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

Synthesis of 2-benzyl N-substituted anilines via imine condensation–isoaromatization of (E)-2-arylidene-3-cyclohexenones and primary amines

• Lu Li,
• Na Li,
• Xiao-Tian Mo,
• Ming-Wei Yuan,
• Lin Jiang and
• Ming-Long Yuan

Beilstein J. Org. Chem. 2024, 20, 1468–1475, doi:10.3762/bjoc.20.130

• reduction. This electrophilic aromatic substitution usually needs harsh reaction conditions, tedious synthetic procedures and sometimes encounters the trouble of separating positional isomers caused by orientation or steric effects of the pre-existed amino group on the aryl moiety. Nevertheless, anilines

A Diels–Alder probe for discovery of natural products containing furan moieties

• Alyssa S. Eggly,
• Namuunzul Otgontseren,
• Carson B. Roberts,
• Amir Y. Alwali,
• Haylie E. Hennigan and
• Elizabeth I. Parkinson

Beilstein J. Org. Chem. 2024, 20, 1001–1010, doi:10.3762/bjoc.20.88

• -carbon chain shown with 8, conversion dropped to an average of 86%. This is likely because the bulkier side chain sterically hinders the molecules from aligning in the optimal orientation for the HOMO and LUMO to interact. Similar high yields were observed with 10 and 11. The maleimide probe also worked

Confirmation of the stereochemistry of spiroviolene

• Yao Kong,
• Yuanning Liu,
• Kaibiao Wang,
• Tao Wang,
• Chen Wang,
• Ben Ai,
• Hongli Jia,
• Guohui Pan,
• Min Yin and
• Zhengren Xu

Beilstein J. Org. Chem. 2024, 20, 852–858, doi:10.3762/bjoc.20.77

• boron migration occurred during the hydroboration process of spiroviolene that resulted in the production of a mixture of 1α-hydroxyspiroviolane, 9α- and 9β-hydroxyspiroviolane after oxidation. The assertion of the cis-orientation of the 19- and 20-methyl groups provided further support for the revised

Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria

• Kara A. Strickland,
• Brenda Martinez Rodriguez,
• Ashley A. Holland,
• Shelby Wagner,
• Michelle Luna-Alva,
• David E. Graham and
• Jonathan D. Caranto

Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75

• °C in deoxygenated 30 mM tricine buffer at pH 7.5. Alpha-fold model of Vs NnlA dimer (cyan) overlayed with Pseudomonas aeruginosa (grey; PDB: 3VOL [35][36]) to estimate the position and orientation of the heme cofactor. Conserved residues in the distal heme pocket are labeled. Conserved basic

Evaluation of the enantioselectivity of new chiral ligands based on imidazolidin-4-one derivatives

• Jan Bartáček,
• Karel Chlumský,
• Jan Mrkvička,
• Lucie Paloušová,
• Miloš Sedlák and
• Pavel Drabina

Beilstein J. Org. Chem. 2024, 20, 684–691, doi:10.3762/bjoc.20.62

• effective transition state includes the electrophile positioned in the equatorial site (strongly coordinated) and the nucleophile in the perpendicular site (weakly coordinated) [19]. The most favourable orientation of aldehyde should be out of the ligand’s molecular parts, thus forming E-configuration at

Pseudallenes A and B, new sulfur-containing ovalicin sesquiterpenoid derivatives with antimicrobial activity from the deep-sea cold seep sediment-derived fungus Pseudallescheria boydii CS-793

• Zhen Ying,
• Xiao-Ming Li,
• Sui-Qun Yang,
• Hong-Lei Li,
• Xin Li,
• Bin-Gui Wang and
• Ling-Hong Meng

Beilstein J. Org. Chem. 2024, 20, 470–478, doi:10.3762/bjoc.20.42

• by analysis of NOESY data (Figure 3). NOE cross peaks from H-15 to H-2, 6-OH, and from H-3 to 6-OH indicated the cofacial orientation of these groups, while correlations from 1-OH to H-8, 7-OH, 2-OMe, and 3-OH suggested the opposite position of these groups. To unambiguously clarify the structure of

• . Key 1H-1H COSY (bond lines), and HMBC (red arrows) correlations of 1–3. NOE correlations of compounds 1 and 2 (solid line indicates β-orientation and dashed lines represent α-orientation). X-ray crystal structure of compounds 1–3 (with a thermal ellipsoid probability of 50%). Proposed biosynthetic

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

• rotated to maximize the distances between the lone pairs of the electron-rich fluorine and oxygen atoms. Usually, one of the fluorine atoms lies in a syn orientation to an oxygen (e.g., 3f has an F–C–C–O dihedral angle of 15.6°) creating a dipole. This dipole appears to aid crystal packing by forming weak

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

• antiparallel orientation of the closely spaced cationic fragments of base 5 can be reversed to the opposite. This can be achieved with 4,6-dichlororesorcinol, a well-known molecular organizer and coordinating agent [20][21]. Thus, the joint crystallization of dipyridoacenaphthene 5 and 4,6-dichlororesorcinol

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

Photoinduced in situ generation of DNA-targeting ligands: DNA-binding and DNA-photodamaging properties of benzo[c]quinolizinium ions

• Julika Schlosser,
• Olga Fedorova,
• Yuri Fedorov and
• Heiko Ihmels

Beilstein J. Org. Chem. 2024, 20, 101–117, doi:10.3762/bjoc.20.11

• ligand and DNA bases [72]. To gain additional information about the orientation of the benzo[c]quinolizinium ligand in the intercalation site, the reduced LD (LDr) spectrum was determined exemplarily for ligand 3f (Supporting Information File 1, Figure S15) [74][75]. The analysis of the data revealed a

• binding angle α = 59° between the ligand 3f and the DNA helix, thus indicating a tilted orientation of the ligand relative to the DNA base pairs within the binding site. The DNA-binding ligands were also generated in situ in the presence of DNA. For that purpose, solutions of the styrylpyridines 2d–g and

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

• this study. On the other hand, despite higher L/D, the CNT orientation in the film prepared from the dispersion was comparable to the previous study. This suggests that further optimization of the deposition process is necessary to create highly oriented CNT films. Results and Discussion To prepare

• (Figure 2e). This indicates that the L/D had a greater impact on the transition concentrations than the ζ-potential. In the biphasic state, the spindle nematic phase droplets, tactoids, were observed (Figure 2c). These were classified into two types depending on the orientation of the DWCNT [22][23][29

• to the randomly oriented DWCNTs beneath the surface, the densification of aligned DWCNTs toward the edge region could account for the similar orientation degree to the previous lower L/D SWCNT film [23]. To obtain highly aligned CNT films, the condition of drying step [33], the surfactant

Aldiminium and 1,2,3-triazolium dithiocarboxylate zwitterions derived from cyclic (alkyl)(amino) and mesoionic carbenes

• Nedra Touj,
• François Mazars,
• Guillermo Zaragoza and
• Lionel Delaude

Beilstein J. Org. Chem. 2023, 19, 1947–1956, doi:10.3762/bjoc.19.145

• attractive coulombic interactions between the opposite charges were held responsible for this orientation [79]. In addition, the presence of bulky aryl substituents in the vicinity of the sulfur atoms should further restrict their conformational freedom. As a matter of fact, the largest deviation from

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

• same atoms as at the start. Visually, only a part of the GAG’s final pose overlaps with the initial one. The final pose adapts a perpendicular conformation to the starting GAG chain orientation (Figure 3). Acidic FGF Ligand 1. RMSD slowly increased during the first phase (windows from 1 to 8) of