Cis Isomerization Research Articles

Theoretical study on the isomerization process of retinal in gas and aqueous phase

B3LYP/6-311++G(d,p) level of theory was carried out to explain the isomerization process of retinal stereoisomer based on the structural and molecular properties in gas phase and implicit aqueous environment. Frequency calculations on the fully optimized molecular geometries of the retinal isomers confirmed them to be true minima. The relative energies, dipole moments, bond orders, theoretically predicted vibrational frequencies, and HOMO–LUMO energy gaps of the retinal isomers were analyzed. The influence of the explicit aqueous environment on the geometrical parameters associated with the geometry of polyene chain and the vibrational spectra of retinal isomers were evident. The geometries of 11-cis and all-trans retinal isomers exhibited delocalized bonds along the polyene chain in the aqueous phase with a pattern of longer double bonds and shorter single bonds. The vibrational frequencies of the retinal isomers calculated at the B3LYP level of theory were in better agreement with the experimental values in the gas phase. The method and results presented in this study may help to better understand the effects of environment on its isomerization process.

Emissive Azobenzenes Delivered on a Silver Coordination Polymer.

Azobenzene has become a ubiquitous component of functional molecules and polymeric materials because of the light-induced trans → cis isomerization of the diazene group. In contrast, there are very few applications utilizing azobenzene luminescence, since the excitation energy typically dissipates via nonradiative pathways. Inspired by our earlier studies with 2,2'-bis[ N,N'-(2-pyridyl)methyl]diaminoazobenzene (AzoAM oP) and related compounds, we investigated a series of five aminoazobenzene derivatives and their corresponding silver complexes. Four of the aminoazobenzene ligands, which exhibit no emission under ambient conditions, form silver coordination polymers that are luminescent at room temperature. AzoAE pP (2,2'-bis[ N,N'-(4-pyridyl)ethyl]diaminoazobenzene) assembles into a three-dimensional coordination polymer (AgAAE pP) that undergoes a reversible loss of emission upon the addition of metal-coordinating analytes such as pyridine. The switching behavior is consistent with the disassembly and reassembly of the coordination polymer driven by displacement of the aminoazobenzene ligands by coordinating analytes.

3D structural analysis of copper(II) complex of glycine – Experimental mass spectrometric and theoretical quantum chemical approach

The focus on this paper is on to continue the research line taken in our more recent studies of mass spectrometric approaches treating quantitatively the intensity of analyte fragment peaks with respect to time within the own model equation, based on stochastic dynamics, and correlating between experimental diffusion parameters of ions and their 3D structures, when this approach is used complementary with high accuracy methods of quantum chemistry. Accordingly, the aims at the work will be undeniably presented. First, we will explore ESI–MS in solution, operating under positive mode and crystallographic data of a CuII–complex of glycine (cis–{[CuII(Gly)2].H2O} (1)) in determining experimental MS diffusions of ions according to the aforementioned methodology. The correlative analysis to quantum chemical diffusions will be carried out, using the Arrhenius' approximation to the theoretical diffusion of charged species under soft–ionization MS conditions. Second, on the base on experimentally observed complex isotope shape of coordination species of ions of copper, a theoretical description of redox processes under ESI–MS conditions will be detailed. There is nothing irreconcilable between both goals, as far as, the experimental data convincingly argued that the relation to MS stochastic dynamic diffusions ⇔ quantum chemical diffusion parameters has direct bearing on how the analysis of the MS intensity of isotope sub–peaks within the aforementioned method can provide direct information about experimental 3D structure of the analyte in condense phase. The cis/trans isomerization of {[CuII(Gly)2]} complex is discussed in detail correlating crystallographic data of (1) with ESI(+)–MS ones. A process of isomerization cis–{[CuII(gly)2]0} → trans–{[CuII(gly)2+H]+} is proposed on the base on crystallographic and mass spectrometric data on (1).

Photo-responsive foam control base on nonionic azobenzene surfactant as stabilizer

A nonionic photo-responsive surfactant (NPS) was synthesized for obtaining photo control of foamability, exposed in ultraviolet (UV) light or visible (Vis) light irradiation. The foamability depended on the surface activity of NPS, which possessed low critical micelle concentration (CMC) and high adsorption capacity compared with the similar type of nonionic surfactants. The azobenzene component in NPS as the light-responsive group, showed high sensitive and reversibility, i.e., the trans → cis isomerization occurred only for 1 s and the time to reach reversible isomerization was 85 s. And the fatigue resistance of isomerization was also outstanding, which remained stable for 14 cycles of alternate irradiation. Due to the lack of free volume and increase of barrier for isomerization, the irradiation time and first-order kinetics of isomerization decreased with the increase of NPS concentration. The foaming ratio and foam stability promoted with the NPS concentration increase, however, the stereospecific blockade amongst cis isomers was stronger than that of trans isomers, resulting in the steep decrease of foam half-life. The sustainable foam stability control of NPS applied into foam dyeing to solve the problem of residual foam.

Fluorescence modulation of CdTe nanowire by azobenzene photochromic switches

Photoinduced electron transfer (ET) and Forster Resonance Energy Transfer (FRET) between azobenzene derivatives (Quencher) and CdTe nanowires have been investigated. Needle-like cadmium telluride (CdTe) 1D nanowires were successfully prepared. The surface modification was done by the capping agent 3-marcaptopropanoic acid (MPA) and NH3. The azobenzene derivatives (E)-5-((4-chlorophenyl) diazenyl)-2-hydroxybenzaldehyde Q(I) and (E)-4-((3-formyl-4-hydroxyphenyl) diazenyl) benzene sulfonic acid Q(II) have been prepared and glued to MPA capped CdTe nanowires. After UV treatment, the azo compounds Q(I) and Q(II) experience a reversible trans–cis isomerization. The photoinduced trans to cis change supports the transfer of electrons from the conduction band (CB) of the CdTe nanowires to the lowest unoccupied molecular orbital (LUMO) of cis isomer of the azo compounds and the overlapping absorbance spectra of acceptor (QI & QII) with the emission spectrum of donor (CdTe nanowires) also suggests quenching of PL due to Forster energy transfer (FRET). Using steady state (SSPL) and time resolved fluorescence (TRPL) measurements, we have noticed that with the increase in Quencher (I) & (II) concentrations, the fluorescence is quenched with a subsequent decrease in decay life time. Hence fluorescence can be modulated at different quencher concentrations.

Charge Transfer Driven Structural Relaxation in a Push-Pull Azobenzene Dye-Semiconductor Complex.

Photoexcited structural dynamics in azo-compounds may differ fundamentally whether the push-pull photochromic azo-compound is isolated or forms a heterogeneous charge transfer complex, due to a sudden oxidation of the chromophore. Herein, we use a quantum-classical self-consistent approach that incorporates nonadiabatic excited-state electronic quantum dynamics into molecular mechanics to study the photoexcited dynamics of the push-pull azo-compound para-Methyl Red in the gas phase and sensitizing the (101) anatase surface of TiO2. We find that the photoinduced S2/S0 trans-to- cis isomerization of para-Methyl Red in the gas phase occurs through a pedal-like torsion around the ϕCNNC dihedral angle, without evidence to support the inversion mechanism, likewise in the parent azobenzene molecule. However, the photoexcited structural relaxation of the charge transfer complex para-Methyl Red/TiO2 contrasts essentially with the isolated azo-compounds. Immediately after photoexcitation, the excited electron flows into the TiO2 conduction band, with an injection time constant of ≃5 fs, and no indication of isomerization is observed during the 1.5 ps simulations. Instead, a strong vibronic relaxation occurs that excites the NN stretching mode of the azo-group, which is ultimately ascribed to the NA relaxation, and delocalization, of the hole wavepacket.

Role of Photoisomerization on the Photodetachment of the Photoactive Yellow Protein Chromophore

The photocycle of photoactive yellow protein (PYP) is initiated by a photoinduced trans-cis isomerization around a C═C bond in the chromophore that lies at the heart of the protein; however, in addition to the desired photochemical pathway, the chromophore can undergo competing electronic relaxation processes. Here we combine gas-phase anion photoelectron spectroscopy and quantum chemistry calculations to investigate how locking the C═C bond in the chromophore controls the competition between these electronic relaxation processes following photoexcitation in the range 400-310 nm. We find evidence to suggest that preventing trans-cis isomerization effectively turns off internal conversion to the ground electronic state and enhances electron emission from the first electronically excited state.

Unique Stereoselective Homolytic C-O Bond Activation in Diketopiperazine-Derived Alkoxyamines by Adjacent Amide Pyramidalization.

Simple monocyclic diketopiperazine (DKP)-derived alkoxyamines exhibit unprecedented activation of a remote C-O bond for homolysis by amide distortion. The combination of strain-release-driven amide planarization and the persistent radical effect (PRE) enables a unique, irreversible, and quantitative trans→cis isomerization under much milder conditions than typically observed for such homolysis-limited reactions. This isomerization is shown to be general and independent of the steric and electronic nature of both the amino acid side chains and the substituents at the DKP nitrogen atoms. Homolysis rate constants are determined, and they significantly differ for both the labile trans diastereomers and the stable cis diastereomers. To reveal the factors influencing this unusual process, structural features of the kinetic trans diastereomers and thermodynamic cis diastereomers are investigated in the solid state and in solution. X-ray crystallographic analysis and computational studies indicate substantial distortion of the amide bond from planarity in the trans-alkoxyamines, and this is believed to be the cause for the facile and quantitative isomerization. Thus, these amino-acid-derived alkoxyamines are the first examples that exhibit a large thermodynamic preference for one diastereomer over the other upon thermal homolysis, and this allows controlled switching of configurations and configurational cycling.

New trans-[Pd(L-κS,O)2] complexes from N,N-dialkyl-N′-aroylthioureas prepared by photo-induced isomerization of their cis-[Pd(L-κS,O)2] counterparts and their thermal trans-cis isomerization

Photo-induced isomerization of cis-[Pd(L1,2-κS,O)2] (HL1 = N,N-diethyl-N′-4-methyl-benzoylthiourea, HL2 = N,N-dimethyl-N′-benzoylthiourea) in acetonitrile solution leads to the reproducible and clean isomerization of rare, new trans-[Pd(L1,2-κS,O)2] complexes, isolated by vapour diffusion crystallization and characterized by single-crystal X-ray diffraction. The isolated trans-[Pd(L1,2-κS,O)2] complexes show higher melting points to the corresponding cis-[Pd(L1,2-κS,O)2] precursors. Time resolved 1H NMR spectroscopy of the isolated trans-[Pd(L1,2-κS,O)2] complexes in chloroform, shows these to spontaneously revert to their cis-[Pd(L1,2-κS,O)2] counterparts in the absence of light by a simple first-order process at relative rates of the order k1 = 0.23 × 10−2 min−1 and k2 = 0.18 × 10−2 min−1 respectively. The reversion trans → cis of these complexes is confirmed also in acetonitrile using reversed-phase HPLC following irradiation of dilute solutions with polychromatic light, at higher relative rates of k1 = 2.6 × 10−2 min−1 and k2 = 4.9 × 10−2 min−1 respectively.

Reversible Photo- and Thermoresponsive, Self-Assembling Azobenzene Containing Zwitterionic Polymers.

Commercially available azo dyes bearing amino groups were grafted to zwitterionic copolymers composed of cyclic anhydride functionality. The zwitterionic copolymers were prepared for the first time by polymerizing sulfobetaine (SB) monomer with maleic anhydride (MA) under conventional free radical polymerization as well as reversible addition-fragmentation chain transfer (RAFT) polymerization. Poly(SB- co-MA) self-assembled in deionized water. Azobenzene grafted zwitterionic poly((SB- co-MA)- g-Azo) exhibited multiresponsive behavior. As confirmed by UV-vis spectroscopy, trans → cis isomerization of the azo group was responsible for the photo- and thermal responsive behavior. The photoisomerization was reversible, and no photoaging was detected during the repeated exposure to UV and visible light. The water-soluble nature of photoresponsive azo dye grafted copolymers makes it suitable for applications in biological systems.

Intersystem Crossing as a Key Component of the Nonadiabatic Relaxation Dynamics of Bithiophene and Terthiophene.

We present a nonadiabatic dynamics study concerning the subpicosecond relaxation of excited states in dimeric and trimeric thiophene chains. The influence of the triplet states in the overall process is, for the first time, taken into account by explicitly including spin-orbit couplings and hence allowing intersystem crossing phenomena. We observe the fundamental role of the triplet state manifold in driving the full relaxation process. In particular we evidence the effect of both, inter-ring rotation and ring-opening, in the process, as compared to the monomer, where the ring-opening process appears as the dominant one. In addition, the evolution of the open structures allows for trans to cis isomerization in the dimer and trimer. The overall relaxation process slows down with chain elongation. The complex decay mechanism characterized by the presence of different competing channels, due to the presence of a quasi degenerate manifold, is explained allowing the rationalization of oligothiophenes photophysics.

Switching behavior induced by different substituents of group in single molecular device

We investigate the electronic transport properties of photochromic azobenzene-based molecular devices with Au electrodes using non-equilibrium Green’s function and density functional theory. A reversible switching behavior between cis and trans isomerization is found in the device. In addition, the substituent of −NH2 on the right end hydrogen atom of azobenzene molecule reduces the switching ratio of current, consequently the disappearance of switching behavior, while the substituent of −NO2 improves the switching ratio of current. We discuss the different electronic transport induced by different substituents through the transmission spectra, localized density of states, molecular projected self-consistent Hamiltonian and transmission pathways. The observed polarization effect under bias is explained by the evolution of molecular projected self-consistent Hamiltonian of LUMO level. The results indicate that the electron-withdrawing group −NO2 substituting right terminal hydrogen of azobenzene molecule becomes a candidate for improving the performance of molecular device.

From nanoscopic to macroscopic photo-driven motion in azobenzene-containing materials

Abstract The illumination of azobenzene molecules with UV/visible light efficiently converts the molecules between trans and cis isomerization states. Isomerization is accompanied by a large photo-induced molecular motion, which is able to significantly affect the physical and chemical properties of the materials in which they are incorporated. In some material systems, the nanoscopic structural movement of the isomerizing azobenzene molecules can be even propagated at macroscopic spatial scales. Reversible large-scale superficial photo-patterning and mechanical photo-actuation are efficiently achieved in azobenzene-containing glassy materials and liquid crystalline elastomers, respectively. This review covers several aspects related to the phenomenology and the applications of the light-driven macroscopic effects observed in these two classes of azomaterials, highlighting many of the possibilities they offer in different fields of science, like photonics, biology, surface engineering and robotics.

Azobenzene Adsorption on the MoS2(0001) Surface: A Density Functional Investigation within van der Waals Corrections

The interest in light-sensitive organic molecules, such as azobenzene, has increased because of their ability to functionalize two-dimensional layered systems and engineer their electronic structure. In this work, we explore the azobenzene trans and cis isomer adsorption on a molybdenum disulfide MoS2(0001) layer employing the density functional theory (DFT) within van der Waals (vdW) corrections to the semilocal exchange–correlation functional. We found that the aromatic rings of azobenzene lay parallel to the surface (two in the trans isomer and one in the cis isomer), which contributes to increasing the configuration stability by vdW interactions. Furthermore, we found a relatively large work function change upon adsorption because of the electron density rearrangement, and hence, it might affect the electronic transport properties within the single MoS2(0001) layer. We observed an increase in the relative DFT + vdW total energy among the azobenzene isomers (trans and cis) from 0.51 eV in the gas-phase...

Laser spectroscopic study on sinapic acid and its hydrated complex in a cold gas phase molecular beam

The S1 (ππ∗)-S0 electronic spectrum and the infrared spectrum in the OH stretching region of sinapic acid (SA) and its 1:1 complex with water (SA-H2O) are observed in a supersonically cooled molecular beam. Supersonically-cooled SA and SA-H2O complex are obtained by a combination of laser ablation with a newly developed pulsed channel nozzle. Both SA and SA-H2O exhibit sharp electronic spectra, and measurements of UV-UV hole-burning spectra and time-dependent density functional theory (TD-DFT) calculation indicate that the observed vibronic bands belong to two conformers, syn and anti, in both SA and the SA-H2O complex. The OH stretching vibrations are observed with IR-UV double resonance spectroscopy. A comparison of the observed IR spectrum and the DFT-calculated one indicates that SA-H2O has the structure in which a carboxylic (COOH) group and the water form a cyclic hydrogen (H)-bond. The OH stretch of COOH is red-shifted as large as 600 cm−1 in the complex. The S1 lifetime of SA at the zero-point energy level is obtained to be 1.9 ns. This S1 lifetime is shorter than the reported one of its ester derivative (methyl sinapate, MS (Dean et al., J. Am. Chem. Soc. 136 (2014) 1478–14795)) but is much longer than the para-substituted cinnamates, p-hydroxy methylcinnamate (p-HMC (Shimada et al., Phys. Chem. Chem. Phys. 14 (2012) 8999–9005)) and p-methoxy methylcinnamate (p-MMC (Miyazaki et al., J. Chem. Phys. 141 (2014) 244313)). A calculation at TD-DFT level indicates that this long lifetime of SA is due to that the 1nπ∗ state and the transition states along the trans → cis isomerization in S1 (ππ∗) are located much higher in energy than p-HMC and p-MMC. This may lead a main nonradiative channel of SA in the low energy region to be the multistep intersystem crossing to T1 (3ππ∗) via the 3nπ∗ state.

The π-conjugation length determines the fluorescence quenching mechanism of aromatic aldehydes in water

Water-soluble distyrylbenzene-based aldehydes are excellent fluorescence turn-on indicators for amine detection, since they are themselves non-fluorescent in water. Here, the fluorescence quenching mechanisms of aldehydes with systematically increasing π-systems are investigated in an aqueous environment using quantum chemical methods. Although the aldehydes are structurally related, with each extension of the π-system the fluorescence quenching mechanism changes from excited-state hydrogen transfer to trans→cis isomerization and nπ∗ state-mediated intersystem crossing, until the aldehydes become fluorescent in water. For distyrylbenzene aldehyde, nπ∗ mediated ISC has been identified as major fluorescence quenching channel, which becomes closed upon reaction with an amine explaining its fluorescence turn-on sensitivity.

Conformationally Regulated Peptide Bond Cleavage in Bradykinin.

Ion mobility and mass spectrometry techniques are used to investigate the stabilities of different conformations of bradykinin (BK, Arg1-Pro2-Pro3-Gly4-Phe5-Ser6-Pro7-Phe8-Arg9). At elevated solution temperatures, we observe a slow protonation reaction, i.e., [BK+2H]2++H+ → [BK+3H]3+, that is regulated by trans → cis isomerization of Arg1-Pro2, resulting in the Arg1- cis-Pro2- cis-Pro3-Gly4-Phe5-Ser6- cis-Pro7-Phe8-Arg9 (all- cis) configuration. Once formed, the all- cis [BK+3H]3+ spontaneously cleaves the bond between Pro2-Pro3 with perfect specificity, a bond that is biologically resistant to cleavage by any human enzyme. Temperature-dependent kinetics studies reveal details about the intrinsic peptide processing mechanism. We propose that nonenzymatic cleavage at Pro2-Pro3 occurs through multiple intermediates and is regulated by trans → cis isomerization of Arg1-Pro2. From this mechanism, we can extract transition state thermochemistry: Δ G‡ = 94.8 ± 0.2 kJ·mol-1, Δ H‡ = 79.8 ± 0.2 kJ·mol-1, and Δ S‡ = -50.4 ± 1.7 J·mol-1·K-1 for the trans → cis protonation event; and, Δ G‡ = 94.1 ± 9.2 kJ·mol-1, Δ H‡ = 107.3 ± 9.2 kJ·mol-1, and Δ S‡ = 44.4 ± 5.1 J·mol-1·K-1 for bond cleavage. Biological resistance to the most favored intrinsic processing pathway prevents formation of Pro3-Gly4-Phe5-Ser6- cis-Pro7-Phe8-Arg9 that is approximately an order of magnitude more antigenic than BK.

Polarisation-free and high-resolution holographic grating recording and optical phase conjugation with azo-dye doped blue-phase liquid crystals

ABSTRACTWe present the results of a detailed study of the mechanism and dynamics of holographic Bragg grating formation in azo-dye doped blue-phase liquid crystals. The principal mechanism leading to refractive index modulation is lattice distortion caused by photo-activated trans–cis isomerism of the azo-dye dopant. High diffraction efficiency bulk (Bragg) gratings with grating spacing as small as 1 μm can be written with low optical power and do not require specific optical field polarisation. Furthermore, the written grating can be prolonged by uniform illumination with another laser, instead of being erased. Azo-doped blue-phase liquid crystals thus present themselves as highly promising photosensitive materials for high-resolution holographic recording and image processing application. An experimental demonstration of holographic image reconstruction via optical phase conjugation with excellent aberration correction capability is presented.

Mapping reversible photoswitching of molecular resistance fluctuations during the conformational transformation of azobenzene-terminated molecular switches

We report a direct mapping and analysis of electrical noise in azobenzene-terminated molecular monolayers, revealing reversible photoswitching of the molecular resistance fluctuations in the layers. In this work, a conducting atomic force microscope combined with a homemade spectrum analyzer was used to image electrical current and noise at patterned self-assembled monolayers (SAMs) of azobenzene-terminated molecular wires on a gold substrate. We analyzed the current and noise imaging data to obtain maps of molecular resistances and amount of mean-square fluctuations in the resistances of the regions of trans-azobenzene and a cis/trans-azobenzene mixture. We revealed that the fluctuations in the molecular resistances in the SAMs were enhanced after the trans–to–cis isomerization, while the resistances were reduced. This result could be attributed to enhanced disorders in the molecular arrangements in the cis-SAMs. Furthermore, we observed that the changes in the resistance fluctuations were reversible with respect to repeated trans–to–cis and cis–to–trans isomerizations, indicating that the effects originated from reversible photoswitching of the molecular structures rather than irreversible damages of the molecules. These findings provide valuable insights into the electrical fluctuations in photoswitchable molecules, which could be utilized in further studies on molecular switches and molecular electronics in general.

Thermally Twistable, Photobendable, Elastically Deformable, and Self‐Healable Soft Crystals

AbstractThe first example of a smart crystalline material, the 2:1 cocrystal of probenecid and 4,4′‐azopyridine, which responds reversibly to multiple external stimuli (heat, UV light, and mechanical pressure) by twisting, bending, and elastic deformation without fracture is reported. This material is also able to self‐heal on heating and cooling, thereby overcoming the main setbacks of molecular crystals for future applications as crystal actuators. The photo‐ and thermomechanical effects and self‐healing capabilities of the material are rooted in reversible trans–cis isomerization of the azopyridine unit and crystal‐to‐crystal phase transition. Fairly isotropic intermolecular interactions and interlocked crisscrossed molecular packing secure high elasticity of the crystals.