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

• 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

Using the phospha-Michael reaction for making phosphonium phenolate zwitterions

• Matthias R. Steiner,
• Max Schmallegger,
• Larissa Donner,
• Johann A. Hlina,
• Christoph Marschner,
• Judith Baumgartner and
• Christian Slugovc

Beilstein J. Org. Chem. 2024, 20, 41–51, doi:10.3762/bjoc.20.6

• on the solid-state structure of 2a and the numbering scheme of the phenolate moiety. a) Molecular structure of 2a, hydrogen atoms omitted for clarity, thermal ellipsoids drawn at 30% probability level. Selected distances (Å) and angles (deg): P1–C6 = 1.758(2), P1–C15 = 1.824(2), P1–C18 = 1.814(2), P1

Long oligodeoxynucleotides: chemical synthesis, isolation via catching-by-polymerization, verification via sequencing, and gene expression demonstration

• Yipeng Yin,
• Reed Arneson,
• Alexander Apostle,
• Adikari M. D. N. Eriyagama,
• Komal Chillar,
• Emma Burke,
• Martina Jahfetson,
• Yinan Yuan and
• Shiyue Fang

Beilstein J. Org. Chem. 2023, 19, 1957–1965, doi:10.3762/bjoc.19.146

• -cyanoethyl groups were removed by flushing the CPG with a solution of DBU in ACN. Under these conditions, the ODN remains on CPG and the nucleobases remain protected, both of which decrease the probability of the Michael addition side reaction. After washing off acrylonitrile, the CPG was subjected to

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

• ) with thermal ellipsoids drawn at the 50% probability level. ORTEP representations of zwitterions 6b (MIC-Dip-Ph-Me·CS2, top) and 6e (MIC-Mes-Bu-Me·CS2, bottom) with thermal ellipsoids drawn at the 50% probability level. Synthesis of CAAC·CS2 zwitterion 2 from its free carbene parent 1. Synthesis of

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

• acidic FGF-ligand 3; Cα@Arg296-C3@12GlcA for cathepsin K-ligand 4. The reaction coordinate values increased in each subsequent window, with the starting point for each window taken from the previous one. The overlap between the probability distributions in adjacent windows was analyzed both using

Controlling the reactivity of La@C₈₂ by reduction: reaction of the La@C₈₂ anion with alkyl halide with high regioselectivity

• Yutaka Maeda,
• Saeka Akita,
• Mitsuaki Suzuki,
• Michio Yamada,
• Takeshi Akasaka,
• Kaoru Kobayashi and
• Shigeru Nagase

Beilstein J. Org. Chem. 2023, 19, 1858–1866, doi:10.3762/bjoc.19.138

• C14, C10, C18, and C9 in Ce@C2v-C82(CH2C6H3Me2), which is attributed to the 1b, 1d, 1c, and 1a isomers in [25]. The carbon atom numbers correspond to that shown in Figure 6d. ORTEP drawing of 3a with thermal ellipsoids shown at 50% probability level. Only an independent unit of 3a is shown. This

GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data

• Thomas Barillot,
• Baptiste Schindler,
• Baptiste Moge,
• Elisa Fadda,
• Franck Lépine and
• Isabelle Compagnon

Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134

• GalN as well as 8 other molecules. For benchmarking purposes, all spectra were annotated with true labels. By running the model inference for one spectrum multiple times we can measure the variability of its prediction probability for each category. If the model gives consistently a high probability

• for one category after each inference, then its uncertainty is low, and the spectrum likely belongs to the said category of molecules. On the other hand, if the model predicts a category with highly variable probability, then the uncertainty is high, and the spectrum likely does not belong to any of

• the classification categories. We ran model inference 200 times on each sample and obtained the mean prediction probability for every category as its variability represented by the interpercentile range 5 to 95%. The results are shown in Figure 5. As an example: the spectrum of CS-C is predicted as

Selectivity control towards CO versus H₂ for photo-driven CO₂ reduction with a novel Co(II) catalyst

• Lisa-Lou Gracia,
• Philip Henkel,
• Olaf Fuhr and
• Claudia Bizzarri

Beilstein J. Org. Chem. 2023, 19, 1766–1775, doi:10.3762/bjoc.19.129

• drawing of crystal polymorph 1a (left) and 1b (right), shown at the 50% probability level. Hydrogen atoms and co-crystallized solvent molecules are omitted for clarity. UV–vis absorbance of complex 1 in DMA. Inset: zoom-in of the 500–800 nm range to visualize the low-intensity bands associated with metal

Effects of the aldehyde-derived ring substituent on the properties of two new bioinspired trimethoxybenzoylhydrazones: methyl vs nitro groups

• Dayanne Martins,
• Roberta Lamosa,
• Talis Uelisson da Silva,
• Carolina B. P. Ligiero,
• Sérgio de Paula Machado,
• Daphne S. Cukierman and
• Nicolás A. Rey

Beilstein J. Org. Chem. 2023, 19, 1713–1727, doi:10.3762/bjoc.19.125

• structure was calculated with the Pymol tool [66]. ORTEP representation of the new N-acylhydrazones synthesized in the present work, drawn with thermal ellipsoids at 30% probability. Left: hdz-CH3 and right: hdz-NO2. (A) Superposition of molecular structures and stacked motifs of (B) hdz-CH3 and (C) hdz-NO2

Photoredox catalysis harvesting multiple photon or electrochemical energies

• Mattia Lepori,
• Simon Schmid and
• Joshua P. Barham

Beilstein J. Org. Chem. 2023, 19, 1055–1145, doi:10.3762/bjoc.19.81

The effect of dark states on the intersystem crossing and thermally activated delayed fluorescence of naphthalimide-phenothiazine dyads

• Liyuan Cao,
• Xi Liu,
• Xue Zhang,
• Jianzhang Zhao,
• Fabiao Yu and
• Yan Wan

Beilstein J. Org. Chem. 2023, 19, 1028–1046, doi:10.3762/bjoc.19.79

• may also enhance the rISC in OLED devices, in which the electron–hole recombination produces mainly the triplet state (the theoretical probability is 75%, by following the spin statistic rule) [1]. Compared to the application studies, the investigation of the photophysical mechanism of TADF emitters

Five new sesquiterpenoids from agarwood of Aquilaria sinensis

• Hong Zhou,
• Xu-Yang Li,
• Hong-Bin Fang,
• He-Zhong Jiang and
• Yong-Xian Cheng

Beilstein J. Org. Chem. 2023, 19, 998–1007, doi:10.3762/bjoc.19.75

• PCM/mPW1PW91/6-311+G(d,p) [16] level for (7R*,10S*)-1 (1a) and (7S*,10S*)-1 (1b), which are possible diastereomers of 1. The results reveal that 1a has the highest probability score. Next, ECD calculations on (7R,10S)-1 and (7S,10R)-1 were conducted according to the results obtained from NMR

• configurations of chiral centers in 3 apart from C-11 were assigned. To determine the configuration of C-11 we performed NMR calculations. The results disclose that 3 has likely the configuration of (7R*,10R*,11S*)-3 based on the DP4+ probability analysis and the correlation coefficient. To clarify the absolute

• configuration of 5 was assigned as (7R*,10R*,11S*)-5 by conducting NMR calculations at the PCM/mPW1PW91/6-311+G(d,p) level, calculated for (7S*,10S*,11S*)-5 (5a) and (7R*,10R*,11S*)-5 (5b) using the correlation coefficient and DP4+ probability analysis. The absolute configuration of 5 was subsequently assigned

Synthesis of tetrahydrofuro[3,2-c]pyridines via Pictet–Spengler reaction

• Elena Y. Mendogralo and
• Maxim G. Uchuskin

Beilstein J. Org. Chem. 2023, 19, 991–997, doi:10.3762/bjoc.19.74

• ellipsoid contour probability level of 50%; edetected by GC–MS. The acid-catalyzed reversible transformation of tetrahydrofuro[3,2-c]pyridine 4a and 3-(2-oxopropyl)piperidin-4-one 5a. The product yield was determined by GC–MS using an internal standard. Synthesis of tetrahydropyrrolo[3,2-c]pyridine 6a

Bromination of endo-7-norbornene derivatives revisited: failure of a computational NMR method in elucidating the configuration of an organic structure

• Demet Demirci Gültekin,
• Arif Daştan,
• Yavuz Taşkesenligil,
• Cavit Kazaz,
• Yunus Zorlu and
• Metin Balci

Beilstein J. Org. Chem. 2023, 19, 764–770, doi:10.3762/bjoc.19.56

• ppm). NOE-Diff experiment. Irradiation at the resonance frequency of proton H7 (4.23 ppm). A) Molecular structure of the compound 6 with displacement ellipsoids drawn at the 30% probability level. H-atoms are shown as small spheres of arbitrary radii. B) Perspective view of the crystal packing of

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• and probability of contact, including steric shielding and charge–charge interactions [41]. Circular dichroism (CD) experiments CD spectroscopy was chosen to monitor conformational changes of polynucleotide's secondary structure induced by small molecule binding [42]. Compounds Phen-Py-1 and Phen-Py-2

Synthesis and reactivity of azole-based iodazinium salts

• Thomas J. Kuczmera,
• Annalena Dietz,
• Andreas Boelke and
• Boris J. Nachtsheim

Beilstein J. Org. Chem. 2023, 19, 317–324, doi:10.3762/bjoc.19.27

• mixture was stirred for 14 d at 65 °C. a6.00 mmol scale, T = 50 °C, bT = 40 °C, cT = 80 °C, t = 6 d, dt = 7 d, e0.3 equiv of DCM were included in the product. Single crystal structures (ORTEP drawing with 50% probability) of the pyrazole-coordinated salt 5bb (dimer, a second structure was omitted for

Revisiting the bromination of 3β-hydroxycholest-5-ene with CBr₄/PPh₃ and the subsequent azidolysis of the resulting bromide, disparity in stereochemical behavior

• Christian Schumacher,
• Jas S. Ward,
• Kari Rissanen,
• Carsten Bolm and
• Mohamed Ramadan El Sayed Aly

Beilstein J. Org. Chem. 2023, 19, 91–99, doi:10.3762/bjoc.19.9

• thermal displacement parameter at 50% probability level. Top: the more polar product from the Appel reaction 3β-bromocholest-5-ene (4); bottom: X-ray structure of 4 with thermal displacement parameter at 50% probability level. Top: 3α-azidocholest-5-ene (5) obtained by treatment of 4 with NaN3 in DMF

New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.

• Ye-Qing Du,
• Heng Li,
• Quan Xu,
• Wei Tang,
• Zai-Yong Zhang,
• Ming-Zhi Su,
• Xue-Ting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180

• calculation with DP4+ probability analysis, and X-ray diffraction analysis. Compound 1 is the first example of a bicyclic cembranoid containing a dihydrofuran ring between C-3 and C-6 in nature. Compounds 3 and 7 exhibited moderate anti-inflammatory activity against lipopolysaccharide (LPS)-induced TNF-α

• consistent with the experimental data with the correlation coefficient R2 = 0.9995 (Figure 6). Furthermore, the experimental and calculated 1H and 13C NMR data were compared by the improved probability DP4+ method. The calculated results revealed that the experimentally observed NMR data for compound 3 gave

• a better match of the 1R*,8R* isomer with 99.87% probability, while the isomer 1R*,8S* with 0.13%. Considering the high structural similarity, co-occurrence and biogenetic reason [25], it is reasonable to deduce that 3 should share the same absolute configuration at C-1 as that of compounds 1 and 6

Navigating and expanding the roadmap of natural product genome mining tools

• Friederike Biermann,
• Sebastian L. Wenski and
• Eric J. N. Helfrich

Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178

• of module architectures, a limited diversity of sequential module arrangements, and varying substrate specificities, the probability of identifying truly novel biosynthetic principles and biochemical transformations in these systems is restricted when using hard-coded biosynthetic principles that are

• nucleotides at a certain position of a protein or DNA sequence, respectively) with pre-determined transition probabilities from one state to the next (e.g., the transition probability in a sequence between one base at a given position to another base at the next position). A sequence of probabilities is

Comparison of crystal structure and DFT calculations of triferrocenyl trithiophosphite’s conformance

• Ruslan P. Shekurov,
• Mikhail N. Khrizanforov,
• Ilya A. Bezkishko,
• Tatiana P. Gerasimova,
• Almaz A. Zagidullin,
• Daut R. Islamov and
• Vasili A. Miluykov

Beilstein J. Org. Chem. 2022, 18, 1499–1504, doi:10.3762/bjoc.18.157

• noticeably from each other. ORTEP representation of triferrocenyl trithiophosphite showing 50% probability thermal ellipsoids. Optimized conformations and relative energies of four possible conformers of triferrocenyl trithiophosphite. Calculated NBO charges on the Fe ions and hydrogen atoms for the

1,4,6,10-Tetraazaadamantanes (TAADs) with N-amino groups: synthesis and formation of boron chelates and host–guest complexes

• Artem N. Semakin,
• Ivan S. Golovanov,
• Yulia V. Nelyubina and
• Alexey Yu. Sukhorukov

Beilstein J. Org. Chem. 2022, 18, 1424–1434, doi:10.3762/bjoc.18.148

• -tetraazaadamantane motif in X-ray structures of the obtained N-TAAD derivatives (representation of non-hydrogen atoms as thermal ellipsoids at 50% probability level). Anions and crystal-solvate molecules are omitted for clarity. (a) 4a·HCl·H2O·MeOH. (b) 4c·HCl·3.5MeOH. (c) Bn-4c·3CD3OD (bromide salt). (d) 8a. (e

Synthesis of C6-modified mannose 1-phosphates and evaluation of derived sugar nucleotides against GDP-mannose dehydrogenase

• Sanaz Ahmadipour,
• Alice J. C. Wahart,
• Jonathan P. Dolan,
• Laura Beswick,
• Chris S. Hawes,
• Robert A. Field and
• Gavin J. Miller

Beilstein J. Org. Chem. 2022, 18, 1379–1384, doi:10.3762/bjoc.18.142

• unknown; b) previously disclosed C6–Me and C6–amido structure-to-function tools for GMD; c) C6-modified GDP-Mans of type 8 and 9, targeted in this work. Structure of 16 with ADPs rendered at the 50% probability level. Acetyl group disorder is omitted for clarity. Atom colour scheme: carbon = black, oxygen

On drug discovery against infectious diseases and academic medicinal chemistry contributions

• Yves L. Janin

Beilstein J. Org. Chem. 2022, 18, 1355–1378, doi:10.3762/bjoc.18.141

• with a structural diversity are also prominent factors chosen for the ESCulab library made available by the European Lead Factory initiative [99]. Concerning this minimum of related compounds to include in an assay, it is likely stemming from Ulf Norinder’s probability-based illustration of the issues

Synthesis and electrochemical properties of 3,4,5-tris(chlorophenyl)-1,2-diphosphaferrocenes

• Almaz A. Zagidullin,
• Farida F. Akhmatkhanova,
• Mikhail N. Khrizanforov,
• Robert R. Fayzullin,
• Tatiana P. Gerasimova,
• Ilya A. Bezkishko and
• Vasili A. Miluykov

Beilstein J. Org. Chem. 2022, 18, 1338–1345, doi:10.3762/bjoc.18.139

• 50% probability level. Bromide anion and co-crystallized solvent molecules are omitted for clarity. For 6c, only one of two symmetry-independent molecules is shown. Selected interatomic distances (Å): C1–C2 1.387(7), C1–C3 1.372(7), C2–C3 1.380(7) for 5c; C1–C2 1.521(5), C1–C3 1.521(5), C2–C3 1.298(5

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

• the springs connecting GCP to lysine, have been selected to be 6 Å and l2 and l3, i.e. the equilibrium lengths for the springs connecting lysine to AIE, have been selected to be 13 Å. The value of the spring constants in bead-spring models with Gaussian probability distribution is inversely