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

HFIP as a versatile solvent in resorcin[n]arene synthesis

• Hormoz Khosravi,
• Valeria Stevens and
• Raúl Hernández Sánchez

Beilstein J. Org. Chem. 2024, 20, 2469–2475, doi:10.3762/bjoc.20.211

• -shaped conformation it precipitates out of solution acting as a thermodynamic sink [5][6]. Shortly after, Cram et al. recognized the potential of resorcin[n]arenes as compounds large enough to encapsulate other simple molecules or ions and group them with other known macrocyclic arene compounds, e.g

• , chlorinated species 1h and 1i, and carboxylic acid-containing 1s, developed high quality crystals from standing solutions in dimethyl sulfoxide for 1h and 1i, and methanol for 1s. Their molecular crystal structures were determined and are shown in Figure 1b displaying the classic cone conformation for both

Synthesis and conformational analysis of pyran inter-halide analogues of ᴅ-talose

• Olivier Lessard,
• Mathilde Grosset-Magagne,
• Paul A. Johnson and
• Denis Giguère

Beilstein J. Org. Chem. 2024, 20, 2442–2454, doi:10.3762/bjoc.20.208

• and nonbonding interactions for the halogen at C4. Finally, density functional theory (DFT) calculations corroborate the preference of talose analogues to adopt a 4C1-like conformation and a natural bonding orbital (NBO) analysis demonstrates the effects of hyperconjugation from C–F antibonding

• orbitals. Keywords: organofluorine; pyran inter-halide; solid-state conformation; solution-state conformation; Introduction Polyfluorinated pyran analogues of carbohydrates have attracted attention over the years. This class of glycomimetics has great biological potential with useful applications [1][2

• ][25][26][27][28][29][30], such as the solution-state conformation of diastereomeric polyfluorohexitols [31]. Herein, we report the synthesis of pyran inter-halide analogues of ᴅ-talopyranose 6, integrating also the 2,3-cis, 3,4-cis relationship for the halogens, from known intermediate 5 (Figure 1b

Phenylseleno trifluoromethoxylation of alkenes

• Clément Delobel,
• Armen Panossian,
• Gilles Hanquet,
• Frédéric R. Leroux,
• Fabien Toulgoat and
• Thierry Billard

Beilstein J. Org. Chem. 2024, 20, 2434–2441, doi:10.3762/bjoc.20.207

• ], electronic effects [17][18], and conformation [19][20][21]. Some trifluoromethoxylated molecules can be used as drugs in the treatment of various pathologies (Figure 1) [22][23][24][25][26][27][28][29]. On the other hand, despite its toxicity at higher doses, selenium is also an essential trace element in

Asymmetric organocatalytic synthesis of chiral homoallylic amines

• Nikolay S. Kondratyev and
• Andrei V. Malkov

Beilstein J. Org. Chem. 2024, 20, 2349–2377, doi:10.3762/bjoc.20.201

• -methylcrotylsilane (product 52) and disubstituted cyclic silanes (such as the silane, leading to 53), locked in syn-conformation. For the 2,3-disubstituted allylation products such as 52 and 53, the diastereomeric ratio spanned across 18:1 to >50:1. Notably, all 2,3-disubstituted silanes required an increased

Factors influencing the performance of organocatalysts immobilised on solid supports: A review

• Zsuzsanna Fehér,
• Dóra Richter,
• Gyula Dargó and
• József Kupai

Beilstein J. Org. Chem. 2024, 20, 2129–2142, doi:10.3762/bjoc.20.183

• catalyst closer to the support, impacting electronic properties and ligand conformation. With large catalyst molecules, the pores of an ordered mesoporous material being similar in size to the catalyst can create significant diffusion barriers as the catalyst attempts to enter the pores. As a result, the

• covalent bonding. These adsorptive interactions can alter the electronic properties and conformation of the supported organocatalyst, thereby influencing its catalytic activity compared to its homogeneous counterpart. For instance, Fotaras et al. showed that the incorporation of a tripeptide-like

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

• , depending on the values adopted by the torsional angles around the glycosidic linkages [10]. The high variability of linkages type, branching, stoichiometry, anomeric configuration (alpha and beta), and conformation contributes to the intricate nature of glycans. The complexity of the glycome is even higher

• 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

• design and discovery providing access to physics-based molecular modelling tools and machine learning technologies from a single modelling environment, however, it is not free-accessible. Further valuable insights into the structure and conformation of saccharides, determined by experiment and simulation

Understanding X-ray-induced isomerisation in photoswitchable surfactant assemblies

• Beatrice E. Jones,
• Camille Blayo,
• Jake L. Greenfield,
• Matthew J. Fuchter,
• Nathan Cowieson and
• Rachel C. Evans

Beilstein J. Org. Chem. 2024, 20, 2005–2015, doi:10.3762/bjoc.20.176

• ) that contains mostly Z isomers. This can be reversed using blue light or heat in a process that is stable over many cycles [7]. Isomerisation of azobenzene leads to a change in its conformation and polarity which, when combined into a surfactant molecule, modifies the resulting molecular geometry and

• . It should be noted that a lag between the time taken to reach the PSS and the time for the new micelle morphology to form is expected. This is due to the additional time that is required for diffusion and reassembly of the AzoTAB in the Z conformation into the new equilibrium structure [22]. The

• , Supporting Information File 1). This morphology change can be attributed to two changes in the AAPTAB on E–Z isomerisation [19]. Firstly, the shape change of the AAPTAB to the bent, “T-shape” conformation prevents the π–π stacking which was previously possible in the more planar, E isomers that were arranged

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

Harnessing unprotected deactivated amines and arylglyoxals in the Ugi reaction for the synthesis of fused complex nitrogen heterocycles

• Javier Gómez-Ayuso,
• Pablo Pertejo,
• Tomás Hermosilla,
• Israel Carreira-Barral,
• Roberto Quesada and
• María García-Valverde

Beilstein J. Org. Chem. 2024, 20, 1758–1766, doi:10.3762/bjoc.20.154

• assayed in our group. Under these conditions, the bis-1,4-benzodiazepines 7 resulting from the reaction of the amino group with the imine on the benzodiazepine were obtained as a single diastereomer. On the basis of the preferred conformation for the 1,4-benzodiazepin-5-ones 5 and 6 [20][22], where the

• amide substituent in C3 is pseudoaxially oriented in an all-trans conformation, only the unlike attack would be allowed (Scheme 3). On the other hand, when 3-bromopropanamine was used, the formation of the pyrrolobenzodiazepinone system 8 was observed albeit along with benzodiazepinone 5c (Scheme 4). In

Ring opening of photogenerated azetidinols as a strategy for the synthesis of aminodioxolanes

• Henning Maag,
• Daniel J. Lemcke and
• Johannes M. Wahl

Beilstein J. Org. Chem. 2024, 20, 1671–1676, doi:10.3762/bjoc.20.148

• ). The corresponding protecting group (PG) was thought to control the conformation of the 1,4-biradical 2, which is known to be important for efficient Norrish–Yang cyclizations [27][28]. Furthermore, the PG was deemed crucial for the development of further functionalizations of the azetidinols (vide

• effect on product formation, potentially by changing the substrate’s conformation. Ring opening Based on its outstanding performance in the photoreaction, we selected Ts-protected azetidinol 3a as our preferred substrate to test ring-opening reactions. However, initial attempts were met with limited

Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry

• Maria-Paula Schröder,
• Isabel P.-M. Pfeiffer and
• Silja Mordhorst

Beilstein J. Org. Chem. 2024, 20, 1652–1670, doi:10.3762/bjoc.20.147

• its β-helical structure; reversion of the N-methylation led to complete conformation loss. The methylated asparagine residues at positions 16, 22, and 28 form an intramolecular chain of hydrogen bonds along the outside of the β-helix. Hydrogen atoms from the amide methyl group form hydrogen bonds with

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

• conformational stability of proline-rich proteins such as collagen [2]. Therefore, pyrrolidine derivatives are particularly susceptible to conformational control induced by a fluorine substituent. The 5-membered pyrrolidine ring is a cyclic alkylamine that adopts a conformation that resembles the familiar

• fluorine gauche effect, commonly observed in compounds containing the F‒C‒C‒X fragment (where X is an electron-withdrawing substituent, such as nitrogen), typically favors a conformation where F and X are gauche to each other. This preference is attributed to stabilizing σCH→σ*CF and σCH→σ*CX

• interactions [4]. Protonation of 3-fluoropyrrolidine generates the 3-fluoropyrrolidinium cation, and this typically results in a highly favored conformation in both the gas phase and solution where the fluorine and nitrogen atoms are cis, mirroring the behavior observed in analagous 4- and 6-membered ring

Mining raw plant transcriptomic data for new cyclopeptide alkaloids

• Draco Kriger,
• Michael A. Pasquale,
• Brigitte G. Ampolini and
• Jonathan R. Chekan

Beilstein J. Org. Chem. 2024, 20, 1548–1559, doi:10.3762/bjoc.20.138

• the β-carbon of leucine ether linkage. Structurally related cyclopeptide alkaloids have similar J-values (Jα-β ≈ 8.0 Hz) and have been assigned as ʟ-erythro (anti) conformation [20][39]. Metabolomic analysis and GNPS networking Live samples of C. americanus and G. jasminoides were separated into

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

• /off or from low to high. This strategy can be used for specific targeting or local drug activation to reduce its toxicity [14]. There is an increasing use of the photoisomerization to control the conformation as well as the activities of various biomolecules with the development of photopharmacology

• the known crystal structure. The extended E-isomer establishes contact through galactoside and the first aryl ring only, while the bent Z-isomer has proper conformation to wrap around the central His53 residue and to establish a more extended interaction with the protein surface. This would be in

• LecA binding by light. Few differences were observed for the meta- (2 and 4) and ortho-substituted azobenzenes (5). Thermodynamics contributions exhibit larger variations with stronger enthalpy of binding for the Z-isomer, probably in relation with a folded conformation generating additional contact

Selectfluor and alcohol-mediated synthesis of bicyclic oxyfluorination compounds by Wagner–Meerwein rearrangement

• Ziya Dağalan,
• Muhammed Hanifi Çelikoğlu,
• Saffet Çelik,
• Ramazan Koçak and
• Bilal Nişancı

Beilstein J. Org. Chem. 2024, 20, 1462–1467, doi:10.3762/bjoc.20.129

• compounds by changing their metabolic stability, hydrogen bonding ability, lipophilicity, solubility, bioavailability, conformation and general structure [1][2][3][4]. About 20% of commercially available drugs contain fluorine, and this ratio is estimated to increase further [5][6]. Among organofluorines

Synthesis of cyclic β-1,6-oligosaccharides from glucosamine monomers by electrochemical polyglycosylation

• Md Azadur Rahman,
• Hirofumi Endo,
• Takashi Yamamoto,
• Shoma Okushiba,
• Norihiko Sasaki and
• Toshiki Nokami

Beilstein J. Org. Chem. 2024, 20, 1421–1427, doi:10.3762/bjoc.20.124

• disaccharide 16 was obtained as an exclusive product. The optimized structure of 15 calculated by DFT (B3LYP/6-31G(d)) suggested that the pyran ring preferred the boat conformation because the chair conformation of the pyran ring was controlled by the introduction of the 2,3-oxazolidinone protecting group (see

Computation-guided scaffold exploration of 2E,6E-1,10-trans/cis-eunicellanes

• Zining Li,
• Sana Jindani,
• Volga Kojasoy,
• Teresa Ortega,
• Erin M. Marshall,
• Khalil A. Abboud,
• Sandra Loesgen,
• Dean J. Tantillo and
• Jeffrey D. Rudolf

Beilstein J. Org. Chem. 2024, 20, 1320–1326, doi:10.3762/bjoc.20.115

• . Scaffold exploration of the eunicellane skeleton During protonation-induced cyclization of 1 and 2, the C6–C7 alkene showed higher nucleophilicity than either of the other two double bonds likely due to the unique conformation of the eunicellane skeleton. This selective reactivity was further supported

Sustainable tandem acylation/Diels–Alder reaction toward versatile tricyclic epoxyisoindole-7-carboxylic acids in renewable green solvents

• Ayhan Yıldırım

Beilstein J. Org. Chem. 2024, 20, 1308–1319, doi:10.3762/bjoc.20.114

• in a much shorter time (Table 1, entry 4) when the temperature of the reaction medium was increased to 50 °C. According to X-ray and Raman spectroscopy techniques, triglyceride molecules in liquid form are arranged in a dynamic chain-like conformation [114][115][116]. As the temperature of the

• in good agreement with those reported for this compound in the literature. In all synthesized compounds, Ha and Hb protons are only in endo conformation and therefore the amide and carboxylic acid functional groups are arranged in exo conformation. The fact that the flexible 2n and 2o compounds in

• reaction medium has been previously demonstrated by 1H NMR studies [129]. The elongation of the alkyl chain attached to the N atom facilitates the formation of the epoxyisoindole product by favoring the s-cis conformation due to steric factors (Thorpe–Ingold effect) [130][131]. Briefly, in this type of

Domino reactions of chromones with activated carbonyl compounds

• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 1256–1269, doi:10.3762/bjoc.20.108

• steric influence of the fluorine atom and of the substituent R1 might have an influence on the conformation which facilitates the intramolecular aldol reaction at the expense of the nitrile addition. In the case of formation of biphenyls 44, these products were generally obtained in good yields (63–79

Introduction of peripheral nitrogen atoms to cyclo-meta-phenylenes

• Koki Ikemoto and
• Hiroyuki Isobe

Beilstein J. Org. Chem. 2024, 20, 1207–1212, doi:10.3762/bjoc.20.103

• structural features of nitrogen-doped [n]CMPs. The crystal molecular structures of 3a and 3b are shown in Figure 3. The hexagonal macrocyclic structure of 3a showed a chair-like conformation with alternating biaryl dihedral angles showing +/– values. The octagonal structure of 3b exhibited a saddle-like

• conformation with an average dihedral angle of 45.0°, which was slightly larger than that of 3a (30.4°). The shapes of nitrogen-doped [n]CMPs did not deviate from those of hydrocarbon [n]CMPs, with similar average dihedral angles (32.4° for [6]CMP and 40.6° for [8]CMP) [15]. Likewise, the crystal packings of

Structure–property relationships in dicyanopyrazinoquinoxalines and their hydrogen-bonding-capable dihydropyrazinoquinoxalinedione derivatives

• Tural N. Akhmedov,
• Ajeet Kumar,
• Daken J. Starkenburg,
• Kyle J. Chesney,
• Khalil A. Abboud,
• Novruz G. Akhmedov,
• Jiangeng Xue and
• Ronald K. Castellano

Beilstein J. Org. Chem. 2024, 20, 1037–1052, doi:10.3762/bjoc.20.92

• measures 1.531 Å, comparatively larger than that of aromatic systems and on the order of Csp3–Csp3 bonds (Figure 6a). This represents the first evidence that the keto form is largely favored. Next, the molecule does not adopt a fully planar conformation, instead exhibiting a torsional angle of 4.33° with

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

• overall conformation of N-glycans comes to that of validated deposited structures [16]. The PDB-REDO [21] database is a separate resource, albeit linked to the PDB in that the entries that compound PDB-REDO are those original PDB crystallographic entries that included experimental data (i.e., reflection

• valid, the ring must be in the 4C1 chair conformation. This can be measured through the Cremer–Pople parameters θ and ψ [27]. Theta angles of 0° < θ < 360° indicate that the sugar may be in a higher-energy confirmation; therefore, caution should be placed on any conclusions drawn from the molecular

• the diagram. For example, a shape with an orange highlight indicates something is abnormal about the ring’s conformation, puckering, or monosaccharide nomenclature [30]. Similarly, a linkage with an orange highlight indicates that the torsion angles between the linkages are unexpected and require

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

• hand, the originally proposed cyclization mechanism (Scheme 1B) involves a 3,6-cyclization of cation IM-1 through a conformation shown as IM-1A to generate cation IM-5, which was proposed to undergo a dyotropic rearrangement, followed by a 1,2-alkyl shift of cation IM-6 to yield the spirocyclic cation

• cyclization mechanism (Scheme 1C) leading to the same spirocyclic skeleton as spiroviolene with an altered stereochemistry at C7 found in GJ1012A (3) could be proposed [11][17][18]. A 3,6- or 3,7-cyclization of cation IM-1 through a conformation shown as IM-1B with β-oriented 20-methyl group, would generate

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

• at C4 determined the resultant ring system, as the σ* orbital is not accessible to external nucleophiles due to steric hindrance and the rigid conformation of the bicyclic ring system. When the C4–OH was equatorial, O8 migrated as it was aligned with the σ* orbital giving a 3,8-dioxabicyclo[3.2.1