EZ Isomers Research Articles

Intramolecular hydrogen bonds interactions in the isomers of the bilirubin molecule: DFT and QTAIM analysis.

Bilirubin is an important molecule, used as a marker of some liver diseases, and it can also be toxic and cause jaundice, especially in newborns. The main treatment for neonatal jaundice is phototherapy with blue light, which is still widely studied because the photophysical processes involved are not fully understood. Calculations based on the density functional theory (DFT) at M062X/6-31G(d,p) level were performed in order to evaluate the structural, electronic, and topological properties of bilirubin isomers. It was found that the ZZ conformation can form a greater number of hydrogen bonds, which gives the isomer greater energy stabilization compared to the other ZE, EZ, and EE isomers, and that the EE isomer is the conformer with the lowest energy of stabilization. The hydrogen bonds were characterized by the quantum theory of atoms in molecules (QTAIM) and for the ZZ isomer four hydrogen bonds (HBs) were found classified as intermediate, ∇2ρ(r) > 0, H(r) > 0. The ZE, EZ, and EE isomers show weak HBs, ∇2ρ(r) > 0, H(r) > 0.

Photoisomerization of Linear and Stacked Isomers of a Charged Styryl Dye: A Tandem Ion Mobility Study.

The photoisomerization behavior of styryl 9M, a common dye used in material sciences, is investigated using tandem ion mobility spectrometry (IMS) coupled with laser spectroscopy. Styryl 9M has two alkene linkages, potentially allowing for four geometric isomers. IMS measurements demonstrate that at least three geometric isomers are generated using electrospray ionization with the most abundant forms assigned to a combination of EE (major) and ZE (minor) geometric isomers, which are difficult to distinguish using IMS as they have similar collision cross sections. Two additional but minor isomers are generated by collisional excitation of the electrosprayed styryl 9M ions and are assigned to the EZ and ZZ geometric isomers, with the latter predicted to have a π-stacked configuration. The isomer assignments are supported through calculations of equilibrium structures, collision cross sections, and statistical isomerization rates. Photoexcitation of selected isomers using an IMS-photo-IMS strategy shows that each geometric isomer photoisomerizes following absorption of near-infrared and visible light, with the EE isomer possessing a S1 ← S0 electronic transition with a band maximum near 680 nm and shorter wavelength S2 ← S0 electronic transition with a band maximum near 430 nm. The study demonstrates the utility of the IMS-photo-IMS strategy for providing fundamental gas-phase photochemical information on molecular systems with multiple isomerizable bonds.

Restriction of Conformation Transformation in Excited State: An Aggregation-Induced Emission Building Block Based on Stable Exocyclic C=N Group.

SummaryThe development of aggregation-induced emission (AIE) building block and deciphering its luminescence mechanism are of great significance. Here a feasible strategy for the construction of AIE unit based on E-Z isomerization (EZI) of exocyclic C=N double bond is proposed. Taking [1,2,4]thiadiazole[4,3-a]pyridine (TZP) derivative as an example, its aryl-substituted derivative (TZPP) shows obvious AIE character. The analysis of spectral data and theoretical calculations indicates that fast structural relaxation of TZPP in the emissive state plays a key role in a low fluorescence quantum yield in dilute solution, which should be caused by the small energy gap between locally excited (LE) state and twisted intramolecular charge transfer state. When in solid state, the bright emission with LE state characteristic reappears due to the large shift barrier of geometry transformation. As a potential building block for AIEgens with special heterocyclic structure, these findings would open up opportunities for developing various functional materials.

Nickel- and Brønsted Acid-Catalyzed Redox-Neutral Coupling of 1,3-Dienes and Aldehydes for Synthesis of Dienols

Dienols are important structural motifs in organic molecules, but most of the traditional synthetic methods required multistep prefunctionalization of substrates, leading to stoichiometric waste an...

Double Molecular Photoswitch Driven by Light and Collisions.

The shapes of many molecules can be transformed by light or heat. Here we investigate collision- and photon-induced interconversions of EE, EZ, and ZZ isomers of the isolated Congo red (CR) dianion, a double molecular switch containing two ─N═N─ azo groups, each of which can have the E or Z configuration. We find that collisional activation of CR dianions drives a one-way ZZ→EZ→EE cascade towards the lowest-energy isomer, whereas the absorption of a single photon over the 270-600nm range can switch either azo group from E to Z or Z to E, driving the CR dianion to lower- or higher-energy forms. The experimental results, which are interpreted with the aid of calculated statistical isomerization rates, indicate that photoisomerization of CR in the gas phase involves a passage through conical intersection seams linking the excited and ground state potential energy surfaces rather than through isomerization on the ground state potential energy surface following internal conversion.

Selectivity in Olefin-Intervened Macrocyclic Ring-Closing Metathesis

The ring-closing metathesis (RCM) of α,m,ω-triene was employed for the syntheses of four slightly different EE, EZ, ZE, and ZZ isomers of macrocycles with two greatly separated type I olefins. Kinetic control of the RCM reaction using G1 was achieved, in which secondary metathesis of the initially formed RCM product that usually afforded the thermodynamically favored product was inhibited, and a reliable model was built to differentiate the kinetic or thermodynamic control in the RCM reaction. Kinetic studies of olefin metathesis using the kinetically controlled Z-selective catalyst Cat-Z were conducted to determine its thermodynamic capability to convert (Z)-olefin to (E)-olefin. Finally, the ring size selectivity of α,ω- vs α,m-/m,ω-products in the RCM reaction of α,m,ω-triene revealed that all types of isomeric α,ω-products are favored for the 18-membered ring and above, and α,m-/m,ω-products are predominant for the rings with 14-members and less. For the 15-, 16-, and 17-membered rings, each of the E/Z-selective RCM reactions of starting (mE)- and (mZ)-trienes has a different performance under the optimized conditions. These studies provide insights into the applications of RCM on the synthesis of macrocycles with two separate type I olefins.

Twist of C═C Bond Plays a Crucial Role in the Quenching of AIE-Active Tetraphenylethene Derivatives in Solution

Aggregation-induced emission (AIE) has emerged as a new class of attractive photoluminescence behavior. Understanding the precise mechanism of the AIE phenomenon will lead to the rational molecular design of novel molecules with AIE properties (AIEgens). In this work, we selected disubstituted derivatives of tetraphenylethene (TPE), a well-known archetypal AIEgen, as the model compounds to elucidate the AIE mechanism. As the result of photochemical experiments and quantum chemical computations, π-bond twist (π twist), including E–Z isomerization (EZI), was found to be the major factor for quenching the photoexcited state of TPE derivatives in the solution state, differently from the well-accepted propeller-like rotation of the side phenyl groups in earlier research. In photochemical experiments, the prepared TPE derivatives exhibited EZI in the solution state upon photoirradiation, and a negative correlation was observed between this isomerization and the AIE phenomenon. The theoretical computations verif...

Study of spontaneous E/Z isomerization of bis[(Z)-cyanomethylidene]-diazapentacyclodienedicarboxylates by 1 H, 13 C, and 15 N NMR spectroscopy, X-ray, and quantum chemical calculation data.

X-ray data show that the diethyl 6,13-bis[(Z)-cyanomethylidene]-5,5,14,14-tetramethyl-4,15-dioxa-7,12-diazapentacyclo[9.5.2.02,10 .03,7 .012,16 ]octadeca-8,17-diene-10,17-dicarboxylate is formed as the ZZ isomer and diastereomer with the (1R*,2R*,3R*,10S*,11R*,12R*,16R*) configuration. The 1 H, 13 C, and 15 N NMR data exhibit that on standing in chloroform-d solution, there is a spontaneous isomerization of this compound resulting in a thermodynamically stable mixture of the ZZ, ZE, EE, and EZ isomers with the same backbone. Using the 2D [1 H-1 H] COSY, [1 H-13 C] HSQC, and [1 H-13 C, 1 H-15 N] HMBC NMR techniques and quantum chemical calculations makes it possible a complete assignment of signals in the 1 H, 13 C, and 15 N NMR spectra of each of the isomers. Such isomerization does not occur for similar compounds with the more bulky substituents at the 1,3-oxazolidine rings. Copyright © 2016 John Wiley & Sons, Ltd.

Dynamic induction of enantiomeric excess from a prochiral azobenzene dimer under circularly polarized light.

The ability to photoinduce enantiomeric excess from the chirality of circularly polarized light (CPL) is pertinent to the study of the origin of homochirality in biomolecules. Such CPL-induced reactions, including both chirality generation and formation of partial enantiomeric imbalance, from nonchiral starting compounds have been known, however, only for the conversion of diarylolefins into chiral helicenes. In this study we synthesized three different prochiral molecules, each featuring a pair of photoisomerizable phenylazo moieties arranged symmetrically upon the phenyl rings of an sp3-hybridized carbon atom (1), the phenyl rings of [2.2]paracyclophane (2), and the ortho positions of a phenyl ring bearing a naphthyl unit (3), and then investigated the possibility of photoinducing enantiomeric excess under CPL. Irradiation of 1-3 with light induced E ↔ Z photoisomerizations of their azobenzene moieties, giving mixtures of their EE, EZ, and ZZ isomers in the photostationary state (PSS). Among these regioisomers, the EZ forms are chiral and existed as racemic mixtures of R and S stereoisomers. Upon CPL irradiation of 3, circular dichroism (CD) revealed enantiomeric enrichment of one of the EZ stereoisomers; furthermore, irradiation with r- or l-CPL gave CD signals opposite in sign, but with equal intensity, in the PSS. In contrast, 1 and 2 did not give any detectable induced CD upon CPL irradiation. These experimental results can be explained by considering the different Kuhn anisotropy factors (g) of the (R)-EZ and (S)-EZ stereoisomers of 1-3, assuming that the origin of the enantiomeric excess is the enantio-differentiating photoisomerization from EZ stereoisomers to nonchiral EE or ZZ regioisomers by r- or l-CPL. In short, we demonstrate the simultaneous induction of chirality and enantiomeric excess from a prochiral azobenzene dimer via a chiral regioisomer formed in situ upon CPL irradiation.

Modulating weak intramolecular interactions through the formation of beryllium bonds: complexes between squaric acid and BeH2

The electronic structure of the two most stable isomers of squaric acid and their complexes with BeH2 were investigated at the B3LYP/6-311 + G(3df,2p)// B3LYP/6-31 + G(d,p) level of theory. Squaric acid forms rather strong beryllium bonds with BeH2, with binding energies of the order of 60 kJ mol(-1). The preferential sites for BeH2 attachment are the carbonyl oxygen atoms, but the global minima of the potential energy surfaces of both EZ and ZZ isomers are extra-stabilized through the formation of a BeH···HO dihydrogen bond. More importantly, analysis of the electron density of these complexes shows the existence of significant cooperative effects between the beryllium bond and the dihydrogen bond, with both becoming significantly reinforced. The charge transfer involved in the formation of the beryllium bond induces a significant electron density redistribution within the squaric acid subunit, affecting not only the carbonyl group interacting with the BeH2 moiety but significantly increasing the electron delocalization within the four membered ring. Accordingly the intrinsic properties of squaric acid become perturbed, as reflected in its ability to self-associate.

Novel dimeric leuco-TAM dyes, 1,4-bis{(1E,3Z)-1,3-bis(1,3,3-trimethylindolin-2-ylidene)propan-2-yl}benzene derivatives: Structure and spectroscopic characterization

Abstract Novel dimeric leuco-triarylmethane (LTAM) dyes, 1,4-bis{(1 E ,3 Z )-1,3-bis(1,3,3-trimethylindolin-2-ylidene)propan-2-yl}benzene derivatives, as precursors of dimeric TAM + and TAM ++ dyes, were synthesized and characterized by 1D and 2D NMR experiments including DEPT, COSY, HSQC, HMBC and NOESY. Judging from the 1H NMR analysis, the dimeric LTAM molecules were suggested to have a dual-propeller shaped structure. For the prepared dimeric leuco-TAM dyes, the ZE / EZ isomers were formed as the sole products from the reaction of 2–3 M excess Fischer base and terephthalaldehyde in absolute ethanol. The ZE / EZ isomers were equilibrated with other diastereomers ( EE / EE and ZZ / ZZ ) in organic solvents. UV–Vis spectroscopy of dimeric TAM ++ dyes in organic solvents show an absorption band at >700 nm in the near-infrared (NIR) region. Formation of the dimeric TAM ++ molecules was further confirmed by comparison of CV diagrams for monomeric TAM + and dimeric TAM ++ molecules.

Study of stereospecificity of 1H, 13C, 15N and 77Se shielding constants in the configurational isomers of the selenophene‐2‐carbaldehyde azine by NMR spectroscopy and MP2‐GIAO calculations

In the (1)H and (13)C NMR spectra of selenophene-2-carbaldehyde azine, the (1)H-5, (13)C-3 and (13)C-5 signals of the selenophene ring are shifted to higher frequencies, whereas those of the (1)H-1, (13)C-1, (13)C-2 and (13)C-4 are shifted to lower frequencies on going from the EE to ZZ isomer or from the E moiety to the Z moiety of EZ isomer. The (15)N chemical shift is significantly larger in the EE isomer relative to the ZZ isomer and in the E moiety relative to the Z moiety of EZ isomer. A very pronounced difference (60-65 mg/g) between the (77)Se resonance positions is revealed in the studied azine isomers, the (77)Se peak being shifted to higher frequencies in the ZZ isomer and in the Z moiety of EZ isomer. The trends in the changes of the measured chemical shifts are reasonably reproduced by the GIAO calculations at the MP2 level of the (1)H, (13)C, (15)N and (77)Se shielding constants in the energy-favorable conformation with the syn orientation of both selenophene rings relative to the C = N groups. The NBO analysis suggests that such an arrangement of the selenophene rings may take place because of a higher energy of some intramolecular interactions.

ChemInform Abstract: Efficient Synthesis of N-Alkylformimidoyl Cyanides.

N-Alkylformimidoyl cyanides (RRCHNCHCN, 1) were obtained through a very efficient oxidation of N-alkylaminoacetonitriles (RRCHNHCH2CN, 2) by aq. NaOCl. The reaction was run under very mild and simple conditions and afforded products (as EZ isomer mixtures; EZ ratio of 70–99%) in short reaction times (30–180 min), and in good to excellent yields (67–97%).

Crystal Phase Transition and Solid-State Photoisomerization of Benzyl (Z,Z)-Muconate Polymorphs Studied by Direct Observation of Crystal Structure Change

We investigated the polymorph structures of benzyl (Z,Z)-muconate crystals (ZZ-Bn-α, β, and γ) and their EZ photoisomerization behavior in order to clarify the EZ isomerization mechanism of diene compounds in the solid state. First, the thermodynamics and crystal phase transition of the polymorphs were investigated by differential scanning calorimetry and X-ray diffraction. A single-crystal-to-single-crystal transition was observed during the change in the polymorph structures from the ZZ-Bn-β to the α form. We also observed in situ the migration of the boundary between the different polymorph domains during the phase transition of the ZZ-Bn-γ to the α form by optical microscopy. We then investigated the change in the crystal structure of ZZ-Bn during the EZ photoisomerization in the solid state. The photoisomerization of ZZ-Bn to the corresponding EE isomer (EE-Bn) proceeded according to a bicycle-pedal model via a single-crystal-to-single-crystal topochemical reaction mechanism, which was directly confi...

The behavior of Gliclazide in solution and in the solid state: a case of organic compound presenting a solid‐solution structure

The structure of the hypoglycemic agent Gliclazide has been studied by (1)H, (13)C, and (15)N NMR in solution (CDCl(3) and DMSO-d(6)) and in the solid state. In the solid state, the compound crystallizes as an EZ isomer without dynamic properties. In CDCl(3) solution, the structure is still EZ but with a slow nitrogen inversion about the pyrrolidine nitrogen: two invertomers have been observed and characterized. In DMSO-d(6), the rate is faster and only averaged signals were observed. GIAO calculated absolute shieldings were used to confirm the nature of the observed species. In the solid state, Gliclazide presents the phenomenon of solid-solution with two disordered conformations present in the crystal at a 90:10 ratio.

Molecular Stacking and Photoreactions of Fluorine-Substituted Benzyl Muconates in the Crystals

The solid-state photoreactions of fluorine-substituted benzyl (Z,Z)- and (E,E)-muconates have been investigated. The reaction of 16 derivatives was carried out under UV- and γ-ray radiations, and the products were characterized by NMR spectroscopy and X-ray diffractions. [2+2] Dimerization, EZ isomerization, and polymerization occurred depending on the monomer structure and provided a highly selective photoproduct during each reaction. The reaction mechanism was discussed based on the monomer packing in the crystals. The single-crystal structure analysis of the monomers has revealed that the reaction pathways and the structure of the products are closely related to the molecular packing formed by intermolecular interactions such as C−H···O and C−H···F interactions. The reactivity and the structure of the dimers as the products of regioselective cyclodimerization are well accounted for by the relative orientation of the reacting monomer molecules in the crystals. The topochemical polymerization of a 2,6-difluorobenzyl ester derivative is also described.

22]Porphyrin-(3.1.1.3), a New Vinylogous Expanded Porphyrin System

Acid-catalyzed condensation of a pyrrole bisacrylaldehyde with a tripyrrane, followed by oxidation with ferric chloride, gave a [22]porphyrin-(3.1.1.3). This stretched macrocycle shows a strong diamagnetic ring current by (1)H NMR spectroscopy and gives red-shifted porphyrin-like UV-vis spectra; coordination with palladium(II) induces an EZ isomerization to accommodate the metal cation while retaining highly diatropic characteristics. [structure: see text]

Polymer Crystal Engineering for Control of Stereochemical Structure of Polymers: Stereospecific Monomer Synthesis and Stereospecific Solid-State Polymerization

ABSTRACT We have successfully synthesized diisotactic and disyndiotactic polymers of (Z,Z)- and (E,E)-muconates with various benzyl ester groups. Muconic acid was conveniently converted into its corresponding ester derivatives without EZ isomerization when reacted with benzyl bromides in the presence of potassium carbonate in hexamethylphosphoramide (HMPA) at room temperature. Several monomers undergo photopolymerization in the crystalline state to give stereoregular polymers according to the monomer configuration and the ester substituents. X-ray single crystal structure analysis of the monomer and polymer crystals has revealed the process of the topochemical polymerization. In the monomer crystals with 4-alkoxybenzyl groups as the ester substituents, a columnar structure is formed by the alternate stacking of monomer molecules with the aid of weak hydrogen bonds such as CH/π and CH/O intermolecular interactions. The alternate stacking is appropriate for syndiotactic polymerization, being different from the crystal structures of many other ester monomers which provide a diisotactic polymer due to the translational monomer stacking in a column, as is seen in the crystals of the 4-chloro-, 4-bromo-, and 4-nitro-substituted benzyl esters. Weak and flexible intermolecular interactions provide a variety of crystal structures and different type of molecular stacking leading to the different tacticity of the polymers.

Synthesis of Structurally Defined Scaffolds for Bivalent Ligand Display Based on Glucuronic Acid Anilides. The Degree of Tertiary Amide Isomerism and Folding Depends on the Configuration of a Glycosyl Azide

[structures: see text] Syntheses and structural analyses of bivalent carbohydrates based on anilides of glucuronic acid are described. Secondary anilides predominantly adopted the Z-anti structure; there is also evidence for population of the Z-syn isomer. Bivalent tertiary anilides displayed two signal sets in their NMR spectra, consistent with the presence of (i) a major isomer where both amides have E configurations (EE) and (ii) a minor isomer where one amide is E and the other Z (EZ). Qualitative NOE/ROE spectroscopic studies in solution support the proposal that the anti conformation is preferred for E amides. The crystal structure of one bivalent tertiary anilide showed E-anti and E-syn structural isomers; intramolecular carbohydrate-carbohydrate stacking was observed and mediated by carbonyl-pyranose, azide-azide, and pyranose-aromatic interactions. The EE to EZ isomer ratio, or the degree of folding, for tertiary amides, was greatest for a bivalent compound containing two alpha-glycosyl azide groups; this was enhanced in water, suggesting that hydrophobic interactions are partially but not wholly responsible. Computational methods predicted azide-aromatic (N...H-C interaction) and azide-azide interactions for folded isomers. The close contact of the azide and aromatic protons (N...H-C interaction) was observed upon examination of the close packing in the crystal structure of a related monomer. It is proposed that the alpha-azide group is more optimally aligned, compared to the beta-azide, to facilitate interaction and minimize the surface area of the hydrophobic groups exposed to water, and this leads to the increased folding. The alkylation of bivalent secondary anilides induces a switch from Z to E amide that alters the scaffold orientation. The synthesis of a bivalent mannoside, based on a secondary anilide scaffold, for investigation of mannose-binding receptor cross-linking and lattice formation is described.

Electrochemical Isomerization and Polymerization of Three Stereoisomers of a Novel Photoluminescent Thienylene-PPV Derivative

Three stereoisomers (EE, EZ, and ZZ) of 1,4-diethoxy-2,5-bis[2-(thien-2-yl)ethenyl]benzene were synthesized and characterized. It is shown that the electrochemical and optical properties depend on the configuration of themolecules. It is also shown that both electrochemical polymerization and photoactivation of the EZ and ZZ isomers cause transformation of the molecules to the most stable EE configuration.