Sequence dependence in base flipping: experimental and computational studies

Base flipping is the movement of a DNA base from an intrahelical, base-stacked position to an extrahelical, solvent-exposed position. As there are favorable interactions for an intrahelical base, both hydrogen bonding and base stacking, base flipping is expected to be energetically prohibitive for an undamaged DNA duplex. For damaged DNA bases, however, the energetic cost of base flipping may be considerably lower. Using a selective, non-covalent assay for base flipping, the sequence dependence of base flipping in DNA sequences containing an abasic site has been studied. The dissociation constants of the zinc-cyclen complex to small molecules and single strands of DNA as well as the equilibrium constants for base flipping have been determined for these sequences. Molecular dynamics simulations of the zinc-cyclen complex bound to both single- and double-stranded DNA have been performed in an attempt to rationalize the differences in the dissociation constants obtained for the two systems. The results are compared to previous studies of base flipping in DNA containing an abasic site.     

过渡金属原子对掺杂g-CN单层作为高效氮电催化剂性能

由于氨是药物、肥料和树脂等领域的基础,氨合成一直广受关注.工业中主要通过Haber-Bosch反应制备氨,反应需要在高温高压下进行.因此,探索其它氨合成技术对减轻能源消耗和缓解温室效应具有重大意义.在溶液条件下,采用水作为氢质子源,电化学还原氮合成氨方法受到了极大关注.然而,大多数电催化剂难以活化氮气分子且电催化氮气还...     

Electron Correlation Effects for Adiabatic Electrochemical Reactions of Electron Transfer in a Model for an Electrode with an Infinitely Wide Conduction Band: Diagrams of Kinetic Modes

For adiabatic electrochemical reactions, within the framework of a model for an electrode with an infinitely wide conduction band, exact results are obtained for critical regions that correspond to different possible types of electron transfer processes (transfer of a single electron with and without an intermediate state, simultaneous transfer of two electrons) and regions that correspond to electroadsorption of the reactant in certain charge states. These regions form a diagram of kinetic modes (DKM) in the space of model parameters. Analytical expressions for outermost curves of DKM are obtained for some extreme cases. For the general case of a model for an electrode with an infinitely wide conduction band, a DKM is constructed and investigated with exact allowance for the effects of electron–electron correlations.     

A biocatalytic redox isomerisation

A bi-enzymatic cascade for the redox-isomerisation of allylic alcohol is presented. Coupling of an alcohol dehydrogenase to an enoate reductase has been successfully applied in one pot for the isomerisation of an allylic alcohol to the corresponding ketone. Critical parameters for yield and selectivity have been investigated.     

Electrostatic control of lipid bilayer self-spreading using a nanogap gate on a solid support

We have demonstrated for the first time that the self-spreading of supported lipid bilayers can be controlled by the temporal switching of an electric field applied between nanogap electrodes. To account for this phenomenon, we propose an electrostatic trapping model in which an electric double layer plays an important role. The validity of this mechanism was verified by the dependence of self-spreading on the nanogap width and the ionic concentration of the electrolyte. Our results provide a promising tool for the temporal and spatial control of lipid bilayer formation for nanobio devices.     

Electron Correlations for Adiabatic Electrochemical Electron Transfer Reactions in a Model for an Electrode with an Infinitely Wide Conduction Band

Fresh general relationships for adiabatic free-energy surfaces (AFES) and corresponding diagrams of kinetic modes for adiabatic electrochemical electron transfer reactions are derived in the framework of an exactly solvable model for a metallic electrode with an infinitely wide conduction band. The model is a limiting case of the Anderson model applicable to the sp metals. In contrast to earlier studies of adiabatic reactions in a model for an electrode with an infinitely wide conduction band, this work accounts for the electron–electron correlation effects exactly. As an illustration, an AFES is calculated and a diagram of kinetic modes is constructed for a special case corresponding to the equilibrium electrode potential of a two-electron reaction. The exact AFES is compared with the AFES computed in the Hartree–Fock approximation and a spinless model. The correlation effects are shown to play a substantial role and lead to a considerable decrease in the activation free energy.     

Diffusiophoresis of a cylindrical colloidal particle oriented parallel to an electrolyte concentration gradient field

We derive the general expression for the diffusiophoretic mobility of a cylindrical particle oriented parallel to an applied electrolyte concentration gradient field in a symmetrical electrolyte solution. From the general mobility expression as combined with an approximate analytic expression with negligible error for the electric potential distribution around a cylinder, an accurate analytic mobility expression is obtained, which is applicable for arbitrary values of the particle zeta potential and the electrical double layer thickness. It is also found that the low zeta potential approximation is an excellent approximation for low-to-moderate values of the particle zeta potential.     

Expeditious and scalable preparation of a Li-Thiele reagent for amine-based bioconjugation

Chemoselective amine bioco njugation has long been a challenge for native protein modification.Inspired by Thiele's seminal discovery,Li and co-workers recently developed an orto-phthalaldehyde(OPA)based reagent for labeling the amino group of a protein.Here we report an expeditious and scalable synthesis of a Li-Thiele reagent featuring an arene construction strategy.The reagent contains an alkyne side chain as a handle for secondary modification.     

Novel strategies for the synthesis of anthrapyran antibiotics: discovery of a new antitumor agent and total synthesis of (S)-espicufolin

Two high-yielding strategies for the synthesis of 4H-anthra[1,2-b]pyran antibiotics have been developed giving access to novel antitumor agent (ED(50) 1.5 microm) and to (S)-espicufolin (3). A key step for the assembly of the tetracyclic 4H-anthra[1,2-b]pyran-4,7,12-trione skeleton is the nucleophilic addition of an aryl lithium species onto an aldehyde which allows the introduction of either an ynone or 1,3-diketo side chain, serving as precursors for an acid-catalysed cyclisation.     

A fully retarded expression for the circular dichroism of polymers in the frenkel exciton model

A theoretical expression for the ellipticity of an exciton band in an oriented rigid polymer is derived by use of the Frenkel exciton model in conjunction with a fully retarded expression for the partial ellipticity of an electronic transition.     

Total synthesis of (-)-apicularen A

Complete details of an asymmetric synthesis of apicularen (1) are described. The synthesis has been accomplished using a highly diastereo- and enantioselective [4 + 2] annulation for the assembly of the functionalized pyran core. An underdeveloped lactonization method involving an NaH promoted transesterification of an advanced intermediate bearing an aryl cyanomethyl ester was used for the macrolactonization step.     

Local inverse inelastic mean free path at interface

We calculated a local inverse inelastic mean free path (local-IIMFP) for electrons crossing a medium–medium interface, considering various incident electron energies, crossing angles and combinations of materials. We used an extension of a classical dielectric model developed by Li and co-workers for an electron crossing a surface (interface vacuum-medium). Moreover, the integration over the distance of the local-IIMFP allows to obtain the interface excitation parameter (or IEP) characterizing the change in excitation probability for an electron crossing an interface once caused by the presence of the interface in comparison with an electron for which only volume excitations are considered. We perform these calculations for angles between 0° and 80°, for electron energies between 500 and 2500 eV and for various pairs of materials, as Al/In for its academic interest or Au/Si and SiO₂/Si for their technological importance. Small but not negligible variations of the local-IIMFP and the IEP were observed for metal–metal or metal–semiconductor interfaces, while quite significant variations are obtained when one of the materials is a insulator.     

Prevention of evaporation of small-volume sample solutions for capillary electrophoresis using a mineral-oil overlay.

The suppression of evaporation of water from small volumes of sample solutions or reagents for capillary electrophoresis by the use of a mineral-oil overlay was investigated in affinophoresis applications, in which the affinity constant of a mutant protein of recombinant human galectin-1 to a lactose affinophore, a triply negative charged ion having a lactoside as an affinity ligand, was determined. When an injection was carried out from a minimum of 20 microL of an aqueous solution beneath the oil overlay, no oil contamination inside the capillary was observed, provided the capillary was cleanly cut so that the end was flat, and the polyimide coating had been removed for a distance of about 2 mm from the end. Affinophoresis was carried out using 20 microL of an affinophore solution covered with an oil overlay. The abnormalities in the electropherograms as the result of the evaporation of the water from the solution during storage prior to use in an automatic operation of a capillary electrophoresis instrument were suppressed, with respect to the formation of a base line gap, an increase in the detection time of a marker ion and an increase in the initial current. A solution in a vial could be used repeatedly for a longer period of time when overlaid with mineral oil than in the absence of an overlay. The use of a mineral-oil overlay is a simple but very efficient technique for solving the problem of the evaporation of water from small volumes of aqueous solutions for use in capillary electrophoresis.     

Manipulating replication processes within a dynamic covalent framework

The reaction of an amine bearing an amidopyridine recognition site and an aldehyde bearing a carboxylic acid recognition site affords an imine that is capable of directing its own formation through a dynamic covalent replication cycle. Additionally, the amine, formed by reduction of the replicating imine, is a more efficient catalyst for the formation of the replicating imine than the imine is a catalyst for its own formation.     

Sur un effet de solvant inhabituel sur une reaction de menschutkin intramoleculaire

The influence of solvation on the reaction rate of an intramolecular quaternisation, may be different from the rate observed for an intermolecular reaction of the same type. In the intermolecular reaction, if the polarity of an aprotic solvent increases, the partially charged transition state is more stable than the initial state. In the contrary, for an intramolecular reaction the conformation of the different states (initial and transition) plays an important role. So that, if the polarity of an aprotic solvent increases, one conformation of the uncharged initial state may be, by its geometry more stable than the partially charged transition state. An interpretation based on the conformation, explains why in one case and in comparison with CH₃CN, methanol accelerates the intramolecular reaction whereas the contrary is always observed for an intermolecular one.     

多种类表面活性剂临界胶束浓度定量构效关系

表面活性剂的临界胶束浓度(CMC)是个非常重要的物质特性参数, CMC在研究表面活性剂的工业应用和生物利用方面发挥着关键作用. 本工作提出了一个新的拓扑指数—扩展距离矩阵, 建立了一个稳定的构效关系模型, 并对175种表面活性剂的临界胶束浓度进行了计算预测. 结果表明, 基于新的拓扑指数建立的构效关系模型计算临界胶束浓度能给出稳定可靠的预测结果, 其预测结果相关性系数R²(training set)=0.9295, 相对标准偏差ARD(training set)=8.20%, R²(testing set)=0.9257, ARD(testing set)=6.76%. 与文献中模型预测结果的对比表明, 本工作在稳定性和可靠性上均有显著改善.     

The all-Cartesian reaction plane Hamiltonian: formulation and application to the H-atom transfer in tropolone

In this work we present an all-Cartesian reaction surface approach, where the large amplitude coordinates span the so-called reaction plane, that is, the unique plane defined by the two minima and the saddle-point structure of an isomerization reaction. Orthogonal modes are treated within harmonic approximation which gives the total Hamiltonian an almost separable form that is suitable for multidimensional quantum dynamics calculations. The reaction plane Hamiltonian is constructed for the H-atom transfer in tropolone as an example for a system with an intramolecular O...H-O hydrogen bond. We find ground-state tunneling splittings of 3.5 and 0.16 cm(-1) for the normal and deuterated species, respectively. We calculated infrared-absorption spectra for a four-dimensional model focusing on the low-frequency region. Here, we identify a reaction mode which is closely connected to the tautomerization that is reflected in the increase of tunneling splitting to 18 cm(-1) upon excitation.     

Computer-aided acquisition and processing of data for caloric measurements with isoperibol calorimeters

The undisturbed temperature equilibration of the vessel in an isoperibol calorimeter must follow an exponential time function. Any caloric effect within this vessel must cause a deviation of this function. A mathematical relation has been derived for linking the extent of this caloric effect and the integral of the temperature-time function.This algorithm has been utilized for a computer program capable for an automatic acquisition of the data of an appropriate digital temperature meter and for the automatic calculation of the calorimetric results.In two different calorimetric units these arrangements have been applied for the following determinations: -specific heat capacities of liquid samples -heats of chemical reactions -reaction rates -heats of vaporization of liquid samples.     

Observation of Single Pt Nanoparticle Collisions: Enhanced Electrocatalytic Activity on a Pd Ultramicroelectrode

Single Pt nanoparticle (NP) collisions on an electrode surface were detected by using an electrocatalytic amplification method with a Pd ultramicroelectrode (UME). Pd is not a preferred material for UMEs for the detection of single Pt NP collisions, because Pd shows similar electrocatalytic activity compared with Pt for hydrazine oxidation, thus resulting in a high background current level. However, a Pt NP colliding on the Pd UME shows greatly enhanced activity compared with a Pt NP on an inert UME, such as a Au UME, which is usually used for the detection of single Pt NP collisions. The use of an electroactive UME material instead of an inert one facilitated the study of single‐NP activity on the various solid supports, which is important in many NP applications.