Theoretical and computational studies of vectorial processes in biomolecular systems

Efficient vectorial processes such as the transduction of bioenergy and signals are characteristics that strikingly distinguish living systems from inanimate materials. Recent developments in biophysical and biochemical techniques have provided new information about the structure, dynamics and interaction of biomolecules involved in vectorial life processes at multiple length and temporal scales. This wealth of data makes it possible to carry out theoretical and computational studied of key mechanistic questions associated with complex life processes at an unprecedented level. Using two “vectorial biomolecular machines”, myosin and cytochrome c oxidase, as examples, we discuss the identification of interesting and biologically relevant questions that require thorough theoretical analysis. Technical challenges and recent progress related to these theoretical investigations are briefly summarized     

电场作用下苏氨酸的电流特性研究

制备了以液态苏氨酸为沟道材料的四端有机场效应晶体管,观测了其随着栅极电压的不同呈现出源漏两极之间不同的电学特异现象;还观测了苏氨酸在外电场作用下,阻抗随着源漏之间电压频率变化的关系,提出一个极性液体模型解释了其导电机理。     

Protein-coated β-ferric hydrous oxide particles: An electrokinetic and electrooptic study

Using microelectrophoresis and electric light scattering techniques, we investigated the adsorption characteristics, surface coverage and surface electric parameters of superstructures from two isoforms of plastocyanin, PCa and PCb, in an oxidized state adsorbed on β-ferric hydrous oxide particles. The surface electric charge and electric dipole moments of the composite particles and the thickness of the protein adsorption layer are determined in a wide pH range, at different ionic strengths and concentration ratios of PC to β-FeOOH. The adsorption of the two proteins was found to shift the particles’ isoelectric point and to alter the total electric charge and the electric dipole moments of the oxide particles to different extent. A “reversal” in the direction of the permanent dipole moment is observed at lower pH for PCb- than for PCa-coated oxide particles. Strict correlation is found between the changes in the electrokinetic charge of the composite particles and the variation in their “permanent” dipole moments. Data suggest that the adsorption of the proteins is driven by electrostatic and/or hydrophobic interactions with the oxide surfaces dependent on pH. The adsorption behaviour is consistent with the involvement of the “eastern” and “northern” patches of the plastocyanin molecules in their adsorption on the oxide surfaces that are differently charged depending on pH.     

Analysis of dielectric relaxations of w/o emulsions in the light of theories of interfacial polarization

An attempt is made to apply dielectric theories of interfacial polarization to observations of dielectric relaxations for W/O emulsions. Approximate formulas for disperse systems in a W/O type were derived from the two theories: one proposed by Maxwell and Wagner for dilute disperse systems of spherical particles, and the other developed by Hanai for concentrated disperse systems. Dielectric measurements were carried out on concentrated W/O emulsions prepared from kerosene and distilled water or KCl aqueous solutions by minimal use of emulsifiers. Marked dielectric relaxations were observed with the emulsions, the dielectric parameters having been determined to characterize the relaxation data. Phase parameters such as relative permittivity, electric conductivity and volume fraction of the disperse phase were evaluated from the dielectric parameters by use of the approximate formulas of the respective theories. The phase parameters evaluated and the frequency dependence of complex permittivity of the W/O emulsions deduced from the theory for concentrated disperse systems are in excellent agreement with the observed data in comparison to that for dilute disperse systems. It is concluded that the dielectric relaxations due to the interfacial polarization of disperse systems of spheres are explained satisfactorily by the theory for concentrated disperse systems.     

Electrochemistry of capillary systems with narrow pores. IV. Dialysis potentials

The dialysis potentials of different collodion membranes with graded pore sizes and electrochemical activities have been measured in dilute aqueous KCl solutions as functions of concentration. It is possible to predict the value of the diffusion potential within a few millivolts on the basis of electrical conductivity data obtained with the same membranes. In general, the measured values are lower than those calculated. It is assumed that this difference is caused by the membranes having a distribution of pore sizes.     

Polyynes and cyanopolyynes synthesis from the submerged electric arc: about the role played by the electrodes and solvents in polyynes formation

The products of the electric arc between graphite electrodes have been investigated by high performance liquid chromatography-diode-array detector (HPLC-DAD) analysis in various media: distilled water, liquid nitrogen, methanol, ethanol, n-hexane and benzene. In distilled water, hydrogen capped polyynes H-(CC)_n-H were the unique products demonstrating that carbon is supplied by the graphite electrodes while hydrogen is supplied by the solvent plasmalysis (in this case water plasmalysis). Arcing graphite electrodes in liquid nitrogen produces cyanopolyynes: NC-(CC)_n-CN demonstrating that in this case the end groups of the polyyne chains are supplied by molecular nitrogen plasmalysis caused by the electric arc. Graphite arcing in methanol and ethanol produces very clean solutions (by-products negligible or absent) of hydrogen-capped polyynes with C₈H₂ as the main product accounting for more than 70 mol percent of the total polyyne concentration. By replacing graphite electrodes with titanium electrodes in methanol or in ethanol, polyynes are not formed at all; only trace amounts of polycyclic aromatic hydrocarbons (PAHs) were detected. When arcing with graphite electrodes is conducted in n-hexane or in benzene, polyyne formation is accompanied by a significant production of PAH, especially in benzene. These results have been rationalized in terms of carbonization or coking tendency of a given solvent. The effect of using titanium electrodes in place of graphite electrodes has been investigated also in n-hexane and in benzene as well as the effects of very high electric current intensity employed to ignite and sustain the submerged electric arc.     

Structure formation and dynamics of water in strong external electric fields

We have performed molecular dynamics computer simulations of water in homogeneous external electric fields which were varied in a wide range of field strengths. The dielectric response is found to be linear up to fields E₀≈0.01 V/Å from where dielectric saturation effects become important. At fields of E₀≈3 V/Å a phase transition into an ordered, ice-like structure is observed, which is stabilized through hydrogen-bonds. With an increasing external electric field, the frequency spectrum of the water dynamics shows a remarkable red shift of the intramolecular modes and a blue shift of the librational motions, where the frequency varies quadratically with the field strength. A simple analytical model is discussed which reproduces the observed behavior.     

碘掺杂的3-乙基-5-[2-(3-乙基-2苯并噻唑啉基)亚乙基]罗丹宁的结构与电性能

The merocyanine dye 3-ethyl-5-(2-(3-ethyl-2-benzothiazolinylidene)-ethylidene)-rhodanine (BTER) known as Agfa-10 has been found to have a good photoconductivity as solution cast film. In this paper iodine-doped BTER was obtained by doping with iodine vapor. Its structure was investigated with the following characteristies. 1 The doped iodine had been excited as I_3~- anion. 2 Because the electron located on the sulphur atom was transferred to iodine, the charge transfer complex of (BTER-I_3) formed. 3 During the iodine doping process, BTER changed from α-form to β-modification. These had been identified by X-ray diffraction, VIS-absorption spectra and SEM picture.4 From the volt-Ampere curve obtained from sandwich cell, when E≤2.2×10~(-1) V·cm~(-1), the room temperature electrical conductivity of BTER and BTER-I_3 were found to be 2.22×10~(-10) s·cm~(-1) and 2.6×10~(-7) S·cm~(-1), respectively.     

Enhanced visible-light-driven photodegradation of Acid Orange 7 azo dye in aqueous solution using Fe-N co-doped TiO2

FeN -co-doped TiO₂ photocatalysts are prepared by sol–gel method using titanium tetraisopropoxide, urea and iron(II) acetylacetonate as precursors of titania, nitrogen and iron, respectively. The prepared samples are analysed from chemical-physical point of view by X-ray diffraction (XRD), Raman spectroscopy, UV–Vis diffuse reflectance spectroscopy (UV–Vis DRS), specific surface area measurements and scanning electron microscopy (FESEM). UV–Vis DRS spectra evidence that the co-doping of TiO₂ with N and Fe leads to the narrowing of the band gap value (2.7 eV) with respect to Fe-doped TiO₂ (2.8 eV) and N-doped TiO₂ (2.9–3 eV). XRD patterns show that photocatalysts are mainly in anatase phase and Fe and N ions are successfully incorporated into the TiO₂ lattice. The average crystallite size of Fe-N co-doped TiO₂ is slightly lower than the other samples and equal to about 7 nm and the specific surface area of the co-doped sample results to be 117 m² g⁻¹. Photocatalytic performances of all prepared samples are evaluated by analysing the degradation of Acid Orange 7 azo dye under visible light irradiation. Photocatalytic efficiency obtained using FeN co-doped TiO₂ strongly increases compared to undoped TiO₂, N-doped TiO₂ and Fe-doped TiO₂ photocatalysts. In detail, using the co-doped photocatalyst, dye discoloration and mineralization result equal to about 90 and 83% after 60 min of LEDs visible light irradiation, underlining the best performances of the FeN co-doped TiO₂ photocatalyst both in terms of treatment time and electric energy consumption.     

Polarisabilites moléculaires et effet diélectrique de milieu à l'état liquide. Étude théorique de la molécule d'eau et de ses diméres

The model of Onsager in which a polar molecule undergoes a reaction field due to the polarization of the molecular surroundings is used to evaluate by a S.C.F. calculation (CNDO/2 approximation) the modifications of a molecular structure in the liquid state.Application to water molecule and to three polar dimers for values of the dielectric constant varying between 3 and 78, shows that most of geometric parameters and dipoles moments vary of few per cent when the molecule is inserted in a liquid. In the liquid state dipole moments do not depend very much on the dielectric constant but energies and relative stabilities of isomers are strongly dependent on the medium.[/p]