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Solvent Stabilization of Protic Oxonium/Ammonium Intermediates in Cation Radical Cyclization Reactions Investigated via Computational Approaches
Anodic intramolecular cyclization reactions have substantial synthetic utility for formation of cyclic carbon–carbon or carbon–heteroatom bonds. For cases of intramolecular trapping of a cation radical by a protic nucleophile, the cyclization step coincides with a substantial increase in substrate acidity and thus may exhibit particularly pronounced solvent effects. In this computational work, we employ both quantum chemical (QM) and quantum mechanics/molecular mechanics (QM/MM) methods to compute solvent effects on free energy profiles for cyclization and deprotonation reaction steps for cation radical intermediates of substrates representative for anodic intramolecular cyclizations. We find substantial solvent contribution to the thermodynamic driving force for cation radical cyclization; for example, methanol and tetrahydrofuran solvents provide ∼30–35 kJ/mol driving force to form cyclic oxonium cation radicals and ∼15–25 kJ/mol driving force to form cyclic ammonium cation radicals, compared to baseline reactions in dichloromethane solvent. Given that these solvent shifts are on par with the innate cyclization reaction thermodynamics, the choice of solvent plays a crucial role in promoting/driving the cation radical cyclization step. Methanol is particularly effective at facilitating rapid deprotonation of the cyclic cation radical intermediate, which may lead to the full electrochemical process (e.g., second electron transfer) proceeding heterogeneously at the anode.
Cyclization of archaeal membrane lipids impacts membrane protein activity and archaellum formation
Enhancement of the cyclization of membrane lipids GDGTs (glycerol dialkyl glycerol tetraethers) is a critical strategy for archaea to adapt to various environmental stresses. However, the physiological function of membrane lipid cyclization remains unclear. Here, we reported that the GDGT ring synthases mutant, deficient in GDGT cyclization, inhibited archaellum formation and reduced cell motility in thermoacidophilic crenarchaeon Sulfolobus acidocaldarius . This inhibition was caused by decreased transcription of the archaellum operon, likely due to cleavage of the C-terminal domains in transmembrane proteins ArnRs, the transcription factors that regulate archaellum operon expression. The transcriptomic and proteomic analysis showed deficiency of GDGT cyclization broadly impacted the expression of membrane associate proteins, including respiratory chain proteins, and decreased cellular ATP concentration. Moreover, phylogenetic analysis demonstrated that the correlation between GDGT cyclization and archaellum formation is widespread among (hyper)thermophilic archaea, and this was further verified in the euryarchaeon Thermococcus kodakarensis. Our findings suggested that archaea modify their membrane lipids to profoundly alter cellular appendages and cell physiology to adapt to environmental fluctuations.
In Situ Cyclized Polyacrylonitrile Coating: Key to Stabilizing Porous High-Entropy Oxide Anodes for High-Performance Lithium-Ion Batteries
High-entropy oxides (HEOs) composed of multiple metal elements have attracted great attention as anode materials for lithium-ion batteries (LIBs) due to the synergistic effects of various metal species. However, the practical applications of HEOs are still plagued by poor conductivity, unstable solid electrolyte interphase (SEI) and poor cycling stability. In this work, nanosized (FeCoNiCrMn) 3 O 4 HEO (NHEO) is prepared successfully by the NaCl-assisted mechanical ball-milling strategy. Novelly, polyacrylonitrile (PAN) is used as the binder and then in situ thermochemically cyclized to construct a cyclized PAN (cPAN) outer layer onto NHEO (NHEO-cPAN). The in situ formed cPAN coating not only improves the electrical conductivity, but also reinforces the structural and interfacial stability, and thereby, the resulted NHEO-cPAN electrode exhibits significantly enhanced rate and cyclic performance. Specifically, NHEO-PAN500 electrode delivers a high reversible capacity of 560 mAh g –1 at 5 A g –1 and a high-capacity retention of 83% over 800 cycles at 3 A g –1 . Furthermore, the structural evolution and electrochemical behavior of NHEO-PAN electrode during discharge/charge is systematically investigated by operando X-ray diffraction, in situ impedance spectroscopy and ex situ high-resolution transmission electron microscopy. Therefore, this work provides new insights into the engineering of electrode and interphase for high-performance HEO electrode materials, potentially enlightening the practical applications of HEO-based LIBs.
Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile
DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications, such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn, which is slightly different from that of native B-form DNA (~10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption.
Synthesis of succinic acid‐based polyamide through direct solid‐state polymerization method: Avoiding cyclization of succinic acid
Abstract Succinic acid is an important synthetic monomer but it is difficult to use it as a precursor for synthesizing high molecular weight polyamide, due to its tendency to perform intra‐cyclization reaction at high temperature. In order to solve this problem, in this paper, the direct solid‐state polymerization (DSSP) method with the initial reactant, nylon salt which was composed of 1, 5‐diaminopentane, succinic acid, and terephthalic acid, was applied to synthesize the bio‐based copolyamide PA 5T/54. In comparison with the conventional melting polymerization method, the DSSP method can prevent the cyclization reaction of succinic acid effectively due to the lower reacting temperature as well as the restriction effect of the nylon salt. As a result, the product fabricated by DSSP method has higher molecular weight and much lighter color from red to white. Therefore, the DSSP method is advantageous for the synthesis of the polymers or copolymers composed of the succinic acid as the monomer. Furthermore, the polymerization mechanism proposed in this work can serve as a guidance for the design of the molecular structure and control of the polymerization process.
Distribution and abundance of tetraether lipid cyclization genes in terrestrial hot springs reflect pH
Many Archaea produce membrane-spanning lipids that enable life in extreme environments. These isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs) may contain up to eight cyclopentyl and one cyclohexyl ring, where higher degrees of cyclization are associated with more acidic, hotter or energy-limited conditions. Recently, the genes encoding GDGT ring synthases, grsAB, were identified in two Sulfolobaceae; however, the distribution and abundance of grs homologs across environments inhabited by these and related organisms remain a mystery. To address this, we examined the distribution of grs homologs in relation to environmental temperature and pH, from thermal springs across Earth, where sequences derive from metagenomes, metatranscriptomes, single-cell and cultivar genomes. The abundance of grs homologs shows a strong negative correlation to pH, but a weak positive correlation to temperature. Archaeal genomes and metagenome-assembled genomes (MAGs) that carry two or more grs copies are more abundant in low pH springs. We also find grs in 12 archaeal classes, with the most representatives in Thermoproteia, followed by MAGs of the uncultured Korarchaeia, Bathyarchaeia and Hadarchaeia, while several Nitrososphaeria encodes >3 copies. Furthermore, our findings highlight the key role of grs-catalysed lipid cyclization in archaeal diversification across hot and acidic environments.
The cyclization of arabinosyladenine-5-prime-phosphorimidazolide
When arabinosyladenine-5-prime-phosphorimidazolide is allowed to decompose in aqueous solution at room temperature and pH 7.2, depending on the buffer, 5-24 percent is converted to the 2-prime,5-prime-cyclic phosphate (V). Although the extent of cyclization is much greater than for adenosine-5-prime-phosphorimidazolide, cyclization is less efficient than hydrolysis and so would not substantially decrease the efficiency of condensation reactions in aqueous solution. The significance of this result for prebiotic chemistry is discussed.
Controlled cyclization of peptoids to form chiral diketopiperazines
The present disclosure provides improved methods for controlled cyclization of peptoid dimers to form N,N′-2,5-diketopiperazines (N,N′-2,5-DKPs) with significant selectivity. In at least some examples, selectivity is based on a serendipitous conglomeration of slow exchange of amide rotamers, steric repulsion from the degree of α-substitution, and the geometric bulk of an amine nucleophile. By varying reaction conditions, the selectivity of the reaction and formation of a particular N,N′-2,5-DKP can be switched. The cyclization works in the presence of a variety of protection groups and diverse functionalities. The teachings herein provide techniques for synthesizing N,N′-2,5-DKPs that can be readily docked with drug candidates for shuttling across the blood brain barrier. This method provides a facile way to produce substituted DKPs containing groups ready for post-modification to include docking drug candidates.
Covalent Organic Frameworks with Irreversible Linkages via Reductive Cyclization of Imines
Covalent organic frameworks (COFs) show great potential for many advanced applications on account of their structural uniqueness. To address the synthetic challenges, facile chemical routes to engineer the porosity, crystallinity, and functionality of COFs are highly sought after. Herein, we report a synthetic approach that employs the Cadogan reaction to introduce nitrogen-containing heterocycles as the linkages in the framework. Irreversible indazole and benzimidazolylidene (BIY) linkages are introduced into COFs for the first time via phosphine-induced reductive cyclization of the common imine linkages following either stepwise or one-pot reaction protocols. Further, the successful linkage transformation introduces new functionalities, as demonstrated in the case of BIY-COF, which displays excellent intrinsic proton conductivity without the need of impregnation with external proton transfer reagents. Such a general strategy will open the window to a broader class of functional porous crystalline materials.
Redox Homeostasis as a Key Regulator of Intramolecular Cyclization in Fungal Perylenequinones
Perylenequinones (PQs) such as hypocrellins and hypomycins are fungal-derived redox-active metabolites with known roles as photosensitizers in the oxidative stress response and applications in photodynamic therapy (PDT). Here, we report that Shiraia sp., a filamentous fungus, can survive and grow under strictly anaerobic (argon) conditions─an unexpected finding for a multicellular eukaryote. Modulating redox homeostasis through chemical reduction and oxygen limitation promotes the intramolecular cyclization of hypocrellins, enhancing hypomycin biosynthesis. Moisture content further influences these transformations, with high water levels favoring keto–enol tautomerization and dry, reducing environments promoting hydride substitution at the peripheral positions. These findings highlight redox modulation as a key driver of perylenequinone metabolism and suggest that PQs may contribute to maintaining redox balance under anaerobic stress, hinting at a broader role in oxygen-independent adaptation in filamentous fungi. This work offers new insights at the interface of redox biology, chemical signaling, and fungal metabolism, with potential implications for the stability and function of PQ-based PDT agents in hypoxic, reducing conditions such as tumor microenvironments.
Formation of 1 H -Phenalene (C 13 H 10 ) in the Taurus Molecular Cloud via Methylidyne Addition-Cyclization-Aromatization (MACA)
The formation of 1H-phenalene (C 13 H 10 ) in cold molecular clouds, such as the Taurus Molecular Cloud-1 (TMC-1), presents a significant challenge to traditional astrochemical models, which predominantly suggest high-temperature pathways for polycyclic aromatic hydrocarbon (PAH) formation. In this study, we explore computationally the Methylidyne Addition-Cyclization-Aromatization (MACA) mechanism as a viable, barrierless pathway for phenalene synthesis under low-temperature conditions. Through electronic structure calculations and Rice–Ramsperger–Kassel–Marcus (RRKM) statistical methods, we demonstrate that the reaction of 1-vinylnaphthalene (C 10 H 7 C 2 H 3 ) with the methylidyne radical (CH) leads to the formation of 1H-phenalene via a bimolecular reaction, a process that is exoergic and without entrance barrier. The MACA mechanism facilitates the growth of the aromatic carbon backbone via a [5 + 1] ring annulation, providing a new insight into PAH formation in cold molecular clouds. Notably, the MACA mechanism has previously been shown to form indene (C9H8), which was detected in TMC-1 as well, via a [4 + 1] annulation, demonstrating its potential to produce a variety of complex PAHs by addition of a five- and six-membered ring to a benzene moiety via [4 + 1] and [5 + 1] annulation, respectively. As a result, this work highlights the importance of barrierless, exoergic reactions involving MACA in the synthesis of complex aromatic molecules in space, expanding our physicochemical understanding of carbon-rich chemistry in cold molecular clouds.
Sulfur ( 3 P) Reaction with Conjugated Dienes Gives Cyclization to Thiophenes under Single Collision Conditions
Here, we combine crossed-beam velocity map imaging with high-level ab initio/transition state theory modeling of the reaction of S( 3 P) with 1,3-butadiene and isoprene under single collision conditions. For the butadiene reaction, we detect both H and H 2 loss from the initial adduct, and from reaction with isoprene, we see both H loss and methyl loss. Theoretical calculations confirm these arise following intersystem crossing to the singlet surface forming long-lived intermediates. For the butadiene reaction, these lose H 2 to form thiophene as the dominant channel, H to form the detected 2H-thiophenyl radical, or ethene, giving thioketene. For isoprene, additional reaction products are suggested by theory, including the observed H and methyl loss radicals, but also methyl thiophene, thioformaldehyde, and thioketene. The results for S( 3 P) + 1,3-butadiene, showing direct cyclization to the aromatic product and yielding few bimolecular product channels, are in striking contrast to those for the analogous O( 3 P) reaction.
Source of Rate Acceleration for Carbocation Cyclization in Biomimetic Supramolecular Cages
The results of quantum chemical and molecular dynamics calculations reveal that polyanionic gallium-based cages accelerate cyclization reactions of pentadienyl alcohols as a result of substrate cage interactions, preferential binding of reactive conformations of substrate/H 3 O + pairs, and increased substrate basicity. However, the increase in basicity dominates. Here, experimental structure–activity relationship studies in which the metal vertices and overall charge of the cage are varied confirm the model derived via calculations.
The cyclization of epoxyolefins. IV.
Epoxyolefins cyclization, discussing bicyclic ethers from citronellal derivative as synthetic entries into diterpene series of natural products
The cyclization of epoxyolefins. V.
Synthesis of model system for diterpenoids using epoxide and acid catalyst cyclization
Carbonyl participation in acid-catalyzed cyclization reactions involving olefinic bonds
Protonation mechanism in acid catalyzed cyclization reactions of 2-acetamido 3-methylbicyclo-heptene
The isocyano group as a carbenoid function cyclization of ortho-isocyanobiphenyl and derivatives
Cyclization of ortho-isocyanobiphenyl and derivatives with insertion of isocyano carbon to form cycloheptbindoles