Human telomere sequence DNA in water-free and high-viscosity solvents: g-quadruplex folding governed by kramers rate theory

Structures formed by human telomere sequence (HTS) DNA are of interest due to the implication of telomeres in the aging process and cancer. We present studies of HTS DNA folding in an anhydrous, high viscosity deep eutectic solvent (DES) comprised of choline choride and urea. In this solvent, the HTS DNA forms a G-quadruplex with the parallel-stranded ("propeller") fold, consistent with observations that reduced water activity favors the parallel fold, whereas alternative folds are favored at high water activity. Surprisingly, adoption of the parallel structure by HTS DNA in the DES, after thermal denaturation and quick cooling to room temperature, requires several months, as opposed to less than 2 min in an aqueous solution. This extended folding time in the DES is, in part, due to HTS DNA becoming kinetically trapped in a folded state that is apparently not accessed in lower viscosity solvents. A comparison of times required for the G-quadruplex to convert from its aqueous-preferred folded state to its parallel fold also reveals a dependence on solvent viscosity that is consistent with Kramers rate theory, which predicts that diffusion-controlled transitions will slow proportionally with solvent friction. These results provide an enhanced view of a G-quadruplex folding funnel and highlight the necessity to consider solvent viscosity in studies of G-quadruplex formation in vitro and in vivo. Additionally, the solvents and analyses presented here should prove valuable for understanding the folding of many other nucleic acids and potentially have applications in DNA-based nanotechnology where time-dependent structures are desired.     

Bis(diisopropylammonium) thiosulfate and bis(tert‐butylammonium) thiosulfate

Two new dialkylammonium thiosulfates, namely bis(diisopropylammonium) thiosulfate, 2C₆H₁₆N⁺·S₂O₃²⁻, (I), and bis(tert‐butylammonium) thiosulfate, 2C₄H₁₂N⁺·S₂O₃²⁻, (II), have been characterized. The secondary ammonium salt (I) crystallizes with Z = 4, while the primary ammonium salt (II), with more hydrogen‐bond donors, crystallizes with Z = 8 and a noncrystallographic centre of inversion. In both salts, the organic cations and thiosulfate anions are linked within extensive N—H...O and N—H...S hydrogen‐bond networks, forming extended two‐dimensional layers. Layers are parallel to (10) in (I) and to (002) in (II), and have a polar interior and a nonpolar hydrocarbon exterior. The layered structure and hydrogen‐bond motifs observed in (I) and (II) are similar to those in related ammonium sulfates.     

Changes of organic acids and phenolic compounds contents in grapevine berries during their ripening

Changes of total content of phenolic substances, alteration in total titratable acidity and differences in tartaric acid content in grapes of four white (Müller-Thurgau — MT, Pinot Blanc — Rulandské bílé in Czech, RB, Sauvignon (Sg), and Muscat Ottonel — Mu?kát Ottonel in Czech, MO) and two blue (Dornfelder — Df and Blue Frankish — Frankovka in Czech, Fr) grapevine varieties throughout their growth, ripening and maturing (July–November). Potentiometric titration was applied for the determination of total titratable acids in grapes (expressed as tartaric acid equivalents in g L^?1). A spectrophotometric method according Rebelein based on the formation of a colored complex of ammonium metavanadate and tartaric acid was used for determination of tartaric acid in green juice made by pressing unripe grapes. A spectrophotometric method based on reduction of phosphomolybdato-tungsten complex in alkaline solution using Folin-Ciocalteau reagent was applied for determination of total content of phenolic substances (TCP).

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Photophysics of Push–Pull Distyrylfurans,Thiophenes and Pyridines by Fast and Ultrafast Techniques

Time‐resolved transient absorption and fluorescence spectroscopy with nano‐ and femtosecond time resolution were used to investigate the deactivation pathways of the excited states of distyrylfuran, thiophene and pyridine derivatives in several organic solvents of different polarity in detail. The rate constant of the main decay processes (fluorescence, singlet–triplet intersystem crossing, isomerisation and internal conversion) are strongly affected by the nature [locally excited (LE) or charge transfer (CT)] and selective position of the lowest excited singlet states. In particular, the heteroaromatic central ring significantly enhances the intramolecular charge‐transfer process, which is operative even in a non‐polar solvent. Both the thiophene and pyridine moieties enhance the S₁→T₁ rate with respect to the furan one. This is due to the heavy‐atom effect (thiophene compounds) and to the ¹(π,π)*→³(n,π)* transition (pyridine compounds), which enhance the spin‐orbit coupling. Moreover, the solvent polarity also plays a significant role in the photophysical properties of these push–pull compounds: in fact, a particularly fast ¹LE*→¹CT* process was found for dimethylamino derivatives in the most polar solvents (time constant, τ≤400 fs), while it takes place in tens of picoseconds in non‐polar solvents. It was also shown that the CT character of the lowest excited singlet state decreased by replacing the dimethylamino side group with a methoxy one. The latter causes a decrease in the emissive decay and an enhancement of triplet‐state formation. The photoisomerisation mechanism (singlet/triplet) is also discussed.     

Correction to: Aziridine-2-Carboxylic Acid Derivatives and Its Open-Ring Isomers as a Novel PDIA1 Inhibitors

Chemistry of Heterocyclic Compounds -     

Nonlinear Optical Switching in Regioregular Porphyrin Covalent Organic Frameworks

Covalent organic frameworks (COFs) have garnered immense scientific interest among porous materials because of their structural tunability and diverse properties. However, the response of such materials toward laser‐induced nonlinear optical (NLO) applications is hardly understood and demands prompt attention. Three novel regioregular porphyrin (Por)‐based porous COFs—Por‐COF‐HH and its dual metalated congeners Por‐COF‐ZnCu and Por‐COF‐ZnNi—have been prepared and present excellent NLO properties. Notably, intensity‐dependent NLO switching behavior was observed for these Por‐COFs, which is highly desirable for optical switching and optical limiting devices. Moreover, the efficient π‐conjugation and charge‐transfer transition in ZnCu‐Por‐COF enabled a high nonlinear absorption coefficient (β=4470 cm/GW) and figure of merit (FOM=σ₁/σ_o, 3565) value compared to other state‐of‐the‐art materials, including molecular porphyrins (β≈100–400 cm/GW), metal–organic frameworks (MOFs; β≈0.3–0.5 cm/GW), and graphene (β=900 cm/GW).     

Analysis of long-term distributions of calibration parameters and calibration intervals for an atomic absorption spectrophotometer

 A combination of "black box" and "calendar-time" methods for the determination of calibration intervals of an analytical measuring instrument is discussed. Since the methods require information on the distributions of the calibration parameters, such information is described for an atomic absorption spectrophotometer, as an example. The hypotheses on the normal distribution of the calibration parameters are tested using the ω²-criterion and accepted at 0.90–0.95 levels of confidence. Corresponding control charts are designed for indication of warning and action limits of the calibration parameters, and diagnoses of outliers in further calibrations. Control charts indicate also when the calibration should be done according to the full program of the equipment manufacturer. Received: 15 April 2000 / Accepted: 24 July 2000     

Calcium-Ligand Cooperation Promoted Activation of N2O,Amine, and H2 as well as Catalytic Hydrogenation of Imines,Quinoline, and Alkenes

Bond activation and catalysis using s-block metals are of great significance. Herein, a series of calcium pincer complexes with deprotonated side arms have been prepared using pyridine-based PNP and PNN ligands. The complexes were characterized by NMR and X-ray crystal diffraction. Utilizing the obtained calcium complexes, unprecedented N₂O activation by metal-ligand cooperation (MLC) involving dearomatization-aromatization of the pyridine ligand was achieved, generating aromatized calcium diazotate complexes as products. Additionally, the dearomatized calcium complexes were able to activate the N−H bond as well as reversibly activate H₂, offering an opportunity for the catalytic hydrogenation of various unsaturated molecules. DFT calculations were applied to analyze the electronic structures of the synthesized complexes and explore possible reaction mechanisms. This study is an important complement to the area of MLC and main-group metal chemistry.     

Sensitivity of the NTB phase formation to the molecular structure of imino-linked dimers

ABSTRACT

Here we report on the synthesis and mesomorphic properties of a series of imino-linked dimeric molecules. In order to improve our understanding of the structure–N_TB phase correlations, we have studied the impact of geometric and electronic factors arising from varying mesogenic units, different spacer lengths and from the ratio (n/m) between the lengths of terminal chains (n) and spacer (m). From the perspective of the molecular geometry, the results show that the stability of the N_TB phase results from increasing effective molecular bending and with the broadening of the mesogenic unit, in particular near the spacer, and that the n/m ratio plays a substantial role in conjunction with the specific mesogenic unit. A computational study of the electronic properties shows that a broadening of the mesogenic core in the vicinity of the spacer is associated with an increased anisotropy of the electrostatic potential distribution. Within a given series of materials our study suggests that the incidence of the N_TB phase and its thermal stability are governed by the synergy of specific geometrical factors and the anisotropy of the electrostatic potential distribution of the mesogenic core.     

Enhancement of the Efficacy of Photodynamic Inactivation of Candida albicans with the Use of Biogenic Gold Nanoparticles

This study reports on successful photodynamic inactivation of planktonic and biofilm cells of Candida albicans using Rose Bengal (RB) in combination with biogenic gold nanoparticles synthesized by the cell‐free filtrate of Penicillium funiculosum BL1 strain. Monodispersed colloidal gold nanoparticles coated with proteins were characterized by a number of techniques including SEM–EDS, TEM, UV–Vis absorption and fluorescence spectroscopy, as well as Fourier transform infrared spectroscopy to be 24 ± 3 nm spheres. A Xe lamp (output power of 20mW, delivering intensity of 53 mW cm^?2) was used as a light source to study the effects of RB alone, the gold nanoparticles alone and the RB‐gold nanoparticle mixture on the viability of C. albicans cells. The most effective reduction in the number of planktonic cells was found after 30 min of Xe lamp light irradiation (95.4 J cm^?2) and was 4.89 log₁₀ that is 99.99% kill for the mixture of RB with gold nanoparticles compared with 2.19 log₁₀ or 99.37% for RB alone. The biofilm cells were more resistant to photodynamic inactivation, and the highest effective reduction in the number of cells was found after 30 min of irradiation in the presence of the RB–gold nanoparticles mixture and was 1.53 log₁₀, that is 97.04% kill compared with 0.6 log₁₀ or 74.73% for RB. The probable mechanism of enhancement of RB‐mediated photodynamic fungicidal efficacy against C. albicans in the presence of biogenic gold nanoparticles is discussed leading to the conclusion that this process may have a multifaceted character.