Conception and Evaluation of a Library of Cleavable Mass Tags for Digital Polymers Sequencing.

A library of phosphoramidite monomers containing a main-chain cleavable alkoxyamine and a side-chain substituent of variable molar mass (i.e. mass tag) was prepared in this work. These monomers can be used in automated solid-phase phosphoramidite chemistry and therefore incorporated periodically as spacers inside digitally-encoded poly(phosphodiester) chains. Consequently, the formed polymers contain tagged cleavable sites that guide their fragmentation in mass spectrometry sequencing and enhance their digital readability. The spacers were all prepared via a seven steps synthetic procedure. They were afterwards tested for the synthesis and sequencing of model digital polymers. Uniform digitally-encoded polymers were obtained as major species in all cases, even though some minor defects were sometimes detected. Furthermore, the polymers were decoded in pseudo-MS3 conditions, thus confirming the reliability and versatility of the spacers library.

Synthesis of oligoarylacetylenes with defined conjugated sequences using tailor-made soluble polymer supports.

Due to their strong tendency to self-aggregate, unfunctionalized oligoarylacetylenes are difficult to synthesize. Here, tailored polystyrene soluble supports, prepared by atom transfer radical polymerization and post-polymerization modification, were tested for preparing sequence-defined oligoarylacetylenes. Controlled aromatic sequences were obtained by iterative Sonogarisha coupling, using phenyl- and pyridine-based building-blocks.

Synthesis of a strained acetylenic macrocycle incorporating a para-oligo[2]cruciform bridge bent over nanoscopic dimensions: structural, electronic, spectroscopic, and ion-sensing properties.

An Eglinton-Galbraith diethyne cyclization preferentially yielded a structurally unusual macrocycle, comprising a strained conjugated oligo[2]cruciform wire, forced into a 2.2 nm bow-shape by a terpyridine rein or tether, and stabilized towards light and heat by four insulating triisopropylsilylacetylene (TIPSA) substituents. Spectroscopic ion-binding studies revealed the macrocycle to exhibit a particularly high UV/Vis selectivity for Pd(II) in dilute solution, and one of its precursors to afford a variety of luminescence quenching and color responses to particular metals, suggestive of promising ion-sensor applications. Under more concentrated conditions, the new macrocycle is able to bind specific metals (e.g., Au(I)) within its cavity despite the steric constraints. Intriguingly, variable-temperature (VT) UV/Vis/(1)H NMR investigations showed the TIPSA substituents to undergo restricted intramolecular motions along with reversible changes in the spectroscopic bandgap of the compound with temperature. In line with the theoretical calculations, the VT UV/Vis observations are consistent with a thermal modulation of the electronic conjugation through the strained oligo[2]cruciform bridge, which is coupled with redistributions within a mixture of conformational isomers of the macrocycle with differing relative twisting between the TIPSA-substituted phenyl rings. Overall, the generation of a para-oligo[2]cruciform, bent and flexed over nanoscopic dimensions through conformational tethering within the macrocyclic ring is noteworthy, and suggests a general approach to nanosized, curved, and strained, yet heat- and light-stable, para-phenyleneethynylene oligomers with unique physicochemical properties and challenging theoretical possibilities.

Quenching dynamics in CdSe nanoparticles: surface-induced defects upon dilution.

We have analyzed the decays of the fluorescence of colloidal CdSe quantum dots (QDs) suspensions during dilution and titration by the ligands. A ligand shell made of a combination of trioctylphosphine (TOP), oleylamine (OA), and stearic acid (SA) stabilizes the as-synthesized QDs. The composition of the shell was analyzed and quantified using high resolution liquid state 1H nuclear magnetic resonance (NMR) spectroscopy. A quenching of the fluorescence of the QDs is observed upon removal of the ligands by diluting the stock solution of the QDs. The fluorescence is restored by the addition of TOP. We analyze the results by assuming a binomial distribution of quenchers among the QDs and predict a linear trend in the time-resolved fluorescence decays. We have used a nonparametric analysis to show that for our QDs, 3.0 ± 0.1 quenching sites per QD on average are revealed by the removal of TOP. We moreover show that the quenching rates of the quenching sites add up. The decay per quenching site can be compared with the decay at saturation of the dilution effect. This provides a value of 2.88 ± 0.02 for the number of quenchers per QD. We extract the quenching dynamics of one site. It appears to be a process with a distribution of rates that does not involve the ligands.

Electronic, spectroscopic, and ion-sensing properties of a dehydro[m]pyrido[14]- and [15]annulene isomer library.

An isomeric series of dehydro[m]pyrido[n]annulenes incorporating strained 1,4-buta-1,3-diyne units have been synthesized, where m = 2, n = 14 (1a-d); m = 2, n = 15 (2a,b); and m = 3, n = 15 (3). The number of pyridine rings and annulene ring π-electrons are denoted by m and n, respectively. The X-ray crystal structures of 1b and 1c confirmed their cyclic formulation. All macrocycles were found to be luminescent chromophores with differing isomer-dependent proton and metal ion-sensory emission responses, which appear collectively as analyte-specific color patterns. Within the series studied, 1a was singular in displaying the highest luminescence quantum yield and sharing the strongest emission energy and molar absorption changes upon protonation and Hg(II) binding. Spectroscopic and electrochemical results were supported by density functional theory calculations in showing 1a, 2a, and 3 to be low bandgap materials with lowest unoccupied molecular orbitals delocalized over the 1,4-di(pyridin-4-yl)buta-1,3-diyne bridges that provide a pathway for electronic communication between the nitrogens. Overall, the investigations suggest that 1a, 2a, and 3 would be excellent ligands for the construction of novel conjugated hybrid metallosupramolecular nanostructures, polymers, and ion-sensory systems.

Studies on bis(halogeno) dioxomolybdenum(VI)-bipyridine complexes: synthesis and catalytic activity.

Dioxomolybdenum(VI) complexes with the general formula [MoO2Cl2L2] (L2=3,3'-dimethyl-2,2'-bipyridine, 5,5'-dimethyl-2,2'-bipyridine, 6,6'-dimethyl-2,2'-bipyridine, 4,4'-dibromo-2,2'-bipyridine, 5,5'-dibromo-2,2'-bipyridine, 5,5'-diamino-2,2'-bipyridine; 5,5'-dinitro-2,2'-bipyridine; 5,5'-di-ethoxycarbonyl-2,2'-bipyridine; 6-phenyl-2,2'-bipyridine; 2,2':6',2''-terpyridine) have been prepared and characterised. [MoO2Cl2(5,5'-di-ethoxycarbonyl-2,2'-bipyridine)] has been examined by single crystal X-ray analysis. The complexes were applied as homogenous catalysts for the epoxidation of cyclooctene with tert-butyl hydroperoxide (TBHP) as oxidising agent. The new compounds show an overall high activity and are highly selective catalysts in the epoxidation of cyclooctene. The stability of the complexes and differences in the catalytic activity can be clearly attributed to electronic contributions of the functional groups on bipyridine ligands and to steric restrictions. DFT calculations have assisted in a better understanding of the stability of the complexes and are in agreement with experiment. The influence of the terminal oxo ligands and the Lewis base ligands on the Mo center keep the compounds on quite a stable level of electron density.

Synthesis and properties of oligo[n]cruciforms: nanosized sterically encumbered tetraethynylphenyl-homologated fluorophores.

A series of nanosized phenyleneethynylenes have been prepared which are sterically insulated from the surrounding environment by multiple functionalization with triisopropylsilyl (TIPS) substituents. The phenyleneethynylenes comprise oligo[n]cruciforms 1-4 (n = 3-5) and a dehydrotribenzo[12]annulene 5, the former of which possess para-acyclic and the latter ortho-cyclic electronic conjugation pathways. All compounds were characterized by (1)H and (13)C NMR, IR, and mass spectroscopic techniques. The X-ray crystal structure of 1 confirmed the sterically isolating properties of the TIPS substituents. A comparison of the physical properties of these electronically differing systems revealed that they were all luminescent upon UV irradiation displayed negligible aggregation in dilute solution and that particular members of the series studied were electrochemically active, undergoing facile reversible reductions. The phenyleneethynylenes also exhibited significantly enhanced thermal stability by virtue of the presence of the TIPS substituents. The properties of 1-5 suggest that they are promising building blocks for the construction of materials for novel molecular electronics applications.

Nitrogen heterocyclic carbon-rich materials: synthesis and spectroscopic properties of dehydropyridoannulene macrocycles.

A new series of nitrogen heterocyclic dehydroannulenes 1-3 have been synthesized and their macrocyclic structures assigned using spectroscopic methods. The chiral and planar ground state conformations of 1 and 3, respectively, were determined by semiempirical theoretical calculations. All dehydropyridoannulenes and precursors possessing four aromatic rings functioned as fluorescent chromophores. A detailed spectroscopic investigation into the cation-binding properties of 3 in dilute solution revealed a particularly selective photoluminescence quenching sensory response for Pd(II) ions. Cycle 3, as well as 1 and 2, also exhibited reversible proton-triggered luminescence quenching behavior. At higher concentrations, 3 afforded a coordination polymer precipitate with Ag(I) ions. Cycles 1 and 2 and precursors 15, 23, and 29 also undergo thermochemical reactions that may potentially lead to carbon-rich polymers. The physicochemical properties of 1-3 suggest that dehydropyridoannulenes may serve as a particularly versatile new class of ligands for the creation of novel heteroatom-containing carbon-rich materials with many potential applications in supramolecular materials science and nanotechnology.

Cyclic donor-acceptor circuits: synthesis and fluorescence ion sensory properties of a mixed-heterocyclic dehydroannulene-type cyclophane.

The new dehydroannulene-type cyclophane 5 comprising a conjugated helical framework of thiophene (electron donor) and pyridine (electron acceptor) heterocyclic units has been prepared. Macrocycle 5 was characterized by FAB MS and (1)H and (13)C NMR spectroscopy. Cycle 5 was found to function as a selective precipitation and fluorescence sensor for specific metal ions such as Ag(I) and also exhibited reversible proton-triggered fluorescence quenching behavior. The unique donor-acceptor architecture and spectroscopic properties of 5 suggest that it represents a novel lead class of molecular sensory platforms, with many potential future applications in 21st century materials science.

Synthesis of a hexagonal nanosized macrocyclic fluorophore with integrated endotopic terpyridine metal-chelation sites.

A rigid nanosized hexagonal phenylethynyl cyclophane 5 has been prepared, which incorporates two 2,2':6',2"-terpyridines as integral structural units, for the purpose of binding metal ions. Macrocycle 5 was obtained by a 14-step synthesis in an overall yield of 11 %, and was characterised by spectroscopic techniques. The efficiency and ease of all transformations, and the relatively enhanced yield of the final macrocyclisation suggests that the entire synthetic pathway should be amenable to scale-up. Cyclophane 5 possesses four bulky triisopropylsilyl(TIPS)-protected ethyne substituents which serve a dual role. Firstly, they solubilise the structure thereby facilitating purification and subsequent handling. Secondly, they enable post-synthetic modification in which additional functionality may be attached to the periphery of the ring. Significantly, 5 was found to be a fluorescent chromophore, and may therefore potentially function as a new sensory platform for the detection of metal ions and H-bond donating biological substrates. The structurally well-defined nanosized morphology of 5, coupled with its interesting spectroscopic properties, supports the expectation that 5 and related architectures will attain a wealth of future applications within the developing fields of nanochemistry and nanoscience.

Synthesis and fluorescence ion-sensory properties of the first dehydropyridoannulene-type cyclophane with enforced exotopic metal ion binding sites.

The new twistophane 4 has been synthesised, which comprises a conjugated dehydropyridoannulene-type macrocyclic scaffold with outwardly projecting nitrogen-donor sites for the purpose of metal ion coordination. The macrocyclíc structure of 4 was assigned by using spectroscopic methods, and shown to exist in a twisted and chiral ground state conformation by semi-empirical theoretical calculations. A detailed spectroscopic investigation into the metal ion binding properties of 4 and precursor 11 revealed that they functioned as selective complexants, affording a fluorescence quenching output response characteristic of Pd(II) and Hg(II) ions. Furthermore, 4 also signalled the presence of Fe(II), Co(II), Ni(II) and Ag(I) ions by the precipitation of coordination polymers, and exhibited reversible proton-triggered fluorescence quenching behaviour. Macrocycle 4 thus represents a unique type of molecular sensory platform, which may find a wealth of potential applications such as the detection of heavy-metal pollutants, as well as for the fabrication of proton-switchable materials and coordination polymers with novel electronic and magnetic properties.

Self-assembly, characterisation, and crystal structure of multinuclear metal complexes of the [2 x 3] and [3 x 3] grid-type.

The self-assembly of new multimetallic complexes of grid-type architecture is described. The binding of a set of tris-terdentate ligands, 1 a-1 d, based on terpyridine-like subunits, with different octahedrally coordinated metal ions leads to the formation of species whose structure depends strongly on the ligand, the metal ion, the counterion, the solvent, and the reaction conditions. Under suitable conditions, the [3 x 3] grid was obtained from the reaction of ligand 1 a with zinc tetrafluoroborate and from ligand 1 b with mercury triflate. The other ligands led to the formation of mainly one compound of composition [M(6)L(5)](12+), which has the structure of an incomplete [2 x 3] grid. The crystal structure of such a [2 x 3] grid, [Co(6)(1 d)(5)](12+), has been determined. In this complex, the three central pyrimidine-pyridine-pyrimidine non-coordinating sites adopt transoid NCbond;CN conformations. The much less stable cisoid conformations, the "pinching" of the coordination sites in the complex, the weaker donor strength of the central binding site, and the steric demand of the substituents are all factors contributing to the reluctance to produce the [3 x 3] structure. A subtle interplay between the nature of the metal, the steric demand of the ligand, the reaction conditions, and the type of counterion determine the product of self-assembly. The results obtained show that by tuning the parameters, complexes containing six or nine octahedrally coordinated metal ions in a well-defined grid-type arrangement are accessible. Both types of arrays, [2 x 3] and [3 x 3 ], are of interest as self-assembled inorganic architectures of well-defined structure and nuclearity that may be suitable prototypes for selective information storage media.

Twistophane macrocyles with integrated 6,6'-connected-2,2'-bipyridine units: a new lead class of fluorescence sensors for metal ions.

The new twistophane macrocycles 2 and 3 have been synthesised; these compounds are composed of a cyclically conjugated dehydrobenzoannulene framework that incorporates 6,6'-connected-2,2'-bipyridine moieties for the purpose of coordinating metal ions. The cyclophanes were characterised by spectroscopic techniques, and shown by molecular mechanics calculations to be helically twisted and chiral molecules that may exist in several possible ground state conformations. UV/vis spectroscopic studies revealed that 2, 3 and precursor 9 bind with different selectivities to particular members of the following small group of metal analytes: CuII, AgI, HgII, Tl1 and PdII. Significantly, 2, 3 and 9 signal the presence of CuII ions through fluorescence emission quenching output responses. Furthermore, cyclophane 3 exhibited a particularly sensitive protontriggered chromogenic fluorescence response. With respect to their unique structural features, high analyte selectivity coupled with their enhanced and characteristic fluorescence emission responses, these molecules are among the first examples representing a new lead class of chemosensory materials. Compounds 2, 3 and 9 and derivatives thereof may, therefore, be expected to find many future applications in the detection of metal-based environmental pollutants, biologically important trace elements and monitoring proton fluxes.

Multicomponent Self-Assembly: Generation of Rigid-Rack Multimetallic Pseudorotaxanes.

The rigid linear ligands 1a-g and the macrocycle 2 undergo self-assembly via coordination with copper(I) ions to generate the series of rigid-rack inorganic pseudorotaxanes 3a-g. These complexes have been characterized by analytical and spectroscopic methods. Their architecture has been confirmed by determination of the crystal structures of 3e,f. The complex [Cu(2)(1e)(2)(2)](PF(6))(2) (3e) crystallizes in the space group C2/c, whereas complex [Cu(2)(1f)(2)(2)](PF(6))(2) (3f) gives crystals containing a single enantiomer in the chiral space group P2(1)2(1)2(1). The synthesis and solution structures of 3a-g and the solid-state structures of 3e,f are discussed in relation to the viability of multicomponent self-assembly as an approach to linear metal-ion arrays.

Self-Assembly of an 11-Component Cylindrical Inorganic Architecture: Electrospray Mass Spectrometry and Thermodynamic Studies.

Two hexaphenylhexaazatriphenylene L(1)()and three quaterpyridine L(2)() ligands are well-known to associate around six copper(I) ions to form a cylindrical inorganic cage 1. Spectrophotometric and electrospray mass spectrometry (ESMS) titrations have been conducted to gain information on the thermodynamics and the formation pathway of the assembly 1. From these data, the nature of intermediates present in solution was determined and the association constants of these species were calculated. It was also found that this assembling process occurs with positive cooperativity.