Solvent-dependent chemoselective synthesis of different isoquinolinones mediated by the hypervalent iodine(III) reagent PISA

• Ze-Nan Hu,
• Yan-Hui Wang,
• Jia-Bing Wu,
• Ze Chen,
• Dou Hong and
• Chi Zhang

Beilstein J. Org. Chem. 2024, 20, 1914–1921, doi:10.3762/bjoc.20.167

• zwitterionic water-soluble hypervalent iodine reagent (phenyliodonio)sulfamate (PISA). In water, PISA is strongly acidic, and the pH value can reach 2.05 in a saturated aqueous solution. With PISA, various indoles have been synthesized via C–H amination of 2-alkenylanilines involving an aryl migration

The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)

• Cristina Martini,
• Muhammad Idham Darussalam Mardjan and
• Andrea Basso

Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162

• compatibility of the GBB reaction with typical KTGS conditions, such as aqueous solvent at near-physiological pH and high dilution, and the achievement of selective ligand amplification. First, molecular modeling studies were carried out to verify that building blocks and intermediates could bind the target

• -reacted with the aldehydes to yield 5-iminoimidazoles 56. When benzamidine (54, R2 = Ph) was used, aldehydes bearing electron-rich groups gave the products in higher yields compared to those with electron-poor groups. This study demonstrated that the GBB reaction could take place when acyclic amidines

A facile three-component route to powerful 5-aryldeazaalloxazine photocatalysts

• Ivana Weisheitelová,
• Radek Cibulka,
• Marek Sikorski and
• Tetiana Pavlovska

Beilstein J. Org. Chem. 2024, 20, 1831–1838, doi:10.3762/bjoc.20.161

• , value for Ar = Ph] [14][15][16][17][18] (Figure 1B). 5-Aryldeazaalloxazines 2 have been found to be even more powerful reductants than 1 due to their more negative ground-state reduction potential by ca. 300 mV. Moreover, 2 exhibits higher photostability than 1. Consequently, 5-aryldeazaalloxazine 2f

Discovery of antimicrobial peptides clostrisin and cellulosin from Clostridium: insights into their structures, co-localized biosynthetic gene clusters, and antibiotic activity

• Moisés Alejandro Alejo Hernandez,
• Katia Pamela Villavicencio Sánchez,
• Rosendo Sánchez Morales,
• Karla Georgina Hernández-Magro Gil,
• David Silverio Moreno-Gutiérrez,
• Eddie Guillermo Sanchez-Rueda,
• Yanet Teresa-Cruz,
• Brian Choi,
• Armando Hernández Garcia,
• Alba Romero-Rodríguez,
• Oscar Juárez,
• Siseth Martínez-Caballero,
• Mario Figueroa and
• Corina-Diana Ceapă

Beilstein J. Org. Chem. 2024, 20, 1800–1816, doi:10.3762/bjoc.20.159

• 0.8. Cultures were incubated for 14 h, at 200 rpm, at 18 °C. Subsequently, cells were centrifuged at 10,000 rpm for 30 min at 4 °C. The resulting cell pellets were resuspended in 20 mL of LanA starting buffer (20 mM Tris pH 7.5, 500 mM KCl, 10% glycerol) and lysed by sonication (4.0 seconds on, 10

• purifications using affinity chromatography with a 1 mL His Trap nickel affinity column. Sonication lysis was performed and centrifuged during 30 min, at 8,000 rpm, 4 °C. The supernatants were loaded into the column. The column was washed with 5 column volumes of LanA wash buffer 1 (20 mM Tris pH 7.5, 500 mM

• KCl, 10% glycerol, 0.5 mM imidazole), followed by 10 column volumes of LanA wash buffer 2 (20 mM Tris pH 7.5, 500 mM KCl, 10% glycerol, 30 mM imidazole). Finally, the elution was performed with 3 column volumes of LanA elution buffer (20 mM Tris pH 7.5, 500 mM KCl, 10% glycerol, 750 mM imidazole

Ugi bisamides based on pyrrolyl-β-chlorovinylaldehyde and their unusual transformations

• Alexander V. Tsygankov,
• Vladyslav O. Vereshchak,
• Tetiana O. Savluk,
• Serhiy M. Desenko,
• Valeriia V. Ananieva,
• Oleksandr V. Buravov,
• Yana I. Sakhno,
• Svitlana V. Shishkina and
• Valentyn A. Chebanov

Beilstein J. Org. Chem. 2024, 20, 1773–1784, doi:10.3762/bjoc.20.156

• moiety under the influence of water. The appearance of HCl in these cases was identified by the specific odor and detected by pH measurements. It is likely that this catalytic amount of HCl is enough for the conversion and formation of the amides 10. To confirm the influence of HCl and its necessity to

Synthesis and characterization of 1,2,3,4-naphthalene and anthracene diimides

• Adam D. Bass,
• Daniela Castellanos,
• Xavier A. Calicdan and
• Dennis D. Cao

Beilstein J. Org. Chem. 2024, 20, 1767–1772, doi:10.3762/bjoc.20.155

• . Heating 5 with hexylamine or aniline in refluxing acetic acid successfully led to the formation of the targeted aromatic diimides bearing either N-hexyl (7-Hex) or N-phenyl (7-Ph) substitutions in good yields. The same strategy was employed to create the imide-capped anthracenes 8-Hex and 8-Ph

• evaporation of CH2Cl2/MeOH solutions and characterized by X-ray crystallography. 7-Ph crystallizes in the Pbcn space group into a solvent superstructure of π-stacked columns of 7-Ph. The imide groups are pointed in alternating directions within a stack. While this may occur in part as a consequence of the

• steric demands of the N-phenyl groups, there are also C–H···π interactions between phenyl groups of adjacent π stacks, with the closest Ph centroid to H distance being 2.613 Å (Figure 2a). Additionally, the middle carbonyl oxygens are in short contact (2.376 Å) with the 7- and 8-H atoms of the

Chemo-enzymatic total synthesis: current approaches toward the integration of chemical and enzymatic transformations

• Ryo Tanifuji and
• Hiroki Oguri

Beilstein J. Org. Chem. 2024, 20, 1693–1712, doi:10.3762/bjoc.20.151

• for methyl malonyl-CoA and malonyl-CoA in the enzymatic conversions. After careful and systematic optimization of the reaction conditions, such as the stoichiometry of the PKS modules and pH, along with the application of a NADPH recycling system, JuvEIV/JuvEV-catalyzed enzymatic conversions of 77–79

Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty

• Weimao Zhong and
• Vinayak Agarwal

Beilstein J. Org. Chem. 2024, 20, 1635–1651, doi:10.3762/bjoc.20.146

• enzyme RagaA7 was produced in a Bacillus subtilis host and characterized to be a neoagarotetraose-producing GH-16 family endo-type β-agarase with a pH and temperature optima being 7.0 and 50 °C, respectively. Another thermostable neoagarotetraose-producing GH-16 endo-type β-agarase rAgaA was identified

• and cloned from deep-sea-derived Microbulbifer sp. JAMB-A94 with pH and temperature optima being 7.0 and 55 °C, respectively [26]. The recombinant enzyme was likewise produced using a B. subtilis host. The crystal structure of the catalytic domain was determined to show a β-jelly roll fold with

• bridges, relatively short length of the surface loops, and the increased number of Pro and Arg residues [29]. A truncated β-agarase gene without the carbohydrate-binding modules (Aga16A-ΔCBM) from the marine Microbulbifer sp. BH-1 was cloned and expressed in Escherichia coli with pH and temperature being

Supramolecular assemblies of amphiphilic donor–acceptor Stenhouse adducts as macroscopic soft scaffolds

• Ka-Lung Hung,
• Leong-Hung Cheung,
• Yikun Ren,
• Ming-Hin Chau,
• Yan-Yi Lam,
• Takashi Kajitani and
• Franco King-Chi Leung

Beilstein J. Org. Chem. 2024, 20, 1590–1603, doi:10.3762/bjoc.20.142

• -responsiveness, and molecular functional tunability of synthetic supramolecular systems can be precisely controlled through the delicate design and synthesis of organic molecules [9][10][11][12][13][14]. Synthetic supramolecular systems can respond to various external stimuli, e.g., light, pH, organic solvents

Divergent role of PIDA and PIFA in the AlX₃ (X = Cl, Br) halogenation of 2-naphthol: a mechanistic study

• Kevin A. Juárez-Ornelas,
• Manuel Solís-Hernández,
• Pedro Navarro-Santos,
• J. Oscar C. Jiménez-Halla and
• César R. Solorio-Alvarado

Beilstein J. Org. Chem. 2024, 20, 1580–1589, doi:10.3762/bjoc.20.141

• an equilibrium of Cl–I(Ph)–OTFA–AlCl3 and [Cl–I(Ph)][OTFA–AlCl3], rather than PhICl2 being the active species. On the other hand, bromination using PIDA and AlBr3 was more efficient, wherein the intermediate Br–I(Ph)–OAc–AlBr3 was formed as active brominating species. Similarly, PhIBr2 was higher in

• bromide is coordinated by an acetate ligand to produce the active brominating species Br–I(Ph)–OAc–AlBr3 (I-3–Br). Then, 2-naphthol adds to the iodine(III) species to release the activated Br3Al–OAc ligand through transition state TS2–Br (ΔG‡ = 11.7 kcal/mol), which leads to the protonated intermediate I

• -4–Br. The next step is a deprotonation assisted by the released Br3Al–OAc species. This allows the formation of the AcO–AlBr2 salt via TS3–Br and the trans intermediate I-5–Br, which contains a Br–I(Ph)–O–naphthyl bond of 2.14 Å length. The last step is the bromination of I-5–Br by isomerization to

Mining raw plant transcriptomic data for new cyclopeptide alkaloids

• Draco Kriger,
• Michael A. Pasquale,
• Brigitte G. Ampolini and
• Jonathan R. Chekan

Beilstein J. Org. Chem. 2024, 20, 1548–1559, doi:10.3762/bjoc.20.138

• . After the extractions were finished and dried by rotary evaporation, the extract was resuspended in basic water (pH 10 using NaOH) and vacuum filtered to remove insoluble particulates. Liquid–liquid extraction was performed three times with basic water and DCM. The DCM layer was collected and dried

Photoswitchable glycoligands targeting Pseudomonas aeruginosa LecA

• Yu Fan,
• Ahmed El Rhaz,
• Stéphane Maisonneuve,
• Emilie Gillon,
• Maha Fatthalla,
• Franck Le Bideau,
• Guillaume Laurent,
• Samir Messaoudi,
• Anne Imberty and
• Juan Xie

Beilstein J. Org. Chem. 2024, 20, 1486–1496, doi:10.3762/bjoc.20.132

• ITC200 isothermal titration calorimeter (Microcal-Malvern Panalytical, Grenoble, France). The lyophilized LecA protein was dissolved in a buffer composed of 20 mM Tris.HCl (pH 7.5), 100 mM NaCl and 100 μM CaCl2 with 5% or 10% DMSO final. All compounds were first dissolved in DMSO then in same buffer for

Synthesis of 2-benzyl N-substituted anilines via imine condensation–isoaromatization of (E)-2-arylidene-3-cyclohexenones and primary amines

• Lu Li,
• Na Li,
• Xiao-Tian Mo,
• Ming-Wei Yuan,
• Lin Jiang and
• Ming-Long Yuan

Beilstein J. Org. Chem. 2024, 20, 1468–1475, doi:10.3762/bjoc.20.130

• to various aryl moieties except for those containing strong electron-withdrawing substituent (i.e., -CN, -NO2). 3-Cyclohexenones 2 bearing a halogen group (i.e., -Cl, -Br) as well as an electron-donating group (i.e., -Me, -OMe, -Ph) worked well under the optimized reaction conditions, delivering the

A comparison of structure, bonding and non-covalent interactions of aryl halide and diarylhalonium halogen-bond donors

• Nicole Javaly,
• Theresa M. McCormick and
• David R. Stuart

Beilstein J. Org. Chem. 2024, 20, 1428–1435, doi:10.3762/bjoc.20.125

• Discussion This study evolved from a parallel exploration of reactions involving unsymmetrical phenyl(mesityl)halonium salts, i.e., Ph(Mes)X+. DFT analysis revealed similar structural trends to our previous work [21] when we expanded the halogens to include astatine (At). Due to its radioactivity and short

Hypervalent iodine-catalyzed amide and alkene coupling enabled by lithium salt activation

• Akanksha Chhikara,
• Fan Wu,
• Navdeep Kaur,
• Prabagar Baskaran,
• Alex M. Nguyen,
• Zhichang Yin,
• Anthony H. Pham and
• Wei Li

Beilstein J. Org. Chem. 2024, 20, 1405–1411, doi:10.3762/bjoc.20.122

• . Acknowledgements We thank Dr. Yong W. Kim (University of Toledo) for NMR assistance. Mr. Babatunde Obadawo (University of Toledo) is acknowledged for collecting the high-resolution mass spectrometry data. We acknowledge Dr. Navdeep Kaur’s Ph. D. for her contributions in her Ph. D. thesis titled “Selective

Domino reactions of chromones with activated carbonyl compounds

• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 1256–1269, doi:10.3762/bjoc.20.108

• a substituent R5 located at carbon C-4 gave good yields, except for methoxy and benzyloxy which did not work at all. Dienes derived from 1,3-diketones (R6 = Me, Ph) gave similar yields to those obtained from dienes derived form β-ketoesters, although yields were slightly lower in case of R6 = Me

• intramolecular nucleophilic attack of the oxygen to the halide to give intermediate U and subsequent ring-cleavage. The reaction of 3-ketoamide 34a (R3 = Me, R4 = Ph) with 3-chloro-, 3-bromo-, and 3-iodochromone showed that the yields strongly depend on the type of halogen atom located at position 3 of the

• chromones, presumably due to the electron-donating character of the methoxy group and the lower electrophilicity of the chromone. But this trend was also not general. Similar yields were obtained for ketones (R3 = Me, Ph) or esters (R3 = OMe). Treatment of 2-(salicyloyl)furan 35a with iodine in the presence

Cofactor-independent C–C bond cleavage reactions catalyzed by the AlpJ family of oxygenases in atypical angucycline biosynthesis

• Jinmin Gao,
• Liyuan Li,
• Shijie Shen,
• Guomin Ai,
• Bin Wang,
• Fang Guo,
• Tongjian Yang,
• Hui Han,
• Zhengren Xu,
• Guohui Pan and
• Keqiang Fan

Beilstein J. Org. Chem. 2024, 20, 1198–1206, doi:10.3762/bjoc.20.102

• -morpholino)propanesulfonic acid (MOPS) buffer (pH 7.5), and the cells were disrupted by ultrasonication to obtain the cell extract. Cell debris was removed by centrifugation (14,000g, 15 min). The proteins were purified by Ni-NTA agarose chromatography, desalted, and concentrated by centrifugation (8,000g

• ]. In vitro enzymatic assay All reactions were performed in 50 mM Tris-HCl buffer at pH 8.0. For conversion of 9 by AlpG or JadH, the reaction mixtures (50 μL) consisting of 10 μM FAD, 125 μM NADPH, 100 μM 9, and 25 μM AlpG or JadH were incubated at 30 °C for 5 min and analyzed by HPLC directly. For

Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A

• Maksim V. Kvach,
• Stefan Harjes,
• Harikrishnan M. Kurup,
• Geoffrey B. Jameson,
• Elena Harjes and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2024, 20, 1088–1098, doi:10.3762/bjoc.20.96

• -neutral phosphinamide and a negatively charged phosphinic acid derivative had excellent stability in water at pH 7.4, but only the charge-neutral compound inhibited human CDA, similar to previously described 2'-deoxyzebularine (Ki = 8.0 ± 1.9 and 10.7 ± 0.5 µM, respectively). However, under basic

• in H2O. Removal of toluoyl groups was accomplished in aq NH3, providing pure α- and β-nucleoside of Va and Vc, respectively, carrying a negatively charged phosphinic acid group. These compounds were found to be stable in sodium phosphate buffer at pH 7.0 as no decomposition was observed in NMR

• equation, such as Lineweaver–Burk, Hanes–Woolf and Eadie–Hofstee transformations [71]. Then, KM for the substrate and Ki for each inhibitor were calculated, assuming competitive nature of the inhibitors (Table 1). Initially, we performed this assay in 50 mM sodium phosphate buffer at pH 7.4 (25 °C) and

Structure–property relationships in dicyanopyrazinoquinoxalines and their hydrogen-bonding-capable dihydropyrazinoquinoxalinedione derivatives

• Tural N. Akhmedov,
• Ajeet Kumar,
• Daken J. Starkenburg,
• Kyle J. Chesney,
• Khalil A. Abboud,
• Novruz G. Akhmedov,
• Jiangeng Xue and
• Ronald K. Castellano

Beilstein J. Org. Chem. 2024, 20, 1037–1052, doi:10.3762/bjoc.20.92

• supramolecular approach in the solar cell arena. π-Conjugated linear and branched oligothiophenes appended to H-bonding capable phthalhydrazide (PH) were prepared [14][15]. These compounds demonstrated a power conversion efficiency (PCE) twice as high as that of non-hydrogen bonding controls upon photovoltaic

• device fabrication with the electron acceptor C60. Subsequently, the design was extended to “ditopic” systems with diverse HB-capable units such as PH, 2,4-diamino-1,3,5-triazine (DAT), and barbiturate (B) that can form trimeric and hexameric “rosettes”, respectively [16]. The Sokolowski and Głowacki

• lactam form would mirror our prior work with phthalhydrazide (PH) and is also consistent with the work later reported by Takeda et al. We additionally envisioned that the DCPQs would serve as valuable comparators as the H-bonding capable DPQDs were studied. Reported here is the synthesis of a library of

(Bio)isosteres of ortho- and meta-substituted benzenes

• H. Erik Diepers and
• Johannes C. L. Walker

Beilstein J. Org. Chem. 2024, 20, 859–890, doi:10.3762/bjoc.20.78

• of physicochemical data showed that the experimentally determined distribution coefficient (logD) and calculated partition coefficient (clogP) are slightly higher for the bioisosteres and the aqueous solubility at pH 7.4 was also increased (Figure 8) [45]. Fluxapyroxad bioisostere (±)-64 had a higher

• fibrosis drug orkambi [67], to its 1,3-cubane bioisostere 183 (Figure 25) [51]. This comparison showed that while the distribution coefficient (logD) did not significantly change upon bioisosteric replacement, the solubility at neutral and low pH as well as the intrinsic clearance rate in human liver

• microsomes (CLint) improved significantly. The increase in solubility is particularly marked at low pH. A related observation was made by Poole and co-workers for quinoline-substituted 1,2,3-BCPs, where larger increases in the lipophilicity of the bioisosteric compound were also found at low pH [68]. One

Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria

• Kara A. Strickland,
• Brenda Martinez Rodriguez,
• Ashley A. Holland,
• Shelby Wagner,
• Michelle Luna-Alva,
• David E. Graham and
• Jonathan D. Caranto

Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75

• deoxygenated 30 mM tricine buffer at pH 7.5 were incubated for one hour at 21 °C in an anaerobic glove box. The samples were analyzed by LC–MS to measure final glyoxylate and NNG concentrations. The extracted ion chromatograms (EICs) showed that NNG was completely consumed and glyoxylate accumulated within the

• degradation was unrelated to E. coli being unable to uptake 2-NAE, in vitro experiments with purified, reduced Vs NnlA incubated with 2 mM 2-NAE at pH 7.5 were performed. The LC–MS EICs monitoring 2-NAE (m/z 105.03 ± 100 ppm) show the prominent peak characteristic for 2-NAE. The intensity of this peak does

• portion of NNG would be expected to exist as the inhibitory nitronate form at physiological pH, suggesting another potential role for nitramine groups as potent warheads in antibiotics. This antibiotic activity may also require further modification of NNG or its incorporation into a larger natural product

Synthesis and characterization of water-soluble C₆₀–peptide conjugates

• Yue Ma,
• Lorenzo Persi and
• Yoko Yamakoshi

Beilstein J. Org. Chem. 2024, 20, 777–786, doi:10.3762/bjoc.20.71

• successfully provide C60–peptide conjugates with one C60 and two peptide anchors as water-soluble moieties. Among three C60–peptide conjugates prepared, C60–oligo-Lys was soluble in water at neutral pH, and C60–oligo-Glu was soluble in buffer with a higher pH value, but C60–oligo-Arg was insoluble in water and

• purified. Solubility in water The water solubility of C60–peptide conjugates 5a–c was tested after the removal of any remaining solvent traces by lyophilization. Upon addition of Milli-Q® water (pH 7.0), C60–oligo-Lys (5a) was immediately and thoroughly solubilized. In contrast, the other conjugates, C60

• –oligo-Glu (5b, purified) and C60–oligo-Arg (5c, crude), did not produce transparent solutions in water at neutral pH value even by sonication (Figure 2). While C60–oligo-Glu (5b) was soluble in buffer with a higher pH value (>8.3), C60–oligo-Arg (5c) was not soluble in most polar and nonpolar solvents

Methodology for awakening the potential secondary metabolic capacity in actinomycetes

• Shun Saito and
• Midori A. Arai

Beilstein J. Org. Chem. 2024, 20, 753–766, doi:10.3762/bjoc.20.69

• carbonate and terminal olefin functionalities [50]. Thus, artificial methods of genetic engineering and chemistry also play an important role in the identification of novel secondary metabolites. Culture conditions Medium composition, pH, oxygen supply, light Simply modifying the culture conditions is an

• Zeeck and co-workers in the early 2000s, is a method in which the target bacteria are cultured under various conditions (medium composition, temperature, pH, oxygen supply, light quality and quantity, addition of precursors and enzyme inhibitors, etc.) and all metabolites obtained from them are analyzed

• to 12-fold increase) the expression of nine secondary metabolite biosynthetic gene clusters in Streptomyces coelicolor A3(2) [65]. Furthermore, it has been reported that changing the pH of the culture medium can also result in the production of new substances (Figure 3d). Jiang et al. achieved a

Research progress on the pharmacological activity, biosynthetic pathways, and biosynthesis of crocins

• Zhongwei Hua,
• Nan Liu and
• Xiaohui Yan

Beilstein J. Org. Chem. 2024, 20, 741–752, doi:10.3762/bjoc.20.68

• are highly soluble in hot water but slightly soluble in anhydrous ethanol and ether. The presence of multiple conjugated double bonds in crocins makes them susceptible to degradation when exposed to certain conditions, such as high temperature, the presence of metal ions or light, certain pH values

SOMOphilic alkyne vs radical-polar crossover approaches: The full story of the azido-alkynylation of alkenes

• Julien Borrel and
• Jerome Waser

Beilstein J. Org. Chem. 2024, 20, 701–713, doi:10.3762/bjoc.20.64

• source. Upon light irradiation, it can release an azide radical by homolysis of the I−N3 bond [46]. We were pleased to see that irradiation of a mixture of styrene (1a), Ph-EBX (2) and Ts-ABZ (3) afforded 17% isolated yield of the desired homopropargylic azide 4a (Table 1, entry 1). Heating the reaction

• to 80 °C instead of using light to form the radical only afforded traces of the product (Table 1, entry 2). Changing the solvent to DCE slightly increased the yield (Table 1, entry 3). Blue light with an emission spectrum centered around 467 nm was initially selected since Ph-EBX is known to absorb

• generate a large quantity of iodanyl radical from Ts-ABZ (3) homolysis and from the addition–elimination on Ph-EBX (2). Since no quencher is present in the mixture, we wondered if the accumulation of those radicals could be responsible for the low yields obtained. Addition of (TMS)3SiH, a H• donor