Sugar Moiety Research Articles

Customizable Glycopolymers as Adjuvants for Cancer Immunotherapy: From Branching Degree Optimization to Cell Surface Engineering.

Engineering dendritic cell (DC) maturation is paramount for robust T-cell responses and immunological memory, critical for cancer immunotherapy. This work unveils a novel strategy using precisely controlled branching in synthetic glycopolymers to optimize DC activation. Using the distinct copolymerization kinetics of 2-(methacrylamido) glucopyranose (MAG) and diethylene glycol dimethacrylate (DEGDMA) in a RAFT polymerization, unique glycopolymers with varying branching degrees are created. These strategically produced gradient branched glycopolymers with sugar moieties on the outer chain potently promote DC maturation. Strikingly, low-branched glycopolymers demonstrate superior activity, both in pure form and when engineered on tumor cell surfaces. Quartz crystal microbalance and theoretical simulations elucidate the crucial role of branching in modulating glycopolymer-DC receptor interactions. Low-branched gradient glycopolymers have shown a notable advantage and are promising adjuvants in DC-based cancer immunotherapy.

Antiplasmodial and Insecticidal Activities of Third-Generation Ivermectin Hybrids.

Preclinical and/or clinical studies have demonstrated the potential of Ivermectin (IVM) for malaria control. In order to improve its antiplasmodial activity and build on previous knowledge, we have designed a third generation of hybrid molecules in which selected pharmacophores were appended to the IVM macrolide, while retaining one or both sugar moieties at the C-13 position. Moreover, we synthesized IVM hybrids that contain structural features of potent IVM metabolites. The evaluation of the in vitro antiplasmodial activity of these compounds against Plasmodium berghei pre-erythrocytic stages and Plasmodium falciparum erythrocytic stages identified molecules that displayed enhanced activity against the latter when compared to IVM. Additionally, two IVM intermediates and one IVM hybrid retained the insecticidal activity of the parental molecule, clarifying the contribution of the sugar moieties to this feature. Altogether, these results provide key structure-activity relationships to guide the rational design of new generations of IVM hybrids.

Discovery and functional characterization of two novel glycosyltransferases associated with the biosynthesis of α-hederin in Dipsacus asperoides

Triterpenoid saponins are crucial natural products widely distributed in various medicinal plants, with Dipsacus asperoides being particularly rich in these compounds. However, the glycosyltransferases responsible for the biosynthesis of α-hederin, one of the primary bioactive secondary metabolites in D. asperoides, have not been elucidated. In this study, transcriptomic and compound analyses revealed 359 differentially expressed genes associated with secondary metabolism, with 271 involved in triterpenoid saponin glycosylation. Through correlation analysis, 71 candidate glycosyltransferases were identified, and two novel glycosyltransferases were functionally characterized. It was shown that DaUGT121 catalyzes the conversion of hederagenin into cauloside A, while DaUGT103 acts as a cauloside A 1,2-rhamnosyltransferase transforming cauloside A into α-hederin. These findings illuminate the biosynthesis of triterpenoid saponins in D. asperoides, providing insights into the molecular mechanisms and offering novel tools for synthesizing natural products with diverse sugar moieties.

Prediction of human O-linked glycosylation sites using stacked generalization and embeddings from pre-trained protein language model.

O-linked glycosylation, an essential post-translational modification process in Homo sapiens, involves attaching sugar moieties to the oxygen atoms of serine and/or threonine residues. It influences various biological and cellular functions. While threonine or serine residues within protein sequences are potential sites for O-linked glycosylation, not all serine and/or threonine residues undergo this modification, underscoring the importance of characterizing its occurrence. This study presents a novel approach for predicting intracellular and extracellular O-linked glycosylation events on proteins, which are crucial for comprehending cellular processes. Two base multi-layer perceptron models were trained by leveraging a stacked generalization framework. These base models respectively employ ProtT5 and Ankh O-linked glycosylation site-specific embeddings whose combined predictions are used to train the meta-multi-layer perceptron model. Trained on extensive O-linked glycosylation datasets, the stacked-generalization model demonstrated high predictive performance on independent test datasets. Furthermore, the study emphasizes the distinction between nucleocytoplasmic and extracellular O-linked glycosylation, offering insights into their functional implications that were overlooked in previous studies. By integrating the protein language model's embedding with stacked generalization techniques, this approach enhances predictive accuracy of O-linked glycosylation events and illuminates the intricate roles of O-linked glycosylation in proteomics, potentially accelerating the discovery of novel glycosylation sites. Stack-OglyPred-PLM produces Sensitivity, Specificity, Matthews Correlation Coefficient, and Accuracy of 90.50%, 89.60%, 0.464, and 89.70%, respectively on a benchmark NetOGlyc-4.0 independent test dataset. These results demonstrate that Stack-OglyPred-PLM is a robust computational tool to predict O-linked glycosylation sites in proteins. The developed tool, programs, training, and test dataset are available at https://github.com/PakhrinLab/Stack-OglyPred-PLM. Supplementary data are available at Bioinformatics online.

Novel quinazolin-4-one based derivatives bearing 1,2,3-triazole and glycoside moieties as potential cytotoxic agents through dual EGFR and VEGFR-2 inhibitory activity

The toxicity that was caused by the developed medications for anticancer treatment is, unfortunately, an earnest problem stemming from the various involved targets, and accordingly, intense research for overcoming such a phenomenon remains indispensable. In the current inquiry, an innovative category of substituted quinazoline-based glycosides incorporating a core of 1,2,3-triazole and attached to distinct acetylated likewise deprotected sugar segments are created and produced synthetically. The resulted 1,2,3-triazolyl-glycosides products were investigated for their ability to cause cytotoxicity to several human cancer cell lines. The quinazoline based glycosyl-1,2,3-triazoles 10–13 with free hydroxy sugar moiety revealed excellent potency against (IC50 range = 5.70–8.10 µM, IC50 Doxorubicin = 5.6 ± 0.30 µM, IC50 Erlotinib = 4.3 ± 0.1 µM). against MCF-7 cancer cell line. In addition, the derived glycosides incorporating quinazolinone and triazole core 6–13 with acetylated and deprotected sugar parts showed excellent and superior potency against HCT-116 (IC50 range = 2.90–6.40 µM). The potent products were revealed as safe cytotoxic agents as indicated by their studied safety profiles. Additional research of promising candidates inhibitory analysis performed against EGFR and VEGFR-2. The hydroxylated glycosides incorporating triazole and quinazoline system 11 and 13 with N-methyl substitution of quinazolinone, gave excellent potency against EGFR (IC50 = 0.35 ± 0.11 and 0.31 ± 0.06 µM, correspondingly) since glycoside 13 revealed comparable IC50 (3.20 ± 0.15 µM) to sorafenib against VEGFR-2. For more understanding of its action mode, it was analyzed how the 1,2,3-triazolyl glycoside 13 made an effect on the apoptosis induction and the arrest of the cell cycle. It was revealed that it had the ability to stop HCT-116 cells in their cell cycle’s G1 stage. Moreover, the influence of quinazolinone-1,2,3-triazole-glycoside 13 upon p53, Bax, and Bcl-2 levels in HCT-116 units was also studied for future approaches toward its behavior. Additionally, the latter derivative may trigger apoptosis, as indicated by a significant increase in apoptotic cells. Furthermore, molecular docking was simulated to make an obvious validation and comprehension acquirement of the binding’s characteristics also attractions among the most forceful compounds side by side with their aimed enzymes.

Multivalent interactions between fully glycosylated influenza virus hemagglutinins mediated by glycans at distinct N-glycosylation sites

The hemagglutinin (HA) glycoprotein of influenza virus binds host cell receptors and mediates viral entry. Here we present cryo-EM structures of fully glycosylated HAs from H5N1 and H5N8 influenza viruses. We find that the H5N1 HA can form filaments that comprise two head-to-head HA trimers. Multivalent interactions between the two HA trimers are mediated by glycans attached to N158. The distal Sia1-Gal2-NAG3 sugar moiety of N158 interacts with the receptor binding site on the opposing HA trimer. Additional interactions are observed between NAG3 and residues K222 and K193. The H5N8 HA lacks the N158 glycosylation site and does not form the filamentous structure. However, the H5N8 HA exhibits an auto-inhibition conformation, where the receptor binding site is occupied by the glycan chain attached to residue N169 from a neighboring protomer. These structures represent native HA-glycan interactions, which may closely mimic the receptor-HA interactions on the cell surface.

The sugar moiety in protopanaxadiol ginsenoside affects its ability to target glucocorticoid receptor to regulate lipid metabolism

Ginsenosides are natural products with hydrophobic rings adorned with sugar molecules. The elucidation of the impact of ginsenosides structure on their activity is crucial for facilitating precision-oriented modifications, thereby enhancing their suitability for drug development. Here, utilizing an ob/ob mouse model, we demonstrated that as the number of sugar moiety on the protopanaxadiol-type ginsenosides decreased, the hypolipidemic potency increased, while the aglycon exhibited negligible activity. Mechanistically, we demonstrated the dependency of ginsenosides on the glucocorticoid receptor (GR) for the regulation of lipid metabolism. Interestingly, ginsenoside CK was found to promote the transcription of lipid metabolism-related genes via GR contrast to the effects of glucocorticoids, suggesting a unique mode of action. Furthermore, we observed that a reduction in the number of sugar molecules strengthened the binding affinity of ginsenosides to GR, as determined by microscale thermophoresis. These findings highlight the critical role of the sugar moiety in modulating the lipid-regulating capacity of ginsenosides, providing valuable insights for the development of these compounds as potential therapeutic agents.

Analyzing hydroxyl radical accessibility related to hydrogen abstraction in a DNA sugar moiety using molecular dynamics simulations

Exposure of water to ionizing radiation induces OH radical formation. Within cellular environments, the presence of OH radicals can stimulate the abstraction of hydrogen atoms from the sugar backbone of DNA. Subsequent damage to DNA structures leads to various diseases. Multiple studies have elucidated this phenomenon, especially computational studies examining the differences in the degree of abstraction between the sugar hydrogens (H1′, H2′, H2″, H3′, H4′, H5′, and H5″). However, the details of this phenomenon have not yet been clarified. It is rare for OH radicals to approach DNA within the simulation time, making it difficult to adequately sample the configurations in which OH radicals immediately precede the abstraction of the hydrogen atoms. To address this problem, we performed molecular dynamics simulation to calculate the relative accessibility by putting a potential on nucleotides and OH radicals. As a result, we found that the accessibility of OH radicals to each hydrogen atom differs from that of water molecules as solvents. A more detailed accessibility analysis revealed that the angle of the OH radicals approaching the hydrogen atoms of ribose and the energy barrier for abstracting the hydrogen atoms can be considered to improve the correspondence with the experimental data. Moreover, we found that the behavior of water molecules and OH radicals toward accessibility to DNA differs significantly and showed that the factors are related to the physicochemical properties of water molecules and OH radicals, as well as the structure of DNA.

Biotransformation of Xanthohumol by Entomopathogenic Filamentous Fungi.

Xanthohumol (1) is a major prenylated flavonoid in hops (Humulus lupulus L.) which exhibits a broad spectrum of health-promoting and therapeutic activities, including anti-inflammatory, antioxidant, antimicrobial, and anticancer effects. However, due to its lipophilic nature, it is poorly soluble in water and barely absorbed from the gastrointestinal tract, which greatly limits its therapeutic potential. One method of increasing the solubility of active compounds is their conjugation to polar molecules, such as sugars. Sugar moiety introduced into the flavonoid molecule significantly increases polarity, which results in better water solubility and often leads to greater bioavailability. Entomopathogenic fungi are well known for their ability to catalyze O-glycosylation reactions. Therefore, we investigated the ability of selected entomopathogenic filamentous fungi to biotransform xanthohumol (1). As a result of the experiments, one aglycone (2) and five glycosides (3-7) were obtained. The obtained (2″E)-4″-hydroxyxanthohumol 4'-O-β-D-(4‴-O-methyl)-glucopyranoside (5) has never been described in the literature so far. Interestingly, in addition to the expected glycosylation reactions, the tested fungi also catalyzed chalcone-flavanone cyclization reactions, which demonstrates chalcone isomerase-like activity, an enzyme typically found in plants. All these findings undoubtedly indicate that entomopathogenic filamentous fungi are still an underexploited pool of novel enzymes.

Spectroscopic determination of Deborah numbers in membrane-mimetic bolaamphiphile assemblies

The remarkable stability of Archaebacteria and their resistance to extreme environmental conditions, such as high temperature (hot springs), high salinity (salt marsh), high acidity (volcanic environment), or low temperature (Arctic or Antarctic) is mostly due to their very stable membranes. Membranes of Archaebacteria are composed of tetraethers from the lipid family of bolaamphiphiles. The concern in our laboratory is to synthesize bolaamphiphiles that could form vectors with function to carry drugs toward target cells in the body. The new family of bolamphiphiles synthesized has one polar head based on a sugar moiety and the other polar head is glycine betaine, both issued from natural sources (sugar beet, wheat). They are interconnected with a hydrocarbon chain of 12 methylène units. One side hydrocarbon chain, of 8 methylène units is attached to the anomeric position of the sugar moiety. These two molecules are named N-(12-Betainylamino-Dodecane)-octyl β-D-Glucofuranosiduronamide Chloride, abbreviated C8C12 and N-(12-Betainylamino-Dodeca-5,7-diynyl)-octyl β-D-Glucofuranosiduronamide Chloride, abbreviated C8C12X2. These bolaamphiphile molecules organize in membrane-mimetic lamellar structures (Lc, Lα, L). They undergo a thermal phase transition upon heating. When cooled back to room temperature, they remain in the undercooled high-temperature phase. To follow the relaxation back to the thermodynamically stable phase at 20 °C, the small-angle and wide-angle X-ray spectra were recorded every hour. The Deborah number (De), defined as De = time of relaxation/time of observation, is a dimensionless number often used in rheology to characterize the fluidity of materials under specific flow conditions. It was evaluated for supramolecular structures of two type of bolaamphiphiles, as the De(C8C12) = 35 and the De(C8C12X2) = 62. These values are typical for solid-like behavior, which is in accordance with the sticky, paste-like, brownish aspect of these bolaamphiphile assemblies. The time of relaxation was the time for bolaamphiphiles to regain their thermodynamically stable phase at 20 °C and the time of observation was 1 h, the typical time of recording between two subsequent spectra.

Cardenolides; calotropin and gomphogenin from Calotropis procera (Aiton) mitigate bone turnover in ovariectomized osteoporotic rats: Targeting RANKL/OPG axis and estrogen receptor-alpha

The present study aimed to examine the effect of Calotropis procera (Aiton) and its major cardenolides; calotropin and gomphogenin on ovariectomy-induced osteoporosis in rats. Osteoporotic rats were orally treated with C. procera alcoholic extract (100 mg/kg), calotropin (CLT; 100 μg/kg) and gomphogenin (GPG; 100 μg/kg) for 14 consecutive days. Bone resorption/formation biomarkers; bone specific alkaline phosphatase (BALP), osteoprotegerin (OPG) and nuclear factor-κβ ligand (RANKL) as well as serum calcium and phosphorus were assessed 24 h after last doses of treatments. Serum levels of estradiol (E2) and catalase were also measured.Oral treatment with C. procera extract, CLT and GPG caused E2 restoration to normal level with a marked regulation in the RANKL/OPG axis. Serum phosphorus and calcium were up-leveled whereas BALP was downregulated. Histopathological examination, bone histomorphometric analysis and immunohistochemical staining for osteopontin (OPN) inspection further emphasized the aforementioned outcomes. The results revealed the superiority of CLT and to a lesser extent GPG osteoporotic effect over C. procera extract. Molecular docking of the two compounds on ER-α and RANKL/OPG complex showed noteworthy binding affinities which also confirmed the supremacy of CLT due to the additional hydrogen bonding of the hydroxyl groups of the sugar moiety with RANKL/OPG complex. Finally, it is concluded that CLT and GPG from C. procera hinder bone turnover by decreasing osteoclastic bone cells activity and increasing calcium mineralization thus suppressing bone remodeling and preventing bone infirmity in OVX osteoporotic rats directly via binding to RANKL/OPG complex and ER-α and indirectly through elevating level of E2.

Advances in glycosyltransferase-mediated glycodiversification of small molecules.

Currently, numerous glycosides have been synthesized and used in clinical applications, neutraceuticals, cosmetics, and food processing. Structurally, a glycoside is composed of aglycone attaching to one or several sugar moieties so-called glycone. It is found that biochemical or biopharmaceutical properties of glycoside are mainly determined by its sugar part and thereby alternation of this glycone resulting in novel structure and characteristics as well. The use of traditional production methods of glycosides such as direct extraction and purification from plants, animals, or microorganisms is very challenging (laborious, time-consuming, technique, high price, low yield, etc.). Alternatively, the use of enzymatic methods for the biosynthesis of glycosides has become a highly promising tool. Particularly, the diverse structure of glycosides can be obtained using the promiscuous catalytic activity of glycosyltransferases (GT) mined from bioresources (plants, fungi, microorganisms, etc.). In addition, the exploration of GT catalytic promiscuity toward diverse aglycones, and glycones has indeed been interesting and played a key role in the production of novel glycosides. This review described the recent advances in glycosyltransferase-mediated glycodiversification of small molecules (flavonoids, steroids, terpenoids, etc.). Mostly, references were collected from 2014 to 2023.

Development of 4′-Oxo-MLN4924 as potential neddylation inhibitors: Design, synthesis, anti-HCMV evaluation, and molecular docking

MLN4924 (1), a neddylation inhibitor, has shown promising anticancer and antiviral properties. In this study, we designed and synthesized new derivatives of 4′-oxo-MLN4924, inspired by the structures of MLN4924 and another known neddylation inhibitor, referred to as compound 2. Like compound 2, we used a specific type of sugar molecule but incorporated a modified building block known as 7-deazapurine for the nucleobase part. Additionally, we arranged the sulfamate and 2′-hydroxyl as key functional groups. We found that the 2′-OH group is essential for activity against human cytomegalovirus (HCMV) using luciferase reporter assay. Molecular docking and molecular dynamics (MD) studies revealed that the conformation of the sugar moiety plays a crucial role in protein–ligand interactions. These studies suggest that derivatives with a bulky aromatic ring at the 6-position of the nucleobase are likely to have enhanced binding, which is supported by experimental findings.

Selectivity Screening and Structure-Cytotoxic Activity Observations of Selected Oleanolic Acid (OA)-Type Saponins from the Amaranthaceae Family on a Wiade Panel of Human Cancer Cell Lines.

Plants from the Amaranthaceae family are a source of oleanolic acid (OA)-type saponins with cytotoxic activity. Two known OA-type saponins, calenduloside E and chikusetsusaponin IVa, were isolated from the roots of Chenopodium strictum Roth. Their structures were confirmed using MS and NMR techniques. This constitutes the inaugural report of the saponins in Ch. strictum. Both the isolated saponins and structurally similar compounds, momordin Ic and OA, were compared for their cytotoxicity against various cancer and normal cell lines (including skin, breast, thyroid, gastrointestinal, and prostate panels). Their effects were dose- and time-dependent, varying with the specific cell line and compound structure. A chemometric approach demonstrated the effects of the compounds on the cell lines. The study discusses the structure-activity observations. The key structural elements for potent cytotoxic activity included the free carboxyl group 28COOH in the sapogenin structure (OA) and the presence of a sugar moiety. The monodesmosides with glucuronic acid (GlcA) at the C3 position of OA were generally more cytotoxic than bidesmosides or OA alone. The addition of xylose in the sugar chain modified the activity towards the cancer cells depending on the specific cell line. OA-type saponins with GlcA (particularly calenduloside E and momordin Ic) represent a promising avenue for further investigation as potential anticancer agents.

Mechanistic Basis for the Translation Inhibition of Cutibacterium acnes by Clindamycin

Inflammation and the Gram-positive anaerobic bacterium Cutibacterium acnes, which is implicated in acne pathogenesis and pilosebaceous unit inflammation, are the main targets of antibiotic-based therapy against acne vulgaris (acne). The most widely used antibiotics in acne therapy are tetracyclines, macrolides, and lincosamides. Unfortunately, C. acnes bacteria over the past several decades have demonstrated increased resistance to these antibiotics, particularly to clindamycin. The precise knowledge of how antibiotics interact with their clinical target is needed to overcome this problem. Toward this goal, we determined the structure of clindamycin in complex with the ribosome of Cutibacterium acnes at 2.53 Å resolution using cryogenic electron microscopy. The galactose sugar moiety of clindamycin interacts with nucleotides of the 23S rRNA directly or through a conserved network of water-mediated interactions. Its propyl pyrrolidinyl group interacts with the 23S rRNA through van der Waals forces. Clindamycin binding to the Cutibacterium acnes ribosome interferes with both: proper orientation of the aminoacyl group of the A-site bound tRNA that is needed for peptide bond formation and with the extension of the nascent peptide. Our data are important for advancing understanding of antibiotic resistance and development of narrow- spectrum antibacterial drugs, which is an urgent need for contemporary antibiotic stewardship.

Synthesis of C-Alkyl Glycosides from Alkyl Bromides and Glycosyl Carboxylic Acids via Ni/Photoredox Dual Catalysis.

C-Alkyl glycosides, an important class of C-glycosides, are widely found in various drugs and natural products. The synthesis of C-alkyl glycosides has attracted considerable attention. Herein, we developed a Ni/photoredox catalyzed decarboxylative C(sp3)-C(sp3) coupling reaction of stable glycosylcarboxylic acids with simple aliphatic bromides to generate C-alkyl glycosides. The method successfully linked several functional molecular fragments (natural products or drugs) to a sugar moiety, showing the extensive application prospects of this transformation. Controlled experiments and DFT calculations demonstrated that the reaction pathway contains a free radical process, and a possible mechanism is proposed.

Application of Monoclonal Antibodies against Naturally Occurring Bioactive Ingredients.

Monoclonal antibodies (Mabs) are widely used in a variety of fields, including protein identification, life sciences, medicine, and natural product chemistry. This review focuses on Mabs against naturally occurring active compounds. The preparation of Mabs against various active compounds began in the 1980s, and now there are fewer than 50 types. Eastern blotting, which was developed as an antibody staining method for low-molecular-weight compounds, is useful for its ability to visually represent specific components. In this method, a mixture of lower-molecular-weight compounds, particularly glycosides, are separated by thin-layer chromatography (TLC). The compounds are then transferred to a membrane by heating, followed by treatment with potassium periodate (KIO4) to open the sugar moiety of the glycoside on the membrane to form an aldehyde group. Proteins are then added to form Schiff base bonds to enable adsorption on the membrane. A Mab is bound to the glycoside moiety on the membrane and reacts with a secondary antibody to produce color. Double Eastern blotting, which enables the simultaneous coloration of two glycosides, can be used to evaluate quality and estimate pharmacological effects. An example of staining by Eastern blotting and a component search based on the results will also be presented. A Mab-associated affinity column is a method for isolating antigen molecules in a single step. However, the usefulness of the wash fractions that are not bound to the affinity column is unknown. Therefore, we designated the wash fraction the "knockout extract". Comparing the nitric oxide (NO) production of a glycyrrhizin (GL)-knockout extract of licorice with a licorice extract revealed that the licorice extract is stronger. Therefore, the addition of GL to the GL-knockout extract of licorice increased NO production. This indicates that GL has synergic activity with the knockout extract. The GL-knockout extract of licorice inhibited high-glucose-induced epithelial-mesenchymal transition in NRK-52E cells, primarily by suppressing the Notch2 pathway. The real active constituent in licorice may be constituents other than GL, which is the causative agent of pseudohyperaldosteronism. This suggests that a GL-knockout extract of licorice may be useful for the treatment of diabetic nephritis.

Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application.

Xeno nucleic acid (XNA) are artificial nucleic acids, in which the chemical composition of the sugar moiety is changed. These modifications impart distinct physical and chemical properties to XNAs, leading to changes in their biological, chemical, and physical stability. Additionally, these alterations influence the binding dynamics of XNAs to their target molecules. Consequently, XNAs find expanded applications as functional materials in diverse fields. This review provides a comprehensive summary of the distinctive biophysical properties exhibited by various modified XNAs and explores their applications as innovative functional materials in expanded fields.

Kanamycin−Cu(II) Complex Catalyzed Ullmann Amine Synthesis at Room Temperature: A Tool for Mechanistic Insights into Methylene Blue Degradation

AbstractThis study highlights the significance of the Ullmann coupling reaction in modern organic synthesis and advances catalytic methodologies through the introduction of a kanamycin−copper complex as a highly efficient catalyst for the synthesis of diverse N−aryl compounds. We demonstrate the catalyst's versatility by synthesizing 20 diaryl−amine instances, 21 Ar(het)−N compounds, and 10 miscellaneous examples. NMR, IR, and UV spectroscopy offer insights into the catalyst's behaviour. Additionally, DFT studies support the catalyst's proficiency in generating SO4−⋅ radicals by stabilizing with amino sugar moieties. Ex‐situ NMR experiments confirm a ternary complex‐based mechanism at concentrations below 0.1 μM. Furthermore, we showcase the degradation of methylene blue to its precursor amine under optimized conditions. Overall, this research underscores the potential of Ullmann condensation reactions in contemporary organic synthesis and contributes significantly to the advancement of catalytic methodologies.

Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotide Fragments.

Accurate calculation of non-covalent interaction energies in nucleotides is crucial for understanding the driving forces governing nucleic acid structure and function, as well as developing advanced molecular mechanics forcefields or machine learning potentials tailored to nucleic acids. Here, we dissect the nucleotides' structure into three main constituents: nucleobases (A, G, C, T, and U), sugar moieties (ribose and deoxyribose), and phosphate group. The interactions among these fragments and between fragments and water were analyzed. Different quantum mechanical methods were compared for their accuracy in capturing the interaction energy. The non-covalent interaction energy was decomposed into electrostatics, exchange-repulsion, dispersion, and induction using two ab initio methods: Symmetry-Adapted Perturbation Theory (SAPT) and Absolutely Localized Molecular Orbitals (ALMO). These calculations provide a benchmark for different QM methods, in addition to providing a valuable understanding of the roles of various intermolecular forces in hydrogen bonding and aromatic stacking. With SAPT, a higher theory level and/or larger basis set did not necessarily give more accuracy. It is hard to know which combination would be best for a given system. In contrast, ALMO EDA2 did not show dependence on theory level or basis set; additionally, it is faster.