To reduce climate change, absorbing CO2 directly from the air (DAC) with high-efficient CO2 absorption, low-cost, and environmentally friendly system has been attracted much attention for several decades. In this work, a series of aqueous diamine solutions was examined for 400ppm CO2 absorption at ambient temperature. The absorbents exhibited CO2 absorption with molar ratio of 1 molCO2/molamine, and aqueous isophorone diamine (IPDA) in particular showed >99% CO2 removal even under a 500 mL min−1 flow of 400ppm CO2-N2 with the contact rate of 13,761.5 h−1 between CO2 and IPDA aqueous solution and the CO2 absorption rate of 4.46 mmol/L·min. A precipitate of carbamic acid of IPDA was formed by reaction with CO2, and the CO2 removal efficiency was enhanced by increasing the solution viscosity by the formation of this precipitate. The CO2 was absorbed in aqueous IPDA solution as carbamic acid of IPDA and bicarbonate/carbonate species, and the absorbed CO2 could desorb by heating under O2-containing gas flow, which indicates our system is applicable to the CO2 condensation for a plant growth. This work provides a fundamental information to establishing a solid–liquid phase change system with a high-efficient and environmentally friendly DAC system using aqueous solvent.
为了减少气候变化，几十年来，直接从空气中吸收二氧化碳（DAC）这一高效吸收二氧化碳、低成本和环保的系统一直备受关注。这项研究考察了一系列二胺水溶液在常温下吸收 400ppm CO2 的能力。吸收剂对二氧化碳的吸收摩尔比为 1 molCO2/摩尔胺，尤其是异佛尔酮二胺水溶液（IPDA），即使在 400ppm CO2-N2 流量为 500 mL min-1 的条件下，二氧化碳去除率仍高达 >99% ，二氧化碳与 IPDA 水溶液的接触速率为 13,761.5 h-1，二氧化碳吸收率为 4.46 mmol/L-min。IPDA 的氨基甲酸与 CO2 反应生成沉淀，沉淀的形成增加了溶液粘度，从而提高了 CO2 去除效率。二氧化碳在 IPDA 水溶液中以 IPDA 氨基甲酸和碳酸氢盐/碳酸盐的形式被吸收，被吸收的二氧化碳可在含氧气的气流中加热解吸，这表明我们的系统适用于植物生长的二氧化碳冷凝。这项研究为利用水性溶剂建立高效环保的 DAC 固液相变系统提供了基础信息。
{"title":"Highly efficient direct air capture using solid–liquid phase separation in aqueous diamine solution as sorbent","authors":"Furong Cao, Soichi Kikkawa, Hidetaka Yamada, Seiji Yamazoe","doi":"10.1093/bulcsj/uoae096","DOIUrl":"https://doi.org/10.1093/bulcsj/uoae096","url":null,"abstract":"To reduce climate change, absorbing CO2 directly from the air (DAC) with high-efficient CO2 absorption, low-cost, and environmentally friendly system has been attracted much attention for several decades. In this work, a series of aqueous diamine solutions was examined for 400ppm CO2 absorption at ambient temperature. The absorbents exhibited CO2 absorption with molar ratio of 1 molCO2/molamine, and aqueous isophorone diamine (IPDA) in particular showed >99% CO2 removal even under a 500 mL min−1 flow of 400ppm CO2-N2 with the contact rate of 13,761.5 h−1 between CO2 and IPDA aqueous solution and the CO2 absorption rate of 4.46 mmol/L·min. A precipitate of carbamic acid of IPDA was formed by reaction with CO2, and the CO2 removal efficiency was enhanced by increasing the solution viscosity by the formation of this precipitate. The CO2 was absorbed in aqueous IPDA solution as carbamic acid of IPDA and bicarbonate/carbonate species, and the absorbed CO2 could desorb by heating under O2-containing gas flow, which indicates our system is applicable to the CO2 condensation for a plant growth. This work provides a fundamental information to establishing a solid–liquid phase change system with a high-efficient and environmentally friendly DAC system using aqueous solvent.","PeriodicalId":9511,"journal":{"name":"Bulletin of the Chemical Society of Japan","volume":"13 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142249875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
N-Alkylated oligo- and poly(p-benzamide)s exist as dynamic helical structures with all-cis amide conformation. Imidazole N-alkylated amides also show cis conformational preference, but their major conformer is changed from cis to trans by addition of acid. Here, based on those findings, we designed and synthesized aromatic triamides 3 and hexaamides 4 containing an imidazole ring as candidate foldamers anticipated to exhibit acid-induced conformational change. X-Ray structure analysis of oligomer 3c showed that it takes all-cis conformation in the crystal. In solution, all the oligoamides examined existed as an equilibrium mixture of four conformers, among which the major conformer was the folded all-cis structure as judged from the low-temperature 1H NMR spectra. When trifluoroacetic acid-d was added to a solution of the oligoamides in methylene chloride-d2, only two conformers were observed in the low-temperature 1H NMR spectra, and the major conformer was the (trans, cis) form with respect to the amide bonds of the imidazole at the 4 and 2 positions. Experimental and theoretical analysis of the CD spectra indicated that the conformation of hexaamides 4 changes upon addition of acid. Our results suggest that N-alkylated imidazoleamide can serve as a key structural motif for the construction of foldamers with acid-switchable conformation.
{"title":"Acid-induced Conformational Switching of Helical Foldamers Containing Imidazole Amide","authors":"Sakiko Kimura, Fumi Takeda, Ayano Ikeda, Asuka Tanimoto, Kosuke Katagiri, Masatoshi Kawahata, Yusuke Okada, Nagao Kobayashi, Hiroyuki Kagechika, Aya Tanatani","doi":"10.1093/bulcsj/uoae094","DOIUrl":"https://doi.org/10.1093/bulcsj/uoae094","url":null,"abstract":"N-Alkylated oligo- and poly(p-benzamide)s exist as dynamic helical structures with all-cis amide conformation. Imidazole N-alkylated amides also show cis conformational preference, but their major conformer is changed from cis to trans by addition of acid. Here, based on those findings, we designed and synthesized aromatic triamides 3 and hexaamides 4 containing an imidazole ring as candidate foldamers anticipated to exhibit acid-induced conformational change. X-Ray structure analysis of oligomer 3c showed that it takes all-cis conformation in the crystal. In solution, all the oligoamides examined existed as an equilibrium mixture of four conformers, among which the major conformer was the folded all-cis structure as judged from the low-temperature 1H NMR spectra. When trifluoroacetic acid-d was added to a solution of the oligoamides in methylene chloride-d2, only two conformers were observed in the low-temperature 1H NMR spectra, and the major conformer was the (trans, cis) form with respect to the amide bonds of the imidazole at the 4 and 2 positions. Experimental and theoretical analysis of the CD spectra indicated that the conformation of hexaamides 4 changes upon addition of acid. Our results suggest that N-alkylated imidazoleamide can serve as a key structural motif for the construction of foldamers with acid-switchable conformation.","PeriodicalId":9511,"journal":{"name":"Bulletin of the Chemical Society of Japan","volume":"32 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142186103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The soot oxidation over platinum group metal oxide/CeO2–ZrO2 (PGM/CZ) catalysts with different ability to capture gas-phase oxygen has been studied herein. The ability to capture gas-phase oxygen was in sequence of Ru/CZ > Rh/CZ > Ir/CZ > Pt/CZ > Pd/CZ. Soot oxidation test by TG-DTA showed that Ru/CZ, Rh/CZ, and Ir/CZ are highly active catalysts. It was found that there is a good correlation between the ability to capture gas-phase oxygen and soot oxidation activity. TEM observation revealed that soot oxidation mainly occurs at the interface between soot and CZ surface. The Ea values and soot oxidation test using labeled oxygen suggested that highly active catalysts oxidize soot by CZ lattice oxygen. For Ir/CZ, soot oxidation at 270°C occurred due to the reduction by soot. Ru/CZ and Rh/CZ captured gas-phase oxygen spontaneously below 250°C, resulting in soot oxidation at 270°C. H2-TPR results suggested that the reactivity of lattice oxygen in CZ surface improved by PGM is also related to soot oxidation activity. It was suggested that the ability to capture gas-phase oxygen and the reactivity of lattice oxygen in CZ surface determine the soot oxidation activity, and that Ru, Rh, and Ir have the effect of enhancing these properties.
{"title":"Effect of the Supported Metal Species on Soot Oxidation over PGM/CeO2–ZrO2","authors":"Hitoshi Kubo, Yusuke Ohshima, Shunsuke Kato, Noriyuki Saitoh, Noriko Yoshizawa, Osamu Nakagoe, Shuji Tanabe","doi":"10.1093/bulcsj/uoae092","DOIUrl":"https://doi.org/10.1093/bulcsj/uoae092","url":null,"abstract":"The soot oxidation over platinum group metal oxide/CeO2–ZrO2 (PGM/CZ) catalysts with different ability to capture gas-phase oxygen has been studied herein. The ability to capture gas-phase oxygen was in sequence of Ru/CZ > Rh/CZ > Ir/CZ > Pt/CZ > Pd/CZ. Soot oxidation test by TG-DTA showed that Ru/CZ, Rh/CZ, and Ir/CZ are highly active catalysts. It was found that there is a good correlation between the ability to capture gas-phase oxygen and soot oxidation activity. TEM observation revealed that soot oxidation mainly occurs at the interface between soot and CZ surface. The Ea values and soot oxidation test using labeled oxygen suggested that highly active catalysts oxidize soot by CZ lattice oxygen. For Ir/CZ, soot oxidation at 270°C occurred due to the reduction by soot. Ru/CZ and Rh/CZ captured gas-phase oxygen spontaneously below 250°C, resulting in soot oxidation at 270°C. H2-TPR results suggested that the reactivity of lattice oxygen in CZ surface improved by PGM is also related to soot oxidation activity. It was suggested that the ability to capture gas-phase oxygen and the reactivity of lattice oxygen in CZ surface determine the soot oxidation activity, and that Ru, Rh, and Ir have the effect of enhancing these properties.","PeriodicalId":9511,"journal":{"name":"Bulletin of the Chemical Society of Japan","volume":"7 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142186102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We synthesized a “cyborg protein,” wherein a synthetic molecule partially substitutes the main peptide chain by linking two protein domains with a synthetic oligomer. Green fluorescent protein (GFP) served as the model for constructing the cyborg proteins. We prepared circularly permuted GFP (cpGFP) with new termini between β10 and β11, where the original N- and C-termini were linked by a cleavable peptide loop. The cyborg GFP was constructed from cpGFP by linking the β10 and β11 with oligo(ethylene glycol) using maleimide-cysteine couplings, followed by the enzymatic cleavage of the N- and C-termini linking loop by thrombin. With the help of machine learning, we were able to obtain the cpGFP mutants that significantly alter the fluorescence activity (53% increase) by thrombin treatment, which splits cpGFP into two fragments (fragmented-GFP), and by heat shock. When the cyborg GFP was constructed using this mutant, the fluorescence intensity increased by 13% after heat treatment, similar to cpGFP (33% increase), and the behavior was significantly different from that of the fragmented-GFP. This result suggests the possibility that the oligo(ethylene glycol) chain in the cyborg protein plays a similar role to the peptide in the main chain of the protein.
{"title":"Design of Cyborg Proteins by Loop Region Replacement with Oligo(ethylene glycol): Exploring Suitable Mutations for Cyborg Protein Construction Using Machine Learning","authors":"Wijak Yospanya, Akari Matsumura, Yukihiro Imasato, Tomoyuki Itou, Yusuke Aoki, Hikaru Nakazawa, Takashi Matsui, Takeshi Yokoyama, Mihoko Ui, Mitsuo Umetsu, Satoru Nagatoishi, Kouhei Tsumoto, Yoshikazu Tanaka, Kazushi Kinbara","doi":"10.1093/bulcsj/uoae090","DOIUrl":"https://doi.org/10.1093/bulcsj/uoae090","url":null,"abstract":"We synthesized a “cyborg protein,” wherein a synthetic molecule partially substitutes the main peptide chain by linking two protein domains with a synthetic oligomer. Green fluorescent protein (GFP) served as the model for constructing the cyborg proteins. We prepared circularly permuted GFP (cpGFP) with new termini between β10 and β11, where the original N- and C-termini were linked by a cleavable peptide loop. The cyborg GFP was constructed from cpGFP by linking the β10 and β11 with oligo(ethylene glycol) using maleimide-cysteine couplings, followed by the enzymatic cleavage of the N- and C-termini linking loop by thrombin. With the help of machine learning, we were able to obtain the cpGFP mutants that significantly alter the fluorescence activity (53% increase) by thrombin treatment, which splits cpGFP into two fragments (fragmented-GFP), and by heat shock. When the cyborg GFP was constructed using this mutant, the fluorescence intensity increased by 13% after heat treatment, similar to cpGFP (33% increase), and the behavior was significantly different from that of the fragmented-GFP. This result suggests the possibility that the oligo(ethylene glycol) chain in the cyborg protein plays a similar role to the peptide in the main chain of the protein.","PeriodicalId":9511,"journal":{"name":"Bulletin of the Chemical Society of Japan","volume":"37 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142186104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lutfia Isna Ardhayanti, Islam Md Saidul, Ze Cai, Masahiro Fukuzaki, Xinyao Liu, Zhongyue Zhang, Yoshihiro Sekine, Shinya Hayami
Nanodiamonds (NDs) offer immense potential in various fields, but graphitic or metal-based impurities hinder their widespread adoption. Conventional purification methods often employ harsh chemicals or high temperatures, raising concerns about ND integrity and surface properties. Herein, we compared various strategies to purify and tailor the surface functional groups in the detonation-derived nanodiamonds. A facile two-step purification strategy combining salt-assisted air oxidation (SAAO) and Fenton chemistry is particularly interesting for efficient and selective removal of graphitic impurities while preserving the diamond lattice structure. SAAO selectively burns off graphitic impurities at 450 °C under controlled oxygen flow, minimizing damage to the diamond core. Subsequently, Fenton's reagent (H2O2/Fe2+) introduces hydrophilic functional groups onto the ND surface, further enhancing diamond purity and promoting subsequent functionalization. This synergistic approach enables i) highly efficient removal of graphitic impurities while preserving ND morphology and crystal structure, ii) controlled introduction of surface functionalities, and iii) improved colloidal stability of purified NDs. This green and efficient purification protocol is beneficial for tailoring ND properties and unlocking their full potential in diverse applications ranging from biomedicine and electronics to catalysis and quantum technologies.
{"title":"Purification and Tailored Functionalities in Detonation Nanodiamond","authors":"Lutfia Isna Ardhayanti, Islam Md Saidul, Ze Cai, Masahiro Fukuzaki, Xinyao Liu, Zhongyue Zhang, Yoshihiro Sekine, Shinya Hayami","doi":"10.1093/bulcsj/uoae089","DOIUrl":"https://doi.org/10.1093/bulcsj/uoae089","url":null,"abstract":"Nanodiamonds (NDs) offer immense potential in various fields, but graphitic or metal-based impurities hinder their widespread adoption. Conventional purification methods often employ harsh chemicals or high temperatures, raising concerns about ND integrity and surface properties. Herein, we compared various strategies to purify and tailor the surface functional groups in the detonation-derived nanodiamonds. A facile two-step purification strategy combining salt-assisted air oxidation (SAAO) and Fenton chemistry is particularly interesting for efficient and selective removal of graphitic impurities while preserving the diamond lattice structure. SAAO selectively burns off graphitic impurities at 450 °C under controlled oxygen flow, minimizing damage to the diamond core. Subsequently, Fenton's reagent (H2O2/Fe2+) introduces hydrophilic functional groups onto the ND surface, further enhancing diamond purity and promoting subsequent functionalization. This synergistic approach enables i) highly efficient removal of graphitic impurities while preserving ND morphology and crystal structure, ii) controlled introduction of surface functionalities, and iii) improved colloidal stability of purified NDs. This green and efficient purification protocol is beneficial for tailoring ND properties and unlocking their full potential in diverse applications ranging from biomedicine and electronics to catalysis and quantum technologies.","PeriodicalId":9511,"journal":{"name":"Bulletin of the Chemical Society of Japan","volume":"69 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142186106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yasutaka Suzuki, Akira Ikeda, Shuji Nakao, Teruyuki Nakato, Kanji Saito, Jun Kawamata
The study explores a novel method for constructing hetero-stacked bilayers of graphene and various inorganic oxide nanosheets by utilizing optical manipulation technique. A graphene oxide (GO) is trapped by a laser beam, and the GO nanosheet is converted to reduced graphene oxide (rGO). The rGO pressed against the substrate, forming a hetero-stacked rGO–GO bilayer. Precise control over the relative location of the nanosheets is achieved by optically manipulating the rGO nanosheet. The technique is demonstrated with rGO-niobate and rGO-titanate bilayers, highlighting its simplicity and versatility.
{"title":"Optical manipulation of graphene oxide nanosheets toward arbitrary hetero-stacking of graphene and niobate and titanate nanosheets","authors":"Yasutaka Suzuki, Akira Ikeda, Shuji Nakao, Teruyuki Nakato, Kanji Saito, Jun Kawamata","doi":"10.1093/bulcsj/uoae086","DOIUrl":"https://doi.org/10.1093/bulcsj/uoae086","url":null,"abstract":"The study explores a novel method for constructing hetero-stacked bilayers of graphene and various inorganic oxide nanosheets by utilizing optical manipulation technique. A graphene oxide (GO) is trapped by a laser beam, and the GO nanosheet is converted to reduced graphene oxide (rGO). The rGO pressed against the substrate, forming a hetero-stacked rGO–GO bilayer. Precise control over the relative location of the nanosheets is achieved by optically manipulating the rGO nanosheet. The technique is demonstrated with rGO-niobate and rGO-titanate bilayers, highlighting its simplicity and versatility.","PeriodicalId":9511,"journal":{"name":"Bulletin of the Chemical Society of Japan","volume":"42 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142186107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The temperature dependences of the spin–spin relaxation times (T2) of 1H and 19F nuclei were measured for N, N-diethylpyrrolidinium bis(fluorosulfonyl)amide with a plastic crystal (PC) phase. In the PC phase, two types of T2 were observed in both 1H and 19F experiments, which was considered to be the appearance of heterogeneous dynamics of diffusive motion. By examining temperature dependences of the T2 values and the existence ratios, the following conclusions were reached. (1) The prepared PC sample was in a polycrystalline state, and each crystallite comprised two phases: the core phase (PC phase) and the surface phase formed to relieve surface stress. (2) The 1H-T2 (19F-T2) values of the two phases differed, and ions in the surface phase were more mobile. The 1H-T2 (19F-T2) values for the two phases increased with temperature rise. In particular, the 1H-T2 (19F-T2) values of the surface phase were smoothly connected to the liquid T2 values. (3) The cations and anions exhibited a cooperative diffusive motion. (4) When the temperature was considerably lower than the melting point, the ratio of the surface phase did not significantly differ from when it first formed. However, it rapidly increased near the melting point and became liquid.
测量了具有塑性晶体（PC）相的 N, N-二乙基吡咯烷双（氟磺酰）酰胺的 1H 和 19F 原子核的自旋-自旋弛豫时间（T2）的温度依赖性。在 PC 相中，1H 和 19F 实验都观察到了两种类型的 T2，这被认为是扩散运动的异质动力学的表现。通过研究 T2 值和存在比的温度相关性，得出了以下结论。(1）制备的 PC 样品处于多晶状态，每个晶粒由两相组成：核心相（PC 相）和为缓解表面应力而形成的表面相。(2) 两相的 1H-T2 (19F-T2) 值不同，表面相中的离子流动性更大。两相的 1H-T2（19F-T2）值随温度升高而增加。尤其是表相的 1H-T2 （19F-T2）值与液相的 T2 值平稳相连。(3) 阳离子和阴离子表现出协同扩散运动。(4) 当温度大大低于熔点时，表面相的比率与最初形成时没有明显差别。然而，当温度接近熔点时，表面相的比例迅速增加并变成液态。
{"title":"Heterogenous Dynamics of Diffusive Motion in Organic Ionic Plastic Crystal Studied Using Spin-Spin Relaxation Time: N, N-Diethylpyrrolidinium Bis(fluorosulfonyl)amide","authors":"Keiko Nishikawa, Kozo Fujii, Kazuhiko Matsumoto, Hiroshi Abe, Masahiro Yoshizawa-Fujita","doi":"10.1093/bulcsj/uoae088","DOIUrl":"https://doi.org/10.1093/bulcsj/uoae088","url":null,"abstract":"The temperature dependences of the spin–spin relaxation times (T2) of 1H and 19F nuclei were measured for N, N-diethylpyrrolidinium bis(fluorosulfonyl)amide with a plastic crystal (PC) phase. In the PC phase, two types of T2 were observed in both 1H and 19F experiments, which was considered to be the appearance of heterogeneous dynamics of diffusive motion. By examining temperature dependences of the T2 values and the existence ratios, the following conclusions were reached. (1) The prepared PC sample was in a polycrystalline state, and each crystallite comprised two phases: the core phase (PC phase) and the surface phase formed to relieve surface stress. (2) The 1H-T2 (19F-T2) values of the two phases differed, and ions in the surface phase were more mobile. The 1H-T2 (19F-T2) values for the two phases increased with temperature rise. In particular, the 1H-T2 (19F-T2) values of the surface phase were smoothly connected to the liquid T2 values. (3) The cations and anions exhibited a cooperative diffusive motion. (4) When the temperature was considerably lower than the melting point, the ratio of the surface phase did not significantly differ from when it first formed. However, it rapidly increased near the melting point and became liquid.","PeriodicalId":9511,"journal":{"name":"Bulletin of the Chemical Society of Japan","volume":"46 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142186108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular dynamics (MD) simulations are frequently used to elucidate the molecular mechanisms underlying protein behaviour. Based on a conformational search with MD simulations, protein structures rich in high-dimensional data can be quantitatively evaluated in free-energy landscapes (FELs). Generally, FELs are defined in low-dimensional subspaces spanned by reaction coordinates (RCs) to characterize biological functions. When calculating FELs of proteins, principal component analysis (PCA) is particularly useful for capturing large-amplitude motions via dimensionality reduction into low-dimensional subspaces. In this study, to efficiently calculate FELs, a simple and convenient method is proposed by accelerating conformational search in a PCA subspace, which is achieved by quick generation of protein configurations. Specifically, inverse transformation driven by PCA facilitates the quick generation of diverse protein configurations from arbitrary grids in a defined PCA subspace. In our conformational search, a set of newly generated configurations serves as initial structures for multiple MD simulations, enabling one to calculate FELs of proteins by building Markov state models from their multiple trajectories. In conclusion, the conformational search from protein configurations broadly distributed in a PCA subspace accelerates FEL calculations, which supports a comprehensive approach to understanding collective protein dynamics.
{"title":"Structural Generation by Inverse Transformation Using Principal Component Analysis Enhances Conformational Sampling of","authors":"Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada","doi":"10.1093/bulcsj/uoae087","DOIUrl":"https://doi.org/10.1093/bulcsj/uoae087","url":null,"abstract":"Molecular dynamics (MD) simulations are frequently used to elucidate the molecular mechanisms underlying protein behaviour. Based on a conformational search with MD simulations, protein structures rich in high-dimensional data can be quantitatively evaluated in free-energy landscapes (FELs). Generally, FELs are defined in low-dimensional subspaces spanned by reaction coordinates (RCs) to characterize biological functions. When calculating FELs of proteins, principal component analysis (PCA) is particularly useful for capturing large-amplitude motions via dimensionality reduction into low-dimensional subspaces. In this study, to efficiently calculate FELs, a simple and convenient method is proposed by accelerating conformational search in a PCA subspace, which is achieved by quick generation of protein configurations. Specifically, inverse transformation driven by PCA facilitates the quick generation of diverse protein configurations from arbitrary grids in a defined PCA subspace. In our conformational search, a set of newly generated configurations serves as initial structures for multiple MD simulations, enabling one to calculate FELs of proteins by building Markov state models from their multiple trajectories. In conclusion, the conformational search from protein configurations broadly distributed in a PCA subspace accelerates FEL calculations, which supports a comprehensive approach to understanding collective protein dynamics.","PeriodicalId":9511,"journal":{"name":"Bulletin of the Chemical Society of Japan","volume":"12 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142186151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Organic photoreactions have received much attention as unique tools to access kinetically and/or thermodynamically prohibited products in the ground state. These photoreactions have been based mainly on using elements with high electronegativity such as carbon (C), oxygen (O), nitrogen (N), halogens (F, Cl, Br, and I) as well as transition metals. On the other hand, we have been interested in the characteristics of elements with low electronegativity, such as boron (B), silicon (Si), and tin (Sn), in the excited state, enabling highly reactive and/or selective photoinduced borylations, silylations, and stannylations. In this account, we highlight our latest findings concerning diverse organic photoreactions utilizing B, Si, and Sn elements, which are challenging when using conventional strategies.
{"title":"Development of organic photoreactions utilizing the characteristics of elements with low electronegativity","authors":"Yuki Nagashima","doi":"10.1093/bulcsj/uoae080","DOIUrl":"https://doi.org/10.1093/bulcsj/uoae080","url":null,"abstract":"Organic photoreactions have received much attention as unique tools to access kinetically and/or thermodynamically prohibited products in the ground state. These photoreactions have been based mainly on using elements with high electronegativity such as carbon (C), oxygen (O), nitrogen (N), halogens (F, Cl, Br, and I) as well as transition metals. On the other hand, we have been interested in the characteristics of elements with low electronegativity, such as boron (B), silicon (Si), and tin (Sn), in the excited state, enabling highly reactive and/or selective photoinduced borylations, silylations, and stannylations. In this account, we highlight our latest findings concerning diverse organic photoreactions utilizing B, Si, and Sn elements, which are challenging when using conventional strategies.","PeriodicalId":9511,"journal":{"name":"Bulletin of the Chemical Society of Japan","volume":"200 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chiral transcription from chiral to achiral organic molecules is a fundamental research area in supramolecular chemistry, organic chemistry, and nanoscience. In this study, we demonstrated that chiral transcription of an achiral azobenzene derivative (Azo) can be achieved by embedding it within helically controlled nanofibers. Helical nanofibers were produced via supramolecular assembly of water-insoluble D-12-hydroxystearic acid (D-HSA) as a chiral source and a water-soluble long-chain amidoamine derivative (C18AA) in water. Azo-incorporated helical nanofibers exhibited a circular dichroism (CD) peak at 350 nm, which was assigned to the π−π* transition band of trans-azobenzene chromophore, suggesting a chiral arrangement of Azo molecules in the nanofibers. Because the nanofibers are dispersed in water and Azo is not soluble in water, the selection of an organic solvent to dissolve Azo is important for the incorporation of Azo molecules. When water-immiscible toluene was used as the solvent, Azo incorporation did not occur, because contact between the nanofibers and Azo was inhibited; however, when water-miscible methanol was used, incorporation was achieved. The incorporation of Azo gradually occurred in the pre-assembled C18AA + D-HSA nanofibers, but co-assembly did not occur during the formation of the C18AA + D-HSA nanofibers. We also showed that Azo-containing nanofibers can undergo a reversible thermal phase transition between gel-to-sol states, switching the CD signal of Azo on and off. Furthermore, trans–cis-photoisomerization of Azo embedded in the nanofibers eliminated the CD peak of the trans-isomer, and no new CD peak corresponding to the cis-isomer appeared.
从手性到非手性有机分子的手性转录是超分子化学、有机化学和纳米科学的一个基础研究领域。在这项研究中，我们证明了通过将非手性偶氮苯衍生物（Azo）嵌入螺旋控制的纳米纤维中，可以实现该衍生物的手性转录。螺旋纳米纤维是由不溶于水的 D-12- 羟基硬脂酸（D-HSA）作为手性源与水溶性长链氨基胺衍生物（C18AA）在水中超分子组装而成。加入偶氮的螺旋纳米纤维在 350 纳米波长处出现圆二色性（CD）峰，该峰被归属于反式偶氮苯发色团的 π-π* 过渡带，表明纳米纤维中偶氮分子呈手性排列。由于纳米纤维分散在水中，而偶氮不溶于水，因此选择溶解偶氮的有机溶剂对于偶氮分子的掺入非常重要。当使用不溶于水的甲苯作为溶剂时，由于纳米纤维与偶氮之间的接触受到抑制，偶氮没有被掺入；但当使用不溶于水的甲醇时，偶氮被掺入。偶氮逐渐掺入到预组装的 C18AA + D-HSA 纳米纤维中，但在形成 C18AA + D-HSA 纳米纤维的过程中没有发生共组装。我们还发现，含偶氮的纳米纤维可以在凝胶态到溶胶态之间发生可逆的热相变，从而开关偶氮的 CD 信号。此外，纳米纤维中嵌入的偶氮的反式-顺式-光异构化消除了反式异构体的 CD 峰，没有出现与顺式异构体相对应的新的 CD 峰。
{"title":"Imparting chiroptical property to achiral azobenzene derivative via incorporation into chiral-controlled helical nanofibers","authors":"Tomoki Ito, Makoto Nakagawa, Takeshi Kawai","doi":"10.1093/bulcsj/uoae075","DOIUrl":"https://doi.org/10.1093/bulcsj/uoae075","url":null,"abstract":"Chiral transcription from chiral to achiral organic molecules is a fundamental research area in supramolecular chemistry, organic chemistry, and nanoscience. In this study, we demonstrated that chiral transcription of an achiral azobenzene derivative (Azo) can be achieved by embedding it within helically controlled nanofibers. Helical nanofibers were produced via supramolecular assembly of water-insoluble D-12-hydroxystearic acid (D-HSA) as a chiral source and a water-soluble long-chain amidoamine derivative (C18AA) in water. Azo-incorporated helical nanofibers exhibited a circular dichroism (CD) peak at 350 nm, which was assigned to the π−π* transition band of trans-azobenzene chromophore, suggesting a chiral arrangement of Azo molecules in the nanofibers. Because the nanofibers are dispersed in water and Azo is not soluble in water, the selection of an organic solvent to dissolve Azo is important for the incorporation of Azo molecules. When water-immiscible toluene was used as the solvent, Azo incorporation did not occur, because contact between the nanofibers and Azo was inhibited; however, when water-miscible methanol was used, incorporation was achieved. The incorporation of Azo gradually occurred in the pre-assembled C18AA + D-HSA nanofibers, but co-assembly did not occur during the formation of the C18AA + D-HSA nanofibers. We also showed that Azo-containing nanofibers can undergo a reversible thermal phase transition between gel-to-sol states, switching the CD signal of Azo on and off. Furthermore, trans–cis-photoisomerization of Azo embedded in the nanofibers eliminated the CD peak of the trans-isomer, and no new CD peak corresponding to the cis-isomer appeared.","PeriodicalId":9511,"journal":{"name":"Bulletin of the Chemical Society of Japan","volume":"20 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141869240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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