The Impact of Retinal Configuration on the Protein–Chromophore Interactions in Bistable Jumping Spider Rhodopsin-1

Bistable rhodopsins have two stable forms that can be interconverted by light. Due to their ability to act as photoswitches, these proteins are considered as ideal candidates for applications such as optogenetics. In this work, we analyze a recently crystalized bistable rhodopsin, namely the jumping spider rhodopsin-1 (JSR1). This rhodopsin exhibits identical absorption maxima for the parent and the photoproduct form, which impedes its broad application. We performed hybrid QM/MM simulations to study three isomers of the retinal chromophore: the 9-cis, 11-cis and all-trans configurations. The main aim was to gain insight into the specific interactions of each isomer and their impact on the absorption maximum in JSR1. The absorption spectra were computed using sampled snapshots from QM/MM molecular dynamics trajectories and compared to their experimental counterparts. The chromophore–protein interactions were analyzed by visualizing the electrostatic potential of the protein and projecting it onto the chromophore. It was found that the distance between a nearby tyrosine (Y126) residue plays a larger role in the predicted absorption maximum than the primary counterion (E194). Geometric differences between the isomers were also noted, including a structural change in the polyene chain of the chromophore, as well as changes in the nearby hydrogen bonding network.

Quantification of Hypochlorite in Water Using the Nutritional Food Additive Pyridoxamine

Chlorine is a widely used disinfectant and oxidant used for an array of municipal and industrial applications, including potable water, swimming pools, and cleaning of membranes. The most popular method to verify the concentration of free chlorine is the colorimetric method based on DPD (N, N-diethyl-p-phenylenediamine), which is fast and reasonably cheap, but DPD and its product are potentially toxic. Therefore, a novel, environmentally friendly colorimetric method for the quantification of residual chlorine based on the food additive pyridoxamine (4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol) was investigated. Pyridoxamine is a B6 vitamin with an absorption maximum at 324 nm and fluorescence emission at 396 nm. Pyridoxamine reacts rapidly and selectively with free chlorine, resulting in a linear decrease both in absorbance and in emission, giving therefore calibration curves with a negative slope. The pyridoxamine method was successfully applied for the quantification of free chlorine from 0.2 to 250 mg/L. Using 1 cm cuvettes, the limit of quantification was 0.12 mg Cl2/L. The pyridoxamine and the DPD methods were applied to actual environmental samples, and the deviation between results was between 4% and 9%. While pyridoxamine does not react with chloramine, quantification of monochloramine was possible when iodide was added, but the reaction is unfavourably slow.

Synthesis of Antibacterially ActiveSilver Nanoparticles by Galvanic Replacement on Magnesium in Solutions of Sodium Polyacrylate in an Ultrasound

“Green” synthesis of silver nanoparticles (AgNPs) by a galvanic replacement (GR) on magnesium in solutions of sodium polyacrylate (NaPA) under ultrasound (42 kHz) is reported. The mechanism of combined action of GR and ultrasound on the formation of nanoparticles is proposed. Synthesized solutions of AgNPs are characterized by an absorption maximum at 410 nm, the value of which does not depend on the concentrations of precursors (AgNO3 and NaPA) and the duration of the process. The dimensions of nanoparticles that have a spherical shape do not exceed 30 nm. With increasing concentration of surfactant, there is a tendency to decrease in size. The rate of synthesis of AgNPs increases almost in proportion to the concentration of AgNO3 in the solution, while the effect of NaPA concentration is negligible. The synthesized nanoparticles efficiently demonstrated a bactericide effect on Escherichia coli and Staphylococcus aureus.

The Impact of Retinal Configuration on the Protein-Chromophore Interactions in Bistable Jumping Spider Rhodopsin-1

Bistable rhodopsins have two stable forms which can be interconverted by light. Due to their ability to act as photoswitches, these proteins are considered as ideal candidates for applica-tions such as optogenetics. In this work we analyze a recently crystalized bistable rhodopsin, namely the jumping spider rhodopsin-1 (JSR1). This rhodopsin exhibits identical absorption maxima for the parent and the photoproduct form, which impedes its broad application. We have performed hybrid QM/MM simulations to study three isomers of the retinal chromo-phore: the 9-cis, 11-cis and all-trans configurations. The main aim was to gain insight into the specific interactions of each isomer and their impact on the absorption maximum in JSR1. The absorption spectra were computed using sampled snapshots from a QM/MM molecular dy-namics trajectory and compared to experimental counterparts. The chromophore-protein in-teractions were analyzed by visualizing the electrostatic potential of the protein and projecting it onto chromophore. It was found that the distance between a nearby tyrosine (Y126) residue plays a larger role in the predicted absorption maximum than the primary counterion (E194). Geometric differences between the isomers were also noted including a structural change in the polyene chain of the chromophore as well as changes in the nearby hydrogen bond network.

Study the fluorescent and conductivity properties of a 4-hydroxy-3-nitro-1,8-naphthalic anhydride

The compound of (4-hydroxy-3-nitro-1,8-naphthalic anhydride) and the dopant material (4-hydroxy-m-benzene-disulfonic acid) were synthesized. The UV-Vis absorption and fluorescence spectra of the compound were recorded. The bathochromic shifts in absorption due to the changes in the solvent polarity was observed, in DMSO solvent, the compound shows different peaks, three bands in the UV region and one band in the visible region, one absorption peak at 402 nm, which might be attributed to the (ICT) band. The emission spectra of this compound were sensitive to the solvent polarity. They moved to lower energies with increasing the polarity of the solvent. The influence of the solvent polarity on the fluorescence maximum was more pronounced compared with the absorption maximum, showing ca. 3 nm red shift on moving from butanol to DMSO. The effect of the dopant material on the conductivities (ionic and specific) of the compound was studied, the ionic conductivity was increased as the weight of the dopant material increases, and the ionic conductivity (G) was measured in water as a solvent. the (G) of the compound was 2.4X10-6 Siemens at 0.01 gm of the dopant material, and was 2.62X10-4 Siemens after the dopant material was added (0.1 gm).

Pd-catalyzed synthesis of C-C (Sonogashira, Suzuki, Heck, Stille), C-P and C-S linked products using gem -dibromovinyl BODIPY

The chemistry of gem-dibromovinyl derivatives has undergone a renaissance through the application of palladium catalysis and has been applied to pyrrole substituted gem-dibromovinyl BODIPY. gem-Dibromovinyl BODIPYs (substituted at either the [Formula: see text]-position of 8-phenyl or the [Formula: see text]-position of the pyrrole rings) were studied for cross-coupling reactions using Sonogashira, Suzuki, Heck and Stille conditions, and with phosphonates and thiols. The assigned structures were supported by MS and 1H NMR, [Formula: see text]C NMR, X-ray diffraction analysis as well as optical spectroscopy. The conjugates were investigated for their absorption, fluorescence and solvatochromic properties in different solvents. Substitution at the [Formula: see text]-position of 8-phenyl derivatives of gem-diethynyl BODIPYs did not induce any shift in the absorption maximum, while the [Formula: see text]-position pyrrole substituted derivatives showed a red shift. Aromatic compounds gave larger red shifts as compared to the aliphatic substituted analogs.

Synthesis and Characterization of Lead Dibutyl Dithiophosphate Nanoparticles

We examined the interaction of aqueous solutions of lead nitrate and sodium dibutyl dithiophosphate and showed the formation nanoparticles of lead dibutyl dithiophosphate. The effect of reaction parameters on the synthesis of nanoparticles was studied and the optimal conditions for the formation of their stable hydrosols were determined. The obtained products were investigated by methods of optical spectroscopy, dynamic light scattering. The average size of 15–20 nm, but due to the low surface charge, they are combined into larger aggregates. The UV‑vis spectra has absorption maximum at about 320 nm. TEM micrographs and Pb 2p, S2p XAS spectra revealed a composition and structure of the particles. These nanoparticles can play an important role in the flotation of sulfide minerals of nonferrous metals

Characterization of polysaccharides from Eremurus hissaricus roots by FTIR spectroscopy

The structure of water'soluble gluco' and galactomannans (GlcMan and GalMan) isolated from the roots of several Eremurus'related plant species has been studied previously. This article characterizes polysaccharides and other extraction products from the root tubers of Eremurus hissaricus by Fourier' transform infrared (FTIR) spectroscopy using an attenuated total reflectance (ATR) accessory. Polysaccharide samples were purified from protein substances with the Sevage method and discoloured through a polyamide column. In the FTIR spectra, the main peaks attributed to asymmetric and symmetric stretching vibrations of CH2 of the pyranose ring (for GluMan - 2886, 1373, 1244 cm-1; for GalGluMan - 2923, 1370, 1238 cm-1) were enhanced by purification after removing bound protein impurities. The KnownitAll and IR-Pal 2 software applications were used to examine the spectra of a sample of purified GalGluMan in the studied polysaccharides. The results show that the intensity of the absorption maximum decreased at 1732 cm-1. At the same time, at 1552.92 cm-1, a new band appeared that refers to the valence vibrations of carboxyl (CO) or nitroso (NO) groups in the purified polysaccharide. This band appeared as a result of the Maillard reaction between the protein and the reducing end of the polysaccharide unit. The intensity of the bands in the 1238-1244 cm-1 region also decreased in the purified samples, which may be due to the elimination of a small fraction of protein. The use of FTIR spectroscopy allows the process of purifying watersoluble GluMan and acid-soluble polysaccharide of GalGluMan from acrylamide impurities to be characterized timely and accurately. Additionally, this method allows a comparative estimation of functional groups in polysaccharides of the root tubers of E. hissaricus.

Structure and Properties of 1,3,3-Trimethyl-6′-chlorospiro[indoline-2,2′-2H-chromene]

Indoline spiropyran containing an σ-acceptor chlorine atom in 6′ position of the 2H-chromene part of the molecule was synthesized and studied. The use of 1,2,3,3-tetramethyl-3H-indolium perchlorate as a starting compound made it possible to achieve higher product yields as compared to previous studies. The molecular structure of the compound was established by single crystal X-ray diffraction analysis. The features of the crystal structure and intermolecular interactions were investigated using CrystalExplorer17 software package. The photochromic behavior in acetonitrile solution was studied for the first time. It was found that the merocyanine form of spiropyran is characterized by an absorption maximum at 592 nm, which is 37 nm closer to the range of the “biological window” in comparison with the nitro-substituted analog.

Identification of dipyrrolone pigments and their precursors formed in the Maillard reaction of carnosine and pentose under weakly acidic conditions

Colored compounds formed by the Maillard reaction of carnosine with xylose or glucose were investigated in this study. Yellow pigments showing an absorption maximum at 450 nm were found in a heated solution of carnosine with xylose at pH 5.0. These pigments were then isolated and identified as dicarnosyl-dipyrrolones A and B. The generation of dipyrrolones in the absence of lysine suggests that dipyrrolone pigments can be formed by pentose as well as every amino compound such as amino acids, peptides and proteins possessing a free amino group. Analysis of α-dicarbonyls using LC-MS/MS showed that pentosone, 1-deoxypentosone, 3-deoxypentosone (3-DP), and methylglyoxal were predominantly generated via degradation of Amadori compounds. Also, a potential formation pathway of dypyrrolones was established, indicating that an Amadori compound which could form 3-DP is likely to play a role as a main precursor for dipyrrolones.