Simulating molecular shuttle movements: towards computer-aided design of nanoscale transport systems

Molecular shuttles based on the motor protein kinesin and microtubule filaments have the potential to extend the lab-on-a-chip paradigm to nanofluidics by enabling the active, directed and selective transport of molecules and nanoparticles. Based on experimentally determined parameters, in particular the trajectory persistence length of a microtubule gliding on surface-adhered kinesin motors, we developed a Monte-Carlo simulation, which models the transport properties of guiding structures, such as channels, rectifiers and concentrators, and reproduces the properties of several experimentally realized systems. Our tool facilitates the rational design of individual guiding structures as well as whole networks, and can be adapted to the simulation of other nanoscale transport systems.     

XPS analysis of NH3 plasma-treated polystyrene films utilizing gas phase chemical modification

Gas phase chemical modification (GCM) is found to be more preferable as a pretreatment for the XPS surface analysis of polymer materials than the conventional liquid phase treatment because it can circumvent problems such as solvent contamination and swelling. We have tried the quantification of the surface composition successfully by estimating the yield of the reaction from model samples. GCM was then applied to correlate the surface composition of NH₃ plasma-treated polystyrene films with their cell-affinity. The amount of primary-amine and that of carboxylic acid were directly determined by GCM. Although the amount of primary-amine, 15–20% of total nitrogen, did not depend on the treatment intensity, the total amine content for the treated samples increased with the plasma treatment intensity. The quantity of carboxylic acid generated was found to be very small. All treated samples had better cell-affinity than the control. The sample N2 (of medium treatment) showed the best cell-affinity. The most strongly treated sample N3, with larger amine content than N2, showed worse cell-affinity because of the interference by the sputtered SiO₂ on the surface.     

"What is This?" A Structure Analysis Tool for Rapid and Automated Solution of Small Molecule Structures

Journal of Chemical Crystallography - The structure of organic compounds, including their absolute configuration, is extremely critical to the activity of medicines, aroma chemicals, and...     

Spectrofluorometric determination of kynurenic acid with horseradish peroxidase in the presence of hydrogen peroxide.

The catalytic activity of horseradish peroxidase (HRP) in the presence of hydrogen peroxide has been investigated for the fluorescent derivatization of kynurenic acid under conditions with no exposure to light. Non-fluorescent kynurenic acid was converted into a fluorescent compound (Ex: 367 nm, Em: 470 nm) with HRP in the presence of hydrogen peroxide, and the optimum conditions of this fluorescent derivatization were investigated. Moreover, this fluorescent derivatization was developed for a spectrofluorometric determination of trace amounts of kynurenic acid by measuring the fluorescence intensity of the fluorescent compound. The calibration curve obtained was linear from 1.0 to 10.0 nmol of kynurenic acid in a 1.0 mL sample solution. The relative standard deviation at 5.0 nmol of kynurenic acid was 5.71% (n=5). By adjusting the bandwidths for both the excitation and emission to 15 nm, the calibration curve was also linear in the range between 0.1 to 1.0 nmol of kynurenic acid in a 1.0 mL sample solution. This method was applied to the fluorometric determination of trace amounts of kynurenic acid in the control sera.     

Central Elements in the Universal Enveloping Algebras for the Split Realization of the Orthogonal Lie Algebras

We construct central elements in the universal enveloping algebra using column-determinants for the split realization of the orthogonal Lie algebra. Our central elements are quite new and simple, though they are closely related to what Howe and Umeda gave for the orthogonal Lie algebra under the different realization as the alternating matrices.     

Development of a simultaneous measurement system of x‐ray diffraction and raman spectra: Application to structural study of crystalline‐phase transitions of chain molecules

The development of a bench‐top‐type system for simultaneous measurement of X‐ray diffraction and Raman spectra has been made to investigate structural changes in the phase transitions of chain molecules such as polyethylene, n‐alkane, and so forth from various viewpoints. For the X‐ray diffraction measurement an imaging plate or a charge‐coupled device camera was used as a two‐dimensional detector. For the Raman spectral measurement a miniature Raman spectrometer was used with optical fibers for the irradiation of incident laser beams and collection of scattered signals. For example, in the heating process of the n‐C₃₀H₆₂ sample, the phase transition from orthorhombic‐to‐hexagonal lattices could be detected clearly by the X‐ray and Raman measurements. By comparing these two different types of data in detail, an intimate relationship between conformational disordering and rotational motion of molecular chains is detected more clearly than before. Also, similar discussion can be made for the orthorhombic‐to‐hexagonal phase transition of the geometrically constrained polyethylene sample occurring immediately below the melting point. Another example concerns the structural change in the photoinduced solid‐state polymerization of cis,cis‐diethylmuconate single crystal. From the shifts in the X‐ray reflection position and Raman frequency characteristic of the produced polymer, it was found that the molecular deformation of the polymer chains and lattice strain was induced in the early stage of the polymerization reaction. For the ferroelectric‐phase transition of vinylidene fluoride copolymer, the simultaneous measurement was made for collecting triple information of small‐angle and wide‐angle X‐ray scatterings and Raman spectra to know the relationship between the structural change in the crystal lattice and the morphological change in the lamellar stacking mode. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 495–506, 2002; DOI 10.1002/polb.10112     

An efficient chemical fixation of nitric oxide: convenient and practical synthesis of 1,2,3-oxadiazole 3-oxides

Nitric oxide reacts efficiently with alkynyllithium at low temperature producing 1,2,3-oxadiazole 3-oxides in good yields.     

Communication: A concerted mechanism between proton transfer of Zundel anion and displacement of counter cation

Ab initio path integral molecular dynamics simulation of M(+)(H(3)O(2)(-)) (M = Li, Na, and K) has been carried out to analyze how the structure and dynamics of a low-barrier hydrogen-bonded Zundel anion, H(3)O(2)(-), can be affected by the counter alkali metal cation, M(+). Our simulation predicts that the quantum proton transfer in Zundel anion can be strongly coupled to the motion of counter cation located nearby. A smaller cation can induce larger structural distortion of the Zundel anion fragment making the proton transfer barrier higher, and hence, lower the vibrational excitation energy. It is also argued that a large H∕D isotope effect is present.