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

• complement the growing glycan content of the PDB. Keywords: carbohydrates; database; N-glycans; N-glycosylation; polysaccharides; validation; website; Introduction Carbohydrate modelling is an important but often cumbersome stage in the macromolecular X-ray structure solution workflow. The accurate

Skeletal rearrangement of 6,8-dioxabicyclo[3.2.1]octan-4-ols promoted by thionyl chloride or Appel conditions

• Martyn Jevric,
• Julian Klepp,
• Johannes Puschnig,
• Oscar Lamb,
• Christopher J. Sumby and
• Ben W. Greatrex

Beilstein J. Org. Chem. 2024, 20, 823–829, doi:10.3762/bjoc.20.74

• levoglucosenone, cyrene and their derivatives, generating a unique set of bicyclic building blocks. Previous work on migration reactions in 6,8-dioxabicyclooctan-4-ols [18]. Mechanism for the rearrangement of 10, and Newman projection and the X-ray structure of 10d projected along the C4–C5 axis. Structures for

• 10a–c, preparation of 10d–f, and X-ray structure of 10e. Rearrangement reactions for 10a–f promoted by SOCl2. Reactions of allylic alcohols 15 and 18 with SOCl2. Appel reactions of dioxabicyclo[3.2.1]octan-4-ols 10a,e,f and 15. Some transformations for the skeletal rearrangement products 11a and 12a

• and X-ray structure for 24. Supporting Information Supporting information includes detailed experimental details and characterisation data, X-ray crystallography, and copies of 1H and 13C spectra for new compounds. Supporting Information File 11: Experimental details, X-ray crystallography and

Advancements in hydrochlorination of alkenes

• Daniel S. Müller

Beilstein J. Org. Chem. 2024, 20, 787–814, doi:10.3762/bjoc.20.72

• forms a dissociated hydrogen chloride aggregate in the form of complexes 103 or 105. An X-ray structure of complex 105 was reported and the reaction 104 → 105 is described in the report by Snyder, though not stoichiometric balanced. These complexes seem to play a pivotal role in the hydrochlorination

Visible-light-induced radical cascade cyclization: a catalyst-free synthetic approach to trifluoromethylated heterocycles

• Chuan Yang,
• Wei Shi,
• Jian Tian,
• Lin Guo,
• Yating Zhao and
• Wujiong Xia

Beilstein J. Org. Chem. 2024, 20, 118–124, doi:10.3762/bjoc.20.12

• Supporting Information Supporting Information File 35: Characterization data and copies of spectra. Supporting Information File 36: Crystallographic information file (cif) of X-ray structure for compound 3m. Funding We are grateful for the financial support from the Science and Technology Plan of Shenzhen

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

• with irreversible C–C fusions [7]. In phase 1, a [2 + 2] cycloadduct C120 dimer is formed, which was initially proposed to be with Cs symmetry, in contrast to the X-ray structure for the C120 dimer that shows D2h symmetry [3][9]. In phase 2, irreversible structural rearrangements occur leading to a

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

• product of interest 2a. Compound 2a was identified by a combination of NMR spectroscopic methods and single-crystal X-ray structure analysis (vide infra) as the zwitterionic phospha-Michael adduct of 1 and acrylonitrile, formally stabilized by proton transfer from the phenol group to the initially formed

• displayed in Scheme 1. All simulations were performed with COPASI, an open-source software [48]. The second-order rate constants were obtained by fitting the experimental time traces until a fully consistent data set, being valid for all experimental conditions, was established. For X-ray structure analyses

Cycloaddition reactions of heterocyclic azides with 2-cyanoacetamidines as a new route to C,N-diheteroarylcarbamidines

• Pavel S. Silaichev,
• Tetyana V. Beryozkina,
• Vsevolod V. Melekhin,
• Valeriy O. Filimonov,
• Andrey N. Maslivets,
• Vladimir G. Ilkin,
• Wim Dehaen and
• Vasiliy A. Bakulev

Beilstein J. Org. Chem. 2024, 20, 17–24, doi:10.3762/bjoc.20.3

• , 174.5; IR (ATR, KBr, cm−1): ν 3400, 3359, 3255, 1625, 1602, 1563, 1554, 1508, 1495, 1483, 1455, 1436, 1425, 1402, 1385, 1356, 1332, 1319, 1303, 1283, 1257, 1215, 1151, 1095, 1067, 1053, 1035, 1011; HRMS–ESI-TOF (m/z): [M + H]+ calcd for C13H14N7S+, 300.1026; found, 300.1031. X-ray structure

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

• , particular three positively charged residues, R101, K106, and K116, maintained strong H-bonds that have been also established in the X-ray structure-based MD simulation [51]. Some of these residues are absent as the most contributing to H-bonding in the less stable complexes (both last windows of the pulling

• away and pulling in processes). At the same time, the essential difference between the H-bonding pattern observed in the unrestrained MD simulation of the X-ray structure is that there were several non-charged residues (N8, A17, Y84) among the top residues contributing to H-bonds, while almost

• exclusively positively charged residues were observed to be substantial H-bond contributors in the US windows. In a microsecond-scale MD simulation of the same X-ray structure, three non-charged residues were identified as the top MM/GBSA free energy contributors [52]. This suggests that despite a very

Tying a knot between crown ethers and porphyrins

• Maksym Matviyishyn and
• Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

• geometry with the cobalt(II) positioned slightly above the N4 donor plane. The X-ray structure of 18b-Co exhibited a similar Pacman motif as its palladium analogue, with the cobalt(II) cation residing in a square-planar environment. The exploitation of a similar synthetic methodology allowed for preparing

Synthesis of 7-azabicyclo[4.3.1]decane ring systems from tricarbonyl(tropone)iron via intramolecular Heck reactions

• Aaron H. Shoemaker,
• Elizabeth A. Foker,
• Elena P. Uttaro,
• Sarah K. Beitel and
• Daniel R. Griffith

Beilstein J. Org. Chem. 2023, 19, 1615–1619, doi:10.3762/bjoc.19.118

• of X-ray structure data for compound 8. Supporting Information File 11: Copies of 1H and 13C NMR spectra of all purified novel compounds. Supporting Information File 12: Chrystallographic information file (cif) of X-ray structure for compound 8. Acknowledgements We acknowledge Prof. Dasan Thamattoor

Application of N-heterocyclic carbene–Cu(I) complexes as catalysts in organic synthesis: a review

• Nosheen Beig,
• Varsha Goyal and
• Raj K. Bansal

Beilstein J. Org. Chem. 2023, 19, 1408–1442, doi:10.3762/bjoc.19.102

• consecutive treatment of the corresponding azolium salts with silver oxide and copper chloride (Scheme 25). The X-ray structure of one of the complexes, [(TPrXyl)CuCl], revealed that the NHC–Cu–Cl bond angle is 177.8°, indicating almost linearity. These synthesized complexes were also used as efficient

• stable monomeric copper complexes. The X-ray structure shows a nearly linear C–Cu–CHF2 bond angle of 178°. Riant, Leyssens and co-workers obtained NHC–Cu(I)–bifluoride complexes 92 by reacting (IPr)CuCl successively with KOt-Bu and NEt3·3HF under inert atmosphere (Scheme 32) [45]. In place of KOt-Bu and

Cyanothioacetamides as a synthetic platform for the synthesis of aminopyrazole derivatives

• Valeriy O. Filimonov,
• Alexandra I. Topchiy,
• Vladimir G. Ilkin,
• Tetyana V. Beryozkina and
• Vasiliy A. Bakulev

Beilstein J. Org. Chem. 2023, 19, 1191–1197, doi:10.3762/bjoc.19.87

• -(substituted)phenylsulfonyl-4-thiocarbamoylpyrazoles in moderate to high yields. It was concluded that in 2-cyanothioacetamides, cyano and enamino groups are more active in the reaction with hydrazines than the thiocarbamoyl function. Experimental X-ray structure determination of 5b, 6a, 7a 5b: Crystal data

Light-responsive rotaxane-based materials: inducing motion in the solid state

• Adrian Saura-Sanmartin

Beilstein J. Org. Chem. 2023, 19, 873–880, doi:10.3762/bjoc.19.64

• -crystal X-ray structure of rotaxane 1a (R1 = Me, R2 = R3 = H) showing two interlocked molecules of the crystalline array [44]. Colour key of the solid structure: light blue = carbon atoms; purple = nitrogen atoms; red = oxygen atoms; and orange = iron atoms. Hydrogen atoms are omitted for clarity. (a

Facile access to 3-sulfonylquinolines via Knoevenagel condensation/aza-Wittig reaction cascade involving ortho-azidobenzaldehydes and β-ketosulfonamides and sulfones

• Ksenia Malkova,
• Andrey Bubyrev,
• Stanislav Kalinin and
• Dmitry Dar’in

Beilstein J. Org. Chem. 2023, 19, 800–807, doi:10.3762/bjoc.19.60

• good to excellent yields (Scheme 3). The product structures were confirmed by the standard set of characterization data as well as the single-crystal X-ray structure of the representative compound 5a. The presence of an electron-withdrawing group in the o-azidobenzaldehyde leads to decreased yields of

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

• NMR data of our structures and confirmed our published structure, and the X-ray structure provided the final piece of evidence in the process. As a side note, we would like to remind scientists that theory is not the ultimate means for structural elucidations and cannot be used to refute experimental

Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives

• Martin Kalník,
• Sergej Šesták,
• Juraj Kóňa,
• Maroš Bella and
• Monika Poláková

Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24

• inhibitory potential of the investigated imino-ᴅ-lyxitol derivatives. Molecular modeling In order to better understand the results of our inhibition study, the inhibitor:enzyme interactions were analyzed by molecular modeling. Structures of the inhibitors were docked into an X-ray structure of dGMII and

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

• at 90–100 °C was reported to give 3β-azidocholest-5-ene [10]. Comparing the respective NMR data with the published ones [12] revealed a difference of about 0.6 ppm for the chemical shift of H3 suggesting a miss-assignment [23]. This assumption was confirmed by the X-ray structure analysis of single

• ][10]. The current results correct the structure of cholesterols II and III to be in the α- and not, as reported before and shown in this Figure, in the β-configuration. Top: cholesterol (1) and the less polar product from the Appel reaction, cholesta-3,5-diene (9); bottom: X-ray structure of 9 with

• 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

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

• the X-ray structure geometries with the other functionals (or even with the PBE0 functional) does not give better agreement of the calculated to the experimental chemical shifts. That is, the P–P bond length in compound 8 is 2.147(6) Å by X-ray [67] and is 2.143 Å using the Latypov PBE0/6-31+G(d)/gas

• optimization, especially with the M06-2X NMR calculation (Table 3)! The X-ray structure of 32 was reported in 2004 [88][89] so the identification is correct, and provides a surprisingly extreme example of how these DFT functionals can differ. Comparison of bond lengths showed that this might be due to

• sensitivity of the DFT chemical shift to bond lengths. The three-membered phosphorus ring in the X-ray structure exhibited C–C and average C–P bond lengths of 1.495(2) and 1.869(5) Å, while the values for the M06-2X, Latypov, and B3LYP optimizations were 1.495/1.869, 1.488/1.882, and 1.489/1.908 Å

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

• ) 19e·3HCl·H2O. (f) 21·HCl·2H2O. (a) General structure of host–guest complexes of 3N-TAADs with water. (b) The general structure of host–guest complexes of 3N-TAADs with methanol. (c) Host–guest motif in the X-ray structure of 4a·HCl·H2O·MeOH (guest molecule is shown in “spacefill” representation). (d

• ) Host–guest motif in the X-ray structure of 4c·HCl·3.5MeOH (guest molecule is shown in “spacefill” representation). (e) Hirshfeld surface of the TAAD cation in 4a·HCl·H2O·MeOH. (e) Hirshfeld surface of the TAAD cation in 4c·HCl·3.5MeOH. (a) Dynamic processes in TAADs 4 and complexation with ROH. (b

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

• hangtaimycin, starting from ʟ-tryptophan is presented. Comparison to TDD isolated from the hangtaimycin producer Streptomyces spectabilis confirmed its S configuration. The X-ray structure of the racemate shows an interesting dimerisation through hydrogen bridges. The results from bioactivity testings of

• ), C) enantiomerically enriched 4 (90% ee) obtained under optimised conditions for the elimination reaction of 14 (Scheme 3), and D) natural enantiomerically pure (S)-TDD isolated from S. spectabilis. X-ray structure of (rac)-4. Bioactivity testing with hangtaimycin (1). A) Growth retardation of model

Synthesis of novel [1,2,4]triazolo[1,5-b][1,2,4,5]tetrazines and investigation of their fungistatic activity

• Anna V. Korotina,
• Svetlana G. Tolshchina,
• Rashida I. Ishmetova,
• Natalya P. Evstigneeva,
• Natalya A. Gerasimova,
• Natalya V. Zilberberg,
• Nikolay V. Kungurov,
• Gennady L. Rusinov,
• Oleg N. Chupakhin and
• Valery N. Charushin

Beilstein J. Org. Chem. 2022, 18, 243–250, doi:10.3762/bjoc.18.29

• been found. All the above-mentioned results demonstrate good prospects for finding new antifungal drugs in this class of compounds. X-ray structure of N-(6-(4-bromo-3,5-dimethylpyrazol-1-yl)-1,2,4,5-tetrazin-3-yl)benzamide. Chemical structures of [1,2,4]triazolo[4,3-b][1,2,4,5]tetrazine (a), [1,2,4

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

• chemoselective in the presence of other oxidisable moieties such as in the cases of 2i and 2j. Additionally, the stereoconfiguration of the styryl moiety was maintained as confirmed via the X-ray structure of 2j (Scheme 3). As a potential application of our previously reported synthesis of useful bicyclo[1.1.1

Regioselective synthesis of methyl 5-(N-Boc-cycloaminyl)-1,2-oxazole-4-carboxylates as new amino acid-like building blocks

• Jolita Bruzgulienė,
• Greta Račkauskienė,
• Aurimas Bieliauskas,
• Vaida Milišiūnaitė,
• Miglė Dagilienė,
• Gita Matulevičiūtė,
• Vytas Martynaitis,
• Sonata Krikštolaitytė,
• Frank A. Sløk and
• Algirdas Šačkus

Beilstein J. Org. Chem. 2022, 18, 102–109, doi:10.3762/bjoc.18.11

• analysis, 1H, 13C, and 15N NMR spectroscopy, HRMS, and single-crystal X-ray diffraction data. Keywords: β-enamino ketoesters; heterocyclic amino acids; 15N-labeled 1,2-oxazole; NMR (1H; 13C; 15N); 1,2-oxazole (isoxazole); X-ray structure analysis; Introduction 1,2-Oxazoles (isoxazoles) constitute an

• sets of signals with different intensities were observed due to the existence of two Boc-group rotational conformers. The X-ray structure of (2S)-2-[4-(methoxycarbonyl)-1,2-oxazol-5-yl]piperidin-1-ium trifluoroacetate (6b) finally supported this structure analysis. Examples of amino-functionalized 1,2

The enzyme mechanism of patchoulol synthase

• Houchao Xu,
• Bernd Goldfuss,
• Gregor Schnakenburg and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 13–24, doi:10.3762/bjoc.18.2

• Supporting Information File 1). A reference sample of 3 was isolated from patchouli oil and its structure was confirmed by NMR spectroscopy (Supporting Information File 1, Table S1 and Figures S3–S10). So far, only the X-ray structure of the chromate diester [6] and a Mo Kα structure of 3 were reported (CCDC

Synthesis of a novel aminobenzene-containing hemicucurbituril and its fluorescence spectral properties with ions

• Qingkai Zeng,
• Qiumeng Long,
• Jihong Lu,
• Li Wang,
• Yuting You,
• Xiaoting Yuan,
• Qianjun Zhang,
• Qingmei Ge,
• Hang Cong and
• Mao Liu

Beilstein J. Org. Chem. 2021, 17, 2840–2847, doi:10.3762/bjoc.17.195

• on host–guest interaction and supramolecular systems. Its applications and modifications are being pursued in our laboratory, and the results will be reported in due course. The X-ray structure of nitrobenzene-containing hemicucurbituril 9 (CCDC 2094879). Fluorescence emission spectra (λmax = 349 nm