A laterally-fused N-heterocyclic carbene framework from polysubstituted aminoimidazo[5,1-b]oxazol-6-ium salts

• Andrew D. Gillie,
• Matthew G. Wakeling,
• Bethan L. Greene,
• Louise Male and
• Paul W. Davies

Beilstein J. Org. Chem. 2024, 20, 621–627, doi:10.3762/bjoc.20.54

• fused imidazolium core (Scheme 2). No reaction was observed between 6a and [Ir(cod)Cl]2 in the presence of NEt3. A solution of the free carbene was prepared from 6 and reacted with [Ir(cod)Cl]2 and then CO to afford the AImOxIr(CO)Cl complex 15. A minor side-product with a strong red colour was formed

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

• 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

• for inositol dehydrogenases. (b) Comparison of the hygromycin A (red) and hygromycin A-like (orange) biosynthetic gene clusters. A more detailed comparison can be found in Supporting Information File 1, Table S2. Kinetic parameters for Hyg17. Supporting Information Supporting Information File 36

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

• graphene Conformations of PASE are interconverted by mutual transition when the molecule is twisted around one of the carbon–carbon single bonds in the alkyl chain. The rotational motion connecting conformation 1 and conformation 2 happens around the single bond indicated by the solid red line in Figure 1a

• activation barrier-type pathway. The pathway connecting conformations 1 and 2 appears as a torsion of the alkyl chain around the carbon–carbon single bond, as indicated by the solid red line in Figure 1a. This is a kind of rotational motion. We determined the dihedral angles formed by the four carbon atoms

• connected by the red line in Figure 3, and the values of dihedral angles for conformations 1, 2, and the conformation at the activation barrier top are collected in Table 1. From these values, we can interpret the torsion as an approximate rotation. We call the rotations 0, π/3, and 2π/3 as an approximation

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

• °, fold angle 4.38°). The molecular packing of compound 3b was characterized by the presence of numerous π–π interactions (Figure 4). Intermolecular interactions in the benzo[b]thiophene fragment (red planes in Figure 4) were characterized by the following parameters: plane centroid–plane centroid

Synthesis and biological profile of 2,3-dihydro[1,3]thiazolo[4,5-b]pyridines, a novel class of acyl-ACP thioesterase inhibitors

• Jens Frackenpohl,
• David M. Barber,
• Guido Bojack,
• Birgit Bollenbach-Wahl,
• Ralf Braun,
• Rahel Getachew,
• Sabine Hohmann,
• Kwang-Yoon Ko,
• Karoline Kurowski,
• Bernd Laber,
• Rebecca L. Mattison,
• Thomas Müller,
• Anna M. Reingruber,
• Dirk Schmutzler and
• Andrea Svejda

Beilstein J. Org. Chem. 2024, 20, 540–551, doi:10.3762/bjoc.20.46

• monocotyledon weeds in wheat, including resistant species, we tested the three selected 2,3-dihydro[1,3]thiazolo[4,5-b]pyridines 7b, 7c, and 13b against commercially relevant weeds in corn, e.g., crabgrass or red fingergrass (DIGSA) and goosegrass or crowsfoot grass (ELEIN), together with Johnson grass (SORHA

A new analog of dihydroxybenzoic acid from Saccharopolyspora sp. KR21-0001

• Rattiya Janthanom,
• Yuta Kikuchi,
• Hiroki Kanto,
• Tomoyasu Hirose,
• Arisu Tahara,
• Takahiro Ishii,
• Arinthip Thamchaipenet and
• Yuki Inahashi

Beilstein J. Org. Chem. 2024, 20, 497–503, doi:10.3762/bjoc.20.44

• to red). Next, the mixtures were incubated at 37 °C for 1 h. After incubation, 25 µL of 1 M HCl was added to each sample for neutralization. The mixtures were concentrated to dryness in vacuo, dissolved in acetonitrile, and analyzed by LC–MS. Biological activity Antioxidant activity The antioxidant

Pseudallenes A and B, new sulfur-containing ovalicin sesquiterpenoid derivatives with antimicrobial activity from the deep-sea cold seep sediment-derived fungus Pseudallescheria boydii CS-793

• Zhen Ying,
• Xiao-Ming Li,
• Sui-Qun Yang,
• Hong-Lei Li,
• Xin Li,
• Bin-Gui Wang and
• Ling-Hong Meng

Beilstein J. Org. Chem. 2024, 20, 470–478, doi:10.3762/bjoc.20.42

• . Key 1H-1H COSY (bond lines), and HMBC (red arrows) correlations of 1–3. NOE correlations of compounds 1 and 2 (solid line indicates β-orientation and dashed lines represent α-orientation). X-ray crystal structure of compounds 1–3 (with a thermal ellipsoid probability of 50%). Proposed biosynthetic

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

• Figure 7e. In the packing shown in red, the host–guest complex is alternately stacked with two counterions to forms a one-dimensional (1D) columnar structure in which the complex is tilted at approximately 45° relative to the short axis (Figure 7f and Supporting Information File 1, Figure S3

• −/1,2-dichloroethane upon scanning in (a) positive and (b) negative directions. UV–vis–NIR spectra of [10]CPP⊃[5]CPP2+[B(C6F5)4−]2 (black), [10]CPP (blue), and [5]CPP2+[B(C6F5)4−]2 (red) in CH2Cl2. Top and side view of [10]CPP⊃[5]CPP2+ complexes a) 1, b) 2, and c) 3 obtained by DFT calculation at the

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

• decarboxylative transformations of NHPI esters using a phenothiazine-based organophotoredox catalyst PTH1. This type of catalyst is believed to facilitate SET to NHPI esters through the formation of EDA complexes. Interestingly, upon addition of RAE 58 to a solution of PTH1, a noticeable red shift in the UV–vis

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

• was detected for carbons 1 and 3 (in red color). The same 1D 13C NMR spectra were measured for guest molecule 1 in host cavities of β-CD and γ-CD, showing almost no split of prochiral carbon peaks and suggesting a higher degree of conformational flexibility of the host–guest complexes than for the

• 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

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• ]. Validating binding in solution and assessing binding affinity As CMA1 both exhibited multiple binding sites and robust binding to blood group epitopes (H-antigen), we hypothesized that it would be capable of agglutinating red blood cells, justifying its new name. When testing the protein recombinantly

• array and dividing the results by the standard deviation. Agglutination assay The hemagglutinating activity of CMA1 was determined in V-bottom 96-well plates by a twofold serial dilution procedure in PBS using rabbit red blood cells (Atlantis France). 25 µL of 4% erythrocyte suspension was added to an

• heatmap via the get_heatmap function of glycowork. Representative glycans are shown. Assessing and quantifying in-solution binding of CMA1. (a) Erythrocyte agglutination assay. Using rabbit red blood cells, CMA1 protein recombinantly produced in mammalian cells was used in a two-fold dilution series to

Unveiling the regioselectivity of rhodium(I)-catalyzed [2 + 2 + 2] cycloaddition reactions for open-cage C₇₀ production

• Cristina Castanyer,
• Anna Pla-Quintana,
• Anna Roglans,
• Albert Artigas and
• Miquel Solà

Beilstein J. Org. Chem. 2024, 20, 272–279, doi:10.3762/bjoc.20.28

• α- and β-bonds were systematically observed at different temperatures. The protons of the two methyl groups around δ 2.30 ppm were used as diagnostic signals. For the major isomer (red dots, Figure 2), the spectrum exhibits two singlets at δ = 2.27 and 2.28 ppm, corresponding to the two different

• methyl groups in the six-membered ring formed in the cycloaddition and coming from the starting diyne 1a (highlighted in red in Scheme 2). In contrast, for the minor isomer (green dots), which has Cs symmetry, the two methyl groups (highlighted in green in Scheme 2) appear as a single peak at δ = 2.40

• protons marked in red and the ones marked in green might be those of the β-isomer (29%). Unfortunately, NMR experiments did not allow to differentiate between α- and β-3a derivatives. The reaction was carried out also with bis(fulleroid) derivative 2b, exhibiting the same behavior. Conclusion In this

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

• in the Full Research Paper by Nath and co-workers. The newly synthesized porphyrin derivatives displayed significant red-shifted absorption and emission compared to simple meso-tetraarylporphyrins [14]. The Carlone group reports an Enders-type triple cascade reaction toward cyclohexenals, using

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

• to the presence of the electron-withdrawing ester groups. Importantly, only the Z-form of 18c was found to be stable enough with a half-life of 2.8 min at room temperature in acetonitrile (77% of Z-isomer in PSS) and 4.1 minutes in toluene (91% of Z-isomer in PSS) after irradiation with red light

• , recently attracted increased attention as red-light photoswitches. The investigation of the photophysical properties of these compounds began in 2017 with the work by Hecht, Jacquemin and co-workers [42]. In their study, a series of symmetrical as well as unsymmetrical N,N'-diaryl-substituted indigos 19a–h

• the existence of the isomeric mixtures in the dark state. Interestingly, the initial E/Z ratio was restored when the compounds were left in darkness after irradiation with red light (660 nm). The time required for the restoration of the initial state varied from 58 s (in the presence of electron

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

Perspectives on push–pull chromophores derived from click-type [2 + 2] cycloaddition–retroelectrocyclization reactions of electron-rich alkynes and electron-deficient alkenes

• Michio Yamada

Beilstein J. Org. Chem. 2024, 20, 125–154, doi:10.3762/bjoc.20.13

• shoulder emission at 612 nm. When the solvent was changed from toluene to benzonitrile and the polarity of the solvent increased, the emission at 612 nm remained almost unchanged, while the emission at 675 nm significantly quenched with a red shift of 35 nm. In the transient absorption spectra of 60 in

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

• derivatives 2b–g showed a slight bathochromic shift mostly in the range of λmax = 333–360 nm, whereas for the nitro-substituted compound 2a a stronger red shift of the absorption maximum was observed, presumably caused by the strong electron-withdrawing property of the nitro group resulting in a more

• general, the absorption maximum of the derivatives 2b–g decreased during the photoreaction with formation of new red-shifted absorption bands. Nevertheless, the new red-shifted absorption band of the amino-substituted styryl derivative 2b in MeCN was weak and very broad, indicating only negligible

• (cf. Supporting Information File 1, Figures S3C–S6C) than in polar, aprotic MeCN solution. In MeOH the photoreactions were inefficient as indicated by the lack of red-shifted bands or by formation of broad, weak absorption bands (cf. Supporting Information File 1, Figures S1, S2A, S3A, S4A, S5A, and

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

• barriers are in kcal mol−1 and distances of the most relevant bonds for the different structures are represented in Å in a zoomed image. Energy profile for C60 + C60+• radical dimerization (phase 1) computed with the periodic (P) approximation (plane waves, VASP) is represented in red, while energy

Optimizing reaction conditions for the light-driven hydrogen evolution in a loop photoreactor

• Pengcheng Li,
• Daniel Kowalczyk,
• Johannes Liessem,
• Mohamed M. Elnagar,
• Dariusz Mitoraj,
• Radim Beranek and
• Dirk Ziegenbalg

Beilstein J. Org. Chem. 2024, 20, 74–91, doi:10.3762/bjoc.20.9

• operation of the reactor design concept of a guided inner circulation around the draft tube. Figure 4 shows the red channel values of ROIs for the mixing experiments with different stirring speeds (430, 560, 740, and 860 rpm). The mixing time in the draft tube only slightly depends on the stirring speed

• shot under red light, which matched the absorption properties of the dye, to obtain optimal optical visualization. Digital images extracted from videos (see Supporting Information File 2) were processed with the Python OpenCV package to quantify the mixing time (see Supporting Information File 3

• , Python code) by following the color evolution in the videos from red towards black under the red-light environment [49]. ROI used as the working zone were defined on the images when these were processed to quantify the mixing time. The three rectangles shown in Figure 3 on frame at 1.2 s showed the

Multi-redox indenofluorene chromophores incorporating dithiafulvene donor and ene/enediyne acceptor units

• Christina Schøttler,
• Kasper Lund-Rasmussen,
• Line Broløs,
• Philip Vinterberg,
• Ema Bazikova,
• Viktor B. R. Pedersen and
• Mogens Brøndsted Nielsen

Beilstein J. Org. Chem. 2024, 20, 59–73, doi:10.3762/bjoc.20.8

• ) and 2 (176 mg, 534 μmol) in anhydrous toluene (5 mL) and P(OEt)3 (10 mL) was heated to reflux for 5 h, resulting in a color change from orange to dark red. The reaction mixture was then allowed to cool to rt before it was concentrated under reduced pressure. The resulting dark red solid was purified

• % CH2Cl2/heptane) yielded 19 (62 mg, 66%) as a purple solid (red in solution). Rf = 0.31 (15% CH2Cl2/heptane); 1H NMR (500 MHz, CDCl3) δ 9.07 (s, 1H), 8.81 (d, J = 1.7 Hz, 1H), 7.91 (s, 1H), 7.76 (d, J = 1.7 Hz, 1H), 7.72 (d, J = 8.0 Hz, 1H), 7.65 (d, J = 8.0 Hz, 1H), 7.41 (dd, J = 8.0, 1.7 Hz, 1H), 7.37

• orbitals), the dianion has an additional 6π-aromatic cyclopentadienyl anion (highlighted in green), while the cation has a 6π-aromatic 1,3-dithiolium ring (highlighted in red). ORTEP plots (50% probability) and crystal packing of compounds a) 25, b) 26, and c) 29. The respective crystal packing of each

Preparing a liquid crystalline dispersion of carbon nanotubes with high aspect ratio

• Keiko Kojima,
• Nodoka Kosugi,
• Hirokuni Jintoku,
• Kazufumi Kobashi and
• Toshiya Okazaki

Beilstein J. Org. Chem. 2024, 20, 52–58, doi:10.3762/bjoc.20.7

• %, respectively, as shown in Supporting Information File 1, Figure S3, which were lower than those previously obtained in the surfactant-assisted SWCNT aqueous dispersions [22][23]. Figure 2e shows the phase transition concentrations obtained in this study (L/D = 1378, red symbols) together with the previously

• examined using scanning electron microscopy (SEM) (HITACHI High-Tech, SU8200) and atomic force microscopy (AFM) (OLYMPUS, OLS-4500). Additionally, the ζ-potential of the DWCNTs was determined by measuring the ζ potential analyzer (Malvern Panalytical, ZETASIZER Pro Red label) in a disposable cell (Malvern

• polarizers (white double arrows). Scale bars are 400 µm. (c) Polarized optical absorption spectra with different angles ranging from 0° (red) to 90° (blue). The sear direction and polarizer are parallel at 0°. (d) SEM image of the DWCNT film. Blue outlined arrows indicate the shear direction of bar-coating

Facile access to pyridinium-based bent aromatic amphiphiles: nonionic surface modification of nanocarbons in water

• Lorenzo Catti,
• Shinji Aoyama and
• Michito Yoshizawa

Beilstein J. Org. Chem. 2024, 20, 32–40, doi:10.3762/bjoc.20.5

• similar to AA [12][13], indicating self-assembly via the hydrophobic effect and π-stacking interactions (Figure 3a,b). The self-assembly in water was further supported by UV–visible analysis, displaying slight red-shifts of the anthracene absorption bands relative to the spectrum in methanol (Δλmax = +3

Aldiminium and 1,2,3-triazolium dithiocarboxylate zwitterions derived from cyclic (alkyl)(amino) and mesoionic carbenes

• Nedra Touj,
• François Mazars,
• Guillermo Zaragoza and
• Lionel Delaude

Beilstein J. Org. Chem. 2023, 19, 1947–1956, doi:10.3762/bjoc.19.145

• instantaneous formation of the desired zwitterionic adducts, as evidenced by the appearance of an intense orange-red color. The solvent was removed and the residues were brought back to air, washed with n-pentane, and dried under high vacuum to afford pseudo-cross-conjugated mesomeric betaines 4a–c in high

• affinity and the higher basicity of CAACs and MICs vs NHCs [25][69][70][71] did not prevent the formation of the desired adducts using Cs2CO3 instead of KN(SiMe3)2 or NaOt-Bu, as evidenced by the appearance of revealing orange-red colors and by the emergence of a characteristic resonance for the CS2− unit

• . Crystallography Crystals of CAAC·CS2 zwitterions 4a and 4c suitable for X-ray diffraction (XRD) analysis were grown by slow diffusion of cyclohexane in a THF solution at 6 °C. Their molecular structures are depicted in Figure 3. The orange-red needles of compound 4a belonged to the trigonal space group, while

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• ). Graphical representation of the ligands’ starting (in red, licorice) and final (in blue, licorice) positions in regard of the binding site of basic fibroblast factor (in yellow, new cartoon). Graphical representation of the ligand’s starting (in red, licorice) and final (in blue, licorice) poses in regard

• of the binding site of acidic fibroblast factor (in yellow, new cartoon). Graphical representation of the ligand 4 starting (in red, licorice) and final (in blue, licorice) position in regard of binding site of cathepsin K (in yellow, new cartoon). Comparison of the last frame of the US simulation

Beyond n-dopants for organic semiconductors: use of bibenzo[d]imidazoles in UV-promoted dehalogenation reactions of organic halides

• Kan Tang,
• Megan R. Brown,
• Chad Risko,
• Melissa K. Gish,
• Garry Rumbles,
• Phuc H. Pham,
• Oana R. Luca,
• Stephen Barlow and
• Seth R. Marder

Beilstein J. Org. Chem. 2023, 19, 1912–1922, doi:10.3762/bjoc.19.142

• representative temporal evolution of % conversion (blue squares), % toluene yield (red diamonds), and % bibenzyl yield (black circles) during the dark dehalogenation reaction of benzyl bromide (BnBr) using (N-DMBI)2 in THF (these data were acquired using 3 mM BnBr and 1.5 mM of (N-DMBI)2. (b) Plot of [D2]0