Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• two series of simulations (in the presence and absence of C-Raf peptides). It should be mentioned that Epitopsy does not model the displacement of structural water molecules and counter-ions when the ligand comes in contact with the protein surface and the ligand dielectric permittivity is

• approximately that of saline water. However, desolvation effects tend to be weak for solvent-exposed binding sites compared to binding pockets which are systematically avoided by Epitopsy due to the strong steric repulsion that is imposed on the ligand. Note that the above approach models only interactions of

Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants

• Karan Malhotra and
• Jakob Franke

Beilstein J. Org. Chem. 2022, 18, 1289–1310, doi:10.3762/bjoc.18.135

• group and an aqua ligand (water), resulting in an octahedral complex [17]. The oxidative reaction is initiated by displacement of the axial water molecule by the substrate (step 1), which pushes the Fe(III) ion out of the porphyrin plane in intermediate B [17]. This geometrical distortion promotes

• hydroxy intermediate H, also known as compound II. This leads to the hydroxylated product coordinated to ferric ion (intermediate I). Lastly, displacement of the product by water regenerates the resting state A (step 9). In addition to simple hydroxylations, slight deviations from this general mechanistic

Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions

• Michael Keppler,
• Sandra Moser,
• Henning J. Jessen,
• Christoph Held and
• Jennifer N. Andexer

Beilstein J. Org. Chem. 2022, 18, 1278–1288, doi:10.3762/bjoc.18.134

• by accounting for molecular repulsion and attraction caused by van-der-Waals forces, hydrogen bonding, and Coulomb forces. The ePC-SAFT parameters of the nucleotides were fitted in previous works to experimental osmotic pressures of pseudo-binary mixtures of nucleotide and water [29][33]. As

• modelling polyP with high chain length is currently not possible with ePC-SAFT, we assumed that only nucleotides were present in water. The consequence of this assumption is that interactions among nucleotides and polyP were considered to be equal to interactions among nucleotides and polyPn−1, and we

Modular synthesis of 2-furyl carbinols from 3-benzyldimethylsilylfurfural platforms relying on oxygen-assisted C–Si bond functionalization

• Sebastien Curpanen,
• Per Reichert,
• Gabriele Lupidi,
• Giovanni Poli,
• Julie Oble and
• Alejandro Perez-Luna

Beilstein J. Org. Chem. 2022, 18, 1256–1263, doi:10.3762/bjoc.18.131

• extracted with cyclohexane/CH2Cl2 9:1 (4 × 10 mL), and the combined organic layer was washed with water (10 mL), dried over MgSO4, and concentrated under reduced pressure. The residue was purified by silica gel column chromatography. C3–Si bond functionalization of biomass-derived 3-silylated furfural

Polymer and small molecule mechanochemistry: closer than ever

• José G. Hernández

Beilstein J. Org. Chem. 2022, 18, 1225–1235, doi:10.3762/bjoc.18.128

• of these two different experimental approaches in the development of mechanochemical reactions. For example, Li and co-workers showed that piezoelectric nanoparticles such as BaTiO3 and ZnO could trigger water electrolysis under ultrasonication [53]. Sonication caused deformation of, or strain on the

• in the formation of H2 and O2 from the water splitting reaction by donating strain-induced electrons and holes [53]. The piezoelectricity obtained upon ultrasonication of BaTiO3 has also been used to trigger and sustain atom transfer radical polymerization (ATRP) reactions of acrylate monomers by

Mechanochemical bottom-up synthesis of phosphorus-linked, heptazine-based carbon nitrides using sodium phosphide

• Blaine G. Fiss,
• Georgia Douglas,
• Michael Ferguson,
• Jorge Becerra,
• Jesus Valdez,
• Trong-On Do,
• Tomislav Friščić and
• Audrey Moores

Beilstein J. Org. Chem. 2022, 18, 1203–1209, doi:10.3762/bjoc.18.125

• ; Introduction The development of heteroatom-doped graphitic carbon nitrides (g-CN) has been a rapidly growing area of research since their first report towards water splitting in 2009 [1]. Since that time, the addition of elements such as boron [2], phosphorus [3][4][5], sulfur and oxygen [6] have shown to help

• powder was then allowed to age under an argon atmosphere for 24 hours, prior to washing via centrifugation in a 3:1 by volume mixture of ethanol and deionized (DI) water. This afforded a material referred to below as g-h-PCN. Alternatively, the sample was annealed for 1 hour at 300 °C under a flow of

• quenching in water and ethanol at the end of the aging step. g-h-PCN300 featured the same three major carbon 1s peaks at 284.8, 286.2 and 288.2 eV for C=N/C=C, C=O and C–OH species, respectively, as well as the charging peak seen in g-h-PCN. In g-h-PCN300, a reduction of the C=N ratio to 37%, reduction of C

Derivatives of benzo-1,4-thiazine-3-carboxylic acid and the corresponding amino acid conjugates

• Péter Kisszékelyi,
• Tibor Peňaška,
• Klára Stankovianska,
• Mária Mečiarová and
• Radovan Šebesta

Beilstein J. Org. Chem. 2022, 18, 1195–1202, doi:10.3762/bjoc.18.124

• significantly accelerated by ultrasonic irradiation [16]. Cyclocondensation of 1,3-dicarbonyl compounds with substituted diaryl disulfides in water in the presence of β-cyclodextrin gave 2,3-disubstituted benzo-1,4-thiazines in 70–91% yield in 50 min [17]. A highly efficient visible-light-mediated one-pot

Thermally activated delayed fluorescence (TADF) emitters: sensing and boosting spin-flipping by aggregation

• Ashish Kumar Mazumdar,
• Gyana Prakash Nanda,
• Nisha Yadav,
• Upasana Deori,
• Upasha Acharyya,
• Bahadur Sk and
• Pachaiyappan Rajamalli

Beilstein J. Org. Chem. 2022, 18, 1177–1187, doi:10.3762/bjoc.18.122

• was obtained for BPy-p3C due to the bulkier donor, leading to a more twisted D–A geometry than that of BPy-pTC. Hence, BPy-p3C exhibited aggregation-induced enhanced emission (AIEE) in a THF/water mixture. Interestingly, the singlet–triplet energy gap (ΔEST) was reduced for both compounds in the

• , facilitating the photon upconversion from the T1 to the S1 state through an RISC process. Aggregation-induced enhanced emission (AIEE) In order to determine the molecular aggregate formation of BPy-pTC and BPy-p3C and the impact on the optical properties, we carried out aggregation studies in THF/water

• mixtures (Figure 3) [33]. BPy-pTC emits in the blue-green region at λem = 497 nm in THF with a PLQY of 12.7% (Figure 3a). The emission intensity was reduced to near 0 upon increasing the water fraction from 10 to 70 vol % in the THF solution of BPy-pTC (Figure 3a and Figure 3c). The formation of a dark

Synthesis of tryptophan-dehydrobutyrine diketopiperazine and biological activity of hangtaimycin and its co-metabolites

• Houchao Xu,
• Anne Wochele,
• Minghe Luo,
• Gregor Schnakenburg,
• Yuhui Sun,
• Heike Brötz-Oesterhelt and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 1159–1165, doi:10.3762/bjoc.18.120

• DBU is a common strategy for the dehydration of serine and threonine units in peptides [16], but unfortunately the acetylation of 10 failed. Interestingly, the direct treatment of 10 with LiClO4 and DBU under prolonged reaction times (3 days) resulted in the elimination of water. This reaction

Electro-conversion of cumene into acetophenone using boron-doped diamond electrodes

• Mana Kitano,
• Tsuyoshi Saitoh,
• Shigeru Nishiyama,
• Yasuaki Einaga and
• Takashi Yamamoto

Beilstein J. Org. Chem. 2022, 18, 1154–1158, doi:10.3762/bjoc.18.119

• in 21% yield. Therefore, it is indicated that the reaction intermediate is the cumyl cation. Second, we carried out the electrolysis of 1 in MeCN–H2O to confirm whether the oxygen source is dissolved oxygen or residual water. When dehydrated MeCN was used, 3 was obtained as the main product (Table 2

• not residual water in MeCN, but dissolved oxygen. The role of dissolved oxygen was further investigated. As the reaction did not proceed without electricity, it is suggested that the superoxide generated on the cathode is involved in the reaction, rather than dissolved molecular oxygen itself

Synthesis of protected precursors of chitin oligosaccharides by electrochemical polyglycosylation of thioglycosides

• Md Azadur Rahman,
• Kana Kuroda,
• Hirofumi Endo,
• Norihiko Sasaki,
• Tomoaki Hamada,
• Hiraku Sakai and
• Toshiki Nokami

Beilstein J. Org. Chem. 2022, 18, 1133–1139, doi:10.3762/bjoc.18.117

• . Then, the reaction temperature was elevated to −30 °C, and the temperature was kept for 1 h. The reaction was quenched with Et3N (0.30 mL), and the reaction mixture was diluted with Et2O and EtOAc and washed with water to remove the electrolyte. The combined organic layer was dried with Na2SO4, and the

A Streptomyces P450 enzyme dimerizes isoflavones from plants

• Run-Zhou Liu,
• Shanchong Chen and
• Lihan Zhang

Beilstein J. Org. Chem. 2022, 18, 1107–1115, doi:10.3762/bjoc.18.113

• General Microbiological Culture Collection Center (CGMCC). Seed culture of this strain was done in ISP-2 medium (yeast extract 0.4 g, malt extract 1 g, glucose 0.4 g, distilled water up to 100 mL, pH 7.2) for 2 days. Isoflavone dimer production was performed on MS agar medium (mannitol 20 g, soy flour 20

• g, agar 20 g, distilled water up to 1 L) for 15 days from the above seed culture. Analytical methods All HPLC analyses were performed using (A) H2O with 0.1% formic acid and (B) acetonitrile with 0.1% formic acid at 40 °C column temperature unless otherwise noted. The HPLC–UV analysis of feeding

Radical cation Diels–Alder reactions of arylidene cycloalkanes

• Kaii Nakayama,
• Hidehiro Kamiya and
• Yohei Okada

Beilstein J. Org. Chem. 2022, 18, 1100–1106, doi:10.3762/bjoc.18.112

• ). Then, the solution was diluted with water and extracted with EtOAc. The combined organic layers were dried over Na2SO4, filtered, and concentrated in vacuo. Yields were determined by 1H NMR analysis using dibromomethane as an internal standard. Silica gel column chromatography (hexane/ethyl acetate

• electrolyzed at 1.3–1.5 V vs Ag/AgCl using carbon felt electrodes (10 mm × 10 mm) in an undivided cell with stirring. Then, the solution was diluted with water and extracted with EtOAc. The combined organic layers were dried over Na2SO4, filtered, and concentrated in vacuo. Yields were determined by 1H NMR

Synthesis of N-phenyl- and N-thiazolyl-1H-indazoles by copper-catalyzed intramolecular N-arylation of ortho-chlorinated arylhydrazones

• Yara Cristina Marchioro Barbosa,
• Guilherme Caneppele Paveglio,
• Claudio Martin Pereira de Pereira,
• Sidnei Moura,
• Cristiane Storck Schwalm,
• Gleison Antonio Casagrande and
• Lucas Pizzuti

Beilstein J. Org. Chem. 2022, 18, 1079–1087, doi:10.3762/bjoc.18.110

• was cooled in an ice bath and cold water (30 mL) was added to give a precipitate. In a Büchner funnel, the solid was filtered off and washed with an additional amount of cold water. After drying the solid in a desiccator, it was recrystallized from methanol/water 1:1 to give the products 1a–i with

• , and then the eluate was washed with water (1 × 10 mL) and a saturated aqueous NaCl solution (2 × 10 mL). The resulting organic solution was dried over anhydrous MgSO4, filtered, and concentrated under reduced pressure. Each product 2a,b,d–i,i’ was isolated using column chromatography with silica gel

Electrochemical formal homocoupling of sec-alcohols

• Kosuke Yamamoto,
• Kazuhisa Arita,
• Masashi Shiota,
• Masami Kuriyama and
• Osamu Onomura

Beilstein J. Org. Chem. 2022, 18, 1062–1069, doi:10.3762/bjoc.18.108

• somewhat lower yield with a high diastereoselectivity. In both cases, the reaction proceeded with the good mass balance of 2a and 3a. On the other hand, the reaction without adding water resulted in a decrease in the dl:meso ratio of 2a, and ketone 3a was transformed into unidentified byproducts. When dl

• reaction conditions. While ketone 3a was obtained in a higher yield when the reaction was performed in the absence of imidazole, a lower yield of 3a and a poor mass balance were observed in the reaction without adding water. These results indicate that imidazole may suppress the formation of the ketone

• from the corresponding vic-1,2-diol. Water may play a role as a proton source to facilitate the formation of the protonated ketyl radical through a concerted proton-electron transfer toward the ketone or smooth protonation of the radical anion species, which readily dimerize to vic-1,2-diol 2a [46][49

Electrochemical hydrogenation of enones using a proton-exchange membrane reactor: selectivity and utility

• Koichi Mitsudo,
• Haruka Inoue,
• Yuta Niki,
• Eisuke Sato and
• Seiji Suga

Beilstein J. Org. Chem. 2022, 18, 1055–1061, doi:10.3762/bjoc.18.107

• achieved. With this reaction system, chemoselective reduction can be performed using only electricity and water, and the product can be easily obtained by simply concentrating the solution coming out of the outlet of the flow system. We are currently trying to reduce various functional groups using this

Synthesis, optical and electrochemical properties of (D–π)₂-type and (D–π)₂Ph-type fluorescent dyes

• Kosuke Takemura,
• Kazuki Ohira,
• Taiki Higashino,
• Keiichi Imato and
• Yousuke Ooyama

Beilstein J. Org. Chem. 2022, 18, 1047–1054, doi:10.3762/bjoc.18.106

• '-bithiophene]-5,5'-diyl)bis(9-butyl-N,N-diphenyl-9H-carbazol-2-amine) (OTT-2): A solution of 1 (87 mg, 0.137 mmol), 1,3-diiodobenzene (14 mg, 0.041 mmol), and Pd(PPh3)4 (2 mg, 0.001 mmol) in toluene (1 mL) was stirred for 29 h at 110 ºC under an argon atmosphere. The reaction mixture was diluted with water

Electrochemical Friedel–Crafts-type amidomethylation of arenes by a novel electrochemical oxidation system using a quasi-divided cell and trialkylammonium tetrafluoroborate

• Hisanori Senboku,
• Mizuki Hayama and
• Hidetoshi Matsuno

Beilstein J. Org. Chem. 2022, 18, 1040–1046, doi:10.3762/bjoc.18.105

• likely nucleophile in this reaction medium was the trifluoroacetate ion, which was produced by electrochemical reduction of TFA at the cathode, although we could not detect the coupling product of trifluoroacetate and the corresponding N-acyliminium ion due to the high solubility in water. In addition to

• M iPr2NHEtBF4 using a quasi-divided cell gave 3-amidomethylated N-methylindole 9 in 47% 1H NMR yield and 44% isolated yield at full conversion (Scheme 4). The moderate yield of 9 is thought to be due to its high solubility in water. A probable reaction pathway is shown in Scheme 5. The present

Electrochemical vicinal oxyazidation of α-arylvinyl acetates

• Yi-Lun Li,
• Zhaojiang Shi,
• Tao Shen and
• Ke-Yin Ye

Beilstein J. Org. Chem. 2022, 18, 1026–1031, doi:10.3762/bjoc.18.103

• , entries 4 and 5). Note that the yield decreased without the addition of water suggesting water may facilitate the formation of the azidoketone (Table 1, entry 6). Interestingly, the H218O labeling experiment confirmed that there was no 18O incorporation in the obtained α-azidoketone (2, for details see

• Supporting Information File 1). Therefore, the oxygen source of the newly formed carbonyl moiety may originate directly from the vinyl acetate. This conclusion is also consistent with the fact that even in the absence of water, the desired α-azidoketone was still obtained. Under the optimal conditions, the

• water to form the desired product E. According to our 18O labeling experiment, the oxygen source of the newly installed carbonyl group probably originates from the vinyl acetate, not from H2O. Conclusion In summary, we have developed an environmentally friendly and efficient electrochemical oxyazidation

New azodyrecins identified by a genome mining-directed reactivity-based screening

• Atina Rizkiya Choirunnisa,
• Kuga Arima,
• Yo Abe,
• Noritaka Kagaya,
• Kei Kudo,
• Hikaru Suenaga,
• Junko Hashimoto,
• Manabu Fujie,
• Noriyuki Satoh,
• Kazuo Shin-ya,
• Kenichi Matsuda and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2022, 18, 1017–1025, doi:10.3762/bjoc.18.102

• Streptomyces sp. RM72 were first partitioned by water and ethyl acetate, and then the organic layer was further fractionated by silica gel column chromatography. Fractionation by reversed-phase HPLC yielded ten compounds (1–10) that generate N2H4 upon acid hydrolysis. The combination of 1H and 13C NMR with a

Automated grindstone chemistry: a simple and facile way for PEG-assisted stoichiometry-controlled halogenation of phenols and anilines using N-halosuccinimides

• Dharmendra Das,
• Akhil A. Bhosle,
• Amrita Chatterjee and
• Mainak Banerjee

Beilstein J. Org. Chem. 2022, 18, 999–1008, doi:10.3762/bjoc.18.100

• an improved yield (77%) of the monobromo product 2a, with a reduced amount of 3a (12%), and a nominal recovery of the starting material were observed (Table 1, entry 2). Incomplete consumption of starting phenol 1a was primarily due to over bromination. The LAG in the presence of water afforded

• not proceed to completion (Table S1, entry 8 in Supporting Information File 1). Further, during aqueous work-up at least 10% loss of the water-soluble crude product 2a was observed in the conventional solution-phase reactions leading to a drop in the isolated yields. Based on the above observations

Molecular diversity of the base-promoted reaction of phenacylmalononitriles with dialkyl but-2-ynedioates

• Hui Zheng,
• Ying Han,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2022, 18, 991–998, doi:10.3762/bjoc.18.99

• be seen that the C–C double bond is connected to two methoxycarbonyl groups. Though one hydroxy group exists on the reactive allyl position and benzyl position, it still is present in the molecule and did not give the cyclopentadiene by further elimination of water. In order to obtain the

• corresponding products with elimination of water, alternative conditions for the base-promoted reaction of phenacylmalononitrile and dialkyl but-2-ynedioates were tested. After carefully examining the reaction conditions, we found that the reaction of phenacylmalononitriles and dialkyl but-2-ynedioates in

Electroreductive coupling of 2-acylbenzoates with α,β-unsaturated carbonyl compounds: density functional theory study on product selectivity

• Naoki Kise and
• Toshihiko Sakurai

Beilstein J. Org. Chem. 2022, 18, 956–962, doi:10.3762/bjoc.18.95

• for 1 h. The mixture was diluted with sat. aqueous NaCl solution (20 mL) and water (20 mL), and then extracted with ethyl acetate (3 × 20 mL). The organic layer was washed with sat. aqueous NaCl solution, dried over MgSO4, and filtered. After removal of the solvent in vacuo, the residue was purified

Introducing a new 7-ring fused diindenone-dithieno[3,2-b:2',3'-d]thiophene unit as a promising component for organic semiconductor materials

• Valentin H. K. Fell,
• Joseph Cameron,
• Alexander L. Kanibolotsky,
• Eman J. Hussien and
• Peter J. Skabara

Beilstein J. Org. Chem. 2022, 18, 944–955, doi:10.3762/bjoc.18.94

• under vacuum. Details of the synthesis are described in Supporting Information File 1. After fresh, anhydrous dichloromethane was added, the mixture was cooled to 0 °C in a water–ice bath, and resublimed aluminium trichloride was added. The mixture was allowed to warm to room temperature, and was then

On Reuben G. Jones synthesis of 2-hydroxypyrazines

• Pierre Legrand and
• Yves L. Janin

Beilstein J. Org. Chem. 2022, 18, 935–943, doi:10.3762/bjoc.18.93

• addition of concentrated hydrochloric acid. When relevant, this is followed by a dilution in an excess of water and then a filtration and washing. This procedure provides average yields of the 3,5-substituted-2-hydroxypyrazine 3 isomer as the major reaction product sometimes along with lesser amounts of

• previously reported [13], the separation (by any mean) of the 2-hydroxypyrazine isomers 3 and 4 is challenging. To overcome this, we used water-heated columns and preheated eluent mixtures (see the experimental part) which allowed to run chromatography over silica gel at 60 °C. At this temperature and using

• , entries 2 and 4) led to a slight drop of the reaction yield but a longer time (4 hours) had no impact (Table 1, entry 5). A neutralization of the reaction medium with ammonium chloride (instead of 37% hydrochloric acid), followed by the addition of an excess of water, also caused a drop of the yield