Conformation of ionizable poly Para phenylene ethynylene in dilute solutions

The conformation of dinonyl poly para phenylene ethynylenes (PPEs) with carboxylate side chains, equilibrated in solvents of different quality have been studied using molecular dynamics simulations. PPEs are of interest because of their tunable electro‐optical properties, chemical diversity, and functionality which are essential in wide range of applications. The polymer conformation determines the conjugation length and their assembly mode and affects electro‐optical properties which are critical in current and potential uses. This study investigates the effect of carboxylate fraction on PPEs side chains on the conformation of chains in the dilute limit, in solvents of different quality. The dinonyl PPE chains are modeled atomistically, where the solvents are modeled both implicitly and explicitly. Dinonyl PPEs maintained a stretched out conformation up to a carboxylate fraction f of 0.7 in all solvents studied. The nonyl side chains are extended and oriented away from the PPE backbone in toluene and in implicit good solvent, whereas in water and implicit poor solvent, the nonyl side chains are collapsed toward the PPE backbone. Rotation around the aromatic ring is fast and no long range correlations are seen within the backbone. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 582–588     

Evidence for the isomerization and decarboxylation in the photoconversion of the red fluorescent protein DsRed

Recently, it has been shown that the red fluorescent protein DsRed undergoes photoconversion on intense irradiation, but the mechanism of the conversion has not yet been elucidated. Upon irradiation with a nanosecond-pulsed laser at 532 nm, the chromophore of DsRed absorbing at 559 nm and emitting at 583 nm (R form) converts into a super red (SR) form absorbing at 574 nm and emitting at 595 nm. This conversion leads to a significant change in the fluorescence quantum yield from 0.7 to 0.01. Here we demonstrate that the photoconversion is the result of structural changes of the chromophore and one amino acid. Absorption, fluorescence, and vibrational spectroscopy as well as mass spectrometry suggest that a cis-to-trans isomerization of the chromophore and decarboxylation of a glutamate (E215) take place upon irradiation to form SR. At the same time, another photoproduct (B) with an absorption maximum at 386 nm appears upon irradiation. This species is assigned as a protonated form of the DsRed chromophore. It might be a mixture of several protonated DsRed forms as there is at least two ways of formation. Furthermore, the photoconversion of DsRed is proven to occur through a consecutive two-photon absorption process. Our results demonstrate the importance of the chromophore conformation in the ground state on the brightness of the protein as well as the importance of the photon flux to control/avoid the photoconversion process.     

Evaluating the Conservation State of Naturally Aged Paper with Raman and Luminescence Spectral Mapping: Toward a Non-Destructive Diagnostic Protocol

Micro-Raman and luminescence spectroscopy were combined with morphological analysis to study the conservation state of differently degraded paper samples, dated from 1873 to 2021. The aim of the work reported in this paper was to obtain ageing markers based on variations of Raman and fluorescence spectral features. Raman and luminescence spectra were acquired by scanning non-printed areas of books, and Raman and fluorescence maps were built by contrasting spectral parameters point by point, obtaining a micron-scale space resolved imaging of the degradation pattern. Complementary information on paper morphology and surface compactness were obtained by high-resolution scanning electron and atomic force microscopy. The proposed non-destructive procedure is particularly interesting for precious and ancient samples to analyze their degradation processes and to evaluate the performance and effectiveness of restoration treatments.     

Effective elastic shear stiffness of a periodic fibrous composite with non-uniform imperfect contact between the matrix and the fibers

In this contribution, effective elastic moduli are obtained by means of the asymptotic homogenization method, for oblique two-phase fibrous periodic composites with non-uniform imperfect contact conditions at the interface. This work is an extension of previous reported results, where only the perfect contact for elastic or piezoelectric composites under imperfect spring model was considered. The constituents of the composites exhibit transversely isotropic properties. A doubly periodic parallelogram array of cylindrical inclusions under longitudinal shear is considered. The behavior of the shear elastic coefficient for different geometry arrays related to the angle of the cell is studied. As validation of the present method, some numerical examples and comparisons with theoretical results verified that the present model is efficient for the analysis of composites with presence of imperfect interface and parallelogram cell. The effect of the non uniform imperfection on the shear effective property is observed. The present method can provide benchmark results for other numerical and approximate methods.     

Cationic calix[4]arenes as anion-selective ionophores

1,3-Alternate cationic calix[4]arene proved highly selective for proton/halogens symport transport and showed antiproliferative activity against murine monocyte/macrophage J774.A1 cancer cells.     

Mutual Support of Ligand- and Structure-Based Approaches—To What Extent We Can Optimize the Power of Predictive Model? Case Study of Opioid Receptors

The process of modern drug design would not exist in the current form without computational methods. They are part of every stage of the drug design pipeline, supporting the search and optimization of new bioactive substances. Nevertheless, despite the great help that is offered by in silico strategies, the power of computational methods strongly depends on the input data supplied at the stage of the predictive model construction. The studies on the efficiency of the computational protocols most often focus on global efficiency. They use general parameters that refer to the whole dataset, such as accuracy, precision, mean squared error, etc. In the study, we examined machine learning predictions obtained for opioid receptors (mu, kappa, delta) and focused on cases for which the predictions were the most accurate and the least accurate. Moreover, by using docking, we tried to explain prediction errors. We attempted to develop a rule of thumb, which can help in the prediction of compound activity towards opioid receptors via docking, especially those that have been incorrectly predicted by machine learning. We found out that although the combination of ligand- and structure-based path can be beneficial for the prediction accuracy, there still remain cases that cannot be reliably predicted by any available modeling method. In addition to challenging ligand- and structure-based predictions, we also examined the role of the application of machine-learning methods in comparison to simple statistical methods for both standard ligand-based representations (molecular fingerprints) and interaction fingerprints. All approaches were confronted in both classification (where compounds were assigned to the group of active and inactive group constructed on the basis of K_i values) and regression (where exact K_i value was predicted) experiments.     

Two new zincophosphates, (H3NCH2CH2NH3)2[Zn(μ-PO4)2] and (NH4)[(H3N)Zn{(μ-PO4)Zn}3]: Crystal structures and relationships to similar open framework zinco- and aluminophospates

Two new zincophosphates, bis(ethylenediammonim) catena-bis(μ-phosphato)zincate, (H₃NCH₂CH₂NH₃)₂[Zn(μ-PO₄)₂] (1), and ammonium ammine-tris(μ-phosphato)tetrazincate, (NH₄)[(H₃N)Zn{(μ-PO₄)Zn}₃] (2), were synthesized under hydrothermal conditions and their crystal structures were determined by single-crystal X-ray diffraction analysis. The crystal structure of 1 consists of infinite macroanionic ZnP₂O₈⁴⁻ chains, running along the [0 0 1] direction, and diprotonated ethylenediammonium cations, H₂en²⁺. The crystal structure of 2 is built up from ZnO₄, Zn(NH₃)O₃ and PO₄ vertex-sharing tetrahedra connected to form an open 3D framework. The ammonium groups, NH₄⁺, are located in the channels formed by 8M-rings extending along [1 0 0]. In order to study vibrational behavior of H₂en²⁺ and NH₄⁺ cations, NH₃ molecules in 1 and 2, single-crystal Raman spectra were obtained. Structural, chemical and topological similarities to the other open framework zinco- and aluminophosphates incorporating different guest species are discussed.     

Amperometric determination of bonded glucose with an MnO(2) and glucose oxidase bulk-modified screen-printed electrode using flow-injection analysis

A screen-printed amperometric biosensor based on carbon ink double bulk-modified with MnO₂ as a mediator and glucose oxidase as a biocomponent was investigated for its ability to serve as a detector for bonded glucose in different compounds, such as cellobiose, saccharose, (-)-4-nitrophenyl-β-d-glucopyranoside, as well as in beer samples by flow-injection analysis (FIA). The biosensor could be operated under physiological conditions (0.1 M phosphate buffer, pH 7.5) and exhibited good reproducibility and stability. Bonded glucose was released with glucosidase in solution, and the free glucose was detected with the modified screen-printed electrode (SPE). The release of glucose by the aid of glucosidase from cellobiose, saccharose and (-)-4-nitrophenyl-β-d-glucopyranoside in solution showed that stoichiometric quantities of free glucose could be monitored in all three cases.The linear range of the amperometric response of the biosensor in the FIA-mode flow rate 0.2 mL min⁻¹, injection volume 0.25 mL, operation potential 0.48 V versus Ag/AgCl) extends from 11 to 13,900 μmol L⁻¹ glucose in free form. The limit of detection (3σ) is 1 μmol L⁻¹ glucose. A concentration of 100 μmol L⁻¹ yields a relative standard deviation of approximately 7% with five injections. These values correspond to the same concentrations of bonded glucose supposed that it is liberated quantitatively (incubation for 2 h with glucosidase).Bonded glucose could be determined in beer samples using the same assay. The results corresponded very well with the reference procedure.