Coupling Dimer Research Articles

Efficient Synthesis of Several Natural Oligostilbenes from the ­Biomimetic Oxidation of Brominated Isorhapontigenin

This study extensively investigated the regioselective oxidative coupling reactions of 5-bromoisorhapontigenin catalyzed by ­FeCl3·6H2O or HRP/H2O2 in different solvent systems and the distinct reductive debromination of the isolated dimeric coupling intermediates. Natural (±)-bisisorhapontigenin A and (±)-lehmbachol A and B were efficiently prepared. (±)-Gnetuhainin I, (±)-gnemontanin E, (±)-7-O-ethylgnetuhainin I, and (±)-gnemontanin F were synthesized for the first time.

Effect of Unsymmetrically Branched Alkyl Chains on the Electrochemical Band Gap and Thermal Stability of the PCDTBT

AbstractThis work introduces a modified poly[N‐9’‐heptadecanyl‐2,7‐carbazole‐alt‐5,5‐(4’,7’‐di‐2‐thienyl‐2’,1’,3’‐benzothiadiazole)] (PCDTBT) with the unsymmetrically branched N‐alkyl chain, which name as poly[N‐9’‐(2‐hexyldecyl)‐2,7‐carbazole‐alt‐5,5‐(4’,7’‐di‐2‐thienyl‐2’,1’,3’‐benzothiadiazole)] (P1). The synthesis of P1 involves dimerization, cyclization, tosylation, N‐alkylation, bromination, Stille's and Suzuki's coupling reactions. Suitable analysis techniques have used to study the chemical, physical, electrochemical, optical, and thermal properties of P1. The analysis results show that P1 possesses higher HOMO and LUMO energy levels than the previously reported PCDTBT, which have been narrowing the electrochemical band gap down to 1.58 eV. However, the P1 experiences 5% thermal degradation at 280 °C, which is relatively less favourable than the PCDTBT. Hence, the replacement of the symmetrically branched alkyl chains of PCDTBT with unsymmetrically branched alkyl chains results in both improvement and drawback on the characteristics of the polymer.

Optical Properties of Vibronically Coupled Cy3 Dimers on DNA Scaffolds.

We examine the effect of electronic coupling on the optical properties of Cy3 dimers attached to DNA duplexes as a function of base pair (bp) separation using steady-state and time-resolved spectroscopy. For close Cy3-Cy3 separations, 0 and 1 bp between dyes, intermediate to strong electronic coupling is revealed by modulation of the absorption and fluorescence properties including spectral band shape, peak wavelength, and excited-state lifetime. Using a vibronic exciton model, we estimate coupling strengths of 150 and 266 cm-1 for the 1 and 0 bp separations, respectively, which are comparable to those found in natural light-harvesting complexes. For the strongest electronic coupling (0 bp separation), we observe that the absorption band shape is strongly affected by the base pairs that surround the dyes, where more strongly hydrogen-bonded G-C pairs produce a red-shifted absorption spectrum consistent with a J-type dimer. This effect is studied theoretically using molecular dynamics simulation, which predicts an in-line dye configuration that is consistent with the experimental J-type spectrum. When the Cy3 dimers are in a standard aqueous buffer, the presence of relatively strong electronic coupling is accompanied by decreased fluorescence lifetime, suggesting that it promotes nonradiative relaxation in cyanine dyes. However, we show that the use of a viscous solvent can suppress this nonradiative recombination and thereby restore the dimer fluorescent emission. Ultrafast transient absorption measurements of Cy3 dimers in both standard aqueous buffer and viscous glycerol buffer suggest that sufficiently strong electronic coupling increases the probability of excited-state relaxation through a dark state that is related to Cy3 torsional motion.

Electron transfer and exciplex chemistry of functionalized nanocarbons: effects of electronic coupling and donor dimerization.

In the past few decades, research on the construction of donor-bridge-acceptor linked systems capable of efficient photoinduced charge separation has fundamentally contributed to the fields of artificial photosynthesis and solar energy conversion. Specifically, the above systems are often fabricated by using carbon-based nanomaterials such as fullerenes, carbon nanotubes, and graphenes, offering limitless possibilities of tuning their optical and electronic properties. Accordingly, since understanding the structure-photodynamics relationships of π-aromatic donor-bridge-nanocarbon linked systems is crucial for extracting the full potential of nanocarbon materials, this review summarizes recent research on their photophysical properties featuring nanocarbon materials as electron acceptors. In particular, we highlight the electronic coupling effects on the photodynamics of donor-bridge-nanocarbon acceptor linked systems, together with the effects of donor dimerization. On a basis of their time-resolved spectroscopic data, the photodynamics of donor-bridge-nanocarbon acceptor linked systems is shown to be substantially influenced by the formation and decay of an exciplex state, i.e., an excited-state consisting of a π-molecular donor and a nanocarbon acceptor with partial charge-transfer character. Such basic information is essential for realizing future application of carbon-based nanomaterials in optoelectronic and energy conversion devices.

Voltage-gated sodium channels assemble and gate as dimers

Fast opening and closing of voltage-gated sodium channels are crucial for proper propagation of the action potential through excitable tissues. Unlike potassium channels, sodium channel α-subunits are believed to form functional monomers. Yet, an increasing body of literature shows inconsistency with the traditional idea of a single α-subunit functioning as a monomer. Here we demonstrate that sodium channel α-subunits not only physically interact with each other but they actually assemble, function and gate as a dimer. We identify the region involved in the dimerization and demonstrate that 14-3-3 protein mediates the coupled gating. Importantly we show conservation of this mechanism among mammalian sodium channels. Our study not only shifts conventional paradigms in regard to sodium channel assembly, structure, and function but importantly this discovery of the mechanism involved in channel dimerization and biophysical coupling could open the door to new approaches and targets to treat and/or prevent sodium channelopathies.

Photoluminescence as a probe of molecular organization in PDI8-CN2 ultra-thin films

Photoexcited ultra-thin films of the organic semiconductor N,N'-bis(n-octyl)-dicyanoperylene-3,4:9,10-bis dicarboximide (DPI8-CN2), grown on thermal Si/SiO2, exhibit an intense room temperature emission, strongly dependent on molecular coverage, even for sub-monolayer thicknesses. The luminescence spectra are characterized by a highly structured, isolated molecule emission in the sub-monolayer regime (coverage <30%) and by a condensed-state singlet exciton fluorescence temporally evolving (within 0.5ns) toward an unstructured, energetically relaxed, excimer-like emission, for thicker films. Once a complete monolayer is formed, only the unstructured excimer emission can be detected. The experimental findings are interpreted in terms of progressive deposition of nearly not interacting molecules, followed by islands formation where a strong dimeric coupling takes place, upon increasing the coverage. A thorough investigation by means of AFM and in-situ X-ray diffraction confirms the proposed picture.

Molecular Orbital Rule for Quantum Interference in Weakly Coupled Dimers: Low-Energy Giant Conductivity Switching Induced by Orbital Level Crossing

Destructive quantum interference (QI) in molecular junctions has attracted much attention in recent years. It can tune the conductance of molecular devices dramatically, which implies numerous potential applications in thermoelectric and switching applications. There are several schemes that address and rationalize QI in single molecular devices. Dimers play a particular role in this respect because the QI signal may disappear, depending on the dislocation of monomers. We derive a simple rule that governs the occurrence of QI in weakly coupled dimer stacks of both alternant and nonalternant polyaromatic hydrocarbons (PAHs) and extends the Tada-Yoshizawa scheme. Starting from the Green's function formalism combined with the molecular orbital expansion approach, it is shown that QI-induced antiresonances and their energies can be predicted from the amplitudes of the respective monomer terminal molecular orbitals. The condition is illustrated for a toy model consisting of two hydrogen molecules and applied within density functional calculations to alternant dimers of oligo(phenylene-ethynylene) and nonalternant PAHs. Minimal dimer structure modifications that require only a few millielectronvolts and lead to an energy crossing of the essentially preserved monomer orbitals are shown to result in giant conductance switching ratios.

Glycosylation Alters Dimerization Properties of a Cell-surface Signaling Protein, Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1)

Human carcinoembryonic antigen-related cell adhesion molecule 1 (C?/Au: EACAM1) is a cell-surface signaling molecule involved in cell adhesion, proliferation, and immune response. It is also implicated in cancer angiogenesis, progression, and metastasis. This diverse set of effects likely arises as a result of the numerous homophilic and heterophilic interactions that CEACAM1 can have with itself and other molecules. Its N-terminal Ig variable (IgV) domain has been suggested to be a principal player in these interactions. Previous crystal structures of the β-sandwich-like IgV domain have been produced using Escherichia coli-expressed material, which lacks native glycosylation. These have led to distinctly different proposals for dimer interfaces, one involving interactions of ABED β-strands and the other involving GFCC'C″ β-strands, with the former burying one prominent glycosylation site. These structures raise questions as to which form may exist in solution and what the effect of glycosylation may have on this form. Here, we use NMR cross-correlation measurements to examine the effect of glycosylation on CEACAM1-IgV dimerization and use residual dipolar coupling (RDC) measurements to characterize the solution structure of the non-glycosylated form. Our findings demonstrate that even addition of a single N-linked GlcNAc at potential glycosylation sites inhibits dimer formation. Surprisingly, RDC data collected on E. coli expressed material in solution indicate that a dimer using the non-glycosylated GFCC'C″ interface is preferred even in the absence of glycosylation. The results open new questions about what other factors may facilitate dimerization of CEACAM1 in vivo, and what roles glycosylation may play in heterophylic interactions.

ChemInform Abstract: Recent Advances in Transition‐Metal‐Catalyzed Synthesis of Conjugated Enynes

AbstractReview: [65 refs.

Excitation Localization/Delocalization Isomerism in a Strongly Coupled Covalent Dimer of 1,3-Diphenylisobenzofuran.

Two isomers of both the lowest excited singlet (S1) and triplet (T1) states of the directly para, para'-connected covalent dimer of the singlet-fission chromophore 1,3-diphenylisobenzofuran have been observed. In one isomer, excitation is delocalized over both halves of the dimer, and in the other, it is localized on one or the other half. For a covalent dimer in solution, such "excitation isomerism" is extremely rare. The vibrationally relaxed isomers do not interconvert, and their photophysical properties, including singlet fission, differ significantly.

What computational chemistry and magnetic resonance reveal concerning the oxygen evolving centre in Photosystem II

Density Functional Theory (DFT) computational studies of the Mn4/Ca Oxygen Evolving Complex (OEC) region of Photosystem II in the paramagnetic S2 and S3 states of the water oxdizing catalytic cycle are described. These build upon recent advances in computationally understanding the detailed S1 state OEC geometries, revealed by the recent high resolution Photosystem II crystal structures of Shen et al., at 1.90Å and 1.95Å (Petrie et al., 2015, Angew. Chem. Int. Ed., 54, 7120). The models feature a ‘Low Oxidation Paradigm’ assumption for the mean Mn oxidation states in the functional enzyme, with the mean oxidation levels being 3.0, 3.25 and 3.5 in S1, S2 and S3, respectively. These calculations are used to infer magnetic exchange interactions within the coupled OEC cluster, particularly in the Electron Paramagnetic Resonance (EPR)-visible S2 and S3 states. Detailed computational estimates of the intrinsic magnitudes and molecular orientations of the 55Mn hyperfine tensors in the S2 state are presented. These parameters, together with the resultant spin projected hyperfine values are compared with recent appropriate experimental EPR data (Continuous Wave (CW), Electron-Nuclear Double Resonance (ENDOR) and ELDOR (Electron-Electron Double Resonance)-Detected Nuclear Magnetic Resonance (EDNMR)) from the OEC. It is found that an effective Coupled Dimer magnetic organization of the four Mn in the OEC cluster in the S2 and S3 states is able to quantitatively rationalize the observed 55Mn hyperfine data. This is consistent with structures we propose to represent the likely state of the OEC in the catalytically active form of the enzyme.

Proton-Transfer Polymerization by N-Heterocyclic Carbenes: Monomer and Catalyst Scopes and Mechanism for Converting Dimethacrylates into Unsaturated Polyesters.

This contribution presents a full account of experimental and theoretical/computational investigations into the N-heterocyclic carbene (NHC)-catalyzed proton-transfer polymerization (HTP) that converts common dimethacrylates (DMAs) containing no protic groups into unsaturated polyesters. This new HTP proceeds through the step-growth propagation cycles via enamine intermediates, consisting of the proposed conjugate addition-proton transfer-NHC release fundamental steps. This study examines the monomer and catalyst scopes as well as the fundamental steps involved in the overall HTP mechanism. DMAs having six different types of linkages connecting the two methacrylates have been polymerized into the corresponding unsaturated polyesters. The most intriguing unsaturated polyester of the series is that based on the biomass-derived furfuryl dimethacrylate, which showed a unique self-curing ability. Four MeO- and Cl-substituted TPT (1,3,4-triphenyl-4,5-dihydro-1H-1,2,4-triazol-5-ylidene) derivatives as methanol insertion products, (Rx)TPT(MeO/H) (R = MeO, Cl; x = 2, 3), and two free carbenes (catalysts), (OMe2)TPT and (OMe3)TPT, have been synthesized, while (OMe2)TPT(MeO/H) and (OMe2)TPT have also been structurally characterized. The structure/reactivity relationship study revealed that (OMe2)TPT, being both a strong nucleophile and a good leaving group, exhibits the highest HTP activity and also produced the polyester with the highest Mn, while the Cl-substituted TPT derivatives are least active and efficient. Computational studies have provided mechanistic insights into the tail-to-tail dimerization coupling step as a suitable model for the propagation cycle of the HTP. The extensive energy profile was mapped out, and the experimentally observed unicity of the TPT-based catalysts was satisfactorily explained with the thermodynamic formation of key spirocyclic species.

Recent advances in transition-metal-catalyzed synthesis of conjugated enynes.

Conjugated enynes are of great importance in organic synthesis, biochemistry and materials sciences. The most commonly used synthetic methods include cross coupling reactions and dimerization reactions of alkynes. Despite many robust strategies being established, the improvement of reaction efficiency and development of novel transformations have still been actively pursued in the past decade. This review covers recent advances in transition-metal-catalyzed reactions in these fields.

Engineering an enzymatic regeneration system for NAD(P)H oxidation

A recently proposed coenzyme regeneration system employing laccase and a number of various redox mediators for the oxidation of NAD(P)H was studied in detail by kinetic characterization of individual reaction steps. Reaction engineering by modeling was used to optimize the employed enzyme, coenzyme as well as redox mediator concentrations. Glucose dehydrogenase from Bacillus sp. served as a convenient model of synthetic enzymes that depend either on NAD+ or NADP+. The suitability of laccase from Trametes pubescens in combination with acetosyringone or syringaldazine as redox mediator was tested for the regeneration (oxidation) of both coenzymes. In a first step, pH profiles and catalytic constants of laccase for the redox mediators were determined. Then, second-order rate constants for the oxidation of NAD(P)H by the redox mediators were measured. In a third step, the rate equation for the entire enzymatic process was derived and used to build a MATLAB model. After verifying the agreement of predicted vs. experimental data, the model was used to calculate different scenarios employing varying concentrations of regeneration system components. The modeled processes were experimentally tested and the results compared to the predictions. It was found that the regeneration of NADH to its oxidized form was performed very efficiently, but that an excess of laccase activity leads to a high concentration of the oxidized form of the redox mediator – a phenoxy radical – which initiates coupling (dimerization or polymerization) and enzyme deactivation.

Reversed Electron Apportionment in Mesolytic Cleavage: The Reduction of Benzyl Halides by SmI2.

The paradigm that the cleavage of the radical anion of benzyl halides occurs in such a way that the negative charge ends up on the departing halide leaving behind a benzyl radical is well rooted in chemistry. By studying the kinetics of the reaction of substituted benzylbromides and chlorides with SmI2 in THF it was found that substrates para-substituted with electron-withdrawing groups (CN and CO2 Me), which are capable of forming hydrogen bonds with a proton donor and coordinating to samarium cation, react in a reversed electron apportionment mode. Namely, the halide departs as a radical. This conclusion is based on the found convex Hammett plots, element effects, proton donor effects, and the effect of tosylate (OTs) as a leaving group. The latter does not tend to tolerate radical character on the oxygen atom. In the presence of a proton donor, the tolyl derivatives were the sole product, whereas in its absence, the coupling dimer was obtained by a SN 2 reaction of the benzyl anion on the neutral substrate. The data also suggest that for the para-CN and CO2 Me derivatives in the presence of a proton donor, the first electron transfer is coupled with the proton transfer.

Reaction of a brominated benzolactone/lactam with 4-methoxythiobenzamide and thiourea: an Eschenmoser coupling reaction, ring transformation, or dimerization?

The reactions of 3-bromo-1-benzofuran-2(3H)-one (1a) and 3-bromo-1,3-dihydro-2H-indol-2-one (1b) with 4-methoxythiobenzamide and thiourea under mildly basic conditions are reported. While brominated lactone 1a gave the expected 5-(2-hydroxyphenyl)-2-(4-methoxyphenyl)-1,3-thiazol-4-ol (2) or 2-amino-5-(2-hydroxyphenyl)-1,3-thiazol-4(5H)-one (5) products, the analogous brominated lactam 1b reacted with the thioamide via an unexpected Eschenmoser coupling reaction to give (3Z)-3-[amino(4-methoxyphenyl)-methylidene]-1,3-dihydro-2H-indol-2-one (3). When lactam 1b was treated with thiourea, isoindigo (4) was the only isolated product. The reaction mechanisms, involving formation of α-thioiminium or isothiouronium salts and their base-catalyzed decomposition are also proposed.

A G protein-coupled receptor dimer imaging assay reveals selectively modified pharmacology of neuropeptide Y Y1/Y5 receptor heterodimers.

The ability of G protein-coupled receptors (GPCRs) to form dimers, and particularly heterodimers, offers potential for targeted therapeutics with improved selectivity. However, studying dimer pharmacology is challenging, because of signaling cross-talk or because dimerization may often be transient in nature. Here we develop a system to isolate the pharmacology of precisely defined GPCR dimers, trapped by bimolecular fluorescence complementation (BiFC). Specific effects of agonist activation on such dimers are quantified using automated imaging and analysis of their internalization, controlled for by simultaneous assessment of endocytosis of one coexpressed protomer population. We applied this BiFC system to study example neuropeptide Y (NPY) Y1 receptor dimers. Incorporation of binding-site or phosphorylation-site mutations into just one protomer of a Y1/Y1 BiFC homodimer had no impact on efficient NPY-stimulated endocytosis, demonstrating that single-site agonist occupancy, and one phosphorylated monomer within this dimer, was sufficient. For two Y1 receptor heterodimer combinations (with the Y4 receptor or β2-adrenoceptor), agonist and antagonist pharmacology was explained by independent actions on the respective orthosteric binding sites. However, Y1/Y5 receptor BiFC dimers, compared with the constituent subtypes, were characterized by reduced potency and efficacy of Y5-selective peptide agonists, the inactivity of Y1-selective antagonists, and a change from surmountable to nonsurmountable antagonism for three unrelated Y5 antagonists. Thus, allosteric interactions between Y1 and Y5 receptors modify the pharmacology of the heterodimer, with implications for potential antiobesity agents that target centrally coexpressed Y1 and Y5 receptors to suppress appetite.

Photoexcited Energy Transfer in a Weakly Coupled Dimer.

Nonadiabatic excited-state molecular dynamics (NA-ESMD) simulations have been performed in order to study the time-dependent exciton localization during energy transfer between two chromophore units of the weakly coupled anthracene dimer dithia-anthracenophane (DTA). Simulations are done at both low temperature (10 K) and room temperature (300 K). The initial photoexcitation creates an exciton which is primarily localized on a single monomer unit. Subsequently, the exciton experiences an ultrafast energy transfer becoming localized on either one monomer unit or the other, whereas delocalization between both monomers never occurs. In half of the trajectories, the electronic transition density becomes completely localized on the same monomer as the initial excitation, while in the other half, it becomes completely localized on the opposite monomer. In this article, we present an analysis of the energy transfer dynamics and the effect of thermally induced geometry distortions on the exciton localization. Finally, simulated fluorescence anisotropy decay curves for both DTA and the monomer unit dimethyl anthracene (DMA) are compared. Our analysis reveals that changes in the transition density localization caused by energy transfer between two monomers in DTA is not the only source of depolarization and exciton relaxation within a single DTA monomer unit can also cause reorientation of the transition dipole.

Dimerization Coupling Reaction of Terminal Alkyne Promoted by CuI/DEAD

Dimerization Coupling Reaction of Terminal Alkyne Promoted by CuI/DEAD

CdII-Mediated Efficient Synthesis and Complexation of Asymmetric Tetra-(2-pyridine)-Substituted Imidazolidine

One convenient CdII-mediated C–C/C–N bond-forming strategy toward asymmetric tetra-(2-pyridine)-substituted imidazolidine (L1), the basic framework of several natural products with bioactivity, has been found for the first time. In the reaction of tridentate N3-set neutral pyridine-type Schiff base ligand (L) possessing a [−HCNCH2−] linkage with CdCl2 at 70 °C for 3 days, one two-dimensional 44 topological layer [Cd3L1Cl6]n (1) could be obtained, in which ligand L1 resulted from [3 + 2] C–C/C–N asymmetric coupling dimerization of L. When equimolar amounts of NaSCN and NaNO3 were added to the reaction mixtures, one-dimensional chain [Cd2L1(SCN)Cl3]n (2) and zero-dimensional dinuclear Cd2L1(NO3)4(MeOH) (3) containing the same ligand L1 were also generated under the same reaction conditions, respectively. Obviously, the medium of the Cd2+ ion plays the key role in solvothermal in situ formation of ligand L1. Moreover, new ligand tetra-substituted imidazolidine (L1) could be obtained effectually from all three complexes 1–3 through the reactions of those compounds with Na2S.