Simultaneous polymer chain growth with the coexistence of bulk and surface initiators: insight from computer simulations.

By Brownian dynamics simulations we study the simultaneous polymer chain growth process with the coexistence of bulk and surface initiators. We find that when the surface initiator density is low enough, the practical experimental way to estimate the dispersity (D) of surface-initiated chains on the basis of the dispersity of bulk-initiated chains remains valid as long as the conformations of grafted chains remain within the mushroom regime (i.e., the grafted chains are sparsely distributed). On the other hand, although the average chain lengths of surface and bulk polymers could be equivalent when certain conditions are met, their mass distributions are still different. We also find that increasing the fraction of surface initiators leads to an enlarged disparity in D and average length between surface and bulk chains, which is inconsistent with previous studies. This study helps in better understanding the cooperative competition and suppressing effect of bulk chains on surface grown chains, as well as the cause of the dispersity of the surface grown chains as compared to their bulk counterparts with the coexistence of bulk and surface initiators.

Polymerization-induced polymer aggregation or polymer aggregation-enhanced polymerization? A computer simulation study.

In this study, using dissipative particle dynamics simulations coupled with the stochastic reaction model, we investigate the polymerization-induced polymer aggregation process and the polymer aggregation-enhanced polymerization process in a binary solution, by simply tuning the solubility of the solvent to one species of copolymerization. Our simulations indicate that it is a complicated interplay of the copolymerization on the formation of aggregates, namely, on one hand the polymerization may induce the aggregation of one species; on the other hand it has an effect of mixing the two species together. We also find that the polymerization process basically follows the first order reaction kinetics. With the increase of insolubility of B species in the solution, it continuously deviates from the first order reaction kinetics. In the symmetric copolymerization system, we find that the dispersity of copolymers monotonically decreases with the increase of reaction probability. This counterintuitive result can be understood via the comparison of diffusion-controlled kinetics and reaction-controlled kinetics. In the asymmetric system, for systems with preferential copolymerization, the mass distribution shapes are Gaussian-like with certain peaks. For comparison, for systems with preferential homopolymerization, the mass distribution shape shows an obviously bimodal form. This study helps to better understand the cooperative competition between the reaction dynamics and the diffusion dynamics during the preparation of copolymer materials, and could act as a guide to better design and improve the copolymerization technologies in laboratories and in industry.

Porous Aromatic Frameworks Enabling Polyiodide Confinement toward High Capacity and Long Lifespan Zinc-Iodine Batteries.

Aqueous zinc-iodine batteries (AZIBs) are attracting increasing attention because of their high safety and abundance of resources. However, the performance of AZIBs is compromised by inadequate confinement of soluble polyiodides, the undesired shuttle effect, and slow reaction kinetics. In this study, a porous aromatic framework (PAF) with abundant benzene motifs and a well-organized pore structure is adopted as the iodine host, which exhibits high iodine adsorption capacity and robust polyiodide confinement. Both experimental characterizations and theoretical simulations indicate that the interactions between iodine species and the PAF-1 facilitate the redox reaction by coupling the electronic structures of the active species in the framework. A comparison of PAF-1, PAF-5, and PAF-11 also emphasizes the structural advantages of the high surface area and interconnected three-dimensional channels of PAF-1. Consequently, the I2@PAF-1 cathode can deliver a high capacity of 328 mAh g-1 at 0.5 C, outstanding rate performance, and a stable cycling life of 20 000 cycles (86 % retention at 10 C). The robust polyiodide confinement and superb electrochemical performance of Zn-I2@PAF-1 provide insights into the practical application of PAFs as excellent electrode materials for AZIBs.

A sustainable approach for the synthesis of recyclable cyclic CO2-based polycarbonates.

It is highly desirable to reduce the environmental pollution related to the disposal of end-of-life plastics. Polycarbonates derived from the copolymerization of CO2 and epoxides have attracted much attention since they can enable CO2-fixation and furnish biorenewable and degradable polymeric materials. So far, only linear CO2-based polycarbonates have been reported and typically degraded to cyclic carbonates. Here we synthesize a homogeneous dinuclear methyl zinc catalyst ((BDI-ZnMe)2, 1) to rapidly copolymerize meso-CHO and CO2 into poly(cyclohexene carbonate) (PCHC) with an unprecedentedly cyclic structure. Moreover, in the presence of trace amounts of water, a heterogeneous multi-nuclear zinc catalyst ((BDI-(ZnMe2·xH2O)) n , 2) is prepared and shows up to 99% selectivity towards the degradation of PCHC back to meso-CHO and CO2. This strategy not only achieves the first case of cyclic CO2-based polycarbonate but also realizes the complete chemical recycling of PCHC back to its monomers, representing closed-loop recycling of CO2-based polycarbonates.

Elucidation of the methyl transfer mechanism catalyzed by chalcone O-methyltransferase: a density functional study.

The mechanism of the methyl transfer catalyzed by chalcone O-methyltransferase has been computationally investigated by employing the hybrid functional B3LYP. Two models are constructed based on the two conformations of the substrate isoliquiritigenin in the X-ray structure. Our calculations show that the overall reaction is divided into two elementary steps: the water-assisted deprotonation of the substrate by His278 as a catalytic base, followed by the methyl transfer from S-adenosyl-L-methionine (SAM) to the substrate. The calculated rate-limiting barriers for the methyl-transfer step indicate that the catalytic reactions are energetically feasible for both conformations adopted by the substrate.

QM/MM study on the catalytic mechanism of heme-containing aliphatic aldoxime dehydratase.

Aliphatic aldoxime dehydratase (Oxd) catalyzes the dehydration of aliphatic aldoximes (R-CH═N-OH) to the corresponding nitriles (R-C≡N). Quantum mechanics/molecular mechanics (QM/MM) calculations are performed to elucidate the catalytic mechanism of the enzyme on the basis of the X-ray crystal structure of the Michaelis complex. On the basis of the calculations, we propose a complete catalytic cycle of Oxd in which the distal histidine (His320) acts as a general acid/base. In the Michaelis complex, the elimination of the hydroxyl group of aldoxime is facilitated by His320 donating a proton to the hydroxyl group in a concerted way, which is the rate-limiting step. The formed intermediate has a ferric heme iron and an unpaired electron on the nitrogen atom of the substrate coupled to a singlet state. The second step is the deprotonation of the ß-hydrogen of the substrate by His320 after the substrate rotates about the Fe-N bond for ∼180° to yield the neutral product. In the meantime, the heme iron goes back to ferrous state by a one-electron transfer from the substrate to the ferric heme iron, and His320 goes back to the protonated state to proceed with the following reaction. The functions of the protein environment and the active site residues are also discussed.

Quantum mechanical/molecular mechanical molecular dynamics and free energy simulations of the thiopurine S-methyltransferase reaction with 6-mercaptopurine.

Quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations were performed to investigate the methylation of 6-mercaptopurine catalyzed by thiopurine S-methyltransferase. Several setups with different tautomeric forms and orientations of the substrate were considered. It is found that, with the orientation in chain A of the X-ray structure, the substrate can form an ideal near-attack configuration for the methylation reaction, which may take place after the deprotonation of the substrate by the conserved residue Asp23 through a water chain. The potential of mean force (PMF) of the methyl-transfer step for the most favorable pathway is 19.6 kcal/mol, which is in good agreement with the available experimental rate constant data.

Catalytic mechanism of hydroxynitrile lyase from Hevea brasiliensis: a theoretical investigation.

Density functional theory (DFT) calculations using the hybrid functional B3LYP have been performed to investigate the catalytic mechanism of hydroxynitrile lyase from Hevea brasiliensis (Hb-HNL). This enzyme catalyzes the cleavage of acetone cyanohydrin to hydrocyanic acid plus acetone. Two models (A and B) of the active site consisting of 105 and 155 atoms, respectively, were constructed on the basis of the crystal structure. Good consistency between the two models provides a verification of the proposed mechanism. Our calculations show that the catalytic reaction proceeds via three elementary steps: (1) deprotonation of the OH-Ser80 by His235 and concomitant abstraction of a proton from the substrate hydroxyl by Ser80; (2) the C-C bond cleavage of the acetone cyanohydrin; and (3) protonation of the cleaved cyanide by His235. The cleavage of the C-C bond is the rate-limiting step with the overall free energy barrier of 13.5 kcal/mol for relatively smaller model A (14.9 kcal/mol for a larger model B) in the protein environment, which is in good agreement with experimental rate. The present results give support to the previously proposed general acid/base catalytic mechanism, in which the catalytic triad acts as a general acid/base. Moreover, the calculated results for model C, with the positive charge of Lys236 removed from model A, show that Lys236 with the positive charge plays a vital role in lowering the reaction barrier of the rate-determining and helps in stabilizing the negatively charged CN(-) by forming a hydrogen bond with the substrate, consistent with the experimental analysis.