Analytical assays based on detecting conformational changes of single molecules.

One common strategy for the detection of biomolecules is labeling either the target itself or an antibody that binds to it. Herein, a different approach, based on detecting the conformational change of a probe molecule induced by binding of the target is discussed. That is, what is being detected is not the presence of the target or the probe, but the conformational change of the probe. Recently, a single-molecule sensor has been developed that exploits this mechanism to detect hybridization of a single DNA oligomer to a DNA probe, as well as specific binding of a single protein to a DNA probe. Biomolecular recognition often involves large conformational changes of the molecules involved, and therefore this strategy may be applicable to other assays.     

Molecular modeling of interactions between L-lysine and functionalized quartz surfaces

Molecular modeling techniques have been used to investigate the interaction of L-lysine in aqueous medium with silanol and methyl sites onto quartz substrates. The substrate effect has been studied for partially hydrophilic surfaces formed by silanol and methyl groups with a ratio of 1:5 and hydrophobic fully methylated surfaces. Molecular dynamics and static calculations indicate that L-lysine does not show any significant interaction with fully methylated surfaces, while its interaction with hydroxylated/methylated surfaces is dominated by electrostatic and H-bond terms. Accordingly, on fully methylated surfaces there is no preferential orientation of L-lysine with respect to the surface, while for hydroxylated/methylated surfaces the L-lysine-surface interaction mainly depends on the molecular orientation, with a preferred geometry involving the ammonium group pointing toward the silanol site. The structure of water shells around L-lysine molecules was shown to be strongly affected by the relative hydrophilic/hydrophobic character of the surfaces. In particular, the order is almost completely lost for partially hydrophilic surfaces, while well-defined hydration shells around L-lysine are obtained for hydrophobic surfaces.     

Ultrafast dynamics of isolated fluorenone

The ultrafast dynamics of isolated 9-fluorenone was studied by femtosecond time-resolved photoionization and photoelectron spectroscopy. The molecule was excited around 264-266 nm into the S(6) state. The experimental results indicate that the excitation is followed by a multistep deactivation. A time constant of 50 fs or less corresponds to a fast redistribution of energy within the initially excited manifold of states, i.e., a motion away from the Franck-Condon region. Internal conversion to the S(1) state then proceeds within 0.4 ps. The S(1) state is long-lived, and only a lower bound of 20 ps can be derived. In addition, we computed excited state energies and oscillator strengths by TD-DFT theory, supporting the interpretation of the experimental data.     

Very long-distance magnetic coupling in a dicopper(II) metallacyclophane with extended π-conjugated diphenylethyne bridges

Self-assembly of the rigid rodlike ligand N,N'-4,4'-diphenylethynebis(oxamate) (dpeba) and Cu(2+) ions affords a novel dinuclear copper(II) metallacyclophane (nBu(4)N)(4)[Cu(2)(dpeba)(2)]·4MeOH·2Et(2)O (1) featuring a very long intermetallic distance (r = 15.0 ?). Magnetic susceptibility measurements for 1 reveal a moderately weak but nonnegligible intramolecular antiferromagnetic coupling between the two metal centers across the double para-substituted diphenylethynediamidate bridge (J = -3.9 cm(-1); H = -JS(1)S(2), where S(1) = S(2) = S(Cu) = (1)/(2)). Density functional electronic structure calculations on 1 support the occurrence of a spin polarization mechanism.     

Structural studies on Ba(II) adducts of the cytosine nucleobase and its derivative 1-Methylcytosine*

Abstract

The use of the cytosine nucleobase or its 1-Methylcytosine derivative as ligands toward barium(II) cations led to the formation of three compounds, {[Ba(1-Mecyt)(H₂O)X₂]}_n [X=Cl (1), Br (2)], and {[Ba(cyt)₂(H₂O)(ClO₄)₂]}_n (3). Depending on the ligand and the counterion employed, 1–3 exhibit different architectures, which serve as a playground to study how the methyl substitution, together with the nature of the counterion are both significant in the self-assembling process of such species. The effect of the nature and size of the alkaline-earth metal ion on the final structural motif is also evident when comparing these structures with parent complexes of the Ca(II) ion.     

One‐Pot Cooperation of Single‐Atom Rh and Ru Solid Catalysts for a Selective Tandem Olefin Isomerization‐Hydrosilylation Process

Realizing the full potential of oxide‐supported single‐atom metal catalysts (SACs) is key to successfully bridge the gap between the fields of homogeneous and heterogeneous catalysis. Here we show that the one‐pot combination of Ru₁/CeO₂ and Rh₁/CeO₂ SACs enables a highly selective olefin isomerization‐hydrosilylation tandem process, hitherto restricted to molecular catalysts in solution. Individually, monoatomic Ru and Rh sites show a remarkable reaction specificity for olefin double‐bond migration and anti‐Markovnikov α‐olefin hydrosilylation, respectively. First‐principles DFT calculations ascribe such selectivity to differences in the binding strength of the olefin substrate to the monoatomic metal centers. The single‐pot cooperation of the two SACs allows the production of terminal organosilane compounds with high regio‐selectivity (>95 %) even from industrially‐relevant complex mixtures of terminal and internal olefins, alongside a straightforward catalyst recycling and reuse. These results demonstrate the significance of oxide‐supported single‐atom metal catalysts in tandem catalytic reactions, which are central for the intensification of chemical processes.     

Identification and assay of underivatized urinary acylcarnitines by paper spray tandem mass spectrometry

A new analytical approach, using paper spray tandem mass spectrometry, has been developed for assay of carnitine and acylcarnitines in urine. Paper spray (PS) is a very promising technique, especially in clinical investigations, because of its simplicity, low cost, and rapid sample preparation. A home-made paper spray device was used for assay of urinary acylcarnitines (C2–C18). The performance of solvents with different elution efficiency and paper substrates with different porosity grade and structure were tested by use of spiked synthetic urine. Tandem mass spectrometry in multiple reaction monitoring (MRM) mode was optimized to obtain better specificity and sensitivity. Analyte signals were evaluated for stability and reproducibility. Calibration with [²H₃]propionylcarnitine (C3-d3), [²H₃]octanoylcarnitine (C8-d3), and [²H₃] palmitoylcarnitine (C16-d3) as internal standards was used for quantification. Very good linearity was obtained, with correlation coefficients >0.99 for C0–C12 and C16 acylcarnitines and >0.96 for C14 and C18 acylcarnitines. Accuracy and precision (RSD, %) of the proposed procedure were tested at concentrations of 0.8, 8, and 20 mg L^?1 with very satisfactory results: overall mean accuracy was 98.9 % and overall mean relative standard deviation 1 %. Limits of detection (LOD) between 6 and 208 μg L^?1 for propionylcarnitine and tetradecanoylcarnitine, respectively, can be regarded as very satisfactory. Application of the method to real urine proved that paper spray tandem mass spectrometry is a simple, rapid, and direct tool (no derivatization is required) for assay of carnitine and C2–C12 acylcarnitines in urine.     

Correction of the interference by mixing the reagents in the bioluminescent determination of ATP in environmental samples by an interfaced PC photometer and a robust regression procedure

 An automated procedure for correcting the interference due to mixing the reagents in the determination of ATP by a bioluminescent technique is described. The measurements were performed by an in-house interfaced PC photometer. An automated procedure based on a robust regression method and outliers detection was applied to exclude the time of the mixing of the reagents from the global time of reaction. In fact the mixing of the reagents is responsible of the poor analytical precision (RSD%>25) and low sensitivity (limit of detection≈2×10^-8 mol/l). By this procedure, the precision (RSD%<7) and sensitivity (limit of detection≈8×10^-10 mol/l) were improved. The method was applied to the determination of ATP in marine sediments and good recovery within 90–108% was obtained. For non-polluted samples the measurement can be carried out by direct comparison with standard solutions. The standard addition procedure is recommended for polluted samples. Received: 25 April 1996/Revised: 28 June 1996/Accepted: 3 July 1996     

Influence of nanodispersed boehmite on polypropylene photooxidation

Nanocomposites containing pure or organically modified nanoboehmites of different sizes were prepared by melt compounding with polypropylene. The samples were UV light irradiated in artificial accelerated conditions representative of solar irradiation (λ > 300 nm) at 60 °C in air. The chemical modifications resulting from photooxidation were followed by IR and UV-visible spectroscopies. The presence of pristine nanoboehmites was shown to change the rate of oxidation of polypropylene by reducing the oxidation induction period due to the presence of residual processing antioxidant. The differences of the oxidation induction periods between the nanocomposites and the pristine polymer disappear after solvent extraction of the antioxidant. The inefficiency of traditional antioxidant in retarding the photooxidation of polypropylene containing nanodispersed boehmite is proved. Antioxidant migration to the boehmite surface induced by the preferential interaction with the polar filler is proposed as an explanation. The oxidative behaviour of the organically modified boehmites was shown to depend on the type of organic substituent. p-Toluenesulfonate reduces the adsorption of antioxidants while the presence of a long-chain alkyl benzensulfonate increased the oxidation rate by generation of radical initiators.     

Self-Assembling of cytosine nucleoside into triply-bound dimers in acid Media. A comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry,X-rays diffractometry,and theoretical calculations

Electrospray tandem mass spectrometry (ESI-MS/MS) is used to evaluate the assembling of cytosine and thymine nucleosides in the gas phase, through the formation of hydrogen bonded supermolecules. Mixtures of cytidine analogues and homologues deliver in the gas phase proton-bound heterodimers stabilized by multiple interactions, as proven by the kinetics of their dissociation into the corresponding protonated monomers. Theoretical calculations, performed on initial structures of methylcytosine homodimers available in the literature, converged to a minimized structure whereby the two pyrimidine rings interact through the formation of three hydrogen bonds of similar energy. The crystallographic data here reported show the equivalency of the two interacting pyrimidines which is attributable to the presence of an inversion center. Thymine and uracil pyrimidyl nucleosides form, by ESI, gaseous proton-bound dimers. The kinetic of their dissociation into the related protonated monomers shows that the nucleobases are weekly interacting through a single hydrogen bond. The minimized structure of the protonated heterodimer formed by thymine and N-1-methylthymine confirmed the existence of mainly one hydrogen bond which links the two nucleobases through the O4 oxygens. No crystallographic data exists on thymine proton-bound species, nor have we been able to obtain these aggregates in the solid phase. The gaseous phase, under high vacuum conditions, seems therefore a suitable environment where vanishing structures produced by ESI can be studied with a good degree of approximation.