Charge-mediated recognition of N-terminal tryptophan in aqueous solution by a synthetic host

The molecular recognition of peptides and proteins in aqueous solution by designed molecules remains an elusive goal with broad implications for basic biochemical research and for sensors and separations technologies. This paper describes the recognition of N-terminal tryptophan in aqueous solution by the synthetic host cucurbit[8]uril (Q8). Q8 is known to form 1:1:1 heteroternary complexes with methyl viologen (MV) and a second aromatic guest. Here, the complexes of Q8.MV with (i) the four natural aromatic alpha-amino acids, (ii) four singly charged tryptophan derivatives, and (iii) four tryptophan-containing tripeptides were characterized by isothermal titration calorimetry, mass spectrometry, and UV-visible, fluorescence, and (1)H NMR spectroscopy. We find that Q8.MV binds Trp-Gly-Gly with high affinity (K(a) = 1.3 x 10(5) M(-1)), with 6-fold specificity over Gly-Trp-Gly, and with 40-fold specificity over Gly-Gly-Trp. Analysis of the nine indole-containing compounds suggests that peptide recognition is mediated by the electrostatic charge(s) proximal to the indole, and that the mode of binding is consistent for these compounds. Complex formation is accompanied by the growth of a visible charge-transfer band and the quenching of indole fluorescence. These optical properties, combined with the stability and selectivity of this system, are promising for applications in sensing and separating specific peptides.     

The cooperative effect in ion-pair recognition by a ditopic hemicryptophane host

The heteroditopic hemicryptophane 1 , which bears a tripodal anion binding site and a cation recognition site in the molecular cavity, proved to be an efficient ion‐pair receptor. The hemicryptophane host binds anions selectively depending on shape and hydrogen‐bond‐accepting ability. It forms an inclusion complex with the Me₄N⁺ ion, which can simultaneously bind anionic species to provide anion@[ 1? Me₄N⁺] complexes. The increased affinity of [ 1? Me₄N⁺] for anionic species is attributed to a strong cooperative effect that arises from the properly positioned binding sites in the hemicryptophane cavity, thus allowing the formation of the contact ion pair. Density functional theory calculations were performed to analyze the Coulomb interactions of the ion pairs, which compete with the ion‐dipole ones, that originate in the ion–hemicryptophane contacts.     

A luminescent receptor with affinity for N-terminal histidine in peptides in aqueous solution

Crown ethers of suitable size are the perfect artificial host compounds for ammonium ion binding, but the rather low affinity in aqueous solution prevents their use at physiological conditions. We report here the synthesis and properties of a luminescent benzo crown ether with a pendant copper imidodiacetic acid complex, which coordinates with high affinity to histidine. The emission intensity of the benzo crown ether increases significantly in the presence of ammonium ions in methanol. At physiological conditions in buffered water at pH 7.5 these interactions are too weak to be detected. If an ammonium ion and an imidazole moiety are present in the analyte, such as in His-Lys-OMe or His-OMe, high binding affinity in aqueous solution is restored. The binding event is signaled by an increase in emission intensity, which can even be observed with the naked eye. This allows the selective detection of small peptides containing N-terminal histidine or histidine among all other amino acids at physiological conditions.     

Thiocyanate removal from aqueous solution by a synthetic hydrotalcite sol

The use of a chloride-containing synthetic hydrotalcite sol (LDHC) as adsorbent to remove thiocyanate from aqueous solution was investigated. LDHC was prepared by coprecipitation and was characterized by HRTEM, particle size, XRD, and FTIR. The experiments showed that LDHC was particularly effective in removing thiocyanate due to its small particle size and high zeta potential. The adsorption of thiocyanate on LDHC was favored when the initial solution pH was in the range 3-10, though the most effective pH range was between 4.0 and 8.0. The adsorption reached equilibrium within 150 min. The interaction between the surface sites of LDHC and thiocyanate ions may be a combination of both anion exchange and surface complexation. The pseudo-second-order model best described the adsorption kinetics of thiocyanate onto LDHC. The equilibrium isotherm showed that the adsorption of thiocyanate on LDHC was consistent with the Langmuir equation and the saturated adsorption capacity of LDHC for thiocyanate was 98.3 mg/g at 20°C. The regenerated LDHC in FeCl(3) solution can be used repeatedly in adsorption-regeneration cycles. The results showed that LDHC can be used as a new adsorbent for thiocyanate removal from aqueous solution because of its high adsorption capacity and rapid adsorption rate.     

Samarium-induced convenient reductive dimerization of aromatic ketones in aqueous methanol: a mechanistic approach

Samarium metal has been used for the reductive dimerization of aromatic ketones in the presence of additives; the most probable mechanism has been advanced to explain the diastereoselectivity of this dimerization reaction.     

Sequence-specific recognition and cleavage of DNA by anti-tumour antibiotics

Abstract

DNA cleavage by a bleomycin—iron complex occurs preferentially at guanine-pyrimidine (5′ → 3′) sequences, in particular at G-C sites. Metallobleomycin binds in the minor groove of B-DNA and the bithiazole moiety probably plays an important role as an anchor on DNA duplex. The 2-amino group of guanine adjacent to the 5′-side of the cleaved pyrimidine base is one key element of the specific 5′-GC recognition by the bleomycin-metal complex. Endiyne anti-tumour antibiotics such as esperamicin A₁ and dynemicin A also interact with the minor groove of DNA, and their strong DNA splitting activity is due to phenylene diradical formation from the enediyne core. A possible binding mode between these antibiotics and B-DNA has been proposed by computer-constructed model building.     

Laccase-catalyzed carbon-carbon bond formation: oxidative dimerization of salicylic esters by air in aqueous solution

The laccase catalyzed oxidative dimerization of salicylic esters, a rare example of a laccase-catalyzed carbon-carbon bond formation, was studied. This reaction allows the use of air as stoichiometric oxidant and proceeds in aqueous solution. The preparative scope and the mechanism of the method, which provides a new and convenient access to functionalized biaryls under mild conditions, were investigated.     

Development of calixarene-based host molecules for peptides in aqueous media

We synthesized a peptidocalix[4]arene library consisting of 1000 members that was suitable for peptide recognition in aqueous media. Some peptidocalix[4]arenes in the library were host molecules for guest peptides. Electrostatic interaction between the host and guest molecules was the most important factor for binding in aqueous media.     

Oxidative amide synthesis and N-terminal alpha-amino group ligation of peptides in aqueous medium

A new method for oxidative synthesis of amides from alkynes and amines in high yields (up to 96%) using [Mn(2,6-Cl2TPP)Cl] 1 as a catalyst and Oxone/H2O2 as an oxidant in aqueous medium has been developed. This method could be used for N-terminal alpha-amino group ligation of unprotected peptides with aryl, aliphatic, and internal alkynes under mild conditions.     

Hydroxylation of aromatic rings in an aqueous solution induced by argon arc plasma

Plasma-induced reaction in an aqueous solution of phenyl-containing amino acids resulted in the formation of several hydroxyphenyl amino acids, which was explained by the action of hydroxyl radicals generated by decomposition of water molecules by the high energy plasma.     

Molecular recognition and fluorescence sensing of monophosphorylated peptides in aqueous solution by bis(zinc(II)-dipicolylamine)-based artificial receptors

The phosphorylation of proteins represents a ubiquitous mechanism for the cellular signal control of many different processes, and thus selective recognition and sensing of phosphorylated peptides and proteins in aqueous solution should be regarded as important targets in the research field of molecular recognition. We now describe the design of fluorescent chemosensors bearing two zinc ions coordinated to distinct dipicolylamine (Dpa) sites. Fluorescence titration experiments show the selective and strong binding toward phosphate derivatives in aqueous solution. On the basis of (1)H NMR and (31)P NMR studies, and the single-crystal X-ray structural analysis, it is clear that two Zn(Dpa) units of the binuclear receptors cooperatively act to bind a phosphate site of these derivatives. Good agreement of the binding affinity estimated by isothermal titration calorimetry with fluorescence titration measurements revealed that these two receptors can fluorometrically sense several phosphorylated peptides that have consensus sequences modified with natural kinases. These chemosensors display the following significant features: (i) clear distinction between phosphorylated and nonphosphorylated peptides, (ii) sequence-dependent recognition, and (iii) strong binding to a negatively charged phosphorylated peptide, all of which can be mainly ascribed to coordination chemistry and electrostatic interactions between the receptors and the corresponding peptides. Detailed titration experiments clarified that the phosphate anion-assisted coordination of the second Zn(II) to the binuclear receptors is crucial for the fluorescence intensification upon binding to the phosphorylated derivatives. In addition, it is demonstrated that the binuclear receptors can be useful for the convenient fluorescent detection of a natural phosphatase (PTP1B) catalyzed dephosphorylation.     

Molecular recognition of ADP over ATP in aqueous solution by a polyammonium receptor containing a pyrimidine residue

The synergistic action of the different binding groups of the polyfunctional HL receptor leads to the recognition of ADP over ATP in water, with a selectivity coefficient of up to 116, a phenomenon which is unprecedented in the context of synthetic receptors in water. The recognition is mostly due to the good matching between H(3)L(2+) and the protonated forms of ADP.     

Photosensitization by phenylalanine of carboxylic acids, amides, and peptides in frozen aqueous solution

Abstract— In order to elucidate the mechanism of the photosensitization of proteins and peptides by aromatic amino acids, the behaviour of aliphatic carboxylic acids and amides upon irradiation in frozen aqueous solution in the presence of phenylalanine (l-Phe) has been studied by EPR spectroscopy. EPR signals are much stronger when acids or amides are irradiated in the presence of l-Phe, showing that they are photosensitized by the aromatic amino acid. The species observed are either alkyl radicals, or radicals formed by abstraction of a hydrogen atom from a molecule of acid or arnide. A mechanism is proposed which involves the capture by carboxyl or amide carbonyl groups of hydrated electrons released by the photo-excited l-Phe, followed by the splitting of the resulting anion free radical with the formation of alkyl radicals, and transfer reactions leading to more stable free radicals. In peptides, which are also photosensitized by l-Phe, electrons are captured preferably by the carboxylic carbonyl groups.     

Fluorescence probes for thiol-containing amino acids and peptides in aqueous solution

A new fluorescence probe is described using the "chemosensing ensemble" method. The probe shows high selectivity and sensitivity for thiol-containing amino acids and peptides, and can detect cysteine and homocysteine from healthy to abnormal levels under physiologically-relevant conditions.     

Adsorption of fluoride on synthetic siderite from aqueous solution

The study has investigated the feasibility of using synthetic siderite for F⁻ removal from aqueous solution. Batch experiments were performed to test effects of adsorbent dosage, contact time, initial F⁻ concentration, temperature, solution pH, and coexisting anions on F⁻ removal. Results show that the kinetic rate of F⁻ adsorption was high in the first 2 h, and thereafter significantly decreased. The kinetic data was better fitted to the pseudo-second order kinetic model than the pseudo-first order kinetic model. In comparison with Langmuir isotherm, both Freundlich and Redlich-Peterson isotherms better described the adsorption process, which indicates that the multilayer adsorption should be involved in the process of F⁻ removal. Thermodynamic study manifests that F⁻ adsorption on synthetic siderite was spontaneous and exothermic in nature. The synthetic siderite had high adsorption capacity for F⁻ removal, which was up to 1.775 mg/g in the batch with an adsorbent dosage of 5 g/L and an initial F⁻ concentration of 20 mg/L at 25 °C. The adsorption was relatively independent on solution pH between 4 and 9. The presence of Cl⁻ and NO₃⁻ had less impact on F⁻ adsorption, while PO₄³⁻ significantly affected F⁻ removal from aqueous solution. Results of X-ray diffraction (XRD) and scanning electron microscopy (SEM) suggest that the high adsorption capacity possibly arose from both coprecipitation of ferric hydroxide with F⁻ and adsorption of F⁻ on the fresh goethite.     

Sequence-specific control of azobenzene assemblies by molecular recognition of DNA

We investigated the molecular recognition between the amphiphile AzoAde, which is composed of azobenzene in the hydrophobic and adenine in the hydrophilic portion of the molecule, and oligonucleotides having a homogeneous base (dA30, dT30, dG30, and dC30) at the air-water interface. On the basis of the complementary base-pairing of DNA in the duplex, orderly arrangement of AzoAde on templated dT30 was examined using pi-A isotherm, UV-vis RAS, FT-IR RAS, and XPS measurements. Although there was little interaction between AzoAde and mismatched oligonucleotides (dA30, dG30, and dC30), AzoAde prepared on a dT30 subphase stoichiometrically assembled and interacted with dT30, subsequently forming a J-form assembly at the air-water interface. AFM observation of the LB films revealed the nanostructure of the J-formed AzoAde monolayer on the dT30 subphase as well as the domain structures of the H-formed monolayers on the other oligonucleotide subphases. Therefore, dT30 has a potential application as a template for assembling AzoAde at the air-water interface.     

Single ion and dimerization studies of the Al(III) ion in aqueous solution

Aqueous trivalent aluminum (Al) ions and their oligomers play important roles in diverse areas, such as environmental sciences and medicine. The geometries of octahedral Al(H(2)O)(6)(3+) and tetrahedral Al(OH)(4)(-) species have been studied extensively. However, structures of intermediate hydrolysis products of the Al(III) ion, such as the penta-coordinated Al(OH)(2+) species, which exists at pH values ranging from 3.0 to 4.3, and their mode of formation have been poorly understood. Here, we present that a trigonal bipyramidal Al(OH)(H(2)O)(4)(2+) structure is formed in aqueous solution and how this monomeric species dimerizes to a dinuclear [(H(2)O)(4)Al(OH)(2)Al(H(2)O)(4)](4+) complex in aqueous solution. The Gibbs free energy change calculations indicate that the formation of the dinuclear complex is preferred over the existence of two single trigonal bipyramidal Al(OH)(H(2)O)(4)(2+) species in aqueous solution. This study captures the solution dynamics and proton transfer in the oligomerization reactions of penta-coordinated Al(OH)(2+) species in aqueous solution.