Base Moiety Research Articles

Birefringence Control of Photoalignable Liquid Crystalline Polymers Based on an In Situ Exchange of Oriented Mesogenic Side Groups

Abstract An in situ exchange of oriented mesogenic side groups containing Schiff base moieties realized birefringence control of photoalignable liquid crystalline polymers between 0.13 and 0.44. Both thermal hydrolysis of the oriented side groups and in situ condensation using phenyl amine derivatives with a high inherent birefringence vary the birefringence and thermal stability of oriented films without distortion of the oriented structure.

Sphingoid base in pineapple glucosylceramide suppresses experimental allergy by binding leukocyte mono-immunoglobulin-like receptor 3.

BACKGROUNDThe increase in patients suffering from type I hypersensitivity, including hay fever and food allergy, is a serious public health issue around the world. Recent studies have focused on allergy prevention by food factors with fewer side effects. The purpose of this study was to evaluate the effect of dietary glucosylceramide from pineapples (P‐GlcCer) on type I hypersensitivity and elucidate mechanisms.RESULTSOral administration of P‐GlcCer inhibited ear edema in passive cutaneous anaphylaxis reaction. In a Caco‐2/RBL‐2H3 co‐culture system, P‐GlcCer inhibited β‐hexosaminidase release from RBL‐2H3 cells. The direct treatment of P‐GlcCer on RBL‐2H3 did not affect β‐hexosaminidase release, but sphingoid base moiety of P‐GlcCer did. These results predicted that sphingoid base, a metabolite of P‐GlcCer, through the intestine inhibited type I hypersensitivity by inhibiting mast cell degranulation. In addition, the inhibitory effects of P‐GlcCer on ear edema and degranulation of RBL‐2H3 cells were canceled by pretreatment of leukocyte mono‐immunoglobulin‐like receptor 3 (LMIR3)‐Fc, which can block LMIR3‐mediated inhibitory signals.CONCLUSIONIt was demonstrated that a sphingoid base, one of the metabolites of P‐GlcCer, may inhibit mast cell degranulation by binding to LMIR3. The oral administration of P‐GlcCer is a novel and attractive food factor that acts directly on mast cells to suppress allergy. © 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Biomass-derived dynamic covalent epoxy thermoset with robust mechanical properties and facile malleability

Biomass-derived dynamic covalent thermoset has been considered as a promising solution to the high dependence on fossil resources and the difficulty in recyclability after curing of conventional bisphenol A epoxy resins. However, the design and preparation of a dynamic covalent biobased epoxy thermoset with both comparable thermal and mechanical performances to bisphenol A epoxy resins and reprocessibility remains a significant challenge. Herein, based on imine chemistry, a novel Schiff base-containing dynamic covalent epoxy thermoset was facilely fabricated from biobased protocatechualdehyde and synthetic siloxane diamine. Due to the more reactive epoxides in the epoxy monomer than in bisphenol A epoxy oligomer, the thermoset exhibited a high cross-linking density, resulting in high thermal stability and glass transition temperature. The rigid aromatic Schiff base moieties endowed the thermoset with excellent mechanical properties: Thanks to the plasticization of the flexible siloxane, the thermoset displayed high impact strength. Meanwhile, owing to the high segmental mobility, the fast exchange of imine bonds was guaranteed; and the thermoset was able to be recycled through reprocessing. Taking these features, this work provided great potential for designing and preparing sustainable substitutes for bisphenol A epoxy resins in the high-performance applications.

Helium Nanodroplet Infrared Action Spectroscopy of the Proton-Bound Dimer of Hydrogen Sulfate and Formate: Examining Nuclear Quantum Effects.

The proton-bound dimer of hydrogen sulfate and formate is an archetypal structure for ionic hydrogen-bonding complexes that contribute to biogenic aerosol nucleation. Of central importance for the structure and properties of this complex is the location of the bridging proton connecting the two conjugate base moieties. The potential energy surface for bridging proton translocation features two local minima, with the proton localized at either the formate or hydrogen sulfate moiety. However, electronic structure methods reveal a shallow potential energy surface governing proton translocation, with a barrier on the order of the zero-point energy. This shallow potential complicates structural assignment and necessitates a consideration of nuclear quantum effects. In this work, we probe the structure of this complex and its isotopologues, utilizing infrared (IR) action spectroscopy of ions captured in helium nanodroplets. The IR spectra indicate a structure in which a proton is shared between the hydrogen sulfate and formate moieties, HSO4–···H+···–OOCH. However, because of the nuclear quantum effects and vibrational anharmonicities associated with the shallow potential for proton translocation, the extent of proton displacement from the formate moiety remains unclear, requiring further experiments or more advanced theoretical treatments for additional insight.

Thermal and Mesomorphic Investigations of 1:1 Supramolecular Assemblies of 4-[(4-(n-Alkoxy)phenylimino)methyl]benzoic Acids Having Symmetrical and Un-Symmetrical Terminal Chain Lengths

Thermal and mesomorphic properties of possible 1:1 supramolecular complexes (SMCs) (Im/In) designed from two members of 4-[(4-(n-alkoxy)phenylimino)methyl]benzoic acid with symmetrical or un-symmetrical alkoxy terminal flexible chains (carbons of m and n = 6, 8 and 16), were analyzed by differential scan-calorimetry (DSC), thermogravemetric (TG) analysis, and their mesophases identified by polarized optical microscopy (POM). The equimolecular mixtures of the two acids possess symmetrical and un-symmetrical terminal lengths. The mesomorphic properties of the binary mixtures were examined as a function of the total alkoxy chain length on both sides. Results revealed that the nematic mesophase temperature range increases as the total terminal length increases for all designed un-symmetrical mixtures. A comparison was constructed between the formed SMCs and of those of the previously prepared 4-n-alkoxyphenylazo benzoic acids as well as the 4-n-alkoxy benzoic acids, to examine the impact of mesogenic core on the mesomorphic properties. The comparison indicated that as the mesogenic portion lengthens the thermal mesophase stability exhibits higher values of phase transition temperatures; whereas, the azo and Schiff base moieties exhibited near thermal properties.

New nematogenic conical-shaped supramolecular H-bonded complexes for solar energy investigations

New conical-shaped geometrical supramolecular H-bonded liquid crystal complexes were formed through 1:2 intermolecular interactions of H-bonding between flexible core (adipic acid, A) and lateral chloro-substituted azopyridines (Bn). The chains of the terminally alkoxy substituted base (n) were changed between 8 and 16 carbons. Mesomorphic and optical examinations of the prepared complexes were measured via differential scanning calorimetry (DSC) and polarizing optical microscopy (POM). Fourier-transform infrared spectroscopy (FT-IR) was used to confirm the Fermi bands of the H- bonding interactions. Induced nematogenic mesophases that cover the whole lengths of alkoxy-chains were detected. The non-linear geometries of the designed supramolecular complexes were also confirmed via Density functional theory (DFT) calculations. It was found that the length of terminal alkoxy chain of the base moiety highly affects the geometrical structure of the investigated complexes. Moreover, it increases the thermodynamic energy and influences the geometrical parameters. The electrical properties of each of the acid component (A), the base (B16) and their 1:2 complex (A/2B16) were evaluated using the Keithley measurement-source unit. The optical properties studies showed that the influences in the optical absorption and the reduction of the energy gap of the complex compared to its individual components made the resulted supramolecular H-bonded complex soft material suitable for solar energy investigations.

Analysis of non-derivatized bacteriohopanepolyols using UHPLC-HRMS reveals great structural diversity in environmental lipid assemblages

Bacteriohopanepolyols (BHPs) are lipids with great chemotaxonomic potential for microbial populations and biogeochemical processes in the environment. The most commonly used methods for BHP analysis are chemical degradation followed by gas chromatography-mass spectrometry (MS) or derivatization followed by high performance liquid chromatography (HPLC)-atmospheric pressure chemical ionization/MS. Here we report on significant advances in the analysis of non-derivatized BHPs using U(ltra)HPLC-electrospray ionization-high resolution MS2. Fragmentation mass spectra provided information on the BHP core, functionalized side chain, as well as the conjugated moiety of composite BHPs. We successfully identified the common bacteriohopanepolyols and their (di)methylated and (di)unsaturated homologues, aminoBHPs, and composite BHPs (e.g., cyclitol ethers and methylcarbamate-aminoBHPs) in biomass of several known BHP-producing bacteria. To show how the method can be exploited to reveal the diversity of BHPs in the environment, we investigated a soil from an active methane seep, in which we detected ca. 130 individual BHPs, including a complex distribution of adenosylhopanes. We identified the nucleoside base moiety of both adenosylhopane type-2 and type-3. Adenosyl hopane type-3 contains a methylated adenine as its nucleobase, while type-2 appears to contain a deaminated and methylated adenine, or N1-methylinosine. In addition, we detected novel adenosylhopanes. Furthermore, we identified a series of novel composite BHPs comprising of bacteriohopanepolyols conjugated to an ethenolamine moiety. The novel ethenolamineBHPs as well as aminoBHPs were also detected acylated to fatty acids. The analytical approach described allows for simultaneous analysis of the full suite of IPLs, now including BHPs, and represents a further step towards environmental lipidomics.

A non-centrosymmetric cocrystal assembled by O[sbnd]H…N and C[sbnd]H…π supramolecular synthons

A novel NLO material, Acridine:Naphthoresorcinol cocrystal (ACRNR) was obtained by solvent assisted grinding method and single crystals were grown from methanol. The charge transfer activity of ACRNR cocrystal was confirmed by UV-Visible study. The photoluminescence (PL) spectrum of ACRNR crystal exhibit violent and green emission at 365 and 551 nm, respectively. The presence of various function groups and intermolecular interaction between acridine and naphthoresorcinol was determined by FT-IR spectral analysis. Single crystal X-ray diffraction analysis shows that ACRNR cocrystal belongs to orthorhombic system with non-centrosymmetric space group, P212121. Further, crystal-packing analysis suggests that there are OH…N and CH…O hydrogen bonds between acid and base moieties in ACRNR crystal. TG/DTA analysis indicates that the crystal is thermally stable up to 173.5 °C. Dielectric and microhardness measurements were performed to investigate the electrical and mechanical properties. Second harmonic generation (SHG) efficiency was identified by Kurtz and Perry technique and compared with KDP. The laser damage threshold value of grown crystal was found to be 3.24 GW/cm2.

Modulation of stimuli‐responsiveness toward acid vapor between real‐time and write‐erase responses based on conjugated polymers containing azobenzene and Schiff base moieties

AbstractWe developed three types of film‐type stimuli‐responsive polymers based on aza‐substituted conjugated polymers involving azobenzene, N_bith, N_fluo and Schiff base moieties, C_bith. All polymer films showed bathochromic shifts in absorption spectra followed by chromic behaviors by fuming trifluoroacetic acid (TFA). In particular, we disclosed that there were three significant differences on acid detecting ability between azobenzene and Schiff base derivatives in terms of absorption wavelengths, stability, and proton holding time. The azobenzene polymers exhibited real‐time responses toward vapor fuming, meanwhile write and erase chromic behaviors were reversibly accomplished with the Schiff base polymer by exposing to acid and amine vapor. Theoretical calculation revealed that red‐shifted absorption bands should be induced by protonation on nitrogen atoms in the aza‐substituted positions. Diverse responses through dynamic regulation of electronic properties of main‐chain conjugation can be accomplished by introducing the aza‐substituents in polymers.

Sphingolipid long-chain base hydroxylation influences plant growth and callose deposition in Physcomitrium patens.

Sphingolipids are enriched in microdomains in the plant plasma membrane (PM). Hydroxyl groups in the characteristic long-chain base (LCB) moiety might be essential for the interaction between sphingolipids and sterols during microdomain formation. Investigating LCB hydroxylase mutants in Physcomitrium patens might therefore reveal the role of certain plant sphingolipids in the formation of PM subdomains. Physcomitriumpatens mutants for the LCB C-4 hydroxylase S4H were generated by homologous recombination. Plants were characterised by analysing their sphingolipid and steryl glycoside (SG) profiles and by investigating different gametophyte stages. s4h mutants lost the hydroxyl group at the C-4 position of their LCB moiety. Loss of this hydroxyl group caused global changes in the moss sphingolipidome and in SG composition. Changes in membrane lipid composition may trigger growth defects by interfering with the localisation of membrane-associated proteins that are crucial for growth processes such as signalling receptors or callose-modifying enzymes. Loss of LCB-C4 hydroxylation substantially changes the P.patens sphingolipidome and reveals a key role for S4H during development of nonvascular plants. Physcomitrium patens is a valuable model for studying the diversification of plant sphingolipids. The simple anatomy of P.patens facilitates visualisation of physiological processes in biological membranes.

RNA modifications as a common denominator between tRNA and mRNA.

Recent studies underscore RNA modifications as a novel mechanism to coordinate expression and function of different genes. While modifications on the sugar or base moieties of tRNA are well known, their roles in mRNA regulation are only starting to emerge. Interestingly, some modifications are present in both tRNA and mRNA, and here we discuss the functional significance of these common features. We describe key modifications that are present in both RNA types, elaborate on proteins that interact with them, and indicate recent works that identify roles in communicating tRNA processes and mRNA regulation. We propose that as tools are developed, the shortlist of features that are common between types of RNA will greatly expand and proteins that interact with them will be identified. In conclusion, the presence of the same modification in both RNA types provides an intersect between tRNA processes and mRNA regulation and implies a novel mechanism for connecting diverse cellular processes.

Synthesis, density functional theory study, molecular dynamics simulation and anti-corrosion performance of two benzidine Schiff bases

In this study, two Schiff bases named (E,E)-N,N’-biphenyl-4–4′diylbis[1-(thiophen-3-yl)methanimine] (BT) and 3-[(Z)-N(4′-aminobiphenyl-4yl)ethanimidoyl]-2-hydroy-6-methyl-4H-pyran-4-one (BD) have been synthesized and characterized using spectroscopic techniques. The XRD technique was employed to study the atomic packing, crystal structure and space group of the developed crystals of BD. The corrosion inhibition performance of BT and BD was investigated for mild steel corrosion in 1 M HCl medium using weight loss method and electrochemical techniques. Density functional theory (DFT) and molecular dynamics (MD) simulations were further applied to explain the adsorption as well as inhibition abilities of the molecules on the mild steel surface. Compounds revealed a good inhibition action in tested medium even at low concentrations and the inhibition efficiency increases with increasing concentration of inhibitors, and revealing a mixed-type inhibitor of predominantly anodic type. SEM and EDX studies revealed the film-forming ability of the molecules on the mild steel surface. DFT and MD studies complement experimental results and demonstrate that Schiff base moieties and functional groups are responsible for corrosion inhibitive performances of studied compounds.

Prebiotic studies on the interaction of zirconia nanoparticles and ribose nucleotides and their role in chemical evolution

AbstractStudies on the interaction of biomolecules with inorganic compounds, mainly mineral surfaces, are of great concern in identifying their role in chemical evolution and origins of life. Metal oxides are the major constituents of earth and earth-like planets. Hence, studies on the interaction of biomolecules with these minerals are the point of concern for the study of the emergence of life on different planets. Zirconium oxide is one of the metal oxides present in earth's crust as it is a part of several types of rocks found in sandy areas such as beaches and riverbeds, e.g. pebbles of baddeleyite. Different metal oxides have been studied for their role in chemical evolution but no studies have been reported about the role of zirconium oxide in chemical evolution and origins of life. Therefore, studies were carried out on the interaction of ribonucleic acid constituents, 5′-CMP (cytidine monophosphate), 5′-UMP (uridine monophosphate), 5′-GMP (guanosine monophosphate) and 5′-AMP (adenosine monophosphate), with zirconium oxide. Synthesized zirconium oxide particles were characterized by using vibrating sample magnetometer, X-Ray Diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy. Zirconia particles were in the nanometre range, from 14 to 27 nm. The interaction of zirconium oxide with ribonucleic acid constituents was performed in the concentration range of 5 × 10−5–300 × 10−5 M. Interaction studies were carried out in three mediums; acidic (pH 4.0), neutral (pH 7.0) and basic (pH 9.0). At neutral pH, maximum interaction was observed. The interaction of zirconium oxide with 5′-UMP was 49.45% and with 5′-CMP 67.98%, while with others it was in between. Interaction studies were Langmurian in nature. Xm and KL values were calculated. Infrared spectral studies of ribonucleotides, metal oxide and ribonucleotide–metal oxide adducts were carried out to find out the interactive sites. It was observed that the nitrogen base and phosphate moiety of ribonucleotides interact with the positive charge surface of metal oxide. SEM was also carried out to study the adsorption. The results of the present study favour the important role of zirconium oxide in concentrating the organic molecules from their dilute aqueous solutions in primeval seas.

Organomercury Nucleic Acids: Past, Present and Future.

Synthetic efforts towards nucleosides, nucleotides, oligonucleotides and nucleic acids covalently mercurated at one or more of their base moieties are summarized, followed by a discussion of the proposed, realized and abandoned applications of this unique class of compounds. Special emphasis is given to fields in which active research is ongoing, notably the use of HgII‐mediated base pairing to improve the hybridization properties of oligonucleotide probes. Finally, this minireview attempts to anticipate potential future applications of organomercury nucleic acids.

Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA

We introduce MADna, a sequence-dependent coarse-grained model of double-stranded DNA (dsDNA), where each nucleotide is described by three beads localized at the sugar and base moieties, and at the phosphate group. The sequence dependence is included by considering a step-dependent parameterization of the bonded interactions, which are tuned in order to reproduce the values of key observables obtained from exhaustive atomistic simulations from literature. The predictions of the model are benchmarked against an independent set of all-atom simulations, showing that it captures with high fidelity the sequence dependence of conformational and elastic features beyond the single step considered in its formulation. A remarkably good agreement with experiments is found for both sequence-averaged and sequence-dependent conformational and elastic features, including the stretching and torsion moduli, the twist-stretch and twist-bend couplings, the persistence length and the helical pitch. Overall, for the inspected quantities, the model has a precision comparable to atomistic simulations, hence providing a reliable coarse-grained description for the rationalization of single-molecule experiments and the study of cellular processes involving dsDNA. Owing to the simplicity of its formulation, MADna can be straightforwardly included in common simulation engines.

Structural Basis of SARS-CoV-2 Polymerase Inhibition by Favipiravir

SummaryThe outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has developed into an unprecedented global pandemic. Nucleoside analogs, such as Remdesivir and Favipiravir, can serve as the first-line broad-spectrum antiviral drugs by targeting the viral polymerases. However, the underlying mechanisms for the antiviral efficacies of these drugs are far from well understood. Here, we reveal that Favipiravir, as a pyrazine derivative, could be incorporated into the viral RNA products by mimicking both adenine and guanine nucleotides. This drug thus inhibits viral replication mainly by inducing mutations in progeny RNAs, different from Remdesivir or other RNA-terminating nucleoside analogs that impair the elongation of RNA products. We further determined the cryo-EM structure of Favipiravir bound to the replicating polymerase complex of SARS-CoV-2 in the pre-catalytic state. This structure provides a missing snapshot for visualizing the catalysis dynamics of coronavirus polymerase, and reveals an unexpected base-pairing pattern between Favipiravir and pyrimidine residues that may explain its capacity for mimicking both adenine and guanine nucleotides. These findings shed light on the mechanism of coronavirus polymerase catalysis and provide a rational basis for developing antiviral drugs to combat the SARS-CoV-2 pandemic.

1,2,4-Thiadiazole acyclic nucleoside phosphonates as inhibitors of cysteine dependent enzymes cathepsin K and GSK-3β

In analogy to antiviral acyclic nucleoside phosphonates, a series of 5-amino-3-oxo-1,2,4-thiadiazol-3(2H)-ones bearing a 2-phosphonomethoxyethyl (PME) or 3-hydroxy-2-(phosphonomethoxy)propyl (HPMP) group at the position 2 of the heterocyclic moiety has been synthesized. Diisopropyl esters of PME- and HPMP-amines have been converted to the N-substituted ureas and then reacted with benzoyl, ethoxycarbonyl, and Fmoc isothiocyanates to give the corresponding thiobiurets, which were oxidatively cyclized to diisopropyl esters of 5-amino-3-oxo-2-PME- or 2-HPMP- 1,2,4-thiadiazol-3(2H)-ones. The phosphonate ester groups were cleaved with bromotrimethylsilane, yielding N5-protected phosphonic acids. The subsequent attempts to remove the protecting group from N5 under alkaline conditions resulted in the cleavage of the 1,2,4-thiadiazole ring. Similarly, compounds with a previously unprotected 5-amino-1,2,4-thiadiazolone base moiety were stable only in the form of phosphonate esters. The series of twenty-one newly prepared 1,2,4-thiadiazol-3(2H)-ones were explored as potential inhibitors of cysteine-dependent enzymes – human cathepsin K (CatK) and glycogen synthase kinase 3β (GSK-3β). Several compounds exhibited an inhibitory activity toward both enzymes in the low micromolar range. The inhibitory potency of some of them toward GSK-3β was similar to that of the thiadiazole GSK-3β inhibitor tideglusib, whereas others exhibited more favorable toxicity profile while retaining good inhibitory activity.

Environmental and morphological behavior of polystyrene films containing Schiff base moiety

Herein novel Schiff base having triazole segment ( 3 ) has been synthesized and characterized. Different techniques have been used to evaluate the photo stability of the polystyrene polymeric films. It was demonstrated that mixing the polystyrene with synthesized Schiff base reduce the formation of carbonyl groups during the irradiation compare to the blank polystyrene film. The determination of weight loss was also studied and it was proved that using the Schiff base with the polymer films reduce the weight loss versus the irradiation time compare to the blank film. The energy-dispersive X-ray spectroscopy (EDX) technique shows that the major component of both Schiff base/polystyrene and blank polystyrene films is the carbon atom. However, it shows the appearance of new band for Schiff base/polystyrene film, related to the oxygen, nitrogen, and sulfur. The Schiff base/polystyrene film demonstrates the formation of terrestrial cracks-like and this might be due to the existence of the Schiff base, by using the scanning electron microscopy (SEM) technique. This work includes important results to reduce the threatening of plastic waste for marine ecosystem through using new photo stabilizers, which leads to decreasing of plastic consuming around the world.

Mechanism of absorption wavelength shifts in anion channelrhodopsin-1 mutants

Using a quantum mechanical/molecular mechanical approach, we show the mechanisms of how the protein environment of Guillardia theta anion channelrhodopsin-1 (GtACR1) can shift the absorption wavelength. The calculated absorption wavelengths for GtACR1 mutants, M105A, C133A, and C237A are in agreement with experimentally measured wavelengths. Among 192 mutant structures investigated, mutations at Thr101, Cys133, Pro208, and Cys237 are likely to increase the absorption wavelength. In particular, T101A GtACR1 was expressed in HEK293T cells. The measured absorption wavelength is 10 nm higher than that of wild type, consistent with the calculated wavelength. (i) Removal of a polar residue from the Schiff base moiety, (ii) addition of a polar or acidic residue to the β-ionone ring moiety, and (iii) addition of a bulky residue to increase the planarity of the β-ionone and Schiff base moieties are the basis of increasing the absorption wavelength.

Chemical Synthesis of Acyclic Nucleoside Phosphonate Analogs Linked with Cyclic Systems between the Phosphonate and the Base Moieties.

The syntheses of acyclic nucleoside phosphonate (ANP) analogs linked with cyclic systems are described in the present review. The purpose of the review is to report the methodology of ANP analogs and to give an idea on the synthesis of a therapeutic structural feature of such analogs. The cyclopropane systems were mainly prepared by diazomethane cyclopropanation catalyzed by Pd(OAc)2, intramolecular alkylation, Kulinkovich cyclopropanation, and use of difluorocyclopropane, and so forth. The preparation of methylenecyclopropane system was made by diazoacetate cyclopropanation catalyzed by Rhodium followed by addition-elimination reactions. For the preparation of a variety of tethered 1,2,3-triazole systems, 1,3-dipolar cycloaddition between azidealkylphosphonates and propargylated nucleobases was mainly applied. The formation of various phosphonate moieties was achieved via phosphonylation of alkoxide, cross-coupling between BrZnCF2P (O)(OEt)2 with iodoalkens catalyzed by CuBr, Michaelis-Arbuzov reaction with phosphite, and Rh(II)-catalyzed O-H insertion, and so forth.