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

• validation report can be generated for each carbohydrate in the molecular model. This report is put out in JSON format for easy consumption by web-based database frontends. The initial report generation was completed in parallel over 64 CPU cores in around 5 h. After the initial surveys through PDB and PDB

Synthesis and properties of 6-alkynyl-5-aryluracils

• Ruben Manuel Figueira de Abreu,
• Till Brockmann,
• Alexander Villinger,
• Peter Ehlers and
• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 898–911, doi:10.3762/bjoc.20.80

• that the distance between the molecules within the unit cell is higher than the distance between the unit cells. In addition, the molecules are arranged parallel-displaced to each other, which is considered to be more stable than the sandwich arrangement [64][65][66][67][68]. Consequently, the distance

• between the layers varies periodically between 3.373 Å and 3.662 Å. This results in different interactions between the layers, as depicted in Figure 3. Furthermore, the layers are arranged in an anti-parallel face-to-face order to reduce the steric hindrance. Within the shorter distance layers (3.373 Å

Switchable molecular tweezers: design and applications

• Pablo Msellem,
• Maksym Dekthiarenko,
• Nihal Hadj Seyd and
• Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

• a parallel direction, as the bulky -OMe groups are located outside the tweezer’s cavity to avoid steric hindrance with each other. When protonated, the pyridinium group acts as a hydrogen-bond donor for the two methoxy groups and triggers the rotation of the respective benzene rings along with the

• release of siRNA or miRNA encapsulated within them into the solution in vitro and in vivo [21]. The closed conformation of 2 with parallel alkyl chains acts as a building block of the bilayer membrane and is packed together with other lipids. When the surrounding medium becomes acidic, the tweezers adopt

• arms with planar Pt complexes are parallel and the distance between them allows for the intercalation of another terpy-Pt complex. The guest intercalation coupled with the induction of short-range Pt–Pt interactions was followed by UV–vis absorption and emission spectroscopies with characteristic MMLCT

Synthesis of 2,2-difluoro-1,3-diketone and 2,2-difluoro-1,3-ketoester derivatives using fluorine gas

• Alexander S. Hampton,
• David R. W. Hodgson,
• Graham McDougald,
• Linhua Wang and
• Graham Sandford

Beilstein J. Org. Chem. 2024, 20, 460–469, doi:10.3762/bjoc.20.41

• anionic 1a–i-enolate species in parallel with N-fluoroammonium ion 6. Fluoride ions formed through the reactions between fluorine and quinuclidine or fluorine and enolate species, may deprotonate 1a–i-enol, to form enolates of 1a–i that are reactive towards both fluorine and N-fluoroammonium ion 6. The

Enhanced host–guest interaction between [10]cycloparaphenylene ([10]CPP) and [5]CPP by cationic charges

• Eiichi Kayahara,
• Yoshiyuki Mizuhata and
• Shigeru Yamago

Beilstein J. Org. Chem. 2024, 20, 436–444, doi:10.3762/bjoc.20.38

• transition corresponds to the CT band. The structure and stability of [10]CPP⊃[5]CPP2+ were estimated by DFT calculations at the ωB97-XD/6-31G* level of theory. Three isomeric structures were optimized, of which complex 1, with two CPPs aligned in parallel, is the most thermodynamically stable (Figure 5a

• ). Furthermore, the tilting of the complex in adjacent columnar structures with respect to the short axis is opposite to each other, as in a herringbone structure, and such columnar structures are parallel to each other through a columnar structure consisting of a host–guest complex in blue and its counterions

• . On the other hand, the complex in blue forms a 1D columnar structure with alternating counterions (Figure 7g), and each column is parallel to the others. Furthermore, the complex is tilted at approximately 30° relative to the long axis of the unit lattice. Conclusion [10]CPP encapsulates [5]CPP2+ in

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

• conditions (Scheme 25A). The general catalytic cycle begins with oxidative addition of an organohalide into a Ni0 catalyst yielding NiII complex 125 (Scheme 25B). In parallel, the initial SET activation of RAE 10, leading to the formation of radical anion 11, takes place in the presence of a stoichiometric

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

• ). In parallel, we also expressed CMA1 in a bacterial expression system, which allowed us to ascertain whether binding was influenced by lectin glycosylation. The full-length mature protein (6–264) and individual N- or C-terminal domains were expressed using a N-terminal fusion comprising DsbC and a

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

• pristine acene with a dienophile to transiently form a cycloadduct with increased solubility for processing purposes, and unmasking it afterwards via a retro-Diels–Alder reaction [16][17][18][19]. In parallel to retro-Diels–Alder reactions, another efficient strategy for the in situ aromatization of target

Substitution reactions in the acenaphthene analog of quino[7,8-h]quinoline and an unusual synthesis of the corresponding acenaphthylenes by tele-elimination

• Ekaterina V. Kolupaeva,
• Narek A. Dzhangiryan,
• Alexander F. Pozharskii,
• Oleg P. Demidov and
• Valery A. Ozeryanskii

Beilstein J. Org. Chem. 2024, 20, 243–253, doi:10.3762/bjoc.20.24

• in a 2:1 ratio leads to the formation of co-crystals, in which, as judged by the X-ray data, the supramolecular organization is again in action (Figure 4). Two molecules of the base are almost parallel to each other (the distance between the π-systems of two molecular planes is 3.551 Å with the

• -axis is shown). Selected images of the supramolecular organization of two molecules of base 5 held by 4,6-dichlororesorcinol in an almost parallel manner showing side view (а), view with the resorcinol molecule directed to the viewer (b), and view above the azaarene cycles showing their almost complete

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

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

• slightly larger than 2 Å in all three cases. Finally, formation of dimer 1-Cs is exothermic for the radical cation profile, but moderately endothermic for the neutral dimer, as previously observed. As general trends, we find that the radical cation profiles are qualitatively parallel with some minimal

Preparing a liquid crystalline dispersion of carbon nanotubes with high aspect ratio

• Keiko Kojima,
• Nodoka Kosugi,
• Hirokuni Jintoku,
• Kazufumi Kobashi and
• Toshiya Okazaki

Beilstein J. Org. Chem. 2024, 20, 52–58, doi:10.3762/bjoc.20.7

• ][30]. If the DWCNTs align parallel to the long axis of the spindle droplet, it is referred to as a homogenous tactoid. Conversely, if the DWCNTs align from one pole to another, it is called a bipolar tactoid. Figure 3 illustrates the aspect ratio of the tactoids (R/r) as a function of the tactoid

• effect [15][33][34]. As a result, the volume fraction of DWCNTs at the edge increased. Notably, the widths of bundled DWCNTs at the edge were larger than in the inner region (Figure 5b,c). The direction of the bundled DWCNTs near the film surface were parallel to the shear direction in both regions. Due

• polarizers (white double arrows). Scale bars are 400 µm. (c) Polarized optical absorption spectra with different angles ranging from 0° (red) to 90° (blue). The sear direction and polarizer are parallel at 0°. (d) SEM image of the DWCNT film. Blue outlined arrows indicate the shear direction of bar-coating

Charge carrier transport in perylene-based and pyrene-based columnar liquid crystals

• Alessandro L. Alves,
• Simone V. Bernardino,
• Carlos H. Stadtlober,
• Edivandro Girotto,
• Giliandro Farias,
• Rodney M. do Nascimento,
• Sergio F. Curcio,
• Thiago Cazati,
• Marta E. R. Dotto,
• Juliana Eccher,
• Leonardo N. Furini,
• Hugo Gallardo,
• Harald Bock and
• Ivan H. Bechtold

Beilstein J. Org. Chem. 2023, 19, 1755–1765, doi:10.3762/bjoc.19.128

• the charge carrier mobility (parallel vs perpendicular to the columnar axis) of up to ten orders of magnitude [3][4][5][6][7]. In 1994, Adam and collaborators obtained a hole-mobility of up to 0.1 cm2 V−1 s−1 for a triphenylene-based columnar liquid crystal [8], motivating intense research activity to

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

• antiparallel dimers (marked as *) sandwiched between two non-parallel molecules. The planes in hdz-NO2 present similar intermolecular interactions, but they grow as (101) planes. The columns also present the antiparallel dimers, but they are intercalated by antiparallel slipped molecules (Figure 2C). The

• spectrum of this precursor at pH 3.8 (dotted dark yellow curve). On the other hand, under similar arguments, the constituent at 284 nm is probably related to a TMP-based transition. In contrast, the intense component at 307 nm has no parallel in the spectra of precursors and was consequently attributed to

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

• endergonic dimer-to-SC ET; subsequent rapid cleavage of the odd-electron dimer cation affords the stable monomer cation and an odd-electron monomer, the latter then undergoing an exergonic ET to another SC molecule. The “ET-first” mechanism occurs in parallel with the “cleavage-first” mechanism for many of

Organic thermally activated delayed fluorescence material with strained benzoguanidine donor

• Alexander C. Brannan,
• Elvie F. P. Beaumont,
• Nguyen Le Phuoc,
• George F. S. Whitehead,
• Mikko Linnolahti and
• Alexander S. Romanov

Beilstein J. Org. Chem. 2023, 19, 1289–1298, doi:10.3762/bjoc.19.95

• benzoguanidine donor ligands around the central 4,6-dicyanobenzene core. Unlike the 4CzIPN compound, the 4BGIPN emitter can crystallize in a chiral P21 space group due to the parallel and antiparallel orientation of the benzoguanidine donors with respect to each other, lack of C2 rotational symmetry and extended

Selective and scalable oxygenation of heteroatoms using the elements of nature: air, water, and light

• Damiano Diprima,
• Hannes Gemoets,
• Stefano Bonciolini and
• Koen Van Aken

Beilstein J. Org. Chem. 2023, 19, 1146–1154, doi:10.3762/bjoc.19.82

• suppress the photochemical reaction while carrying out another light-induced transformation. Aromatic additives (Table 2): In parallel we observed the significant influence on the reaction rate when the substrate contained an aromatic moiety (e.g., the thioanisole oxidation is over 10 times faster than the

Eschenmoser coupling reactions starting from primary thioamides. When do they work and when not?

• Lukáš Marek,
• Jiří Váňa,
• Jan Svoboda and
• Jiří Hanusek

Beilstein J. Org. Chem. 2023, 19, 808–819, doi:10.3762/bjoc.19.61

• desirable ECR product 9a in 62% or 55% yield (entries 3 and 7 in Table 1) together with other decomposition products from which only thiobenzamide and benzonitrile were identified. In pure trimethyl phosphite (Table 1, entry 8) that acts simultaneously as polar solvent and mild thiophile, the parallel

• where triethylamine behaves as a much stronger base. A much weaker base – solid KHCO3 – is probably still strong enough to generate free imidothioates 6a,b''' which undergo parallel base-catalyzed elimination (minor route to nitriles) and intramolecular proton-transfer between the carbon and nitrogen to

Palladium-catalyzed enantioselective three-component synthesis of α-arylglycine derivatives from glyoxylic acid, sulfonamides and aryltrifluoroborates

• Bastian Jakob,
• Nico Schneider,
• Luca Gengenbach and
• Georg Manolikakes

Beilstein J. Org. Chem. 2023, 19, 719–726, doi:10.3762/bjoc.19.52

• situ generation of reactive imine species, we have disclosed iron- and bismuth-catalyzed three-component reactions for the synthesis of α-arylglycines [14][15][16], in which the arylboronic acid could be replaced with an electron-rich (hetero)arene as nucleophile. In parallel, we have developed

Synthesis, structure, and properties of switchable cross-conjugated 1,4-diaryl-1,3-butadiynes based on 1,8-bis(dimethylamino)naphthalene

• Semyon V. Tsybulin,
• Ekaterina A. Filatova,
• Alexander F. Pozharskii,
• Valery A. Ozeryanskii and
• Anna V. Gulevskaya

Beilstein J. Org. Chem. 2023, 19, 674–686, doi:10.3762/bjoc.19.49

• formally symmetrical structure of diynes 5, naphthalene rings A and B of molecules 5b and 5d differ in their structural parameters. At the same time, the monomer fragments of the nitro derivative 5e are identical. In the case of 5e, the naphthalene rings lie in parallel planes, while in crystals of 5b and

Combretastatins D series and analogues: from isolation, synthetic challenges and biological activities

• Jorge de Lima Neto and
• Paulo Henrique Menezes

Beilstein J. Org. Chem. 2023, 19, 399–427, doi:10.3762/bjoc.19.31

• convergent route by which it was possible to reach both, compound 2 and 1. Initially, the authors prepared the protected alcohol 66 from aldehyde 52 in a linear sequence (Scheme 12). In parallel, the monobenzylation of 3,4-dihydroxybenzaldehyde (67), followed by chain elongation using the Wittig reaction

• proved to be important for the selectivity of the reaction, where significant cleavage of the benzyl group resulted when ethanol was the solvent of choice. Subsequent ester hydrolysis gave compound 112 (Scheme 22) [55]. In parallel, a Still–Gennari olefination using aldehyde 52 lead to the cis-alkene 113

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

• in α-position to the keto function. This terminal double bond prefigures the late RCM cyclization. trans-Hydrindanone 87 was isolated as a single diastereomer and possesses 5 out of the 10 stereogenic centers of nitidasin (93). In parallel, (−)-citronellene (88) was converted into derivative 89

Inclusion complexes of the steroid hormones 17β-estradiol and progesterone with β- and γ-cyclodextrin hosts: syntheses, X-ray structures, thermal analyses and API solubility enhancements

• Alexios I. Vicatos,
• Zakiena Hoossen and
• Mino R. Caira

Beilstein J. Org. Chem. 2022, 18, 1749–1762, doi:10.3762/bjoc.18.184

• host–guest complexation, as a consequence of a mutual-induced fit of host and guest molecules [39]. With reference to γ-CD·PRO, the asymmetric unit (ASU) comprises three pairs of glucose rings that generate three complete γ-CD molecules when rotation of these units around the four-fold axis parallel to

• to the cavities of the γ-CD molecules. The distinct packing arrangement of the repeat unit of the host molecules in γ-CD·PRO. The four-fold axis (blue line) runs through the centre of the channel, parallel to the c-axis. The water molecules are omitted for clarity. A stereoscopic view of γ-CD·PRO

Inline purification in continuous flow synthesis – opportunities and challenges

• Jorge García-Lacuna and
• Marcus Baumann

Beilstein J. Org. Chem. 2022, 18, 1720–1740, doi:10.3762/bjoc.18.182

• chromatography system which utilizes multiple columns in parallel with a series of valves to stagger the injection of crude material to each of the column lines. The columns are filled with a diethylaminopropyl-functionalized polymer, followed by an UV–vis detector to identify and separate the different peaks

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

• prediction but are no longer interpretable as a result of their high level of abstraction [73]. NeuRiPP, for instance, utilizes a parallel convolutional neural network to predict novel RiPP precursor genes independent of their RiPP family. The neural network is trained on a RiPP precursor training set that