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

• decreases concomitantly to the appearance of two new bands at 312 and 438 nm (Figure 2, blue line). Two isosbestic points can also be observed at 310 and 429 nm. The back Z→E photoisomerization can be achieved by illumination at 485 nm (Figure 2, red line). 1H NMR spectroscopy has been used to determine the

• ). The S-galactosyl azobenzenes 3–5 also displayed excellent photoswitching properties, with a red shift for the π→π* transition (λmax = 348–364 nm) compared to the O-galactosyl derivatives (Table 1, entries 5–8). However, the absorption coefficient and the thermostability of the Z-isomers are increased

• ) designed general structure of photoswitchable ligands 1–5 targeting LecA. (Left) Absorption spectra and (right) fatigue resistance of 1 under alternated 370/485 nm irradiations in Tris buffer/DMSO 95:5 at rt: E-1 (black line), PSS370 (blue line), PSS485 (red line). Irradiation conditions at 370 nm: 12.8

Bioinformatic prediction of the stereoselectivity of modular polyketide synthase: an update of the sequence motifs in ketoreductase domain

• Changjun Xiang,
• Shunyu Yao,
• Ruoyu Wang and
• Lihan Zhang

Beilstein J. Org. Chem. 2024, 20, 1476–1485, doi:10.3762/bjoc.20.131

• rings. The triangles indicate a product having α-substituents. (c) Crystal structure of DH-ER-KR tridomain (PDB ID 8G7W) [24]. DH, KRS, ER, KRC are colored in cyan, pink, yellow, and purple, respectively. The lid of KR catalytic pocket is colored in red. The co-crystallized cofactor is represented as

• classification of their products. The key catalytic residues are marked by red stars, and the NADPH-binding residues (partially) are marked by blue triangles. The numbers at the top indicate the fingerprint motifs. Sequence logo comparation of γ- and δ-module KRC based on the classification of their products

• . Top five rows show KRs associated with an inactive DH that produces the hydroxy products. The key catalytic residues are marked by red stars, and the NADPH-binding residues (partially) are marked by blue triangles. The motif numbers at the top are corresponding to the location of fingerprints in

Computation-guided scaffold exploration of 2E,6E-1,10-trans/cis-eunicellanes

• Zining Li,
• Sana Jindani,
• Volga Kojasoy,
• Teresa Ortega,
• Erin M. Marshall,
• Khalil A. Abboud,
• Sandra Loesgen,
• Dean J. Tantillo and
• Jeffrey D. Rudolf

Beilstein J. Org. Chem. 2024, 20, 1320–1326, doi:10.3762/bjoc.20.115

• diterpenoids and their biosyntheses. (A) The 6/10-bicyclic hydrocarbon framework is conserved in eunicellane diterpenoids. Selected natural products consisting of cis- (red) and trans-eunicellane skeletons (blue) are shown. (B) Four types of diterpene synthases are known to form the eunicellane skeleton, each

• of DFT calculations on the atropisomers 10a/10b and the free energy barriers for clockwise (blue) and counter-clockwise (red) rotations. Scaffold exploration of the 2E-trans-eunicellane skeleton. Supporting Information Supporting Information File 90: Experimental methods, NMR and MS spectra, and

Diameter-selective extraction of single-walled carbon nanotubes by interlocking with Cu-tethered square nanobrackets

• Guoqing Cheng and
• Naoki Komatsu

Beilstein J. Org. Chem. 2024, 20, 1298–1307, doi:10.3762/bjoc.20.113

• complexation, a significant red-shift of the dipyrrin band to 465 nm was observed due to the metal coordination with the dipyrrin moieties in 4b. To compare the structures of 1a and 1b, they are calculated through geometry optimization with the density functional theory (DFT) method. The alkyl chains at the

• existence of SWNTs in the extract. Actually, the absorption bands in the range of 500–1400 nm are attributed to the extracted SWNTs. The absorption band of Cu-nanobrackets 1b is red-shifted from 465 to 495 nm in the extract, suggesting the complexation of 1b with SWNTs. To further investigate whether the

• p-SWNTs. Red and black characters indicate metallic and semiconducting SWNTs, respectively. (a, b) Enriched (n,m)-SWNTs are shown in orange. (a) Binding energy between SWNTs of various (n,m)-structures with Cu-nanobrackets 1a and 1b; GFN2-xTB-optimized structures of (b) 1a@(9,4)-SWNT and (c) 1b

Synthesis and physical properties of tunable aryl alkyl ionic liquids based on 1-aryl-4,5-dimethylimidazolium cations

• Stefan Fritsch and
• Thomas Strassner

Beilstein J. Org. Chem. 2024, 20, 1278–1285, doi:10.3762/bjoc.20.110

• start at 0 V. Structures of the imidazolium cations obtained by DFT calculations (B3LYP/6-311++G (d,p)). The electrostatic potentials are indicated by color (blue: positive; red: negative). Overview of the synthesis of compounds 1–63. Thermal decomposition point at 5% mass loss in °C for NTf2− TAAILs 37

Synthesis of indano[60]fullerene thioketone and its application in organic solar cells

• Yong-Chang Zhai,
• Shimon Oiwa,
• Shinobu Aoyagi,
• Shohei Ohno,
• Tsubasa Mikie,
• Jun-Zhuo Wang,
• Hirofumi Amada,
• Koki Yamanaka,
• Kazuhira Miwa,
• Naoyuki Imai,
• Takeshi Igarashi,
• Itaru Osaka and
• Yutaka Matsuo

Beilstein J. Org. Chem. 2024, 20, 1270–1277, doi:10.3762/bjoc.20.109

• future. Characterization data. (a) FTIR spectra of t-Bu-FIDO and t-Bu-FIDS. (b) UV–vis spectra of fullerene derivatives normalized at 270 nm. (c) Vacuum TGA curves of t-Bu-FIDO (black), t-Bu-FIDS (red), and C60 (blue). The measurements were conducted under 0.1 Pa. (d) HPLC analyses before deposition of t

• -Bu-FIDS (black) and of toluene used to rinse the evaporated film of t-Bu-FIDS (red). Single-crystal structure of t-Bu-FIDS. (a) The π–π distance between two molecules. (b) Crystal packing. Cyclic voltammograms of fullerene derivatives in o-DCB solution containing Bu4N+(CF3SO2)2N− (0.1 M) as

• supporting electrolyte at 25 °C with a scan rate of 0.05 V/s, for C60 (blue), t-Bu-FIDO (red), and t-Bu-FIDS (black). Glassy carbon, platinum wire, and Ag/Ag+ electrodes were used as the working, counter, and reference electrodes, respectively. J–V curves of BHJ OPV devices. (a) ITO/ZnO/fullerene:P3HT (1:1

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

• under otherwise identical conditions gave a completely different spectrum (Figure 1B, red) and we assume that the triplet state of Aza-H is almost fully quenched by oxygen at the selected delay, which is supported by additional kinetic measurements (see below). The second transient species is identified

• Aza-H•+ (red) were computed using TD-DFT (see Supporting Information File 1 for details). These computational results, which are included in Figure 1B, align well with the experimentally observed absorption bands in the visible region, supporting our assignment. The observed behavior of the Aza-H

• contribution of the radical cation to the TA signal at 640 nm is only minor, which allows us to estimate a triplet lifetime of ≈28 µs at this detection wavelength. Based on our observations, an isolated triplet spectrum can be obtained from the spectral difference between the black and the red spectrum in

The Ugi4CR as effective tool to access promising anticancer isatin-based α-acetamide carboxamide oxindole hybrids

• Carolina S. Marques,
• Aday González-Bakker and
• José M. Padrón

Beilstein J. Org. Chem. 2024, 20, 1213–1220, doi:10.3762/bjoc.20.104

• ]. Carboxylic acids 2 and aldehydes/ketones 3 used in the Ugi4CR. GI50 range plot against human solid tumor cell lines of investigated α-acetamide carboxamide isatin hybrids. Green most potent, yellow intermediate, red less potent. (A) Library of isatin-based α-acetamide carboxamide oxindole derivatives

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

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

• + ʟ-isoleucine; (i) 8 + JadG; (j) 8 + AlpJ + ʟ-isoleucine. UV absorptions at 266 nm (black line) and 313 nm (red line) are displayed for each reaction. HPLC traces of reactions of JadG, AlpJ, or Flu17 quenched by SOD. (a) 8 + JadG + ʟ-isoleucine; (b) 8 + JadG + ʟ-isoleucine + SOD (5,000 U/mL); (c) 8

• + AlpJ; (d) 8 + AlpJ + SOD (5,000 U/mL); (e) 8 + Flu17 + SOD (5,000 U/mL). UV absorption at 266 nm (black line) and 313 nm (red line) are displayed for each reaction. Ring cleavage and ring rearrangement reactions in the biosynthesis of atypical angucyclines. Proposed catalytic mechanism of cofactor

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

Novel route to enhance the thermo-optical performance of bicyclic diene photoswitches for solar thermal batteries

• Akanksha Ashok Sangolkar,
• Rama Krishna Kadiyam and
• Ravinder Pawar

Beilstein J. Org. Chem. 2024, 20, 1053–1068, doi:10.3762/bjoc.20.93

• the UV region hinders its practical applicability in MOST systems [8][9][10][13]. Several attempts have been made to red-shift the absorption wavelength in direction of the visible region by introducing different substitutions which often compromised the thermochemical properties [8][9][10][13]. Thus

• 202.79 nm, respectively (Table 2). Therefore, the optical absorption spectra unveil that the extension of the unsaturated bridge length with –(CO)– and –NH– units as in type Ib, Ic, IIb, and IIc photoswitches red-shifts the excitation wavelength of the bicyclic diene and helps improving the photophysical

• energy reaching the Earth’s surface requires efforts to be devoted to red-shift the absorption wavelengths of the bicyclic diene in the visible range. As previous reports have demonstrated, this can be practically achieved by substitution with electron-releasing or accepting groups [8][9][33]. The energy

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

• equiv of 1,2-aceanthrylenedione, the reaction provided pure 3a product in moderate yield (41%). Subsequent recrystallization with boiling DMSO provided pristine red-brown crystals of 3a. The synthesis of DCPQ 4a was simple and proceeded with the condensation of a 1:1 mixture of acenaphthenequinone and

• , brown solids precipitated out. The tube was adequately cooled, and the solid residue was filtered and washed with copious amounts of methanol, ethyl acetate and dichloromethane, to afford pure red-brown colored amorphous material (36 mg, 0.10 mmol, 41%). The material could be further purified by

• recrystallization from boiling DMSO to obtain highly insoluble red-brown microcrystalline material. 1H and 13C NMR could not be recorded for the compound 3a given its extremely poor solubility in common organic solvents. Rf (CH2Cl2): 0.75, fluorescent orange spot; HRMS (DART): [M + NH4]+ calcd for C22H8N6, 374.1154

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

• Fe2p peaks and the increase in shake-up peak intensity of the C1s in the XPS spectrum proved the emergence of charge-transfer host–guest interaction in FeCp2-ACFs-150, supported by the red-shift of the G-band in the Raman spectrum. The six-times enhancement in the spin concentration in FeCp2-ACFs-150

• for FeCp2-ACFs-150 due to their tiny abundance, the G-band for FeCp2-ACFs-150 shifts by 3 cm−1 to the lower wavenumber side compared to ACFs. The red shift indicates the weakening of C=C bonding in nanographene caused by filling anti-bonding states (π* states) due to electron injection into

• 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

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

• production of antibiotics such as actinorhodin (ACT, 8), undecylprodigiosin (RED, 21), and calcium-dependent antibiotic (CDA, 22) in Streptomyces coelicolor M145 (Figure 3b). Chen et al. and Shu et al. reported that under stress associated with high concentrations of glutamate, AfsQ1/Q2 is important not only

• for maintaining the metabolic homeostasis of nutrient utilization but also for biosynthesis of antibiotics such as ACT, RED, CDA and the yellow pigment coelimycin P2 in Streptomyces coelicolor strains M145 [60][61]. Depletion of a metal component essential for growth activates the production of

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

• isolated from the fruit of Gardenia jasminoides Ellis and the stigma tissue of Crocus sativus L. Crocins are the main active ingredients of C. sativus, a precious medicinal plant known as the "gold of spices". They are also responsible for the characteristic red color of saffron. Compounds of the crocin

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

• -ketoisocaproate starter unit with introduction of an S configured stereocentre (highlighted in red in Scheme 1) [15]. The domain organisation of module 3 containing no enoylreductase (ER) domain furthermore suggests the formation of an α,β-unsaturated intermediate, and not a full reduction at this stage, in

Isolation and structure determination of a new analog of polycavernosides from marine Okeania sp. cyanobacterium

• Kairi Umeda,
• Naoaki Kurisawa,
• Ghulam Jeelani,
• Tomoyoshi Nozaki,
• Kiyotake Suenaga and
• Arihiro Iwasaki

Beilstein J. Org. Chem. 2024, 20, 645–652, doi:10.3762/bjoc.20.57

• . Polycavernoside E (1) exhibited moderate antitrypanosomal activity against Trypanosoma brucei rhodesiense. Furthermore, the isolation of polycavernoside E (1) from marine cyanobacteria provides additional evidence that marine cyanobacteria, and not red algae, are responsible for the biosynthesis of

• polycavernosides. Keywords: macrolide glycoside; marine cyanobacterium; marine natural products; polycavernosides; terminal alkyne; Introduction In 1991, an outbreak of food poisoning caused by a species of red algae known as ‘Polycavernosa tsudai’ occurred in Guam, which resulted in killing of three people. Two

• novel macrolide glycosides, polycavernosides A (2) and B (3), were reported as the causative compounds for the illness [1]. After that, the second fatal food poisoning incidents occurred in the Philippines caused by the ingestion of polycavernoside A (2)-contaminated red algae [2]. Subsequently

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