Mechanisms for radical reactions initiating from N-hydroxyphthalimide esters

• Carlos R. Azpilcueta-Nicolas and
• Jean-Philip Lumb

Beilstein J. Org. Chem. 2024, 20, 346–378, doi:10.3762/bjoc.20.35

• photosensitizer in an energy-transfer (EnT) mechanism. This proposal was supported by fluorescence quenching measurements, as well as the direct excitation of 44 by UV irradiation, resulting in the formation of 45 in a 45% yield. According to this hypothesis, NHPI ester 44 would adopt a favorable conformation (46

Spatial arrangements of cyclodextrin host–guest complexes in solution studied by ¹³C NMR and molecular modelling

• Konstantin Lebedinskiy,
• Ivan Barvík,
• Zdeněk Tošner,
• Ivana Císařová,
• Jindřich Jindřich and
• Radim Hrdina

Beilstein J. Org. Chem. 2024, 20, 331–335, doi:10.3762/bjoc.20.33

• , we reveal the conformation (spatial arrangement) of the host–guest complex in solution spectroscopically by measuring the 13C NMR spectra of a suitable guest molecule. We decided to take Cs symmetric guest molecules, CD as a host and measure the 13C NMR spectra of these complexes. We expect that the

• carbons (Figure 1). The degree of the signal split correlates with the distance of prochiral atoms (carbons) to the host cavity and thus gives information about the conformation of the guest molecule in the host cavity. First, we measured simple 1D 13C NMR spectra and indeed observed the split of the

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• nitrogen. CH−π stacking and hydrophobic interactions occur between the aromatic ring of Trp36 and the alpha face of the ring as well as the hydroxymethyl moiety of the galactose residue, additionally ensuring specificity for galactoside over glucoside as an equatorial conformation of the O4 hydroxy group

Synthesis of π-conjugated polycyclic compounds by late-stage extrusion of chalcogen fragments

• Aissam Okba,
• Pablo Simón Marqués,
• Kyohei Matsuo,
• Naoki Aratani,
• Hiroko Yamada,
• Gwénaël Rapenne and
• Claire Kammerer

Beilstein J. Org. Chem. 2024, 20, 287–305, doi:10.3762/bjoc.20.30

• conformation of the thiepine ring, thus weakening the π–π stacking intermolecular interactions. Finally, solid-state S-extrusion could be triggered in a controlled way upon thermal activation of 21, as observed in thermogravimetric analysis, with the loss of sulfur detected at 223 °C to yield the planar S

• ) and side view (b) of the X-ray crystal structure of thiepine 3b showing its bent conformation. Thermal ellipsoids are shown at the 50% probability level, and all hydrogen atoms as well as propyl groups on imide substituents have been omitted for clarity. Reprinted with permission from [57]. Copyright

Photochromic derivatives of indigo: historical overview of development, challenges and applications

• Gökhan Kaplan,
• Zeynel Seferoğlu and
• Daria V. Berdnikova

Beilstein J. Org. Chem. 2024, 20, 228–242, doi:10.3762/bjoc.20.23

• melting point of indigo is bifurcated intra- and intermolecular hydrogen bonding [11], and face-to-face π–π stacking of parallel aromatic rings (Figure 2) [12]. Single crystal X-ray diffraction analysis showed that the indigo molecule is almost planar and exists in the E-conformation. The central C=C bond

Comparison of glycosyl donors: a supramer approach

• Anna V. Orlova,
• Nelly N. Malysheva,
• Maria V. Panova,
• Nikita M. Podvalnyy,
• Michael G. Medvedev and
• Leonid O. Kononov

Beilstein J. Org. Chem. 2024, 20, 181–192, doi:10.3762/bjoc.20.18

• ][33][34][37][39][43][44][46]. During a study of a possible influence of remote acyl protective groups [23] on the sialylation outcome (which could become possible through participation in stabilization of glycosyl cation [24][47][48] in a conformation with all-axial substituents in the pyranose ring

• merely changing the reaction conditions” [73][74]. In our opinion, these “environmental variables” [73] (including concentration of reagents) can influence structure and/or composition of supramers of reagents formed in reaction solutions. These changes may result in a modulation of the conformation or

• concerning their relative reactivity and selectivity. This prevented us from revealing a possible influence of remote acyl protective groups at O-9 on the sialylation outcome and their role in stabilization of glycosyl cation in a conformation with all-axial substituents in the pyranose ring. According to

Perspectives on push–pull chromophores derived from click-type [2 + 2] cycloaddition–retroelectrocyclization reactions of electron-rich alkynes and electron-deficient alkenes

• Michio Yamada

Beilstein J. Org. Chem. 2024, 20, 125–154, doi:10.3762/bjoc.20.13

• of 63 in toluene revealed that the lowest singlet excited state (S1) decays mono-exponentially to the ground state (S0) within approximately 1 ps, suggesting the existence of an accessible CI between S1 and S0. In the S1 minimum conformation of 63, the PCBD moiety adopted a planar orientation

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

• shown in Figure 2a (for 2f see Supporting Information File 1, Figure S1). Both molecules crystallize in a conformation in which the phenolate is oriented toward the methylene group in α-position (C16 in Figure 2b) to the electron-withdrawing group (either CN in case of 2a or COOt-Bu in case of 2f). The

• can be represented by the resonance structures shown in Figure 2d. The phosphonium center exhibits a somewhat distorted tetrahedral conformation in both zwitterions. The largest angles found are 115.3(1)° in 2a and 114.0(2)° in 2f (in both cases C6–P1–C15) and the smallest angles are 105.0(1)° in 2a

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

• 1C4 conformation for the IdoA2S ring was chosen as it was shown to be the essentially dominant conformation in the microsecond scale simulations performed by Sattelle et al. as it is energetically more favorable than the 2SO conformation [40]. Complex preparation The obtained ligands were docked using

• restore any native contacts. This suggests that the GAG gets close to the binding site but does not return to a similar conformation as the initial (experimental) pose. A similar trend is observed with hydrogen bonds where the number of H-bonds drops when the ligand is pulled away but never gets fully

• suggesting a more favorable novel ligand conformation. During relaxation, MD energies only improved slightly which is in agreement with the high RMSD that suggests that GAG did not return to the initial binding pose. The number of native contacts decreased drastically during the first windows of US from 1800

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

• coordinating nitrogen of the 1,2,3-triazole units. The nitrogen atoms of the two quinoline moieties are therefore trans to each other. This conformation might be induced by the cobalt precursor Co(NCS)2(py)4, which has already the NCS monodentate ligands cis to each other, as it was not the case for other Co

Unprecedented synthesis of a 14-membered hexaazamacrocycle

• Anastasia A. Fesenko and
• Anatoly D. Shutalev

Beilstein J. Org. Chem. 2023, 19, 1728–1740, doi:10.3762/bjoc.19.126

• deviation of 0.054 Å from the mean-square plane. The nuclear-independent chemical shift (NICS) [48][49][50] values of 5 in its optimized conformation were used as a magnetic criterion of aromaticity. The NICS(0) value for the macrocyclic ring (+2.23 ppm in DMSO), calculated at the HF/6-31+G(d) level, shows

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

• liquors and, in both cases, XRD confirmed the obtention of the (E)-isomer, in an anti-conformation. Computational calculations (gas and water phases) were performed in order to confirm some of the structural and vibrational aspects of the compounds. An important intramolecular H bond involving the

• , were isolated from the respective mother liquors. The structures of hdz-CH3 and hdz-NO2 are displayed in Figure 1 and an overview of the crystallographic data can be found in Table 1. Both molecules are near planar and correspond to the (E)-isomer, in an antiperiplanar conformation. Superposition of

• only one NH signal around 12 ppm, indicating the presence exclusively of the (E)-isomer in solution. Furthermore, steric hindrance in these cases allow only for the formation of the antiperiplanar conformation around the conjugated amide single bond. Full assignments, with the chemical shifts and

Quinoxaline derivatives as attractive electron-transporting materials

• Zeeshan Abid,
• Liaqat Ali,
• Sughra Gulzar,
• Faiza Wahad,
• Raja Shahid Ashraf and
• Christian B. Nielsen

Beilstein J. Org. Chem. 2023, 19, 1694–1712, doi:10.3762/bjoc.19.124

• range of 4.03–4.81% in PSC devices [36]. The team further explored side-chain engineering (phenyl groups) and end-group modification (2-(1,1-dicyanomethylene)thiazolidin-4-one) of new NFAs, i.e., Qx28–Qx30. While removal of all side chains supported a planar conformation of the molecule, it hampered

• quinoxaline-4,4'-dicyanobenzene by manipulating the donor–acceptor conformation. The efficient TADF emission at room temperature highlighted the potential of these emitters for achieving high-performance OLEDs. The tunability of the emission peak through appropriate donor selection further demonstrates the

Benzoimidazolium-derived dimeric and hydride n-dopants for organic electron-transport materials: impact of substitution on structures, electrochemistry, and reactivity

• Swagat K. Mohapatra,
• Khaled Al Kurdi,
• Samik Jhulki,
• Georgii Bogdanov,
• John Bacsa,
• Maxwell Conte,
• Tatiana V. Timofeeva,
• Seth R. Marder and
• Stephen Barlow

Beilstein J. Org. Chem. 2023, 19, 1651–1663, doi:10.3762/bjoc.19.121

• crystallographic inversion (Ci) symmetry, and approximate molecular C2h symmetry, and so has a perfectly staggered conformation around the central C–C bond and thus a Y–C–C–Y torsion angle of precisely 180°; the structure closely resembles those of the two inequivalent molecules in the structure of the previously

• °. The conformation found in the structure of the Y = cyclohexyl, R’ = OMe derivative, 1h2 (Figure 3), is somewhat similar to that previously reported for its non-methoxylated analogue 1e2 [14]; the 1h2 molecule does not have the crystallographic C2 symmetry of the latter, but does have approximate

• molecular C2 symmetry, while the Y–C–C–Y torsion angles for 1h2 and 1e2 are 149.4° and 140.3°, respectively, and thus both intermediate between the perfectly staggered (180° torsion) and neighboring eclipsed conformation (120°). The imidazole rings in the previously reported and present dimer structures are

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

• with Zn(II) was crucial to achieving the final strapping reaction, affording 11. The presence of the diaza-crown-6 caps resulted in the meso-bridge carbon atoms being slightly pulled out of the porphyrin plane, causing 11 to adopt a ruffled conformation. The penta-coordinated Zn(II) contained an

• ligands. Compound 19-Co (structure not shown) retained the cobalt(II) oxidation state with a water molecule within the cleft. The XRD analysis of the structures of 19-Co and 18b-Co exhibited Pacman conformation. The X-ray molecular structure of 19-Co provided further insights, showing a square-planar

Complexes of resorcin[4]arene with secondary amines: synthesis, solvent influence on “in-out” structure, and theoretical calculations of non-covalent interactions

• Waldemar Iwanek

Beilstein J. Org. Chem. 2023, 19, 1525–1536, doi:10.3762/bjoc.19.109

• ; Introduction Resorcin[4]arenes are macrocyclic compounds with a cavity structure formed from resorcinol and aldehydes [1]. Of particular significance is their crown conformation, which stems from the presence of 8 hydroxy groups on the upper rim and a hydrophobic cavity [2]. This property plays an important

• a slight change in its conformation towards the boat conformation. The length of the hydrogen bond between the oxygen atom of the hydroxy group forming the hydrogen bond with pyrrolidine and the adjacent hydroxy group is 1.746 Å and is only slightly shorter than the other intramolecular hydrogen

Exploring the role of halogen bonding in iodonium ylides: insights into unexpected reactivity and reaction control

• Carlee A. Montgomery and
• Graham K. Murphy

Beilstein J. Org. Chem. 2023, 19, 1171–1190, doi:10.3762/bjoc.19.86

• 63a induced an energetically-disfavoured twist in the fluorine adduct’s conformation (INTA’), raising its energy over that of 63b and decreasing the energy barrier between it and the reductive elimination transition state TSA’. Additionally, the role of the halogen bond acceptor in 61d is also poorly

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

• conformation of the force field was optimized. DFT was used to calculate the gauge-independent atomic orbital [30] for 1H and 13C NMR chemical shifts using the PCM solvent model in Gaussian 09 software [29]. The NMR chemical shift was corrected by the isotope shift of TMS [31]. The calculated 13C NMR chemical

First synthesis of acylated nitrocyclopropanes

• Kento Iwai,
• Rikiya Kamidate,
• Khimiya Wada,
• Haruyasu Asahara and
• Nagatoshi Nishiwaki

Beilstein J. Org. Chem. 2023, 19, 892–900, doi:10.3762/bjoc.19.67

• the enol form, a C-attack (path a) furnishes cyclopropane 1, and an O-attack (path b) furnishes dihydrofuran 8. When the R1 group becomes bulkier, the hydroxy group may be far from the reaction site because of the steric repulsion in the stable conformation. Another possibility is that the bulky

Construction of hexabenzocoronene-based chiral nanographenes

• Ranran Li,
• Di Wang,
• Shengtao Li and
• Peng An

Beilstein J. Org. Chem. 2023, 19, 736–751, doi:10.3762/bjoc.19.54

• designed NGs with tailor-made sizes and structures not only show planar conformation as fragments of graphene, but also evolved with a diversity of other shapes, including bowls [10], saddles [11][12][13], helixes [14][15], belts [16], rings [17], and their hybrid conformations such as helical bilayers [18

• helical conformation was confirmed by the single-crystal X-ray crystallography of its methoxy-substituted analogue. Another method to obtain the incompletely cyclized seco-HBC is the introduction of a non-hexagonal ring into the precursors of HBC. Due to the large ring strain, the precursors are not prone

• . And the derivative 16 was also synthesized by allylic oxidation of compound 15 using selenium dioxide. As helical chiral NGs, helicene 14 and its derivatives 15 and 16 showed highly distorted helical conformation and also exhibited a relatively high isomerization barrier (over 28.9 kcal/mol determined

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

• signalize complex formation (interaction with a biomolecule, cyclodextrine, metal cation, etc.) or change of receptor conformation [5][6]. Employment of pyrene as a biosensor is complicated due to its large aromatic surface's hydrophobicity and fluorescence sensitivity to oxygen. Therefore, modifications of

• ), differing only in the linker length between the aromatic units, have been prepared by condensation of two different pyrenecarboxylic acids with phenanthridine-labelled amino acid (Scheme 2). The influence of the linker length on the molecule flexibility, intramolecular conformation, spectroscopic properties

• electrostatic binding of the dye along the polynucleotide backbone. The reorganized intramolecular conformation of the ligand could explain the quenching of excimer fluorescence and/or redistribution of chromophore charges upon binding since fluorescence quenching is sensitive to factors that affect the rate

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

• inhibition of Golgi-type α-mannosidases [22]. It seems that the slightly bulkier (R)-1-hydroxyethyl group at C-5 of 29 compared to the hydroxymethyl at C-5 of 30 allows for a different conformation of the N-2-naphthylmethyl group in the active site of α-mannosidases (Figure 4). This would induce a shift in

• the N-2-naphthylmethyl group and the methyl component of (R)-1-hydroxyethyl group at C-5 of 28. In case of 31, the smaller hydroxymethyl group at C-5 allows for a different binding conformation of the N-2-naphthylmethyl group. FMO-PIEDA total pair interaction energies (ΔElinker-E) (in kcal mol−1

Strategies to access the [5-8] bicyclic core encountered in the sesquiterpene, diterpene and sesterterpene series

• Cécile Alleman,
• Charlène Gadais,
• Laurent Legentil and
• François-Hugues Porée

Beilstein J. Org. Chem. 2023, 19, 245–281, doi:10.3762/bjoc.19.23

Identification and determination of the absolute configuration of amorph-4-en-10β-ol, a cadinol-type sesquiterpene from the scent glands of the African reed frog Hyperolius cinnamomeoventris

• Angelique Ladwig,
• Markus Kroll and
• Stefan Schulz

Beilstein J. Org. Chem. 2023, 19, 167–175, doi:10.3762/bjoc.19.16

• synthesis by Taber that used dichromate as an oxidant [13] led to a less diastereoselective reaction furnishing the three ketones 9, 10, and 11 in a ratio of 36:2:5. The cis-conformation of the decalin backbone of 9 and 11 originates from the endo-selectivity of the Diels–Alder reaction and the boat

• conformation of the transition state. A chair transition state is less preferred because of inherent non-bonding interactions of some hydrogens. This has been discussed in detail in the original publication by Taber and Gunn, favoring 9 as the main diastereomer [13]. Our results confirm these data. To increase

• conformation was determined by calculation using force field methods (MMFF94 [16]) and is shown in Figure S2 of Supporting Information File 1. Key NOE couplings were observed between bridgehead H-8a, H-4a and H-4. The latter also couples with the methyl group at C-1, indicating a cis-decalin configuration with

1,4-Dithianes: attractive C2-building blocks for the synthesis of complex molecular architectures

• Bram Ryckaert,
• Ellen Demeyere,
• Frederick Degroote,
• Hilde Janssens and
• Johan M. Winne

Beilstein J. Org. Chem. 2023, 19, 115–132, doi:10.3762/bjoc.19.12

• , antiaromaticity is usually not a very relevant concept, as there will be no degeneration of the molecular orbitals. Nevertheless, 1,4-dithiin does adopt a non-planar boat-like conformation, which can rapidly interconvert through a planar, but nonaromatic geometry (with a shallow folding energy curve of less than

• single-cis conformation. Ando and co-workers prepared the symmetrical 1,4-dithiane 41 (Scheme 9a) [55], and amply illustrated the concept by reacting it in a [4 + 2] cycloaddition with a highly reactive diazo dienophile (Cookson’s reagent or 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD)) to afford the bis

• -adduct dithiin 42 in quantitative yield. Although 2,5-dimethylhexa-2,4-diene cannot possibly adopt a coplanar single-cis conformation, and is therefore completely unreactive in Diels–Alder reactions as a diene, its 1,4-dithiane-tethered version in 41 must show a sufficient proximity between the terminal