Synthesis and structure of 1,3,5-tris(diorganohydroxysilyl)benzenes. Novel building blocks in supramolecular silanol chemistry

The 1,3,5-tris(diorganohydroxysilyl)benzenes 1,3,5-(HOR₂Si)₃C₆H₃ (TMSB, R = Me; TPSB, R = Ph) have been prepared and fully characterized by X-ray crystallography. The crystal structure of TMSB features pairwise connected layers, in which the molecules are involved in interlayer hydrogen bonding. The supramolecular hydrogen bond motif may be described as a 12-membered ring that adopts a chair conformation. TPSB forms an equimolar inclusion complex with water, which is associated via hydrogen bonding and apparently fills a void in the crystal packing. In this case, the supramolecular hydrogen bond motif may be described as an eight-membered ring. Two of the water molecules are also associated, giving rise to a water dimer entrapped in the silanol matrix. Besides the hydrogen bonds, the crystal structure of the TPSB·H₂O complex reveals intra- and intermolecular C-H··· π stacking of most of the phenyl groups. Electrospray mass spectrometry shows that TPSB undergoes supramolecular complex formation with a variety of N-donors such as 4-(dimethylamino)pyridine, N,N,N',N'-tetramethylethylenediamine, imidazole, 2-(dimethylamino)pyridine, and 2,2'-dipyridylamine.

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2-(2-Pyridylamino)Pyridinium2-(2-Pyridylamino)pyridinium chloride phosphorous acid: one-dimensional hydrogen-bonded and [π]-[π] stacked supramolecular chains

In the crystal structure of the title compound, C₁₀H₁₀N₃⁺·Cl-^·[P(O)(OH)₂H], the chloride ion and phosphorous acid form a one-dimensional hydrogen-bonded chain, while the 2-(2-pyridylamino)pyridinium cations form a second chain through [π]-[π] stacking. The two parallel chains are connected via a PO...H-N hydrogen bond and a weak pyridinium-to-chloride interaction.

Order–disorder transitions in poly(3,4-ethylenedioxythiophene)

The commonly held perception that high conductivity in conducting polymers is linked to a high level of π-stacking order in the material is shown here to be of lesser importance in highly conducting poly(3,4-ethylenedioxythiophene) (PEDT), which has been prepared by chemical vapour phase polymerisation. Despite the fact that there is a highly energetic phase transition about 130 °C (110 J/g), and that this transition corresponds to a loss of the long-range π-stacking as observed in grazing angle XRD, the conductivity remains unchanged beyond the transition and only decreases by a factor of two when heating to above 200 °C. The XRD data suggest that order in two dimension remains above the phase transition measured by DSC and this order is sufficient to maintain a high level of electronic conductivity. Furthermore, as the ligand on the iron salt used in the synthesis is varied, the conductivity of the PEDT varies over two orders of magnitude. These phenomena cannot be explained by different degree of doping or crystallinity and it is proposed that the iron salt has an ordering effect during the vapour phase polymerisation.

Synthesis, characterization, and multilayer assembly of pH sensitive graphene−polymer nanocomposites

pH sensitive graphene−polymer composites have been prepared by the modification of graphene basal planes with pyrene-terminated poly(2-N,N′-(dimethyl amino ethyl acrylate) (PDMAEA) and poly(acrylic acid) (PAA) via π−π stacking. The pyrene-terminal PDMAEA and PAA were synthesized using reversible addition−fragmentation chain transfer (RAFT) polymerization with a pyrene-functional RAFT agent. The graphene−polymer composites were found to demonstrate phase transfer behavior between aqueous and organic media at different pH values. Atomic force microscopy (AFM) analysis revealed that the thicknesses of the graphene−polymer sheets were approximately 3.0 nm when prepared using PDMAEA (M_n: 6800 and PDI: 1.12). The surface coverage of polymer chains on the graphene basal plane was calculated to be 5.3 × 10⁻¹¹ mol cm⁻² for PDMAEA and 1.3 × 10⁻¹⁰ mol cm⁻² for PAA. The graphene−polymer composites were successfully characterized using X-ray photoelectron spectroscopy (XPS), attenuated total reflection infrared (ATR-IR) spectroscopy, and thermogravimetric analysis (TGA). Self-assembly of the two oppositely charged graphene−polymer composites afforded layer-by-layer (LbL) structures as evidenced by high-resolution scanning electron microscopy (SEM) and quartz crystal microbalance (QCM) measurements.

Protonated melonate Ca[HC6N7(NCN)3]·7H2O – synthesis, crystal structure, and thermal properties

Calcium hydrogenmelonate heptahydrate Ca[HC6N7(NCN)3]·7H2O was obtained by metathesis reaction in aqueous solution. The structure of the molecular salt was elucidated by single-crystal X-ray diffraction. The crystal structure consists of alternating layers of planar monopronated melonate ions, Ca2+ and crystal water molecules. The anions of adjacent layers are staggered so that no π–π stacking occurs. The melonate entities are interconnected by hydrogen bonds within and between the layers. Ca[HC6N7(NCN)3]·7H2O was investigated by solid-state NMR and FTIR spectroscopy, TG and DTA measurements.

The influence of graphene on the electrical communication through organic layers on graphite and gold electrodes

The influence of graphene on the electrical communication through organic layers fabricated on graphite and gold electrodes is investigated. These layers were prepared by in situ reductive adsorption of 4-aminobenzoic acid in the presence of NaNO2 and HCl to have surface bound carboxylic acid functionalities, followed by covalent attachment of 1-aminopyrene via an amide coupling reaction to have surface bound pyrene groups for graphene immobilization via noncovalent π-π stacking interaction. The coverage of the layers created via reductive adsorption on graphite electrodes was found to be much higher than that on gold electrodes. It was revealed that graphene significantly enhances the electrical communication through the layers on graphite electrodes but on gold electrodes the enhancement effect through the layers was only minor. However, when gold electrodes were modified with a self-assembled monolayer (SAM) of propanethiol the subsequent immobilization of graphene resulted in a significant enhancement of the electrical communication. It is also found that immobilization of graphene could affect the electron transfer between the redox probe, pyrene and the underlying electrodes. Atomic force microscopy (AFM) and scanning electron microscopy (SEM) were used to characterize the graphene sheets. Cyclic voltammetry, electrochemical impedance spectroscopy (EIS), and X-ray photoelectron spectroscopy (XPS) were also used to characterize the stepwise modified electrodes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Alisertib, an Aurora kinase A inhibitor, induces apoptosis and autophagy but inhibits epithelial to mesenchymal transition in human epithelial ovarian cancer cells.

Ovarian cancer is a leading killer of women, and no cure for advanced ovarian cancer is available. Alisertib (ALS), a selective Aurora kinase A (AURKA) inhibitor, has shown potent anticancer effects, and is under clinical investigation for the treatment of advanced solid tumor and hematologic malignancies. However, the role of ALS in the treatment of ovarian cancer remains unclear. This study investigated the effects of ALS on cell growth, apoptosis, autophagy, and epithelial to mesenchymal transition (EMT), and the underlying mechanisms in human epithelial ovarian cancer SKOV3 and OVCAR4 cells. Our docking study showed that ALS, MLN8054, and VX-680 preferentially bound to AURKA over AURKB via hydrogen bond formation, charge interaction, and π-π stacking. ALS had potent growth-inhibitory, proapoptotic, proautophagic, and EMT-inhibitory effects on SKOV3 and OVCAR4 cells. ALS arrested SKOV3 and OVCAR4 cells in G2/M phase and induced mitochondria-mediated apoptosis and autophagy in both SKOV3 and OVCAR4 cell lines in a concentration-dependent manner. ALS suppressed phosphatidylinositol 3-kinase/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) and p38 mitogen-activated protein kinase pathways but activated 5'-AMP-dependent kinase, as indicated by their altered phosphorylation, contributing to the proautophagic activity of ALS. Modulation of autophagy altered basal and ALS-induced apoptosis in SKOV3 and OVCAR4 cells. Further, ALS suppressed the EMT-like phenotype in both cell lines by restoring the balance between E-cadherin and N-cadherin. ALS downregulated sirtuin 1 and pre-B cell colony enhancing factor (PBEF/visfatin) expression levels and inhibited phosphorylation of AURKA in both cell lines. These findings indicate that ALS blocks the cell cycle by G2/M phase arrest and promotes cellular apoptosis and autophagy, but inhibits EMT via phosphatidylinositol 3-kinase/Akt/mTOR-mediated and sirtuin 1-mediated pathways in human epithelial ovarian cancer cells. Further studies are warranted to validate the efficacy and safety of ALS in the treatment of ovarian cancer.

Graphene/tri-block copolymer composites prepared via RAFT polymerizations for dual controlled drug delivery via pH stimulation and biodegradation

A novel tri-block copolymer poly(oxopentanoate ethyl methacrylate)-block-poly(pyridyl disulfide ethyl acrylate)-block-poly(ethylene glycol acrylate) [poly(OEMA-b-PDEA-b-PEGA)], retaining active keto groups and pyridyl disulfide (PDS) side functionalities, was synthesized as a drug delivery vehicle using reversible addition-fragmentation chain transfer (RAFT) polymerization method. One mimic drug pyridine-2-thione (PT) was introduced into the monomer, PDEA for copolymerization. The other mimic drug O-benzylhydroxylamine (BHA) was conjugated with tri-block copolymer via efficient oxime coupling chemistry, followed by the attachment onto graphene via π-π stacking interaction to obtain a graphene/tri-block copolymer composite. 1H NMR, UV-vis absorption spectroscopy, fluorescence spectroscopy, gel permeation chromatography (GPC), atomic force microscope (AFM) and transmission electron microscope (TEM) were used to verify the successful step-wise preparation of the tri-block copolymer and drug loaded composite. In vitro release behaviors of BHA and PT from graphene/tri-block copolymer composite via dual drug release mechanisms were investigated. BHA can be released under acid environment, while PT will be released in the presence of reducing agents, such as dithiothreitol (DTT) or glutathione (GSH). It can be envisioned that this novel composite could be exploited as a novel intracellular drug delivery system via dual release mechanisms.

Tetrafenilciclopentadienon-derivati ed analoghi: sintesi, "self-assembly" e caratterizzazione reologica

Gels are materials that are easier to recognize than to define. For all practical purpose, a material is termed a gel if the whole volume of liquid is completely immobilized as usually tested by the ‘tube inversion’ method. Recently, supramolecular gels obtained from low molecular weight gelators (LMWGs) have attracted considerable attention in materials science since they represent a new class of smart materials sensitive to external stimuli, such as temperature, ultrasounds, light, chemical species and so on. Accordingly, during the past years a large variety of potentialities and applications of these soft materials in optoelectronics, as electronic devices, light harvesting systems and sensors, in bio-materials and in drug delivery have been reported. Spontaneous self-assembly of low molecular weight molecules is a powerful tool that allows complex supramolecular nanoscale structures to be built. The weak and non-covalent interactions such as hydrogen bonding, π–π stacking, coordination, electrostatic and van der Waals interactions are usually considered as the most important features for promoting sol-gel equilibria. However, the occurrence of gelation processes is ruled by further “external” factors, among which the temperature and the nature of the solvents that are employed are of crucial importance. For example, some gelators prefer aromatic or halogenated solvents and in some cases both the gelation temperature and the type of the solvent affect the morphologies of the final aggregation. Functionalized cyclopentadienones are fascinating systems largely employed as building blocks for the synthesis of polyphenylene derivatives. In addition, it is worth noting that structures containing π-extended conjugated chromophores with enhanced absorption properties are of current interest in the field of materials science since they can be used as “organic metals”, as semiconductors, and as emissive or absorbing layers for OLEDs or photovoltaics. The possibility to decorate the framework of such structures prompted us to study the synthesis of new hydroxy propargyl arylcyclopentadienone derivatives. Considering the ability of such systems to give π–π stacking interactions, the introduction on a polyaromatic structure of polar substituents able to generate hydrogen bonding could open the possibility to form gels, although any gelation properties has been never observed for these extensively studied systems. we have synthesized a new class of 3,4-bis (4-(3-hydroxy- propynyl) phenyl) -2, 5-diphenylcyclopentadienone derivatives, one of which (1a) proved to be, for the first time, a powerful organogelator. The experimental results indicated that the hydroxydimethylalkynyl substituents are fundamental to guarantee the gelation properties of the tetraarylcyclopentadienone unit. Combining the results of FT-IR, 1H NMR, UV-vis and fluorescence emission spectra, we believe that H-bonding and π–π interactions are the driving forces played for the gel formation. The importance of soft materials lies on their ability to respond to external stimuli, that can be also of chemical nature. In particular, high attention has been recently devoted to anion responsive properties of gels. Therefore the behaviour of organogels of 1a in toluene, ACN and MeNO2 towards the addition of 1 equivalent of various tetrabutylammonium salts were investigated. The rheological properties of gels in toluene, ACN and MeNO2 with and without the addition of Bu4N+X- salts were measured. In addition a qualitative analysis on cation recognition was performed. Finally the nature of the cyclic core of the gelator was changed in order to verify how the carbonyl group was essential to gel solvents. Until now, 4,5-diarylimidazoles have been synthesized.

Aggregation of hybrid molecules and film formation of colloidal monolayers

A unique characteristic of soft matter is its ability to self-assemble into larger structures. Characterizing these structures is crucial for their applications. In the first part of this work, I investigated DNA-organic hybrid material by means of Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Cross-Correlation Spectroscopy (FCCS). DNA-organic hybrid materials, a novel class of hybrid materials composed of synthetic macromolecules and oligodeoxynucleotide segmenta, are mostly amphiphilic and can self-assemble into supramolecular structures in aqueous solution. A hybrid material of a fluorophore, perylenediimide (PDI), and a DNA segment (DNA-PDI) has been developed in Prof. A. Hermann’s group (University of Groningen). This novel material has the ability to form aggregates through pi-pi stacking between planar PDIs and can be traced in solution due to the fluorescence of PDI. I have determined the diffusion coefficient of DNA-PDI conjugates in aqueous solution by means of FCS. In addition, I investigated whether such DNA-PDIs form aggregates with certain structure, for instance dimers. rnOnce the DNA hybrid material self-assemble into supermolecular structures for instance into micelles, the single molecules do not necessarily stay in one specific micelle. Actually, a single molecule may enter and leave micelles constantly. The average residence time of a single molecule in a certain micelle depends on the nature of the molecule. I have chosen DNA-b-polypropylene oxide (PPO) as model molecules and investigated the residence time of DNA-b-PPO molecules in their according micelles by means of FCCS.rnBesides the DNA hybrid materials, polymeric colloids can also form ordered structures once they are brought to an air/water interface. Here, hexagonally densely packed monolayers can be generated. These monolayers can be deposited onto different surfaces as coating layers. In the second part of this work, I investigated the mechanical properties of such colloidal monolayers using micromechanical cantilevers. When a coating layer is deposited on a cantilever, it can modify the elasticity of the cantilever. This variation can be reflected either by a deflection or by a resonance frequency shift of the cantilever. In turn, detecting these changes provides information about the mechanical properties of the coating layer. rnIn the second part of this work, polymeric colloidal monolayers were coated on a cantilever and homogenous polymer films of a few hundred nanometers in thickness were generated from these colloidal monolayers by thermal annealing or organic vapor annealing. Both the film formation process and the mechanical properties of these resulting homogenous films were investigated by means of cantilever. rnElastic property changes of the coating film, for example upon absorption of organic vapors, induce a deflection of the cantilever. This effect enables a cantilever to detect target molecules, when the cantilever is coated with an active layer with specific affinity to target molecules. In the last part of this thesis, I investigated the applicability of suitably functionalized micromechanical cantilevers as sensors. In particular, glucose sensitive polymer brushes were grafted on a cantilever and the deflection of this cantilever was measured during exposure to glucose solution. rn

Molecular Dynamics Simulation of a PNA·DNA·PNA Triple Helix in Aqueous Solution

Molecular dynamics simulations have been used to explore the conformational flexibility of a PNA·DNA·PNA triple helix in aqueous solution. Three 1.05 ns trajectories starting from different but reasonable conformations have been generated and analyzed in detail. All three trajectories converge within about 300 ps to produce stable and very similar conformational ensembles, which resemble the crystal structure conformation in many details. However, in contrast to the crystal structure, there is a tendency for the direct hydrogen-bonds observed between the amide hydrogens of the Hoogsteen-binding PNA strand and the phosphate oxygens of the DNA strand to be replaced by water-mediated hydrogen bonds, which also involve pyrimidine O2 atoms. This structural transition does not appear to weaken the triplex structure but alters groove widths and so may relate to the potential for recognition of such structures by other ligands (small molecules or proteins). Energetic analysis leads us to conclude that the reason that the hybrid PNA/DNA triplex has quite different helical characteristics from the all-DNA triplex is not because the additional flexibility imparted by the replacement of sugar−phosphate by PNA backbones allows motions to improve base-stacking but rather that base-stacking interactions are very similar in both types of triplex and the driving force comes from weak but definate conformational preferences of the PNA strands.

Hydrogen bonding of nucleotide base pairs: Application of the PM3 method

The ability of the pm3 semiempirical quantum mechanical method to reproduce hydrogen bonding in nucleotide base pairs was assessed. Results of pm3 calculations on the nucleotides 2′-deoxyadenosine 5′-monophosphate (pdA), 2′-deoxyguanosine 5′-monophosphate (pdG), 2′-deoxycytidine 5′-monophosphate (pdC), and 2′-deoxythymidine 5′-monophosphate (pdT) and the base pairs pdA–pdT, pdG–pdC, and pdG(syn)–pdC are presented and discussed. The pm3 method is the first of the parameterized nddo quantum mechanical models with any ability to reproduce hydrogen bonding between nucleotide base pairs. Intermolecular hydrogen bond lengths between nucleotides displaying Watson–Crick base pairing are 0.1–0.2 Å less than experimental results. Nucleotide bond distances, bond angles, and torsion angles about the glycosyl bond (χ), the C4′C5′ bond (γ), and the C5′O5′ bond (β) agree with experimental results. There are many possible conformations of nucleotides. pm3 calculations reveal that many of the most stable conformations are stabilized by intramolecular CHO hydrogen bonds. These interactions disrupt the usual sugar puckering. The stacking interactions of a dT–pdA duplex are examined at different levels of gradient optimization. The intramolecular hydrogen bonds found in the nucleotide base pairs disappear in the duplex, as a result of the additional constraints on the phosphate group when part of a DNA backbone. Sugar puckering is reproduced by the pm3 method for the four bases in the dT–pdA duplex. pm3 underestimates the attractive stacking interactions of base pairs in a B-DNA helical conformation. The performance of the pm3 method implemented in SPARTAN is contrasted with that implemented in MOPAC. At present, accurate ab initio calculations are too timeconsuming to be of practical use, and molecular mechanics methods cannot be used to determine quantum mechanical properties such as reaction-path calculations, transition-state structures, and activation energies. The pm3 method should be used with extreme caution for examination of small DNA systems. Future parameterizations of semiempirical methods should incorporate base stacking interactions into the parameterization data set to enhance the ability of these methods.

Spectroscopic properties of pyrene-containing DNA mimics

DNA mimics containing non-nucleosidic pyrene building blocks are described. The modified oligomers form stable hybrids, although a slight reduction in hybrid stability is observed in comparison to the unmodified DNA duplex. The nature of the interaction between the pyrene residues in single and double stranded oligomers is analyzed spectroscopically. Intra- and inter-strand stacking interactions of pyrenes are monitored by UV-absorbance as well as fluorescence spectroscopy. Excimer formation is observed in both single and double strands. In general, intrastrand excimers show fluorescence emission at shorter wavelengths (approx. 5-10 nm) than excimers formed by interstrand interactions. The existence of two different forms of excimers (intra- vs. interstrand) is also revealed in temperature dependent UV-absorbance spectra. (C) 2007 Elsevier Ltd. All rights reserved.

From Ribbons to Networks: Hierarchical Organization of DNA-Grafted Supramolecular Polymers

DNA-grafted supramolecular polymers (SPs) allow the programmed organization of DNA in a highly regular, one-dimensional array. Oligonucleotides are arranged along the edges of pyrene-based helical polymers. Addition of complementary oligonucleotides triggers the assembly of individual nanoribbons resulting in the development of extended supramolecular networks. Network formation is enabled by cooperative coaxial stacking interactions of terminal GC base pairs. The process is accompanied by structural changes in the pyrene polymer core that can be followed spectroscopically. Network formation is reversible, and disassembly into individual ribbons is realized either via thermal denaturation or by addition of a DNA separator strand.

Supramolecular Polymers in DNA Nanotechnology

Creation of biocompatible functional materials is an important task in supramolecular chemistry. In this contribution, we report on noncovalent synthesis of DNA-grafted supramolecular polymers (SPs). DNA-grafted SPs enable programmed arrangement of oligonucleotides in a regular, tightly packed one-dimensional array. Further interactions of DNA-grafted SPs with complementary DNA strands leads to the formation of networks through highly cooperative G-C blunt-end stacking interactions. The structural changes in the polymeric core enable to monitor spectroscopically the stepwise formation of networks. Such stimuli-responsive supramolecular networks may lead to the development of DNA-based smart materials.