Synthesis and properties of 6-alkynyl-5-aryluracils

• Ruben Manuel Figueira de Abreu,
• Till Brockmann,
• Alexander Villinger,
• Peter Ehlers and
• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 898–911, doi:10.3762/bjoc.20.80

• molecules within and between a layer with two molecules at the top and the bottom of the unit cell. b) Determined from X-ray structural analysis at 123 K. Element color: carbon (grey), hydrogen (white), oxygen (red) and nitrogen (blue). The thermal ellipsoids are drawn at the 50% probability level. UV–vis

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

• residues outside of the heme pocket are colored in magenta. Nitrogen, oxygen, and iron atoms are colored blue, red, and orange, respectively. Figure generated using PyMOL. Phylogenetic tree of NnlA homologs with accession numbers. Branch lengths correspond to amino acid substitutions per position. Numbers

Advancements in hydrochlorination of alkenes

• Daniel S. Müller

Beilstein J. Org. Chem. 2024, 20, 787–814, doi:10.3762/bjoc.20.72

• . The acridinium ion 161 now takes on the additional role of a phase-transfer catalyst, facilitating the transport of the chloride ion into the lipophilic alkene phase. Subsequently, under irradiation with blue LEDs, the acridinium cation 161 and the chloride anion engage in a single-electron-transfer

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

• . In addition, 5a was not highly soluble in most nonpolar solvents, including toluene and CH2Cl2, but slightly soluble in other polar solvents, including MeOH and DMSO. The solubility of C60–peptide conjugates 5a–c was in line with DLS data of the aqueous solutions or dispersions. While 5a (blue line

Substrate specificity of a ketosynthase domain involved in bacillaene biosynthesis

• Zhiyong Yin and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2024, 20, 734–740, doi:10.3762/bjoc.20.67

• ]. These intermediates consistently showed masses two Da higher than expected, in agreement with a fully saturated intermediate at module 3 [16]. Subsequent investigations demonstrated that the C22=C23 double bond in 1 is incorporated in a post-PKS step through the action of BaeS (highlighted in blue) [18

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

• 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

• light of lower wavelength, which is expected to cause degradation [47]. Indeed, when the reaction was carried out using 440 nm blue light a lower yield of 10% was obtained and full conversion of the EBX reagent was observed (Table 1, entry 4). Next, we wanted to test different additives in the

• under blue light irradiation afforded 4a in 17% NMR yield (Table 2, entry 1). The major byproduct formed during the transformation was identified as diazide 6. When a copper photocatalyst is involved, a lot of diazidation can be observed. We assumed it could be caused by the reaction of Ts-ABZ (3) with

Palladium-catalyzed three-component radical-polar crossover carboamination of 1,3-dienes or allenes with diazo esters and amines

• Geng-Xin Liu,
• Xiao-Ting Jie,
• Ge-Jun Niu,
• Li-Sheng Yang,
• Xing-Lin Li,
• Jian Luo and
• Wen-Hao Hu

Beilstein J. Org. Chem. 2024, 20, 661–671, doi:10.3762/bjoc.20.59

• started our studies with the palladium-catalyzed MCR of ethyl diazoacetate (1a), 1,3-butadiene (2a), and 1-phenylpiperazine (3a) in the presence of 5 mol % Pd(OAc)2 and 10 mol % Xantphos as ligand. To our delight, after irradiation with blue LED light in dimethylformamide (DMF) for 12 h at room

• , hydride shift process, and photoinduced homolytic cleavage of the C–Pd bond, furnishing hybrid α-ester alkylpalladium radical I. In path b, upon irradiation with blue light, photoexcited Pd(0)Ln* reduces ethyl diazoacetate (1a) to Pd-radical species I by a proton-coupled electron transfer (PCET) process

• strategy with diazo esters to access unsaturated γ- and ε-AA derivatives. Substrate scope of diazo compounds, 1,3-dienes and amines. aReactions (1/2/3/Pd(OAc)2/Xantphos = 0.3:0.4:0.2:0.01:0.02 mmol) were irradiated with blue LED light (467 nm) in 2.0 mL DMF at rt for 12 h under argon. Isolated yields

Introduction of a human- and keyboard-friendly N-glycan nomenclature

• Friedrich Altmann,
• Johannes Helm,
• Martin Pabst and
• Johannes Stadlmann

Beilstein J. Org. Chem. 2024, 20, 607–620, doi:10.3762/bjoc.20.53

• are shown in blue [45]. Multi-antennary N-glycans. In addition to regular proglycan abbreviation, intended ambiguity style (see chapter below) is shown in grey for selected structures. The colored codes are just for illustration. Proglycan annotation of LacNAc-repeats. A: Development of the annotation

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A

• Michael O. Akintubosun and
• Melanie A. Higgins

Beilstein J. Org. Chem. 2024, 20, 589–596, doi:10.3762/bjoc.20.51

• imidazole in binding buffer (10, 20, 50, and 500 mM imidazole). Fractions were run on an ExpressPlusTM PAGE Gel (GenScript) and protein was visualized using Coomassie Brilliant Blue G-250 (VWR). Fractions containing Hyg17 were pooled and further purified using a HiLoad 16/600 Superdex 75 pg size exclusion

• inositols with NAD+, (b) myo-inositol with NAD+ or NADP, and (c) myo-inositol at different pH values (orange is HEPEs, green is Tris, blue is CHES, and red is CAPS). NAD(P)H concentrations were measured after 20 minutes. Michaelis–Menten plots for Hyg17 using varying concentrations of (d) myo-inositol, (e

Possible bi-stable structures of pyrenebutanoic acid-linked protein molecules adsorbed on graphene: theoretical study

• Yasuhiro Oishi,
• Motoharu Kitatani and
• Koichi Kusakabe

Beilstein J. Org. Chem. 2024, 20, 570–577, doi:10.3762/bjoc.20.49

• conformation 1, 2, and the conformation at the saddle point, we measured the dihedral angles and the distance between two hydrogen atoms using Xcrysden [10]. (a) Molecular structure of 1-pyrenebutanoic acid succinimidyl ester (PASE). The black, white, red, and blue balls represent C, H, O, and N atoms

Synthesis of photo- and ionochromic N-acylated 2-(aminomethylene)benzo[b]thiophene-3(2Н)-ones with a terminal phenanthroline group

• Vladimir P. Rybalkin,
• Sofiya Yu. Zmeeva,
• Lidiya L. Popova,
• Irina V. Dubonosova,
• Olga Yu. Karlutova,
• Oleg P. Demidov,
• Alexander D. Dubonosov and
• Vladimir A. Bren

Beilstein J. Org. Chem. 2024, 20, 552–560, doi:10.3762/bjoc.20.47

• distance 3.6153(10) Å (shift 1.6063(18) Å, twist and fold angles 0.0°). The closest contact in the phenanthroline fragment (blue plane–blue plane, top fragment in Figure 4) had a plane centroid–plane centroid distance of 3.5398(9) Å (shift 0.4273(18) Å, twist and fold angles 0.00°). One pyridine cycle of

• the phenanthroline unit was also involved in a π–π-stacking interaction (blue plane–green plane in Figure 4), with the plane centroid–plane centroid distance being 3.6998(8) Å (plane shift 1.4919(17) Å, twist and fold angles 1.54° and 1.92°, respectively). Cation-induced transformations of the

Development of a chemical scaffold for inhibiting nonribosomal peptide synthetases in live bacterial cells

• Fumihiro Ishikawa,
• Sho Konno,
• Hideaki Kakeya and
• Genzoh Tanabe

Beilstein J. Org. Chem. 2024, 20, 445–451, doi:10.3762/bjoc.20.39

• modular synthases [5]. They used the inhibitors of individual domains to investigate the biosynthetic pathway of blue pigment synthetase A, which produces the blue pigment indigoidine, and demonstrated that their results complement the proposed biosynthetic pathway. Furthermore, among the catalytic domain

• probe 3 (10 µM) in either the absence or presence of ʟ-Phe-AMS inhibitors 1, 2, or 4–9 (10 or 100 µM). GrsA, gramicidin S synthetase; AMS, 5′-O-sulfamoyladenosine; FL, fluorescent gel; CBB; Coomassie brilliant blue. Synthesis of 2′-OH-substituted ʟ-Phe-AMS derivatives. Reagents and conditions: (a) NaH

Enhanced host–guest interaction between [10]cycloparaphenylene ([10]CPP) and [5]CPP by cationic charges

• Eiichi Kayahara,
• Yoshiyuki Mizuhata and
• Shigeru Yamago

Beilstein J. Org. Chem. 2024, 20, 436–444, doi:10.3762/bjoc.20.38

• between the Hirshfeld surface and the contacting atoms, most sp2-hybridzed carbon atoms of the [10]CPP host have short contact with the Hirshfeld surface, as shown in green, despite the tilting of [10]CPP and [5]CPP. In the crystal packing, there were two orientations, as highlighted in blue and red in

• ). Furthermore, the tilting of the complex in adjacent columnar structures with respect to the short axis is opposite to each other, as in a herringbone structure, and such columnar structures are parallel to each other through a columnar structure consisting of a host–guest complex in blue and its counterions

• . On the other hand, the complex in blue forms a 1D columnar structure with alternating counterions (Figure 7g), and each column is parallel to the others. Furthermore, the complex is tilted at approximately 30° relative to the long axis of the unit lattice. Conclusion [10]CPP encapsulates [5]CPP2+ in

Green and sustainable approaches for the Friedel–Crafts reaction between aldehydes and indoles

• Periklis X. Kolagkis,
• Eirini M. Galathri and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2024, 20, 379–426, doi:10.3762/bjoc.20.36

Mechanisms for radical reactions initiating from N-hydroxyphthalimide esters

• Carlos R. Azpilcueta-Nicolas and
• Jean-Philip Lumb

Beilstein J. Org. Chem. 2024, 20, 346–378, doi:10.3762/bjoc.20.35

• deprotonation of 21 to provide radical intermediate 22 [45]. Finally, the iridium excited state (*IrIII) formed under blue light irradiation oxidizes 22 to form product 23 and the corresponding reduced IrII complex, beginning a new photocatalytic cycle. Photocatalytic oxidative quenching mechanism The

• irradiation at 390 nm or through RuII-mediated EnT under blue light irradiation (456 nm). Following excitation, SET from the enamide to the active ester forms intermediate 53, which undergoes fragmentation and radical recombination to afford intermediate 54. At this stage, the indole nucleophile substitutes

• hydrogen atom to terminate the radical reaction. The proposed mechanism of the hydroalkylation cascade is depicted in Scheme 13B. Upon excitation of complex 59 with blue light, intra-complex SET takes place from the HE to the NHPI ester, leading to the formation of tert-butyl radical 64 and radical cation

Spatial arrangements of cyclodextrin host–guest complexes in solution studied by ¹³C NMR and molecular modelling

• Konstantin Lebedinskiy,
• Ivan Barvík,
• Zdeněk Tošner,
• Ivana Císařová,
• Jindřich Jindřich and
• Radim Hrdina

Beilstein J. Org. Chem. 2024, 20, 331–335, doi:10.3762/bjoc.20.33

• peaks of all prochiral carbon signals of the guest upon complexation with α-CD. The biggest split, 22.5 Hz, was observed for prochiral carbons 8 and 10, depicted in Figure 1 in green color, followed by a split of carbons 3 and 9 (in blue color) and the smallest difference in the magnetic field shielding

• α-CD cavity. The NMR splitting is generally larger if the prochiral guest atoms are located closer to the cavity of the α-CD. In other words, the splitting is larger, if the radius of a density is bigger or the density runs deeper into the α-CD cavity. In Figure 3, the green and blue densities with

• well-separated light and dark clouds (belonging to different prochiral carbons from a pair) have larger radii and run deeper into the α-CD cavity than the red density with mixed light and dark clouds. Accordingly, our NMR experiment only showed splitting for the green and blue atoms (see Figure 1

Synthesis of π-conjugated polycyclic compounds by late-stage extrusion of chalcogen fragments

• Aissam Okba,
• Pablo Simón Marqués,
• Kyohei Matsuo,
• Naoki Aratani,
• Hiroko Yamada,
• Gwénaël Rapenne and
• Claire Kammerer

Beilstein J. Org. Chem. 2024, 20, 287–305, doi:10.3762/bjoc.20.30

• reactive as a thin-film on a glass substrate, with the generation of the desired perylene upon photoirradiation with a blue LED (λ = 470 nm) [62]. Finally, cooperativity of light and heat was demonstrated on a crystalline sample of sulfoxide 4a, where photoirradiation enhanced the SO-extrusion process at

• ]. Copyright 2023 American Chemical Society. This content is not subject to CC BY 4.0. Constant-height STM measurement of decacene on Au(111) using a CO-functionalized tip (sample voltage V = 20 mV), with the chemical structure of decacene superimposed in blue as a guide to the eye. Two different tip height

Additive-controlled chemoselective inter-/intramolecular hydroamination via electrochemical PCET process

• Kazuhiro Okamoto,
• Naoki Shida and
• Mahito Atobe

Beilstein J. Org. Chem. 2024, 20, 264–271, doi:10.3762/bjoc.20.27

• current (Figure 2B, blue line). We considered that the inter- and intramolecular chemoselectivities were derived from the pKa of the proton sources. The pre-organization of the amide substrate and phosphate bases is an important process in PCET [13]. Recently, Gschwind et al. published a detailed NMR

• (Figure 2B, blue line). However, in the presence of AcOH, the N-alkylation yield was low (Table 1, entry 6) owing to the competitive Kolbe oxidation of the cathodically generated acetate anion. In fact, the oxidation potential of Bu4NOAc is lower than that of 1 (Figure 2C, orange line). A decrease in the

• affect the oxidation current. In cathodic events, the reduction of CH2Cl2 primally occurred under standard conditions because the reduction wave of the blank solution appeared at approximately −1.0 V (Figure 2D, blue line). The resulting cathodically generated chloride ion (Cl−) has a lower oxidation

Catalytic multi-step domino and one-pot reactions

• Svetlana B. Tsogoeva

Beilstein J. Org. Chem. 2024, 20, 254–256, doi:10.3762/bjoc.20.25

• trisubstituted 3-iodoindoles, which are valuable substrates for the synthesis of, e.g., blue emitters in good yield [16]. The power of double click reactions toward functionalized bis(1,2,3-triazole) derivatives has been demonstrated in the Full Research Paper by Reissig and Yu. The authors successfully combined

Substitution reactions in the acenaphthene analog of quino[7,8-h]quinoline and an unusual synthesis of the corresponding acenaphthylenes by tele-elimination

• Ekaterina V. Kolupaeva,
• Narek A. Dzhangiryan,
• Alexander F. Pozharskii,
• Oleg P. Demidov and
• Valery A. Ozeryanskii

Beilstein J. Org. Chem. 2024, 20, 243–253, doi:10.3762/bjoc.20.24

• undergo a nucleophilic substitution. Indeed, upon boiling with an excess of sodium methoxide in methanol, the crude dinitration product 10(12) gives up to 6% of a new substance with low mobility on sorbents and blue luminescence under UV light. Its spectral analysis confirmed the symmetrical structure

• approach to acenaphthylene systems. Suggested amination products 6 and two resonance forms of dianion 7. Targeted dipyridoacenaphthylene 8. Molecular and crystal structure of salt 5·HCl·2H2O is strongly dominated by severe H-bonding (blue dotted lines) and π-stacking (one preorganized layer along the c

• overlap (с). Again, π-stacking and H-bonding (blue dotted lines) strongly dominate in this structure. Fragment of the crystal packing of neutral dipyridoacenaphthene 5 showing self-association via multiple C–H…N contacts (blue dotted lines) between three independent molecules. Structure of

Photochromic derivatives of indigo: historical overview of development, challenges and applications

• Gökhan Kaplan,
• Zeynel Seferoğlu and
• Daria V. Berdnikova

Beilstein J. Org. Chem. 2024, 20, 228–242, doi:10.3762/bjoc.20.23

• towards indigo and its derivatives have been recently reviewed in detail by Hecht and Huang [9]. Strucutre and photophysical properties of indigo Indigo dye is blue crystalline powder, which starts to melt at above 390 °C and sublimes in vacuum at above 170 °C [2]. In 1980, it was discovered that indigo

• -chromophores” after the shape of the main structural fragment resembling the Latin letter “H” (Figure 4) [19]. The small HOMO–LUMO gap and, thus, the long-wavelength absorption are responsible for the purple color of indigo in vapors, which changes into deep blue color in the crystalline state due to formation

• these compounds especially attractive for the design of new biocompatible photochemical tools due to the possibility of performing the switching close to or within the biooptical transparency window (650–900 nm) [87]. The negative photochromism of indigos, which implies a blue-shift of absorption during

Optimizations of lipid II synthesis: an essential glycolipid precursor in bacterial cell wall synthesis and a validated antibiotic target

• Milandip Karak,
• Cian R. Cloonan,
• Brad R. Baker,
• Rachel V. K. Cochrane and
• Stephen A. Cochrane

Beilstein J. Org. Chem. 2024, 20, 220–227, doi:10.3762/bjoc.20.22

• in red and antimicrobial-binding motifs highlighted with blue arcs. R1 = H or Ac; R2 = H or Ac; R3 = OH, OMe or NH2; R4 = H or COOH; R5 = Gly5, Ala2, Ala-Ser/Ala or ᴅ-Asp; R6 = OH, OMe or NH2. These structural modifications are described in detail by Münch and co-workers [9]. For more details on

Tandem Hock and Friedel–Crafts reactions allowing an expedient synthesis of a cyclolignan-type scaffold

• Viktoria A. Ikonnikova,
• Cristina Cheibas,
• Oscar Gayraud,
• Alexandra E. Bosnidou,
• Nicolas Casaretto,
• Gilles Frison and
• Bastien Nay

Beilstein J. Org. Chem. 2024, 20, 162–169, doi:10.3762/bjoc.20.15

• ]. Results and Discussion To test the feasibility of this reaction sequence, the aromatic substrate 1 readily accessible by the prenylation of commercial diethyl benzylmalonate [21] was first used. The photooxygenation of 1 was performed in CH2Cl2 in the presence of methylene blue (MB) as a photosensitizer

Photoinduced in situ generation of DNA-targeting ligands: DNA-binding and DNA-photodamaging properties of benzo[c]quinolizinium ions

• Julika Schlosser,
• Olga Fedorova,
• Yuri Fedorov and
• Heiko Ihmels

Beilstein J. Org. Chem. 2024, 20, 101–117, doi:10.3762/bjoc.20.11

• ), 137.3 (C4a), 139.5 (C10a), 153.1 (C9), 155.6 (C8), 171.5 (COCH3); HRMS–ESI+ (m/z): [M]+ calcd. for C17H17N2O3+, 297.1234; found, 297.1235. Absorption spectra of styrylpyridine derivatives 2a (black), 2b (red), 2c (blue), 2d (green), 2e (magenta), 2f (orange), and 2g (purple) in MeCN (A) and H2O (B) (c

• = 20 µM). Changes of the absorption spectra during the irradiation of 2a in MeCN for 16 min (A), 2b in MeCN for 4 min (B), and 2b in H2O/MeCN 49:1 for 6 min (C) (c = 20 µM, λex > 220 nm, irradiated in a cuvette). Blue: spectrum of the starting material before irradiation; red: spectrum at the end of

• the irradiation. Changes of the absorption spectra during the irradiation of 2c for 13 min (A), 2d for 12 min (B), 2e for 15 min (C), 2f for 10 min (D), and 2g for 7 min (E) (in MeCN, c = 20 µM, λex > 220 nm, irradiated in a cuvette). Blue: spectrum of the starting material before irradiation; red

Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations

• Laura Abella,
• Gerard Novell-Leruth,
• Josep M. Ricart,
• Josep M. Poblet and
• Antonio Rodríguez-Fortea

Beilstein J. Org. Chem. 2024, 20, 92–100, doi:10.3762/bjoc.20.10

• profiles for C60 + C60+• radical and C60 + C60 neutral dimerizations computed with the standard molecular (M) approach (atomic basis functions, ADF) are represented in grey and blue, respectively. Energy profiles for the dimerization of 2 C60 (neutral) and C60 + C60•+ (radical cation) fullerenes inside the