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Phototransformations of 6-nitro-8-methoxy-substituted indoline spiropyran in acetonitrile have been studied by laser kinetic spectroscopy (laser photolysis) with single- and double-pulse excitation. The role of the triplet state in the kinetics of photocoloration of spiropyran has been revealed. It has been shown that photochromic transformations of spiropyran involve unstable trans-isomers (conformers) of the open merocyanine form of spiropyran. Data on the transformation kinetics of the trans-isomers are presented. [ABSTRACT FROM AUTHOR]

Polyfunctional macrocycles have been studied extensively for their responsive properties. In this study, three electron- deficient novel azo-containing crown ethers were successfully synthesized. The synthesized macrocycles were characterized and their photophysical along with photoisomerization were studied. The results were compared with their acyclic derivative. It was found that these compounds did not convert to their cis-isomer completely due to the rigidity of the cycles. The fluorescence studies revealed that the macrocycles were fluorescent while the acyclic azo derivative was found not to show fluorescence. The macrocycles were also tested for alkali metal cation-binding abilities. It was shown with DFT calculations that not only the ring size of macrocycles but also the conformation places an important role in recognition of these cations. [ABSTRACT FROM AUTHOR]

Trimethylamine N-Oxide (TMAO) is an important metabolite, which is derived from choline, betaine, and carnitine in various organisms. In humans, it is synthesized through gut microbiota and is abundantly found in serum and cerebrospinal fluid (CSF). Although TMAO is a stress protectant especially in urea-rich organisms, it is an atherogenic agent in humans and is associated with various diseases. Studies have also unveiled its exceptional role in protein folding and restoration of mutant protein functions. However, most of these data were obtained from studies carried on fast-folding proteins. In the present study, we have investigated the effect of TMAO on the folding behavior of a well-characterized protein with slow folding kinetics, carbonic anhydrase (CA). We discovered that TMAO inhibits the folding of this protein via its effect on proline cis–trans isomerization. Furthermore, TMAO is capable of inducing cell cycle arrest. This study highlights the potential role of TMAO in developing proteopathies and associated diseases. [ABSTRACT FROM AUTHOR]

Peptidyl Prolyl Isomerases (PPIases) accelerate cis–trans isomerization of prolyl peptide bonds. In rice, the PPIase LRT2 is essential for lateral root initiation. LRT2 displays in vitro isomerization of a highly conserved W–P peptide bond (104W–P105) in the natural substrate OsIAA11. OsIAA11 is a transcription repressor that, in response to the plant hormone auxin, is targeted to ubiquitin-mediated proteasomal degradation via specific recognition of the cis isomer of its 104W–P105 peptide bond. OsIAA11 controls transcription of specific genes, including its own, that are required for lateral root development. This auxin-responsive negative feedback circuit governs patterning and development of lateral roots along the primary root. The ability to tune LRT2 activity via mutagenesis is crucial for understanding and modeling the role of this bimodal switch in the auxin circuit and lateral root development. We present characterization of the thermal stability and isomerization rates of several LRT2 mutants acting on the OsIAA11 substrate. The thermally stable mutants display activities lower than that of wild-type (WT) LRT2. These include binding diminished but catalytically active P125K, binding incompetent W128A, and binding capable but catalytically incompetent H133Q mutations. Additionally, LRT2 homologs hCypA from human, TaCypA from Triticum aestivum (wheat) and PPIB from E. coli were shown to have 110, 50 and 60% of WT LRT2 activity on the OsIAA11 substrate. These studies identify several thermally stable LRT2 mutants with altered activities that will be useful for establishing relationships between cis–trans isomerization, auxin circuit dynamics, and lateral root development in rice. [ABSTRACT FROM AUTHOR]

In the present work, first time the molecular structures of three newly synthesized azomethine dyes: (1Z)-N-benzylidene-4-((E)-1-(oxim)ethyl)benzenamine (AAFOX-1), 4-((1Z)-(4-((E)-1-(oxim)ethyl)phenylimino)methyl)phenol (AAFOX-7), (Z)-1-(4-((Z)-(4-methoxybenzylidene)amino)phenyl)ethanone oxime (AAFOX-8) have been investigated using Density Functional Theory (DFT) in dimethylformamide (DMF). The electronic spectra of azomethine dyes in a DMF solvent was carried out by TD-DFT method. After quantum-chemical calculations three new azomethine dyes for optoelectronic applications were synthesized. FT-IR spectra of the title compounds are recorded and discussed. The computed absorption spectral data of the azomethine dyes are in good agreement with the experimental data, thus allowing an assignment of the UV spectra. The molecular HOMO-LUMO, excitation energies and oscillator strengths for E and Z isomers of the dyes have also been calculated and presented. Optical Properties of the PVA-films containing new substances have been also investigated. Polarizing Efficiency (PE) of obtained PVA-film is 70-80 % at Stretching Degree (Rs) 3.5. First time anisotropy of thermal and electrical conductivity of PVA-films containing E and Z isomers of the dyes was also measured and discussed. It is new result for physical chemistry of organic dyes.We studied anisotropy of thermal and electrical conductivity of new azomethine dyes in stretched polymer matrix and electronic properties of new azomethines have been also investigated using Density Functional Theory (DFT) in dimethylformamide (DMF). [ABSTRACT FROM AUTHOR]

The main constituents of a typical medicinal herb, Polygonum multiflorum (Heshouwu in Chinese), that induces idiosyncratic liver injury remain unclear. Our previous work has shown that cotreatment with a nontoxic dose of lipopolysaccharide (LPS) and therapeutic dose of Heshouwu can induce liver injury in rats, whereas the solo treatment cannot induce observable injury. In the present work, using the constituent 'knock-out' and 'knock-in' strategy, we found that the ethyl acetate (EA) extract of Heshouwu displayed comparable idiosyncratic hepatotoxicity to the whole extract in LPS-treated rats. Results indicated a significant elevation of plasma alanine aminotransferase, aspartate aminotransferase, and liver histologic changes, whereas other separated fractions failed to induce liver injury. The mixture of EA extract with other separated fractions induced comparable idiosyncratic hepatotoxicity to the whole extract in LPS-treated rats. Chemical analysis further revealed that 2,3,5,4′-tetrahydroxy trans-stilbene-2-O-β-glucoside ( trans-SG) and its cis-isomer were the two major compounds in EA extract. Furthermore, the isolated cis-, and not its trans-isomer, displayed comparable idiosyncratic hepatotoxicity to EA extract in LPS-treated rats. Higher contents of cis-SG were detected in Heshouwu liquor or preparations from actual liver intoxication patients associated with Heshouwu compared with general collected samples. In addition, plasma metabolomics analysis showed that cis-SG-disturbing enriched pathways remarkably differed from trans-SG ones in LPS-treated rats. All these results suggested that cis-SG was closely associated with the idiosyncratic hepatotoxicity of Heshouwu. Considering that the cis-trans isomerization of trans-SG was mediated by ultraviolet light or sunlight, our findings serve as reference for controlling photoisomerization in drug discovery and for the clinical use of Heshouwu and stilbene-related medications. [ABSTRACT FROM AUTHOR]

Photoalignment of thin films of dipotassium 3,7-bis[1-(4-hydroxy-3-carboxylate)phenylazo]-5,5′-dioxodibenzothiophene (AtA-2) that were prepared by spin-coating of dye solutions in HO and DMF and aqueous solutions of polyvinylpyrrolidone (PVP) was studied. The UV absorption band of the dye cis-isomer, the position and intensity of which depended on the PVP concentration in the stock solutions, was recorded upon irradiation of films of AtA-2 in a PVP matrix [AtA-2(PVP)] with unfi ltered light from a DRT-1000 lamp in a vacuum or an Ar atmosphere. PVP facilitated trans-cis isomerization of AtA-2 and increased the stability of the cis-isomer with respect to thermal relaxation into the initial trans-isomer. The dichroic ratio (DR) of AtA-2(PVP) films irradiated with linearly polarized light (blue LED with λ = 450 nm, I = 15 mW/cm) increased by 1.5 times as the PVP concentration in the stock solutions increased from 1.0 to 10.0 mass%. The morphology and roughness of the films depended on the nature of the solvents used to prepare them. [ABSTRACT FROM AUTHOR]

The presence of energetically less favourable cis peptides in protein structures has been observed to be strongly associated with its structural integrity and function. Inter-conversion between the cis and trans conformations also has an important role in the folding process. In this study, we analyse the extent of conservation of cis peptides among similar folds. We look at both the amino acid preferences and local structural changes associated with such variations. Nearly 34% of the Xaa-Proline cis bonds are not conserved in structural relatives; Proline also has a high tendency to get replaced by another amino acid in the trans conformer. At both positions bounding the peptide bond, Glycine has a higher tendency to lose the cis conformation. The cis conformation of more than 30% of β turns of type VIb and IV are not found to be conserved in similar structures. A different view using Protein Block-based description of backbone conformation, suggests that many of the local conformational changes are highly different from the general local structural variations observed among structurally similar proteins. Changes between cis and trans conformations are found to be associated with the evolution of new functions facilitated by local structural changes. This is most frequent in enzymes where new catalytic activity emerges with local changes in the active site. Cis- trans changes are also seen to facilitate inter-domain and inter-protein interactions. As in the case of folding, cis- trans conversions have been used as an important driving factor in evolution. [ABSTRACT FROM AUTHOR]

It has long been understood that the proline residue has lower configurational entropy than any other amino acid residue due to pyrrolidine ring hindrance. The peptide bond between proline and its preceding amino acid (Xaa-Pro) typically exists as a mixture of cis- and trans-isomers in the unfolded protein. Cis–trans isomerization of Xaa-Pro peptide bonds are infrequent, but still occur in folded proteins. Therefore, the effects of the cis–trans isomerization equilibrium in both unfolded and folded states should be taken into account when estimating the stability contribution of a specific proline residue. In order to study the stability contribution of the four proline residues to the hyperthermophilic protein Ssh10b, in this work, we expressed and purified a series of Pro→Ala mutants of Ssh10b, and performed correlative unfolding experiments in detail. We proposed a new unfolding model including proline isomerization. The model predicts that the contribution of a proline residue to protein stability is associated with the thermodynamic equilibrium between cis- and trans-isomers both in the unfolded and folded states, agreeing well with the experimental results. [ABSTRACT FROM AUTHOR]

Doping two alkali-metal atoms (Li and Na) into the saddle-shaped saddle[4]pyrrole forms four new two-alkali-metal-doped compounds with alkalide or electride characteristic. They are cis-LiNa(saddle[4]pyrrole) isomers 1(singlet) and 2(triplet), and trans-Li(saddle[4]pyrrole)Na isomers 3(singlet) and 4(triplet). The four structures with all-real frequencies are obtained at the density functional theory (DFT) B3LYP/6-311+G(d) level. All calculations of electric properties have been carried out at the second order Møller–Plesset perturbation theory (MP2) level. The order of the β0 values is 3.54 × 103 for trans- 4(triplet) <1.51 × 104 for cis- 1(singlet) <3.57 × 104 for cis- 2(triplet) <2.34 × 105 a.u. for trans- 3(singlet). The static first hyperpolarizability ( β0) depends on the cis– trans isomerization and spin multiplicity. The result demonstrates that the cis– trans isomerization and spin multiplicity controls of the second-order NLO response are possible. [ABSTRACT FROM AUTHOR]

A solvate [Cu(CF3COCHCOCH3)2(CH3COCH3)] has been synthesized and characterized for the first time. According to X-ray structural data (diffractometer X8 APEX BRUKER, radiation Mo Kα, T = 150 K), it crystallizes in the monoclinic crystal system, space group P21/ c, a = 8.9940(4) Å, b = 22.3966(11) Å, c = 8.1884(3) Å, β = 92.705(2)°, V = 1647.59(12) Å3, Z = 4, dcalc = 1.725 g/cm3, final R = 0.0272. The structure is molecular. In the equatorial plane the atom Cu(II) is surrounded with four oxygen atoms of two chelating ligands (CF3COCHCOCH3)−; Cu-O distances 1.927–1.937 Å, O-Cu-O angles 86.18–93.30° and 170.18–175.67°. Square coordination of Cu is complemented to the square-pyramidal one by the oxygen atom of an acetone molecule behaving as an axial ligand; Cu-Oacetone 2.342 Å, O-Cu-Oacetone 89.66–100.11°. In the studied compound disorder of one of the chelate ligands implies the co-existance of the molecules in the cis- and trans-configuration in the crystal under ratio 54.6:45.4. In air the solvate rapidly degrades losing acetone, while in a sealed vessel melts around 313 K. Temperature dependence of equilibrium vapor pressure of acetone over the complex was measured with the static spoon gauge technique, thermodynamic characteristics of its dissociation process being derived: [Cu(CF3COCHCOCH3)2(CH3COCH3)]s = [Cu(CF3COCHCOCH3)2]s + CH3COCH3g, Δ H = 49.6(3) kJ/mol, Δ S = 152(1) J/(mol K), Δ G = 4.30(2) kJ/mol. [ABSTRACT FROM AUTHOR]

Thiyl radicals are intermediates of enzyme- and radical-driven biochemical processes, and their potential as reactive species in the biological environment has been somehow underestimated. From organic chemistry, however, it is known that thiyl radicals isomerize the double bonds of unsaturated fatty acids to a mixture with very dominatingtransisomers. Recently, this reaction has been particularly studied for biosystems, focusing on the effect of thiyl radicals on the natural all-cis double bonds of unsaturated phospholipids, which undergo a conversion to the unnaturaltransform. In this paper we report briefly the role of thiyl radicals in biosystems, describe the main features of the radical-inducedcis-transisomerization process under both in vitro and in vivo conditions, and reflect on some consequences for membrane structures, lipid metabolism and enzymatic reactions. [ABSTRACT FROM AUTHOR]

Different syntheses of cis- and trans-2-aminocyclopentanecarboxamides were studied. A convenient and effective method was devised for the preparation of cis-2-aminocyclopentanecarboxamide derivatives starting from the readily available 6- tert-butoxycarbonyl-6-azabicyclo[3.2.0]heptan-7-one. [ABSTRACT FROM AUTHOR]

A burst phase occurs in the refolding kinetics of guanidine-denatured creatine kinase due to formation of an intermediate within the mixing dead time, with further refolding to the native state after the burst phase along a path following biphasic kinetics. In the presence of cyclophilin, the refolding rates of the two slow processes are accelerated and the values are proportional to the cyclophilin concentration. The activity of cyclophilin in accelerating the slow refolding processes of creatine kinase is totally inhibited by cyclosporin A, indicating that the cis—trans isomerization of the peptidyl—prolyl bonds is involved in the two slow refolding processes. [ABSTRACT FROM AUTHOR]

The chromophore in halorhodopsin (HR) which acts as a light-driven chloride pump in halobacteria shares many properties with its counterpart in bacteriorhodopsin (BR): ( i) a similar retinal protein interaction, ( ii) trans to cis isomerization and ( iii) similar intermediates of its photocycle. One major difference between the two chromoproteins is that the HR chromophore does not become deprotonated during its photocycle. A mechanism for the photocycle of HR is presented, which, in close analogy to an earlier proposed mechanism for BR, involves the sequence of all- trans → 13- cis, 14 s-cis → 13- cis → all- trans isomerizations of the chromophore, a Schiff base of retinal. In contrast to the situation in BR the 13- cis, 14 s-cis→13- cis isomerization is induced not by deprotonation of the retinal Schiff base chromophore but rather by the movement of an anion (Cl) towards the protonated nitrogen of the Schiff's base. The suggested mechanism involves the Schiff base directly in the chloride translocation in halorhodopsin. [ABSTRACT FROM AUTHOR]

Some new complexes between the cis-4,4′-dinitrodibenzo-18-crown-6 and rare earth chlorides LnCl3 ( Ln=Nd, Gd, Yb) were synthesized in acetonitrile. Ligand cis-4,4′-dinitrodibenzo-18-crown-6 and its complexes were identified by infrared spectroscopy, X-ray diffraction and thermal analysis (TG and DTA). A cis-trans isomerisation of the complexed ligand is observed about 148°C when heating the rare earth complex. [ABSTRACT FROM AUTHOR]

Spectral and kinetic properties of photoisomers and triplet molecules of a number of anionic polymethine dyes, namely, differential absorption spectra, rate constants ( k) and activation parameters of reverse cis-trans-isomerization, and triplet-state-decay rate constants k are studied by flash photolysis. CINDP/2 calculations of electron density in anionic dyes show that k and k in polar solvents are determined primarily by the electronic effect of the substituents in the meso-position of the polymethine chain of a dye. The increase in kdue to the formation of ion pairs consisting of a dye with a counterion is observed in nonpolar solvents. [ABSTRACT FROM AUTHOR]

The effect of ion pair formation on the kinetics of the decay of the photoisomers and triplet states of cationic benzimidazolocyanine dyes is studied by flash photolysis. An increase in the rate constant of the reverse cis-trans isomerization of the photoisomers is observed when ion pairs are formed (in nonpolar solvents). In the case of benzimidazolocyanine dyes with the I anion, ion-pair formation causes an increase in the rate constant of decay of the triplet state. Acceleration of S ⇝ S internal conversion is discovered for the dyes with I [ABSTRACT FROM AUTHOR]

The analysis of the vibrational spectrum of the retinal chromophore in bacteriorhodopsin with isotopic derivatives provides a powerful "structural dictionary" for the translation of vibrational frequencies and intensities into structural information. Of importance for the proton-pumping mechanism is the unambiguous determination of the configuration about the C13=C14 and C=N bonds, and the protonation state of the Schiff base nitrogen. Vibrational studies have shown that in light-adapted BR568 the Schiff base nitrogen is protonated and both the C13=C14 and C=N bonds are in a trans geometry. The formation of K625 involves the photochemical isomerization about only the C13=C14 bond which displaces the Schiff base proton into a different protein environment. Subsequent Schiff base deprotonation produces the M412 intermediate. Thermal reisomerization of the C13=C14 bond and reprotonation of the Schiff base occur in the M412------O640 transition, resetting the proton-pumping mechanism. The vibrational spectra can also be used to examine the conformation about the C--C single bonds. The frequency of the C14--C15 stretching vibration in BR568, K625, L550 and O640 argues that the C14--C15 conformation in these intermediates is s-trans. Conformational distortions of the chromophore have been identified in K625 and O640 through the observation of intense hydrogen out-of-plane wagging vibrations in the Raman spectra (see Fig. 2). These two intermediates are the direct products of chromophore isomerization. Thus it appears that following isomerization in a tight protein binding pocket, the chromophore cannot easily relax to a planar geometry. The analogous observation of intense hydrogen out-of-plane modes in the primary photoproduct in vision (Eyring et al., 1982) suggests that this may be a general phenomenon in protein-bound isomerizations. Future resonance Raman studies should provide even more details on how bacterio-opsin and retinal act in concert to produce an efficient light-energy convertor. Important unresolved questions involve the mechanism by which the protein catalyzes deprotonation of the L550 intermediate and the mechanism of the thermal conversion of M412 back to BR568. Also, it has been shown that under conditions of high ionic strength and/or low light intensity two protons are pumped per photocycle (Kuschmitz & Hess, 1981). How might this be accomplished?(ABSTRACT TRUNCATED AT 400 WORDS) [ABSTRACT FROM AUTHOR]

The catalytic effect of metmyoglobin on the back thermal cis → trans isomerization reaction of stilbazolium betaine M is reported. This reaction shows substantial acceleration in the presence of metmyoglobin in comparison to the same reaction without the protein or in the presence of metmyoglobin cyanide. It is suggested that the observed thermal reaction acceleration may arise from the coordination of the protonated stilbazolium betaine molecule to the sixth ligand position of the heme iron and subsequent chromophore deprotonation or from the low polarity of the heme pocket microenvironment. [ABSTRACT FROM AUTHOR]