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. The propagation process is simulated via Red Moon methodology, which is a cost-effective method for handling complex chemical reaction systems. By the multiple pathway analysis for the propagation reaction model composed of the dimer radical and the monomer using density functional theory, we obtained the relative energies in multiple transition states, whose energy differences are partly explained by the π-π stacking interactions. Via performing Red Moon simulations from 30 to 190 °C, we confirmed that meso contents moderately increase as the temperature increases, which is explained by the influence of temperature on the probability density of the reaction conformations of each pathway. The successful prediction and explanation for tacticity demonstrate the potential of Red Moon methodology in unveiling the microbehaviors of propagation.

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. In addition, gram-scale PEGs with only cyclic structures were successfully obtained from a crude reaction mixture by using MOF as an adsorbent.

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). The GNR was synthesized by the polymerization of perylene (PER) or its derivative within the nanochannels of the MOF. Molecular dynamics simulations showed that PER was uniaxially aligned along the nanochannels of the MOF through host-guest interactions, which allowed for regulated growth of the nanoribbons. A series of characterizations of the GNR, including NMR, UV/vis/NIR, and Raman spectroscopy measurements, confirmed the formation of the GNR with well-controlled edge structure and width.

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). In addition, we also proposed a macroscopic simulation based on chemical kinetics simulation. Then, we performed two simulations and compared them in terms of the effective time evolution of the three macroscopic physical quantities, the number-average molecular weight Mn , the mass-average molecular weight Mw , and the molar-mass dispersity DM . The comparison showed that the two simulations are in quantitative or partially qualitative agreement with each other. Therefore, it is concluded that the RM simulation could not only simulate the CP reaction process microscopically, but also it is connected essentially to reproduce the time evolution of the macroscopic physical quantities on the basis of its microscopic simulation data. © 2018 Wiley Periodicals, Inc.

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. Selected termini can be adjusted by tuning the MOF structure, and the insertion methodology. Accordingly, MOFs with permanently opened pores allow for the complete separation of poly(ethylene glycol) (PEG) based on steric hindrance of the terminal groups. Excellent separation is achieved, even for high molecular weights (20 kDa). Furthermore, the dynamic character of a flexible MOF is used to separate PEG mixtures with very similar terminal moieties, such as OH, OMe, and OEt, as the slight difference of polarity in these groups significantly changes the pore opening kinetics.

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. However, for the polymerization reaction, the active species is known to be the cationic form of the Zr-catalyst. The Zr-cation can exist in three different isomers, viz., cis-N/trans-O (A), cis-N/cis-O (B), and trans-N/cis-O (C), and the presence of flexible ligands makes the modeling considerably challenging to determine the most preferable isomers. For the efficient modeling, altogether 80 different structures for each of the three cationic isomers have been generated by using molecular dynamics simulations, and subsequently, the quantum mechanical optimization of these structures has been performed to obtain the most preferable conformation for each isomer. The existing probability derived from the obtained free energy values suggests that isomer C is comparable with isomer A. Even more, isomer A of the cation can be present in two different conformations, where the orientation of side groups is altered at the imine nitrogen atoms. The transition state calculations also confirm that the Zr-cation can exist as a mixture of three structures, "up-down" and "down-down" orientations of the isomers A along with isomer C's "up-up" orientation. However, by varying the substituents at imine nitrogen atoms, one could modulate multimodal to unimodal polymerization behavior of the Zr-catalysts. We believe that this study should provide a starting point for theoretically exploring the mechanistic pathway of the complicated polymerization reactions.

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 Cu2+ ion and styrene-3,5-dicarboxylic acid (S) produces a PCP, [Cu(styrene-3,5-dicarboxylate)] n , with the styryl groups periodically immobilized along the one-dimensional channels. After the introduction of acrylonitrile (A) into the host PCP, radical copolymerization between A and the immobilized S is performed inside the channel, followed by decomposing the PCP to isolate the resulting copolymer. The predominant repetitive SAAA sequence in the copolymer is confirmed by monomer composition, NMR spectroscopy and theoretical calculations. Copolymerization using methyl vinyl ketone also provides the same type of sequence-regulated copolymer, showing that this methodology has a versatility to control the copolymer sequence via transcription of PCP periodicity at the molecular level.

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 ß-cyclodextrin (ß-CD) molecules in δ-valerolactone (VL) solvent and explored the reactant complex structures satisfying three conditions (VL inclusion in the ß-CD cavity, hydrogen bonding, and nucleophilic attack) at the same time. As a result, we confirmed the formation of the reactant complex structure. Comparison between the single and multiple ß-CD models revealed that the formation is more frequent and the distance for the nucleophilic attack is shorter in the multiple model. Therefore, we anticipate that the reaction proceeds more efficiently by the cooperation of multiple ß-CDs. This finding will contribute to understanding the reaction mechanism from the atomistic point of view.

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. It still remains a matter of debate whether Na(+)-binding actually promotes the reaction. To solve this problem, we examined the effect of Na(+) on the reaction by employing molecular dynamics (MD) simulations. By executing independent 210 MD simulations of apo and holo systems, we obtained 80 and 26 trajectories undergoing substrate access to S1-pocket, respectively. Interestingly, Na(+)-binding results in a 3-fold reduction of the substrate access. Furthermore, we examined works for the substrate access and release, and found that Na(+)-binding is disadvantageous for the presence of the substrate in the S1-pocket. These observations provide the insight that the bound Na(+) is essentially a negative effecter in thrombin-substrate stereospecific complex formation. The insight rationalizes an enigmatic feature of thrombin, relatively low Na(+)-binding affinity. This is essential to reduce the disadvantage of Na(+)-binding in the substrate-binding.

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. During the MD simulation, ArgP1 in a substrate accessed thrombin's substrate-binding pocket and formed specific hydrogen bonds (H-bonds) with Asp189 in thrombin, while the catalytic serine of thrombin was still away from the substrate's active site. It is assumed that the thrombin-substrate association reaction is regulated by a stepwise mechanism. Furthermore, in the earlier stage of ArgP1 access to the pocket, we observed that ArgP1 was spatially separated from Asp189 by two water molecules in the pocket. These water molecules transferred from the pocket, followed by the specific H-bond formation between thrombin and the substrate. Interestingly, they were not evacuated directly from the pocket to the bulk solvent, but moved to the water channel of thrombin. This observation indicates that the channel plays functional roles in dewetting upon the 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. Under these circumstances, we have examined the roles of unbound Na(+) molecule in maximization of thrombin-substrate association reaction rate. We performed all-atomic molecular dynamics (MD) simulations of thrombin in the presence of three different cations; Li(+), Na(+), and Cs(+). Although these cations are commonly observed in the vicinity of the S1-pocket of thrombin, smaller cations are distributed more densely and extensively than larger ones. This suggests the two observation rules: (i) thrombin surrounded by Na(+) is at an advantage in the initial step of association reaction, namely, the formation of an encounter complex ensemble, and (ii) the presence of Na(+) molecules does not necessarily have an advantage in the final step of association reaction, namely, the formation of the stereospecific complex. In conclusion, we propose a conjecture that unbound Na(+) molecules also affect the maximization of rate constant of thrombin-substrate association reaction through optimally forming an encounter complex ensemble.

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. Nonetheless, such a conformational change was still incomplete. Helix-C was often partially or even fully unfolded and in an infrequent RNA-accessible conformation, which can be detected using state-of-the-art nuclear magnetic resonance methodology. These results suggest that the formation of an energetically stabilized complex is promoted by specific interactions between U1A and RNA. In conclusion, in the recognition of RNA by U1A protein, we propose a combined mechanism that requires the reorientation of Helix-C and the subsequent contact with RNA through conformational selection, although the stabilization of the U1A-RNA complex is caused by induced fit. We further propose a modification to the conventional assumption regarding the mechanism of U1A-RNA molecular recognition.

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. However, here we show that the site-specific allosteric effect is not necessarily only a unique mechanism of O2 allostery. Our simulation results revealed that the solution environment of high O2 partial pressure enhances the quaternary change from T to R without binding to the heme, suggesting an additional "non-site-specific" allosteric effect of O2. The latter effect should play a complementary role in the quaternary change by affecting the intersubunit contacts. This analysis must become a milestone in comprehensive understanding of the allosteric regulation of HbA from the molecular point of view.

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 ß 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 ß subunits of HbA, respectively. We developed the intrinsic pathway identification by clustering method to achieve a persuasive visualization of the multiple entry pathways including both the shapes and relative importance of each pathway. The rate constants of O2 entry estimated from the MD simulations correspond to the experimentally observed values, suggesting that O2 ligands enter the binding site through multiple pathways. The obtained multiple pathway map can be utilized for future detailed analysis of HbA O2 binding process.

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. The calculated structural changes after 20 ps of the photodissociation are consistent with those by time-resolved X-ray diffraction at 100 ps delay time. In the heme proximal side region including the F and H helices, both helices displaced in the proximal direction. Meanwhile, in the heme distal side region including E and A helices, both helices moved toward the heme group after photodissociation. These proximal and distal side displacements occur on a fast time scale (almost complete within 3 ps) and are consistent with the clamshell rotation. Moreover, it was found that the ensemble-averaged structural dynamics of the photodissociated MbCO is independent of the amount of initial excess vibrational energy of the heme, or the difference of excitation photon wavelength. These results provide atomistic details on the functionally important dynamics of the clamshell rotation. Application of the present methodology to Hb will give new insight into the incipient stereochemical mechanism of hemoglobin allostery.

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. Furthermore, using the surficial Kirkwood-Buff approach, spatial distributions of PMV were analyzed as a function of the distance from the CI2 surface. The profiles of the new R-dependent PMV indicate that, in denatured CI2, the reduction in the solvent electrostatic interaction volume is canceled out mainly by an increment in thermal volume in the vicinity of its surface. In addition, the PMV of the denatured CI2 was found to increase in the region in which the number density of water atoms is minimum. These results provide a direct and detailed picture of the mechanism of the protein volume paradox suggested by Chalikian et al.

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. The results suggest that Citrus unshiu powder has an immunomodulatory effect in vitro and that its use could improve seasonal allergic rhinitis symptoms.

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. In addition, it is suggested that the expansion contributes strongly to the fast energy-transfer process to the water solvent because it is undergone almost within several picoseconds. The mechanical work done on the solvent by the expansion within 1 ps was thermodynamically estimated to be 4.8 kcal/mol.