Cooperative motions of protein and hydration water molecules: molecular dynamics study of scytalone dehydratase

Two molecular dynamics (MD) simulations totaling 25 ns of simulation time of monomeric scytalone dehydratase (SD) were performed. The enzyme has a ligand-binding pocket containing a cone-shaped alpha+beta barrel, and the C-terminal region covers the binding pocket. Our simulations clarified the difference in protein dynamics and conformation between the liganded protein and the unliganded protein. The liganded protein held the ligand molecule tightly and the initial structure was maintained during the simulation. The unliganded protein, on the other hand, fluctuated dynamically and its structure changed largely from the initial structure. In the equilibrium state, the binding pocket was fully solvated by opening of the C-terminal region, and the protein dynamics was connected with hydration water molecules entry into and release from the binding pocket. In addition, the cooperative motions of the unliganded protein and the hydration water molecules produced the path through the protein interior for ligand binding.     

Magnetic circular dichroism and anomalous fluorescence spectra of [2,2] (2,6)azulenophanes

The electronic absorption spectra of syn-[2,2] (2,6) azulenophane (1) and anti-[2,2] (2,6)azulenophane (2) were investigated via magnetic circular dichroism spectra. The anomalous fluorescence spectra were also observed. From the assignment of the absorption spectra, it was concluded that molecules 1 and 2 emitted the fluorescence from the third excited singlet state.     

Chelate and intramolecular ion-pair formation: A guiding concept for structure/selectivity relationships in the liquid-liquid extraction of alkali and alkaline earth metal ions by anionic crown ether derivatives

Crown ether dyes with pendent anionic side-arms were synthesized for extractionspectrophotometry of alkali and alkaline earth metal ions. Dramatic changes in metal selectivity were obtained simply by changing the nature of the anionic side-arm on the same crown ether skeleton. A structure/metal selectivity relationship is discussed in detail in terms of “chelate” and “intramolecular ion-pair” formation. Small metal cations (high charge density) are preferred in the extraction by a crown ether reagent with a charge-localized anionic side-arm through the formation of a “chelate”. Large metal cations (low charge density) are preferred in the extraction by reagents with a charge-delocalized anionic side-arm through the formation of an “intramolecular ion-pair”. Steric restrictions imposed by the side-arm on the metal ion approaching the crown ether are also important factor in controlling the selectivity of these reagents.     

Mass spectrometric studies on gibberellins

Based on the element maps of twenty-two gibberellin methyl esters fragmentations are discussed, which are characteristic of the common structural features as well as structural modification in gibberellin homologues.     

Magnetic circular dichroism of theA andB bands in KI:Ga+, KI:In+, and KI:Sn2+

Magnetic circular dichroism (MCD) of theA- andB-absorption band region has been obtained at 4.2 K and 50 kG in KI:Ga⁺, KI:In⁺, and KI:Sn²⁺. The MCD spectra indicate the complex nature of these bands more clearly than the absorption spectra themselves do. TheA-band MCD consists in all cases of a positive and a negative part reflecting the structure of the absorption band. TheB-band MCD shows three peaks, two positive peaks at 4.34 and 4.41₅ eV (4.09 and 4.17₅ eV) and a negative peak at 4.38 eV (4.12₅ eV) in KI:Ga⁺ (KI:In⁺). TheB-band in KI:Sn²⁺ consists of a shoulder (b ₀) at 3.76 eV and a main band which has at least 5 sub-peaks (b ₁~b ₅) at 3.82₁, 3.84₁, 3.86₁, 3.88₀, and 3.89₅ eV; each of the subpeaks (b ₁~b ₅) gives a derivative-like MCD.The MCD shape functionf() for the transitiona _1g ² a _1g t _1u has been obtained for one set of parameter values by using the classical Franck-Condon approximation and the Monte Carlo integration method. The result can explain the observed salient features of theB- as well asA-band MCD's, indicating the validity of the Franck-Condon approximation and the interaction mode coordinates.     

Dipeptide-induced chirality organization

This review describes an outline of dipeptide-induced chirality organization by using molecular scaffolds. A variety of ferrocene-dipeptide conjugates as bioorganometallics are designed to induce chirality-organized structures of peptides. The ferrocene serves as a reliable organometallic scaffold with a central reverse-turn unit for the construction of protein secondary structures via intramolecular hydrogen bondings, wherein the attached dipeptide strands are constrained within the appropriate dimensions. Another interesting feature of ferrocene-dipeptide conjugates is their strong tendency to self-assemble through contribution of available hydrogen bonding sites for helical architectures in solid states. Symmetrical introduction of two dipeptide chains into a urea molecular scaffold is performed to induce the formation of the chiral hydrogen-bonded duplex, wherein each hydrogen-bonded duplex is connected by continuous intermolecular hydrogen bonds to form a double helix-like arrangement.     

Efficient Synthesis of Cyclic Block Copolymers by Rotaxane Protocol by Linear/Cyclic Topology Transformation

High‐yielding synthesis of cyclic block copolymer (CBC) using the rotaxane protocol by linear‐cyclic polymer topology transformation was first demonstrated. Initial complexation of OH‐terminated sec‐ammonium salt and a crown ether was followed by the successive living ring‐opening polymerizations of two lactones to a linear block copolymer having a rotaxane structure by the final capping of the propagation end. CBC was obtained in a high yield by an exploitation of the mechanical linkage through the translational movement of the rotaxane component to transform polymer structure from linear to cyclic. Furthermore, the change of the polymer topology was translated into a macroscopic change in crystallinity of the block copolymer.     

On global stability of a nonresident computer virus model

In this paper, we establish new sufficient conditions for the infected equilibrium of a nonresident computer virus model to be globally asymptotically stable. Our results extend two kind of known results in recent literature.     

Synthesis and characterization of 9,9‐bis(4‐hydroxyphenyl and 4‐aminophenyl)dibenzofluorenes: Novel fluorene‐based monomers

Two novel 9,9‐difunctionalized fluorene‐type monomers, 9,9‐bis(4‐hydroxyphenyl‐ and 4‐aminophenyl)‐2,3:6,7‐dibenzofluorenes, are synthesized by the reaction of dibenzenzofluorenone with phenol and aniline. These monomers are used for the preparation of polyester and polyimide as the typical polymers to evaluate the property change such as thermal stability caused by the benzene rings fused to the fluorene skeleton with keeping good solubility, in comparison with the polymers derived from simple fluorenone. In fact, these two new polymers have the fairly enhanced thermal stability and refractive index value along with satisfactory solubility in organic solvents, enough to emphasize the fusion effect. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019 , 57, 2602–2605