Chemical Reviews最新文献

{"title":"The Analysis of Electron Densities: From Basics to Emergent Applications","authors":"Daniel Koch,&nbsp;Michele Pavanello*,&nbsp;Xuecheng Shao,&nbsp;Manabu Ihara,&nbsp;Paul W. Ayers,&nbsp;Chérif F. Matta*,&nbsp;Samantha Jenkins* and Sergei Manzhos*,&nbsp;","doi":"10.1021/acs.chemrev.4c0029710.1021/acs.chemrev.4c00297","DOIUrl":"https://doi.org/10.1021/acs.chemrev.4c00297https://doi.org/10.1021/acs.chemrev.4c00297","url":null,"abstract":"<p >The electron density determines all properties of a system of nuclei and electrons. It is both computable and observable. Its topology allows gaining insight into the mechanisms of bonding and other phenomena in a way that is complementary to and beyond that available from the molecular orbital picture and the formal oxidation state (FOS) formalism. The ability to derive mechanistic insight from electron density is also important with methods where orbitals are not available, such as orbital-free density functional theory (OF-DFT). While density topology-based analyses such as QTAIM (quantum theory of atoms-in-molecules) have been widely used, novel, vector-based techniques recently emerged such as next-generation (NG) QTAIM. Density-dependent quantities are also actively used in machine learning (ML)-based methods, in particular, for ML DFT functional development, including machine-learnt kinetic energy functionals. We review QTAIM and its recent extensions such as NG-QTAIM and localization-delocalization matrices (LDM) and their uses in the analysis of bonding, conformations, mechanisms of redox reactions excitations, as well as ultrafast phenomena. We review recent research showing that direct density analysis can circumvent certain pitfalls of the FOS formalism, in particular in the description of anionic redox, and of the widely used (spherically) projected density of states analysis. We discuss uses of density-based quantities for the construction of DFT functionals and prospects of applications of analyses of density topology to get mechanistic insight with OF-DFT and recently developed time-dependent OF-DFT.</p>","PeriodicalId":32,"journal":{"name":"Chemical Reviews","volume":"124 22","pages":"12661–12737 12661–12737"},"PeriodicalIF":51.4,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142719327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tackling Undruggable Targets with Designer Peptidomimetics and Synthetic Biologics","authors":"Colin S. Swenson, Gunasheil Mandava, Deborah M. Thomas, Raymond E. Moellering","doi":"10.1021/acs.chemrev.4c00423","DOIUrl":"https://doi.org/10.1021/acs.chemrev.4c00423","url":null,"abstract":"The development of potent, specific, and pharmacologically viable chemical probes and therapeutics is a central focus of chemical biology and therapeutic development. However, a significant portion of predicted disease-causal proteins have proven resistant to targeting by traditional small molecule and biologic modalities. Many of these so-called “undruggable” targets feature extended, dynamic protein–protein and protein–nucleic acid interfaces that are central to their roles in normal and diseased signaling pathways. Here, we discuss the development of synthetically stabilized peptide and protein mimetics as an ever-expanding and powerful region of chemical space to tackle undruggable targets. These molecules aim to combine the synthetic tunability and pharmacologic properties typically associated with small molecules with the binding footprints, affinities and specificities of biologics. In this review, we discuss the historical and emerging platforms and approaches to design, screen, select and optimize synthetic “designer” peptidomimetics and synthetic biologics. We examine the inspiration and design of different classes of designer peptidomimetics: (i) macrocyclic peptides, (ii) side chain stabilized peptides, (iii) non-natural peptidomimetics, and (iv) synthetic proteomimetics, and notable examples of their application to challenging biomolecules. Finally, we summarize key learnings and remaining challenges for these molecules to become useful chemical probes and therapeutics for historically undruggable targets.","PeriodicalId":32,"journal":{"name":"Chemical Reviews","volume":"128 1","pages":""},"PeriodicalIF":62.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142610524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tackling Undruggable Targets with Designer Peptidomimetics and Synthetic Biologics","authors":"Colin S. Swenson,&nbsp;Gunasheil Mandava,&nbsp;Deborah M. Thomas and Raymond E. Moellering*,&nbsp;","doi":"10.1021/acs.chemrev.4c0042310.1021/acs.chemrev.4c00423","DOIUrl":"https://doi.org/10.1021/acs.chemrev.4c00423https://doi.org/10.1021/acs.chemrev.4c00423","url":null,"abstract":"<p >The development of potent, specific, and pharmacologically viable chemical probes and therapeutics is a central focus of chemical biology and therapeutic development. However, a significant portion of predicted disease-causal proteins have proven resistant to targeting by traditional small molecule and biologic modalities. Many of these so-called “undruggable” targets feature extended, dynamic protein–protein and protein–nucleic acid interfaces that are central to their roles in normal and diseased signaling pathways. Here, we discuss the development of synthetically stabilized peptide and protein mimetics as an ever-expanding and powerful region of chemical space to tackle undruggable targets. These molecules aim to combine the synthetic tunability and pharmacologic properties typically associated with small molecules with the binding footprints, affinities and specificities of biologics. In this review, we discuss the historical and emerging platforms and approaches to design, screen, select and optimize synthetic “designer” peptidomimetics and synthetic biologics. We examine the inspiration and design of different classes of designer peptidomimetics: (i) macrocyclic peptides, (ii) side chain stabilized peptides, (iii) non-natural peptidomimetics, and (iv) synthetic proteomimetics, and notable examples of their application to challenging biomolecules. Finally, we summarize key learnings and remaining challenges for these molecules to become useful chemical probes and therapeutics for historically undruggable targets.</p>","PeriodicalId":32,"journal":{"name":"Chemical Reviews","volume":"124 22","pages":"13020–13093 13020–13093"},"PeriodicalIF":51.4,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142719194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Noncanonical Amino Acid Incorporation in Animals and Animal Cells","authors":"Joo-Chan Kim,&nbsp;YouJin Kim,&nbsp;Suho Cho and Hee-Sung Park*,&nbsp;","doi":"10.1021/acs.chemrev.3c0095510.1021/acs.chemrev.3c00955","DOIUrl":"https://doi.org/10.1021/acs.chemrev.3c00955https://doi.org/10.1021/acs.chemrev.3c00955","url":null,"abstract":"<p >Noncanonical amino acids (ncAAs) are synthetic building blocks that, when incorporated into proteins, confer novel functions and enable precise control over biological processes. These small yet powerful tools offer unprecedented opportunities to investigate and manipulate various complex life forms. In particular, ncAA incorporation technology has garnered significant attention in the study of animals and their constituent cells, which serve as invaluable model organisms for gaining insights into human physiology, genetics, and diseases. This review will provide a comprehensive discussion on the applications of ncAA incorporation technology in animals and animal cells, covering past achievements, current developments, and future perspectives.</p>","PeriodicalId":32,"journal":{"name":"Chemical Reviews","volume":"124 22","pages":"12463–12497 12463–12497"},"PeriodicalIF":51.4,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142719136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Spies in Action: Genetically Encoded Fluorescent Biosensors Light up Cellular Signals","authors":"Anneliese M. M. Gest, Ayse Z. Sahan, Yanghao Zhong, Wei Lin, Sohum Mehta, Jin Zhang","doi":"10.1021/acs.chemrev.4c00293","DOIUrl":"https://doi.org/10.1021/acs.chemrev.4c00293","url":null,"abstract":"Cellular function is controlled through intricate networks of signals, which lead to the myriad pathways governing cell fate. Fluorescent biosensors have enabled the study of these signaling pathways in living systems across temporal and spatial scales. Over the years there has been an explosion in the number of fluorescent biosensors, as they have become available for numerous targets, utilized across spectral space, and suited for various imaging techniques. To guide users through this extensive biosensor landscape, we discuss critical aspects of fluorescent proteins for consideration in biosensor development, smart tagging strategies, and the historical and recent biosensors of various types, grouped by target, and with a focus on the design and recent applications of these sensors in living systems.","PeriodicalId":32,"journal":{"name":"Chemical Reviews","volume":"6 1","pages":""},"PeriodicalIF":62.1,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142601599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Additions and Corrections to Cleavage of Si-H, B-H and C-H Bonds by Metal-Ligand Cooperation.","authors":"Takuya Higashi, Shuhei Kusumoto, Kyoko Nozaki","doi":"10.1021/acs.chemrev.4c00563","DOIUrl":"10.1021/acs.chemrev.4c00563","url":null,"abstract":"","PeriodicalId":32,"journal":{"name":"Chemical Reviews","volume":" ","pages":"12381"},"PeriodicalIF":51.4,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single Atom Catalysts Based on Earth-Abundant Metals for Energy-Related Applications.","authors":"Štĕpán Kment, Aristides Bakandritsos, Iosif Tantis, Hana Kmentová, Yunpeng Zuo, Olivier Henrotte, Alberto Naldoni, Michal Otyepka, Rajender S Varma, Radek Zbořil","doi":"10.1021/acs.chemrev.4c00155","DOIUrl":"10.1021/acs.chemrev.4c00155","url":null,"abstract":"<p><p>Anthropogenic activities related to population growth, economic development, technological advances, and changes in lifestyle and climate patterns result in a continuous increase in energy consumption. At the same time, the rare metal elements frequently deployed as catalysts in energy related processes are not only costly in view of their low natural abundance, but their availability is often further limited due to geopolitical reasons. Thus, electrochemical energy storage and conversion with earth-abundant metals, mainly in the form of single-atom catalysts (SACs), are highly relevant and timely technologies. In this review the application of earth-abundant SACs in electrochemical energy storage and electrocatalytic conversion of chemicals to fuels or products with high energy content is discussed. The oxygen reduction reaction is also appraised, which is primarily harnessed in fuel cell technologies and metal-air batteries. The coordination, active sites, and mechanistic aspects of transition metal SACs are analyzed for two-electron and four-electron reaction pathways. Further, the electrochemical water splitting with SACs toward green hydrogen fuel is discussed in terms of not only hydrogen evolution reaction but also oxygen evolution reaction. Similarly, the production of ammonia as a clean fuel via electrocatalytic nitrogen reduction reaction is portrayed, highlighting the potential of earth-abundant single metal species.</p>","PeriodicalId":32,"journal":{"name":"Chemical Reviews","volume":" ","pages":"11767-11847"},"PeriodicalIF":5.1,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11565580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141532883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Spies in Action: Genetically Encoded Fluorescent Biosensors Light up Cellular Signals","authors":"Anneliese M. M. Gest,&nbsp;Ayse Z. Sahan,&nbsp;Yanghao Zhong,&nbsp;Wei Lin,&nbsp;Sohum Mehta and Jin Zhang*,&nbsp;","doi":"10.1021/acs.chemrev.4c0029310.1021/acs.chemrev.4c00293","DOIUrl":"https://doi.org/10.1021/acs.chemrev.4c00293https://doi.org/10.1021/acs.chemrev.4c00293","url":null,"abstract":"<p >Cellular function is controlled through intricate networks of signals, which lead to the myriad pathways governing cell fate. Fluorescent biosensors have enabled the study of these signaling pathways in living systems across temporal and spatial scales. Over the years there has been an explosion in the number of fluorescent biosensors, as they have become available for numerous targets, utilized across spectral space, and suited for various imaging techniques. To guide users through this extensive biosensor landscape, we discuss critical aspects of fluorescent proteins for consideration in biosensor development, smart tagging strategies, and the historical and recent biosensors of various types, grouped by target, and with a focus on the design and recent applications of these sensors in living systems.</p>","PeriodicalId":32,"journal":{"name":"Chemical Reviews","volume":"124 22","pages":"12573–12660 12573–12660"},"PeriodicalIF":51.4,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.chemrev.4c00293","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142719296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Introduction: Fluorescent Probes in Biology","authors":"Christopher J. Chang","doi":"10.1021/acs.chemrev.4c00552","DOIUrl":"https://doi.org/10.1021/acs.chemrev.4c00552","url":null,"abstract":"Published as part of &lt;i&gt;Chemical Reviews&lt;/i&gt; special issue “Fluorescent Probes in Biology”. Seeing is believing! Chemistry makes the invisible visible through the use of imaging agents that can monitor the elements and molecules of life at a variety of length scales with both spatial and temporal resolution. In this context, fluorescence and luminescence provide visual readouts that can be widely adopted by specialists and nonspecialists alike, from laboratory researchers to medical clinicians and field technicians to children playing with glowsticks and fireflies during the long nights of summer. This thematic issue, Fluorescent Probes in Biology, delves into the latest research achievements in this storied and highly active field in the design and development of chemical reagents to decipher new fundamental biology and to translate this knowledge to advanced diagnostic and/or therapeutic platforms. Each paper in this issue focuses on molecular principles of probe design, applied to a particular biological question for analyte detection, chemical platform consisting of a small molecule, macromolecule, nanomaterial, or hybrid scaffold, or disease biomarker. State-of-the art research and future prospects in unmet needs pervade all these informative reviews. A key emerging theme in this collection is the broad use of activity-based sensing, a termed coined by our laboratory and advanced by our team and many others across the world, which is defined as using molecular reactivity rather than molecular recognition for analyte detection. (1) We organize this discussion across fluorescent probes for specific bioanalytes, fluorescent probes derived from a specific type of scaffold (e.g., small molecule, protein, nanomaterial, or hybrid), or fluorescent probes for biomedical applications. A foundational use of fluorescent probes in biology is their application in detecting the chemistry of elements and molecules of life to decipher their physiological and/or pathological contributions to living systems. New and our laboratory have collaborated to write a review on small-molecule sensors for transition metal ions in biological specimens (10.1021/acs.chemrev.3c00819). A focus is on the use of binding-based sensing and activity-based sensing approaches, where the former strategy exploits traditional lock-and-key metal–ligand coordination bonding for selective metal chelation and detection, whereas the latter concept leverages the diverse reactivity of metal ions for their sensing. These approaches are applied to image bioavailable metal pools, termed the labile metal pool, over a variety of biological length scales and in a variety of cell and animal models with metal and oxidation state selectivity, revealing new biological concepts such as transition metal signaling and metalloallostery in health and disease. Activity-based sensing offers a powerful approach to use reaction chemistry as a strategy for analyte detection. Lippert and Domaille and their teams","PeriodicalId":32,"journal":{"name":"Chemical Reviews","volume":"20 1","pages":""},"PeriodicalIF":62.1,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142601600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lone Pair−π Interactions in Organic Reactions","authors":"Yu Chen, Qianqian Zhen, Fan-Jie Meng, Peiyuan Yu, Chen Xu","doi":"10.1021/acs.chemrev.4c00516","DOIUrl":"https://doi.org/10.1021/acs.chemrev.4c00516","url":null,"abstract":"Noncovalent interactions between a lone pair of electrons and π systems can be categorized into two types based on the nature of π systems. Lone pair−π(C═O) interactions with π systems of unsaturated, polarized bonds are primarily attributed to orbital interactions, whereas lone pair−π(Ar) interactions with π systems of aromatic functional groups result from electrostatic attractions (for electron-deficient aryls) or dispersion attractions and Pauli repulsions (for electron-rich/neutral aryls). Unlike well-established noncovalent interactions, lone pair−π interactions have been comparatively underappreciated or less used to influence reaction outcomes. This review emphasizes experimental and computational studies aimed at integrating lone pair−π interactions into the design of catalytic systems and utilizing these interactions to regulate the reactivity and selectivity of chemical transformations. The role of lone pair−π interactions is highlighted in the stabilization or destabilization of transition states and ground-state binding. Examples influenced by lone pair−π interactions with both unsaturated, polarized bonds and aromatic rings as π systems are included. At variance with previous reviews, the present review is not structured according to the physical origin of particular classes of lone pair−π interactions but is divided into chapters according to ways in which lone pair−π interactions affect kinetics and/or selectivity of reactions.","PeriodicalId":32,"journal":{"name":"Chemical Reviews","volume":"72 1","pages":""},"PeriodicalIF":62.1,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142601604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}