Special Issue "Radically Different—A Themed Issue in Honor of Professor Bernd Giese on the Occasion of His 80th Birthday"

A special issue of Chemistry (ISSN 2624-8549).

Deadline for manuscript submissions: closed (30 April 2020).

Special Issue Editor

Prof. Dr. Katharina M. Fromm
E-Mail Website
Guest Editor
Department of Chemistry, University of Fribourg, Chemin du Musée 9, 1700 Fribourg, Switzerland
Interests: crystallography; antimicrobial compounds; bioinorganic chemistry of silver; nanomaterials; coordination compounds; nanomaterials; batteries
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Special Issue Information

Dear Colleagues,

This Special Issue of Chemistry is dedicated to Professor Bernd Giese on behalf of his 80th birthday. Professor Giese is a pioneer in selective radical chemistry, electron transfer through biomolecules, and, recently, electron transfer through bacterial membranes. The “Giese Reaction” has never been cited more often than in the past few months!Bernd’s interest in Chemistry and his curiosity remain unbowed and are so broad that we decided to open this Special Issue to all areas of Chemistry. I am sure that Bernd will enjoy reading every paper with great interest and fascination. Therefore, all contributions are welcome.

Only manuscripts submitted until April 30 can be taken into account for the printed version of the special issue—all later submission are not guaranteed and will only appear in the online issue.

Prof. Dr. Katharina M. Fromm
Guest Editor

Manuscript Submission Information

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Keywords

  • physical organic chemistry
  • nanoparticles
  • electron transfer reactions
  • synthesis
  • kinetics.

Published Papers (16 papers)

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Research

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Open AccessArticle
On the Importance of the Thiazole Nitrogen in Epothilones: Semisynthesis and Microtubule-Binding Affinity of Deaza-Epothilone C
Chemistry 2020, 2(2), 499-509; https://doi.org/10.3390/chemistry2020030 - 23 May 2020
Viewed by 1081
Abstract
Deaza-epothilone C, which incorporates a thiophene moiety in place of the thiazole heterocycle in the natural epothilone side chain, has been prepared by semisynthesis from epothilone A, in order to assess the contribution of the thiazole nitrogen to microtubule binding. The synthesis was [...] Read more.
Deaza-epothilone C, which incorporates a thiophene moiety in place of the thiazole heterocycle in the natural epothilone side chain, has been prepared by semisynthesis from epothilone A, in order to assess the contribution of the thiazole nitrogen to microtubule binding. The synthesis was based on the esterification of a known epothilone A-derived carboxylic acid fragment and a fully synthetic alcohol building block incorporating the modified side chain segment and subsequent ring-closure by ring-closing olefin metathesis. The latter proceeded with unfavorable selectivity and in low yield. Distinct differences in chemical behavior were unveiled between the thiophene-derived advanced intermediates and what has been reported for the corresponding thiazole-based congeners. Compared to natural epothilone C, the free energy of binding of deaza-epothilone C to microtubules was reduced by ca. 1 kcal/mol or less, thus indicating a distinct but non-decisive role of the thiazole nitrogen in the interaction of epothilones with the tubulin/microtubule system. In contrast to natural epothilone C, deaza-epothilone C was devoid of antiproliferative activity in vitro up to a concentration of 10 μM, presumably due to an insufficient stability in the cell culture medium. Full article
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Open AccessArticle
Combining the Sensitivity of LAMP and Simplicity of Primer Extension via a DNA-Modified Nucleotide
Chemistry 2020, 2(2), 490-498; https://doi.org/10.3390/chemistry2020029 - 14 May 2020
Viewed by 828
Abstract
LAMP is an approach for isothermal nucleic acids diagnostics with increasing importance but suffers from the need of tedious systems design and optimization for every new target. Here, we describe an approach for its simplification based on a single nucleoside-5′-O-triphosphate (dNTP) that is [...] Read more.
LAMP is an approach for isothermal nucleic acids diagnostics with increasing importance but suffers from the need of tedious systems design and optimization for every new target. Here, we describe an approach for its simplification based on a single nucleoside-5′-O-triphosphate (dNTP) that is covalently modified with a DNA strand. We found that the DNA-modified dNTP is a substrate for DNA polymerases in versatile primer extension reactions despite its size and that the incorporated DNA indeed serves as a target for selective LAMP analysis. Full article
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Open AccessArticle
Oxidative Repair of Pyrimidine Cyclobutane Dimers by Nitrate Radicals (NO3): A Kinetic and Computational Study
Chemistry 2020, 2(2), 453-469; https://doi.org/10.3390/chemistry2020027 - 09 May 2020
Viewed by 714
Abstract
Pyrimidine cyclobutane dimers are hazardous DNA lesions formed upon exposure of DNA to UV light, which can be repaired through oxidative electron transfer (ET). Laser flash photolysis and computational studies were performed to explore the role of configuration and constitution at the cyclobutane [...] Read more.
Pyrimidine cyclobutane dimers are hazardous DNA lesions formed upon exposure of DNA to UV light, which can be repaired through oxidative electron transfer (ET). Laser flash photolysis and computational studies were performed to explore the role of configuration and constitution at the cyclobutane ring on the oxidative repair process, using the nitrate radical (NO3) as oxidant. The rate coefficients of 8–280 × 107 M−1 s−1 in acetonitrile revealed a very high reactivity of the cyclobutane dimers of N,N’-dimethylated uracil (DMU), thymine (DMT), and 6-methyluracil (DMU6-Me) towards NO3, which likely proceeds via ET at N(1) as a major pathway. The overall rate of NO3 consumption was determined by (i) the redox potential, which was lower for the syn- than for the anti-configured dimers, and (ii) the accessibility of the reaction site for NO3. In the trans dimers, both N(1) atoms could be approached from above and below the molecular plane, whereas in the cis dimers, only the convex side was readily accessible for NO3. The higher reactivity of the DMT dimers compared with isomeric DMU dimers was due to the electron-donating methyl groups on the cyclobutane ring, which increased their susceptibility to oxidation. On the other hand, the approach of NO3 to the dimers of DMU6-Me was hindered by the methyl substituents adjacent to N(1), making these dimers the least reactive in this series. Full article
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Open AccessFeature PaperArticle
OH Group Effect in the Stator of β-Diketones Arylhydrazone Rotary Switches
Chemistry 2020, 2(2), 374-389; https://doi.org/10.3390/chemistry2020024 - 04 May 2020
Cited by 1 | Viewed by 1051
Abstract
The properties of several hydrazon-diketone rotary switches with OH groups in the stators (2-(2-(2-hydroxy-4-nitrophenyl)hydrazono)-1-phenylbutane-1,3-dione, 2-(2-(2-hydroxyphenyl)hydrazono)-1-phenylbutane-1,3-dione and 2-(2-(4-hydroxyphenyl)hydrazono)-1-phenylbutane-1,3-dione) were investigated by molecular spectroscopy (UV-Vis and NMR), DFT calculations (M06-2X/TZVP) and X-ray analysis. The results show that, when the OH group is in ortho position, [...] Read more.
The properties of several hydrazon-diketone rotary switches with OH groups in the stators (2-(2-(2-hydroxy-4-nitrophenyl)hydrazono)-1-phenylbutane-1,3-dione, 2-(2-(2-hydroxyphenyl)hydrazono)-1-phenylbutane-1,3-dione and 2-(2-(4-hydroxyphenyl)hydrazono)-1-phenylbutane-1,3-dione) were investigated by molecular spectroscopy (UV-Vis and NMR), DFT calculations (M06-2X/TZVP) and X-ray analysis. The results show that, when the OH group is in ortho position, the E’ and Z’ isomers are preferred in DMSO as a result of a stabilizing intermolecular hydrogen bonding with the solvent. The availability, in addition, of a nitro group in para position increases the possibility of deprotonation of the OH group in the absence of water. All studied compounds showed a tendency towards formation of associates. The structure of the aggregates was revealed by theoretical calculation and confirmed by X-ray analysis. Full article
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Open AccessFeature PaperArticle
Size and Surface Charge Dependent Impregnation of Nanoparticles in Soft- and Hardwood
Chemistry 2020, 2(2), 361-373; https://doi.org/10.3390/chemistry2020023 - 02 May 2020
Viewed by 776
Abstract
Recent progress in wood preservative research has led to the use of insoluble copper carbonate in the form of nano- to micron-sized particles in combination with known triazole fungicides to combat fungal decay and thus decrease physical material properties. Evidently, particle-based agents could [...] Read more.
Recent progress in wood preservative research has led to the use of insoluble copper carbonate in the form of nano- to micron-sized particles in combination with known triazole fungicides to combat fungal decay and thus decrease physical material properties. Evidently, particle-based agents could lead to issues regarding impregnation of a micro-structured material like wood. In this study, we analyzed these limitations via silicon dioxide particles in impregnation experiments of pine and beech wood. In our experiments, we showed that limitations already existed prior to assumed particle size thresholds of 400–600 nm. In pine wood, 70 nm sized particles were efficiently impregnated, in contrast to 170 nm particles. Further we showed that surface functionalized silica nanoparticles have a major impact on the impregnation efficiency. Silica surfaces bearing amino groups were shown to have strong interactions with the wood cell surface, whereas pentyl chains on the SiO2 surfaces tended to lower the particle–wood interaction. The acquired results illustrate an important extension of the currently limited knowledge of nanoparticles and wood impregnation and contribute to future improvements in the field of particle-based wood preservatives. Full article
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Open AccessFeature PaperArticle
A Procedure for Computing Hydrocarbon Strain Energies Using Computational Group Equivalents, with Application to 66 Molecules
Chemistry 2020, 2(2), 347-360; https://doi.org/10.3390/chemistry2020022 - 30 Apr 2020
Viewed by 752
Abstract
A method is presented for the direct computation of hydrocarbon strain energies using computational group equivalents. Parameters are provided at several high levels of electronic structure theory: W1BD, G-4, CBS-APNO, CBS-QB3, and M062X/6-31+G(2df,p). As an illustration of the procedure, strain energies are computed [...] Read more.
A method is presented for the direct computation of hydrocarbon strain energies using computational group equivalents. Parameters are provided at several high levels of electronic structure theory: W1BD, G-4, CBS-APNO, CBS-QB3, and M062X/6-31+G(2df,p). As an illustration of the procedure, strain energies are computed for 66 hydrocarbons, most of them highly strained. Full article
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Open AccessArticle
Towards a Real Knotaxane
Chemistry 2020, 2(2), 305-321; https://doi.org/10.3390/chemistry2020020 - 26 Apr 2020
Viewed by 785
Abstract
Two classes of mechanically interlocked molecules, [3]rotaxanes and knotted [1]rotaxanes, were the subject of this investigation. The necessary building blocks, alkyne-terminated axles containing two ammonium ions and azide-terminated stoppers, and azide-containing substituted macrocycles, have been synthesized and characterized. Different [3]rotaxanes were synthesized by [...] Read more.
Two classes of mechanically interlocked molecules, [3]rotaxanes and knotted [1]rotaxanes, were the subject of this investigation. The necessary building blocks, alkyne-terminated axles containing two ammonium ions and azide-terminated stoppers, and azide-containing substituted macrocycles, have been synthesized and characterized. Different [3]rotaxanes were synthesized by copper-catalyzed “click” reactions between the azide stoppers and [3]pseudorotaxanes formed from the dialkyne axles and crown ethers (DB24C8). Methylation of the triazoles formed by the “click” reaction introduced a second binding site, and switching via deprotonation/protonation was investigated. In preliminary tests for the synthesis of a knotted [1]rotaxane, pseudorotaxanes were formed from azide-containing substituted macrocycles and dialkyne substituted diammonium axles, and copper-catalyzed “click” reactions were carried out. Mass spectral analyses showed successful double “click” reactions between two modified macrocycles and one axle. Whether a knotted [1]rotaxane was formed could not be determined. Full article
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Open AccessFeature PaperArticle
Topological Dynamics of a Radical Ion Pair: Experimental and Computational Assessment at the Relevant Nanosecond Timescale
Chemistry 2020, 2(2), 219-230; https://doi.org/10.3390/chemistry2020014 - 31 Mar 2020
Viewed by 726
Abstract
Chemical processes mostly happen in fluid environments where reaction partners encounter via diffusion. The bimolecular encounters take place at a nanosecond time scale. The chemical environment (e.g., solvent molecules, (counter)ions) has a decisive influence on the reactivity as it determines the contact time [...] Read more.
Chemical processes mostly happen in fluid environments where reaction partners encounter via diffusion. The bimolecular encounters take place at a nanosecond time scale. The chemical environment (e.g., solvent molecules, (counter)ions) has a decisive influence on the reactivity as it determines the contact time between two molecules and affects the energetics. For understanding reactivity at an atomic level and at the appropriate dynamic time scale, it is crucial to combine matching experimental and theoretical data. Here, we have utilized all-atom molecular-dynamics simulations for accessing the key time scale (nanoseconds) using a QM/MM-Hamiltonian. Ion pairs consisting of a radical ion and its counterion are ideal systems to assess the theoretical predictions because they reflect dynamics at an appropriate time scale when studied by temperature-dependent EPR spectroscopy. We have investigated a diketone radical anion with its tetra-ethylammonium counterion. We have established a funnel-like transition path connecting two (equivalent) complexation sites. The agreement between the molecular-dynamics simulation and the experimental data presents a new paradigm for ion–ion interactions. This study exemplarily demonstrates the impact of the molecular environment on the topological states of reaction intermediates and how these states can be consistently elucidated through the combination of theory and experiment. We anticipate that our findings will contribute to the prediction of bimolecular transformations in the condensed phase with relevance to chemical synthesis, polymers, and biological activity. Full article
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Open AccessFeature PaperArticle
Appropriate Buffers for Studying the Bioinorganic Chemistry of Silver(I)
Chemistry 2020, 2(1), 193-202; https://doi.org/10.3390/chemistry2010012 - 22 Mar 2020
Viewed by 917
Abstract
Silver(I) is being largely studied for its antimicrobial properties. In parallel to that growing interest, some researchers are investigating the effect of this ion on eukaryotes and the mechanism of silver resistance of certain bacteria. For these studies, and more generally in biology, [...] Read more.
Silver(I) is being largely studied for its antimicrobial properties. In parallel to that growing interest, some researchers are investigating the effect of this ion on eukaryotes and the mechanism of silver resistance of certain bacteria. For these studies, and more generally in biology, it is necessary to work in buffer systems that are most suitable, i.e., that interact least with silver cations. Selected buffers such as 4-(2-hydroxyethyl)-1-piperazineethane sulfonic acid (HEPES) were therefore investigated for their use in the presence of silver nitrate. Potentiometric titrations allowed to determine stability constants for the formation of (Ag(Buffer)) complexes. The obtained values were adapted to extract the apparent binding constants at physiological pH. The percentage of metal ions bound to the buffer was calculated at this pH for given concentrations of buffer and silver to realize at which extent silver was interacting with the buffer. We found that in the micromolar range, HEPES buffer is sufficiently coordinating to silver to have a non-negligible effect on the thermodynamic parameters determined for an analyte. Morpholinic buffers were more suitable as they turned out to be weaker complexing agents. We thus recommend the use of MOPS for studies of physiological pH. Full article
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Review

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Open AccessReview
Giant Polymer Compartments for Confined Reactions
Chemistry 2020, 2(2), 470-489; https://doi.org/10.3390/chemistry2020028 - 12 May 2020
Viewed by 1529
Abstract
In nature, various specific reactions only occur in spatially controlled environments. Cell compartment and subcompartments act as the support required to preserve the bio-specificity and functionality of the biological content, by affording absolute segregation. Inspired by this natural perfect behavior, bottom-up approaches are [...] Read more.
In nature, various specific reactions only occur in spatially controlled environments. Cell compartment and subcompartments act as the support required to preserve the bio-specificity and functionality of the biological content, by affording absolute segregation. Inspired by this natural perfect behavior, bottom-up approaches are on focus to develop artificial cell-like structures, crucial for understanding relevant bioprocesses and interactions or to produce tailored solutions in the field of therapeutics and diagnostics. In this review, we discuss the benefits of constructing polymer-based single and multicompartments (capsules and giant unilamellar vesicles (GUVs)), equipped with biomolecules as to mimic cells. In this respect, we outline key examples of how such structures have been designed from scratch, namely, starting from the application-oriented selection and synthesis of the amphiphilic block copolymer. We then present the state-of-the-art techniques for assembling the supramolecular structure while permitting the encapsulation of active compounds and the incorporation of peptides/membrane proteins, essential to support in situ reactions, e.g., to replicate intracellular signaling cascades. Finally, we briefly discuss important features that these compartments offer and how they could be applied to engineer the next generation of microreactors, therapeutic solutions, and cell models. Full article
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Open AccessFeature PaperReview
Recent Studies on the Antimicrobial Activity of Transition Metal Complexes of Groups 6–12
Chemistry 2020, 2(2), 418-452; https://doi.org/10.3390/chemistry2020026 - 09 May 2020
Cited by 5 | Viewed by 1189
Abstract
Antimicrobial resistance is an increasingly serious threat to global public health that requires innovative solutions to counteract new resistance mechanisms emerging and spreading globally in infectious pathogens. Classic organic antibiotics are rapidly exhausting the structural variations available for an effective antimicrobial drug and [...] Read more.
Antimicrobial resistance is an increasingly serious threat to global public health that requires innovative solutions to counteract new resistance mechanisms emerging and spreading globally in infectious pathogens. Classic organic antibiotics are rapidly exhausting the structural variations available for an effective antimicrobial drug and new compounds emerging from the industrial pharmaceutical pipeline will likely have a short-term and limited impact before the pathogens can adapt. Inorganic and organometallic complexes offer the opportunity to discover and develop new active antimicrobial agents by exploiting their wide range of three-dimensional geometries and virtually infinite design possibilities that can affect their substitution kinetics, charge, lipophilicity, biological targets and modes of action. This review describes recent studies on the antimicrobial activity of transition metal complexes of groups 6–12. It focuses on the effectiveness of the metal complexes in relation to the rich structural chemical variations of the same. The aim is to provide a short vade mecum for the readers interested in the subject that can complement other reviews. Full article
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Open AccessFeature PaperReview
Reactive Sterol Electrophiles: Mechanisms of Formation and Reactions with Proteins and Amino Acid Nucleophiles
Chemistry 2020, 2(2), 390-417; https://doi.org/10.3390/chemistry2020025 - 06 May 2020
Cited by 6 | Viewed by 1034
Abstract
Radical-mediated lipid oxidation and the formation of lipid hydroperoxides has been a focal point in the investigation of a number of human pathologies. Lipid peroxidation has long been linked to the inflammatory response and more recently, has been identified as the central tenet [...] Read more.
Radical-mediated lipid oxidation and the formation of lipid hydroperoxides has been a focal point in the investigation of a number of human pathologies. Lipid peroxidation has long been linked to the inflammatory response and more recently, has been identified as the central tenet of the oxidative cell death mechanism known as ferroptosis. The formation of lipid electrophile-protein adducts has been associated with many of the disorders that involve perturbations of the cellular redox status, but the identities of adducted proteins and the effects of adduction on protein function are mostly unknown. Both cholesterol and 7-dehydrocholesterol (7-DHC), which is the immediate biosynthetic precursor to cholesterol, are oxidizable by species such as ozone and oxygen-centered free radicals. Product mixtures from radical chain processes are particularly complex, with recent studies having expanded the sets of electrophilic compounds formed. Here, we describe recent developments related to the formation of sterol-derived electrophiles and the adduction of these electrophiles to proteins. A framework for understanding sterol peroxidation mechanisms, which has significantly advanced in recent years, as well as the methods for the study of sterol electrophile-protein adduction, are presented in this review. Full article
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Open AccessReview
Natural and Engineered Electron Transfer of Nitrogenase
Chemistry 2020, 2(2), 322-346; https://doi.org/10.3390/chemistry2020021 - 27 Apr 2020
Cited by 2 | Viewed by 1310
Abstract
As the only enzyme currently known to reduce dinitrogen (N2) to ammonia (NH3), nitrogenase is of significant interest for bio-inspired catalyst design and for new biotechnologies aiming to produce NH3 from N2. In order to reduce [...] Read more.
As the only enzyme currently known to reduce dinitrogen (N2) to ammonia (NH3), nitrogenase is of significant interest for bio-inspired catalyst design and for new biotechnologies aiming to produce NH3 from N2. In order to reduce N2, nitrogenase must also hydrolyze at least 16 equivalents of adenosine triphosphate (MgATP), representing the consumption of a significant quantity of energy available to biological systems. Here, we review natural and engineered electron transfer pathways to nitrogenase, including strategies to redirect or redistribute electron flow in vivo towards NH3 production. Further, we also review strategies to artificially reduce nitrogenase in vitro, where MgATP hydrolysis is necessary for turnover, in addition to strategies that are capable of bypassing the requirement of MgATP hydrolysis to achieve MgATP-independent N2 reduction. Full article
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Open AccessFeature PaperReview
Before Radicals Were Free – the Radical Particulier of de Morveau
Chemistry 2020, 2(2), 293-304; https://doi.org/10.3390/chemistry2020019 - 20 Apr 2020
Viewed by 898
Abstract
Today, we universally understand radicals to be chemical species with an unpaired electron. It was not always so, and this article traces the evolution of the term radical and in this journey, monitors the development of some of the great theories of organic [...] Read more.
Today, we universally understand radicals to be chemical species with an unpaired electron. It was not always so, and this article traces the evolution of the term radical and in this journey, monitors the development of some of the great theories of organic chemistry. Full article
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Open AccessFeature PaperReview
Amino Acids and Peptides as Versatile Ligands in the Synthesis of Antiproliferative Gold Complexes
Chemistry 2020, 2(2), 203-218; https://doi.org/10.3390/chemistry2020013 - 27 Mar 2020
Cited by 2 | Viewed by 956
Abstract
Gold complexes have been traditionally employed in medicine, and currently, some gold(I) complexes, such as auranofin, are clinically used in the treatment of rheumatoid arthritis. In the last decades, both gold(I) and gold(III) complexes with different types of ligands have gained considerable attention [...] Read more.
Gold complexes have been traditionally employed in medicine, and currently, some gold(I) complexes, such as auranofin, are clinically used in the treatment of rheumatoid arthritis. In the last decades, both gold(I) and gold(III) complexes with different types of ligands have gained considerable attention as potential antitumor agents, showing superior activity both in vitro and in vivo to some of the clinically used agents. The present review article summarizes the results achieved in the field of synthesis and evaluation of gold complexes with amino acids and peptides moieties for their cytotoxicity. The first section provides an overview of the gold(I) complexes with amino acids and peptides, which have shown antiproliferative activity, while the second part is focused on the activity of gold(III) complexes with these ligands. A systematic summary of the results achieved in the field of gold(I/III) complexes with amino acids and peptides could contribute to the future development of metal complexes with these biocompatible ligands as promising antitumor agents. Full article
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Open AccessFeature PaperReview
Addition of Heteroatom Radicals to endo-Glycals
Chemistry 2020, 2(1), 80-92; https://doi.org/10.3390/chemistry2010008 - 20 Feb 2020
Cited by 1 | Viewed by 906
Abstract
Radical reactions have found many applications in carbohydrate chemistry, especially in the construction of carbon–carbon bonds. The formation of carbon–heteroatom bonds has been less intensively studied. This mini-review will summarize the efforts to add heteroatom radicals to unsaturated carbohydrates like endo-glycals. Starting [...] Read more.
Radical reactions have found many applications in carbohydrate chemistry, especially in the construction of carbon–carbon bonds. The formation of carbon–heteroatom bonds has been less intensively studied. This mini-review will summarize the efforts to add heteroatom radicals to unsaturated carbohydrates like endo-glycals. Starting from early examples, developed more than 50 years ago, the importance of such reactions for carbohydrate chemistry and recent applications will be discussed. After a short introduction, the mini-review is divided in sub-chapters according to the heteroatoms halogen, nitrogen, phosphorus, and sulfur. The mechanisms of radical generation by chemical or photochemical processes and the subsequent reactions of the radicals at the 1-position will be discussed. This mini-review cannot cover all aspects of heteroatom-centered radicals in carbohydrate chemistry, but should provide an overview of the various strategies and future perspectives. Full article
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