Topologically-Interlocked Minicircles as Probes of DNA Topology and DNA-Protein Interactions

DNA minicircles exist in biological contexts, such as kinetoplast DNA, and are promising components for creating functional nanodevices. They have been used to mimic the topological features of nucleosomal DNA and to probe DNA-protein interactions such as HIV-1 and PFV integrases, and DNA gyrase. Here, we synthesized the topologically-interlocked minicircle rotaxane and catenane inside a frame-shaped DNA origami. These minicircles are 183 bp in length, constitute six individual single-stranded DNAs that are ligated to realize duplex interlocking, and adopt temporary base pairing of single strands for interlocking. To probe the DNA-protein interactions, restriction reactions were carried out on DNAs with different topologies such as free linear duplex or duplex constrained inside origami and free or topologically-interlocked minicircles. Except the free linear duplex, all tested structures were resistant to restriction digestion, indicating that the topological features of DNA, such as flexibility, curvature, and groove orientation, play a major role in DNA-protein interactions.     

Skeletal Transformation Triggered by C−F Bond Activation after Photochemical Rearrangement of Fluorinated [7]Helicenes

Tri- and tetra-fluorinated [7]helicenes are photolabile and undergo a double fluorine atom transfer. Herein, we show that the transferred product further undergoes a skeletal transformation on silica gel. The transformation begins with activation of the allylic C−F bond on the silanol surface. Then, the resulting carbocation readily undergoes a regioselective nucleophilic aromatic substitution with water, depending on the position of the fluorine substituents. Hexafluoro-2-propanol also activated the allylic C−F bond and acted as a nucleophile. These findings support the generation of a highly reactive cationic electrophilic intermediate in the successive transformations involving fluorine atoms.     

Investigation of Molecular Diffusion at Block Copolymer Thin Films Using Maximum Entropy Method-Based Fluorescence Correlation Spectroscopy and Single Molecule Tracking

Fluorescence correlation spectroscopy (FCS) has been widely used to investigate molecular diffusion behavior in various samples. The use of the maximum entropy method (MEM) for FCS data analysis provides a unique means to determine multiple distinct diffusion coefficients without a priori assumption of their number. Comparison of the MEM-based FCS method (MEM-FCS) with another method will reveal its utility and advantage as an analytical tool to investigate diffusion dynamics. Herein, we measured diffusion of fluorescent probes doped into nanostructured thin films using MEM-FCS, and validated the results with single molecule tracking (SMT) data. The efficacy of the MEM code employed was first demonstrated by analyzing simulated FCS data for systems incorporating one and two diffusion modes with broadly distributed diffusion coefficients. The MEM analysis accurately afforded the number of distinct diffusion modes and their mean diffusion coefficients. These results contrasted with those obtained by fitting the simulated data to conventional two-component and anomalous diffusion models, which yielded inaccurate estimates of the diffusion coefficients. Subsequently, the MEM analysis was applied to FCS data acquired from hydrophilic dye molecules incorporated into microphase-separated polystyrene-block-poly(ethylene oxide) (PS-b-PEO) thin films characterized under a water-saturated N₂ atmosphere. The MEM analysis revealed distinct fast and slow diffusion components attributable to molecules diffusing on the film surface and inside the film, respectively. SMT studies of the same materials yielded trajectories for mobile molecules that appear to follow the curved PEO microdomains. Diffusion coefficients obtained from the SMT data were consistent with those obtained for the slow diffusion component detected by MEM-FCS. These results highlight the utility of MEM-FCS and SMT for gaining complementary information on molecular diffusion processes in heterogeneous material systems.

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On the six-field model of fluids based on extended thermodynamics

We study the six-field model of fluids (ET6) derived from extended thermodynamics. The six fields are the mass density, the velocity, the temperature, and the dynamic pressure (nonequilibrium pressure). We present the basic system of field equations of ET6. And we elucidate its characteristic features through the studies of the singular limit from polyatomic to monatomic rarefied gases, of hydrodynamic fluctuation, and of a hard-sphere system. Open problems remained in ET6 at present are also pointed out.     

Synthesis,Structure, Optical,and Electrochemical Properties of Triple‐ and Quadruple‐Decker Co‐facial Tetrathiafulvalene Arrays

Understanding the details of the electronic structure in face‐to‐face arranged tetrathiafulvalenes (TTFs) is very important for the design of supramolecular functional materials and superior conductive organic materials. This article is a comprehensive study of the interactions among columnar stacked TTFs using trimeric (trimer) and tetrameric (tetramer) TTFs linked by alkylenedithio groups (‐S(CH₂)_nS‐, n=1–4) as models of triple‐ and quadruple‐decker TTF arrays. Single‐crystal X‐ray analyses of neutral trimeric TTFs revealed that the three TTF moieties are oriented in a zigzag arrangement. Cyclic voltammetry measurements (CV) reveal that the trimer and tetramer exhibited diverse reversible redox processes with multi‐electron transfers, depending on the length of the ‐S(CH₂)_nS‐ units and substituents. The electronic spectra of the radical cations, prepared by electrochemical oxidation, showed charge resonance (CR) bands in the NIR/IR region (1630–1850 nm), attributed to a mixed valence (MV) state of the triple‐ and quadruple‐decker TTF arrays. In the trimeric systems, the dicationic state (+2; 0.66 cation per TTF unit) was found to be a stable state, whereas the monocationic state (+1) was not observed in the electronic spectra. In the tetrameric system, substituent‐dependent redox processes were observed. Moreover, π‐trimers and π‐tetramers, which show a significant Davydov blueshift in the spectra, are formed in the tricationic (trimer) and tetracationic (tetramer) state. In addition, these attractive interactions are strongly dependent on the length of the linkage unit.     

Global dynamics of a reaction–diffusion system with mass conservation

We study global dynamics of a mass conserved reaction–diffusion system. First, we show the global-in-time existence of the solution with compact orbit. Then the dynamical stability of local minima associated with a variational function is proven.     

Chiral Ammonium Betaine‐Catalyzed Highly Stereoselective Aza‐Henry Reaction of α‐Aryl Nitromethanes with Aromatic N‐Boc Imines

A highly stereoselective aza‐Henry reaction of α‐aryl nitromethanes with aromatic N‐Boc imines was established by using C₁‐symmetric chiral ammonium betaine as a bifunctional organic base catalyst. Various substituted aryl groups for both imines and nitromethanes were tolerated in the reaction, and a series of precursors for the synthesis of unsymmetrical anti‐1,2‐diaryl ethylenediamines was provided.     

Investigation on the Surface‐Confined Self‐Assembly Stabilized by Hydrogen Bonds of Urea and Amide Groups: Quantitative Analysis of Concentration Dependence of Surface Coverage

Formation of a hydrogen‐bond network via an amide group is a key driving force for the nucleation–elongation‐type self‐assembly that is often seen in biomolecules and artificial supramolecular assemblies. In this work, rod‐coil‐like aromatic compounds bearing an amide ( 1 a – 3 a ) or urea group ( 1 u – 3 u ) were synthesized, and their self‐assemblies on a 2‐D surface were investigated by scanning tunneling microscopy (STM). According to the quantitative analysis of the concentration dependence of the surface coverage, it was revealed that the strength of the hydrogen bond (i.e., amide or urea) and the number of non‐hydrogen atoms in a molecular component (i.e., size of core and length of alkyl side chain) play a primary role in determining the stabilization energy during nucleation and elongation processes of molecular ordering on the HOPG surface.     

Progress in the demonstration and understanding of water splitting using particulate photocatalysts

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Interaction between Divalent Copper Fluoride and Carboxamide Group Enabling Stereoretentive Fluorination of Tertiary Alkyl Halides

Herein, we report a copper-catalyzed stereospecific fluorination involving CsF and α-bromocarboxamides as tertiary alkyl sources that, unlike traditional stereospecific routes involving stereoinversive S_N2 reactions, proceeds with retention of stereochemistry. The developed stereospecific Cu-catalyzed reaction is among the most efficient methods for synthesizing fluorinated molecules that possess highly congested stereogenic carbon centers. Mechanistic studies revealed that the combined reactivity of CuF₂ and Cs salt is essential for completing the catalytic cycle. Our catalytic system underwent fluorination exclusively with tertiary alkyl bromides and did not react with primary alkyl bromides, indicating that this stereospecific fluorination methodology is suitable for synthesizing fluorinated building blocks possessing stereo-defined F-containing tertiary carbon stereogenic center.