Study on the Single Crystals of Poly(3-octylthiophene) Induced by Solvent-Vapor Annealing

Needle-like single crystals of poly(3-octylthiophene) (P3OT) have been prepared by tetrahydrofuran-vapor annealing. The morphology and structure of the crystals were characterized with optical microscopy, scanning electron microscopy, atomic force microscopy, transmission electron microscopy, and wide-angle X-ray diffraction. It is observed that the P3OT molecules are packed with the backbones parallel to the length axis of the crystal and the alkyl side chains perpendicular to the substrate. The field effect transistor based on the P3OT single crystal exhibited a charge carrier mobility of 1.54 x 10(-4) cm(2)/(Vs) and on/off current ratio of 37, and the molecular orientation of the crystal is ascribed to account for the device performance. The time-dependent morphological evolution demonstrated that the crystals underwent Ostwald ripening when annealed.

Adaptive recognition of small molecules by nucleic acid aptamers through a label-free approach

We report a novel label-free method for the investigation of the adaptive recognition of small molecules by nucleic acid aptamers using capillary electrophoresis analysis. Cocaine and argininamide were chosen as model molecules, and the two corresponding DNA aptamers were used. These single-strand DNAs folded into their specific secondary structures, which were mainly responsible for the binding of the target molecules with high affinity and specificity. For molecular recognition, the nucleic acid structures then underwent additional conformational changes, while keeping the target molecules stabilized by intermolecular hydrogen bonds. The intrinsic chemical and physical properties of the target molecules enabled them to act as indicators for adaptive binding. Thus any labeling or modification of the aptamers or target molecules were made obsolete. This label-free method for aptamer-based molecular recognition was also successfully applied to biological fluids and therefore indicates that this approach is a promising tool for bioanalysis.

Extended-chain lamellar packing of poly(3-butylthiophene) in single crystals

We developed an approach, i.e. solvent-assist crystallization (SAC), for growing high quality single crystals of head-to-tail regio-regular poly(3-butylthiophene) (P3BT). By means of atomic force microscopy, electron diffraction and X-ray diffraction, we found that P3BT macromolecules formed lamella single crystals through gradient crystallization, and in the single crystals, molecules packed normal to the lamella with extended-chain conformation with alkyl side chains in the growth front during crystallization.

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold.

Manipulations of atoms and molecules by scanning probe microscopyk

Scanning probe microscopy (SPM), including scanning tunneling microscopy (STM) and atomic force microscopy (AFM), has become a powerful tool in building nanoscale structures required by modern industry. In this article, the use of SPM for the manipulation of atoms and molecules for patterning nanostructures for opt-electronic and biomedical applications is reviewed. The principles and procedures of manipulation using STM and AFM-based technologies are presented with an emphasis on their ability to create a wide variety of nanostructures for different applications. The interaction among the atoms/molecules, surface, and tip are discussed. The approaches for positioning the atom/molecule from and to the desired locations and for precisely controlling its movement are elaborated for each specific manipulation technique. As an AFM-based technique, the dip-pen nanolithography is also included. Finally, concluding remarks on technological improvement and future research is provided.

Atomic force microscope investigation of large-circle DNA molecules

A circular bacterial artificial chromosome of 148.9 kbp on human chromosome 3 has been extended and fixed on bare mica substrates using a developed fluid capillary flow method in evaporating liquid drops. Extended circular DNA molecules were imaged with an atomic force microscope (AFM) under ambient conditions. The measured total lengths of the whole DNA molecules were in agreement with sequencing analysis data with an error range of +/-3.6%. This work is important groundwork for probing single nucleotide polymorphisms in the human genome, mapping genomic DNA, manipulating biomolecular nanotechnology, and studying the interaction of DNA-protein complexes investigated by AFM.

Functionalization of single-walled carbon nanotubes with Prussian blue

Chemical functionalization of single-walled carbon nanotubes (SWNTs) has constructed plenty of new structures with ample new properties into them. But the modification was often confined to organic molecules, either by covalence or non-covalence. In this report, SWNTs were successfully functionalized with one kind of electroactive inorganic compounds: Prussian blue (PB). And the molecular interactions between them were firstly investigated. Interestedly, pi-pi stacking interaction coupled with ionic interaction was found between SWNTs and PB. The electrochemical properties of SWNTs-PB were also investigated. It would pave a new pathway to manipulate molecular entities of SWNTs by cooperation with functional inorganic electroactive compounds.

Poly-L-lysine functionalization of single-walled carbon nanotubes

Single-walled carbon nanotubes (SWNTs) were covalently functionalized with biocompatible poly-L-lysine, which is useful in promoting cell adhesion. SWNTs played an important role as connectors to assemble these active amino groups of poly-L-lysine, which provided a relative "friendly" and "soft" environment for further derivation, such as attaching bioactive molecules. As an application example, by further linking peroxidase, an amplified biosensing toward H2O2 concerning this assembly was investigated.

Highly enhanced luminescence from single-crystalline C-60 center dot 1m-xylene nanorods

Single-crystalline C-60 center dot 1m-xylene nanorods with a hexagonal structure were successfully synthesized by evaporating a C-60 solution in m-xylene at room temperature. The ratio of the length to the diameter of the nanorods can be controlled in the range of approximate to 10 to over 1000 for different applications. The photoluminescence (PL) intensity of the nanorods is about 2 orders of magnitude higher than that for pristine C-60 crystals in air. Both UV and Raman results indicate that there is no charge transfer between C-60 and m-xylene. It was found that the interaction between C-60 and m-xylene molecules is of the van der Waals type. This interaction reduces the icosahedral symmetry of C-60 molecule and induces strong PL from the solvate nanorods.

Fabrication of Au(111) single-crystal nanoisland-arrayed electrode ensembles by template-directed seeding growth

A new and simple approach for preparation of Au(111) single-crystal nanoisland - arrayed electrode ensembles, based on fine colloidal Au monolayer-directed seeding growth, is reported.

Single-crystal X-ray structure and properties of K-10[Ni-4(H2O)(2)(AsW9O34)(2)]center dot 4H(2)O

The rational synthesis and the structural and magnetic characterization of a nickel cluster are presented. The compound comprises a rhomblike Ni4O16 group encapsulated between two-heptadentate tungstoarsenate ligands [AsW9O34](9-). The crystal structure of K-10[Ni-4(H2O)(2)(AsW9O34)(2)](.)4H(2)O was solved in monoclinic, P2(1)/n symmetry, with a = 12.258(3) Angstrom, b = 21.232(4) Angstrom, c = 15.837(3) Angstrom, beta = 92.05(3)degrees, V = 4119.1(14) Angstrom(3), Z = 2, and R = 0.0862. The crystal structure of the Ni(II) derivative was compared with that of the Cu(II), Zn(II), Co(II) and Mn(II) derivatives. The Ni4O14(H2O)(2) unit in the compound shows no Jahn-Teller distortion. On the other hand, the Ni(II) derivative shows ferromagnetic exchange interactions within the Ni4O16 group (J = 7.8 cm(-1), J' = 13.7 cm(-1)) and an S = 4 ground state, the highest spin state reported in a heteropoly complex. Its redox electrochemistry has been studied in acid buffer solutions using cyclic voltammetry. It exhibited two steps of one-electron redox waves attributed to redox processes of the tungsten-oxo framework. The new catalyst showed an electrocatalytic effect on the reduction of NO2-.

Study on polymer micelles of hydrophobically modified ethyl hydroxyethyl cellulose using single-molecule force spectroscopy

Individual hydrophobically modified ethyl hydroxyethyl cellulose (HM-EHEC) molecules under different conditions were elongated using a new atomic force microscope (AFM) based technique-single-molecule force spectroscopy (SMFS). The critical concentration of HM-EHEC for micelle-like clusters at a solid/liquid interface was around 0.8 wt %, which is lower than that in solution. The different mechanical properties of HM-EHEC below and above the critical concentration were displayed on force-extension curves. Through a comparison with unmodified hydroxyethyl cellulose, substituent-induced effects on nanomechanical features of HM-EHEC were investigated. Because of hydrophobic interactions and cooperative binding with the polymer, surfactants such as sodium dodecyl sulfate (SDS) dramatically influence the elastic properties of HM-EHEC below the critical concentration, and further addition of SDS reduces the interactions between the hydrophobic groups and the surfactant.

Molecular dynamics-based approach to study the anisotropic self-diffusion of molecules in porous materials with multiple cage types: Application to H-2 in losod

Van den Berg, A. W. C., Flikkema, E., Lems, S., Bromley, S. T., Jansen, J. C. (2006). Molecular dynamics-based approach to study the anisotropic self-diffusion of molecules in porous materials with multiple cage types: Application to H-2 in losod. Journal of physical chemistry b, 110 (1), 501-506. RAE2008

Properties of molecules in tunnel junctions

Molecular tunnel junctions involve studying the behaviour of a single molecule sandwiched between metal leads. When a molecule makes contact with electrodes, it becomes open to the environment which can heavily influence its properties, such as electronegativity and electron transport. While the most common computational approaches remain to be single particle approximations, in this thesis it is shown that a more explicit treatment of electron interactions can be required. By studying an open atomic chain junction, it is found that including electron correlations corrects the strong lead-molecule interaction seen by the ΔSCF approximation, and has an impact on junction I − V properties. The need for an accurate description of electronegativity is highlighted by studying a correlated model of hexatriene-di-thiol with a systematically varied correlation parameter and comparing the results to various electronic structure treatments. The results indicating an overestimation of the band gap and underestimation of charge transfer in the Hartree-Fock regime is equivalent to not treating electron-electron correlations. While in the opposite limit, over-compensating for electron-electron interaction leads to underestimated band gap and too high an electron current as seen in DFT/LDA treatment. It is emphasised in this thesis that correcting electronegativity is equivalent to maximising the overlap of the approximate density matrix to the exact reduced density matrix found at the exact many-body solution. In this work, the complex absorbing potential (CAP) formalism which allows for the inclusion metal electrodes into explicit wavefunction many-body formalisms is further developed. The CAP methodology is applied to study the electron state lifetimes and shifts as the junction is made open.

An entirely cell-based system to generate single-chain antibodies against cell surface receptors.

The generation of recombinant antibodies (Abs) using phage display is a proven method to obtain a large variety of Abs that bind with high affinity to a given antigen. Traditionally, the generation of single-chain Abs depends on the use of recombinant proteins in several stages of the procedure. This can be a problem, especially in the case of cell-surface receptors, because Abs generated and selected against recombinant proteins may not bind the same protein expressed on a cell surface in its native form and because the expression of some receptors as recombinant proteins is problematic. To overcome these difficulties, we developed a strategy to generate single-chain Abs that does not require the use of recombinant protein at any stage of the procedure. In this strategy, stably transfected cells are used for the immunization of mice, measuring Ab responses to immunization, panning the phage library, high-throughput screening of arrayed phage clones, and characterization of recombinant single-chain variable regions. This strategy was used to generate a panel of single-chain Abs specific for the innate immunity receptor Toll-like receptor 2. Once generated, individual single-chain variable regions were subcloned into an expression vector allowing the production of recombinant Abs in insect cells, thus avoiding the contamination of recombinant Abs with microbial products. This cell-based system efficiently generates Abs that bind to native molecules on the cell surface, bypasses the requirement of recombinant protein production, and avoids risks of microbial component contamination.