Recent advances and future challenges in the bottom-up synthesis of azulene-embedded nanographenes

• Bartłomiej Pigulski

Beilstein J. Org. Chem. 2025, 21, 1272–1305, doi:10.3762/bjoc.21.99

• -workers (Scheme 20) [98]. The starting polymer 152 was synthesized using Suzuki cross coupling and is regiorandom, meaning the orientation of the azulene units within the main chain is not defined. Polymer 152 was annulated using MsOH (methanesulfonic acid) yielding the non-alternant graphene nanoribbon

Supramolecular assembly of hypervalent iodine macrocycles and alkali metals

• Krishna Pandey,
• Lucas X. Orton,
• Grayson Venus,
• Waseem A. Hussain,
• Toby Woods,
• Lichang Wang and
• Kyle N. Plunkett

Beilstein J. Org. Chem. 2025, 21, 1095–1103, doi:10.3762/bjoc.21.87

• °, displaying a closer arrangement of two HIMs. In contrast, the sodium complex exhibits a more open orientation of two HIMs with an oxygen–sodium–oxygen bond angle close to 167.98°. Lastly, a comparative study of association constants and binding energies for phenylalanine-based HIM with LiBArF20 and NaBArF24

Orthogonal photoswitching of heterobivalent azobenzene glycoclusters: the effect of glycoligand orientation in bacterial adhesion

• Leon M. Friedrich and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2025, 21, 736–748, doi:10.3762/bjoc.21.57

• glycophotoswitches in their different isomeric states led to new insights into the role of ligand orientation in carbohydrate recognition. The experimental results were underpinned by molecular modeling. Keywords: azobenzene glycoconjugates; carbohydrate recognition; docking; FimH; orthogonal photoswitching

• diverse interactions with primary and secondary carbohydrate binding sites of the protein [13]. For example, when an α-ᴅ-mannopyranosyl (Man) and a β-ᴅ-glucopyranosyl (Glc) unit were conjugated such that the relative orientation of the two sugar portions is varied – be it on enantiomeric or regioisomeric

• scaffold molecules, respectively [14][15], – differing inhibitory properties in carbohydrate-specific bacterial adhesion resulted. To further investigate the effect of relative ligand orientation in carbohydrate recognition, we and others have utilized photoswitchable glycoconjugates [16][17][18][19

Acyclic cucurbit[n]uril bearing alkyl sulfate ionic groups

• Christian Akakpo,
• Peter Y. Zavalij and
• Lyle Isaacs

Beilstein J. Org. Chem. 2025, 21, 717–726, doi:10.3762/bjoc.21.55

• the C1·guest complexes. In uncomplexed C1 the tips of the aromatic rings are pointing toward each other which places Ha in the magnetically shielding region of the opposing sidewall. Upon formation of the C1·guest complexes, the tips of the aromatic sidewall change their orientation to accommodate the

• hydrophobic region of the guest which changes the orientation of Ha with respect to the magnetically shielding region [54][63][64]. X-ray crystal structure of C1 We were fortunate to obtain single crystals of the C1·Me6CHDA complex and solved the crystal structure by X-ray diffraction (CCDC 2411723). Figure 5

Origami with small molecules: exploiting the C–F bond as a conformational tool

• Patrick Ryan,
• Ramsha Iftikhar and
• Luke Hunter

Beilstein J. Org. Chem. 2025, 21, 680–716, doi:10.3762/bjoc.21.54

• (I, Figure 2). This has several implications. For example, if the C–C(F) bond rotates, the orientation of the terminal C–F bond dipole changes, and this can alter the overall dipole moment of the molecule. Indoles 1–3 illustrate this point (Figure 2) [9]. The non-fluorinated indole 1 has an unvarying

• leads to a low molecular dipole moment, because every C–F bond can be paired with another that has the opposite orientation. In contrast, compound 29 (Figure 4) divides the six fluorines into two groups of three, separated by an ethylene spacer [47]. The same helical conformation is maintained, but the

• ) bond, such that the endo orientation of the C–F bond (as depicted in I, Figure 6) is lower in energy than the exo conformer (not shown). This is an example of the anomeric effect [77]. The anomeric effect can be visualised perhaps most clearly when the ether moiety is embedded within a small ring [78

Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages

• Keith G. Andrews

Beilstein J. Org. Chem. 2025, 21, 421–443, doi:10.3762/bjoc.21.30

• polarization (enthalpic) (Figure 1). Organization, the control of the position(s) and orientation(s) of reacting molecules, has been achieved historically in supramolecular chemistry using “pre-organized” catalyst designs (vide infra). More recently, organization has been mooted by List as a unifying concept

• are linear molecules able to direct functionality toward each other in a relatively rigid pincer orientation. One example featuring a pair of antipodal carboxylic acids demonstrated acetal hydrolysis catalysis (Figure 3B) [110]. However, as linear molecules, the clefts are difficult to develop past

• active site (binding a substrate in an orientation that directs internally catalyzed reactivity) [347][348]. The examples of cavities with functionality discussed above, from Cram’s “full serine protease model” [87], to MOCs with flexible peripheral groups [349], to frameworks with internal proline

Synthesis of new condensed naphthoquinone, pyran and pyrimidine furancarboxylates

• Kirill A. Gomonov,
• Vasilii V. Pelipko,
• Igor A. Litvinov,
• Ilya A. Pilipenko,
• Anna M. Stepanova,
• Nikolai A. Lapatin,
• Ruslan I. Baichurin and
• Sergei V. Makarenko

Beilstein J. Org. Chem. 2025, 21, 340–347, doi:10.3762/bjoc.21.24

• structural analysis were obtained by crystallization from MeOH (5a), EtOH (5b), or DMFA (6b, 6c, and 7a). Single crystals of a suitable size were glued to the top of a glass fiber in a random orientation. The preliminary unit cell parameters were determined using three runs at different ω angle positions

Antibiofilm and cytotoxic metabolites from the entomopathogenic fungus Samsoniella aurantia

• Rita Toshe,
• Syeda J. Khalid,
• Blondelle Matio Kemkuignou,
• Esteban Charria-Girón,
• Paul Eckhardt,
• Birthe Sandargo,
• Kunlapat Nuchthien,
• J. Jennifer Luangsa-ard,
• Till Opatz,
• Hedda Schrey,
• Sherif S. Ebada and
• Marc Stadler

Beilstein J. Org. Chem. 2025, 21, 327–339, doi:10.3762/bjoc.21.23

• (Figure 2, Figure S10, Supporting Information File 1) that revealed key ROE correlations from H-2’ and H-3’ indicating their cofacial orientation whereas 3’-OH and 2’-NH are facing the opposite side of the molecule. In addition, further key ROE correlations were distinguished from H-11 to two methyl

Cu(OTf)₂-catalyzed multicomponent reactions

• Sara Colombo,
• Camilla Loro,
• Egle M. Beccalli,
• Gianluigi Broggini and
• Marta Papis

Beilstein J. Org. Chem. 2025, 21, 122–145, doi:10.3762/bjoc.21.7

• orientation between the electron-rich nitrogen of the diene and the electron-poor carbon of the alkyne. A different one-pot procedure affording tetrahydropyridines was developed employing two molecules of aromatic aldehydes, ethyl acetoacetate and two molecules of aniline. The copper triflate catalyst acts in

Recent advances in organocatalytic atroposelective reactions

• Henrich Szabados and
• Radovan Šebesta

Beilstein J. Org. Chem. 2025, 21, 55–121, doi:10.3762/bjoc.21.6

• organocatalyst C21. A considerable drop in yield and enantioselectivity was also observed in the reaction with dibenzylaniline. Interactions with and steric effects of the CPA C21 guiding the orientation of the substrates dictate the stereocontrol of the reaction. The utilization of CPA (R)-C23 in a dynamic

Non-covalent organocatalyzed enantioselective cyclization reactions of α,β-unsaturated imines

• Sergio Torres-Oya and
• Mercedes Zurro

Beilstein J. Org. Chem. 2024, 20, 3221–3255, doi:10.3762/bjoc.20.268

• alcohol E isomer and it coordinated to the squaramide in an effective orientation, a stepwise mechanism is taking place. Firstly, the dienolate adds to the azadiene which is followed by cyclization with formation of the C–N bond. Finally, protonation leads to the formation of the desired derivative. The

Hypervalent iodine-mediated intramolecular alkene halocyclisation

• Charu Bansal,
• Oliver Ruggles,
• Albert C. Rowett and
• Alastair J. J. Lennox

Beilstein J. Org. Chem. 2024, 20, 3113–3133, doi:10.3762/bjoc.20.258

• is then attacked by a nucleophile. The use of chiral iodine catalysts is essential for controlling the stereochemistry of the reaction. The specific arrangement of the catalyst influences the orientation of this nucleophilic attack as supported by density functional theory (DFT) calculations. In 2022

Advances in the use of metal-free tetrapyrrolic macrocycles as catalysts

• Mandeep K. Chahal

Beilstein J. Org. Chem. 2024, 20, 3085–3112, doi:10.3762/bjoc.20.257

• orientation of p-nitrophenyl units, due to the shielding of the bound aldehyde substrate from the incoming diene. The catalytic inactivity of 5 demonstrated the requirement of macrocyclic character for the potential catalysts. Later in 2009, the same group reported an organocatalyzed diastereoselective aldol

Tailored charge-neutral self-assembled L₂Zn₂ container for taming oxalate

• David Ocklenburg and
• David Van Craen

Beilstein J. Org. Chem. 2024, 20, 3007–3015, doi:10.3762/bjoc.20.250

• backbone adopt a nearly parallel orientation with a slight tilt compared to the horizontal axis which results in one short (Figure 3a, left ligand: 2.2 Å, and right ligand: 2.3 Å) and one longer Htriazole···Hquinolate (Hg···Ha) distance (left ligand: 2.8 Å, and right ligand: 2.8 Å). Contradictory, the

Interaction of a pyrene derivative with cationic [60]fullerene in phospholipid membranes and its effects on photodynamic actions

• Hayato Takagi,
• Çetin Çelik,
• Ryosuke Fukuda,
• Qi Guo,
• Tomohiro Higashino,
• Hiroshi Imahori,
• Yoko Yamakoshi and
• Tatsuya Murakami

Beilstein J. Org. Chem. 2024, 20, 2732–2738, doi:10.3762/bjoc.20.231

• membrane potential (Vm) in living cells. These previous studies indicated that the localization of the triad molecules in a specific intra-membrane orientation and the suppression of the photodynamic actions of the [60]fullerene (C60) moiety are likely important to achieve fast and safe control of Vm

• light irradiation [7], with the C60 species becoming negatively charged while the ferrocene moiety became positively charged (Figure 1a). This charge-separated state can be used to initiate nanoscale electric fields, e.g., Vm. The design of the triad molecules may also help to keep their orientation

Deciphering the mechanism of γ-cyclodextrin’s hydrophobic cavity hydration: an integrated experimental and theoretical study

• Stiliyana Pereva,
• Stefan Dobrev,
• Tsveta Sarafska,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2024, 20, 2635–2643, doi:10.3762/bjoc.20.221

• oppositely oriented intramolecular hydrogen bonds on the two edges: viewed from above (the narrow rim side; O6 side), the orientation of the hydrogen bonds on the wide rim (O2/O3 side of the truncated cone) is clockwise (CW), while the orientation of the hydrogen bonds on the narrow rim is counterclockwise

Applications of microscopy and small angle scattering techniques for the characterisation of supramolecular gels

• Connor R. M. MacDonald and
• Emily R. Draper

Beilstein J. Org. Chem. 2024, 20, 2608–2634, doi:10.3762/bjoc.20.220

• increasing shear [67]. This plateau had been observed in various systems, but an origin of the phenomenon had not been described. However, the unexpected behaviour could be rationalised as friction effects by quantifying the degree of orientation, as determined from anisotropic 2D-SANS scattering patterns

Metal-free double azide addition to strained alkynes of an octadehydrodibenzo[12]annulene derivative with electron-withdrawing substituents

• Naoki Takeda,
• Shuichi Akasaka,
• Susumu Kawauchi and
• Tsuyoshi Michinobu

Beilstein J. Org. Chem. 2024, 20, 2234–2241, doi:10.3762/bjoc.20.191

• the experimental observation that no monotriazoles were obtained. During the second azide addition, the orientation of benzyl azide is once more controlled. The benzyl group positioned on the inner side results in a thermodynamically less stable transition state (in-in-ts) compared to that on the

Natural resorcylic lactones derived from alternariol

• Joachim Podlech

Beilstein J. Org. Chem. 2024, 20, 2171–2207, doi:10.3762/bjoc.20.187

• (Figure 14) [249]. While most of the investigations including the X-ray data suggested that this natural product occurs as a racemate [38][74][147][162][248][249], it was occasionally obtained as the (−)-enantiomer [250][251]. The assumption that the methyl group in (−)-altenuene has the same orientation

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• (Figure 1): 1C4, 4C1 (chair forms) and an additional skew-boat shape (2S0) [9]. The glycosidic torsion angles Φ (H1–C1–Ox–Cx) and Ψ (C1–Ox–Cx–Hx) describe the relative orientation of two connected monosaccharide units; moreover, when dealing with monosaccharides containing an exocyclic hydroxymethyl group

• only by their chemical composition but also by their conformation. As mentioned above, glycans are characterised by a huge conformational diversity (see Figure 1): even individual furanoid or pyranoid monosaccharides can assume various shapes and in longer glycans the relative orientation of the

• complexes. 6. DOCK [137]: It is a molecular docking program (free for academic research) that predicts the orientation and conformation of ligands within the binding site of proteins or nucleic acids. It uses an incremental construction approach ("anchor-and-grow") to handle ligand flexibility and employs a

Multicomponent syntheses of pyrazoles via (3 + 2)-cyclocondensation and (3 + 2)-cycloaddition key steps

• Ignaz Betcke,
• Alissa C. Götzinger,
• Maryna M. Kornet and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2024, 20, 2024–2077, doi:10.3762/bjoc.20.178

Diastereoselective synthesis of highly substituted cyclohexanones and tetrahydrochromene-4-ones via conjugate addition of curcumins to arylidenemalonates

• Deepa Nair,
• Abhishek Tiwari,
• Banamali Laha and
• Irishi N. N. Namboothiri

Beilstein J. Org. Chem. 2024, 20, 2016–2023, doi:10.3762/bjoc.20.177

• strain destabilizes TSII where R is equatorial. Such a strain is avoided by R adopting axial orientation as in TSI, which is favoured, leading to the observed product 3. This has also been seen in previous cases where nitroalkenes and chalcones have been employed as acceptors in the reaction of curcumins

The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)

• Cristina Martini,
• Muhammad Idham Darussalam Mardjan and
• Andrea Basso

Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162

• its nucleophilicity and improving its orientation. Furthermore, Ser105 formed a strong hydrogen bond also with benzaldehyde, making it a better electron acceptor. Interestingly, also the imine intermediate showed strong interaction with Thr40 and Ser105 residues, so becoming a good electrophile for

• the addition of tert-butyl isocyanide. On the other hand, the addition of tert-butyl isocyanide on the imine altered the orientation of adduct 19, suppressing the interaction with Ser105 (Scheme 8). Very recently, Tyagi et al. reported the double encapsulation of CALB and Pd(PPh3)4 within silica

Regio- and stereochemical stability induced by anomeric and gauche effects in difluorinated pyrrolidines

• Ana Flávia Candida Silva,
• Francisco A. Martins and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2024, 20, 1572–1579, doi:10.3762/bjoc.20.140

• only slightly more stable than the other three conformers in both the gas phase and implicit water [4]. Hence, it appears that strong intramolecular interactions, and not only hydrogen bonding, govern the orientation of the fluorine atom in the F‒C‒C‒N fragment, favoring the cis-isomer of 3

• -fluoropyrrolidine. To investigate potential changes in the preferred orientation of the fluorine substituent in 3-fluoropyrrolidine and the respective cation, an additional fluorine atom was introduced into the molecule for theoretic studies (Figure 2). The subsequent evaluation focused on the role of anomeric and

• Figure 5 and Table 2. This disparity in stability was largely attributed to the relative orientation of the nitrogen electron lone pair and the adjacent C–F bond, facilitating an anomeric interaction characterized by nN→σ*CF electron delocalization. Isomer 2 also demonstrated such an orientation, but the

Photoswitchable glycoligands targeting Pseudomonas aeruginosa LecA

• Yu Fan,
• Ahmed El Rhaz,
• Stéphane Maisonneuve,
• Emilie Gillon,
• Maha Fatthalla,
• Franck Le Bideau,
• Guillaume Laurent,
• Samir Messaoudi,
• Anne Imberty and
• Juan Xie

Beilstein J. Org. Chem. 2024, 20, 1486–1496, doi:10.3762/bjoc.20.132

• ] or to mannosyl azobenzene-modified human cells [21] through photoswitching the orientation of the attached mannoside [22]. Photoswitchable glycooligomers [23] or glycodendrimers [24] have been investigated for the inhibition of PA lectin PA-IL or LecA and LecB. A variation of the IC50 value by a

• ][34], confirming the favorable interaction of the aryl group with the protein surface. For all compounds, no significant differences of affinities are observed between the E- and Z-isomer, with the exception of compounds 1 and 3 with para-orientation between the two aryl groups. The affinity of the E