Asymmetric Dimer Research Articles

Artificial iono- and photosensitive membranes based on an amphiphilic aza-crown-substituted hemicyanine.

Artificial iono- and photosensitive membranes based on an amphiphilic aza-crown-substituted hemicyanine are assembled on liquid and solid supports and their aggregation behaviour, which is influenced by the binding of metal cations and surface density, is studied. The photoinduced charge-transfer properties of an analogous non-amphiphilic hemicyanine in solution are also demonstrated. An asymmetric sandwich dimer model is proposed and existence of such dimers in solution is evidenced by transient absorption and fluorescence anisotropy experiments. Changes in absorption and emission spectra, as well as compression isotherms of the amphiphile observed in the presence of cations, are discussed in terms of 2D molecular reorganisation. Surface-pressure-controlled reversible excimer formation at the air-water interphase and excimer-type emission of Langmuir-Blodgett films in the presence of cations are demonstrated and are discussed on the basis of fibre-optic fluorimetry and fluorescence microscopy results.

The resonant, near-resonant, and off-resonant plasmon coupling effects for the bonding modes in two types of asymmetric dimer

The resonant, near-resonant, and off-resonant plasmon coupling effects for the bonding modes in asymmetric dimers are illustrated by two types of configuration, one formed by a gold nanoparticle and a TiO2–Ag core–shell nanoparticle and the other formed by two TiO2–Ag core–shell nanoparticles with suitable sizes. The redshift and blueshift behaviours of the coupled bonding modes with decreasing gap are found under longitudinal and transverse polarization of light for these dimers in the resonant situation, respectively. Under the near-resonant situation, the redshift behaviours of the coupled bonding modes still remain under longitudinal polarization, whereas the two separated modes of monomers after coupling under transverse polarization exhibit no obvious peak-shift behaviours, and the one on the lower frequency side shows an apparent attenuation in the strength. Under the off-resonant situation, the redshift behaviours not only occur in the coupled modes under longitudinal polarization, but also occur in two separated modes under transverse polarization.

Surface second-harmonic generation from coupled spherical plasmonic nanoparticles: Eigenmode analysis and symmetry properties

The surface second-harmonic generation from interacting spherical plasmonic nanoparticles building different clusters (symmetric and asymmetric dimers, trimers) is theoretically investigated. The plasmonic eigenmodes of the nanoparticle clusters are first determined using an ab initio approach based on the Green's functions method. This method provides the properties, such as the resonant wavelengths, of the modes sustained by a given cluster. The fundamental and second-harmonic responses of the corresponding clusters are then calculated using a surface integral method. The symmetry of both the linear and nonlinear responses is investigated, as well as their relationship. It is shown that the second-harmonic generation can be significantly enhanced when the fundamental field is such that its second harmonic matches modes with suitable symmetry. The role played by the nanogaps in second-harmonic generation is also underlined. The results presented in this article demonstrate that the properties of the second-harmonic generation from coupled metallic nanoparticles cannot be fully predicted from their linear response only, while, on the other hand, a detailed knowledge of the underlying modal structure can be used to optimize the generation of the second harmonic.

Auger intensity anomalies from the Si(001)2 × 1 surface excited by the wave field of RHEED

The Auger intensity of Si‐LVV from the Si(001)2 × 1 surface has been measured at room temperature while changing the glancing angle of the incident electron beam of reflection high‐energy electron diffraction (RHEED). Such a beam‐rocking Auger electron spectroscopy (BRAES) profile shows intensity anomalies under surface wave resonance conditions. The surface structure of Si(001)2 × 1 has been analyzed by rocking curves of diffraction spots within the 0th Laue zone. Since RHEED intensities limited to the 0th Laue zone can be determined by the projected potential of Si atomic rows along the incident azimuth, the phase of asymmetric dimers with flip‐flop motion can be neglected. According to the Si(001)2 × 1 surface structure model which was confirmed by the rocking curve analysis, it was found that the calculated wave‐field intensity profile for Si atoms reveals similar intensity anomalies to those of the experimental BRAES profile. The background profile is also discussed in terms of the beam irradiation area and its transmissivity. Copyright © 2014 John Wiley & Sons, Ltd.

Slab photonic crystals with dimer colloid bases

The photonic band gap properties for centered rectangular monolayers of asymmetric dimers are reported. Colloids in suspension have been organized into the phase under confinement. The theoretical model is inspired by the range of asymmetric dimers synthesized via seeded emulsion polymerization and explores, in particular, the band structures as a function of degree of lobe symmetry and degree of lobe fusion. These parameters are varied incrementally from spheres to lobe-tangent dimers over morphologies yielding physically realizable particles. The work addresses the relative scarcity of theoretical studies on photonic crystal slabs with vertical variation that is consistent with colloidal self-assembly. Odd, even and polarization independent gaps in the guided modes are determined for direct slab structures. A wide range of lobe symmetry and degree of lobe fusion combinations having Brillouin zones with moderate to high isotropy support gaps between odd mode band indices 3-4 and even mode band indices 1-2 and 2-3.

Charge transfer in time-dependent density-functional theory: Insights from the asymmetric Hubbard dimer

We show that propagation with the best possible adiabatic approximation in time-dependent density-functional theory fails to properly transfer charge in an asymmetric two-site Hubbard model when beginning in the ground state. The approximation is adiabatic but exact otherwise, constructed from the exact ground-state exchange-correlation functional that we compute via constrained search. The model shares the essential features of charge-transfer dynamics in a real-space long-range molecule, so the results imply that the best possible adiabatic approximation, despite being able to capture nonlocal ground-state step features relevant to dissociation and charge-transfer excitations, cannot capture fully time-resolved charge-transfer dynamics out of the ground state.

An asymmetric PAN3 dimer recruits a single PAN2 exonuclease to mediate mRNA deadenylation and decay.

The PAN2-PAN3 complex functions in general and microRNA-mediated mRNA deadenylation. However, mechanistic insight into PAN2 and its complex with the asymmetric PAN3 dimer is lacking. Here, we describe crystal structures that show that Neurospora crassa PAN2 comprises two independent structural units: a C-terminal catalytic unit and an N-terminal assembly unit that engages in a bipartite interaction with PAN3 dimers. The catalytic unit contains the exonuclease domain in an intimate complex with a potentially modulatory ubiquitin-protease-like domain. The assembly unit contains a WD40 propeller connected to an adaptable linker. The propeller contacts the PAN3 C-terminal domain, whereas the linker reinforces the asymmetry of the PAN3 dimer and prevents the recruitment of a second PAN2 molecule. Functional data indicate an essential role for PAN3 in coordinating PAN2-mediated deadenylation with subsequent steps in mRNA decay, which lead to complete mRNA degradation.

Property of the Valence-Bond Ordering in Molecular Superconductor with a Quasi-Triangular Lattice

We have investigated the property of the non-magnetic insulating state of a pressure-induced molecular superconductor with a quasi-triangular lattice consisting of tight dimer units applying vibrational and reflectance spectroscopy to monoclinic-phase of C2H5(CH3)3P[Pd(dimt)2]2 (dmit = 1,3-dithiole-2-thione-4,5-dithiolate). From the analyses of the spectra, it is founded that two asymmetric dimers form a weakly bounded tetramer and the 2D layer is a slightly anisotropic. Theses results indicate that the cooperation between nearest Coulomb repulsions and valence bond order, which is operative for the anisotropic system of triclinic-phase of C2H5(CH3)3P[Pd(dimt)2]2, inhibits spin frustration in the monoclinic-phase. Our result also suggests that a half-filled picture does not always hold for the molecular superconductors consisting of tight dimer units.

Study of “Racemic Compound-Like” Behavior of Diastereomeric Mixture of Pinanyl Sulfoxides by X-Ray Diffraction, IR Spectroscopy, and DFT Calculations

The oxidation of a β-hydroxysulfide in the pinane series by use of m-chloroperbenzoic acid resulted in the formation of the corresponding β-hydroxysulfoxide as a mixture of two diastereomers in 4:5 ratio. According to single-crystal X-ray diffraction (XRD) results, it is established that the diastereomeric mixture of sulfoxides crystallizes in the “racemic compound-like” manner under formation of asymmetric dimers through S=O··H–O interactions. This asymmetric dimer formed from diastereomeric molecules is a structural unit in both crystal modifications, the triclinic and the monoclinic one. The behavior of the diastereomeric mixture of pinane derived sulfoxides in crystals, melts and in tetrachloromethane solutions was studied by IR spectroscopy. The density functional theory (DFT) method with 6-31G (d, p) basis set was used to calculate the optimized geometrical parameters and vibrational frequencies of different associates in solutions. The calculated vibrational frequencies are compared with experimental IR spectra.

The EGFR Family: Not So Prototypical Receptor Tyrosine Kinases

The epidermal growth factor receptor (EGFR) was among the first receptor tyrosine kinases (RTKs) for which ligand binding was studied and for which the importance of ligand-induced dimerization was established. As a result, EGFR and its relatives have frequently been termed "prototypical" RTKs. Many years of mechanistic studies, however, have revealed that--far from being prototypical--the EGFR family is quite unique. As we discuss in this review, the EGFR family uses a distinctive "receptor-mediated" dimerization mechanism, with ligand binding inducing a dramatic conformational change that exposes a dimerization arm. Intracellular kinase domain regulation in this family is also unique, being driven by allosteric changes induced by asymmetric dimer formation rather than the more typical activation-loop phosphorylation. EGFR family members also distinguish themselves from other RTKs in having an intracellular juxtamembrane (JM) domain that activates (rather than autoinhibits) the receptor and a very large carboxy-terminal tail that contains autophosphorylation sites and serves an autoregulatory function. We discuss recent advances in mechanistic aspects of all of these components of EGFR family members, attempting to integrate them into a view of how RTKs in this important class are regulated at the cell surface.

Stable electro-optic response in wide-temperature blue phases realized in chiral asymmetric bent dimers [Invited

We report that an asymmetric bent dimer, consisting of a rod mesogen and a cholesterol mesogen linked by a flexible spacer with 9 carbon atoms, was found to form blue phases with a record-wide temperature range. Moreover, highly stable, fast electro-optic switching is possible. In addition to the stable Kerr effect, the electrostriction effect was also observed.

Structural and thermodynamic basis of the inhibition of Leishmania major farnesyl diphosphate synthase by nitrogen-containing bisphosphonates.

Farnesyl diphosphate synthase (FPPS) is an essential enzyme involved in the biosynthesis of sterols (cholesterol in humans and ergosterol in yeasts, fungi and trypanosomatid parasites) as well as in protein prenylation. It is inhibited by bisphosphonates, a class of drugs used in humans to treat diverse bone-related diseases. The development of bisphosphonates as antiparasitic compounds targeting ergosterol biosynthesis has become an important route for therapeutic intervention. Here, the X-ray crystallographic structures of complexes of FPPS from Leishmania major (the causative agent of cutaneous leishmaniasis) with three bisphosphonates determined at resolutions of 1.8, 1.9 and 2.3 Å are reported. Two of the inhibitors, 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium (300B) and 3-butyl-1-(2,2-diphosphonoethyl)pyridinium (476A), co-crystallize with the homoallylic substrate isopentenyl diphosphate (IPP) and three Ca(2+) ions. A third inhibitor, 3-fluoro-1-(2-hydroxy-2,2-diphosphonoethyl)pyridinium (46I), was found to bind two Mg(2+) ions but not IPP. Calorimetric studies showed that binding of the inhibitors is entropically driven. Comparison of the structures of L. major FPPS (LmFPPS) and human FPPS provides new information for the design of bisphosphonates that will be more specific for inhibition of LmFPPS. The asymmetric structure of the LmFPPS-46I homodimer indicates that binding of the allylic substrate to both monomers of the dimer results in an asymmetric dimer with one open and one closed homoallylic site. It is proposed that IPP first binds to the open site, which then closes, opening the site on the other monomer, which closes after binding the second IPP, leading to the symmetric fully occupied FPPS dimer observed in other structures.

Visualizing autophosphorylation in histidine kinases

Reversible protein phosphorylation is the most widespread regulatory mechanism in signal transduction. Autophosphorylation in a dimeric sensor histidine kinase is the first step in two-component signalling, the predominant signal-transduction device in bacteria. Despite being the most abundant sensor kinases in nature, the molecular bases of the histidine kinase autophosphorylation mechanism are still unknown. Furthermore, it has been demonstrated that autophosphorylation can occur in two directions, cis (intrasubunit) or trans (intersubunit) within the dimeric histidine kinase. Here, we present the crystal structure of the complete catalytic machinery of a chimeric histidine kinase. The structure shows an asymmetric histidine kinase dimer where one subunit is caught performing the autophosphorylation reaction. A structure-guided functional analysis on HK853 and EnvZ, two prototypical cis- and trans-phosphorylating histidine kinases, has allowed us to decipher the catalytic mechanism of histidine kinase autophosphorylation, which seems to be common independently of the reaction directionality.

Studying the Structural Origins of Microtubule Dynamic Instability through Combining Computational Modeling and cryoEM

Despite the importance of microtubule dynamic instability for their function in cell division and for the effect of anticancer drugs like taxol, understanding this macroscopic microtubule behavior at the structural level has been so far hindered by the limitations in cryoEM resolution available for this system. To gain mechanistic molecular understanding of the dynamic nature of microtubules, we have used real space refinement helical reconstruction to obtain cryoEM maps of microtubules in various ligand-bound states: GMPCPP, (a non-hydrolyzable GTP analog), GDP (dynamic microtubules), and GDP+taxol (drug-stabilized). These maps, ranging from 4.5 to 5 Angstrom resolution, represent the most detailed description of alpha and beta tubulin in the microtubule lattice to date. In order analyze the differences between the maps, we performed molecular refinement using the software Rosetta guided by the EM density, as well as information from available crystal structures. With this new approach, we were successful in obtaining well-converged ensembles of models that fit their respective maps significantly better than they fit the maps of other ligand-bound states. We find that the major differences between the GMPCPP and GDP bound microtubules is a compression along the longitudinal axis, accompanied by subtle structural rearrangements within the asymmetric dimer. This compression is not observed when comparing the GMPCPP and GDP+taxol bound structures, which are highly similar. The M-loop involved in lateral contacts between tubulins is modeled well in all of the maps by a short helical structure that is similar to that described recently in the zampanolide bound crystal structure of Steinmetz and colleagues. More detailed structural analysis is underway and will be presented at the conference.

Designed Hsp90 Heterodimers Reveal an Asymmetric ATPase-Driven Mechanism In Vivo

Hsp90 is a homodimeric ATPase that is essential in eukaryotes for the maturation of client proteins frequently involved in signal transduction, including many kinases and nuclear steroid hormone receptors. Competitive inhibitors of ATP binding to Hsp90 prevent client maturation and show promise as anticancer agents in clinical trials. However, the role of ATP binding and hydrolysis in each subunit of the Hsp90 dimer has been difficult to investigate because of an inability to assemble and study dimers of defined composition. We used protein engineering to generate functional Hsp90 subunits that preferentially assemble as heterodimers. We analyzed dimers wherein one subunit harbors a disruptive mutation and observed that ATP binding by both subunits is essential for function in yeast, whereas ATP hydrolysis is only required in one subunit. These findings demonstrate important functional contributions from both symmetric and asymmetric Hsp90 dimers and provide valuable reagents for future investigations of Hsp90 mechanism.

Dimerization-based control of cooperativity.

Cooperativity of ligand-receptor binding influences the input-output behavior of a biochemical system and thus is an important determinant of its physiological function. Canonically, such cooperativity is understood in terms of ligand-receptor binding affinity, where an initial binding event changes the affinity for subsequent binding events. Here, we demonstrate that dimerization-a simple yet pervasive signaling motif across biology-can have significant control over cooperativity and even dominate over the canonical mechanism. Through an exhaustive parameter sensitivity analysis of a general kinetic model for signal-mediated dimerization, we show that quantitative modulation of dimerization processes can reinforce, eliminate, and even reverse cooperativity imposed by the canonical allosteric ligand-receptor binding affinity mechanism. The favored accumulation of stoichiometrically asymmetric dimers (those with ligand-receptor stoichiometry of 1 : 2) is a major determinant of dimerization-based cooperativity control. However, simulations demonstrate that favoring accumulation of such stoichiometrically asymmetric dimers can either increase or decrease cooperativity, and thus the quantitative relationship between stoichiometrically asymmetric dimers and cooperativity is highly dependent on the parameter values of the particular system of interest. These results suggest that the dimerization motif provides a novel mechanism for both generating and quantitatively tuning cooperativity that, due to the ubiquity of dimerization motifs in biochemical systems, may play a major role in a host of biological functions. Thus, the canonical, allosteric view of cooperativity is incomplete without considering dimerization effects, which is of particular importance as dimerization is often a necessary feature of the allosteric mechanism.

Colloidal structures of asymmetric dimers via orientation-dependent interactions.

We apply an AC electric field to induce anisotropic interactions among asymmetric colloidal dimers. These anisotropic interactions, being shape-specific and orientation-dependent, can create complex and unique structures that are not possible for spherical particles or symmetric dimers. More specifically, we show a series of novel structures that closely resemble one- and two-dimensional antiferromagnetic lattices, including small clusters, linear chains, square lattices, and frustrated triangular arrays. All of them are uniquely formed by alternating association between dimers with opposite orientations. Our theoretical model attributes those patterns to an exquisite balance between electrostatic (primarily dipolar) and electrohydrodynamic interactions. Although similarly oriented dimers are strongly repulsive, the oppositely oriented dimers possess a concave shoulder in the pair interaction, which favors clustering to minimize the number of overlaps between neighboring particles. By combining the anisotropy in both particle geometry and field-induced interaction, our work suggests a new way to tailor colloidal interactions on anisotropic particles, which is important for both scientific understanding and practical applications.

Optical Sensing Using Dark Mode Excitation in an Asymmetric Dimer Metamaterial

We study the presence of dark and bright modes in a planar metamaterial with a double rod unit cell introducing geometric asymmetry in rod lengths. The dark mode displays a Fano-type resonance with a sharp asymmetric profile, rendering it far more sensitive than the bright mode to slight variations of the dielectric environment. This peculiar feature may envisage the possible application of the asymmetric dimer metamaterial as an optical sensor for chemical or biological analysis, provided that the effect of material losses on the dark mode quality factor is properly taken into account.

Structures and stabilities of asymmetric fullerene dimers: A density functional theory study

The molecular structure and the relative stability of asymmetric fullerene dimers were systematically investigated using density functional theory calculations. The most stable geometries for a directly-linked dimer of C130, and bridged dimers of C130O and C131 were identified among several isomers by using a total energy comparison. The relative stability of asymmetric dimers was defined by calculating the dissociation energy barrier of a fullerene dimer into two unit fullerenes. We found that the directly-linked asymmetric dimer C130 was not energetically stable and that the carbon-bridged dimer C131 was more stable than the oxygen-bridged dimer C130O. The electronic structures of the stable asymmetric dimers were also investigated.

Large group index induced by asymmetric split ring resonator dimer

In this manuscript, we experimentally and numerically demonstrate group delay enhancement of an asymmetric split ring resonators (SRRs) metamaterial dimer. By introducing minor different magnetic resonances between dimer SRRs, a sharp transmission peak located between two dips is observed, which is in analogy to classical electromagnetically induced transparency. Transmission phase of asymmetric SRR dimer experiences steep dispersion, resulting in an increase of group index to 150. Furthermore, the underlying physics can be explained by suppressed mode formed by opposite magnetic dipoles of asymmetric SRRs.