Molecular-shape imprinting and immobilization of biomolecules on a polymer containing azo dye

We demonstrate a novel technique for molecular imprinting and immobilization on a surface of a polymer containing azo dyes (azopolymer). The azopolymer was found to be capable of immobilizing micrometer- and nanometer-scale macromolecules (e.g., lambda-DNA, immunoglobulin G (IgG), bacterial protease, and 1-mum polystyrene particles) through photoirradiation with blue-wavelength light. Fluorescence and atomic force microscopy studies revealed that the azopolymer surface deformed along with the shape of the macromolecules, holding them in place after photoirradiation. The desorption of the immobilized macromolecules from the azopolymer surface in an aqueous medium was observed to be very slow, on the time scale of 10 min to weeks, depending on the photoirradiation time. Immunological and enzymatic studies showed that IgG and bacterial protease immobilized on the azopolymer surface retained their original functionality. These results suggest that the azopolymer physically, not chemically, binds the macromolecules because of the increase in contact area between the macromolecules and the azopolymer surface after photoirradiation.     

Topographic, electrochemical, and optical images captured using standing approach mode scanning electrochemical/optical microscopy

We developed a high-resolution scanning electrochemical microscope (SECM) for the characterization of various biological materials. Electrode probes were fabricated by Ti/Pt sputtering followed by parylene C-vapor deposition polymerization on the pulled optical fiber or glass capillary. The effective electrode radius estimated from the cyclic voltammogram of ferrocyanide was found to be 35 nm. The optical aperture size was less than 170 nm, which was confirmed from the cross section of the near-field scanning optical microscope (NSOM) image of the quantum dot (QD) particles with diameters in the range of 10-15 nm. The feedback mechanism controlling the probe-sample distance was improved by vertically moving the probe by 0.1-3 microm to reduce the damage to the samples. This feedback mode, defined as "standing approach (STA) mode" (Yamada, H.; Fukumoto, H.; Yokoyama, T.; Koike, T. Anal. Chem. 2005, 77, 1785-1790), has allowed the simultaneous electrochemical and topographic imaging of the axons and cell body of a single PC12 cell under physiological conditions for the first time. STA-mode feedback imaging functions better than tip-sample regulation by the conventionally available AFM. For example, polystyrene beads (diameter approximately 6 microm) was imaged using the STA-mode SECM, whereas imaging was not possible using a conventional AFM instrument.     

Cell-permeant small-molecule modulators of NAADP-mediated Ca2+ release

Nicotinic acid adenine dinucleotide phosphate (NAADP, 1) is the most potent intracellular Ca2+ mobilizing agent in important mammalian cells and tissues, yet the identity of the NAADP receptor is elusive. Significantly, the coenzyme NADP is completely inactive in this respect. Current studies are restricted by the paucity of any chemical probes beyond NAADP itself, and importantly, none is cell permeant. We report simple nicotinic acid-derived pyridinium analogs as low molecular weight compounds that (1) inhibit Ca2+ release via the NAADP receptor (IC50 approximately 15 microM - 1 mM), (2) compete with NAADP binding, (3) cross the cell membrane of sea urchin eggs to inhibit NAADP-evoked Ca2+ release, and (4) selectively ablate NAADP-dependent Ca2+ oscillations induced by the external gastric peptide hormone agonist cholecystokinin (CCK) in murine pancreatic acinar cells.     

Electron-transfer fluorescence quenching of aromatic hydrocarbons by europium and ytterbium ions in acetonitrile

To make the effects of molecular size on photoinduced electron-transfer (ET) reactions clear, the ET fluorescence quenching of aromatic hydrocarbons by trivalent lanthanide ions M3+ (europium ion Eu3+ and ytterbium ion Yb3+) and the following ET reactions such as the geminate and free radical recombination were studied in acetonitrile. The rate constant k(q) of fluorescence quenching, the yields of free radical (phi(R)) and fluorescer triplet (phi(T)) in fluorescence quenching, and the rate constant k(rec) of free radical recombination were measured. Upon analysis of the free energy dependence of k(q), phi(R), phi(T), and k(rec), it was found that the switchover of the fluorescence quenching mechanism occurs at deltaG(fet) = -1.4 to -1.6 eV: When deltaG(fet) < -1.6 eV, the fluorescence quenching by M3+ is induced by a long-distance ET yielding the geminate radical ion pairs. When deltaG(fet) > -1.4 eV, it is induced by an exciplex formation. The exciplex dissociates rapidly to yield either the fluorescer triplet or the geminate radical ion pairs. The large shift of switchover deltaG(fet) from -0.5 eV for aromatic quenchers to -1.4 to -1.6 eV for lanthanide ions is almost attributed to the difference in the molecular size of the quenchers. Furthermore, it was substantiated that the free energy dependence of ET rates for the geminate and free radical recombination is satisfactorily interpreted within the limits of the Marcus theory.     

A simple picture for the rotational enhancement of the rate for the F + HCl --> HF + Cl reaction: a dynamical study using a new ab initio potential energy surface

Quantum scattering calculations for the reaction F + HCl --> HF + Cl are performed on a new ground-state ab initio potential energy surface. The reagent rotation is found to have a dramatic effect on the reaction probability. Furthermore, the exit channel rotational thresholds leave a strong imprint on the reaction probabilities and even on the cumulative reaction probability. A very simple vibrationally adiabatic model is shown to account for most aspects of the reaction dynamics. In this model, the fast vibrational motion is adiabatically eliminated leaving the key reaction dynamics represented by a reduced atom + rotor collision. The shape of the adiabatic potential surface immediately yields to a simple and intuitive interpretation for the rotational enhancement of the rate. The rotational enhancement is shown to be an effect of the entrance channel dynamics of the atom-rotor problem.     

Evaluation of energy transfer in perylene-cored anthracene dendrimers

Quantitative evaluation of F?rster-type fluorescence resonance energy transfer (FRET) was undertaken by statistical investigations on perylene-cored anthracene dendrimers.     

Theory and experiment agree: single-walled carbon nanotube caps grow catalyst-free with chirality preference on a SiC surface

High-temperature quantum chemical molecular dynamics simulations have been performed on model systems of thin SiC crystal surfaces with two graphene sheets placed on top of either C or Si face. In agreement with experiment, we find that (a) the C-face-attached graphene layer warps readily to form small diameter, stable nanocaps, suitable for further perpendicular growth of nanotubes, (b) the Si-face-attached graphene sheet does not readily wrap and forms more volatile Si-graphene bonds, and (c) C face nanocaps appear to anneal to dome-shape structures with zigzag chirality.     

Multireference configuration interaction calculations for the F(2P)+HCl-->HF+Cl(2P) reaction: a correlation scaled ground state (1 2A') potential energy surface

This paper presents a new ground state (1 (2)A(')) electronic potential energy surface for the F((2)P)+HCl-->HF+Cl((2)P) reaction. The ab initio calculations are done at the multireference configuration interaction+Davidson correction (MRCI+Q) level of theory by complete basis set extrapolation of the aug-cc-pVnZ (n=2,3,4) energies. Due to low-lying charge transfer states in the transition state region, the molecular orbitals are obtained by six-state dynamically weighted multichannel self-consistent field methods. Additional perturbative refinement of the energies is achieved by implementing simple one-parameter correlation energy scaling to reproduce the experimental exothermicity (DeltaE=-33.06 kcalmol) for the reaction. Ab initio points are fitted to an analytical function based on sum of two- and three-body contributions, yielding a rms deviation of <0.3 kcalmol for all geometries below 10 kcalmol above the barrier. Of particular relevance to nonadiabatic dynamics, the calculations show significant multireference character in the transition state region, which is located 3.8 kcalmol with respect to F+HCl reactants and features a strongly bent F-H-Cl transition state geometry (theta approximately 123.5 degrees ). Finally, the surface also exhibits two conical intersection seams that are energetically accessible at low collision energies. These seams arise naturally from allowed crossings in the C(infinityv) linear configuration that become avoided in C(s) bent configurations of both the reactant and product, and should be a hallmark of all X-H-Y atom transfer reaction dynamics between ((2)P) halogen atoms.     

On the validity range of the Born-Oppenheimer approximation: a semiclassical study for all-particle quantization of three-body Coulomb systems

The validity range of the Born-Oppenheimer (BO) approximation is studied with respect to the variation of the mass (m) of negatively charged particle by substituting an electron (e) with muon (mu) and antiproton (p) in hydrogen molecule cation. With the use of semiclassical quantization applied to these (ppe), (ppmu), and (ppp) under a constrained geometry, we estimate the energy difference of the non-BO vibronic ground state from the BO counterpart. It is found that the error in the BO approximation scales to the power of 3/2 to the mass of negative particles, that is, m(1.5). The origin of this clear-cut relation is analyzed based on the original perturbation theory due to Born and Oppenheimer, with which we show that the fifth order term proportional to m(5/4) is zero and thereby the first correction to the BO approximation should arise from the sixth order term that is proportional to m(6/4). Therefore, the validity range of the Born-Oppenheimer approximation is wider than that often mistakenly claimed to be proportional to m(1/4).     

High-throughput and high-resolution two dimensional mapping of pI and m/z using a microchip in a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer

We have developed a high-throughput, two-dimensional-mapping (isoelectric point [pI], mass-to-charge ratio [m/z]) method by combining a capillary isoelectric focusing chip sealed with removable resin tape and a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer. Sample proteins are separated in a meandering channel on the chip and immediately frozen. The tape is then removed and the proteins are freeze-dried. The freeze-drying maintains the separation state of the proteins and prevents movement of the sample solution, which can reduce pI resolution. A matrix solution is then applied and mass spectrometry is carried out by laser irradiation. The whole process takes less than 70 min, more than 10 times faster than with two-dimensional, polyacrylamide gel electrophoresis.