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Chemistry, Volume 2, Issue 2 (June 2020) – 25 articles

Cover Story (view full-size image): The structures and properties of rotary switches bearing an OH group in the stator have been investigated through the combined use of molecular spectroscopy (UV–Vis, NMR), DFT calculations, and X-ray analysis. The position of the OH group determines the isomerization ratio, aggregation pattern, and the extent of deprotonation in proton acceptor solvents. View this paper.
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13 pages, 2329 KiB  
Article
Synthesis of Naphthoxazinones in a One-Pot Two-Step Manner by the Application of Propylphosphonic Anhydride (T3P®)
by Valentina Varga, Péter Ábrányi-Balogh and Mátyás Milen
Chemistry 2020, 2(2), 600-612; https://doi.org/10.3390/chemistry2020037 - 16 Jun 2020
Cited by 1 | Viewed by 3690
Abstract
A sequential one-pot two-step protocol has been elaborated for the synthesis of naphthoxazinones from 2-naphthol, methyl carbamate, and aromatic aldehydes. First, a three-component reaction was optimized with the dehydrating additive propylphosphonic anhydride (T3P®), resulting in 1-carbamatoalkyl 2-naphthols in good to excellent [...] Read more.
A sequential one-pot two-step protocol has been elaborated for the synthesis of naphthoxazinones from 2-naphthol, methyl carbamate, and aromatic aldehydes. First, a three-component reaction was optimized with the dehydrating additive propylphosphonic anhydride (T3P®), resulting in 1-carbamatoalkyl 2-naphthols in good to excellent yields. Following the successful multicomponent approach, intramolecular acylation was performed at high temperature, again with the contribution of T3P®, resulting in naphthoxazinone derivatives in moderate yields. These two steps were optimized together in one-pot as well, and the sequential rise in the requisite temperature eventuated the optimal procedure for the multistep cascade. Full article
(This article belongs to the Special Issue Organic Chemistry Research in Hungary)
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9 pages, 1690 KiB  
Article
Synthesis and Crystallographic Characterization of X-Substituted 2,4-Dinitrophenyl-4′-phenylbenzenesulfonates
by Brock A. Stenfors, Richard J. Staples, Shannon M. Biros and Felix N. Ngassa
Chemistry 2020, 2(2), 591-599; https://doi.org/10.3390/chemistry2020036 - 15 Jun 2020
Cited by 5 | Viewed by 3363
Abstract
Treatment of 2,4-dinitrophenol with sulfonyl chlorides in the presence of pyridine results in the formation of undesired pyridinium salts. In non-aqueous environments, the formation of the insoluble pyridinium salt greatly affects the formation of the desired product. A facile method of producing the [...] Read more.
Treatment of 2,4-dinitrophenol with sulfonyl chlorides in the presence of pyridine results in the formation of undesired pyridinium salts. In non-aqueous environments, the formation of the insoluble pyridinium salt greatly affects the formation of the desired product. A facile method of producing the desired sulfonate involves the use of an aqueous base with a water-miscible solvent. Herein, we present the optimization of methods for the formation of sulfonates and its application in the production of desired x-substituted 2,4-dinitrophenyl-4′-phenylbenzenesulfonates. This strategy is environmentally benign and supports a wide range of starting materials. Additionally, the intermolecular interactions of these sulfonate compounds were investigated using single-crystal x-ray diffraction data. Full article
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14 pages, 3195 KiB  
Article
Complementarity in Cyclotricatechylene Assemblies: Symmetric Cages Linked within 3D Cubic Hydrogen Bonded Networks
by Jessica L. Holmes, Steven M. Russell, Brendan F. Abrahams, Timothy A. Hudson and Keith F. White
Chemistry 2020, 2(2), 577-590; https://doi.org/10.3390/chemistry2020035 - 11 Jun 2020
Cited by 1 | Viewed by 2738
Abstract
A serendipitous discovery has led to the generation of a family of four compounds in which six components combine to form symmetric metal-cyclotricatechylene (H6ctc) cages. The four compounds, which have the compositions, [Cs((CH3)2CO)6][K4(H [...] Read more.
A serendipitous discovery has led to the generation of a family of four compounds in which six components combine to form symmetric metal-cyclotricatechylene (H6ctc) cages. The four compounds, which have the compositions, [Cs((CH3)2CO)6][K4(H6ctc)4(H2O)8][Cs4(H2O)6](PO4)3, [Rb((CH3)2CO)6][Rb2K2(H6ctc)4(H2O)6][Rb4(H2O)6](PO4)3, [Cs((CH3)2CO)6][K4(H6ctc)4(H2O)8]-[Cs(H2O)9](SO4)3 and [Rb((CH3)2CO)6][Rb2K2(H6ctc)4(H2O)6][Rb(H2O)9](SO4)3 possess cubic symmetry that arises from the complementary interactions that govern the assembly of the components. The cage cavities contain water molecules and either one or four large alkali metal ions (either Rb+ or Cs+) which interact with the internal aromatic surfaces of the cage. Each cage is linked to six tetrahedral anions (PO43− or SO42−) through 24 equivalent hydrogen bonds and each anion bridges a pair of cages through eight such hydrogen bonds. An unusual octahedral complex M((CH3)2CO)6+ (M = Rb or Cs), in which the M-C=O link is linear, appears to be a key structural component. A feature of this family of crystalline compounds is the presence of a range of complementary interactions which combine to generate materials that exhibit high crystallographic symmetry. Full article
(This article belongs to the Special Issue Supramolecular Chemistry in the 3rd Millennium)
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12 pages, 3226 KiB  
Review
Combining Coordination and Hydrogen Bonds to Develop Discrete Supramolecular Metalla-Assemblies
by Bruno Therrien
Chemistry 2020, 2(2), 565-576; https://doi.org/10.3390/chemistry2020034 - 08 Jun 2020
Cited by 11 | Viewed by 3246
Abstract
In Nature, metal ions play critical roles at different levels, and they are often found in proteins. Therefore, metal ions are naturally incorporated in hydrogen-bonded systems. In addition, the combination of metal coordination and hydrogen bonds have been used extensively to develop supramolecular [...] Read more.
In Nature, metal ions play critical roles at different levels, and they are often found in proteins. Therefore, metal ions are naturally incorporated in hydrogen-bonded systems. In addition, the combination of metal coordination and hydrogen bonds have been used extensively to develop supramolecular materials. However, despite this win-win combination between coordination and hydrogen bonds in many supramolecular systems, the same combination remains scarce in the field of coordination-driven self-assemblies. Indeed, as illustrated in this mini-review, only a few discrete supramolecular metalla-assemblies combining coordination and hydrogen bonds can be found in the literature, but that figure might change rapidly. Full article
(This article belongs to the Special Issue Supramolecular Chemistry in the 3rd Millennium)
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20 pages, 5439 KiB  
Article
The Photophysical Properties of Triisopropylsilyl-ethynylpentacene—A Molecule with an Unusually Large Singlet-Triplet Energy Gap—In Solution and Solid Phases
by Fabio A. Schaberle, Carlos Serpa, Luis G. Arnaut, Andrew D. Ward, Joshua K. G. Karlsson, Alparslan Atahan and Anthony Harriman
Chemistry 2020, 2(2), 545-564; https://doi.org/10.3390/chemistry2020033 - 03 Jun 2020
Cited by 14 | Viewed by 4525
Abstract
The process of singlet-exciton fission (SEF) has attracted much attention of late. One of the most popular SEF compounds is TIPS-pentacene (TIPS-P, where TIPS = triisopropylsilylethynyl) but, despite its extensive use as both a reference and building block, its photophysical properties are not [...] Read more.
The process of singlet-exciton fission (SEF) has attracted much attention of late. One of the most popular SEF compounds is TIPS-pentacene (TIPS-P, where TIPS = triisopropylsilylethynyl) but, despite its extensive use as both a reference and building block, its photophysical properties are not so well established. In particular, the triplet state excitation energy remains uncertain. Here, we report quantitative data and spectral characterization for excited-singlet and -triplet states in dilute solution. The triplet energy is determined to be 7940 ± 1200 cm−1 on the basis of sensitization studies using time-resolved photoacoustic calorimetry. The triplet quantum yield at the limit of low concentration and low laser intensity is only ca. 1%. Self-quenching occurs at high solute concentration where the fluorescence yield and lifetime decrease markedly relative to dilute solution but we were unable to detect excimer emission by steady-state spectroscopy. Short-lived fluorescence, free from excimer emission or phosphorescence, occurs for crystals of TIPS-P, most likely from amorphous domains. Full article
(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)
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20 pages, 3245 KiB  
Article
Solvent Effect on the Regulation of Urea Hydrolysis Reactions by Copper Complexes
by Caio B. Castro, Rafael G. Silveira, Felippe M. Colombari, André Farias de Moura, Otaciro R. Nascimento and Caterina G. C. Marques Netto
Chemistry 2020, 2(2), 525-544; https://doi.org/10.3390/chemistry2020032 - 02 Jun 2020
Cited by 3 | Viewed by 4533
Abstract
Abiotic allosterism is most commonly observed in hetero-bimetallic supramolecular complexes and less frequently in homo-bimetallic complexes. The use of hemilabile ligands with high synthetic complexity enables the catalytic center by the addition or removal of allosteric effectors and simplicity is unusually seen in [...] Read more.
Abiotic allosterism is most commonly observed in hetero-bimetallic supramolecular complexes and less frequently in homo-bimetallic complexes. The use of hemilabile ligands with high synthetic complexity enables the catalytic center by the addition or removal of allosteric effectors and simplicity is unusually seen in these systems. Here we describe a simpler approach to achieve kinetic regulation by the use of dimeric Schiff base copper complexes connected by a chlorido ligand bridge. The chlorido ligand acts as a weak link between monomers, generating homo-bimetallic self-aggregating supramolecular complexes that generate monomeric species in different reaction rates depending on the solvent and on the radical moiety of the ligand. The ligand exchange was observed by electron paramagnetic resonance (EPR) and conductivity measurements, indicating that complexes with ligands bearing methoxyl (CuIIL2) and ethoxyl (CuIIL5) radicals were more prone to form dimeric complexes in comparison to ligands bearing hydrogen (CuIIL1), methyl (CuIIL3), or t-butyl (CuIIL4) radicals. The equilibrium between dimer and monomer afforded different reactivities of the complexes in acetonitrile/water and methanol/water mixtures toward urea hydrolysis as a model reaction. It was evident that the dimeric species were inactive and that by increasing the water concentration in the reaction medium, the dimeric structures dissociated to form the active monomeric structures. This behavior was more pronounced when methanol/water mixtures were employed due to a slower displacement of the chlorido bridge in this medium than in the acetonitrile/water mixtures, enabling the reaction kinetics to be evaluated. This effect was attributed to the preferential solvation shell by the organic solvents and in essence, an upregulation behavior was observed due to the intrinsic nature of the complexes to form dimeric structures in solution that could be dismantled in the presence of water, indicating their possible use as water-sensors in organic solvents. Full article
(This article belongs to the Special Issue Supramolecular Chemistry in the 3rd Millennium)
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15 pages, 4670 KiB  
Article
Interactions of Small-Molecule Guests with Interior and Exterior Surfaces of a Coordination Cage Host
by Christopher G. P. Taylor, Jennifer S. Train and Michael D. Ward
Chemistry 2020, 2(2), 510-524; https://doi.org/10.3390/chemistry2020031 - 02 Jun 2020
Cited by 8 | Viewed by 4169
Abstract
Coordination cages are well-known to act as molecular containers that can bind small-molecule guests in their cavity. Such cavity binding is associated with interactions of the guests with the surrounding set of surfaces that define the cavity; a guest that is a good [...] Read more.
Coordination cages are well-known to act as molecular containers that can bind small-molecule guests in their cavity. Such cavity binding is associated with interactions of the guests with the surrounding set of surfaces that define the cavity; a guest that is a good fit for the cavity will have many favourable interactions with the interior surfaces of the host. As cages have exterior as well as interior surfaces, possibilities also exist for ‘guests’ that are not well-bound in the cavity to interact with the exterior surface of the cage where spatial constraints are fewer. In this paper, we report a combined solid-state and solution study using an octanuclear cubic M8L12 coordination cage which illustrates the occurrence of both types of interaction. Firstly, crystallographic studies show that a range of guests bind inside the cavity (either singly or in stacked pairs) and/or interact with the cage exterior surface, depending on their size. Secondly, fluorescence titrations in aqueous solution show how some flexible aromatic disulfides show two separate types of interaction with the cage, having different spectroscopic consequences; we ascribe this to separate interactions with the exterior surface and the interior surface of the host cage with the former having a higher binding constant. Overall, it is clear that the idea of host/guest interactions in molecular containers needs to take more account of external surface interactions as well as the obvious cavity-based binding. Full article
(This article belongs to the Special Issue 2020 Profile Papers by Chemistry' Editorial Board Members)
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11 pages, 1804 KiB  
Article
On the Importance of the Thiazole Nitrogen in Epothilones: Semisynthesis and Microtubule-Binding Affinity of Deaza-Epothilone C
by Adriana Edenharter, Lucie Ryckewaert, Daniela Cintulová, Juan Estévez-Gallego, José Fernando Díaz and Karl-Heinz Altmann
Chemistry 2020, 2(2), 499-509; https://doi.org/10.3390/chemistry2020030 - 23 May 2020
Viewed by 2902
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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10 pages, 1301 KiB  
Article
Combining the Sensitivity of LAMP and Simplicity of Primer Extension via a DNA-Modified Nucleotide
by Moritz Welter and Andreas Marx
Chemistry 2020, 2(2), 490-498; https://doi.org/10.3390/chemistry2020029 - 14 May 2020
Viewed by 3252
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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20 pages, 4512 KiB  
Review
Giant Polymer Compartments for Confined Reactions
by Elena C. dos Santos, Alessandro Angelini, Dimitri Hürlimann, Wolfgang Meier and Cornelia G. Palivan
Chemistry 2020, 2(2), 470-489; https://doi.org/10.3390/chemistry2020028 - 12 May 2020
Cited by 6 | Viewed by 5174
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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17 pages, 3144 KiB  
Article
Oxidative Repair of Pyrimidine Cyclobutane Dimers by Nitrate Radicals (NO3): A Kinetic and Computational Study
by Tomas Haddad, Joses G. Nathanael, Jonathan M. White and Uta Wille
Chemistry 2020, 2(2), 453-469; https://doi.org/10.3390/chemistry2020027 - 09 May 2020
Viewed by 2476
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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35 pages, 4076 KiB  
Review
Recent Studies on the Antimicrobial Activity of Transition Metal Complexes of Groups 6–12
by Sara Nasiri Sovari and Fabio Zobi
Chemistry 2020, 2(2), 418-452; https://doi.org/10.3390/chemistry2020026 - 09 May 2020
Cited by 70 | Viewed by 8210
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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28 pages, 3474 KiB  
Review
Reactive Sterol Electrophiles: Mechanisms of Formation and Reactions with Proteins and Amino Acid Nucleophiles
by Ned A. Porter, Libin Xu and Derek A. Pratt
Chemistry 2020, 2(2), 390-417; https://doi.org/10.3390/chemistry2020025 - 06 May 2020
Cited by 17 | Viewed by 5134
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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16 pages, 6443 KiB  
Article
OH Group Effect in the Stator of β-Diketones Arylhydrazone Rotary Switches
by Silvia Hristova, Fadhil S. Kamounah, Aurelien Crochet, Nikolay Vassilev, Katharina M. Fromm and Liudmil Antonov
Chemistry 2020, 2(2), 374-389; https://doi.org/10.3390/chemistry2020024 - 04 May 2020
Cited by 4 | Viewed by 2813
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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13 pages, 4224 KiB  
Article
Size and Surface Charge Dependent Impregnation of Nanoparticles in Soft- and Hardwood
by David Bossert, Christoph Geers, Maria Inés Placencia Peña, Thomas Volkmer, Barbara Rothen-Rutishauser and Alke Petri-Fink
Chemistry 2020, 2(2), 361-373; https://doi.org/10.3390/chemistry2020023 - 02 May 2020
Cited by 4 | Viewed by 2961
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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12 pages, 1397 KiB  
Article
A Procedure for Computing Hydrocarbon Strain Energies Using Computational Group Equivalents, with Application to 66 Molecules
by Paul R. Rablen
Chemistry 2020, 2(2), 347-360; https://doi.org/10.3390/chemistry2020022 - 30 Apr 2020
Cited by 17 | Viewed by 3971
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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24 pages, 2669 KiB  
Review
Natural and Engineered Electron Transfer of Nitrogenase
by Wenyu Gu and Ross D. Milton
Chemistry 2020, 2(2), 322-346; https://doi.org/10.3390/chemistry2020021 - 27 Apr 2020
Cited by 11 | Viewed by 5546
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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16 pages, 3401 KiB  
Article
Towards a Real Knotaxane
by Torben Duden and Ulrich Lüning
Chemistry 2020, 2(2), 305-321; https://doi.org/10.3390/chemistry2020020 - 26 Apr 2020
Cited by 1 | Viewed by 3068
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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12 pages, 1908 KiB  
Review
Before Radicals Were Free – the Radical Particulier of de Morveau
by Edwin C. Constable and Catherine E. Housecroft
Chemistry 2020, 2(2), 293-304; https://doi.org/10.3390/chemistry2020019 - 20 Apr 2020
Cited by 3 | Viewed by 4412
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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19 pages, 3895 KiB  
Article
Metals, n-Alkanes, Hopanes, and Polycyclic Aromatic Hydrocarbon in Sediments from Three Amazonian Streams Crossing Manaus (Brazil)
by Moacir G. de Melo, Leonildo G. de Castro, Laís A. Reis, Gilcllys de S. Costa, Felipe M. A. da Silva, Marcos A. Bolson, Jamal da S. Chaar, Hector H. F. Koolen, Ézio Sargentini Junior and Giovana A. Bataglion
Chemistry 2020, 2(2), 274-292; https://doi.org/10.3390/chemistry2020018 - 18 Apr 2020
Cited by 6 | Viewed by 3127
Abstract
Pollution is increasing in the Amazon region and its real impact is still unclear. Since this region is of great interest to the global community, this study aimed to assess geochemical biomarkers and metals in sediments from three streams crossing Manaus, a Brazilian [...] Read more.
Pollution is increasing in the Amazon region and its real impact is still unclear. Since this region is of great interest to the global community, this study aimed to assess geochemical biomarkers and metals in sediments from three streams crossing Manaus, a Brazilian city of 2.1 million inhabitants located in the heart of the Amazon rainforest. The Mindu and Quarenta streams criss-cross the urban area of Manaus and receive domestic effluents from many heavily populated districts. In addition, the Quarenta stream is subjected to effluents from the industrial district of Manaus. The Tarumã-Açu stream is mostly covered by vegetation, although the region presents some occurrence of family farming, floating petrol station, marinas, and floating restaurants and bars. n-Alkanes were determined by Gas Chromatography with Flame Ionization Detection (GC-FID), whereas hopanes and polycyclic aromatic hydrocarbons (PAHs) were determined by Gas Chromatography coupled to Mass Spectrometry (GC-MS). The metals Ag, Cd, Cr, Co, Cu, Mn, Ni, Pb, and Zn were determined by Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES) after microwave-assisted acid digestion. Concentrations of total PAHs and metals were higher in sediments from the urban streams Mindu and Quarenta because of the occurrence of more intense and diverse sources of pollution. In addition, some sediment samples from both these streams presented concentrations of fluoranthene, phenanthrene, and metals higher than the limits of low probability of adverse effects on biota established by the international guideline and by the Brazilian legislation. A similar total n-alkane concentration for sediments from all streams associated with profiles of n-alkanes with no odd/even hydrocarbon predominance suggests that biomass burning is an important source of hydrocarbons. Petroleum-derived products also represented a source for n-alkanes, as confirmed by the presence of α,β-hopanes, including an α,β-homohopane series from C31 to C35 with the presence of both 22S and 22R epimers. This is the first report on n-alkanes, PAHs, and hopanes in sediments from the Mindu, Quarenta, and Tarumã-Açu streams. The concentrations reported herein may be considered as baseline data in future monitoring programs of these streams. Full article
(This article belongs to the Section Green and Environmental Chemistry)
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12 pages, 3227 KiB  
Article
A Study of the Interaction between Cucurbit[7]uril and Alkyl Substituted 4-Pyrrolidinopyridinium Salts
by Weitao Xu, Xinyi Zhu, Bing Bian, Xin Xiao, Zhu Tao and Carl Redshaw
Chemistry 2020, 2(2), 262-273; https://doi.org/10.3390/chemistry2020017 - 14 Apr 2020
Cited by 4 | Viewed by 2280
Abstract
The interaction between cucurbit[7]uril (Q[7]) and a series of 4-pyrrolidinopyridinium salts bearing aliphatic substituents at the pyridinium nitrogen, namely 4-(C4H8N)C5H5NRBr, where R = H (C0), Et (C2), n-butyl (C4), n-hexyl (C6), has been [...] Read more.
The interaction between cucurbit[7]uril (Q[7]) and a series of 4-pyrrolidinopyridinium salts bearing aliphatic substituents at the pyridinium nitrogen, namely 4-(C4H8N)C5H5NRBr, where R = H (C0), Et (C2), n-butyl (C4), n-hexyl (C6), has been studied in aqueous solution by 1H NMR spectroscopy, electronic absorption spectroscopy, and mass spectrometry. Full article
(This article belongs to the Special Issue Supramolecular Chemistry in the 3rd Millennium)
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9 pages, 2949 KiB  
Communication
A Brucite-Like Mixed-Valent Cluster Capped by [MnIIIp-tBu-calix[4]arene] Moieties
by Marco Coletta, Maria A. Palacios, Euan K. Brechin and Scott J. Dalgarno
Chemistry 2020, 2(2), 253-261; https://doi.org/10.3390/chemistry2020016 - 09 Apr 2020
Cited by 2 | Viewed by 3126
Abstract
p-tBu-calix[4]arene (H4TBC[4]) has proven to be an incredibly versatile ligand for the synthesis of 3d- and 3d/4f- clusters, in particular those containing mixed-valent Mn ions. These are of interest to the magnetochemist [...] Read more.
p-tBu-calix[4]arene (H4TBC[4]) has proven to be an incredibly versatile ligand for the synthesis of 3d- and 3d/4f- clusters, in particular those containing mixed-valent Mn ions. These are of interest to the magnetochemist for the diversity of magnetic behaviours that can be shown, along with a huge variety of nuclearities and topologies accessible, which allow one to outline magneto-structural correlations and a quantitative understanding of their properties. This contribution reports the synthesis, analysis and magnetic properties of a Brucite-like Mn-oxo/hydroxo octanuclear fragment encapsulated within/capped by four [MnIII-TBC[4]] moieties. A diol coligand in the reaction mixture plays a seemingly important role in determining the outcome, though it is not incorporated in the final structure. Full article
(This article belongs to the Special Issue Supramolecular Chemistry in the 3rd Millennium)
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22 pages, 5528 KiB  
Article
The Tyranny of Arm-Wrestling Methyls on Iron(II) Spin State in Pseudo-Octahedral [Fe(didentate)3] Complexes
by Neel Deorukhkar, Timothée Lathion, Laure Guénée, Céline Besnard and Claude Piguet
Chemistry 2020, 2(2), 231-252; https://doi.org/10.3390/chemistry2020015 - 02 Apr 2020
Cited by 2 | Viewed by 3967
Abstract
The connection of a sterically constrained 3-methyl-pyrazine ring to a N-methyl-benzimidazole unit to give the unsymmetrical α,α’-diimine ligand L5 has been programmed for the design of pseudo-octahedral spin-crossover [Fe(L5)3]2+ units, the transition temperature (T1/2) [...] Read more.
The connection of a sterically constrained 3-methyl-pyrazine ring to a N-methyl-benzimidazole unit to give the unsymmetrical α,α’-diimine ligand L5 has been programmed for the design of pseudo-octahedral spin-crossover [Fe(L5)3]2+ units, the transition temperature (T1/2) of which occurs in between those reported for related facial tris-didentate iron chromophores fitted with 3-methyl-pyridine-benzimidazole in a LaFe helicate (T1/2 ~ 50 K) and with 5-methyl-pyrazine-benzimidazole L2 ligands (T1/2 ~350 K). A thorough crystallographic analysis of [Fe(L5)3](ClO4)2 (I), [Ni(L5)3](ClO4)2 (II), [Ni(L5)3](BF4)2∙H2O (III), [Zn(L5)3](ClO4)2 (IV), [Ni(L5)3](BF4)2∙1.75CH3CN (V), and [Zn(L5)3](BF4)2∙1.5CH3CN (VI) shows the selective formation of pure facial [M(L5)3]2+ cations in the solvated crystals of the tetrafluoroborate salts and alternative meridional isomers in the perchlorate salts. Except for a slightly larger intra-strand interannular twist between the aromatic heterocycles in L5, the metric parameters measured in [Zn(L5)3]2+ are comparable to those reported for [Zn(L2)3]2+, where L2 is the related unconstrained ligand. This similitude is reinforced by comparable ligand-field strengths (∆oct) and nephelauxetic effects (as measured by the Racah parameters B and C) extracted from the electronic absorption spectra recorded for [Ni(L5)3]2+ and [Ni(L2)3]2+. In this context, the strictly high-spin behavior observed for [Fe(L5)3]2+ within the 5–300 K range contrasts with the close to room-temperature spin-crossover behavior of [Fe(L2)3]2+ (T1/2 = 349(5) K in acetonitrile). This can be unambiguously assigned to an intraligand arm wrestling match operating in bound L5, which prevents the contraction of the coordination sphere required for accommodating low-spin FeII. Since the analogous 3-methyl-pyridine ring in [Fe(L3)3]2+ derivatives are sometimes compatible with spin-crossover properties, the consequences of repulsive intra-strand methyl–methyl interactions are found to be amplified in [Fe(L5)3]2+ because of the much lower basicity of the 3-methyl-pyrazine ring and the resulting weaker thermodynamic compensation. The decrease of the stability constants by five orders of magnitude observed in going from [M(L2)3]2+ to [M(L5)3]2+ (M = NiII and ZnII) is diagnostic for the operation of this effect, which had been not foreseen by the authors. Full article
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12 pages, 2726 KiB  
Article
Topological Dynamics of a Radical Ion Pair: Experimental and Computational Assessment at the Relevant Nanosecond Timescale
by Helmut Quast, Georg Gescheidt and Martin Spichty
Chemistry 2020, 2(2), 219-230; https://doi.org/10.3390/chemistry2020014 - 31 Mar 2020
Viewed by 2782
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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16 pages, 3713 KiB  
Review
Amino Acids and Peptides as Versatile Ligands in the Synthesis of Antiproliferative Gold Complexes
by Tina P. Andrejević, Biljana Đ. Glišić and Miloš I. Djuran
Chemistry 2020, 2(2), 203-218; https://doi.org/10.3390/chemistry2020013 - 27 Mar 2020
Cited by 9 | Viewed by 3047
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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