Designing Sustainable Hydrophilic Interfaces via Feature Selection from Molecular Descriptors and Time-Domain Nuclear Magnetic Resonance Relaxation Curves.

Surface modification using hydrophilic polymer coatings is a sustainable approach for preventing membrane clogging due to foulant adhesion to water treatment membranes and reducing membrane-replacement frequency. Typically, both molecular descriptors and time-domain nuclear magnetic resonance (TD-NMR) data, which reveal physicochemical properties and polymer-chain dynamics, respectively, are required to predict the properties and understand the mechanisms of hydrophilic polymer coatings. However, studies on the selection of essential components from high-dimensional data and their application to the prediction of surface properties are scarce. Therefore, we developed a method for selecting features from combined high-dimensional molecular descriptors and TD-NMR data. The molecular descriptors of the monomers present in polyethylene terephthalate films were calculated using RDKit, an open-source chemoinformatics toolkit, and TD-NMR spectroscopy was performed over a wide time range using five-pulse sequences to investigate the mobility of the polymer chains. The model that analyzed the data using the random forest algorithm, after reducing the features using gradient boosting machine-based recursive feature elimination, achieved the highest prediction accuracy. The proposed method enables the extraction of important elements from both descriptors of surface properties and can contribute to the development of new sustainable materials and material-specific informatics methodologies encompassing multiple information modalities.

Exploring the Optimal Alloy for Nitrogen Activation by Combining Bayesian Optimization with Density Functional Theory Calculations.

Binary alloy catalysts have the potential to exhibit higher activity than monometallic catalysts in nitrogen activation reactions. However, owing to the multiple possible combinations of metal elements constituting binary alloys, an exhaustive search for the optimal combination is difficult. In this study, we searched for the optimal binary alloy catalyst for nitrogen activation reactions using a combination of Bayesian optimization and density functional theory calculations. The optimal alloy catalyst proposed by Bayesian optimization had a surface energy of ∼0.2 eV/Å2 and resulted in a low reaction heat for the dissociation of the N≡N bond. We demonstrated that the search for such binary alloy catalysts using Bayesian optimization is more efficient than random search.

Complex Network Representation of the Structure-Mechanical Property Relationships in Elastomers with Heterogeneous Connectivity.

The complicated structure-property relationships of materials have recently been described using a methodology of data science that is recognized as the fourth paradigm in materials science. In network polymers or elastomers, the manner of connection of the polymer chains among the crosslinking points has a significant effect on the material properties. In this study, we quantitatively evaluate the structural heterogeneity of elastomers at the mesoscopic scale based on complex network, one of the methods used in data science, to describe the elastic properties. It was determined that a unified parameter with topological and spatial information universally describes some parameters related to the stresses. This approach enables us to uncover the role of individual crosslinking points for the stresses, even in complicated structures. Based on the data science, we anticipate that the structure-property relationships of heterogeneous materials can be interpretatively represented using this type of "white box" approach.

Kinetic analyses and structure-activity relationship studies of synthetic lysine acetylation catalysts.

Lysine acylation of proteins is a crucial chemical reaction, both as a post-translational modification and as a method for bioconjugation. We previously developed a chemical catalyst, DSH, which activates a chemically stable thioester including acyl-CoA, allowing the site-selective lysine acylation of histones under physiological conditions. However, a more active catalyst is required for efficient lysine acylation in more complex biological milieu, such as in living cells, but there are no rational guidelines for developing efficient lysine acylation catalysts for use under physiological conditions as opposed to in organic solvents. We, herein, conducted a kinetic analysis of the ability of DSH and several derivatives to mediate lysine acetylation to better understand the structural elements essential for high acetylation activity under physiological conditions. Interestingly, the obtained trend in reactivity was different from that observed in organic solvents, suggesting that a different principle is necessary for designing chemical catalysts specifically for use under physiological conditions compared to catalysts for use in organic solvents. Based on the obtained information, we identified a new catalyst scaffold with high activity and structural flexibility for further modification to improve this catalyst system.

Orientational cross correlations between entangled branch polymers in primitive chain network simulations.

Although it has not been frequently discussed, contributions of the orientational cross-correlation (OCC) between entangled polymers are not negligible in the relaxation modulus. In the present study, OCC contributions were investigated for 4- and 6-arm star-branched and H-branched polymers by means of multi-chain slip-link simulations. Owing to the molecular-level description of the simulation, the segment orientation was traced separately for each molecule as well as each subchain composing the molecules. Then, the OCC was calculated between different molecules and different subchains. The results revealed that the amount of OCC between different molecules is virtually identical to that of linear polymers regardless of the branching structure. The OCC between constituent subchains of the same molecule is significantly smaller than the OCC between different molecules, although its intensity and time-dependent behavior depend on the branching structure as well as the molecular weight. These results lend support to the single-chain models given that the OCC effects are embedded into the stress-optical coefficient, which is independent of the branching structure.

Primitive chain network simulations of probe rheology.

Probe rheology experiments, in which the dynamics of a small amount of probe chains dissolved in immobile matrix chains is discussed, have been performed for the development of molecular theories for entangled polymer dynamics. Although probe chain dynamics in probe rheology is considered hypothetically as single chain dynamics in fixed tube-shaped confinement, it has not been fully elucidated. For instance, the end-to-end relaxation of probe chains is slower than that for monodisperse melts, unlike the conventional molecular theories. In this study, the viscoelastic and dielectric relaxations of probe chains were calculated by primitive chain network simulations. The simulations semi-quantitatively reproduced the dielectric relaxation, which reflects the effect of constraint release on the end-to-end relaxation. Fair agreement was also obtained for the viscoelastic relaxation time. However, the viscoelastic relaxation intensity was underestimated, possibly due to some flaws in the model for the inter-chain cross-correlations between probe and matrix chains.

Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin.

Posttranslational modifications (PTMs) of histones play an important role in the complex regulatory mechanisms governing gene transcription, and their dysregulation can cause diseases such as cancer. The lack of methods for site-selectively modifying native chromatin, however, limits our understanding of the functional roles of a specific histone PTM, not as a single mark, but in the intertwined PTM network. Here, we report a synthetic catalyst DMAP-SH (DSH), which activates chemically stable thioesters (including acetyl-CoA) under physiological conditions and transfers various acyl groups to the proximate amino groups. Our data suggest that DSH, conjugated with a nucleosome ligand, such as pyrrole-imidazole-polyamide and LANA (latency-associated nuclear antigen)-peptide, promotes both natural (including acetylation, butyrylation, malonylation, and ubiquitination) and non-natural (azido- and phosphoryl labeling) PTMs on histones in recombinant nucleosomes and/or in native chromatin, at lysine residues close to the DSH moiety. To investigate the validity of our method, we used LANA-DSH to promote histone H2B lysine-120 (K120) acylation, the function of which is largely unknown. H2BK120 acetylation and malonylation modulated higher-order chromatin structures by reducing internucleosomal interactions, and this modulation was further enhanced by histone tail acetylation. This approach, therefore, may have versatile applications for dissecting the regulatory mechanisms underlying chromatin function.

Self-healing of covalently cross-linked polymers by reshuffling thiuram disulfide moieties in air under visible light.

Self-healing of covalently cross-linked polymers under an ambient visible light in the bulk state, in air, at room temperature using radical exchange of thiuram disulfide units is reported. The successful attachment of surfaces of cut pieces proceeded under ambient conditions under exposure to visible light from a commercial tabletop lamp, as confirmed by bending and tensile tests.

Changes in Network Structure of Chemical Gels Controlled by Solvent Quality through Photoinduced Radical Reshuffling Reactions of Trithiocarbonate Units.

Changes in the structure of networks of chemical gels cross-linked by covalent bonds have been investigated using reshuffling (i.e., degenerative exchange) reactions of the covalent bonds. These reactions can be applied to form functional materials including self-healing polymers, plasticity in cross-linked polymers, and shape-memory polymers. Herein, network structures of chemical gels were changed through radical reshuffling reactions of trithiocarbonate (TTC) units, and swelling degrees or network sizes were controlled by solvent quality. The chemical gels were prepared by RAFT copolymerizations of butyl acrylate and a TTC cross-linker, and the swelling degree was different for polymers prepared by solution or bulk polymerization. The cross-linked polymers were swollen in either good or nonsolvents and then exposed to UV light to trigger the radical reshuffling of the TTC units. The degree of swelling and network size in toluene increased in the presence of good solvents, whereas they decreased in nonsolvents. The repetitive changes in the degree of swelling were accomplished by changing the order of exposure to solvents.

Rational approach to star-like nanogels with different arm lengths: formation by dynamic covalent exchange and their imaging.

The formation of star-like nanogels with different arm lengths via a radical crossover reaction of alkoxyamine units in diblock copolymers and direct observation of the star-like nanogels by scanning force microscopy were successfully accomplished.

Programmed thermodynamic formation and structure analysis of star-like nanogels with core cross-linked by thermally exchangeable dynamic covalent bonds.

Programmed thermodynamic formation of star-like nanogels from designed diblock copolymers with thermally exchangeable dynamic covalent bonds in their side chains and structure analysis of the nanogels were performed. Linear diblock copolymers that consist of poly(methyl methacrylate) block and random copolymer block of methyl methacrylate (MMA) and methacrylic esters with alkoxyamine moiety were prepared by atom transfer radical polymerization (ATRP). By heating the diblock copolymers in anisole, a cross-linking reaction occurred as a result of the radical crossover reaction of alkoxyamine moieties to afford star-like nanogels. Kinetic studies have revealed that the cross-linking behavior reaches equilibrium at a given reaction time, with characteristic reaction behaviors for thermodynamic reactions being observed. The equilibrium structures of the star-like nanogels were controlled by the initial concentrations of diblock copolymers as well as their compositions and molecular weights. Furthermore, by heating the star-like nanogels with excess alkoxyamine, linear polymers were successfully regenerated. The molecular weights and sizes of the nanogels were evaluated by gel permeation chromatography-multiangle laser light scattering (GPC-MALLS) and small-angle X-ray scattering (SAXS) measurements, respectively, and the morphologies of the nanogels were directly observed by scanning force microscopy (SFM).