Mathematical Relationships Between Bond-Bending Force Fields

Molecular mechanics softwares adopt various set of force field functions. In some cases, reliable data from one set of force field parameters cannot be used in a software that adopts another set of force field. Using mathematical approach, exact relationships between parameters from three bond-bending force fields, namely the (i) harmonic cosine angle, (ii) polynomial series, and (iii) Fourier series, are herein developed. Parameters from these three potential functions are further related to the approximate form, the harmonic angle function, which is valid for small change in chemical bond angle.     

Formation and atomic structures of boron nitride nanohorns encaging boron nitride cluster

Boron nitride (BN) nanohorns were synthesized by arc-melting YB₆ powders. Method, and atomic structure models for BN nanohorns encaging Y@B₃₆N₃₆ were proposed from high-resolution electron microscopy. The molecular mechanics calculation indicated that BN clusters with metal atoms would be stabilized by being encaged in double-walled BN nanohorns.     

Dependence on substrate topography of growth of nanosized dendritic structures in an electron-beam-induced deposition process

Nanometer-sized W-dendrites are fabricated on Al₂O₃ substrates with an electron-beam-induced deposition process. Dependence of growth of nanodendrite on surface topography is investigated with transmission electron microscopy. It is confirmed that the nanodendrite grows on convex surfaces but not around a hole on a substrate. These are attributed to different distribution of charges on surfaces with different topographies during electron beam irradiation when charges are produced on the surface due to emission of second electrons. The charges accumulate on convex surface and do not distribute around a hole. Therefore, the nanodendrite grows on the former and not on the latter.     

Effects of guest microparticles on the swelling behavior of polyacrylamide gels

We report the effects of guest particles on the swelling properties of bulk polyacrylamide gels. The guest particles were the spheres of poly(N‐isopropylacrylamide) gel with submicrometer diameter, which were synthesized by an emulsion‐polymerized reaction in water. Polyacrylamide gels were prepared by a free radical polymerization reaction, immobilizing the gel microparticles with different concentrations at gelation. The macroscopic swelling ratio of this hybrid gel in a cylindrical shape was measured as functions of temperature and acetone concentration. The presence of guest particles was found to strongly affect the swelling behavior in the bulk gels when the concentration of incorporated particles exceeded a threshold. The experimental results indicated that the macroscopic volume in response to the temperature change should be determined by the guest particles above the threshold. On the other hand, the hybrid gel could not evidently shrink by adding acetone when the concentration of guest particles exceeded the threshold. To make clear the distribution of guest particles in the bulk networks, the fractured surfaces of dried gels were imaged by tapping mode atomic force microscopy. The guest particles were found to aggregate in the bulk homogeneous networks to form microdomains with densely connected structure, which became larger with increasing particle concentration. The roles of bulk networks as well as guest particles on the swelling behavior of hybrid gels were qualitatively discussed on the basis of the incorporated structure of guest particles, depending on the concentration of guest particles. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1696–1704, 2005     

Greenish‐yellow‐, yellow‐, and orange‐light‐emitting iridium(III) polypyridyl complexes with poly(ε‐caprolactone)–bipyridine macroligands

A set of novel greenish‐yellow‐, yellow‐, and orange‐light‐emitting polymeric iridium(III) complexes were synthesized with the bridge‐splitting method. The respective dimeric precursor complexes, [Ir(ppy)₂‐μ‐Cl]₂ (ppy = 2‐phenylpyridine) and [Ir(ppy? CHO)₂‐μ‐Cl]₂ [ppy? CHO = 4‐(2‐pyridyl)benzaldehyde], were coordinated to 2,2′‐bipyridine carrying poly(ε‐caprolactone) tails. The resulting emissive polymers were characterized with one‐dimensional (¹H) and two‐dimensional (¹H? ¹H correlation spectroscopy) nuclear magnetic resonance and infrared spectroscopy, gel permeation chromatography, and matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry, and the successful coordination of the iridium(III) centers to the 2,2′‐bipyridine macroligand was revealed. The thermal behavior was studied with differential scanning calorimetry and correlated with atomic force microscopy. Furthermore, the quantitative coordination was verified by both the photophysical and electrochemical properties of the mononuclear iridium(III) compounds. The photoluminescence spectra showed strong emissions at 535 and 570 nm. The color shifts depended on the substituents of the cyclometallating ligands. Cyclic voltammetry gave oxidation potentials of 1.23 V and 1.46 V. Upon the excitation of the films at 365 nm, yellow light was observed, and this could allow potential applications in light‐emitting devices. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2765–2776, 2005     

Molecular design,synthesis, and properties of Y‐type nonlinear optical polyester containing tricyanovinylthiophene with enhanced thermal stability of second harmonic generation

1‐{3,4‐Di‐(2‐hydroxyethoxy)phenyl}‐2‐(2‐thiophenyl)ethene (5) was prepared and condensed with terephthaloyl chloride to yield polyester (6). Polymer 6 was reacted with tetracyanoethylene to give a new Y‐type polyester (7) containing 1‐(3,4‐dioxyethoxy)phenyl‐2‐{5‐(2,2,3‐tricyanovinyl)‐2‐thiophenyl)}ethenyl groups as NLO‐chromophores, which are components of the polymer backbones. Polyester 7 is soluble in common organic solvents such as N,N‐dimethylformamide and acetone. Polymer 7 showed a thermal stability up to 300 °C in thermogravimetric analysis with glass transition temperature (T_g) obtained from differential scanning calorimetry near 126 °C. The second harmonic generation (SHG) coefficient (d₃₃) of poled polymer film at the 1560 nm fundamental wavelength was around 6.57 × 10^?9 esu. The dipole alignment exhibited high thermal stability up to the T_g, and there was no SHG decay below 125 °C due to the partial main‐chain character of polymer structure, which is acceptable for NLO device applications. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1911–1919, 2009     

Self-assembly formation of the ordered nanostructure arrays induced by Be interaction with Si(1 1 1) surface

Formation of the beryllium (Be) submonolayers on the Si(1 1 1)7 × 7 surface has been studied using scanning tunneling microscopy. It has been found that Be interaction with Si(1 1 1) at 500-700 °C results in a self-assembly formation of the four various types of the highly-ordered nanostructure arrays. The nanostructure arrays develop on top of the “soft” silicide layer, which period and orientation alter with the nanostructure growth: the shorter the nanostructure period, the larger the rotation angle. The main structural parameters of the silicide layer and nanostructure arrays have been established.     

Coalescence process of monodispersed Co cluster assemblies

Cluster-cluster coalescence process of monodispersed Co clusters with mean diameter d = 8.5 and 13 nm deposited a plasma-gas-condensation-type cluster beam deposition system was investigated by in situ electrical conductivity measurements and ex situ scanning electron microscopy (SEM) and transmission electron microscopy (TEM), and analyzed by percolation concept. The electrical conductivity measurement and TEM observation indicated that, below temperature T≈ 100^°C, the Co clusters in the assemblies maintain their original structure as deposited at room temperature, while that the inter-cluster coalescence takes place at T > 100^°C, although the size distribution and the interface morphology of the clusters showed no marked change at substrate temperatures T _s≤200^°C. Received 29 November 2000     

IDENTIFICATION OF MEMBRANE PROTEINS IMAGED BY ATOMIC FORCE MICROSCOPY USING A TEMPLATE MATCHING ALGORITHM

The atomic force microscope allows to image biological samples in their native environment. But the identification and the topography of individual randomly distributed membrane proteins is still a challenge. We used membranes of isolated vacuoles of barley mesophyll cells. Images at low resolution indicate that vacuoles spontaneously attach, rupture and finally adsorb completely as planar membrane to mica. Height profiles indicate that the membrane at the peripheral boundary exposes the extravacuolar surface to the scanning tip. At molecular resolution a template matching correlation algorithm was used to identify the most abundant membrane protein, the vacuolar H⁺-ATPase by the characteristic extravacuolar head of the transport molecule. The data indicate the possibility to analyse single randomly distributed membrane proteins in their native environment with the knowledge of a suitable template.