Cis Form Research Articles

Photoinduced Regeneration of an Aptamer-Based Electrochemical Sensor for Sensitively Detecting Adenosine Triphosphate.

Electrochemical aptasensors generally include three elements, that is, recognition element, signal-transformation element, and regeneration element. In this study, a new adenosine triphosphate (ATP) aptasensor is developed by combining three elements into one DNA oligonucleotide chain. In the DNA oligonucleotide chain, DNA aptamer is used as the recognition element, ferrocene group attached at the 3'-end of the aptamer is used as the signal-transformation element, and azobenzene moiety embedded into the DNA chain is used as the regeneration element. In addition to the similar analytical properties with the traditional ones, the aptasensor developed here is easily regenerated with UV-light irradiation. The current response recorded on the aptasensor increases with increasing the concentration of ATP in the incubation solution and is linear with the logarithm of ATP concentration in the range from 1 nM to 100 μM. The limit of detection is 0.5 nM (S/N = 3). The basal level of ATP in the rat brain cortex microdialysate is determined to be 21.33 ± 4.1 nM ( n = 3). After being challenged with ATP, the aptasensor could be readily regenerated by UV-light irradiation for more than seven cycles. The regeneration of the aptasensor is proposed to be regulated by conversing azobenzene from its trans to cis form under UV irradiation.

Smart collectors: Control of the wettability and floatability of quartz with UV irradiation

Quartz is a hydrophilic mineral that usually associates with other ores. In this paper, the effect of UV stimuli on the wettability and floatability of quartz was studied. An azobenzene-containing surfactant was synthesized and its structure was identified by 1H NMR. We used UV–vis and 1H NMR spectra of the surfactant to study its photoisomerization. After UV irradiation of the surfactant molecular, the trans isomer concentration decreases and the cis isomer concentration increases; both the aromatic protons of the azobenzene moiety and aliphatic protons experience an upfield shift, indicating that the surfactant molecular isomerizes from the trans isomer to the cis form. We used contact angle measurements to demonstrate that UV irradiation decreases the hydrophobicity of the quartz and increases the adhesion tension of the surfactant on quartz. The results of flotation tests demonstrate that the azobenzene-containing surfactant has higher performances than alkyl amine salt, and UV irradiation improves the selectivity of the azobenzene-containing surfactant in the flotation of quartz. This study demonstrates that the azobenzene-containing surfactant can be used as a light-responsive collector for quartz in the flotation of phosphate ores.

Near-infrared in situ generation of the higher-energy trans conformer of tribromoacetic acid: Observation of a large-scale matrix-site changing mediated by conformational conversion.

The first observation of the higher-energy conformer of tribromoacetic acid (trans-TBAA) is reported. The conformer was produced in cryogenic matrices (Ar, Kr, and N2) by in situ selective narrowband near-infrared excitation of the lower-energy cis-TBAA conformer and characterized both structurally and vibrationally. The novel trans-TBAA conformer is shown to spontaneously decay to the most stable cis-TBAA form in all studied matrix media, by tunneling, and the measured decay rates in the different matrices were compared with those of the trans conformers of other carboxylic acids in similar experimental conditions. In the N2 matrix, where trans-TBAA establishes a specific stabilizing intermolecular interaction with the host N2 molecules via its OH group and is about 11 times more stable than in rare gas matrices, the effect of changing the irradiation wavenumber within the 2νOH absorption profile was investigated in detail. An interesting phenomenon of matrix-site changing mediated by conformational conversion was observed in the N2 matrix: vibrational excitation of cis-TBAA in the 2νOH wavenumber range predominantly converts the molecules located in a specific "matrix site" into trans-TBAA; then, relaxation (by tunneling) of the produced higher-energy conformer back to the cis form populates almost exclusively another "matrix site." The experimental studies received support from quantum chemistry calculations, which allowed a detailed characterization of the relevant regions of the potential energy surface of the molecule and the detailed assignment of the infrared spectra of the two conformers in the various matrices.

Photocontrolled Reversible Guest Uptake, Storage, and Release by Azobenzene-Modified Microporous Multilayer Films of Pillar[5]arenes.

Using the pillar-shaped architecture of pillar[5]arenes, we constructed microporous multilayer films with azobenzene groups on the top surface by layer-by-layer assembly of cationic and anionic pillar[5]arenes. Guest uptake, storage, and release by the microporous films were regulated through photoreversible isomerization of azobenzene groups attached to the pore outlets. Azobenzene was regarded as a "molecular valve" to control guest access: the trans form of the azobenzene acted as an open valve, allowing guest-free access from/to the micropores. Conversely, the cis form of the azobenzene behaved as a closed valve, completely blocking guest access from/to the micropores. Photoresponsive reversible uptake, storage, and release of guest molecules were demonstrated through photoisomerization of the azobenzene valves by irradiation with ultraviolet and visible light.

Moderately Flexible Trans-Chelating Diphosphine Ligands Consisting of a Triazine Unit Showing High Ligand Acceleration Effect for Heck Reaction

Abstract Originally designed trans-chelating diphosphine ligands with moderate flexibility that allows trans- to cis-isomerization and bidentate to monodentate complex form were developed. The novel ligand shows high ligand acceleration effect (LAE) for Heck reaction. The catalyst loading was decreased to 0.0001 mol%, and the turnover number (TON) reached 970,000. The catalytic cycle was evaluated by DFT calculations. The calculations revealed the following: 1) the insertion step in monodentate pathway was the rate-determining step, 2) the high LAE effect of the novel ligand was due to a facile change of conformation from trans to cis form and flexibility to avoid steric repulsion between substrate and catalyst in the insertion step as well.

A rare complex mutation in FMF gene; genetics and treatment decisions in Familial Mediterranean Fever patients

Introduction: FMF is an autosomal-recessive autoinflammatory disease characterized by episodic, self-limiting attacks characterized by fever, abdominal pain, pleurisy, arthritis and erysipelas-like-erythema. Systemic amyloidosis is the most severe manifestation of the disease. Case: 3 year old patient for evaluation of FMF who was referred because of gastrointestinal symptoms and a paternal family history of FMF. He had a number of gastrointestinal symptoms as an infant up to the age of 8 months, since the age of 1 year the patient had had 2 episodes each lasting 2 months, during which he would be sick every week with fever and severe abdominal pain and vomiting. The patient met the criteria for FMF based on the criteria from the Sheba medical center of Tel Hashomer in Israel. The patient was determined to have rare heterozygous complex mutation with E148Q-P369S-R408Q in cis state. Testing of his parents revealed that he had inherited all of the mutations from his mother despite the paternal familial history of FMF. Since amyloidosis is rare in Ashkenazi families and due to absence of mutations liked with high risk of amyloidosis, it was determined that he did not need chronic colchicine therapy. To best of our knowledge this is the third reported case of FMF with this gene complex and the first reported case in a patient of Shephardic and Ashkenazi Jewish ancestry. Conclusion: E148Q, P369S and R408Q when present separately are associated with a mild phenotype and incomplete penetrance, but when present together in cis form on same allele may lead to increased penetrance and clinical disease.

THE EFFECT OF INTRAMOLECULAR H-BOND INTERACTIONS IN THE ISOMERIZATION PROCESS IN AMINO ACIDS

The effect of intramolecular hydrogen bond (H-bond) interactions in the cis - trans isomerization of the amino acids such as, cysteine, serine, threonine and valine have been studied using density functional theory method. Our calculations have shown that the geometrical parameters are significantly changed during the isomerization process. This is due to the presence of intramolecular H-bonds within main chain or in between side chain and main chain. The barrier energies have been calculated for isomerization process in all the amino acids, which is more for cysteine and less for valine. The Fourier decomposition potential has been obtained for the above named amino acids which show that V2 potential has higher value. The vibrational frequency analysis has been carried out for the cis and trans forms of cysteine, serine, threonine and valine amino acids and the results are discussed.

Solid‐state polymerization process for the preparation of poly(cyclohexane‐1,4‐dimethylene cyclohexane‐1,4‐dicarboxylate) polymers with high melting temperature and crystallinity

Poly(cyclohexane‐1,4‐dimethylene cyclohexane‐1,4‐dicarboxylate) has been prepared by solid‐state polymerization using 1,4‐cyclohexanedicarboxylic acid or its di‐methylester and 1,4‐cyclohexanedimethanol as monomers. The process consists in a first step in which a prepolymer with high crystallinity is prepared by melt polycondensation and then submitted to solid‐state polymerization (SSP) at a temperature below the melting temperature of the polymer. The use of the solid state process permits to minimize the isomerization from the trans to the cis form in the polymer chain and therefore a polyester with higher crystallinity and melting temperature, compared to those synthesized by the traditional polycondensation routes, can be obtained. For this reason, the SSP process allows to obtain materials with thermo‐mechanical properties that cannot be achieved using the standard polycondensation method. Moreover, the process does not involve a complex multi‐step temperature ramp as in the case of the polycondensation process. POLYM. ENG. SCI., 58:1981–1986, 2018. © 2017 Society of Plastics Engineers

Genetic toxicological comparison of nano- and micro-sized iron oxide nanoparticles

The cis- (5 and 6) and trans-dispiroferrocenylphosphazenes (7 and 8) containing ferrocenyl pendant arms were synthesized from the reactions of hexachlorocyclotriphosphazene, N3P3Cl6, with two equimolar amounts of the sodium salts of the ligands; [2-(N-ferrocenylmethylamino)-1-ethanoxide (1) and 3-(N-ferrocenylmethylamino)-1-propanoxide (2)]. The monospiroferrocenylcyclotriphosphazenes (3 and 4) were also isolated from the reaction mixtures as by-products. The characterizations of the new compounds (5–8) were elucidated using MS, FTIR and 1H, 13C and 31P NMR techniques. The molecular structure of 6 was established by X-ray crystallography. As expected, compounds 5, 6, 7 and 8 have two stereogenic P-atoms. The compounds 5 and 6 are likely to be in cis (meso) forms, whereas the compounds 7 and 8 are in trans (racemic) forms. Besides, the antimicrobial activities of the cyclotriphosphazenes against G(+) and G(−) bacteria and fungi were evaluated. The interactions of the compounds with pBR322 plasmid DNA were also investigated.

Electromagnetic Field of Plasmonic Nanoparticles Extends the Photoisomerization Lifetime of Azobenzene

The thermodynamically stable azobenzene trans conformation photoisomerizes to the cis form on an ultrashort time scale when photoirradiated with photons of sufficient energy. Irradiating p,p′-dimercaptoazobenzene (DMAB) adsorbed on the surface of plasmonic nanoparticles with a 532 nm laser led to the appearance of Raman bands corresponding to a ring stretching. The torsion of DMAB during the photoisomerization is responsible for the appearance of the ring stretching, which disappeared after several minutes. Colloidally prepared gold nanorods (AuNRs) are assembled into two-dimensional (2-D) arrays on the surface of a glass substrate. AuNR 2-D arrays on a glass substrate are coated with silver half-shells (AgHAuNRs) of different thicknesses. The irradiation time required to induce the isomerization of DMAB adsorbed on the surface of AgHAuNRs and the lifetime of the isomerization is increased by increasing the thickness of the silver layer. The plasmon field calculated with the discrete-dipole approximation ...

Protonation-Enhanced Antiferromagnetic Couplings in Azobenzene-Bridged Diradicals

Proton-induced magnetic enhancement in an organic diradical is an appealing phenomenon. Here, taking two nitroxide groups as spin sources, we predict the magnetic properties of the trans and cis forms of azobenzene (AB)-bridged diradicals in which the central −N═N– unit can undergo single protonation to convert to its protonated counterpart or vice versa. The calculated results for these two pairs of diradicals (protonated versus unprotonated trans and cis forms) indicate that the signs of their magnetic coupling constants J do not change, but the magnitudes remarkably increase after protonation from −716.4 to −1787.1 cm–1 for the trans form and from −388.1 to −1227.9 cm–1 for the cis form, respectively. Such noticeable magnetic enhancements induced by protonation are mainly attributed to the strong mediating role of the coupler AB between two radical groups through its lowest unoccupied molecular orbital (LUMO) with a lower energy level after protonation. The planar structure for the protonated trans dir...

Smart Biointerface with Photoswitched Functions between Bactericidal Activity and Bacteria-Releasing Ability.

Smart biointerfaces with capability to regulate cell-surface interactions in response to external stimuli are of great interest for both fundamental research and practical applications. Smart surfaces with "ON/OFF" switchability for a single function such as cell attachment/detachment are well-known and useful, but the ability to switch between two different functions may be seen as the next level of "smart". In this work reported, a smart supramolecular surface capable of switching functions reversibly between bactericidal activity and bacteria-releasing ability in response to UV-visible light is developed. This platform is composed of surface-containing azobenzene (Azo) groups and a biocidal β-cyclodextrin derivative conjugated with seven quaternary ammonium salt groups (CD-QAS). The surface-immobilized Azo groups in trans form can specially incorporate CD-QAS to achieve a strongly bactericidal surface that kill more than 90% attached bacteria. On irradiation with UV light, the Azo groups switch to cis form, resulting in the dissociation of the Azo/CD-QAS inclusion complex and release of dead bacteria from the surface. After the kill-and-release cycle, the surface can be easily regenerated for reuse by irradiation with visible light and reincorporation of fresh CD-QAS. The use of supramolecular chemistry represents a promising approach to the realization of smart, multifunctional surfaces, and has the potential to be applied to diverse materials and devices in the biomedical field.

Distinguishing Cis and Trans Isomers in Intact Complex Lipids Using Electron Impact Excitation of Ions from Organics Mass Spectrometry.

We present a mass spectrometry-based method for the identification of cis and trans double-bond isomers within intact complex lipid mixtures using electron impact excitation of ions from organics (EIEIO) mass spectrometry. EIEIO involves irradiating singly charged lipid ions with electrons having kinetic energies of 5-16 eV. The resulting EIEIO spectra can be used to discern cis and trans double-bond isomers by virtue of the differences in the fragmentation patterns at the carbon-carbon single bonds neighboring the double bonds. For trans double bonds, these characteristic fragments include unique closed-shell and open-shell (radical) products. To explain this fragmentation pattern in trans double bonds, we have proposed a reaction mechanism involving excitation of the double bond's π electrons followed by hydrogen atom rearrangement. Several lipid standards were analyzed using the EIEIO method, including mixtures of these standards. Prior to EIEIO, some of the lipid species in these mixtures were separated from their isomeric forms by using differential mobility spectrometry (DMS). For example, mixed cis and trans forms of triacylglycerols and phosphatidylcholines were identified by this DMS-EIEIO workflow. With this combined gas-phase separation and subsequent fragmentation, we could eliminate the need for authentic standards for identification. When DMS could not separate cis and trans isomers completely, as was the case with sphingomyelins, we relied upon the aforementioned diagnostic EIEIO fragment peaks to determine the relative contribution of the trans double-bond isomer in the mixed samples. We also applied the DMS-EIEIO methodology to natural samples extracted from a ruminant (bovine), which serve as common origins of trans fatty acids in a typical Western diet that includes dairy products.

First-principles study on photoswitching behavior and negative differential resistance in single molecule junction

We investigate the electronic transport of a photochromic molecule, a 1,2-dithienyl-1,2-dicyanoethene sandwiched between two Au electrodes using first-principles based on non-equilibrium Green’s function and density functional theory. This molecule can be reversibly transformed between trans and cis state through irradiation. The calculated current of the cis form is larger than the trans form, indicating an obvious switching behavior in the present device. We discuss the electronic transport properties for cis and trans forms in detail by the transmission spectra and molecular projected self-consistent Hamiltonian states. The observed negative differential resistance effect in the cis form is explained discussing the transmission eigenstates of HOMO energy level. The results suggest that this photochromic molecule can become one of the good candidates for single molecular photoswitching in the future.

Tuning Luminescence and Conductivity through Controlled Growth of Polymorphous Molecular Crystals

AbstractClear structure–property correlation is of crucial importance for molecular materials for optical and electronic application. Here, a new intramolecular charge transfer compound (E)‐2‐{4‐[4‐(9H‐carbazol‐9‐yl)styryl]benzylidene}malononitrile (TCBR) with a dicyanovinyl group as the electron acceptor and a carbazole group as the electron donor is designed and synthesized. Four different single crystals based on the cis and trans isomeric forms of this compound are grown simultaneously, which are both kinetically and thermodynamically stable. The different packing modes give rise to a dynamic crystal structure change, leading to dramatically different optical and electronic properties. The closer packing can effectively promote the π–π interactions to increase the exciton coupling and orbital overlap between neighbor molecules in crystals, which produces a redshift fluorescence emission and good conductivity. This permits one to tune the packing molecules in the solid state to specific applications in a more precise way. The results of this study highlight the power of designing new functional molecules for optical and electronic applications.

FTIR Analysis of a Light-driven Inward Proton-pumping Rhodopsin at 77 K.

Parvularcula oceani xenorhodopsin (PoXeR) is a light-driven inward proton pump that was discovered from deep ocean marine bacteria. PoXeR is categorized into the same family of Anabaena sensory rhodopsin (ASR) that functions as a photochromic sensor. In this study, we applied light-induced difference Fourier-transform infrared (FTIR) spectroscopy to PoXeR at 77 K, and the obtained spectra were compared with those of ASR. The structure and structural changes in the primary processes of PoXeR are common to all microbial rhodopsins. The red-shifted K formation (PoXeRK ) was accompanied by retinal photoisomerization from the all-trans to 13-cis form resulting in a distorted structure of the retinal. The observed hydrogen out-of-plane (HOOP) vibrations were sensitive to H/D exchange, indicating that the chromophore distortion by retinal isomerization is located near the Schiff base region in PoXeR. The hydrogen-bonding strength of the protonated Schiff base is similar between PoXeR and ASR, whose acceptor is presumably a water molecule. Unlike ASR, however, PoXeR contains strongly hydrogen-bonded water (O-D stretch at 2277 cm-1 in D2 O), which is also the case for outward proton pumps. The detailed structure, structural changes upon retinal photoisomerization, as well as functional correlation in PoXeR are discussed based on the present FTIR study.

Reactivity of 4‐Pyridyltellurolate with Pd(II)/Pt(II) Complexes

AbstractReactions of 4‐pyridyltellurolate with various palladium and platinum complexes have been investigated. Treatment of MCl2(dppe) and two equivalents of Na(4‐TeC5H4N) gave cis‐[M(4‐TeC5H4N)2(dppe)] (M=Pd (1), Pt (2)). Similar reactions of MCl2(dppm) exclusively yielded unexpected products, [Pd2(μ3‐Te)(μ2‐4‐TeC5H4N)(4‐TeC5H4N)(μ‐dppm)]2 (M=Pd (3)) and [Pt{(Ph2P)2C(4‐TeC5H4N)}2] (M=Pt (4)). The cis and trans forms of [PdCl(4‐TeC5H4N)(PPh3)]2 (6 a, 6 b) could be isolated from the reaction of polymeric complex [PdCl2(4,4′‐(C5H4N)2Te2)]n (5) and PPh3. All the phosphine complexes have been characterized by NMR and X‐ray crystallography. Complex 3 contains bridging dppm ligand whereas 4 is formed via deprotonation of methylene carbon of dppm ligand.

Effects of ageing on stilbenes and biogenic amines in red grape winemaking with stem contact maceration

Stem contact maceration is a technique used in red winemaking for wines poor of phenolic constituents (tannins) in order to improve organoleptic characteristics and ensure color stability over time. This article investigates how the presence of different amounts of de-stemmed bunches affects stilbenoids, known for their nutraceutical properties and biogenic amines (BAs), known for their adverse physiological and toxicological effects, at racking and after 24 months of storage in Primitivo wine. Stilbenes found in Primitivo were not influenced by the stems during maceration/fermentation. The ageing period resulted in isomerization phenomena of trans forms of piceid and resveratrol to the corresponding cis forms. The presence of stems during the winemaking did not induced the production or enhanced BAs content. Therefore, this enological practice does not represent a limit in terms of food safety and product quality. Practical applications Red wines poor in proanthocyanidins are subjected to color loss and decrease of organoleptic properties over time. Stem contact maceration is a technique used in red winemaking in order to enforce structure and stabilize color over time. Since food safety and product quality are of paramount importance, this study for the first time examines the presence of dangerous biogenic amines (BAs) and potent antioxidant stilbenoids throughout the production and aging of red wines produced with this technique. Results may benefit the winemaking industry and researchers who are striving to improve the processing and marketing of red wine.

Effects of hydrogen bonding between pyrrole-2-carboxaldehyde and nearest polar and nonpolar environment

The present paper represents dominant effects of hydrogen bonding on the existence of different molecular aggregates in one of the heterocyclic pyrrole system: pyrrole-2-carboxaldehyde (PCL). Theoretical and experimental Raman spectral evidence verifies the existence of different molecular aggregates like dimeric, monomeric, hydrated complex states in PCL. Atoms in molecules (AIMs) analysis and fluorescence decay profile provide a strong signature of intermolecular hydrogen bonding (IerHB) as the possible reason for the existence of cis form of dimeric (X) molecular aggregates. The high remnant polarization of 3.13μCcm−2 and smaller dielectric loss in solid form of PCL arise due to in X by ordering of dipoles as a result of IerHB. A remarkable high ferroelectric response in solid phase makes PCL a desirable candidate to be used as raw material for energy storage devices. For solution phase, in presence of external hydroxylic environment, PCL reacts with external water molecules through weak IerHB and creates different hydrated PCL/(H2O)n complexes by creating water bridge with number of water molecules from 1 to n. An increasing number of water molecules helps to form stronger hydrated complex by separation of charges by lowering the transferring energy barrier.

A Study of Electrocyclic Reactions in a Molecular Junction: Mechanistic and Energetic Requirements for Switching in the Coulomb Blockade Regime.

Molecular photoswitches incorporated in molecular junctions yield the possibility of light-controlled switching of conductance due to the electronic difference of the photoisomers. Another isomerization mechanism, dark photoswitching, promoted by a voltage stimulus rather than by light, can be operative in the Coulomb blockade regime for a specific charge state of the molecule. Here we elucidate theoretically the mechanistic and thermodynamic restrictions for this dark photoswitching for donor-acceptor substituted 4n and 4n+2 π-electron open-chain oligoenes (1,3-butadiene and 1,3,5-hexatriene) by considering the molecular energies and orbitals of the molecules placed in a junction. For an electrocyclic ring closure reaction to occur for these compounds, we put forward two requirements: a) the closed stereoisomer (cis or trans form) must be of lower energy than the open form, and b) the reaction pathway must be in accordance to the orbital symmetry rules expressed by the Woodward-Hoffmann rules (when the electrodes do not significantly alter the molecular orbital appearances). We find these two requirements to be valid for the dianion of (1E,3Z,5E)-hexa-1,3,5-triene-1,6-diamine, and the Coulomb blockade diamonds were therefore modeled for this compound to elucidate how a dark photoswitching event would manifest itself in the stability plot. From this modeling of conductance as a function of gate and bias potentials, we predict a collapse in Coulomb diamond size, that is, a decrease in the height of the island of zero conductance.