Electronic excitation is usually accomplished using light (photoexcitation) and is a key step in a vast number of important physical and biological processes. However, in instances where photoexcitation is not possible, a photosensitizer can excite the target molecule in a process called photosensitization. Unfortunately, full details of its mechanism are still unknown. This perspective gives an overview of the current understanding of photosensitization and describes how instanton theory can be used to fill the gaps, especially with regard tothe importance of quantum tunnelling effects.
{"title":"Using Instanton Theory to Study Quantum Effects in Photosensitization","authors":"Meghna A. Manae, Jeremy O. Richardson","doi":"10.2533/chimia.2024.231","DOIUrl":"https://doi.org/10.2533/chimia.2024.231","url":null,"abstract":"Electronic excitation is usually accomplished using light (photoexcitation) and is a key step in a vast number of important physical and biological processes. However, in instances where photoexcitation is not possible, a photosensitizer can excite the target molecule in a process called photosensitization. Unfortunately, full details of its mechanism are still unknown. This perspective gives an overview of the current understanding of photosensitization and describes how instanton theory can be used to fill the gaps, especially with regard tothe importance of quantum tunnelling effects.","PeriodicalId":9957,"journal":{"name":"Chimia","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140665503","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}
Fluorescence imaging is an invaluable tool to study biological processes, and fluorogenic dyes are crucial to enhance cell permeability and target intracellular structures with high specificity. Polymethine dyes are vitally important fluorophores in single-molecule localization microscopy and in vivo imaging, but their use in live cells has been limited by high background fluorescence and low membrane permeability. Here, we present a general strategy to transform polymethine compounds into fluorogenic dyes by implementing a 5-exo-trig ring-closure. This method provides access to bright, fluorogenic polymethine dyes with emissions across the visible and near-infrared spectrum.
{"title":"A Baldwin-favored Cyclization Inspires the Development of Fluorogenic Polymethine Dyes for Bioimaging","authors":"Annabell Martin, Pablo Rivera Fuentes","doi":"10.2533/chimia.2024.196","DOIUrl":"https://doi.org/10.2533/chimia.2024.196","url":null,"abstract":"Fluorescence imaging is an invaluable tool to study biological processes, and fluorogenic dyes are crucial to enhance cell permeability and target intracellular structures with high specificity. Polymethine dyes are vitally important fluorophores in single-molecule localization microscopy and in vivo imaging, but their use in live cells has been limited by high background fluorescence and low membrane permeability. Here, we present a general strategy to transform polymethine compounds into fluorogenic dyes by implementing a 5-exo-trig ring-closure. This method provides access to bright, fluorogenic polymethine dyes with emissions across the visible and near-infrared spectrum.","PeriodicalId":9957,"journal":{"name":"Chimia","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140665982","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}
Das von Josef Fried erfundene Verfahren zur Einführung von 9a-Fluorsubstituenten in Glucocorticoide wird erläutert und ein kurzer Einblick in das Leben dieses bedeutenden Synthetikers und Wirkstoffforschers gegeben.
{"title":"Der Fried-Prozess als Quelle von 9alpha-Fluorglucocorticoiden","authors":"Carsten A. Vock","doi":"10.2533/chimia.2024.264","DOIUrl":"https://doi.org/10.2533/chimia.2024.264","url":null,"abstract":"Das von Josef Fried erfundene Verfahren zur Einführung von 9a-Fluorsubstituenten in Glucocorticoide wird erläutert und ein kurzer Einblick in das Leben dieses bedeutenden Synthetikers und Wirkstoffforschers gegeben.","PeriodicalId":9957,"journal":{"name":"Chimia","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140660278","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}
Kasimir Kienbeck, Lukas Malfertheiner, Susann Zelger-Paulus, S. Johannsen, Christian von Mering, R. Sigel
RNA, widely recognized as an information-carrier molecule, is capable of catalyzing essential biological processes through ribozymes. Despite their ubiquity, specific functions in a biological context and phenotypes based on the ribozymes' activity are often unknown. Here, we present the discovery of a subgroup of minimal HDV-like ribozymes, which reside 3' to viral tRNAs and appear to cleave the 3'-trailers of viral premature tRNA transcripts. This proposed tRNA-processing function is unprecedented for any ribozymes, thus, we designate this subgroup as theta ribozymes. Most theta ribozymes were identified in Caudoviricetes bacteriophages, the main constituent (>90%) of the mammalian gut virome. Intriguingly, our findings further suggest the involvement of theta ribozymes in the transition of certain bacteriophages between distinct genetic codes, thus possibly contributing to the phage lysis trigger. Our discovery expands the limited repertoire of biological functions attributed to HDV-like ribozymes and provides insights into the fascinating world of RNA catalysis.
{"title":"From Enigma to Revelation: Unravelling Biological Functions of Ubiquitous Small Ribozymes","authors":"Kasimir Kienbeck, Lukas Malfertheiner, Susann Zelger-Paulus, S. Johannsen, Christian von Mering, R. Sigel","doi":"10.2533/chimia.2024.200","DOIUrl":"https://doi.org/10.2533/chimia.2024.200","url":null,"abstract":"RNA, widely recognized as an information-carrier molecule, is capable of catalyzing essential biological processes through ribozymes. Despite their ubiquity, specific functions in a biological context and phenotypes based on the ribozymes' activity are often unknown. Here, we present the discovery of a subgroup of minimal HDV-like ribozymes, which reside 3' to viral tRNAs and appear to cleave the 3'-trailers of viral premature tRNA transcripts. This proposed tRNA-processing function is unprecedented for any ribozymes, thus, we designate this subgroup as theta ribozymes. Most theta ribozymes were identified in Caudoviricetes bacteriophages, the main constituent (>90%) of the mammalian gut virome. Intriguingly, our findings further suggest the involvement of theta ribozymes in the transition of certain bacteriophages between distinct genetic codes, thus possibly contributing to the phage lysis trigger. Our discovery expands the limited repertoire of biological functions attributed to HDV-like ribozymes and provides insights into the fascinating world of RNA catalysis.","PeriodicalId":9957,"journal":{"name":"Chimia","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140663370","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}
From energy-related transformations to organic syntheses, single-atom heterogeneous catalysts (SACs) are offering new prospects to tackle sustainability challenges. However, scarce design guidelines and poor mechanistic understanding due to a lack of discovery and operando characterization tools impede theirbroader development. This perspective offers a glimpse into how droplet-based microfluidic technologies mayhelp solve both of these issues, and provides technical considerations for platform design to systematically fabricate SACs and study them under operational conditions during liquid-phase organic syntheses.
{"title":"Extending Droplet-Based Microfluidic Tools to Single-Atom Heterogeneous Catalysis","authors":"Thomas Moragues","doi":"10.2533/chimia.2024.226","DOIUrl":"https://doi.org/10.2533/chimia.2024.226","url":null,"abstract":"From energy-related transformations to organic syntheses, single-atom heterogeneous catalysts (SACs) are offering new prospects to tackle sustainability challenges. However, scarce design guidelines and poor mechanistic understanding due to a lack of discovery and operando characterization tools impede theirbroader development. This perspective offers a glimpse into how droplet-based microfluidic technologies mayhelp solve both of these issues, and provides technical considerations for platform design to systematically fabricate SACs and study them under operational conditions during liquid-phase organic syntheses.","PeriodicalId":9957,"journal":{"name":"Chimia","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140659214","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}
{"title":"Northwest to Southwest – The Conference Reports of the 5th and 6th Swiss Symposium in Point-of-Care Diagnostics held in Muttenz 2022 and Sion 2023","authors":"Marc E Pfeifer, D. Prim","doi":"10.2533/chimia.2024.267","DOIUrl":"https://doi.org/10.2533/chimia.2024.267","url":null,"abstract":"","PeriodicalId":9957,"journal":{"name":"Chimia","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140659272","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}
Understanding the impact of human activities on the metabolic state of soil and aquatic environments is of paramount importance to implement measures for maintaining ecosystem services. Variations of naturalabundance 18O/16O ratios in phosphate have been proposed as proxies for the holistic assessment of metabolic activity given the crucial importance of phosphoryl transfer reactions in fundamental biological processes. However, instrumental and procedural limitations inherent to oxygen isotope analysis in phosphate and organophosphorus compounds have so far limited the stable isotope-based evaluation of metabolic processes. Here, we discuss how recent developments in Orbitrap high resolution mass spectrometry enable measurements of 18O/16O ratios in phosphate and outline the critical mass spectrometry parameters for accurate and precise analysis. Subsequently, we evaluate the types of 18O kinetic isotope effects of phosphoryl transfer reactions and illustrate how novel analytical approaches will give rise to an improved understanding of 18O/16O ratio variations from biochemical processes affecting the microbial phosphorus metabolism.
{"title":"Advances in Oxygen Isotope Analysis of Phosphate by Electrospray Orbitrap Mass Spectrometry for Studying the Microbial Metabolism of Microorganisms","authors":"Nora M. Bernet, T. Hofstetter","doi":"10.2533/chimia.2024.256","DOIUrl":"https://doi.org/10.2533/chimia.2024.256","url":null,"abstract":"Understanding the impact of human activities on the metabolic state of soil and aquatic environments is of paramount importance to implement measures for maintaining ecosystem services. Variations of naturalabundance 18O/16O ratios in phosphate have been proposed as proxies for the holistic assessment of metabolic activity given the crucial importance of phosphoryl transfer reactions in fundamental biological processes. However, instrumental and procedural limitations inherent to oxygen isotope analysis in phosphate and organophosphorus compounds have so far limited the stable isotope-based evaluation of metabolic processes. Here, we discuss how recent developments in Orbitrap high resolution mass spectrometry enable measurements of 18O/16O ratios in phosphate and outline the critical mass spectrometry parameters for accurate and precise analysis. Subsequently, we evaluate the types of 18O kinetic isotope effects of phosphoryl transfer reactions and illustrate how novel analytical approaches will give rise to an improved understanding of 18O/16O ratio variations from biochemical processes affecting the microbial phosphorus metabolism.","PeriodicalId":9957,"journal":{"name":"Chimia","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140661910","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}
Antibiotics reach agricultural soils via fertilization with manure and biosolids as well as irrigation withwastewater and have the potential to be taken up by growing crops. The fate of antibiotics in terms of uptakefrom soil to plants, as well as translocation from root to leaves, is determined by a combination of antibiotic’sphysio-chemical (e.g. speciation, lipophilicity), soil (e.g. organic carbon content, pH) and plant (e.g.transpiration rates) characteristics. In this meta-analysis, a literature search was executed to obtain an overview of antibiotic uptake to plants, with an aim to identify uptake and translocation patterns of different antibiotic classes. Overall, we found that higher uptake of tetracyclines to plant leaves was observed compared to sulfonamides. Differences were also observed in translocation within the plants, where tetracyclines were found in roots and leaves with close to equal concentrations, while the sulfonamides represented a tendency to accumulate to the root fraction. The antibiotic’s characteristics have a high influence on their fate, for example, the high water-solubility and uncharged speciation in typical agricultural soil pH ranges likely induces tetracycline uptake from soil and translocation in plant. Despite the advances in knowledge over the past decade, our meta-analysis indicated that the available research is focused on a limited number of analytes and antibiotic classes. Furthermore, fastgrowing plant species (e.g. spinach, lettuce, and radish) are overly represented in studies compared to crop species with higher significance for human food sources (e.g. corn, wheat, and potato), requiring more attention in future research.
{"title":"Antibiotics Uptake from Soil and Translocation in the Plants – Meta-analysis","authors":"Inna Nybom, Thomas D. Bucheli, Gina Garland","doi":"10.2533/chimia.2024.209","DOIUrl":"https://doi.org/10.2533/chimia.2024.209","url":null,"abstract":"Antibiotics reach agricultural soils via fertilization with manure and biosolids as well as irrigation withwastewater and have the potential to be taken up by growing crops. The fate of antibiotics in terms of uptakefrom soil to plants, as well as translocation from root to leaves, is determined by a combination of antibiotic’sphysio-chemical (e.g. speciation, lipophilicity), soil (e.g. organic carbon content, pH) and plant (e.g.transpiration rates) characteristics. In this meta-analysis, a literature search was executed to obtain an overview of antibiotic uptake to plants, with an aim to identify uptake and translocation patterns of different antibiotic classes. Overall, we found that higher uptake of tetracyclines to plant leaves was observed compared to sulfonamides. Differences were also observed in translocation within the plants, where tetracyclines were found in roots and leaves with close to equal concentrations, while the sulfonamides represented a tendency to accumulate to the root fraction. The antibiotic’s characteristics have a high influence on their fate, for example, the high water-solubility and uncharged speciation in typical agricultural soil pH ranges likely induces tetracycline uptake from soil and translocation in plant. Despite the advances in knowledge over the past decade, our meta-analysis indicated that the available research is focused on a limited number of analytes and antibiotic classes. Furthermore, fastgrowing plant species (e.g. spinach, lettuce, and radish) are overly represented in studies compared to crop species with higher significance for human food sources (e.g. corn, wheat, and potato), requiring more attention in future research.","PeriodicalId":9957,"journal":{"name":"Chimia","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140664959","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}
N-heterocycles are key building blocks for many pharmaceutical products. An efficient and sustainable method for the synthesis of this class of compounds consists of the recently established intramolecular C–H amination reaction. Development of new iron-based catalysts for this transformation is of paramount importance. Herein, three major challenges in this field are addressed: the accessibility of the catalyst, the lack of mechanisticunderstanding, and the limited activity and robustness of the catalyst. These challenges are tackled by threedifferent catalysts. The first catalyst is the commercially available FeI2, that shows good activities, but is limitedto substrates with activated C–H bonds. The Fe(HMDS)2 catalyst is used to perfom in-depth mechanistic studies, revealing key intermediates of the C–H amination reaction. The third catalyst, featuring mesoionic carbene ligands, displays unprecedented activities and aminates various C–H bonds.
{"title":"From C–H to C–N Bonds: Three Challenges, Three Catalysts, Three Solutions","authors":"Wowa Stroek, Martin Albrecht","doi":"10.2533/chimia.2024.205","DOIUrl":"https://doi.org/10.2533/chimia.2024.205","url":null,"abstract":"N-heterocycles are key building blocks for many pharmaceutical products. An efficient and sustainable method for the synthesis of this class of compounds consists of the recently established intramolecular C–H amination reaction. Development of new iron-based catalysts for this transformation is of paramount importance. Herein, three major challenges in this field are addressed: the accessibility of the catalyst, the lack of mechanisticunderstanding, and the limited activity and robustness of the catalyst. These challenges are tackled by threedifferent catalysts. The first catalyst is the commercially available FeI2, that shows good activities, but is limitedto substrates with activated C–H bonds. The Fe(HMDS)2 catalyst is used to perfom in-depth mechanistic studies, revealing key intermediates of the C–H amination reaction. The third catalyst, featuring mesoionic carbene ligands, displays unprecedented activities and aminates various C–H bonds.","PeriodicalId":9957,"journal":{"name":"Chimia","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140665944","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}
Enzymes are natural catalysts which are gaining momentum in chemical synthesis due to their exquisiteselectivity and their biodegradability. However, the cost-efficiency and the sustainability of the overall biocatalytic process must be enhanced to unlock completely the potential of enzymes for industrial applications. To reach this goal, enzyme immobilization and the integration into continuous flow reactors have been the cornerstone of our research. We showed key examples of the advantages of those tools for the biosynthesis of antivirals, anticancer drugs, and valuable fragrance molecules. By combining new strategies to immobilize biocatalysts, innovative bioengineering approaches, and process development, the performance of the reactions could be boosted up to 100-fold.
{"title":"Towards Greener and More Cost-efficient Biosynthesis of Pharmaceuticals and Fragrance Molecules","authors":"Ana I. Benítez Mateos","doi":"10.2533/chimia.2024.222","DOIUrl":"https://doi.org/10.2533/chimia.2024.222","url":null,"abstract":"Enzymes are natural catalysts which are gaining momentum in chemical synthesis due to their exquisiteselectivity and their biodegradability. However, the cost-efficiency and the sustainability of the overall biocatalytic process must be enhanced to unlock completely the potential of enzymes for industrial applications. To reach this goal, enzyme immobilization and the integration into continuous flow reactors have been the cornerstone of our research. We showed key examples of the advantages of those tools for the biosynthesis of antivirals, anticancer drugs, and valuable fragrance molecules. By combining new strategies to immobilize biocatalysts, innovative bioengineering approaches, and process development, the performance of the reactions could be boosted up to 100-fold.","PeriodicalId":9957,"journal":{"name":"Chimia","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140659266","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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