Mechanistic investigations of polyaza[7]helicene in photoredox and energy transfer catalysis

• Johannes Rocker,
• Till J. B. Zähringer,
• Matthias Schmitz,
• Till Opatz and
• Christoph Kerzig

Beilstein J. Org. Chem. 2024, 20, 1236–1245, doi:10.3762/bjoc.20.106

• as the radical cation, Aza-H•+, which is in perfect agreement with our proposed photoinduced electron transfer step, while no triplet-excited Aza-H is observed (Figure 2A, blue spectrum). Since the direct ionization of Aza-H also contributes to this spectrum, we recorded a spectrum of only Aza-H in

• (blue) and phosphorescence (green) spectra measured at 77 K in MeOH/EtOH (4:1). B) Transient absorption spectra of 25 µM (initial ground-state absorbance at the laser wavelength, 0.2) Aza-H in Ar-saturated (black) and air-saturated (red) MeCN/H2O (9:1) recorded after 250 ns and the difference spectrum

• . Mechanistic LFP experiments of 25 µM Aza-H with 4CP in MeCN/H2O (9:1) after 355 nm laser pulses. A) TA spectra recorded after 250 ns of solely Aza-H in air-saturated solution (red), in Ar-saturated solution with 200 mM 4CP (blue) and the difference spectrum of both (green). Inset: Kinetic traces of Aza-H with

Introduction of peripheral nitrogen atoms to cyclo-meta-phenylenes

• Koki Ikemoto and
• Hiroyuki Isobe

Beilstein J. Org. Chem. 2024, 20, 1207–1212, doi:10.3762/bjoc.20.103

• shown. (b) Packing structures. Chloroform molecules in the crystal of 3b are omitted for clarity. X-ray charge density analyses of 3a and [6]CMP. (a) Deformation map (Fo – Fc) of a pyridine ring in 3a (contour interval: 0.05 e·Å−3, positive: red, negative: blue). (b) Electrostatic potential maps mapped

• on the 0.0067 e·Å−3 isosurface for the electron density. Response towards acid treatment with nitrogen-doped CMPs. (a) Absorption spectra of 3a (CHCl3, 2.3 × 10−6 M) in the absence (black) and presence of trifluoroacetic acid (green: 4.3 × 10−2 M, blue: 2.1 × 10−1 M, red: 4.2 × 10−1 M). (b

• ) Absorption spectra of 6 (CHCl3, 1.9 × 10−6 M) in the absence (black) and presence of trifluoroacetic acid (green: 4.3 × 10−2 M, blue: 2.1 × 10−1 M, red: 4.2 × 10−1 M). Syntheses of 3a and 3b. Supporting Information Supporting Information File 50: Experimental and copies of spectra. Supporting Information

Stability trends in carbocation intermediates stemming from germacrene A and hedycaryol

• Naziha Tarannam,
• Prashant Kumar Gupta,
• Shani Zev and
• Dan Thomas Major

Beilstein J. Org. Chem. 2024, 20, 1189–1197, doi:10.3762/bjoc.20.101

• electron density (ρ) and the reduced-density gradient (RDG, s). The NCIplot provides qualitative information, and it can successfully map real-space regions where non-covalent interactions are prominent. The resulting plots have a color scheme of red–green–blue scale, where red represents attractive

• interactions and blue represents repulsive interactions. Additionally, we carried out natural bonding orbital (NBO) analysis using the NBO 3.1 program [42] as implemented in the Gaussian 16 package. The computations are performed at the same level of theory that we chose initially for optimization (M06-2X/6-31

• , with a larger blue isosurface than A, has greater steric hindrance than A (Figure 3). Although this difference is not directly quantified here, this is likely part of the reason behind the greater stability of A over B. A similar analysis can be performed for C and D (Figure S2 in Supporting

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

• from 388 to 423 nm, indicative of π–π* transitions. On the contrary, DPQDs exhibited more structured, blue-shifted bands with λmax from 357–400 nm. At the same time, DCPQs exhibit intramolecular charge transfer (ICT) bands at lower energy due to the dicyanopyrazinopyrazine moiety as a strong acceptor

• intermolecular N–H∙∙∙N and C–H∙∙∙O=C distances (d). Unit cell comprised of four molecules of 2b (e). Herringbone packing of 2b showing the distance between adjacent ring centroids (f). Herringbone backing of 2b shown as a spacefilling model (g). Atom color code: blue N, gray C, red O, and white H. Synthesis of

Auxiliary strategy for the general and practical synthesis of diaryliodonium(III) salts with diverse organocarboxylate counterions

• Naoki Miyamoto,
• Daichi Koseki,
• Kohei Sumida,
• Elghareeb E. Elboray,
• Naoko Takenaga,
• Ravi Kumar and
• Toshifumi Dohi

Beilstein J. Org. Chem. 2024, 20, 1020–1028, doi:10.3762/bjoc.20.90

• benzoate in 70% yield (Scheme 6A). Furthermore, iodonium salt 7aj with an umbelliferone-3-carboxylate counterion displayed extremely weak blue fluorescence emission under 365 nm UV light compared to free carboxylic acid 6j. This unique property was utilized for tracing the counterion exchange process of

• the diaryliodonium(III) salt by irradiating with 365 nm UV light. The counterion exchange in umbelliferone carboxylate salt 7aj with trifluoroacetic acid was rapid, and after 30 s, the completion of the reaction was confirmed by the emergence of strong blue fluorescence emission due to the liberation

Spin and charge interactions between nanographene host and ferrocene

• Akira Suzuki,
• Yuya Miyake,
• Ryoga Shibata and
• Kazuyuki Takai

Beilstein J. Org. Chem. 2024, 20, 1011–1019, doi:10.3762/bjoc.20.89

• clarification. XPS spectrum for FeCp2-ACFs-150 in the Fe2p region shown with fitting curves. XPS spectra of (left) FeCp2-ACFs-150 and (right) ACFs in the C1s region with fitting curves. Raman spectra for ACFs and FeCp2-ACFs-150. Each raw data (black) was fitted to the G-band (blue) and D-band (red) components

A Diels–Alder probe for discovery of natural products containing furan moieties

• Alyssa S. Eggly,
• Namuunzul Otgontseren,
• Carson B. Roberts,
• Amir Y. Alwali,
• Haylie E. Hennigan and
• Elizabeth I. Parkinson

Beilstein J. Org. Chem. 2024, 20, 1001–1010, doi:10.3762/bjoc.20.88

• utilizing the probe in additional strains to probe for novel natural products similar to the MMFs. A) Bioactive natural products containing a furan ring (blue) or 3-furoic acid moiety (red): plakorsin D, wortmannin, tournefolin C, rosefuran, and flufuran and their respective biological activities. B) MMF

Monitoring carbohydrate 3D structure quality with the Privateer database

• Jordan S. Dialpuri,
• Haroldas Bagdonas,
• Lucy C. Schofield,
• Phuong Thao Pham,
• Lou Holland and
• Jon Agirre

Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83

• conformational landscape of pyranose sugars. A well-modelled ᴅ-sugar would be expected to be in the lowest-energy conformation and have a theta angle close to 0° and would be indicated by a blue point; deviations from the ideal conformation are highlighted with a red cross. Right: Real space correlation

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