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3‐Methylglutaconic (3MGC) aciduria is a common phenotypic feature of a growing number of inborn errors of metabolism. “Primary” 3MGC aciduria is caused by deficiencies in leucine pathway enzymes while “secondary” 3MGC aciduria results from inborn errors of metabolism that impact mitochondrial energy production. The metabolic precursor of 3MGC acid is trans‐3MGC CoA, an intermediate in the leucine catabolism pathway. Gas chromatography‐mass spectrometry (GC‐MS) analysis of commercially available trans‐3MGC acid yielded a mixture of cis and trans isomers while 1H‐NMR spectroscopy of trans‐3MGC acid at 25°C provided no evidence for the cis isomer. When trans‐3MGC acid was incubated under conditions used for sample derivatization prior to GC‐MS (but with no trimethylsilane added), 1H‐NMR spectroscopy provided evidence of trans to cis isomerization. Incubation of trans‐3MGC acid at 37°C resulted in time‐dependent isomerization to cis‐3MGC acid. Cis‐3MGC acid behaved in a similar manner except that, under identical incubation conditions, less isomerization occurred. In agreement with these experimental results, molecular modeling studies provided evidence that the energy minimized structure of cis‐3MGC acid is 4 kJ/mol more stable than that for trans‐3MGC acid. Once generated in vivo, trans‐3MGC acid is proposed to isomerize via a mechanism involving π electron delocalization with formation of a resonance structure that permits bond rotation. The data presented are consistent with the occurrence of both diastereomers in urine samples of subjects with 3MGC aciduria.

Arylazopyrazoles show significant potential as next‐generation photoswitches, in particular because of the high thermal stability of their Z‐isomers. Herein we investigate the potential to perform Z−E isomer chemical switching of arylazopyrazoles using acid. We show that acid‐accelerated isomerisation allows for robust Z−E switching using mild acids and opens up the possibility to use light‐acid cycles to near quantitatively and reversibly switch the arylazopyrazoles at room temperature. We attribute the chemical switching to azonium formation, facilitated by mesomeric stabilisation by the pyrazole ring. Coupled with their exceptionally long Z‐isomer half‐lives, we believe our study may open up a wider array of functional opportunities for the arylazopyrazoles.

Chiroptical molecular switches play an important role in responsive materials and dynamic molecular systems. Here we present the synthesis of four chiral overcrowded alkenes and the experimental and computational study of their photochemical and thermal behavior. By irradiation with UV light, metastable diastereoisomers with opposite helicity were generated through high yielding E–Z isomerizations. Kinetic studies on metastable 1–4 using CD spectroscopy and HPLC analysis revealed two pathways at higher temperatures for the thermal isomerization, namely a thermal E–Z isomerization (TEZI) and a thermal helix inversion (THI). These processes were also studied computationally whereby a new strategy was developed for calculating the TEZI barrier for second-generation overcrowded alkenes. To demonstrate that these overcrowded alkenes can be employed as bistable switches, photochromic cycling was performed, which showed that the alkenes display good selectivity and fatigue resistance over multiple irradiation cycles. In particular, switch 3 displayed the best performance in forward and backward photoswitching, while 1 excelled in thermal stability of the photogenerated metastable form. Overall, the alkenes studied showed a remarkable and unprecedented combination of switching properties including dynamic helicity, reversibility, selectivity, fatigue resistance, and thermal stability.

Dehydrophenylalanine, ΔPhe, is the most commonly studied α,β-dehydroamino acid. In nature, further modifications of the α,β-dehydroamino acids were found, for example, replacement of the C-terminal amide group by oxazole ring. The conformational properties of oxazole-dehydrophenylalanine residue (ΔPhe-Ozl), both isomers Z and E, were investigated. To determine all possible conformations, theoretical calculations were performed using Ac-(Z/E)-ΔPhe-Ozl(4-Me) model compounds at M06-2X/6-31++G(d,p) level of theory. Ac-(Z/E)-ΔPhe-Ozl-4-COOEt compounds were synthesized and the conformational preferences of each isomer, Z and E, were investigated using FTIR and NMR-NOE in solutions of increasing polarity (CHCl3 , DMSO-d6). The solid-state low-temperature structures of Ac-(Z)-ΔPhe-Ozl-4-COOEt and its intermediate analog Ac-(Z)-ΔPhe-Ozn(4-OH)-4-COOEt were also determined. In a weakly polar environment, the ΔPhe-Ozl residue has a tendency to adopt the conformation β2 with the calculated φ and ψ angles of -127° and 0° for the isomer Z and -170° and 26° for the isomer E. The increase of environment polarity favors the helical conformation α and the beta-turn like conformation β, but the conformation β2 seems to be still accessible. The (E)-ΔPhe-Ozl residue can be obtained from the isomer Z in photoisomerization reaction. However, hydroxyl-oxazoline-dehydrophenylalanine ΔPhe-Ozn(4-OH) decomposes in such conditions. Alternatively, (E)-ΔPhe-NH2 can be applied as a substrate in the Hantzsch reaction. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 283-294, 2016.

Peptidylprolyl-isomerases (PPIases) comprise of the protein families of FK506 binding proteins (FKBPs), cyclophilins, and parvulins. Their common feature is their ability to expedite the transition of peptidylprolyl bonds between the cis and the trans conformation. Thus, it seemed highly plausible that PPIase enzymatic activity is crucial for protein folding. However, this has been difficult to prove over the decades since their discovery. In parallel, more and more studies have discovered scaffolding functions of PPIases. This essay discusses the hypothesis that PPIase enzymatic activity might be the consequence of binding to peptidylprolyl protein motifs. The main focus of this paper is the large immunophilins FKBP51 and FKBP52, but other PPIases such as cyclophilin A and Pin1 are also described. From the hypothesis, it follows that the PPIase activity of these proteins might be less relevant, if at all, than the organization of protein complexes through versatile protein binding. Also see the video abstract here https://youtu.be/A33la0dx5LE.

Manufacturing machines converting energy to mechanical work at the molecular level is a vital pathway to explore the microscopic world. A kind of operable molecular engines, composed of β-cyclodextrin (β-CD), aryl, alkene and amide moiety was investigated using molecular dynamics simulations combined with free-energy calculations. To understand how the integrated alkene double bond controls the work performed on the engines, two alkene isomers of the prototype were considered as two molecular engines. The free-energy profiles delineating the binding process of the amide (Z)- and (E)-isomers for each alkene isomer with 1-adamantanol indicate that for the alkene (E)-isomer, the apparent work performed on the amide bond is 1.6 kcal/mol, while the alkene (Z)-isomer is incapable to perform work. Direct switch on/off of engines caused by the isomerization of the alkene bond was, therefore, witnessed, in line with experimental measurements. Decomposition of the free-energy profile into different components and structural analyses suggest that the isomerization of the alkene bond controls the position of the aryl unit relative to the cavity of the CD, resulting in the difference among the free-energy profiles and the stark contrast of the work performed on engines.

A pyrazoline derivative, 3-(1,1-dicyanoethenyl)-1-phenyl-4,5-dihydro-1H-pyrazole (DCNP), is studied by using optical spectroscopy methods in several solvents at room and at low temperatures. The DCNP molecule reveals a complex photophysics behavior, which is sensitive to solvent polarity, proticity, temperature and viscosity and arises from the presence of two rotational degrees of freedom of the dicyanovinyl group--the torsion around the double C=C bond and the s-trans-s-cis isomerization around the single C-C bond--that differently behave in various environmental conditions. The fluorescence yield of a few percent and sub-nanosecond decay times observed at room temperature make the compound useful for optical studies of liquid environments. The proticity of polar solvents can be detected with two-exponential fluorescence decays. At low temperatures, DCNP can be used as solvent viscosity or temperature fluorescent sensor.

Self-association of proteins can be triggered by a change in the distribution of the conformational ensemble. Posttranslational modification, such as phosphorylation, can induce a shift in the ensemble of conformations. In the brain of Alzheimer's disease patients, the formation of intra-cellular neurofibrillary tangles deposition is a result of self-aggregation of hyper-phosphorylated tau protein. Biochemical and NMR studies suggest that the cis peptidyl prolyl conformation of a phosphorylated threonine-proline motif in the tau protein renders tau more prone to aggregation than the trans isomer. However, little is known about the role of peptidyl prolyl cis/trans isomerization in tau aggregation. Here, we show that intra-molecular electrostatic interactions are better formed in the trans isomer. We explore the conformational landscape of the tau segment containing the phosphorylated-Thr(231)-Pro(232) motif using accelerated molecular dynamics and show that intra-molecular electrostatic interactions are coupled to the isomeric state of the peptidyl prolyl bond. Our results suggest that the loss of intra-molecular interactions and the more restricted conformational ensemble of the cis isomer could favor self-aggregation. The results are consistent with experiments, providing valuable complementary atomistic insights and a hypothetical model for isomer specific aggregation of the tau protein.

The peptidyl-proyl isomerase Pin1 plays a key role in the regulation of phospho(p)-Ser/Thr-Pro proteins, acting as a molecular timer of the cell cycle. After recognition of these motifs, Pin1 catalyzes the rapid cis-trans isomerization of proline amide bonds of substrates, contributing to maintain the equilibrium between the two conformations. Although a great interest has arisen on this enzyme, its catalytic mechanism has long been debated. Here, the cis-trans isomerization of a model peptide system was investigated by means of umbrella sampling simulations in the Pin1-bound and unbound states. We obtained free energy barriers consistent with experimental data, and identified several enzymatic features directly linked to the acceleration of the prolyl bond isomerization. In particular, an enhanced autocatalysis, the stabilization of perturbed ground state conformations, and the substrate binding in a procatalytic conformation were found as main contributions to explain the lowering of the isomerization free energy barrier.

In the present work, chromophoric system (E)-4-(naphthalen-1-yl diazenyl)benzoic acid was synthesized and incorporated into lignin core. The end hydroxyl group of lignin was modified with the free carboxyl group of the chromophoric systems by dicyclohexylcarbodiimide coupling. The products were characterized by means of UV–visible, fluorescence, FT-IR, and NMR spectroscopic methods and subjected to photoresponsive studies. The results show that modification enhances the light absorption and light fastening properties of the chromophoric system. The photoinduced trans–cis isomerization on the newly developed photosensitive biopolymeric system and the chromophoric system were investigated. Results also show that the trans–cis photoisomerization and the reverse cis–trans thermal conversions of the photoactive groups were also assisted by the incorporation onto biopolymeric core. Copyright © 2014 John Wiley & Sons, Ltd.

Azobenzenes have been used as photoresponsive units for the control of numerous biological processes. Primary prerequisites for such applications are site-selective incorporation of photoswitchable units into biomolecules and the possibility of using non-destructive and deep-tissue-penetrating visible light for the photoisomerization. Here we report a push-pull azobenzene that readily undergoes a Staudinger-Bertozzi ligation with azide groups, that can be addressed with visible light (>440nm) and exhibits the solvato- and acidochromism typical for push-pull systems. The thermal relaxation in aqueous environment proceeds on the low-millisecond timescale, thus enabling control over biological processes on similar timescales. The approach is demonstrated in the modification of a quartz surface and in the incorporation of an azobenzene unit into a functional peptide, the third zinc finger in the mammalian factor Sp1.

The highly hydrophobic β‐carotene is often distributed or dissolved in triglycerides to enhance either nutritional or coloring effects. This study aims at elucidating the physical state of β‐carotene that at high concentrations are mixed into a solid high‐melting tri‐glyceride matrix by dissolution at high temperatures (165 °C) in the melted triglyceride. Extensive isomerization of β‐carotene is observed by HPLC after melting crystalline all‐trans β‐carotene and in the solid mixtures of β‐carotene and fully hydrogenated sunflower oil. Crystalline triglyceride is found in the mixed samples by XRPD analysis whereas no signs of crystalline lattice structures of β‐carotene are detected. DSC thermograms show only the melting and recrystallization events of triglycerides, which are affected by the presence of β‐carotene. Severe line broadening is observed in the ¹³C CP/MAS NMR spectra of the β‐carotene‐triglyceride mixtures when compared to crystalline β‐carotene, demonstrating the lack of long‐range order of the carotene. Altogether, the results demonstrate that β‐carotene is present as an amorphous mixture of trans‐ and cis‐isomers dispersed into a structure of crystalline triglyceride in the solid carotene‐triglyceride mixtures. Practical applications: The amorphous structure of trans‐ and cis‐isomers in solid formulations of β‐carotene‐triglyceride mixtures will strongly affect their functional properties related to nutrition and color as food ingredients.

Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is a key enzyme of the purine recycling pathway that catalyzes the conversion of 5-phospho-ribosyl-α-1-pyrophosphate and guanine or hypoxanthine to guanosine monophosphate (GMP) or inosine monophosphate (IMP), respectively, and pyrophosphate (PPi). We report the first crystal structure of a fungal 6-oxopurine phosphoribosyltransferase, the Saccharomyces cerevisiae HGPRT (Sc-HGPRT) in complex with GMP. The crystal structures of full length protein with (WT1) or without (WT2) sulfate that mimics the phosphate group in the PPi binding site were solved by molecular replacement using the structure of a truncated version (Δ7) solved beforehand by multiwavelength anomalous diffusion. Sc-HGPRT is a dimer and adopts the overall structure of class I phosphoribosyltransferases (PRTs) with a smaller hood domain and a short two-stranded parallel β-sheet linking the N- to the C-terminal end. The catalytic loops in WT1 and WT2 are in an open form while in Δ7, due to an inter-subunit disulfide bridge, the catalytic loop is in either an open or closed form. The closure is concomitant with a peptide plane flipping in the PPi binding loop. Moreover, owing the flexibility of a GGGG motif conserved in fungi, all the peptide bonds of the phosphate binding loop are in trans conformation whereas in nonfungal 6-oxopurine PRTs, one cis-peptide bond is required for phosphate binding. Mutations affecting the enzyme activity or the previously characterized feedback inhibition by GMP are located at the nucleotide binding site and the dimer interface.

The influence of lithium cations on the cis/trans isomerization of prolyl peptide bonds was investigated in a quantitative manner in trifluoroethanol (TFE) and acetonitrile, employing NMR techniques. The focus was on various environmental and structural aspects, such as lithium cation and water concentrations, the type of the partner amino acid in the prolyl peptide bond, and the peptide sequence length. Comparison of the thermodynamic parameters of the isomerization in LiCl/TFE and TFE shows a lithium cation concentration dependence of the cis/trans ratio, which saturates at cation concentrations >200mM. A pronounced increase in the cis isomer content in the presence of lithium cations occurs with the exception of peptides with Gly-Pro and Asp-Pro moieties. The cation effect appears already at the dipeptide level. The salt concentration can considerably be reduced in solvents with a lower number of nucleophilic centers like acetonitrile. The lithium cationeffect decreases with small amounts of waterand disappears at a water concentration of about 5%. The isomerization kinetics under the influence of lithium cations suggests a weak cation interaction with the carbonyl oxygen of the peptide bond. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.

Dehydroamino acids with the methylated N-terminal peptide group occur in natural small cyclic peptides. The structural analysis was used to investigate the cis-trans isomerization of the N-terminal tertiary amide group of diamides: Ac-(Z)-Δ(Me)Abu-NHMe (1), Ac-(Z)-Δ(Me)Phe-NHMe (2), Ac-(E)-Δ(Me)Phe-NHMe (3), Ac-Δ(Me)Ala-NHMe (4), and Ac-(Me)Ala-NHMe (5). The compounds were analyzed in the solid state by an X-ray crystallography (1-3), and in the solution by FTIR (MeCN and CHCl(3) ) and NMR (DMSO-d6 and CDCl(3) ) methods (1-5). In the solid state, the studied compounds adopt the cis configuration of N-terminal amide. In solution, this configuration also prevails for the dehydroamino acids 1-4, in contrast to the saturated analog 5. The results indicate that N-methyldehydroamino acids present a promising tool to induce the cis configuration of the amide bond.

The bridge photoisomerization of the chromophores of fluorescent proteins has been suggested as the possible mechanism of radiationless decay in fluorescent proteins. It indicates that this internal structure changing of chromophores great influence the optical properties of fluorescent proteins. The two-photon absorption (TPA) properties of fluorescent proteins might also be influenced by the bridge photoisomerization of the chromophores. In this work, we simulate the dynamic conformations through rotating the bridge bond of chromophore of green fluorescent protein, and employ the time dependent density functional theory combining with the sum-over-states method to study their TPA characters. With our study, we find that the TPA characters of chromophore will be improved through controlling rotation of the bridge bond of chromophore. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011

UV resonance Raman spectroscopic study of six short proline-containing peptides with antioxidant activity isolated from human breast milk was performed. The amide II′ proline spectroscopic band was used to estimate relative cis trans isomerization state of proline amide bonds in the different peptides. Antioxidant activity of the peptides was determined using 1,1-diphenyl-2-picryl-hydrazyl (DPPH) assay and linoleic acid emulsion assay. Although no clear correlation between the amide II′p position and antioxidant activity of the peptides was observed, they both were found to be sensitive to the presence and/or relative position of proline and tyrosine residues in the peptide. Copyright © 2011 John Wiley & Sons, Ltd.

Polymers including chromophores, which can be switched by light, have been studied extensively during the last years due to a host of potential applications which arise from the marked changes in physical properties on switching. Even though there is clear evidence that the free volume has a significant influence on the isomerization kinetics, the question of free volume changes on switching was only addressed recently. Using a pulsed low-energy positron beam the ortho-positronium lifetime tau(3) was taken as a very sensitive free volume probe, and no change in free volume was detected on isomerization in an azobenzene-polymethylmethacrylate (PMMA) copolymer containing about 8 wt of the azobenzene moiety. Here, we report for the first time on free volume changes in an azobenzene-PMMA blend with an azobenzene moiety concentration as high as 40 wt . Using the same pulsed low-energy positron beam, small but significant changes of tau(3) were observed between the structurally relaxed dark and the UV-illuminated states suggesting a decrease in free volume of the order of 10. (C) 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 404-408, 2011

We established a polymerization condition of 3-hydroxycinnamic acid, 3HCA, having photoreactive units over all the main chains. The polymers showed two types of photoreaction, that is, intramolecular E–Z isomerization and interchain [2 + 2] cycloaddition. Spectroscopic studies showed that the rate of the isomerization was higher than that of the cycloaddition. Although the original fiber was very brittle, the short-time UV-irradiation made the fiber softer and more elastic because the chain bending by the isomerization preferentially occurred. On the other hand, the long-time irradiation made the fiber harder because of the cross-linking by the cycloaddition, and simultaneously enhanced the elasticity. Besides we found that the cast film of P3HCA showed a photo-bending behavior with the convex surface facing the UV-lamp by the initial E–Z isomerization. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011

Advances in the field of Femtosecond Stimulated Raman Spectroscopy (FSRS), a new time-resolved structural technique that provides complete vibrational spectra on the ultrafast timescale, are reviewed. When coupled with a femtosecond optical trigger, the time evolution of a reacting species can be monitored with unprecedented

β2-Microglobulin has been a model system for the study of fibril formation for 20 years. The experimental study of β2-microglobulin structure, dynamics, and thermodynamics in solution, at atomic detail, along the pathway leading to fibril formation is difficult because the onset of disorder and aggregation prevents signal resolution in Nuclear Magnetic Resonance experiments. Moreover, it is difficult to characterize conformers in exchange equilibrium. To gain insight (at atomic level) on processes for which experimental information is available at molecular or supramolecular level, molecular dynamics simulations have been widely used in the last decade. Here, we use molecular dynamics to address three key aspects of β2-microglobulin, which are known to be relevant to amyloid formation: (1) 60 ns molecular dynamics simulations of β2-microglobulin in trifluoroethanol and in conditions mimicking low pH are used to study the behavior of the protein in environmental conditions that are able to trigger amyloid formation; (2) adaptive biasing force molecular dynamics simulation is used to force cis-trans isomerization at Proline 32 and to calculate the relative free energy in the folded and unfolded state. The native-like trans-conformer (known as intermediate 2 and determining the slow phase of refolding), is simulated for 10 ns, detailing the possible link between cis-trans isomerization and conformational disorder; (3) molecular dynamics simulation of highly concentrated doxycycline (a molecule able to suppress fibril formation) in the presence of β2-microglobulin provides details of the binding modes of the drug and a rationale for its effect. Proteins 2011. © 2010 Wiley-Liss, Inc.

The Epstein–Barr virus determinant peptide EENLLDFVRF shows high immunogenicity when presented by HLA-B*4405 allotype. This fact is accompanied by a cis–trans isomerization of the Leu5-Asp6 peptide bond upon TCR binding of the pMHC complex. Molecular dynamics simulations of pMHC/TCR structures, with the EENLLDFVRF peptide in cis and trans conformations have been employed in order to examine the structure and dynamics of the pMHC complex with such an unusual conformation. The results, based on MM-PBSA free energy computations as well as buried surface area analysis and interactions at the pMHC/TCR interface, indicate that the TCR binds preferably the pMHC complex with the Leu5-Asp6 peptide bond in cis conformation. It is the first time that this notable conformational feature of T-cell epitope is investigated.

Photoreorientation of a stripe pattern consisting of an MPS structure in a Langmuir-Blodgett monolayer by irradiation with linearly polarized light is achieved for the first time using a PDMS/poly(methacrylate) diblock copolymer with a liquid crystalline azobenzene-containing side chain. The stripe MPS pattern in the trans azobenzene state is diminished by photoisomerization to the cis form upon UV light irradiation. By the erasure of the MPS structure, the anisotropic photo-oriented stripe pattern is generated upon irradiation with linearly polarized visible light, the orientation of the stripe pattern being orthogonal to the electric vector of the light.

The gas‐phase cis‐trans isomerization of 1,3‐pentadiene, photosensitized by a thin polymeric film, has been studied at λ ≥ 300 mμ and 50°C in the pressure range 5 to 200 torr. The observed photostationary state and the influence of substrate pressure on the rate of isomerization suggest a reaction mechanism similar to that proposed for triplet photosensitized isomerizations in solutions[2]. Copyright © 1971 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim

Isomerization of vitamin D2 in apolar solvents at room temperature under the influence of small amounts of iodine in diffuse daylight yields a compound that could be isolated in the form of the crystalline phenylazobenzoate. Spectra of solutions of the free vitamin D isomer obtained upon saponification of the ester are presented. They support the view that the isomer should be considered as trans-vitamin D2 having structure A (fig. 3).

Series of high-cis and cis/trans poly[(fluorophenyl)acetylene]s (PFPhA) have been prepared by polymerization of (2-fluorophenyl)acetylene, (3-fluorophenyl)acetylene, and (4-fluorophenyl)acetylene with catalysts: [Rh(1,5-cyclooctadiene) OCH3]2 (high-cis PFPhAs) and tungsten(VI) oxychloride/tetraphenyltin (cis/trans PFPhAs). The molecular weight and configurational stability under various conditions at room temperature were studied for both PFPhAs series by means of size exclusion chromatography, 1H-NMR, and UV-vis techniques. All samples exhibited slow degradation when exposed to the atmosphere in the solid state; the rate of degradation was independent on the F-position on the Ph ring. The rate of degradation increased up to three orders of magnitude in the tetrahydrofuran solution where it was higher for high-cis polymers compared with their cis/trans counterparts. The degradation of high-cis PFPhAs was accompanied by significant cis-to-trans isomerization in aerated tetrahydrofuran solution. Rate of degradation and isomerization exhibited the same dependence on the F-position on the Ph ring. The hypothesis was postulated that the degradation of high-cis PFPhAs in solution was accelerated by cis-to-trans isomerization due to which the content of unpaired electrons on the main chains is enhanced. In both high-cis and cis/trans series of polymers the ortho-substituted isomers exhibited an enhanced stability compared with meta- and para-substituted isomers. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 4296–4309, 2010

Conformational preferences and prolyl cis−trans isomerizations of the (2S,4S)-4-methylproline (4S-MePro) and (2S,4R)-4-methylproline (4R-MePro) residues are explored at the M06-2X/cc-pVTZ//M06-2X/6-31+G(d) level of theory in the gas phase and in water, where solvation free energies were calculated using the implicit SMD model. In the gas phase, the down-puckered γ-turn structure with the trans prolyl peptide bond is most preferred for both Ac-4S-MePro-NHMe and Ac-4R-MePro-NHMe, in which the C7 hydrogen bond between two terminal groups seems to play a role, as found for Ac-Pro-NHMe. Because of the C7 hydrogen bonds weakened by the favorable direct interactions between the backbone CO and HN groups and water molecules, the 4S-MePro residue has a strong preference of the up-puckered polyproline II (PPII) structure over the down-puckered PPII structure in water, whereas the latter somewhat prevails over the former for the 4R-MePro residue. However, these two structures are nearly equally populated for Ac-Pro-NHMe. The calculated populations for the backbone structures of Ac-4S-MePro-NHMe and Ac-4R-MePro-NHMe in water are reasonably consistent with CD and NMR experiments. In particular, our calculated results on the puckering preference of the 4S-MePro and 4R-MePro residues with the PPII structures are in accord with the observed results for the stability of the (X-Y-Gly)7 triple helix with X = 4R-MePro or Pro and Y = 4S-MePro or Pro. The calculated rotational barriers indicate that the cis−trans isomerization may in common proceed through the anticlockwise rotation for Ac-4S-MePro-NHMe, Ac-4R-MePro-NHMe, and Ac-Pro-NHMe in water. The lowest rotational barriers become higher by 0.24−1.43 kcal/mol for Ac-4S-MePro-NHMe and Ac-4R-MePro-NHMe than those for Ac-Pro-NHMe in water. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 51–61, 2011.

A series of optically inactive polythiophene derivatives bearing the azobenzene moiety are synthesized in an isotropic toluene solution. The polymers are then dissolved in a cholesteric liquid crystal (Ch * LC) medium within the liquid crystal (LC) temperature range. The dissolution process in Ch * LC produces intermolecular π-stacking with structural chirality. Although the polymers thus prepared have no chiral center or axial chirality in the primary structure, they do exhibit consistent chiroptical activity derived from three-dimensional chiral aggregations. Furthermore, photochemical cis-trans isomerization of the substituents allows light-driven chiroptic modulation of the polymer.

We report the synthesis and investigation of a new type of photoresponsive block copolymers (BCPs). They were designed to comprise two water-soluble polymers containing two different photoisomerizable moieties (either azobenzene and spiropyran or two different azobenzenes), with the two constituting blocks that, when separated, exhibit a lower critical solution temperature (LCST) in water and can shift their LCST in opposite directions upon photoisomerization (decrease of LCST for one polymer and increase for the other). A variety of such doubly photoresponsive BCPs were synthesized using either azobenzene- or spiropyran-containing poly(N,N-dimethylacrylamide) (PDMA), poly(N-isopropylacrylamide) (PNIPAM) and poly[methoxydi(ethylene glycol) methacrylate] (PDEGMMA). Their thermal phase transition behaviors in aqueous solution before and after simultaneous photoreactions on the two blocks were investigated in comparison with their constituting blocks, by means of solution transmittance (turbidity) and variable-temperature 1H NMR measurements. The results show that BCPs displayed a single LCST whose shift upon two photoisomerizations appeared to be determined by the competing and opposing photoinduced effects on the two blocks. Moreover, optically controlling the relative photoisomerization degrees of trans azobenzene-to-cis azobenzene and spiropyran-to-merocyanine could be used to tune the LCST of BCP solution. This study demonstrates the potential of exploring a more complex photoreaction scheme to optically control the solution properties of water-soluble thermosensitive BCPs. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 4055–4066, 2010

Various triazatriangulenes are synthesized by nucleophilic attack at the central C atom of triazatriangulenium ions. The molecular functions, especially azobenzenes, are fixed via an ethynyl linker by in situ deprotection of trimethylsilyl-alkynes. The structure of two of these molecules is further investigated by X-ray crystallography. The photo-induced trans/cis-isomerization of the azobenzene substituted derivatives is analyzed in solution and shows great promise for the preparation of switchable functionalized monolayers, as the triazatriangulenes are known for their self-assembly on gold surfaces. [1] .

The naturally occurring macrotetrolide antibiotic nonactin is used in ammonium ion selective electrodes. To increase the lifetime of nonactin in the semipermeable membrane of these sensors we have developed methods for the introduction of hydrophobic side-chains. Simple model compounds for nonactic acid such as 5 and 7 were synthesised. Maintaining the cis arrangement of the substituents in the 2,5-disubstituted tetrahydrofurans proved to be difficult. Three different routes were studied. The enolates obtained by treatment with NaHMDS or KHMDS could be alkylated with benzyl or allyl iodide as electrophiles. Under these conditions a cis/trans isomerisation of the substituents on the tetrahydrofuran ring occurred. A multistep methodology was developed as a synthetic alternative. The sequence consisted of a selective retro-Michael reaction, a 5-exo-tet iodocyclisation and a radical substitution. The products obtained by the two methodologies could be correlated, and thereby a tentative assignment of the relative configurations could be achieved. In the third route the thione ester 18 was deprotonated with tBuOK. At temperatures below -78 °C, the enolate maintained the cis configuration of the substituents at the tetrahydrofuran ring. The alkylated product 12 could be isolated with a satisfactory cis/trans ratio of 85:15. The model compound 12 could be successfully transformed into more hydrophobic derivatives by using either the Heck coupling or the cross-coupling metathesis transformation.

Three accessible azobenzene mesogen-substituted diacetylene monomers (DA1, DA2, and DA3) were synthesized and the effect of the molecular structure on the photopolymerization behavior and self-assembled structures of the resulting azobenzene-substituted polydiacetylene (PDA) films had been investigated in detail. The films derived from DA1 were substantially polymerized into blue phase. However, the films derived from DA2 and DA3 were polymerized into red phase directly. The morphology, packing structure, and thermal stability of the resulting azobenzene-substituted PDA films were characterized in detail by SEM, XRD as well as POM measurements. PDA1 formed micrometer-sized lamellar crystal structures, while PDA2 and PDA3 both formed spherulitic crystal structures. The strong π-π stacking interaction among side chains was essential for maintaining high stability upon thermal stimulus.

A novel amphiphilic diblock copolymer composed of a hydrophilic poly(ethylene oxide) block and a hydrophobic block copolymerized by azobenzene-containing methacrylate and N-isopropylacrylamide was synthesized using ATRP. The polymer micelles showed dual responsiveness to heat and light. The size of the micelles was dependent on temperature and the encapsulated substance in the hydrophobic cores was released during heating and cooling processes. The hydrophobicity of the micellar cores appeared as a reversible change in response to light with neither disruption of the micelles nor leakage of the encapsulated substance while H-aggregation of the azobenzene moieties was detected.

Here, we describe a procedure to manufacture smart hybrid probes that exhibit tunable optical properties as a function of multiple environmental variations. Initially, we achieved a one-pot synthesis of gold-PREP (photo-responsive elastin-like polymer) conjugate Gold-AzoGlu15 via reduction of auric acid in the presence of PREP AzoGlu15. Outstandingly, Gold-AzoGlu15 exhibited pH and temperature sensitiveness. However, Gold-AzoGlu15 was not UV-vis sensitive. We noticed that photo-isomerisation of azobenzene moieties in Gold-AzoGlu15 could not be detected by UV-vis spectroscopy. In a subsequent step, we explored the use of cyclodextrins and the formation of alkanethiol mixed-monolayers over mother Gold-Azo-Glu15 by thiol-place exchange reactions in order to decouple photo-isomerisation of azobenzene from the bulk phase absorption. In this sense we achieved the synthesis of β-cyclodextrin capped Gold-CD-AzoGlu15. Notable was that cis-trans photo-conversion of azobenzene groups in Gold-CD-AzoGlu15 could be successfully detected. Finally, we present the optical properties exhibited by multi-sensitive probe Gold-CD-AzoGlu15 as a function of pH, temperature and UV-vis irradiation. We think that gold-PREP hybrids could be of great interest in the design of multi-functional chromophore-metal nanocomposites that operate in aqueous media for the development of multi-stimuli sensitive detectors for biosensing applications.

A photoresponsive oil sorber (POS) with a hydrophobic, photoresponsive core and shell has been synthesized via suspension polymerization. Lauryl acrylate, isodecyl acrylate, and tert-butylstyrene were used as monomers, 4-(methacrylamino)azobenzene (Azo-M) used as photoresponsive monomer, and bis(methacryloylamino)azobenzene (Azo-CL-M) used as photoresponsive surface crosslinker. The POS prefers nonpolar solvents. It absorbed 15 times its dry weight in toluene, 19 times its dry weight in chloroform, and 16 times its dry weight in dichloromethane. Rapid and photoresponsive desorption of solvent (86% of solvent expulsed in 30 min) was characteristic. POS is an excellent gasoline absorber rapidly increasing its body weight in its presence. The new POS is less dense than water, and can potentially be used for cleaning oil spills on water.

Two new polyethers, bearing azobenzene moiety in the side chain, were synthesized in excellent yields by means of anionic polymerization of 4-glycidyloxyazobenzene and 4-cyano-4′-glycidyloxyazobenzene (leading to azo-P1 and azo-P2 polymers, respectively) with the system polyiminophosphazene base t-Bu-P4/3,5-di-tert-butylphenol as initiator. The polymers were characterized with respect to their molecular weights, structure, and calorimetric features. The polyether bearing cyanoazobenzene group in the side chain was found to exhibit nematic phase up to 200 °C. E–Z isomerization of both polymers in tetrahydrofuran solution, after irradiating with UV light at 364 nm for 15 min, was investigated by means of UV–visible absorption spectroscopy. In the case of glycidylic monomers as well as the resulting polymers, E–Z isomerization was also investigated by means of 1H NMR, by direct irradiation in the NMR probe in deuterated 1,1,2,2-tetrachloroethane solution. By this technique, in the case of 4-cyano-4′-glycidyloxyazobenzene, it was found that irradiation led to a photostationary state corresponding to an amount of Z isomer equal to 25%. For azo-P1 polymer, Z–E or “reverse” isomerization was investigated at 60, 70, or 80 °C directly in the NMR probe; as expected, the process followed a first-order rate law. The kinetic constants as well as the activation energy for the process were determined in this temperature range. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5426–5436, 2009

BACKGROUND: Star-shaped polymers are very attractive because of their interesting properties such as reduced viscosity, good solubility, low glass transition temperature and fast response to external stimuli. The incorporation of azobenzene moieties in star-shaped polymers could significantly widen their potential applications in various optical devices. One of the most important properties of the azobenzene chromophore is its reversible trans–cis photoisomerization induced by UV or visible light. Photoisomerization induces conformational changes in azopolymer chains, which in turn lead to macroscopic variations in chemical and physical properties of the surroundings and media. RESULTS: This study reports the synthesis of azobenzene-functionalized two-, three- and four-arm telomers via free radical telomerization using the di-, tri- and tetrafunctional chain transfer agents 1,2- and 1,4-benzenedimethanethiol, trimethylolpropane-tris(2-mercaptoacetate) and pentaerythritol-tetrakis(3-mercaptopropionate), respectively, in the presence of azobisisobutyronitrile. Azotelomers were characterized using gel permeation chromatography and 1H NMR and Fourier transform infrared spectroscopy. Thermal phase transition behaviors were investigated using differential scanning calorimetry and polarized optical microscopy. Azotelomers synthesized in this study showed reversible photoisomerization and a fast generation of birefringence. CONCLUSION: Considering the photoisomerization behavior and birefringence of the two-, three- and four-arm azotelomers, it can be concluded that they could be potential candidates for use in various optical devices. Copyright © 2009 Society of Chemical Industry

This article studies the influence of the network structure on the activation energies of the α and β relaxations in vulcanized styrene butadiene rubber, SBR. A cure system based on sulphur and TBBS (N-t-butyl-2-benzothiazole sulfenamide) was used in the formulation of several compounds cured at 433 K. The activation energies were evaluated from internal friction (loss tangent) data of the compounds using an automated subresonant forced pendulum in a wide frequency range and between 80 K and 273 K. The internal friction data of the samples reveal two transitions, α and β, characterized by the temperatures T α and T β , due to the glass transition and the phenyl group rotation of the copolymer, respectively. Although T α increases at higher crosslink density, it shows also a dependence with the amount of polysulphide and monosulphide linkages present in the samples. The highest activation energy for this process is obtained for the samples with high crosslink density and 30% of monosulphides in this structure. In the case of the β-relaxation, there is a pronounced change in the activation energy between the uncured and the cured samples. The type of structure formed during vulcanization has an important effect in the activation energy of the segmental mode-process. In the case of the β-process, the cis-trans isomerization that takes place during vulcanization in the butadiene part of the SBR, might be the cause of conformational changes in the surrounding of the phenyl rings that affect the energy barrier associated to the phenyl rotation.

A series of polystyrene-block-poly(n-butyl methacrylate) (PS-b-PnBMA) diblock copolymers (diBCPs) with an azobenzene moiety [trans-4-methacryloyloxyazobenzene (MOAB)] in the PnBMA segment was prepared by atom transfer radical polymerization (ATRP). P(nBMA-co-MOAB) macroinitiators were prepared by activators regenerated by electron transfer (ARGET) ATRP. The MOAB was slightly more reactive than nBMA, resulting in a weak gradient fashion of copolymer. The macroinitiators were subsequently chain-extended with styrene. Acceleration of the ATRP rate was observed in the presence of a reducing agent. P(nBMA-co-MOAB)-b-PS di-BCPs were obtained with relatively narrow molecular weight distributions (Mw/Mn ¼ 1.16–1.49) and the molecular weights were in good agreement with the theoretical values. The efficiency of photoisomerization of the MOAB units was above 80%. DSC traces showed a single Tg suggesting the block copolymers were miscible before UV irradiation. After UV irradiation, the X-ray reflectivity measurements showed the beating of two frequencies, indicating the formation of island-hole structure.