Molecular Spacer Research Articles

Resonant tunnelling diodes based on molecular wiresincorporating saturated spacers: a quantum-chemical study

The demand for increased miniaturization of integratedcircuits has opened the way to the emerging field of molecularelectronics. Recent experimental studies have established thatsingle molecules or a finite ensemble of self-assembledmolecules can perform the basic functions of conventionalelectronic components (i.e., transistors, wires and diodes). Inparticular, it has been demonstrated that molecular wiresinserted into nanopores can be used as active elements for thefabrication of resonant tunnelling diodes (RTDs), whose I/Vcharacteristics reveal a negative differential resistance (NDR)behaviour (i.e., a negative slope in the I/V curve). Here, weprovide a detailed quantum-chemical description of a possiblemechanism leading to NDR in polyphenylene-based molecular wiresincorporating saturated spacers. This mechanism can beunderstood from the evolution of the molecular wire one-electronstructure upon application of a static electric field alignedalong the molecular axis, which simulates the driving voltageapplied between the two electrodes in the RTD devices. The mainparameters controlling the NDR behaviour can be fine tunedthrough molecular engineering of the wires.

Supramolecular Recognition: Use of Cofacially Disposed Bis-terpyridyl Square-Planar Complexes in Self-Assembly and Molecular Recognition

A molecular receptor consisting of a molecular spacer that constrains two terpyridyl-palladium(II) complexes to be disposed in a parallel cofacial geometry has been prepared. The separation between the two terpyridyl-palladium units is enforced to be ca. 7 A, a distance sufficient to incarcerate aromatic molecules and square-planar complexes. A number of molecules are shown to associate with this spacer-chelator complex. In particular, 9-methylanthracene (9-MA) is found to form a 1 : 2 host-guest complex. A crystal structure of this complex shows one 9-MA in the molecular cleft formed by the two terpyridyl-palladium units and the other 9-MA molecule to lie above one of the terpyridyl-palladium units. Nuclear Overhauser effects on analogous molecules that contain two anthracene guests tethered intramolecularly indicate that the structure found in the solid is similar to that in solution. Low-temperature 1H-NMR studies indicate rapid exchange between the two binding sites. The spacer-chelator complexes, when combined with appropriate molecular linkers, readily form molecular rectangles, trigonal prisms, and tetragonal prisms. One molecular rectangle is shown to associate with up to five 9-MA molecules.

Synthesis and polymerization of amphiphilic methacrylates containing permanent dipole azobenzene chromophores

AbstractNew amphiphilic photochromic methacrylates with the structures of 4‐[ω‐methacryloyloxyoligo(ethyleneglycol)]‐4′‐cyanoazobenzene (MEn) and 4‐methacryloyloxy‐4′‐{2‐cyano‐3‐oxy‐3‐[ω‐methoxyoligo(ethyleneglycol)]prop‐1‐en‐1‐yl}azobenzene (MEnMe) and oligo(oxyethylene) segments of different lengths were synthesized. These methacrylates were characterized by the presence of permanent dipole azobenzene chromophores and hydrophilic oligo (oxyethylene) segments. The methacrylates were obtained with six‐step and five‐step synthetic sequences, respectively, in 12–47% overall yields. The radical polymerization of the MEn monomers afforded a 50% yield of the corresponding polymers as orange solids with a number‐average molecular weight of about 40 kD. No solid polymer was obtained from the radical polymerization of the MEnME compounds. Two‐dimensional NMR spectra allowed the unequivocal assignment of the NMR signals and demonstrated a significant contribution of internal charge transfer to the electronic distribution of the azobenzene chromophore. Relaxation time measurements confirmed that the flexible polyether segment effectively decoupled photochromic groups from the polymer backbone. Optical microscopy, differential scanning calorimetry analysis, and X‐ray diffraction data demonstrated the presence of interdigitated smectic mesophases. The stability of mesophases showed a significant dependence on the chemical structure of the analyzed compounds. The glass‐transition temperatures of the polymers were rather low because of the plasticizing effect of the spacers. The monomers and polymers were used for the deposition of Langmuir films and Langmuir–Blodgett–Kuhn multilayers. A strong influence of the macromolecular structure on the film properties was observed. The photoresponsive properties of monomers and polymers were investigated with irradiation at different wavelengths. Isomerization kinetics were independent of both molecular weight and spacer length. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 2957–2977, 2001

Supramolecular chemistry: molecular recognition and self-assembly using rigid spacer-chelators bearing cofacial terpyridyl palladium(II) complexes separated by 7 A.

Partially and fully aromatic molecular spacers bearing two symmetrically bound terpyridyl chelators have been prepared. These spacer-chelators were constructed to dispose the two terpyridyl ligands and their complexes with square planar metals cofacially with a separation of about 7 A between the two metals. Dipalladium(II) complexes of these spacer-chelators were prepared and characterized. These palladium complexes readily form large molecular rectangles with a linear linker such as 4,4'-dipyridyl. The dichlorodipalladium complex of the partially reduced spacer-chelator is capable of incarcerating planar aromatic and coordination compounds as guests. A crystal structure showing the incorporation of 9-methylanthracene has been determined. A 9-methylanthracene lies completely within the approximately 7 A space provided by the cleft formed by the two cofacially disposed chloro-palladium-terpyridyl units. The crystal structure shows additional pi-stacking interactions between a second 9-methylanthracene and neighboring receptors.

Supramolecular Chemistry. Supramolecular Rectangles and Their Guests

Two molecular spacers which cofacially dispose terpyridyl-palladium(II)-acetonitrile units separated by ∼ 7 Å are described. The spacers are polyaromatic molecules, one spacer is fully aromatic whereas the other has two symmetrically disposed reduced aromatic rings. Addition of the linker, 4,4′-dipyridyl, to solutions of these spacer-chelator complexes leads to the rapid and quantitative formation of supramolecular rectangles. It is found that the reduced rectangle forms a 4 : 1 adduct with 9-methylanthracene whereas the oxidized rectangle forms a 5 : 1 adduct with 9-methylanthracene. The possible reasons for this high level of agglomeration and the difference in adduct formation for the two systems are discussed.

Cis- and trans-Acting determinants for translation of psbD mRNA in Chlamydomonas reinhardtii.

Chloroplast translation is mediated by nucleus-encoded factors that interact with distinct cis-acting RNA elements. A U-rich sequence within the 5' untranslated region of the psbD mRNA has previously been shown to be required for its translation in Chlamydomonas reinhardtii. By using UV cross-linking assays, we have identified a 40-kDa RNA binding protein, which binds to the wild-type psbD leader, but is unable to recognize a nonfunctional leader mutant lacking the U-rich motif. RNA binding is restored in a chloroplast cis-acting suppressor. The functions of several site-directed psbD leader mutants were analyzed with transgenic C. reinhardtii chloroplasts and the in vitro RNA binding assay. A clear correlation between photosynthetic activity and the capability to bind RNA by the 40-kDa protein was observed. Furthermore, the data obtained suggest that the poly(U) region serves as a molecular spacer between two previously characterized cis-acting elements, which are involved in RNA stabilization and translation. RNA-protein complex formation depends on the nuclear Nac2 gene product that is part of a protein complex required for the stabilization of the psbD mRNA. The sedimentation properties of the 40-kDa RNA binding protein suggest that it interacts directly with this Nac2 complex and, as a result, links processes of chloroplast RNA metabolism and translation.

Model peptide studies of sequence repeats derived from the intracrystalline biomineralization protein, SM50. II. Pro,Asn-rich tandem repeats.

In the biomineralization process, a number of Pro-rich proteins participate in the formation of three-dimensional supramolecular structures. One such protein superfamily, the Pro,Gly-rich sea urchin intracrystalline spicule matrix proteins, form protein-protein supramolecular assemblies that modify the microstructure of the inorganic mineral phase (calcite) within embryonic sea urchin spicules and adult sea urchin spines. These proteins represent a useful model for understanding Pro sequence usage and the resulting generation of extended or "open" structures for protein-protein and/or protein-crystal recognition. In the sea urchin spicule matrix protein, SM50 (Strongylocentrotus purpuratus), there exists an unusual 20-residue Pro,Asn-containing repeat, &bond;PNNPNNPNPNNPNNPNNPNPbond which links the upstream 15-residue C-terminal domain and the downstream 211-residue beta-spiral repeat domain. To define the structural preferences of this 20-residue repeat, we created a 20-residue N- and C-terminal "capped" peptidomimetic of this sequence. Using far-uv CD dichroism, CH(alpha) and alpha-(15)N conformational shifts, (3)J(NH-CHalpha) coupling constants, sequential d(NN(i, i + 1)) rotating frame nuclear Overhauser effect connectivities, d(alphaN(i, i + 1))/d(NN(i, i + 1)) intensity ratios, amide temperature shift coefficients, amide solvent exchange, and simulated annealing refinement protocols, we have determined that this 20-residue repeat motif adopts an extended "twist" structure consisting of turn- and coil-like regions. These findings are consistent with previous studies, which have shown that Pro-rich tandem repeats adopt extended, flexible structures in solution. We hypothesize that this 20-residue repeat may fulfill the role of a mineral-binding domain, a protein-protein docking domain, or as an internal "molecular spacer" for the SM50 protein during spicule biocomposite formation.

Dinuclear metallo-phosphodiesterase models: application of calix[4]arenes as molecular scaffolds

An important goal in supramolecular chemistry is the synthesis of molecules that exhibit catalytic activity analogous to the activity of enzymes. In this respect, studies toward the biomimetic catalysis of phosphate diester cleavage have received particular attention. In nature this process is catalyzed by enzymes that possess often two or three divalent metal ions in their active sites. In order to mimic the active sites of these metallo-phosphodiesterases chemists generally attempt to connect ligated metal ions by a molecular spacer in such a way that the metal–metal distance matches with the anionic pentacoordinate phosphorus transition state. However, in contrast to enzymes, which bind the transition state by multiple contacts via an induced fit mechanism, many of the low molecular weight model systems exhibit only minor catalytic activity due to lack of catalytic groups and too much rigidity or flexibility. Our approach is to use calix[4]arenes as a molecular scaffold for the dynamic preorganization of multiple catalytic groups. In this review models for dinuclear metallo-phosphodiesterases and the use of calix[4]arenes in such models are described.

Roles for glycosylation of cell surface receptors involved in cellular immune recognition

The majority of cell surface receptors involved in antigen recognition by T cells and in the orchestration of the subsequent cell signalling events are glycoproteins. The length of a typical N-linked sugar is comparable with that of an immunoglobulin domain (30 Å). Thus, by virtue of their size alone, oligosaccharides may be expected to play a significant role in the functions and properties of the cell surface proteins to which they are attached. A databank of oligosaccharide structures has been constructed from NMR and crystallographic data to aid in the interpretation of crystal structures of glycoproteins. As unambiguous electron density can usually only be assigned to the glycan cores, the remainder of the sugar is then modelled into the crystal lattice by superimposing the appropriate oligosaccharide from the database. This approach provides insights into the roles that glycosylation might play in cell surface receptors, by providing models that delineate potential close packing interactions on the cell surface. It has been proposed that the specific recognition of antigen by T cells results in the formation of an immunological synapse between the T cell and the antigen-presenting cell. The cell adhesion glycoproteins, such as CD2 and CD48, help to form a cell junction, providing a molecular spacer between opposing cells. The oligosaccharides located on the membrane proximal domains of CD2 and CD48 provide a scaffold to orient the binding faces, which leads to increased affinity. In the next step, recruitment of the peptide major histocompatibility complex (pMHC) by the T-cell receptors (TCRs) requires mobility on the membrane surface. The TCR sugars are located such that they could prevent non-specific aggregation. Importantly, the sugars limit the possible geometry and spacing of TCR/MHC clusters which precede cell signalling. We postulate that, in the final stage, the sugars could play a general role in controlling the assembly and stabilisation of the complexes in the synapse and in protecting them from proteolysis during prolonged T-cell engagement.

Biological properties of synthetic glycoconjugate mimics of heparin comprising different molecular spacers.

The in vitro antithrombotic activity of synthetic glycoconjugates I and II, comprising a flexible polyethylene glycol type and a rigid polyglucose type spacer, respectively, are compared to heparin.

Transient Shear Flow Behavior of Dilute Solutions of Side-Chain Liquid-Crystalline Polysiloxanes in 4,4‘-(n-Pentyloxy)cyanobiphenyl

The transient stress response of homeotropic monodomains of dilute nematic solutions of side-chain liquid-crystalline polysiloxanes (LCPs) in 4,4‘-(n-pentyloxy)cyanobiphenyl (5OCB) is investigated. In contrast to the flow-aligning behavior of 5OCB, strong stress oscillations are observed for the dilute LCP solutions, characteristic of flow-tumbling behavior. The dependence of the oscillation periodicity on LCP concentration and LCP structure (molecular weight and spacer length) is presented. From analysis of the stress transients, the Leslie viscosity coefficients, α2 and α3, are calculated. For all LCP structures, the increment δα2 on dissolution of LCP is negative, whereas the increment δα3 is positive. The magnitude and signs of these viscosity increments are strictly inconsistent with earlier electrorheological measurements of the Miesowicz viscosity increments, δηb and δηc, of these solutions, using as a guide a hydrodynamic model that computes the contribution of the chains to viscous dissipation in a simple shear flow. We propose that an additional dissipation mechanism should be considered, which derives from the presence of an elastic torque between director rotation and LCP orientation. Corresponding modification of the theory leads to improved agreement with experiment.

Electronic energy transfer in solution in naphthalene-anthracene, naphthalene-acridine and benzene-DANS bichromophoric compounds

Intramolecular energy transfer (intraEET) in naphthalene-anthracene ( I), naphthalene-acridine ( II) and benzene-DANS ( III) bichromophoric compounds was investigated by stationary absorption and fluorescence measurements in solution. Computer simulations of conformational distributions of compounds I (with n = 1, 3 and 6 methylene units as spacer groups) in the gas phase were performed and predict similar molecular structures for n = 3 and 6, which is consistent with previous observations in a supersonic jet expansion. In compounds I, fast intraEET (rate constant k EET > 1 × 10 10 s −1) was observed upon electronic excitation of the naphthalene moieties, whereas in compound III with 6 methylene units and an amide group as molecular spacer, a significantly slower intraEET was found ( k EET = (1.0 0 5) × 10 8 s −1 ). The result is discussed within the framework of the Fermi Golden Rule expression. Differences in Franck-Condon weighted density of EET acceptor states and of the mutual orientation of the two chromophoric units were found to account for the different intraEET efficiencies. This work provides no evidence for intraEET in compounds III.

Electrorheological Behavior of Side-Chain Liquid-Crystalline Polysiloxanes in Nematic Solvents

The electrorheological properties of well-characterized side-chain liquid-crystalline polysiloxanes with different backbone and spacer lengths were studied in two nematic solvents: 4‘-(pentyloxy)-4-biphenylcarbonitrile (5OCB), which has positive dielectric anisotropy, and N-(4-methoxybenzylidene)-4-butylaniline (MBBA), which has negative dielectric anisotropy. Specifically, we measured the steady-shear viscosities, ηoff and ηon, in the absence and presence, respectively, of a saturation electric field. For 5OCB solutions, the electrorheological (ER) effect is positive, i.e., ηon > ηoff. For the intrinsic viscosities, we find [ηoff] ≫ [ηon], and [ηoff] shows a strong dependence on molecular weight ([ηoff] ∼ M0.4) and spacer length, whereas [ηon] is insensitive to the change of molecular weight and spacer length. In contrast, the ER effect of MBBA solutions is very small and slightly negative, i.e., ηon < ηoff. In addition, [ηoff] and [ηon] are of comparable magnitude and each shows a strong dependence on molecular weight ([ηoff] ∼ [ηon] ∼ M0.3). These distinctive patterns of ER behavior can be explained by a hydrodynamic model which assumes the side-chain liquid-crystalline polysiloxane has an asymmetric conformation, such that the root-mean-square end-to-end distance parallel to the director, R∥, is different from that perpendicular to the director, R⊥. R∥ is aligned along the shear gradient in 5OCB when the field is on but is tilted toward the flow direction with the field off. In MBBA, R∥ is oriented perpendicular to the shear gradient both with the field on and with the field off.

SERS spectroscopy with Ag colloids

The possibilities of overcoming some drawbacks encountered in SERS spectroscopy with Ag colloids are presented and discussed. Modification of Ag colloidal surface by molecular spacer is shown to be a suitable way for obtaining SERRS spectra of unperturbed free-base prophyrin species as well as of a metalloporphyrin which cannot be spontaneously adsorbed on a bare Ag colloidal surface. Furthermore, preparation of stable, long-term SERS-active two-dimensional Ag colloid-adsorbate films is described and the effect of the adsorbate structure on the morphology of the films, expressed in terms of fractal dimension, is discussed.

Influence of Backbone Rigidity on the Thermotropic Behavior of Side-Chain Liquid Crystalline Polymers Synthesized by Ring-Opening Metathesis Polymerization

The effect of backbone flexibility on the mesomorphic behavior of side-chain liquid crystalline polymers synthesized by ring-opening metathesis polymerization was investigated. The synthesis of norbornene and cyclobutene monomers containing a p-nitrostilbene moiety as the mesogenic group and polymerization of these monomers to produce side-chain liquid crystalline polymers with low polydispersities and defined molecular weights was accomplished. The relatively rigid poly(norbornene)s displayed enantiotropic nematic mesomorphism with glass transitions from 44 to 64 °C and isotropization temperatures between 108 and 121 °C, whereas the more flexible poly(butadiene)s showed enantiotropic smectic A mesomorphism with glass transition temperatures from 14 to 31 °C and isotropization temperatures between 74 and 111 °C. A diblock copolymer containing a 1:1 mixture of the poly(norbornene) and poly(butadiene) also exhibited a smectic A mesophase, clearly demonstrating the dominance of the poly(butadiene) backbone. The dependence of the degree of polymerization and flexible spacer length on the phase transitions of these systems was determined, demonstrating stabilization of the mesophase by both increasing molecular weight and flexible spacer length.

Space‐Separated 1,10‐Phenanthroline, 4,5‐Diazafluorene, or 3,6‐Di(2‐pyridyl)pyridazine Units as Ligands in Diruthenium Complexes: Preliminary Studies of Metal–Metal Interactions

In new bridging ligands the chelating groups listed in the title are fused to the termini of rigid molecular spacers. The resulting bisbidentate ligands such as those shown below have been prepared with matching and different terminal groups, and the coordination centers are arranged with varying separations and orientations. Selected bridging ligands and polypyridylruthenium(II) moieties were used to prepare dinuclear complexes, which were examined in electrochemical experiments. E  CO2CH3.

Surface-enhanced resonance Raman spectra of water-insoluble tetraphenylporphyrin and chlorophyll a on silver hydrosols with a dioxane molecular spacer

A surface-enhanced resonance Raman spectroscopic (SERRS) study of tetraphenylporphyrin (TTP) on a silver hydrosol, obtained by mixing a dioxane solution of the water-insoluble TPP with the hydrosol, indicates that there is no metallation of the porphyrin. By contrast, water-soluble porphyrins such as tetra-N-methylpyridylporphyrin (TMPyP) have been shown to undergo metallation. We suggest that the TPP is encapsulated within a dioxane envelope which is co-adsorbed to the surface of the silver hydrosol and functions as a molecular spacer. This spacer does not eliminate the analytical advantages afforded by SERRS, but does prevent significant perturbation from the native conformation, as is demonstrated by results obtained using chlorophyll a.

Evidence for Inefficient Chain-to-Chain Coupling in Electron Tunneling through Liquid Alkanethiol Monolayer Films on Mercury

Distance dependence and the intervening medium effects continue to pin the attention of a large number of scientists as the key unresolved problems in the area of electron transfer kinetics.1-3 In this communication, we report electrochemical results describing long-range electron transfer kinetics across two types of alkanethiol monolayer films of variable thickness. Our data show that the geometric distance decay constant involving a chain-to-chain tunneling pathway obtained for liquid monolayers is approximately 5 times smaller than the throughchain decay constant characteristic for ordered alkylthiol monolayers. Many recent advances in the studies of intervening medium effects in electron tunneling have been made using the following two experimental approaches. In the first, synthetic donor/ acceptor pairs are separated by rigid molecular spacer groups of controlled length and structure.4-6 In the second, investigations involve redox proteins in which an electron acceptor (or donor) is attached to a specific site on the periphery of a protein.3,7,8 In addition, electrochemical measurements in which molecules are tethered to the electrode surface at a specific distance have also been successfully explored.9 In related research, recent studies of electron tunneling using selfassembled monolayers of alkanthiols as barrier films on gold electrodes have been particularly successful.10-15 The experiments described below rely on alkanethiol monolayers assembled on mercury. The use of Hg electrodes allows us, for the first time, to vary the thickness of the monolayers in two different ways. The first involves the usual formation of ordered monolayers of thiols with alkyl chains of different length.16 The second method is intrinsic only to Kublik type hanging mercury drop electrodes (HMDE).17 Variation of the monolayer thickness is accomplished by careful expansion of the mercury drop using a micrometric screw that controls the volume of mercury extruded at the tip of the HMDE capillary. Formation structure and properties of alkanethiol monolayers on gold are well documented in the literature.18-21 Similar procedures lead to the formation of ordered thiol monolayers on mercury.22,23 Indeed, our results suggest that impermeable monolayers of alkanethiols with chain length from 9 to 18 carbon atoms are formed essentially instantaneously on HMDE.24 As shown in Figure 1, analysis of the differential capacitance (C) measurements25 gave linear plots of 1/C vs number of the alkyl chain carbon atoms. This is consistent with the Helmholtz model of the double layer in which its capacitance is dominated by the hydrocarbon film of variable thickness (d)12,26 and is expressed by C ) oA/d (1)

Polyphosphazenes with High Refractive Indices: Synthesis, Characterization, and Optical Properties

This work was carried out in order to demonstrate that polymers with tunable, high refractive index values can be designed and synthesized to fit a variety of optical applications. A series of polyphosphazenes bearing conjugated, organic side groups were synthesized and their refractive indices were measured. Refractive index values ranging from 1.60 to 1.75 were obtained. A systematic approach to tailoring various polymer properties such as refractive index, optical absorption, solubility, and glass transition temperature was utilized in the synthesis of these polymers. Control over the extent of conjugation of the side group, side group molecular symmetry, and the use of a molecular spacer group were employed to achieve this goal. These polymers can be cast from solution and used in applications that require optically transparent films.

Self-order in flexible non-mesogenic macromolecules

Some very flexible linear poly(di-n-alkylsiloxane)s and cyclolinear oligo- and polyorganosiloxanes, which do not contain classical rigid rodlike or disclike mesogens, similar to other semi-organic polymers like polyphosphazenes and polysilanes, can form thermodynamically stable two-dimensionally ordered thermotropic mesophases. In many respects the mesophases in polysiloxanes resemble columnar liquid crystals which seems to be the result of the amphiphilic constitution of the polyorganosiloxanes. The origin of the mesomorphic state seems to be closely related to the competition between the interaction of the polar inorganic backbones and those of the organic side chains facilitated by the high flexibility of the inorganic main chain. Similarily to discotic liquid crystals, mesophases in polysiloxanes consist mostly of columns packed hexagonally (or closely so) with lateral long-range positional order, but with only short-range order along the columns. The unique feature of the columnar mesophases is that the axes of macromolecules lie along the column axes. The influence of molecular structure and molecular mass of linear macromolecules is discussed. It has been demonstrated that the temperature interval of mesophase stability is critically dependent on the length of the alkyl side chains. Both the process of formation of the mesophase from the isotropic melt and the crystallization of the mesophase are nucleation controlled processes, although the crystallization of the mesomorphic state is characterized by some specific features. The phase behaviour of cyclolinear polyorganosiloxanes is described with particular emphasis on the temperature stability as a function of molecular structure, tacticity, substituents and flexible spacers.