Modeling diffusion in white matter in the brain: a composite porous medium

We model diffusion in white matter fascicles as a problem of diffusion in an array of identical thick-walled cylindrical tubes immersed in an outer medium and arranged periodically in a regular lattice. The diffusing molecules have different diffusion coefficients and concentrations (or densities) within the tubes' inner core, membrane, myelin sheath, and within the outer medium. For an impermeable myelin sheath, diffusing molecules within the inner core are completely restricted, while molecules in the outer medium are hindered due to the tortuosity of the array of impenetrable tubes.     

Dipolar bosons in a planar array of one-dimensional tubes

We investigate bosonic atoms or molecules interacting via dipolar interactions in a planar array of one-dimensional tubes. We consider the situation in which the dipoles are oriented perpendicular to the tubes by an external field. We find various quantum phases reaching from a "sliding Luttinger liquid" phase to a two-dimensional charge density wave ordered phase. Two different kinds of charge density wave order occur: a stripe phase in which the bosons in different tubes are aligned and a checkerboard phase. We further point out how to distinguish the occurring phases experimentally.     

Analysis of water molecules around GTP in Hras-GTP complex and GDP in Hras-GDP complex by molecular dynamics simulations

We investigate the structures of the Hras-GTP and the Hras-GDP complexes in water solvents in order to understand the mechanism of GTP hydrolysis in the Hras-GTP complex. We performed MD simulations of these complexes in order to study the positions and the orientations of water molecules around the guanosine nucleotides. Using trajectories we calculated the angular distribution of water molecules around the most distant phosphorus from guanosine in our previous work. It was shown that water molecules are distributed evenly in GTP, although unevenly in GDP. This suggests that the trigger of GTP hydrolysis is possibly the attack of water molecule to γ?phosphate from the appropriate direction. In this paper, in order to investigate the role of water molecules in GTP hydrolysis in detail, we calculate the orientation of water molecules. The distribution of the orientation is different between GTP and GDP. In order to investigate the cause of this difference, we examine the hydrogen bonds between water molecules and oxygen atom of the most distant phosphate from guanosine. We find that these hydrogen bonds are formed. We also find that the oxygen atom of hydrogen bond is determined by the position of the water molecule of hydrogen bond.     

Raman and SERS studies of carbon nanotube systems

In this paper, we report on Raman studies carried out on different carbon nanotube systems, namely single-walled and multi-walled carbon nanotubes and polymer/nanotube composites. We focus on different types of interactions which can take place in these materials. In single-walled nanotubes, the introduction of van der Waals interactions between tubes when arranged in bundles leads to an upshift of the radial breathing mode (RBM) ranging from 11 to 16 cm⁻¹ depending on the size of the bundle. In multi-walled carbon nanotubes, similar interactions between concentric tubes permit to interpret the low frequency Raman modes. In composites, PMMA/nanotubes, an upshift of the RBM is also observed, explained by the dynamical strain applied by the polymer on the bundles, in response to the breathing vibration. In addition, surface enhanced Raman scattering experiments have demonstrated the occurrence of interfacial reactions between the nanotubes and the metallic support. This is put in evidence by the degradation of tubes, especially metallic ones, and reconstruction of C₆₀-like molecules are in some cases observed.     

Luminescence of Nile red as indicator of composition of nanoparticles from diketonate complexes of trivalent metals

We study the sensitization of fluorescence of Nile red in nanoparticles formed in aqueous solutions of complexes of Al, In, Sc, and Lu with DBM, DBM, and phen and of complexes of In with MBTA and phen. We show that, at concentrations of Nile red of 2–50 nM and complexes of 10–30 μM, the fluorescence intensity of Nile red in aqueous solutions increases by 1.5–2 orders of magnitude compared to its fluorescence in H₂O. We find that, at these concentrations of Nile red in solutions of complexes Al, the dye is completely contained in nanoparticles from these complexes. We show that Nile red molecules are inhomogeneously distributed in nanoparticles from complexes and, upon the completion of the formation of nanoparticles, dye molecules tend to be localized in regions of nanoparticles formed from diketonate complexes M(diketone)₃phen (M is Lu or In) and Al(DBM)₃. Upon the localization of Nile red in these regions, the maximum of its fluorescence spectrum shifts toward ∼600 nm and, upon the penetration of Nile red into nanoparticles from Sc complexes, the shift of the maximum of its fluorescence spectrum compared to the spectrum in water does not exceed 10 nm. The shifts of the spectra are collated with the ability of ions to form diketonate and hydroxy diketonate complexes. We demonstrate that the fluorescence of Nile red is efficiently sensitized, not only upon its penetration into nanoparticles formed from complexes, but also upon its adsorption on the nanoparticle surface when Nile red molecules are introduced in solutions of already formed nanoparticles.     

Anisotropic packing and one-dimensional fluctuations of C60 molecules in carbon nanotubes

The confinement of a C60 molecule encapsulated in a cylindrical nanotube depends on the tube radius. In small tubes with radius RT approximately < 7 A, a fivefold axis of the molecule coincides with the tube axis. The interaction between C60 molecules in the nanotube is then described by a O2-rotor model on a 1D liquid chain with coupling between orientational and displacive correlations. This coupling leads to chain contraction. The structure factor of the 1D liquid is derived. In tubes with a larger radius the molecular centers of mass are displaced off the tube axis. The distinction of two groups of peapods with on- and off-axis molecules suggests an explanation of the apparent splitting of Ag modes of C60 in nanotubes measured by resonant Raman scattering.     

Spectral-luminescence properties of the complexes formed by similarly charged CdTe quantum dots and tetrasulfophthalocyanine molecules

The interaction between negatively charged CdTe quantum dots (QDs) and tetrasulfophthalocy-anine (TSPC) molecules in weak-acid and alkaline media has been investigated by spectral-luminescence methods. Similarly charged QDs and TSPC molecules are found to form complexes that exhibit energy transfer from QDs to TSPC according to the mechanism of fluorescent resonance energy transfer. The channels of QD-luminescence quenching that compete with the intracomplex energy transfer and their contribution to the total QD-luminescence quenching are discussed. A model of the formation of complexes between similarly charged QDs and molecules is proposed.     

Direct Observation of Fluorescently Labeled Single-stranded λDNA Molecules in a Micro-Flow Channel

We developed two labeling methods for the direct observation of single-stranded DNA (ssDNA), using a ssDNA binding protein and a ssDNA recognition peptide. The first approach involved protein fusion between the 70-kDa ssDNA-binding domain of replication protein A and enhanced yellow fluorescent protein (RPA-YFP). The second method used the ssDNA binding peptide of Escherichia coli RecA labeled with Atto488 (ssBP-488; Atto488-IRMKIGVMFGNPETTTGGNALKFY). The labeled ssλDNA molecules were visualized over time in micro-flow channels. We report substantially different dynamics between these two labeling methods. When ssλDNA molecules were labeled with RPA-YFP, terminally bound fusion proteins were sheared from the free ends of the ssλDNA molecules unless 25-mer oligonucleotides were annealed to the free ends. RPA-YFP-ssλDNA complexes were dissociated by the addition of 0.2 M NaCl, although complex reassembly was possible with injection of additional RPA-YFP. In contrast to the flexible dynamics of RPA-YFP-ssλDNA complexes, the ssBP-488-ssλDNA complexes behaved as rigid rods and were not dissociated even in 2 M NaCl.     

Structural and Interaction Properties of Porphyrin Layers — A Quantum Chemical Study

This paper is proposed to understand the interaction of porphyrin layers with diatomic molecules interacting at their interior regions by applying ab initio and density functional theory(DFT) methods. We have used NO, CO, and O2 diatomic molecules to interact with the porphyrin layers. The most common Fe-centered metalloporphyrin structure with tetra-pyrrlic rings having N4 core is chosen for the study. The optimization of Porphyrin-Porphyrin(P I-P II)and Porphyrin-Diatomic molecule-Porphyrin(P I-AB-P II)(AB = NO, CO, and O2) complexes are performed using HF method. In order to understand the planarity and appropriate stacking size of porphyrins and also to infer the separation of diatomic molecules between porphyrin layers the behavior of P I-AB-P II complexes(where AB = NO, CO, and O2)are analyzed using structural properties and molecular electrostatic potentials(MEP). The MEPs are calculated using hybrid exchange correlation functional B3PW91 of DFT along with 6-31+G* basis set for the P I-P II and P I-AB-P II complexes obtained from HF method.     

Taking into account universal intermolecular interactions by the Hückel molecular orbital method

We show that interactions between molecules according to a universal mechanism can be interpreted as changes in the Coulomb integrals in their Hamiltonians. Supplementing the ? technique with the assumption that there is a proportionality between the relative change in the π-electronic charge on the atom and the interaction energy causing these changes allows us to calculate the electronic spectra for solvated dye molecules and their van der Waals complexes. We show that in the molecular orbital calculation, a universal interaction function can act as a semiempirical parameter.     

Titanium-functional group complexes for high-capacity hydrogen storage materials

Using first-principles density-functional electronic structure calculations, we propose functionalized organic molecules decorated with titanium atoms as high-capacity hydrogen storage materials. We study six kinds of functional groups which form complexes with Ti atoms and find that each complex is capable of binding up to six H₂ molecules. Among such complexes, Ti-decorated ethane-1,2-diol can store H₂’s with the maximum gravimetric density of 13 wt% and, under ambient conditions, a practically usable capacity of 5.5 wt%. We also present various forms of storage materials which are obtained by modifying well-known nanomaterials using Ti-functional group complexes.     

Sensitization of fluorescence of dye molecules in nanoparticles of metal complexes

We studied the dependence of absorption and fluorescence spectra of complexes of Al, In, Sc, Y, and La with dibenzoylmethane and naphthoyltrifluoroacetone, as well as the dependence of sensitized fluorescence of dyes in nanoparticles of these complexes, in relation to the water pH, the ratio between ions and diketones, and the ion selection. We showed that the ability of complexes of ions to form nanoparticles that efficiently sensitize dye molecules incorporated into them is determined by stability constants of these ions with organic ligands and by their ability to compete with the formation of hydroxy complexes of these ions. We found that nanoparticles consist of diketonates of different compositions and that Nile red incorporated into nanoparticles is an indicator of the dependence of the composition of nanoparticles on the selection of the central ion of complexes and conditions of their formation. We revealed that complexes M(diketone)(OH)₂ self-assemble into nanoparticles with an admixture of dye molecules and efficiently sensitize dyes upon excitation into absorption bands of complexes. We showed that, at concentrations of rhodamine 6G in water smaller than 50 nM, the use of a solution that contains 50 μM of Al(III), In(III), or Sc(III) + 50 μM of naphthoyltrifluoroacetone makes it possible to increase the sensitivity of the luminescence analysis by 20-fold for the presence of rhodamine 6G in an aqueous solution.     

Quantum chemical and NMR investigations on structure of surface complexes

The semiempirical quantum chemical CNDO/2 method is used to calculate models of specific interaction between benzene, toluene, and butene molecules, respectively, and ions or hydroxyls representing active sites of adsorption on zeolitic surfaces. From energy minima of full potential curves the stabilization energies of the surface complexes have been obtained. On the basis of proposed complexes theoretical carbon-13 NMR chemical shifts of adsorbed molecules are calculated. The theoretical results are in rather good agreement with the experimental ones, confirming the conception of surface complexes. Moreover, experimental paramagnetic shifts of surface complexes containing Co²⁺ ions are tried to interprete in a quite similar way.     

木犀草素和鸟嘌呤间相互作用的理论研究

采用密度泛函理论中的B3LYP方法对木犀草素和鸟嘌呤之间的相互作用和机理进行研究,分别找到了十八种木犀草素和鸟嘌呤复合物. 结果表明这些复合物是通过氢键相互作用而稳定存在的. 利用分子中的原子理论(AIM)和自然键轨道理论(NBO)对体系中的氢键进行研究. 通过基组重叠误差校正的复合物间的相互作用能为6.04～56.94 kJ/mol,计算结果表明在木犀草素-鸟嘌呤复合物中有很强的氢键相互作用. 比较了木犀草素和四个DNA碱基间的相互作 用,发现木犀草素-胸腺嘧啶是最强的,木犀草素-腺嘌呤是最弱的.     

Single walled nanotubes/amylose/SDBS complex

In this study, we prepare and characterize single walled carbon/amylose complexes formed in aqueous medium in presence of a surfactant, where amylose is an helical polysaccharide. We show that at low amylose content, nanotubes based complexes are formed which show a strong infra-red fluorescence. Electron microscopy and atomic force microscopy suggest that the complex morphology implies also the surfactant. We propose a supramolecular architecture of the complex where the nanotubes are protected from the aqueous environment by the surfactant/amylose molecules. These complexes may be of interest for biosensing applications.     

Nonlinear dipole-dipole interactions and spectroscopic properties of van der waals complexes in the gas phase

We suggest a semiempirical approach to describing the influence of local nonlinear dipole-dipole interactions on the formation of van der Waals complexes of 1: 1 composition in the gas phase. Based on this approach, we quantitatively interpret the experimental data on the patterns of the shift in the electronic (complexes of a 3-aminophthalimide molecule with water and methanol molecules) and vibrational (complexes of a HCl molecule with acetone and acetonitrile molecules) absorption spectra attributable to the processes of complex formation. We confirm the conclusion that a nonlinear dipole-dipole interaction should be considered as one of the most important physical mechanisms that result in the association of molecules both in the gas phase and, under certain conditions, in the condensed state.     

Nanotube field and one-dimensional fluctuations of C<Subscript>60</Subscript> molecules in carbon nanotubes

C₆₀ molecules encapsulated in carbon nanotubes interact by van der Waals forces with the tube walls. The nanotube field leads to orientational confinement of the C₆₀ molecules which depends on the nanotube radius. In small tubes with radius R_T≤7 ? a fivefold symmetry axis of the molecule coincides with the tube axis, the center of mass of the molecule being located on the tube axis. The interaction between C₆₀ molecules encapsulated in the nanotube is then described by a O₂-rotor model on a one-dimensional (1-d) liquid chain with coupling between orientational and displacive degrees of freedom but no long-range order. This coupling leads to a temperature-dependent chain contraction. The structure factor of the 1-d liquid is derived. In tubes with larger radius the molecular centers of mass are displaced off the tube axis. The distinction of two groups of peapods with on- and off-axis molecules suggests an explanation of the apparent splitting of A_g modes of C₆₀ in nanotubes measured by resonant Raman scattering.     

应用分子梳技术对DNA与组蛋白相互作用的研究

利用分子梳技术对λ DNA和组蛋白的相互作用进行了研究. 通过这种简单有效的方法，我们将λ DNA分子拉伸到26—28 μm，相当于其原长（约162 μm）的16—17倍. 当组蛋白与DNA结合后，DNA分子发生凝聚现象，复合体的拉伸长度明显变短，其峰值分布在10—14 μm之间. DNA 组蛋白复合体的拉伸长度与组蛋白的浓度、与碱基对和荧光染料的比例有显著的关系. 关键词： 分子梳 组蛋白 DNA 荧光显微     

Packing configurations for methane storage in carbon nanotubes

In this paper we investigate methane packing in single-walled carbon nanotubes. We employ classical applied mathematical modelling using the basic principles of mechanics to exploit the Lennard-Jones potential function and the continuous approximation, which assumes that intermolecular interactions can be approximated by average atomic surface densities. We consider both zigzag and spiral configurations formed by packing methane molecules into (9, 5), (8, 8) and (10, 10) carbon nanotubes, and we derive analytical expressions for the interaction potential energy of these configurations. Our findings indicate that for the zigzag configuration for a (9, 5) tube, the potential energy of the system is minimized when the methane molecules simply form a linear chain along the tube axis, but genuine zigzag patterns are found as the tube size increases such as for the (8, 8) and (10, 10) tubes. For the spiral configuration, the potential energy of the system is minimized when the angular spacing is approximately equal to π for the (9, 5) and (8, 8) tubes, and π/2 for the (10, 10) tube. Overall, our results are in good agreement with molecular dynamics simulations in the literature and show that the most energetically efficient packing configuration of the three tubes studied, occurs for a (10, 10) tube with a zigzag packing, while a (10, 10) tube with a spiral packing configuration has the largest free-cavity volume for methane adsorption at higher temperatures.     

Multiexciton molecules in the hexaborides

We investigate multiexciton bound states in a semiconducting phase of divalent hexaborides. Due to three degenerate valleys in both the conduction and valence bands the binding energy of a 6-exciton molecule is greatly enhanced by the shell effect. The ground state energies of multiexciton molecules are calculated using the density functional formalism. We also show that charged impurities stabilize multiexciton complexes leading to condensation of localized excitons. These complexes can act as nucleation centers of local moments. Received 24 October 2000