Construction of a protein-detection system using a loop peptide library with a fluorescence label

Construction of a novel protein-detection system was carried out using a designed peptide library with fluorescent labels based on loop structures. As a basic model study, detection of alpha-amylase using fluorescent-labeled peptides derived from an active loop of tendamistat was examined. The detection methods for proteins with immobilized peptides as well as peptides in solution have been successfully established. Based on these results, a loop peptide library that has various turn sequences grafted on a stable loop structure has been constructed. Various proteins with recognition patterns corresponding, for instance, to "protein fingerprints" could be detected using an immobilized peptide library. The present results suggest that the system can be applied to the development of a peptide microarray that behaves as a protein chip.     

Chaperone-assisted translocation of a polymer through a nanopore

Using Langevin dynamics simulations, we investigate the dynamics of chaperone-assisted translocation of a flexible polymer through a nanopore. We find that increasing the binding energy ε between the chaperone and the chain and the chaperone concentration N(c) can greatly improve the translocation probability. Particularly, with increasing the chaperone concentration a maximum translocation probability is observed for weak binding. For a fixed chaperone concentration, the histogram of translocation time τ has a transition from a long-tailed distribution to a gaussian distribution with increasing ε. τ rapidly decreases and then almost saturates with increasing binding energy for a short chain; however, it has a minimum for longer chains at a lower chaperone concentration. We also show that τ has a minimum as a function of the chaperone concentration. For different ε, a nonuniversal dependence of τ on the chain length N is also observed. These results can be interpreted by characteristic entropic effects for flexible polymers induced by either the crowding effect from a high chaperone concentration or the intersegmental binding for the high binding energy.     

Design and performance of a high resolution electrospray ion source for a magnetic sector mass spectrometer with a heated capillary inlet

The design and performance of an electrospray ion source for a high resolution magnetic sector mass spectrometer that utilizes a heated capillary has been presented. Low pressure, high sensitivity, stable electrospray, low flow rates, and low electronic noise were important factors in achieving high resolution electrospray mass spectrometry. A unit mass resolution has been achieved for biomolecules with MW > 12,000, and an accuracy of 1.4 ppm has been achieved for the average molecular weight of bovine insulin.     

Diffusional release of a solute from a polymeric matrix — approximate analytical solutions

A refined integral method has been successfully applied to moving boundary problems encountered in the diffusional release of a solute from a polymeric matrix. The release kinetics has been analyzed for both erodible and non-erodible matrices with perfect sink and constant, finite external volume conditions. The range of applicability of these approximate analytical solutions has been established by comparison with available exact solutions. p]The approximate analytical solutions presented here are much more accurate than the pseudosteady-state results and much easier to use routinely than the exact solutions. For a dispersed solute, the results presented here are particularly useful for cases where the solute loading is not in great excess of the solute solubility in the matrix.     

Cooperativity during binding of a ligand to a multidentate oligomer

A matrix method to describe the equilibrium binding of a ligand by a multidentate oligomer with a system of binding centers differing in the affinity for the binding ligand has been proposed. The example of a complexation process simulating the formation of a complex between an oligonucleotide and zinc phthalocyanine ZnPc is considered. With the use of the proposed method, diagrams of the relative contents of different forms of DNA-ligand complexes have been constructed and analyzed. It is shown that the cooperativity of complexation has a considerable effect on the equilibrium of the ligand with the system of nonequivalent centers of binding. The experimental data on changes in the intensity of luminescence in the course of binding between zinc tetrakis(diisopropylguanidinio)phthalocyanine and a DNA molecule with the nucleotide sequence GTTA(GAGTTA)4GG have been analyzed.     

Thermal Marangoni Convection of a Fluid Film Coating a Deformable Membrane

The thermal Marangoni instability of a fluid film coating a deformable membrane has been investigated by taking into account the deformation of the fluid free surface. Numerical calculations for different thermal boundary conditions are presented. The prestressed membrane is supposed to be very thin and therefore its behavior is similar to that of an isothermal fluid free surface with a surface tension but with a different mechanical boundary condition; that is, the fluid should stick on its surface and thus the fluid velocity is zero. An important assumption is that the membrane has no temperature dependence and therefore that only one Marangoni number exists for the free surface of the fluid. Numerical results are presented for stationary and oscillatory thermocapillary instability in both the sinuous and the varicose modes. It is shown that membrane deformation has important implications on the Marangoni instability of the fluid layer for positive and negative Marangoni numbers. Copyright 2001 Academic Press.     

A capsule with a fractal shell in a uniform liquid flow

The problem of a liquid flow, which is uniform at infinity, around a capsule comprising a fractal shell filled with a liquid identical to the ambient liquid has been solved. The flow in the fractal layer is described by the Brinkman equation, assuming that the viscosity of the effective medium differs from the viscosity of the pure liquid. Velocity and pressure distributions have been found, and the viscous drag force applied to the capsule has been calculated.     

Molecular ordering of a cyano compound at a displacive transition temperature: a statistical analysis based on quantum mechanics and computer simulations

A statistical analysis has been carried out to determine the configurational preference of a pair of 4-cyanophenyl 4-n-pentylbenzoate (CPPB) molecules with respect to translatory and orientational motions. The CNDO/2 method has been employed to evaluate the net atomic charge and atomic dipole components at each atomic centre of the molecule. Configurational energy has been computed using the Rayleigh—Schodinger perturbation method. The total interaction energy values obtained through these computations were used to calculate the probability of each configuration at the phase transition temperature using the Maxwell—Boltzmann formula. An attempt has been made to identify the most probable configuration at the phase transition temperature. Further, the flexibility of various configurations has been studied in terms of variation of probability due to small departures from the most probable configuration. On the basis of stacking, in-plane and terminal interaction energy calculations, all possible geometrical arrangements of the molecular pair have been considered. The results are discussed in the light of experimental as well as theoretical observations. The nature of the mesophase has been correlated with the parameter introduced in this paper.     

Molecular ordering of a cyano compound at a displacive transition temperature: a statistical analysis based on quantum mechanics and computer simulations

A statistical analysis has been carried out to determine the configurational preference of a pair of 4-cyanophenyl 4- n -pentylbenzoate (CPPB) molecules with respect to translatory and orientational motions. The CNDO/2 method has been employed to evaluate the net atomic charge and atomic dipole components at each atomic centre of the molecule. Configurational energy has been computed using the Rayleigh-Schodinger perturbation method. The total interaction energy values obtained through these computations were used to calculate the probability of each configuration at the phase transition temperature using the Maxwell-Boltzmann formula. An attempt has been made to identify the most probable configuration at the phase transition temperature. Further, the flexibility of various configurations has been studied in terms of variation of probability due to small departures from the most probable configuration. On the basis of stacking, in-plane and terminal interaction energy calculations, all possible geometrical arrangements of the molecular pair have been considered. The results are discussed in the light of experimental as well as theoretical observations. The nature of the mesophase has been correlated with the parameter introduced in this paper.     

Use of a long-spacer-side-chain liquid crystalline polysiloxane containing a crown ether as a stationary phase for capillary gas chromatography

A new kind of side chain liquid crystalline polysiloxane containing a crown ether with a longer spacer (PSC-11) has been prepared and coated on a fused silica capillary column. The main chroma-tographic characteristics including efficiency, polarity, and selectivity have been examined. The phase exhibits the retention properties of both liquid crystal and crown ether stationary phases and possesses higher efficiency and better selectivity than PSC-3, which has a shorter spacer between the main polysiloxane chain and liquid crystalline side chain.     

Water vapor nucleation on a crystal surface in a strong electric field

Water vapor nucleation at 260 K in a transverse electric field has been simulated by the Monte Carlo method under conditions corresponding to an internal wall of a spatially extended microcrack in a silver iodide crystal. The bicanonical statistical ensemble method has been employed to calculate, at the molecular level, the free energy of addition and the work of formation of dense phase nuclei in fields with different strengths. In a moderate field, the film mechanism of nucleation characterized by intense distortions on the film surface remains preserved. A domain structure of a film layer in contact with the surface exhibits a high stability with respect to an external field and remains preserved until the film is completely destroyed. In a strong electric field, the nucleation mechanism is fundamentally changed; i.e., the film is destroyed to yield threadlike structures. Therewith, the area of the contact with the surface drastically decreases. The orientation of nanothreads along the electric field lines overcomes a low free energy barrier. The point of equilibrium of nanothreads with vapor depends on the presence of hydrogen bonds, while their stability is determined by longer-range dipole-dipole interactions. The observed form of existence of the condensate as polarized nanothreads seems to be analogous to the superpolarized state previously revealed for water microdroplets, the transition to which has the character of the first-order phase transition.     

Evaporation dynamics of a binary sessile droplet: Theory and comparison with experimental data on a droplet of a sulfuric-acid solution

Diffusion evaporation of a sessile binary droplet in an atmosphere of a noncondensable carrier gas has been considered. For a droplet consisting of two infinitely miscible liquids, a relation between the current values of solution concentration and volume of the droplet has been derived in an explicit form under the ideal solution approximation. It has been shown that the volume of a sessile binary droplet may, as well as the volume of a free binary droplet, vary nonmonotonically with time. The evaporation of a droplet of an aqueous sulfuric-acid solution has been considered in detail taking into account the nonideality of the solution. Time variations in the volume, base area, and contact angle have been experimentally measured for the sessile droplet of an aqueous sulfuric-acid solution on a hydrophobized substrate. The experimental data obtained at different initial humidities of water-vapor and droplet-solution concentrations have been analyzed within the theory of the stationary isothermal diffusion evaporation of a sessile binary droplet.     

Determination of percent composition of a mixture analyzed by gas chromatography. Comparison of a helium pulsed-discharge photoionization detector with a flame ionization detector

We present the results of a study of percent composition for a mixture which has been separated by gas chromatography and analyzed using helium pulsed-discharge photoionization detection (He-PDPID) and flame ionization detection (FID). FID has long been the means by which the percent composition of a hydrocarbon mixture has been determined since it has been previously established as a "carbon counting device". However, in this study we present results which show that He-PDPID is more accurate in determining the percent composition of a hydrocarbon mixture and, because it is a universal detection method and can detect compounds that FID cannot, it is also more effective for determining the percent composition of mixtures containing organic compounds with a variety of other functional groups.     

Platinum solubility of a substance designed as a model for emissions of automobile catalytic converters

Automobile catalytic converters emit nanocrystalline platinum attached to alumina particles. For investigations about the bioavailability of Pt from these particles a model substance with approx. 5% Pt on alumina has been prepared and characterized by physical methods (ESCA, XRD, TEM, DTA, TG). Measuring the platinum solubility of these samples in different solvents revealed high amounts that can be explained assuming a corrosion process. The portion of soluble platinum is dependent on the particle size distribution. For a comparative study platinum black has been used. In general the platinum determination has been carried out by electrothermal atomic absorption spectrometry (ET-AAS). The comparison of ET-AAS results with determinations by adsorptive voltammetry (formazone method) allowed to distinguish between elemental and ionic platinum; in solution samples only ionic platinum has been present. UV spectra of extracts have been used for the semi-quantitative platinum speciation in solutions.     

Angular intensity distribution of a molecular oxygen beam scattered from a graphite surface

The scattering of the oxygen molecule from a graphite surface has been studied using a molecular beam scattering technique. The angular intensity distributions of scattered oxygen molecules were measured at incident energies from 291 to 614 meV with surface temperatures from 150 to 500 K. Every observed distribution has a single peak at a larger final angle than the specular angle of 45° which indicates that the normal component of the translation energy of the oxygen molecule is lost by the collision with the graphite surface. The amount of the energy loss by the collision has been roughly estimated as about 30-41% based on the assumption of the tangential momentum conservation during the collision. The distributions have also been analyzed with two theoretical models, the hard cubes model and the smooth surface model. These results indicate that the scattering is dominated by a single collision event of the particle with a flat surface having a large effective mass. The derived effective mass of the graphite surface for the incoming oxygen is 9-12 times heavier than that of a single carbon atom, suggesting a large cooperative motion of the carbon atoms in the topmost graphene layer.     

Synthesis and Properties of a New Polyesterimide from a Forest Product

Polyesterimide offers a class of resin which combines the advantage of high temperature stability with ease of process-ability. Gum rosin, the exudate of pine trees, has been developed as the raw material for preparation of polyesterimide. Abietic acid of rosin reacts readily with maleic anhydride to form the Diels-Alder adduct, which reacts with p-amino benzoic acid to produce a dicarboxylic acid containing an internal imide group. The dicarboxylic acid reacts with diethylene glycol under melt polycondensation at higher temperature (260–300°C)to produce polyesterimide. The polymer is found to be soluble in highly polar solvents. The polymer is amorphous and of low molecular weight. Thermal stability of the polymer has been characterized, and the polymer was found to be thermostable.     

Is there a quantum definition of a molecule?

The paper surveys how chemistry has developed over the past two centuries starting from Lavoisier’s classification of the chemical elements at the end of the eighteenth century; the subsequent development of the atomic–molecular model of matter preoccupied chemists throughout the nineteenth century, while the results of the application of quantum theory to the molecular model has been the story of this century. Whereas physical chemistry originated in the nineteenth century with the measurement of the physical properties of groups of chemical compounds that chemists identified as families, the goal of chemical physics is the explanation of the facts of chemistry in terms of the principles and theories of physics. Chemical physics as such was only possible after the discovery of the quantum theory in the 1920’s. By then the first of the sub‐atomic particles had been discovered and seemingly it is no longer possible to discuss chemical facts purely in terms of atoms and molecules – one has to recognize the electron and the nucleus, the parts of atoms. The combination of classical molecular structure with the quantum properties of the electron has given us a tremendously successful account of chemistry called ‘quantum chemistry’. Yet from the perspective of the quantum theory the deepest part of chemistry, the existence of chemical isomers and the very idea of molecular structure that rationalizes it, remains a central problem for chemical physics. This revised version was published online in July 2006 with corrections to the Cover Date.     

Platinum solubility of a substance designed as a model for emissions of automobile catalytic converters

Automobile catalytic converters emit nanocrystalline platinum attached to alumina particles. For investigations about the bioavailability of Pt from these particles a model substance with approx. 5% Pt on alumina has been prepared and characterized by physical methods (ESCA, XRD, TEM, DTA, TG). Measuring the platinum solubility of these samples in different solvents revealed high amounts that can be explained assuming a corrosion process. The portion of soluble platinum is dependent on the particle size distribution. For a comparative study platinum black has been used. In general the platinum determination has been carried out by electrothermal atomic absorption spectrometry (ET-AAS). The comparison of ET-AAS results with determinations by adsorptive voltammetry (formazone method) allowed to distinguish between elemental and ionic platinum; in solution samples only ionic platinum has been present. UV spectra of extracts have been used for the semi-quantitative platinum speciation in solutions.     

Synthesis of a Phlorin from a Meso‐Fused Anthriporphyrin by a Diels–Alder Strategy

An anthracene‐containing meso‐fused carbaporphyrin, which has extended π‐conjugation pathways as compared to the corresponding naphthalene‐containing carbaporphyrin, has been synthesized. The weak global aromaticity of the anthriporphyrin also allowed its use as the diene for a Diels–Alder reaction with dimethyl acetylenedicarboxylate (DMAD). The resulting phlorin contains an interesting bicyclic structure. Moreover, to the best of our knowledge, this phlorin is the first Diels–Alder adduct of a diene forming part of the global π‐conjugation pathway of an aromatic porphyrinoid.     

Valgran, a program for potentiometric titrations with a versatile automatic modular system

A very flexible modular system for use with a portable IBM PC for potentiometric titrations is described. The appropriate software has been developed in order to obtain automatic end-points, and conventional, first-derivative, second-derivative and Gran curves, as well as a listing of the potentiometric points expressed in different ways. All these alternatives are selectable on menu presentations. The potentiometric system has been applied both the research and routine problems.