on laterally mobile, supported phospholipid bilayers and non-mobile PLL-g-PEG were recognized by the anti-IKVAV antibody in a dose-dependent manner, indicating that the amount of available IKVAV ligands increases proportionally with ligand density over the concentrations tested. Attachment of AHP cells to IKVAV-functionalized PLL-g-PEG and supported phospholipid bilayers followed a sigmoidal dependence on peptide concentration, with a critical concentration of approximately 3 pmol/cm2 IKVAV ligands required to support initial AHP cell attachment for both surface modifications. There appeared to be little influence of IKVAV peptide mobility on the initial attachment of AHP cells. Although the spread in the cell attachment data was larger for the PLL-g-PEG surface modification, this was reduced when observed after 24 h, indicating that the cells might need longer times to establish attachment strengths equivalent to those observed on peptide-functionalized supported lipid bilayers. The present study is a step toward understanding the influence of extracellular-matrix-derived ligand mobility on cell fate. Further analysis should focus on the systematic tuning of lateral ligand diffusion, as well as a comparison between the response of non-spreading cells (i.e., AHPs), versus spreading cells (i.e., fibroblasts).     

Influence of alkyl chain length on phosphate self-assembled monolayers

A series of alkyl phosphates with alkyl chain lengths ranging from C10 to C18 have been synthesized. Self-assembled monolayers (SAMs) of these molecules were prepared on titanium oxide surfaces by immersion of the substrates in alkyl phosphate solutions of 0.5 mM concentration in n-heptane/isopropanol. The SAMs were characterized by means of dynamic water contact angle (dCA) measurements, variable-angle spectroscopic ellipsometry (VASE), X-ray photoelectron spectroscopy (XPS), and polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS). A higher degree of order and packing density within the monolayers was found for alkyl phosphates with alkyl chain lengths exceeding 15 carbon atoms. This is reflected in a lower dCA hysteresis, as well as a film thickness measured by VASE and XPS close to the expected values for SAMs with an average alkyl chain tilt angle of 30 degrees to the surface normal. Additionally a shift of the symmetric and antisymmetric C-H stretching modes in the PM-IRRAS spectra to lower wave numbers was observed. These findings imply a higher two-dimensional crystallinity of the films derived from alkyl phosphates with a longer alkyl chain length.     

Straightforward access to pyrazines, piperazinones, and quinoxalines by reactions of 1,2-diaza-1,3-butadienes with 1,2-diamines under solution, solvent-free, or solid-phase conditions

The preparation of tetrahydropyrazines, dihydropyrazines, pyrazines, piperazinones, and quinoxalines by 1,4-addition of 1,2-diamines to 1,2-diaza-1,3-butadienes bearing carboxylate, carboxamide, or phosphorylated groups at the terminal carbon and subsequent internal heterocyclization is described. The solvent-free reaction of carboxylated 1,2-diaza-1,3-butadienes with the same reagents affords piperazinones, while phosphorylated 1,2-diaza-1,3-butadienes yield phosphorylated pyrazines. The solid-phase reaction of polymer-bound 1,2-diaza-1,3-butadienes with 1,2-diamines produces pyrazines.     

Synthesis and spectral studies on Ni(II) complexes involving N-furfuryl-N-substituted benzyldithiocarbamates and PPh3: Anagostic and C–H…π(chelate) interactions in (N-furfuryl-N-(4-fluorobenzyl)dithiocarbamato-S,S′)(thiocyanato-N)(triphenylphosphine)nickel(II)

Twelve new nickel(II) complexes of functionalized dithiocarabamates [Ni(S₂CNRR')₂](1-6) and [Ni(S₂CNRR')(NCS)(PPh₃)](7-12) [where R=furfuryl; R'=2-hydroxy benzyl (1,7), 3-hydroxy benzyl (2,8), 4-hydroxy benzyl (3,9), 4-methoxy benzyl (4,10), 4-fluoro benzyl (5,11), 4-chloro benzyl (6,12)] have been prepared and characterized by elemental analysis, IR, UV-Vis and NMR (¹H and ¹³C) spectroscopy. IR spectra of the complexes support the bidentate coordination of dithiocarbamate ligands. Electronic spectral studies on complexes 1-12 indicate square planar geometry around the nickel(II) central atom. In the ¹³C NMR spectra, the upfield shift of NCS₂ carbon signal for heteroleptic complex (7-12) compared to homoleptic complexes (1-6) is due to the effect of PPh₃ on the mesomeric drift of electron density toward nickel through thioureide C-N bond. Single crystal X-ray structural analysis of complex 11 confirms that the coordination geometry about the Ni(II) is distorted square planar. A rare intramolecular anagostic interaction C–H^…Ni [Ni???H=2.804 Å] is observed. The packing of complex 11 is stabilized by non-conventional C–H^…S, C–H?F and C–H?π(chelate, NiS₂C) bonding interactions.