Designing novel catalysts is pivotal for overcoming numerous energy and environmental challenges. Although data science approaches, particularly machine learning (ML) approaches, hold promise for accelerating catalyst development, discovering truly novel catalysts through ML remains rare. This is largely due to the perceived inability of the ML models to extrapolate and identify exceptional materials. In this Review, I present our approach taken to tackle this limitation. Specifically, we employed an advanced ML methodology that could make extrapolative predictions. This approach led to the discovery of multielemental solid catalysts for CO2 hydrogenation to CO. The results not only demonstrate the immense potential of ML in catalysis research but also set a new standard for the rapid development of high-performance catalysts.
设计新型催化剂对于克服众多能源和环境挑战至关重要。尽管数据科学方法，特别是机器学习（ML）方法，有望加速催化剂的开发，但通过 ML 发现真正新型催化剂的情况仍然很少见。这主要是由于人们认为 ML 模型无法推断和识别特殊材料。在本综述中，我将介绍我们为解决这一局限性而采取的方法。具体来说，我们采用了一种先进的 ML 方法，可以进行外推预测。通过这种方法，我们发现了将 CO2 加氢转化为 CO 的多元素固体催化剂。这些成果不仅证明了 ML 在催化研究中的巨大潜力，还为高性能催化剂的快速开发树立了新的标准。
{"title":"Toward accelerated discovery of solid catalysts using extrapolative machine learning approach","authors":"Takashi Toyao","doi":"10.1093/chemle/upae163","DOIUrl":"https://doi.org/10.1093/chemle/upae163","url":null,"abstract":"Designing novel catalysts is pivotal for overcoming numerous energy and environmental challenges. Although data science approaches, particularly machine learning (ML) approaches, hold promise for accelerating catalyst development, discovering truly novel catalysts through ML remains rare. This is largely due to the perceived inability of the ML models to extrapolate and identify exceptional materials. In this Review, I present our approach taken to tackle this limitation. Specifically, we employed an advanced ML methodology that could make extrapolative predictions. This approach led to the discovery of multielemental solid catalysts for CO2 hydrogenation to CO. The results not only demonstrate the immense potential of ML in catalysis research but also set a new standard for the rapid development of high-performance catalysts.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"2 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A novel series of hybrid indole–thiazolidinedione–triazole derivatives (6a-l) were synthesized and assessed for their in vitro inhibitory activity against porcine pancreatic α-amylase. The synthetic procedure consists of 3 steps. A crucial step in this process involves the generation of novel target molecules using a Cu(I)-catalyzed azide–alkyne cycloaddition reaction. The α-amylase inhibition IC50 value of the targeted compounds ranged from 0.51 ± 0.02 to 7.99 ± 0.28 μM as compared with 0.68 ± 0.02 μM with acarbose as the standard drug. Using the Autodock technique, all the derivatives 6a-l were subjected to molecular docking investigations against porcine pancreatic α-amylase (PDB ID: 1OSE). Moreover, it was discovered that the docked compounds had excellent binding affinities that ranged from −10.1 to −10.8 kcal/mol as compared with the standard −7.9 kcal/mol. Additionally, a comprehensive analysis of the physicochemical and pharmacokinetic properties associated with absorption, distribution, metabolism and excretion (ADME) was conducted for all the synthesized compounds.
{"title":"Indole–thiazolidinedione–triazole hybrids: synthesis, molecular docking, absorption, distribution, metabolism and excretion (ADME) profiling, and biological evaluation as α-amylase inhibitors","authors":"Monil P Dholariya, Anilkumar S Patel","doi":"10.1093/chemle/upae162","DOIUrl":"https://doi.org/10.1093/chemle/upae162","url":null,"abstract":"A novel series of hybrid indole–thiazolidinedione–triazole derivatives (6a-l) were synthesized and assessed for their in vitro inhibitory activity against porcine pancreatic α-amylase. The synthetic procedure consists of 3 steps. A crucial step in this process involves the generation of novel target molecules using a Cu(I)-catalyzed azide–alkyne cycloaddition reaction. The α-amylase inhibition IC50 value of the targeted compounds ranged from 0.51 ± 0.02 to 7.99 ± 0.28 μM as compared with 0.68 ± 0.02 μM with acarbose as the standard drug. Using the Autodock technique, all the derivatives 6a-l were subjected to molecular docking investigations against porcine pancreatic α-amylase (PDB ID: 1OSE). Moreover, it was discovered that the docked compounds had excellent binding affinities that ranged from −10.1 to −10.8 kcal/mol as compared with the standard −7.9 kcal/mol. Additionally, a comprehensive analysis of the physicochemical and pharmacokinetic properties associated with absorption, distribution, metabolism and excretion (ADME) was conducted for all the synthesized compounds.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"408 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Recently, liquid desiccant air conditioners (LDACs) have gained rapidly growing interest as an important candidate for an energy-efficient air conditioner. By enabling moisture absorption from the air, ionic liquids (ILs) can serve as a novel desiccant source for LDACs. For insights into the design and optimization of ILs to this end, we herein present a survey of studies on dehumidification and other relevant properties of ILs and offer some molecular perspective on their feasibility as a desiccant.
{"title":"Design of Ionic Liquids as a Desiccant for the Liquid Desiccant Type Air-Conditioning System","authors":"Toshiyuki Itoh, Hyung J Kim","doi":"10.1093/chemle/upae172","DOIUrl":"https://doi.org/10.1093/chemle/upae172","url":null,"abstract":"Recently, liquid desiccant air conditioners (LDACs) have gained rapidly growing interest as an important candidate for an energy-efficient air conditioner. By enabling moisture absorption from the air, ionic liquids (ILs) can serve as a novel desiccant source for LDACs. For insights into the design and optimization of ILs to this end, we herein present a survey of studies on dehumidification and other relevant properties of ILs and offer some molecular perspective on their feasibility as a desiccant.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"71 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The effects of TiO2 nanoparticle (NP) morphology on the photocatalytic activity of physically assembled TiO2 NP/g-C3N4 heterojunctions (TCNPHY) was investigated. Spherical, spindle and cubic TiO2 NPs were synthesized and separately supported on g-C3N4 nanosheets to form physically assembled TCNPHY catalysts. The photocatalytic activity for methylene blue (MB) degradation observed for TCNPHY with the cubic TiO2 NPs supported higher light absorption and a lower recombination rate; therefore, this was an adequate catalyst for the construction of catalytically active heterojunctions. The cubic-TiO2 TCNPHY exhibited a degradation rate that was 2.2 times higher than that for the g-C3N4 nanosheets alone.
{"title":"Morphological effect of TiO2 nanoparticles in TiO2/g-C3N4 heterojunctions on photocatalytic dye degradation","authors":"Zijian Deng, Ryota Osuga, Masaki Matsubara, Kiyoshi Kanie, Atsushi Muramatsu","doi":"10.1093/chemle/upae171","DOIUrl":"https://doi.org/10.1093/chemle/upae171","url":null,"abstract":"The effects of TiO2 nanoparticle (NP) morphology on the photocatalytic activity of physically assembled TiO2 NP/g-C3N4 heterojunctions (TCNPHY) was investigated. Spherical, spindle and cubic TiO2 NPs were synthesized and separately supported on g-C3N4 nanosheets to form physically assembled TCNPHY catalysts. The photocatalytic activity for methylene blue (MB) degradation observed for TCNPHY with the cubic TiO2 NPs supported higher light absorption and a lower recombination rate; therefore, this was an adequate catalyst for the construction of catalytically active heterojunctions. The cubic-TiO2 TCNPHY exhibited a degradation rate that was 2.2 times higher than that for the g-C3N4 nanosheets alone.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"73 1 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Koki Ishii, Yoshihide Hattori, Hajime Shigeto, Shohei Yamamura, Mizuki Kitamatsu
We have developed peptide nucleic acids (PNAs) modified with boronic acid (Boa) and its ligand 2-(pyridin-2-yl)phenol (Pyp) as a probe for fluorescence detection of a target nucleic acid. Boa and Pyp successfully showed fluorescence by complexing via hybridization with PNA and the target. This fluorescent PNA probe also successfully responded to the target RNA in cells.
{"title":"A fluorescent complex with PNAs modified by boronic acid and its ligand detects target RNA in cells","authors":"Koki Ishii, Yoshihide Hattori, Hajime Shigeto, Shohei Yamamura, Mizuki Kitamatsu","doi":"10.1093/chemle/upae169","DOIUrl":"https://doi.org/10.1093/chemle/upae169","url":null,"abstract":"We have developed peptide nucleic acids (PNAs) modified with boronic acid (Boa) and its ligand 2-(pyridin-2-yl)phenol (Pyp) as a probe for fluorescence detection of a target nucleic acid. Boa and Pyp successfully showed fluorescence by complexing via hybridization with PNA and the target. This fluorescent PNA probe also successfully responded to the target RNA in cells.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"14 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Utilizing photoreactive oligodeoxyribonucleotides (ODNs) presents a promising avenue for significantly enhancing antisense effects with high spatiotemporal resolution. This enhancement arises from the increased stability of RNA–DNA heteroduplexes achieved through photo-cross-linking with complementary RNAs upon light illumination. In this study, we propose a post-introduction approach for preparing ODNs incorporating diazirine and aryl azide warheads, employing 2′-amino-2′-deoxyuridine. We investigate the photo-cross-linking efficiencies, rates, and nucleobase preferences of these photoreactive ODNs when paired with their complementary RNAs.
{"title":"Photo-cross-linking reactions in RNA–DNA heteroduplexes using photoreactive DNA incorporated with diazirine and aryl azide warheads","authors":"Kazuya Matsuo, Machiko Kitamura, Kentaro Kobata, Daiki Unita, Tomonori Waku, Akio Kobori","doi":"10.1093/chemle/upae152","DOIUrl":"https://doi.org/10.1093/chemle/upae152","url":null,"abstract":"Utilizing photoreactive oligodeoxyribonucleotides (ODNs) presents a promising avenue for significantly enhancing antisense effects with high spatiotemporal resolution. This enhancement arises from the increased stability of RNA–DNA heteroduplexes achieved through photo-cross-linking with complementary RNAs upon light illumination. In this study, we propose a post-introduction approach for preparing ODNs incorporating diazirine and aryl azide warheads, employing 2′-amino-2′-deoxyuridine. We investigate the photo-cross-linking efficiencies, rates, and nucleobase preferences of these photoreactive ODNs when paired with their complementary RNAs.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"35 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Allenoates are versatile reagents that can be used for numerous (formal) cycloaddition reactions under (chiral) Lewis base catalysis. Most commonly, the catalysts of choice are phosphines, amines, and N-heterocyclic carbenes. We have recently established the use of readily available chiral isochalcogenoureas as catalysts for asymmetric (4+2)-heterocycloadditions of allenoates with various vinylogous acceptors. This represents a complementary approach for allenoate activation and gives access to various highly functionalized chiral dihydropyrans with good to excellent enantioselectivities and diastereoselectivities.
{"title":"Isochalcogenourea-Catalyzed Asymmetric (4+2)-Heterocycloadditions of Allenoates","authors":"Mario Waser","doi":"10.1093/chemle/upae168","DOIUrl":"https://doi.org/10.1093/chemle/upae168","url":null,"abstract":"Allenoates are versatile reagents that can be used for numerous (formal) cycloaddition reactions under (chiral) Lewis base catalysis. Most commonly, the catalysts of choice are phosphines, amines, and N-heterocyclic carbenes. We have recently established the use of readily available chiral isochalcogenoureas as catalysts for asymmetric (4+2)-heterocycloadditions of allenoates with various vinylogous acceptors. This represents a complementary approach for allenoate activation and gives access to various highly functionalized chiral dihydropyrans with good to excellent enantioselectivities and diastereoselectivities.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"11 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The inhibitory activity of puerarin on the CYP1B1 enzyme was evaluated by the 7-ethoxyresorufin O-dealkylation method. At the same time, the density functional theory algorithm, molecular docking, and molecular dynamics simulations were used to verify the stability of the puerarin–CYP1B1 complex. It has been found that puerarin is a potent uncompetitive inhibitor of CYP1B1 (IC50: 1.06 ± 0.15 μM).
{"title":"Quantum chemical analysis and biochemical evaluation of the inhibitory activity of puerarin on CYP1B1 enzyme","authors":"Xue Li, Jinyue Lu, Lianrong Yang, Yuan Tian, Liwei Jia, Xin Meng","doi":"10.1093/chemle/upae160","DOIUrl":"https://doi.org/10.1093/chemle/upae160","url":null,"abstract":"The inhibitory activity of puerarin on the CYP1B1 enzyme was evaluated by the 7-ethoxyresorufin O-dealkylation method. At the same time, the density functional theory algorithm, molecular docking, and molecular dynamics simulations were used to verify the stability of the puerarin–CYP1B1 complex. It has been found that puerarin is a potent uncompetitive inhibitor of CYP1B1 (IC50: 1.06 ± 0.15 μM).","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"62 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AlphaFold3 can predict protein–ligand complex structures. In this study, we examined the accuracy of prediction of heme–protein interactions by AlphaFold3. AlphaFold3 succeeded in predicting heme–protein interactions for most heme proteins except for those without homologous proteins in the Protein Data Bank. Our comparison of predictions by AlphaFold3 and AlphaFold2 suggests that heme–protein structures can be predicted from amino acid sequences of proteins alone using AlphaFold2.
{"title":"Structure comparison of heme-binding sites in heme protein predicted by AlphaFold3 and AlphaFold2","authors":"Hiroko X Kondo, Yu Takano","doi":"10.1093/chemle/upae148","DOIUrl":"https://doi.org/10.1093/chemle/upae148","url":null,"abstract":"AlphaFold3 can predict protein–ligand complex structures. In this study, we examined the accuracy of prediction of heme–protein interactions by AlphaFold3. AlphaFold3 succeeded in predicting heme–protein interactions for most heme proteins except for those without homologous proteins in the Protein Data Bank. Our comparison of predictions by AlphaFold3 and AlphaFold2 suggests that heme–protein structures can be predicted from amino acid sequences of proteins alone using AlphaFold2.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"408 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Methanol dehydrogenase is a promising biocatalyst for industrial use, converting methanol to formaldehyde. Our molecular modeling revealed methanol binds to methanol dehydrogenase with ∼7 kcal/mol free energy, while formaldehyde binds with ∼4 kcal/mol. This suggests that methanol remains longer in the active site, and formaldehyde exits more readily postreaction. These insights are crucial for designing more efficient methanol dehydrogenase variants for industrial applications.
{"title":"Computational insights into the molecular dynamics of the binding of ligands in the methanol dehydrogenase","authors":"One-Sun Lee, Sung Haeng Lee","doi":"10.1093/chemle/upae153","DOIUrl":"https://doi.org/10.1093/chemle/upae153","url":null,"abstract":"Methanol dehydrogenase is a promising biocatalyst for industrial use, converting methanol to formaldehyde. Our molecular modeling revealed methanol binds to methanol dehydrogenase with ∼7 kcal/mol free energy, while formaldehyde binds with ∼4 kcal/mol. This suggests that methanol remains longer in the active site, and formaldehyde exits more readily postreaction. These insights are crucial for designing more efficient methanol dehydrogenase variants for industrial applications.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"2 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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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