Verification for Temperature Dependence of Tacticity in Polystyrene Radical Polymerization with the Combination of Reaction Pathway Analysis and Red Moon Methodology.

Radical polymerization is an economic and practical polymerization method over ionic and coordination polymerizations and is widely used for polymer production. Although many efforts have been made to improve the convenience and controllability of radical polymerization, it is still a challenge to directly observe the microbehaviors of propagation, which may provide inspiration for the development of polymerization processes. In this study, we focused on the tacticity of polystyrene produced by bulk radical polymerization since there is a debate over the temperature dependence.

Metal-Organic Frameworks for Practical Separation of Cyclic and Linear Polymers.

The purification step in the manufacturing of cyclic polymers is difficult as complete fractionation to eliminate linear impurities requires considerable effort. Here, we report a new polymer separation methodology that uses metal-organic frameworks (MOFs) to discriminate between linear and cyclic polyethylene glycols (PEGs) via selective polymer insertion into the MOF nanopores. Preparation of a MOF-packed column allowed analytical and preparative chromatographic separation of these topologically distinct pairs.

Scalable and Precise Synthesis of Armchair-Edge Graphene Nanoribbon in Metal-Organic Framework.

Graphene nanoribbons (GNRs), narrow and straight-edged stripes of graphene, attract a great deal of attention because of their excellent electronic and magnetic properties. As of yet, there is no fabrication method for GNRs to satisfy both precision at the atomic scale and scalability, which is critical for fundamental research and future technological development. Here, we report a methodology for bulk-scale synthesis of GNRs with atomic precision utilizing a metal-organic framework (MOF).

Atomistic chemical computation of Olefin polymerization reaction catalyzed by (pyridylamido)hafnium(IV) complex: Application of Red Moon simulation.

We have realized the microscopic simulation of olefin polymerization, that is, the simulation of the catalytic polymerization (CP) reaction system composed of (pyridylamido)hafnium(IV) complex as the catalyst. For this purpose, we adopted Red Moon (RM) method, a novel molecular simulation method to simulate the complex reaction system. First, according to the previous research, with the help of the QM calculation, we proposed a model system and elementary processes and explained the theoretical treatment of the simulation by the RM method (the RM simulation).

Selective sorting of polymers with different terminal groups using metal-organic frameworks.

Separation of high-molecular-weight polymers differing just by one monomeric unit remains a challenging task. Here, we describe a protocol using metal-organic frameworks (MOFs) for the efficient separation and purification of mixtures of polymers that differ only by their terminal groups. In this process, polymer chains are inserted by threading one of their extremities through a series of MOF nanowindows.

Probing the Most Stable Isomer of Zirconium Bis(phenoxy-imine) Cation: A Computational Investigation.

The possibility of coexistence of multiple isomers for zirconium bis(phenoxy-imine) catalyst has been systematically studied by computational approaches. The energetics among the five different isomers of neutral Zr-catalyst have been assessed quantum mechanically. The results suggest that isomer cis-N/trans-O/cis-Me is the most stable among the five isomers in accordance with the general observations of these kinds of phenoxy-imine catalyst.

Sequence-regulated copolymerization based on periodic covalent positioning of monomers along one-dimensional nanochannels.

The design of monomer sequences in polymers has been a challenging research subject, especially in making vinyl copolymers by free-radical polymerization. Here, we report a strategy to obtain sequence-regulated vinyl copolymers, utilizing the periodic structure of a porous coordination polymer (PCP) as a template. Mixing of Cu ion and styrene-3,5-dicarboxylic acid (S) produces a PCP, [Cu(styrene-3,5-dicarboxylate)] , with the styryl groups periodically immobilized along the one-dimensional channels.

Formation of Reactant Complex Structure for Initiation Reaction of Lactone Ring-Opening Polymerization by Cooperation of Multiple Cyclodextrin.

Ring-opening polymerization of lactones initiated by cyclodextrins has been reported as a promising polymer synthetic method. To investigate the unknown molecular level mechanism of the initiation reaction, we executed molecular dynamics simulations of model systems composed of single or multiple β-cyclodextrin (β-CD) molecules in δ-valerolactone (VL) solvent and explored the reactant complex structures satisfying three conditions (VL inclusion in the β-CD cavity, hydrogen bonding, and nucleophilic attack) at the same time. As a result, we confirmed the formation of the reactant complex structure.

Bound Na(+) is a Negative Effecter for Thrombin-Substrate Stereospecific Complex Formation.

Thrombin has been studied as a paradigmatic protein of Na(+)-activated allosteric enzymes. Earlier structural studies suggest that Na(+)-binding promotes the thrombin-substrate association reaction. However, it is still elusive because (1) the structural change, driven by Na(+)-binding, is as small as the thermal fluctuation, and (2) the bound Na(+) is close to Asp189 in the primary substrate binding pocket (S1-pocket), possibly preventing substrate access via repulsive interaction.

Dewetting of S1-Pocket via Water Channel upon Thrombin-Substrate Association Reaction.

Upon protein-substrate association reaction, dewetting of the substrate-binding pocket is one of the rate-limiting processes. However, understanding the microscopic mechanism still remains challenging because of practical limitations of experimental methodologies. We have addressed the problem here by using molecular dynamics (MD) simulation of the thrombin-substrate association reaction.

Toward understanding allosteric activation of thrombin: a conjecture for important roles of unbound Na(+) molecules around thrombin.

We shed light on important roles of unbound Na(+) molecules in enzymatic activation of thrombin. Molecular mechanism of Na(+)-activation of thrombin has been discussed in the context of allostery. However, the recent challenge to redesign K(+)-activated thrombin revealed that the allosteric interaction is insufficient to explain the mechanism.

Combined mechanism of conformational selection and induced fit in U1A-RNA molecular recognition.

In this study, we demonstrate that U1A-RNA molecular recognition is mediated by a combined mechanism of conformational selection and induced fit. The binding of U1A to RNA has been discussed in the context of induced fit that involves the reorientation of the α-helix in the C-terminal region (Helix-C) of U1A to permit RNA access only when U1A correctly recognizes RNA. However, according to our molecular dynamics simulations, even in the absence of RNA, Helix-C spontaneously reoriented to permit RNA access.

Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure.

Protein allostery is essential for vital activities. Allosteric regulation of human hemoglobin (HbA) with two quaternary states T and R has been a paradigm of allosteric structural regulation of proteins. It is widely accepted that oxygen molecules (O2) act as a "site-specific" homotropic effector, or the successive O2 binding to the heme brings about the quaternary regulation.

Oxygen entry through multiple pathways in T-state human hemoglobin.

The heme oxygen (O2) binding site of human hemoglobin (HbA) is buried in the interior of the protein, and there is a debate over the O2 entry pathways from solvent to the binding site. As a first step to understand HbA O2 binding process at the atomic level, we detected all significant multiple O2 entry pathways from solvent to the binding site in the α and β subunits of the T-state tetramer HbA by utilizing ensemble molecular dynamics (MD) simulation. By executing 128 independent 8 ns MD trajectories in O2-rich aqueous solvent, we simulated the O2 entry processes and obtained 141 and 425 O2 entry events in the α and β subunits of HbA, respectively.

Structural dynamics of clamshell rotation during the incipient relaxation process of photodissociated carbonmonoxy myoglobin: statistical analysis by the perturbation ensemble method.

The structural dynamics of the clamshell rotation of photodissociated carbonmonoxy myoglobin, which is expected to be important for hemoglobin allostery, is investigated by the perturbation ensemble method. In this method, many pairs of perturbed and unperturbed molecular dynamics trajectories are ensemble-averaged to cancel out thermal noises and to detect subtle changes. The number of MD trajectory pairs, in this work 2000 pairs, should be determined to obtain physical properties of interest with statistically meaningful precisions.

Intrinsic alterations in the partial molar volume on the protein denaturation: surficial Kirkwood-Buff approach.

The partial molar volume (PMV) of the protein chymotrypsin inhibitor 2 (CI2) was calculated by all-atom MD simulation. Denatured CI2 showed almost the same average PMV value as that of native CI2. This is consistent with the phenomenological question of the protein volume paradox.

Effects of Citrus unshiu powder on the cytokine balance in peripheral blood mononuclear cells of patients with seasonal allergic rhinitis to pollen.

We evaluated the effects of a 50% methanol extract of Citrus unshiu powder (MEC) on cytokines in peripheral blood mononuclear cells (PBMCs) obtained from patients with seasonal allergic rhinitis to cedar pollen. The levels of cytokines, such as TNF-alpha, IFN-gamma, IL-2, IL-4, IL-5, IL-10, IL-12 (p70), IL-13, and GM-CSF, produced by pollen-stimulated PBMC were measured. We found that MEC suppressed pollen-induced TNF-alpha release and increased IFN-gamma release from PBMCs.

Anisotropic structural relaxation and its correlation with the excess energy diffusion in the incipient process of photodissociated MbCO: high-resolution analysis via ensemble perturbation method.

The effectiveness of the ensemble perturbation method, in which many pairs of perturbed and unperturbed molecular dynamics simulations are executed for the ensemble average, has been demonstrated by calculating the subtle anisotropic structural change of carbonmonoxy myoglobin (MbCO) triggered by ligand photolysis. The results show that Mb largely expands in the direction perpendicular to the heme plane and slightly contracts in the horizontal one. This agrees well with the report in the transient grating experiment.