Teaching old indicators new tricks

Synthesis and preferred all-syn conformation of C3-symmetrical N-(hetero)arylmethyl triindoles

A new series of C(3)-symmetrical N-(hetero)arylmethyl triindoles has been synthesized in a straightforward procedure. The structure and conformation in the solid state have been determined for three derivatives (3, 4, and 6) by X-ray crystallographic analysis. In all three cases, the molecules adopt a tripodal conformation with all of the flexible arms directed towards the same side, thereby delimiting an inner cavity. Compound 6 crystallizes and forms C(3)-symmetric dimeric cagelike complexes. Guest molecules of chloroform and water are confined within the resulting cavities with stabilization by different intermolecular interactions; this highlights the potential of these compounds in the construction of supramolecular systems. A computational analysis has been performed to predict the most stable conformers. As a general trend, a preference for a conformation with all branches directed to the same side has been predicted. Comparison between theoretical and experimental results indicates that the computational level selected for the present study, B3LYP/6-31G*, is able to reproduce both the minimum energy conformations and the rotation barriers about the N--CH(2) bond.

Synthesis and photophysical investigation of squaraine rotaxanes by "clicked capping"

Pseudorotaxane complexes of squaraine dyes and tetralactam macrocycles are converted into permanently interlocked rotaxane structures using copper-catalyzed and copper-free cycloaddition reactions with bulky stopper groups. The photophysical properties of the encapsulated squaraine depend on the structure of the macrocycle. In one case, squaraine rotaxanes are produced in near-quantitative yields and with intense near-IR fluorescence. In another case, squaraine fluorescence is greatly diminished upon macrocyclic encapsulation but the signal can be restored by dye displacement with anions.

A coumarin-derived fluorescence probe selective for magnesium

Two different coumarin derivatives have been connected via an imine linkage to obtain a new fluorescence signaling system. This compound itself does not show any emission due to rapid isomerization around the C[double bond]N bond. However, in the presence of a Mg(II) ion, this isomerization is stopped because of bonding to the metal ion resulting in high-intensity (approximately 550-fold) emission. Other metal ions like Li(I), Ca(II), and Zn(II) show very little emission, while biologically relevant transition-metal ions do not show any emission. In this way, the Mg(II) ion can be detected in the presence of these ions.

Optimalization of Poly(neutral red) Coated-wire Electrode for Determination of Citrate in Soft Drinks

This report presents an optimization of potentiometric measurements with citrate-selective electropolymerized poly(neutral red) electrodes. The optimal background electrolyte for these measurements is a TRIS buffer with nitrate at pH 8.5. The electrodes described here exhibit stable and reproducible near-Nernstian response to citrates with a low detection limit of 6 × 10^-6 M. Electrodes polymerized from sulfuric acid and acetonitrile are compared in detail. Simple and sensitive method for quantification of citrate in real-life samples by potentiometry with poly(neutral red) electrodes are presented. Data from potentiometric measurements of citrate are compared with capillary electrophoresis.

A fluorescent fluoride ion probe based on a self-organized ensemble of 5-hydroxyflavone-Al(III) complex

In the presence of Al(III) ions, 5-hydroxyflavone (5HF) through a complexation reaction in MeOH, shows dual fluorescence, characterized by a newly developed peak at 554nm upon excitation at 363nm. In this communication, the subsequent ligand exchange reaction of the complex with fluoride ion causing a fluorescence enhancement followed by a decrease in fluorescence intensity involving an intermediate mechanistic pathway, delivering a quantitative estimation route for fluoride ion in the concentration range from 5x10(-5) to 7x10(-4)M, has been reported. The ligand exchange reaction, without interference from other common anions, has been investigated by UV-vis and fluorescence spectroscopies combined with the AM1 semi-empirical self-consistent field quantum chemical calculations within UHF formalism in their ground state.

Study of thiazole orange in aptamer-based dye-displacement assays

We screened a series of RNA and DNA aptamers for their ability to serve in the dye displacement assays in which analytes compete with TO dye. We conclude that, while the performance of the TO dye displacement approach is not always predictable, it is still a simple and sensitive assay to detect binding between RNA aptamers and small molecules. In particular, we describe efficient assays for tobramycin and theophylline, with up to 90% displacement of TO observed, and we describe the first aptameric assay for cAMP.

Dizinc enzyme model/complexometric indicator pairs in indicator displacement assays for inorganic phosphates under physiological conditions

A dizinc phosphohydrolase enzyme model complex employing the dinucleating ligand 2,6-bis-[(bis-pyridin-2-ylmethyl-amino)methyl]-4-methylphenol (L1) was tested for binding to a series of 11 commercially available complexometric indicators in aqueous N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid (HEPES) buffer at pH 7.4, with the aim of determining the applicability of these indicators in indicator displacement assays (IDAs) under physiological conditions. Dissociation constants (Kd) were determined for 11 indicator-Zn2L1 complexes, spanning 2 orders of magnitude from 2.8 x 10(-4) M (alizarin red S) to 2.7 x 10(-6) M (bromo pyrogallol red). Phosphate and pyrophosphate were tested for their ability to displace bound indicator and produce a detectable colorimetric response. Three indicators (bromo pyrogallol red, mordant blue 9, and zincon) complex to Zn2L1 to form an indicator displacement assay selective for pyrophosphate over phosphate. Because selection of an indicator/analyte pair having appropriate relative Kd values is critical for their successful application in IDAs, the binding data for these 11 indicators should assist their extension to IDAs for other analytes.

Encapsulation of Electron Donor−Acceptor Dyads in β-Cyclodextrin Cavity: Unusual Planarization and Enhancement in Rate of Electron-Transfer Reaction

Interaction of beta-cyclodextrin (beta-CD) with a few novel electron donor acceptor dyads 1a-c and 2a-c, having aryl and flexible methylene spacer groups, has been investigated through photophysical, chiroptical, electrochemical, NMR, and microscopic techniques. Dyads 1a and 1c, with p-tolyl and biphenyl spacer groups, respectively, exhibited significantly decreased fluorescence quantum yields and lifetimes in the presence of beta-CD, while negligible changes were observed for dyad 1b with an o-tolyl spacer. In contrast, spacer-length-dependent significant enhancement in fluorescence quantum yields and lifetimes was observed for dyads 2a-c, with flexible polymethylene (n = 1, 3, 11) spacer groups. Association constants of beta-CD encapsulated complexes have been determined and the contrast behavior observed in these systems is explained through an electron transfer (kET) mechanism based on calculated favorable change in free energy (DeltaGET = -1.27 eV) and the redox species characterized through laser flash photolysis studies. Rates of kET have been estimated and are found to increase ca. 2-fold in the case of dyads 1a and 1c when encapsulated in beta-CD, while significantly decreased kET values were observed for the dyads 2a-c with flexible spacer (ca. 9-fold for 2c). As characterized through cyclic voltammetry, 2D NMR [correlated (COSY) and nuclear Overhauser enhancement (NOESY) spectroscopy], and laser flash photolysis studies, the beta-CD encapsulation of dyads with aliphatic spacer groups leads to the conformational unfolding of a sandwich type of structure, whereas dyads with rigid aryl spacer groups undergo unusual planarization as compared to the uncomplexed dyads, resulting in enhanced electron-transfer reaction between the donor and acceptor moieties.

"Turn-on" fluorescent sensor for the selective detection of zinc ion by a sterically-encumbered bipyridyl-based receptor

A sterically-encumbered 5,5'-distyryl-2,2'-bipyridyl derivative that enforces a 1:1 metal-to-ligand ratio acts as a selective turn-on sensor for Zn(2+) in THF.

Selective sensing of metalloproteins from nonselective binding using a fluorogenic amphiphilic polymer

Nonconjugated fluorogenic amphiphilic polymers containing an anthracene chromophore exhibit fluorescence quenching in the presence of metalloproteins, although the binding of the polymer to proteins is not selective. The reason for this difference is that the possible conformational changes that protein binding could bring about on a polymer do not affect the fluorescence properties of a pendent chromophore in nonconjugated polymers. This is in contrast to the nonspecific binding and response found with conjugated polymers to proteins.

Pattern-based peptide recognition

Nature's use of sensor arrays in the mammalian olfactory and gustatory systems has encouraged supramolecular chemists to take a new approach to molecular recognition. Pattern-based recognition involves the use of sensor arrays to create fingerprints for analytes. The use of sensing arrays has paved the way for systems capable of identifying biological analytes that would have been difficult targets using the traditional "lock-and-key" approach to sensor design.

A supramolecular ON-OFF-ON fluorescence assay for selective recognition of GTP

With the objective of developing small molecule based receptors for nucleosides and nucleotides, interactions of a cyclic donor-acceptor conjugate 1 with adenosine, AMP, ADP, CTP, UTP, ITP, ATP, and GTP have been investigated by absorption, steady-state, and time-resolved fluorescence, cyclic voltammetry (CV), NMR, and fluorescence indicator displacement techniques. Titration of 1 with the fluorescent indicator, 8-hydroxy-1,3,6-pyrene trisulfonate (HPTS), resulted in nearly complete fluorescence quenching of HPTS, along with 25% hypochromicity in its absorption spectrum. Benesi-Hildebrand analysis gave a 1:1 stoichiometry for the complex between the receptor 1 and HPTS with an association constant (Kass) of 4.66 x 104 M-1 in buffer. The driving force for such a complexation was evaluated to be the synergistic effects of pi-stacking and electrostatic interactions inside the cavity as confirmed by the effect of ionic strength, temperature, and the negative results obtained with the model compound 2. Titration of the nonfluorescent complex [1.HPTS] with various nucleosides and nucleotides resulted in revival of fluorescence of the indicator, HPTS. It was observed that GTP induces maximum displacement of HPTS from the complex [1.HPTS] with an overall fluorescence enhancement of ca. 150-fold. The addition of adenosine, AMP, ADP, CTP, and UTP showed negligible changes, whereas ca. 45- and 50-fold enhancement was observed with ATP and ITP, respectively. The competitive displacement of the indicator by various analytes is found to be in the order GTP (buffer) approximately GTP (biofluid) > ITP approximately ATP > UTP > CTP approximately ADP approximately AMP approximately Ade. By virtue of having a better pi-electron cloud, GTP undergoes effective electronic, pi-stacking, and electrostatic interactions inside the cavity and forms a stable complex with the receptor 1. The uniqueness of this assay is that it differentiates GTP from ATP and other nucleotides and signals the event through a visual "turn on" fluorescence mechanism in buffer as well as in biological fluids.