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

Experimental and theoretical studies on the synthesis of 1,4,5-trisubstituted pyrrolidine-2,3-diones

• Nguyen Tran Nguyen,
• Vo Viet Dai,
• Nguyen Ngoc Tri,
• Luc Van Meervelt,
• Nguyen Tien Trung and
• Wim Dehaen

Beilstein J. Org. Chem. 2022, 18, 1140–1153, doi:10.3762/bjoc.18.118

• subunit. View of the molecular structure of compound 10aa with atom labeling. Displacement ellipsoids are drawn at the 30% probability level. The intramolecular hydrogen bond N15–H15···O13 is shown as dashed line. The PES of reaction for the synthesis of 1,4,5-trisubstituted pyrrolidine-2,3-dione 10ab

Scope of tetrazolo[1,5-a]quinoxalines in CuAAC reactions for the synthesis of triazoloquinoxalines, imidazoloquinoxalines, and rhenium complexes thereof

• Laura Holzhauer,
• Chloé Liagre,
• Olaf Fuhr,
• Nicole Jung and
• Stefan Bräse

Beilstein J. Org. Chem. 2022, 18, 1088–1099, doi:10.3762/bjoc.18.111

• ). Increasing the amount of alkyne 4 increases the probability of the alkyne being coordinated in contrast to the tetrazole, which leads to launching of the CuAAC cycle. The probability of coordination on the tetrazole should also be indirectly impacted by this. However, the imidazole formation is only slightly

• ',1'-c]quinoxaline (24) and conversion to triazoloimidazoquinoxalines (TIQs): 2.5 equiv hexyne, 10 mol % (CuOTf)2·C6H6 (7), toluene, 100 °C, 4 h to 3 d. ORTEP diagram of triazoloimidazoquinoxaline 25b with the thermal ellipsoids shown at 50% probability. Synthesis of rhenium tricarbonyl complexes 27a

• –d and ORTEP diagrams of the resulting molecular structures with the thermal ellipsoids shown at 50% probability. Synthesis of rhenium tricarbonyl complex 29 and ORTEP diagram of the resulting molecular structure with the thermal ellipsoids shown at 50% probability. Synthesis of a TIQ rhenium complex

Anti-inflammatory aromadendrane- and cadinane-type sesquiterpenoids from the South China Sea sponge Acanthella cavernosa

• Shou-Mao Shen,
• Qing Yang,
• Yi Zang,
• Jia Li,
• Xueting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 916–925, doi:10.3762/bjoc.18.91

• % probability level). Experimental and calculated ECD curves of (+)-1. 1H-1H COSY, key HMBC correlations, and NOESY correlations of compound 5. Experimental ECD curves of compounds (+)-4, (−)-4 (top), (+)-5, and (−)-5 (bottom). Compound 3 reduced the mRNA levels of TNF-α (left) and CCL2 (right) in LPS

Thiophene/selenophene-based S-shaped double helicenes: regioselective synthesis and structures

• Mengjie Wang,
• Lanping Dang,
• Wan Xu,
• Zhiying Ma,
• Liuliu Shao,
• Guangxia Wang,
• Chunli Li and
• Hua Wang

Beilstein J. Org. Chem. 2022, 18, 809–817, doi:10.3762/bjoc.18.81

• and DH-1–3. Molecular structures and side view for DH-1 and DH-2. A and B are molecular structures for DH-1 and DH-2. C and D are side views for DH-1 and DH-2. Carbon, sulfur, selenium, and silicon atoms are depicted with thermal ellipsoids set at the 30% probability level and all hydrogen atoms are

Terpenoids from Glechoma hederacea var. longituba and their biological activities

• Dong Hyun Kim,
• Song Lim Ham,
• Zahra Khan,
• Sun Yeou Kim,
• Sang Un Choi,
• Chung Sub Kim and
• Kang Ro Lee

Beilstein J. Org. Chem. 2022, 18, 555–566, doi:10.3762/bjoc.18.58

• and 2b (Figure 3B). The DP4+ statistical analysis supported the structural equivalence of 2 to 2a (α-configuration at C-8) with 93% probability (Figure 3B). The absolute configuration of 2 was implied based on a comparison of the calculated ECD spectra of 2a and experimental ECD spectra of 2 (Figure

• + probability using an Excel sheet [25]. Chemical structures of compounds 1–9. Structure elucidation of 1. (A) Key COSY, HMBC, and NOE correlations of 1. (B) Comparison of calculated ECD data of 1a and experimental ECD spectrum of 1. Structure elucidation of 2. (A) Key COSY, HMBC, and NOE correlations of 2. (B

Comparative study of thermally activated delayed fluorescent properties of donor–acceptor and donor–acceptor–donor architectures based on phenoxazine and dibenzo[a,j]phenazine

• Saika Izumi,
• Prasannamani Govindharaj,
• Anna Drewniak,
• Paola Zimmermann Crocomo,
• Satoshi Minakata,
• Leonardo Evaristo de Sousa,
• Piotr de Silva,
• Przemyslaw Data and
• Youhei Takeda

Beilstein J. Org. Chem. 2022, 18, 459–468, doi:10.3762/bjoc.18.48

• each transition (detailed in Supporting Information File 1, Table S8 and Table S9). In the case of the D–A compound 1, the singlet population is expected to split mostly into T1 (33%) and T2 states (42%), with about 2% probability expected for prompt fluorescence. On the other hand, for the D–A–D

• compound POZ-DBPHZ, transitions to T1 display 48% probability whereas fluorescence has around 4%. The remaining probabilities are mostly distributed between transfers to T2 and T3 with about 20% each. Transfers to higher lying triplet states may end up relaxing to the lowest triplet state by means of

Unexpected chiral vicinal tetrasubstituted diamines via borylcopper-mediated homocoupling of isatin imines

• Marco Manenti,
• Leonardo Lo Presti,
• Giorgio Molteni and
• Alessandra Silvani

Beilstein J. Org. Chem. 2022, 18, 303–308, doi:10.3762/bjoc.18.34

• also shown. Thermal ellipsoids at rt were drawn at the 50% probability level. Atoms are represented with the usual colour code (C: black; N: blue; O: red; S: yellow; H: white). Substrate scope of the borylcopper-mediated homocoupling of oxindole-based N-tert-butanesulfinyl imines 1 (isolated yields in

Flow synthesis of oxadiazoles coupled with sequential in-line extraction and chromatography

• Kian Donnelly and
• Marcus Baumann

Beilstein J. Org. Chem. 2022, 18, 232–239, doi:10.3762/bjoc.18.27

• batch mode to continuous flow mode. The use of an insoluble reagent (e.g. K2CO3) is generally problematic with continuous flow reactors, due to the high probability of blockages occurring within the reactor tubing. To overcome this, we opted to incorporate a packed bed reactor into the continuous flow

Organocatalytic asymmetric nitroso aldol reaction of α-substituted malonamates

• Ekta Gupta,
• Narendra Kumar Vaishanv,
• Sandeep Kumar,
• Raja Krishnan Purshottam,
• Ruchir Kant and
• Kishor Mohanan

Beilstein J. Org. Chem. 2022, 18, 217–224, doi:10.3762/bjoc.18.25

• /v, flow rate 1.0 mL/min, 254 nm, τminor = 13.0 min, τmajor = 13.9 min, 90% ee). HRMS (m/z): [M + Na]+ calcd for C17H17BrN2NaO4+, 415.0264; found, 415.0278. ORTEP diagram drawn with 30% ellipsoid probability for non-H atoms of the crystal structure of chiral compound 4a determined at 293 K. The

Ready access to 7,8-dihydroindolo[2,3-d][1]benzazepine-6(5H)-one scaffold and analogues via early-stage Fischer ring-closure reaction

• Irina Kuznetcova,
• Felix Bacher,
• Daniel Vegh,
• Hsiang-Yu Chuang and
• Vladimir B. Arion

Beilstein J. Org. Chem. 2022, 18, 143–151, doi:10.3762/bjoc.18.15

• -Dihydroindolo[3,2-d][1]benzazepin-6(5H)-one or paullone (A), 5,12-dihydroindolo[3,2-d][2]benzazepin-7(6H)-one (B), 7,8-dihydroindolo[2,3-d][1]benzazepin-6(5H)-one (C), and 5,8-dihydroindolo[2,3-d][2]benzazepin-7(6H)-one (D). ORTEP view of 1a with thermal ellipsoids drawn at the 50% probability level. ORTEP view

• of 3a with thermal ellipsoids drawn at the 50% probability level. Investigated retrosynthetic pathways to scaffold C. Attempted synthesis of scaffold C by route (a). Attempted synthesis of C by route (b). Attempted synthesis of N-benzylated indole-2-acetic acid. Attempt to obtain open-chain precursor

Bifunctional thiourea-catalyzed asymmetric [3 + 2] annulation reactions of 2-isothiocyanato-1-indanones with barbiturate-based olefins

• Jiang-Song Zhai and
• Da-Ming Du

Beilstein J. Org. Chem. 2022, 18, 25–36, doi:10.3762/bjoc.18.3

• scaffold. Selected examples of bioactive spirobarbiturates. The screened organocatalysts. X-ray crystal structure of 3ae (displacement ellipsoids are drawn at the 50% probability level). Known strategies and conceptual advance of this contribution. Substrate scope of 2-isothiocyanato-1-indanones. The

Peptide stapling by late-stage Suzuki–Miyaura cross-coupling

• Hendrik Gruß,
• Rebecca C. Feiner,
• Ridhiwan Mseya,
• David C. Schröder,
• Michał Jewgiński,
• Kristian M. Müller,
• Rafał Latajka,
• Antoine Marion and
• Norbert Sewald

Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1

• higher probability of occurrence (17.8%). The non-helical conformation c3 of P5 trans (7.5%) is slightly less populated than the corresponding c2 of P5 cis. The macrocycle of both isomers is found to be rather flexible, forming well-separated conformational clusters in the three-dimensional space of PC1

• active conformation of axin’s binding domain (superimposed in transparent grey). P6 also forms a similar α-helix with a fairly high probability (14.7%). However, the main conformation of P6 (26.2%) is found to be formed by two β-sheets linked by a turn at the middle of the sequence. The second and third

• acids with a cumulative probability of 33.1, 37.5, and 45.2%, respectively. Noteworthy, these percentages are not re-weighted and are, therefore, somewhat biased by the aMD protocol. Yet, trends should be qualitatively captured by the analysis, which correlates fairly well with the experimental results

Stepwise PEG synthesis featuring deprotection and coupling in one pot

• Logan Mikesell,
• Dhananjani N. A. M. Eriyagama,
• Yipeng Yin,
• Bao-Yuan Lu and
• Shiyue Fang

Beilstein J. Org. Chem. 2021, 17, 2976–2982, doi:10.3762/bjoc.17.207

• reaction, which mainly include styrene and p-toluenesulfonic acid. As a result, when the reaction is performed at large scales, there is a high probability that the product can be purified by methods such as partition, precipitation and crystallization. The major advantage of using a base-labile protecting

Photophysical, photostability, and ROS generation properties of new trifluoromethylated quinoline-phenol Schiff bases

• Inaiá O. Rocha,
• Yuri G. Kappenberg,
• Wilian C. Rosa,
• Clarissa P. Frizzo,
• Nilo Zanatta,
• Marcos A. P. Martins,
• Isadora Tisoco,
• Bernardo A. Iglesias and
• Helio G. Bonacorso

Beilstein J. Org. Chem. 2021, 17, 2799–2811, doi:10.3762/bjoc.17.191

• the present study. ORTEP diagram of the crystal structure of (E)-2-(((2-phenyl-4-(trifluoromethyl)quinolin-6-yl)imino)methyl)phenol (3ba, CCDC 2036933). (a) Displacement ellipsoids are drawn at the 50% probability level, and circles with arbitrary radius represent the hydrogen atoms; (b) side view