Light-induced molecular cutting: localized reaction on a single DNA molecule

A short focused pulse of light was used to selectively cut lambda-phage DNA molecules at specific restriction sites. Lambda DNA (48.5 kbp) was stretched and placed in a solution containing a restriction enzyme (Sma 1), caged magnesium ions (using a DM-Nitrophen complex), and a chelating agent (EDTA). When a pulse of UV light was directed at a particular location on the stretched DNA molecule, magnesium ions were released into solution. A series of binding reactions then occur in which the enzyme and the chelating agent compete for free Mg2+ ions. Since Sma 1 functions only in the presence of Mg2+, as is true of most endonucleases, the site(s) in the vicinity of the pulse (typically approximately 6 microm) were cut while other sites (three total for this DNA/enzyme pair) were not. The ratio of the concentration of the chelating agent to that of the magnesium ions was used to control the radius of this reaction zone with higher ratios leading to smaller, localized reaction areas. This optically based reaction mechanism could be useful to understand single molecule enzymatic kinetics, and when coupled with other DNA analysis techniques, this could be used to construct complex genotyping and sequencing devices that would analyze parts of single DNA molecules.     

The relation between structure and quantum interference in single molecule junctions

Quantum interference (QI) of electron pathways has recently attracted increased interest as an enabling tool for single-molecule electronic devices. Although various molecular systems have been shown to exhibit QI effects and a number of methods have been proposed for its analysis, simple guidelines linking the molecular structure to QI effects in the phase-coherent transport regime have until now been lacking. In the present work we demonstrate that QI in aromatic molecules is intimately related to the topology of the molecule's π system and establish a simple graphical scheme to predict the existence of QI-induced transmission antiresonances. The generality of the scheme, which is exact for a certain class of tight-binding models, is proved by a comparison to first-principles transport calculations for 10 different configurations of anthraquinone as well as a set of cross-conjugated molecular wires.     

Label-free identification of single dielectric nanoparticles and viruses with ultraweak polarization forces

Label-free detection of the material composition of nanoparticles could be enabled by the quantification of the nanoparticles' inherent dielectric response to an applied electric field. However, the sensitivity of dielectric nanoscale objects to geometric and non-local effects makes the dielectric response extremely weak. Here we show that electrostatic force microscopy with sub-piconewton resolution can resolve the dielectric constants of single dielectric nanoparticles without the need for any reference material, as well as distinguish nanoparticles that have an identical surface but different inner composition. We unambiguously identified unlabelled ~10 nm nanoparticles of similar morphology but different low-polarizable materials, and discriminated empty from DNA-containing virus capsids. Our approach should make the in situ characterization of nanoscale dielectrics and biological macromolecules possible.     

Contact formation dynamics: Mapping chemical bond formation between a molecule and a metallic probe

We present a study that maps out chemical bond formation between a Pt-inked probe and a single 1,3-cyclohexadiene (1,3-CHD) molecule on Si(100). By separating the mechanical and electronic contributions to the current during the approach to contact, we show that there are significant forces between the probe and the C=C of the molecule and we track the relaxation of the molecule, the emergence of a chemical bond feature in the LDOS, and the quenching of specific molecular vibrations during bond formation.     

The scanning tunnelling microscope as an operative tool: doing physics and chemistry with single atoms and molecules

The scanning tunnelling microscope, initially invented to image surfaces down to the atomic scale, has been further developed in the last few years to an operative tool, with which atoms and molecules can be manipulated at will at low substrate temperatures in different manners to create and investigate artificial structures, whose properties can be investigated employing spectroscopic dI/dV measurements. The tunnelling current can be used to selectively break chemical bonds, but also to induce chemical association. These possibilities give rise to startling new opportunities for physical and chemical experiments on the single atom and single molecule level. Here we provide a short overview on recent results obtained with these techniques.     

Thermal resistance of nanoscopic liquid-liquid interfaces: dependence on chemistry and molecular architecture

Systems with nanoscopic features contain a high density of interfaces. Thermal transport in such systems can be governed by the resistance to heat transfer, the Kapitza resistance (RK), at the interface. Although soft interfaces, such as those between immiscible liquids or between a biomolecule and solvent, are ubiquitous, few studies of thermal transport at such interfaces have been reported. Here we characterize the interfacial conductance, 1/RK, of soft interfaces as a function of molecular architecture, chemistry, and the strength of cross-interfacial intermolecular interactions through detailed molecular dynamics simulations. The conductance of various interfaces studied here, for example, water-organic liquid, water-surfactant, surfactant-organic liquid, is relatively high (in the range of 65-370 MW/m2 K) compared to that for solid-liquid interfaces ( approximately 10 MW/m2 K). Interestingly, the dependence of interfacial conductance on the chemistry and molecular architecture cannot be explained solely in terms of either bulk property mismatch or the strength of intermolecular attraction between the two phases. The observed trends can be attributed to a combination of strong cross-interface intermolecular interactions and good thermal coupling via soft vibration modes present at liquid-liquid interfaces.     

Assessment of small fatigue crack growth driving forces in single crystals with and without slip bands

Strain localization under low amplitude cyclic loading is a manifestation of plastic irreversible deformation associated with early crack growth. However, traditional constitutive models cannot usually reproduce strain localization in smooth single crystals, which can affect crack growth predictions for crystallographic fatigue cracks. This work analyzes the influence of bands of localized plastic shear strain on the cyclic crack tip displacement and on a fatigue indicator parameter by making special provision of a crack along the interface of a deformation band. Furthermore, the quality of local and volume-averaged fatigue indicator parameters are assessed using finite element models of a Cu single crystal cycled to induce plastic deformation under multiple loading conditions.     

Mechanics of discontinuous ceramic tile core sandwich structure: Influence of thermal and interlaminar stresses

The stress states in a discontinuous ceramic tile core sandwich structure due to mechanical and thermal loading are investigated. The influence of coefficient of thermal expansion (CTE) mismatch between the tile and face sheet layer on the in-plane and interlaminar stresses in the sandwich structure is evaluated. The factors affecting the interlaminar stresses in the structure are of particular interest. The influence of an adhesive layer between the face sheet and core on the effective properties of the sandwich is also discussed. A study is performed to evaluate tailoring of the adhesive properties to reduce interlaminar stresses for increased durability. A parametric study is performed to study how various geometric parameters such as tile and adhesive layer thickness affect the effective properties (e.g. axial modulus and CTE). Failure of the discontinuous core sandwich structure under in-plane tension loading is analyzed. It is observed that thermal property mismatch in the structure can significantly reduce the failure loads for the tile layer. Finally, failure of the sandwich corresponding to various failure modes is discussed.     

The aluminum/polythiophene interface: a case study in molecular electronics and computational chemistry

Conjugated polymer/metal interfaces are formed during the construction of thin-film polymer light-emitting diodes. The nature of the interface may affect device operation. This paper describes the use of computational chemical methods in modelling the interface formed when aluminum is deposited onto a thin film of polythiophene.     

Photo-stability study of a solution-processed small molecule solar cell system: correlation between molecular conformation and degradation

Solution-processed organic small molecule solar cells (SMSCs) have achieved efficiency over 11%. However, very few studies have focused on their stability under illumination and the origin of the degradation during the so-called burn-in period. Here, we studied the burn-in period of a solution-processed SMSC using benzodithiophene terthiophene rhodamine:[6,6]-phenyl C₇₁ butyric acid methyl ester (BTR:PC₇₁BM) with increasing solvent vapour annealing time applied to the active layer, controlling the crystallisation of the BTR phase. We find that the burn-in behaviour is strongly correlated to the crystallinity of BTR. To look at the possible degradation mechanisms, we studied the fresh and photo-aged blend films with grazing incidence X-ray diffraction, UV–vis absorbance, Raman spectroscopy and photoluminescence (PL) spectroscopy. Although the crystallinity of BTR affects the performance drop during the burn-in period, the degradation is found not to originate from the crystallinity changes of the BTR phase, but correlates with changes in molecular conformation – rotation of the thiophene side chains, as resolved by Raman spectroscopy which could be correlated to slight photobleaching and changes in PL spectra.     

Diamond deposition onto WC-6%Co cutting tool material: coating structure and interfacial bond strength

Diamond coatings were grown on WC-6%Co cutting tool material. Measurements were carried out to investigate the effects of diamond seeding of the substrate before deposition, removal of cobalt from the substrate before deposition, and boron incorporation into the coating during growth on the growth rate, morphology and structure of the coating, and coating-substrate edhesion. Diamond seeding of the substrate resulted in a higher growth rate and diamond fraction of the coating relative to a polished and unseeded surface. Etching of cobalt from the substrate resulted in a higher growth rate, diamond fraction and adhesion strength relative to the unetched surface. Introduction of methanol into the gas phase led to a lower growth rate, diamond fraction and adhesion strength relative to the case when no methanol was injected. Introduction of boron oxide (B₂O₃) along with methanol into the gas phase did not affect the growth rate but increased both the diamond fraction and adhesion strength relative to the case when only methanol was added. It is believed that adhesion failure occurs at the diamond-substrate interface, possibly within a soft nanocrystalline graphite transition layer.     

Aqueous co-precipitation of Pd-doped cerium oxide nanoparticles: chemistry, structure, and particle growth

Nanoparticles of palladium-doped cerium oxide (Pd–CeO₂) have been prepared by aqueous co-precipitation resulting in a single phase cubic structure after calcination according to X-ray diffraction (XRD). Inhomogeneous strain, calculated using the Williamson–Hall method, was found to increase with palladium content, and the lattice contracts slightly, relative to nano-cerium oxide, as palladium content is increased. Moreover, high resolution transmission electron microscopy reveals some instances of defective microstructure. These factors combined imply that palladium is in solid solution with CeO₂ in these nanoparticles, but palladium (II) oxide (PdO) peaks in the Raman spectra indicate that solid solution formation is partial and that highly dispersed PdO is present as well as the solid solution. Nevertheless, the addition of palladium to the CeO₂ lattice inhibits the growth of the 6% Pd–CeO₂ particles compared to pure CeO₂ between 600 and 850 °C. Activation energies for grain growth of 54 ± 7 and 79 ± 8 kJ/mol were determined for 6% Pd–CeO₂ and pure CeO₂, respectively, along with pre-exponential Arrhenius factors of 10 for the doped sample and 600 for pure cerium oxide.     

Hybrid resins from polyisocyanate,epoxy resin and water glass: chemistry,structure and properties

Epoxy resin (EP) was selected as potential reactive emulsifier for polyurea-based thermoset resins produced from polyisocyanate/water glass/emulsifier systems. As emulsifier diphenyl-2-ethylhexylphosphate and/or EP served for the initial water-in-oil type emulsions whereby “water” means water glass, and “oil” the organic phase, composed of polyisocyanate and emulsifier, respectively. The EP content of the systems has been varied from 15 to 35 wt% and from 35 to 45 wt% for the hybrid resins with and without DPO emulsifier, respectively. Effects of EP hybridization on the structure, mechanical, thermal and flammability properties of the final polyurea-based systems were studied. EP proved to be a suitable emulsifier based on the fact that the mean size of the polysilicate, generated from the dispersed WG, was markedly reduced. EP could even fully replace the phosphate emulsifier without sacrificing the mechanical properties of the resulting hybrid thermosets. Moreover, the hybridization with EP was accompanied with improved stiffness and fracture toughness.     

Electron microscopy: probing the atomic structure and chemistry of grain boundaries, interfaces and defects

At the heart of ‘ dynamic embrittlement’ phenomena is the stress-induced segregation of microscopic quantities of embrittling impurities to fracture surfaces. Grain boundaries and interfaces are often the natural weak links in a material. The structural and chemical information of such internal interfaces can be probed on an atomic scale using transmission electron microscopy. High-resolution electron microscopy can be used to determine the atomic coordinates of crystalline interfaces. Electron-energy-loss spectroscopy (EELS) and energy-dispersive X-ray spectroscopy can be performed on any boundary or defect and can provide chemical information such as composition and bonding. The spatial resolution of EDS is limited by low collection efficiency to around 10 Å. The more efficient signal collection for EELS allows almost atomic resolution for light elements. EELS fine structure offers a fingerprint of the local boundary arrangements, and also insight into the bonding (and possible reactivity) of boundaries and other defects. Overall, electron microscopy can be used to identify the atomistic characteristics of those interfaces susceptible to dynamic embrittlement. The structural and electronic information obtained can be used as a starting point for semi-empirical and ab initio simulations.     

TEM and molecular simulation studies on the hydroxylapatite structure with Si and Mg impurities

Transmission electron microscopy (TEM) and molecular simulation studies of traces of chemical elements such as Mg, Si, and OH in the hydroxylapatite (CaHAP) crystal structure obtained from the sand dollar were carried out. Two different types of CaHAP crystal morphologies in the samples synthesized by the hydrothermal method used were observed. Reflections with regular intensity in the experimental electron diffraction patterns obtained from these morphologies were observed. However, when these results were compared with a simulated electron diffraction pattern (which was obtained using the crystalline structure proposed for the hydroxylapatite) some forbidden reflections in the experimental pattern were observed. Then, in order to reproduce the experimental patterns Si and Mg atoms in the crystalline lattice were introduced. These elements in the elemental chemical analysis carried out by X-ray energy dispersive spectroscopy (EDS) in the typical CaHAP morphologies were detected. The positions of these atoms in the asymmetric unit were obtained using molecular simulation and during the relaxation process, the structure did not show changes in the lattice parameters. Subsequently, the crystalline structure was reproduced and matched the electron diffraction patterns simulated resulting in the experimental electron diffraction pattern. Experimental and simulated X-ray diffraction spectra were also matched.     

Materials belonging to the CrVO4 structure type: preparation, crystal chemistry and physicochemical properties

Crystallographic data of vanadates, phosphates, chromates, sulphates and selenates belonging to the CrVO4 (-CrPO4) structure type and of some of its most important polymorphs, are reported. Characteristic structural peculiarities and the effect of pressure on the phase transformations are discussed. A definitive stability field for this structure type could be established. Synthetic procedures for the preparation of the different compounds adopting this and closely related structures are presented and its thermal, spectroscopic and magnetic properties are discussed. A brief overview on the most important characteristics of materials adopting the -CrPO4 structure is also presented. © 1998 Chapman & Hall     

Direct comparison of solution- and vacuum-processed small molecular organic light-emitting devices with a mixed single layer

It will be interesting and valuable information can be achieved if a direct comparison between organic light emitting devices (OLEDs) fabricated by vacuum evaporated method (vac) and solution-based manufacturing processes (sol) was realized. Small molecular OLEDs with a mixed organic layer structure (MOLOLEDs) make it possible for direct comparison between devices with the same materials but fabricated by the two processing methods. This article shows a direct comparison of the luminescence characteristics, charge conduction, and device physics between MOLOLEDs fabricated by vac- and sol-processing techniques. It gives an elementary explain how the organic/metal interfaces influence the charge conduction and device performance.