Intermolecular Junctions Research Articles

'Molecular Beam Epitaxy' on Organic Semiconductor Single Crystals: Characterization of Well-Defined Molecular Interfaces by Synchrotron Radiation X-ray Diffraction Techniques.

Epitaxial growth, often termed “epitaxy”, is one of the most essential techniques underpinning semiconductor electronics, because crystallinities of the materials seriously dominate operation efficiencies of the electronic devices such as power gain/consumption, response speed, heat loss, and so on. In contrast to already well-established epitaxial growth methodologies for inorganic (covalent or ionic) semiconductors, studies on inter-molecular (van der Waals) epitaxy for organic semiconductors is still in the initial stage. In the present review paper, we briefly summarize recent works on the epitaxial inter-molecular junctions built on organic semiconductor single-crystal surfaces, particularly on single crystals of pentacene and rubrene. Experimental methodologies applicable for the determination of crystal structures of such organic single-crystal-based molecular junctions are also illustrated.

Crosslinking dextran electrospun nanofibers via borate chemistry: Proof of concept for wound patches

Dextran-based formulations represent promising candidates for the fabrication of biocompatible scaffolds in tissue engineering or as vehicles for drug delivery. Previous investigations showed that, on its own, dextran is able to promote wound healing in vivo in rat models. Its inherent solubility in water, however, must be overcome by inserting inter-molecular junctions via the use of cross-linkers. While conventional cross-linking methods tend to utilize toxic compounds, such as glutaraldehyde, we demonstrate that simple mixtures of dextran and boric acid, in aqueous solutions, can be electrospun to obtain membranes with controlled degradation times. Boric acid covalently links to the hydroxyls moieties present in the dextran chains yielding boronate ester bridges between dextran chains. Variation in the cross-linking density enhanced the average drug release time up to 500% compared to pristine dextran electrospun scaffolds.

Association of κ-carrageenan subjected to deep alkaline hydrolysis.

κ-carrageenan is a linear sulfated anionic gelling polysaccharide obtained from red seaweed algae by an alkaline hydrolysis. We applied static and dynamic light scattering (DLS), capillary viscometry, FT-IR, and electrophoretic DLS to gain insight into the effect of deep alkaline hydrolysis (95 °C, pH = 10 during Th = 60, 75, and 90 min) on κ-carrageenan macromolecules in a coil conformation. As DLS of coil-like κ-carrageenans is usually complicated by spurious permanent aggregates, the alkaline hydrolysis of κ-carrageenans has not been studied by DLS. By applying a double-dialysis procedure (first against water, then against 0.1 M NaCl), we succeeded in obtaining dilute solutions of coil-like κ-carrageenans with unimodal DLS distributions. Association that started with increasing concentration was attributed to attractive dipole-dipole interactions between ion-pairs formed by condensed counter-ions in the vicinity of carboxyl groups of the reducing ends. The second type of stickers resulted from the compositional heterogeneity of κ-carrageenan, namely, from the traces of ι-carrageenan blocks which amount increased with hydrolysis. With increasing Th we observed both the progressive decrease of molecular mass and the growth of association. Lowering the temperature and increasing concentration during lyophilization strengthened the intermolecular junctions, leading to the formation of permanent aggregates.

Steric Influence and Intermolecular Interactions of Formamidinate Ligands in Lanthanide (Sm, Yb) Arylchalcogenolate Complexes

The complexes [Ln(DippForm)2(QAr)(THF)] [DippForm = N,N′‐(2,6‐diisopropylphenyl)formamidinate; Ln = Sm, Yb; QAr = SPh, SePh, TePh, SeC6F5, Se(p‐C6F4OMe)] were synthesized by reduction of corresponding dichalcogenides Ar2Q2 with the LnII formamidinates, [Ln(DippForm)2(THF)2]. All complexes with QPh ligands have similar molecular structure (determined by X‐ray diffraction), they are mononuclear due to the effective shielding of the central atom by the bulky amidinate ligands, and possess transoid disposition of the latter. The complexes with fluorinated phenyl groups (ArF) possess an additional coordination of an o‐F atom to the lanthanide ion. Only the compounds [Yb(DippForm)2(QArF)(THF)] easily lose the coordinated THF due to the sterically crowded coordination sphere, and the addition of THF is reversible even at ambient temperature. The Sm compounds are stable towards elimination of THF upon moderate heating. Similar crystal packing is found for most of the complexes, except for [Sm(DippForm)2(SPh)(THF)], [Yb(DippForm)2(SeC6F4OMe)(THF)] and [Yb(DippForm)2(SeC6F5)], which was rationalized as a consequence of interaction of FormDipp ligands from neighboring molecules to form intermolecular junctions. Analogous junctions were found in the majority of known complexes with Ln(DippForm)2 moiety (for all lanthanides). In the IR spectra the bands characteristic to the C–N, C–F and C–O bonds were revealed, some of which are noticeably influenced by the type of co‐ligands.

Two-Dimensional FTIR Spectroscopic Characterization of Functional Groups of NaOCl-Exposed Alginate: Insights into Membrane Refouling after Online Chemical Cleaning

In-depth understandings of the interactions between NaOCl and foulants (e.g., alginate) at a molecular level can provide a deeper insight into the optimization of chemical cleaning. In this study, two-dimensional Fourier transform infrared correlation spectroscopic (2D-FTIR-COS) analysis was used to probe the hypochlorite oxidation of alginate at normal wastewater treatment operating pH (i.e., 6, 7, and 8). The 2D-FTIR-COS characterization indicated that the groups in alginate were degraded by NaOCl in a similar sequence at all investigated pHs: carboxylate groups (-COOH at pH 6 and 7) > C-O-C bonds, C-O bonds of uronic acids > C-O-C bonds. The results also showed that the presence of hemiacetals, which are formed by uronic acids, can protect alginate chains from oxidation during their initial exposure to NaOCl (30 min) and thus maintain alginate at a constant molecular size. Additionally, the rupture of C-O-C bonds resulting from initial oxidation (30 min) increased the viscosity of alginate solution because of the decreased stiffness of alginate chains and the rise of stronger intermolecular junctions. Long-term exposure to NaOCl (480 min) largely degraded uronic acids and the C-O-C bonds of alginate molecules, leading to decreases in molecular weight and viscosity at pH 6 and 7. However, because of the low degree of oxidation at pH 8, molecular weight and viscosity of alginates were slightly changed after long-term exposure (480 min) to NaOCl. Our results imply that the partial oxidation of alginate during hypochlorite scavenging enhanced its fouling propensity, which could have a potential implication for the implementation of chemical cleaning.

Chitosan-Based Material for Cellular Tissue Engineering

Aqueous dispersed media and films based on edible or succinate chitosan with single-walled carbon nanotubes (SWCNTs) were manufactured. Infrared spectroscopy and Raman spectroscopy were used to study the structural changes associated with formation of intermolecular junctions between chitosan and SWCNT. Nonlinear optical characteristics of liquid samples exposed to pulsed laser radiation of nanosecond duration were determined experimentally and calculated theoretically. The composition of the medium based on succinate chitosan and SWCNT providing the largest nonlinear absorption coefficient (902 cm/GW) was determined. The sample with this composition had lower threshold radiation intensity (2.7 MW/cm2), at which nonlinear effects are generated in the medium and liquid-to-solid transition occurs. The results obtained in this work are useful for laser-based production of three-dimensional cellular and tissue-engineered structures used in cardiovascular surgery.

Density variant carbon nanotube interconnected solids.

The scalable fabrication of 3D macroscopic solids with controllable densities of nano­scale junctions between carbon nanotubes (CNTs) is reported using chemical vapor deposition. The nanoscale intermolecular junctions result in porous solids with high thermal stability, electrical conductivity, excellent mechanical properties, and structural stability in concentrated acids, bases, and organic solvents. Such CNT solids represent the next generation of carbon-based materials with potential for a broad range of applications.

Small metal–organic molecular sandwiches: Versatile units for induced structure manipulation

Interfaces between metal atoms and organic molecules are key units of many important metal–organic systems. Presented are results of ab initio calculations for a series of complexes of 2nd-row metal atoms sandwiched between small unsaturated hydrocarbon molecules. Evolution of the system structure and stability is studied for different metal atoms, as well as upon excitation, ionization and electron attachment. Predicted interesting features include cooperative stabilization, unusual geometries, reversible charge- or excitation-governed geometry alterations. The observed variety of properties suggests potential applications of such species as intermolecular junctions and units with charge- or spin-controlled shapes in molecular devices and/or machines.

Controlled Fabrication of Intermolecular Junctions of Single‐Walled Carbon Nanotube/Graphene Nanoribbon

Intramolecular junctions can be formed in single-walled carbon nanotubes (SWNTs) by introducing a pentagon and/or heptagon into the hexagonal carbon lattice. The realization of these carbon-based molecular electronics is still quite challenging. Here, it is reported that nickel or cobalt catalyzed etching can be applied to partially unzip an SWNT into an intermolecular junction of SWNT/graphene nanoribbon, directly confirmed by atomic force microscopy and Raman spectroscopy.

ELECTRON TRANSFER THROUGH NON-HYDROGEN AND HYDROGEN BONDED INTERMOLECULAR TUNNEL JUNCTIONS: A COMPUTATIONAL STUDY

The nature of electron transfer through intermolecular tunnel junctions has been studied. Intermolecular junctions feature non-hydrogen and hydrogen bonded interactions and are defined by the end groups of pairs of functionalized conjugated alkenes. We compared the distant dependent electron transfer from donor to acceptor group attached to the other sides of those functionalized conjugated alkenes. Study shows electron transfer coupling matrix element for these intermolecular junctions decays exponentially as a function of junction separation and quite substantial in energetically favourable hydrogen bonded intermolecular junctions.

Interface bands in carbon nanotube superlattices

AbstractWe study the electronic band structure of several carbon nanotube superlattices built of two kinds of intermolecular junctions: (12, 0)/(6, 6) and (8, 0)/(14, 0). In particular, we focus on the energy bands originating from interface states. We find that in case of the metallic (12, 0)/(6, 6) superlattices, the interface bands change periodically their character from bonding‐ to antibonding‐like vs. increasing length of the (6, 6) tube.We show that these changes are related to the decay of the charge density Friedel oscillations in the metallic (6, 6) tube. However, when we explore other chiralities without rotational symmetry, no changes in bondingantibonding character are observed for semiconductor superlattices, as exemplified in the case of (8, 0)/(14, 0) superlattices. Our results indicate that unless metallic tubes are employed in the junctions, the bondingantibonding crossings are not present (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Tropomyosin Flexibility Evaluated by Electron Microscopy Image Analysis

Movement of tropomyosin (Tm) on thin filaments in response to Ca2+-binding to troponin and myosin binding to actin is an inherent feature of muscle regulation. As part of this process, the cable-like mechanical properties of the Tm coiled-coil are thought to underlie cooperative on and off switching of contraction. In principle, movement of Tm over the flat surface of actin may not require significant molecular flexibility. However, local perturbations caused, for example, by myosin binding on actin may necessitate some plasticity of the Tm molecule. In contrast, any large-scale Tm flexibility might dampen its cooperative movement. In the current study, we directly assessed the flexibility of Tm by examining EM images of both rotary shadowed and negatively stained molecules. Single Tm molecules in both image sets showed no obvious signs of sharp bending or kinks, and displayed contours close to those predicted from a high-resolution 3D model of Tm (Lorenz et al., 1995). Short multimeric strings of end-to-end bonded Tm were commonly observed in the rotary shadowed images. These showed no pronounced bending or joints at the intermolecular junctions. The persistence length of Tm was calculated to be over twice the length of the molecule based on these EM images. The data as a whole imply that Tm molecules exhibit an intrinsic stiffness sufficient to contribute to cooperativity on thin filaments and thus are consistent with models of muscle regulation (e.g. Lehrer & Geeves, 1998; Lehman et al., 2000). A tropomyosin mutant in which the coiled-coil interface was destabilized by introduction of Ala clusters in the 2nd and 3rd periodic repeats (Y60A-L64A-L106A; Singh & Hitchcock-DeGregori, unpublished) was also examined by EM. No obvious extra bending was observed, although the calculated persistence length was significantly shortened, showing the sensitivity of the technique.

Structure of the N terminus of a nonmuscle alpha-tropomyosin in complex with the C terminus: implications for actin binding.

Tropomyosin is a coiled-coil actin binding protein that stabilizes the filament, protects it from severing, and cooperatively regulates actin's interaction with myosin. Depending on the first coding exon, tropomyosins are low molecular weight (LMW), found in the cytoskeleton and predominant in transformed cells, or high molecular weight (HMW), found in muscle and nonmuscle cells. The N- and C-terminal ends form a complex that allows tropomyosin to associate N terminus-to-C terminus along the actin filament. We determined the structure of a LMW tropomyosin N-terminal model peptide complexed with a smooth/nonmuscle tropomyosin C-terminal peptide. Using NMR and circular dichroism we showed that both ends become more helical upon complex formation but that the C-terminal peptide is partially unfolded at 20 degrees C. The first five residues of the N terminus that are disordered in the free peptide are more helical and are part of the overlap complex. NMR data indicate residues 2-17 bind to the C terminus in the complex. The data support a model for the LMW overlap complex that is homologous to the striated muscle tropomyosin complex in which the ends are oriented in parallel N terminus-to-C terminus with the plane of the N-terminal coiled coil perpendicular to the plane of the C terminus. The main difference is that the overlap spans 16 residues in the LMW tropomyosin complex compared to 11 residues in the HMW striated muscle overlap complex. We discuss the relevance of a stable but dynamic intermolecular junction for high-affinity binding to actin.

Carbon Nanotube T Junctions: Formation and Properties

The formation of carbon nanotube T junctions (CNTJs) and their transport properties are reviewed. The CNTJs were formed by coupling chemically functionalized nanotubes with linker molecules. Both end-to-side and end-to-end intermolecular junctions can be assembled by reacting chloride terminated nanotubes with aliphatic diamines. The functionalized nanotube mats were characterized by Raman spectroscopy and X-ray photoelectron spectroscopy. The incorporation of functional groups into nanotubes is indicated by the pronounced shift of tangential vibration modes in Raman spectra and of carbon is binding energy in X-ray photoelectron spectra. For transport measurements the functionalized nanotubes were adsorbed on Si substrates, and subsequent electrodes were painted on top of the selected T junctions by lithography and lift-off techniques. The bar of the "T" is used as the transistor channel and the stem of the "T" is used as the gate. In this configuration, the active area is confined to a few nanometers in all three dimensions.

Bimolecular Networks and Supramolecular Traps on Au(111)

We demonstrate the formation of intermixed phases and self assembled molecular templates on the Au(111) surface. The templates are stabilized by hydrogen bonding between melamine molecules with trigonal symmetry and linear PTCDI (perylene tetra-carboxylic di-imide) molecules. When annealed, these molecules spontaneously form either a chiral intermixed phase or a honeycomb arrangement in which vertexes and edges correspond respectively to melamine and PTCDI molecules. We also observe minority phases with more complex intermolecular junctions. The use of these networks as templates is demonstrated by the controlled capture of fullerenes within the pores of the network to form dimers, hexamers, and heptamers. Our results confirm that bimolecular templates can be realized on a range of substrates.

Association under shear flow in aqueous solutions of pectin

Effects of oscillatory and steady shear flows on intermolecular associations in dilute and semidilute aqueous solutions of pectin in the absence and presence of the hydrogen bond breaking agent urea are reported. A weak oscillatory shear perturbation builds up, depending on polymer concentration, multichain aggregates or networks in the course of time and these association structures are mainly stabilized through hydrogen bonds. The association effect is more pronounced at higher concentrations, and the growth of intermolecular interactions is inhibited by the addition of urea. Steady shear measurements on the pectin–water solutions reveal shear thickening at low shear rates for all the concentrations, except the lowest one, and disruption of intermolecular junctions at high shear rates. In the presence of urea, no shear thickening is detected. The polymer concentration dependence of the viscosity at a low shear rate can be described by a power law η ∼ c x , with x = 1.9 and 1.4 without and with urea, respectively. When a low constant shear rate is applied to pectin solutions and this monitoring shear rate is interrupted periodically by transitory high shear rates perturbations during a short time, prominent association structures evolve upon return to the monitoring shear rate. This effect is more evident at a lower polymer concentration, and in the presence of urea, the growth of the association complexes is damped. The shear-induced alignment and stretching of polymer chains and the formation of hydrogen-bonded structures are analyzed in the framework of a model, where cooperative zipping of stretched chains play an important role. Viscosity enhancement is found for a semidilute pectin–water solution in the presence of moderate levels of salt addition (NaCl), suggesting that partial screening of electrostatic interactions promotes growth of energetic cross-links.

Solution rheology of hydrophobically modified associative polymers: Effects of backbone composition and hydrophobe concentration

We investigate the effects of polymer molecular structure on the solution rheology of a hydrophobically modified associative polymer comprised of macromonomers with alkyl hydrophobes attached to a poly(ethyl acrylate-co-methacrylic acid) backbone. In particular, the effect of polymer backbone composition with variable proportions of methacrylic acid (MAA) and ethyl acrylate (EA) are examined. We find that the concentration of the MAA monomer has a large impact on polymer viscoelasticity. Polymers with low MAA content have smaller hydrodynamic size that result in lower viscosities and dynamic elastic moduli compared to polymers with high MAA content. Moreover, the balance between the polymer hydrodynamic size, the chain flexibility, and the aggregation of the EA blocks yield maxima in these material functions with respect to the MAA concentration. The scaling of shear viscosity, high frequency elastic modulus, and creep compliance with polymer concentration exhibits power-law behavior with different exponents. In all cases, three power-law regimes, regardless of the MAA content, are observed that can be attributed to the presence of different modes of hydrophobic interaction. However, the transitions shift to lower concentrations as the MAA content increases. With regards to the effects of the macromonomer side-chain concentration, we observe a substantial increase in viscosity at intermediate macromonomer content (1 mol %), possibly due to an increase in the number of intermolecular junctions as the number of hydrophobes per chain increases. This is in contrast to (i) low macromonomer concentration (0.3 mol %) behavior that reveals low viscosity due to weak hydrophobic associations, and (ii) high macromonomer concentration (1.9 mol %) behavior that favors more intramolecular association resulting in lower viscoelastic properties compared to intermediate macromonomer concentrations.

Modeling and simulations of carbon nanotubes and their junctions on surfaces

Recent experiments demonstrated lattice-oriented growth, controlled manipulation of carbon nanotubes and their nanoelectronic devices on surfaces. Using molecular dynamics simulation method and by performing electronic structure and electron transport calculations, we investigate nanotubes and their intermolecular junctions on surfaces. It is demonstrated that local atomic structure in nanotube–surface and nanotube–nanotube contacts plays important roles in friction and electronic transport at the nanoscale. Each nanotube has unique equilibrium orientations with respect to surface structure. Electronic transport is strongly enhanced when the atomic structures of the objects in contact are commensurate.

Interconnection of carbon nanotubes by chemical functionalization

Intermolecular carbon nanotube junctions were formed by coupling chemically functionalized nanotubes with molecular linkers. An end-to-side or end-to-end heterojunction can be formed by reacting chloride terminated nanotubes with aliphatic diamine. The chemically modified nanotube mats were characterized by Raman spectroscopy. The peak shift in the tangential vibration mode reveals that the attached chemical functional groups can behave as either an electron donor or an acceptor, and facilitate charge transfer with the nanotube host. The charge transfer is also verified by transport measurements on individual end-to-side intermolecular junctions, which show diode-like behavior. The charge transfer can be attributed to amide functionality at the junction.

Metal chelates of the amide-substituted nitroxides: the influence of hydrogen bonding on the structure of metal-nitroxide complexes

The amide function was introduced into metal chelates derived from 3-imidazoline-1-oxyl enaminoketones (MCo, Ni) with the aim of investigation of the influence of hydrogen bonding upon the structure and properties of metal-nitroxide complexes. The complexes obtained manifest strong tendency to include different solvents due to clathration, hydrogen bonding, or hydrogen bonding combined with coordinative bonding. The hydrogen bond patterns vary from linear chains arising from amide–amide interactions to complex 3D motifs formed with participation of the solvent molecules (water, methanol). The hydrogen bonds can act as magnetically innocent intermolecular junctions as well as exchange pathways between the paramagnetic centers. The magnetic properties of the complexes are presented and discussed in connection with their structure.