The effect of neighbouring group participation and possible long range remote group participation in O-glycosylation

• Rituparna Das and
• Balaram Mukhopadhyay

Beilstein J. Org. Chem. 2025, 21, 369–406, doi:10.3762/bjoc.21.27

• pathway. The benchmark for the SN1 spectrum of the mechanistic continuum has been elaborately illustrated and supported by Codee et al. by mapping full ensemble of conformations that the glycosyl oxocarbenium ions can adopt by a complete conformational energy landscape (CEL) study in a quantitative manner

Synthesis, structure and π-expansion of tris(4,5-dehydro-2,3:6,7-dibenzotropone)

• Yongming Xiong,
• Xue Lin Ma,
• Shilong Su and
• Qian Miao

Beilstein J. Org. Chem. 2025, 21, 1–7, doi:10.3762/bjoc.21.1

• analysis of it with X-ray crystallography. Interestingly, it is observed that tris(4,5-dehydro-2,3:6,7-dibenzotropone) crystallized from its solution in hexane resulting in colorless and yellow crystal polymorphs, where it adopts conformations of approximate Cs and C2 symmetry, respectively. Furthermore

• conformations of approximate Cs and C2 symmetry, respectively. Furthermore, the expansion of the π-skeleton of 1 through the Barton–Kellogg and Scholl reactions enabled the synthesis of compound 3, whose curved polycyclic skeleton containing three heptagons and two pentagons was identified with X-ray

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

• conformational flexibility, allowing them to adopt four key conformations: 1,3-alternate, cone, partial cone, and 1,2-alternate [1][2]. Calix[4]pyrroles are one of the most studied hosts in supramolecular chemistry, finding use in applications of molecular recognition and extraction, drug delivery, ion transport

• calix[4]pyrroles as catalysts may be related to their conformational flexibility, that leads to less preorganized binding and catalytic sites. Calix[4]pyrroles in solution exist in four-different conformations (cone, partial cone, 1,3-alternate, and 1,2-alternate); this macrocyclic flexibility arises

Synthesis and antimycotic activity of new derivatives of imidazo[1,2-a]pyrimidines

• Dmitriy Yu. Vandyshev,
• Daria A. Mangusheva,
• Khidmet S. Shikhaliev,
• Kirill A. Scherbakov,
• Oleg N. Burov,
• Alexander D. Zagrebaev,
• Tatiana N. Khmelevskaya,
• Alexey S. Trenin and
• Fedor I. Zubkov

Beilstein J. Org. Chem. 2024, 20, 2806–2817, doi:10.3762/bjoc.20.236

• the formation of a coordination bond; the benzene moiety is located in a hydrophobic pocket. bThe conformations of compounds 4a–e are identical, whereas the position of compound 5e (red) is significantly different. Reaction of 2-aminoimidazole (1) with N-substituted maleimides (2) and N

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

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

• halo-divergent strategy from known 1,6-anhydro-2,3-dideoxy-2,3-difluoro-β-ᴅ-mannopyranose. In solution and in the solid-state, all analogues adopt standard 4C1-like conformations despite 1,3-diaxial repulsion between the F2 and the C4 halogen. Moreover, the solid-state conformational analysis of

• order to decipher the key physical properties of complex pyran inter-halides, we performed 19F NMR analysis of halogenated talose analogues 12–15 (Figure 2). First, all analogues adopt standard 4C1-like conformations. Comparison of the vicinal and geminal coupling constants for each organohalogen

• suggests that there is little change in the conformations (although there is an increasing chair distortion for larger halogens, see below). Because F3 is adjacent to the C4 halogen, 19F resonance of F3 occurs at lower field than F2 for analogues 13–15. There is a strong increase in chemical shift of F3

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

• of different and particular structures [7][8]. Additionally, glycans can adopt a wide variety of different shapes; five-membered ring sugars can exhibit envelope and twist conformations usually represented on a pseudo-rotational wheel; while six-membered ring structures can adopt chair (C), boat (B

• ), skew (S), and half-chair (H) conformations (Figure 1). Among them, chair’ shapes typically have the lowest energy and are thus preferred, except few cases in which different conformations can exist in a dynamic equilibrium, as for the iduronic acid that can adopt three low-energy solution conformations

• files of the minimised resulting structures but also files for input to an AMBER simulation (https://glycam.org/). Notably, among the currently available interfaces for modelling oligosaccharide conformations on glycam website, one is dedicated to GAG modelling [51] (https://glycam.org/gag/). 3. CHARMM

Regioselective alkylation of a versatile indazole: Electrophile scope and mechanistic insights from density functional theory calculations

• Pengcheng Lu,
• Luis Juarez,
• Paul A. Wiget,
• Weihe Zhang,
• Krishnan Raman and
• Pravin L. Kotian

Beilstein J. Org. Chem. 2024, 20, 1940–1954, doi:10.3762/bjoc.20.170

• subsequently set to 0 kcal/mol leading to the energy diagram in Figure 5. Two TSs leading to each product were found, all four of which utilized a coordinating Cs+ cation. The N1-s-cis and N1-s-trans TSs were the lowest in energy (27.5 kcal/mol and 29.1 kcal/mol, respectively), leading to two conformations of

Syntheses and medicinal chemistry of spiro heterocyclic steroids

• Laura L. Romero-Hernández,
• Ana Isabel Ahuja-Casarín,
• Penélope Merino-Montiel,
• Sara Montiel-Smith,
• José Luis Vega-Báez and
• Jesús Sandoval-Ramírez

Beilstein J. Org. Chem. 2024, 20, 1713–1745, doi:10.3762/bjoc.20.152

• of a new chiral centre. Advances in understanding ligand–receptor interactions have facilitated the determination of optimal molecular conformations to enhance binding affinity, which can be achieved, in part, by introducing a spiro annelated ring to impart rigidity to the molecule. From a medicinal

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

• crystallographic data using the 3-fluoropyrrolidinium cation and 3-fluoropyrrolidine. Subsequently, we explored the relative energy of all favored conformations of all different stereoisomers of 2,3-, 2,4-, and 3,4-difluoropyrrolidines at the B3LYP-D3BJ/6-311++G** level. A generalized anomeric effect, arising from

• -fluoroalkylamines and the respective cations [6]. Intramolecular hydrogen bonds involving either the carboxy or hydroxy group of 4R- and 4S-hydroxyproline have been identified as key factors in stabilizing the favored conformations in the gas phase. Therein, the contribution of a gauche effect due to electron

• pyrrolidinium salt [11] with the CCSD/DGTZVP geometry of the pyrrolidinium cation (with an exclusively axial C–F bond) and the energy of 3-fluoropyrrolidine conformations. Various combinations of DFT methods (B3LYP-D3BJ, ωB97XD, and PBEPBE) and basis sets (DGTZVP and 6-311++G**) were evaluated. The selection of

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

• rather similar Kd values. In order to rationalize this difference in binding mechanism, molecular models were obtained for selected low-energy conformations of E- and Z-isomers of a “model” scaffold of the para-azobenzene derivative in the binding site of LecA (Figure 5), by simple superpositioning of

• represents a ΔG value of −30 kJ/mol, corresponding to a Kd of approx 5 μM in the experimental conditions. (B) Manual docking of scaffold for compound 3 with selected low energy conformations of the E-isomer (yellow sticks) and Z-isomer (cyan sticks) superimposed on conserved position of galactose in all LecA

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

• activation energy may allow for oxy-Cope rearrangement at 28 °C. DFT calculations (in toluene) of 5-hydroxyalbireticulene for both the pseudo-axial and pseudo-equatorial conformations of the C5 hydroxy moiety suggest that there is not a significant difference in the free energy barriers for the oxy-Cope

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

• case of compound 2p, unlike the other two compounds, the equilibrium is largely in favor of the product of interest and the NMR spectra confirm this. From the mechanistic point of view of the IMDAF reaction, the presence of both s-cis and s-trans conformations of maleamic acid intermediates in the

Kinetically stabilized 1,3-diarylisobenzofurans and the possibility of preparing large, persistent isoacenofurans with unusually small HOMO–LUMO gaps

• Qian Liu and
• Glen P. Miller

Beilstein J. Org. Chem. 2024, 20, 1099–1110, doi:10.3762/bjoc.20.97

• phenyl substituents, have been synthesized and shown to adopt non-planar conformations with the ortho-alkyl groups located above and below the most reactive 1,3-carbons of the furan ring. These bulky substituents provide a strong measure of kinetic stabilization. Thus, 1,3-dimesitylisobenzofuran and 1,3

• semiconductors. However, such syntheses must account for the projected lack of stability associated with isoacenofurans. We demonstrated that sterically congesting ortho groups on 1,3-diarylisobenzofurans like 3 and 23 force the molecules to adopt non-planar conformations in which the aryl groups rotate out-of

• -plane. The out-of-plane rotations provide for enhanced steric congestion both above and below the most reactive 1,3-carbons of the furan ring, dramatically reducing their reactivity with dienophiles including DMAD, acrylonitrile and singlet oxygen. Due to these non-planar conformations, the HOMO and

Enhancing structural diversity of terpenoids by multisubstrate terpene synthases

• Min Li and
• Hui Tao

Beilstein J. Org. Chem. 2024, 20, 959–972, doi:10.3762/bjoc.20.86

• properties (Figure 4c) [45]. Notably, one tetrahydrofuranoterpenoid 59 is also formed as a major product in the BcBoT2 reaction, despite the low sequence similarity between these sesqui-TSs, which could be explained by similar active-site conformations to stabilize prenyl substrates. Similarly, limonene

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

• and, therefore, poorly resolved density regions, whereas in electron cryo-microscopy different conformations and compositions are averaged out during image classification and volume reconstruction [5]. Owing to these difficulties, it is not uncommon to find problematic carbohydrate structures in the

• glycoprotein as pointed out by Crispin and collaborators [8], and more recently the realisation that high-energy ring conformations, a rare event in six-membered pyranosides, were present in ca. 15% of the N-glycan components of glycoproteins in the PDB [3]. Many of these findings originated the development of

• filtering by linkage type is also possible, allowing niche glycosylation targets to be obtained. For example, filtering for C-glycans with a ‘BMA-1,1-TRP’ (the correct pair would be ‘MAN-1,1-TRP’, as the linkage in the modification is an alpha linkage) returns nine instances of incorrect sugar conformations

Recent developments in the engineered biosynthesis of fungal meroterpenoids

• Zhiyang Quan and
• Takayoshi Awakawa

Beilstein J. Org. Chem. 2024, 20, 578–588, doi:10.3762/bjoc.20.50

• cyclizations and post-cyclization modifications are especially important in fungal meroterpenoid biosynthesis, contributing to the structural diversity of this class of compounds. Fungal meroterpenoid cyclases (CYCs) are seven-membrane-spanning transporter-like enzymes that regulate the conformations of

• approach led to the discovery of new CYCs, InsA7 (32% identity with Trt1) and InsB2 (40% identity with Trt1) from Aspergillus insuetus [13]. These enzymes catalyze the formation of the terpenoid skeleton from 6, adopting chair–boat and chair–chair conformations to create two distinct 6-6-6-6-membered ring

Possible bi-stable structures of pyrenebutanoic acid-linked protein molecules adsorbed on graphene: theoretical study

• Yasuhiro Oishi,
• Motoharu Kitatani and
• Koichi Kusakabe

Beilstein J. Org. Chem. 2024, 20, 570–577, doi:10.3762/bjoc.20.49

• Yasuhiro Oishi Motoharu Kitatani Koichi Kusakabe Graduate School of Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan 10.3762/bjoc.20.49 Abstract We theoretically analyze possible multiple conformations of protein molecules immobilized by 1-pyrenebutanoic acid succinimidyl ester (PASE

• ) linkers on graphene. The activation barrier between two bi-stable conformations exhibited by PASE is confirmed to be based on the steric hindrance effect between a hydrogen on the pyrene group and a hydrogen on the alkyl group of this molecule. Even after the protein is supplemented, this steric hindrance

• effect remains if the local structure of the linker consisting of an alkyl group and a pyrene group is maintained. Therefore, it is likely that the kinetic behavior of a protein immobilized with a single PASE linker exhibits an activation barrier-type energy surface between the bi-stable conformations on

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

• , conformational analysis performed by variable temperature NMR led to the conclusion that the open and closed conformations have similar energies and are in fast exchange at ambient temperature. This fluxionality resulted in a relatively low affinity for the electron-poor aromatic guest 2,4,7-trinitro-9

• electrostatic repulsion between the doubly charged redox-active units. Thus, it can be concluded that, although the tweezers exhibit different conformations in neutral and oxidized states, at room temperature

Ligand effects, solvent cooperation, and large kinetic solvent deuterium isotope effects in gold(I)-catalyzed intramolecular alkene hydroamination

• Ruichen Lan,
• Brock Yager,
• Yoonsun Jee,
• Cynthia S. Day and
• Amanda C. Jones

Beilstein J. Org. Chem. 2024, 20, 479–496, doi:10.3762/bjoc.20.43

• of complex 7a. Our preliminary hypothesis is that two conformations exist in solution, one of which is symmetrical (presenting as a singlet), one of which is not. A lack of symmetry in one conformation would mean that each phosphorous is magnetically inequivalent, and thus shows splitting to the

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

• calorimetry [13]. Single crystals for many host–guest complexes have been prepared, and their structure elucidated by X-ray crystallography [14][15]. Conformations of host–guest complexes in solution have been studied by 2D NMR experiments [11] (NOESY, ROESY) or proposed computationally [16][17] based on

• compound 4, we were thus able to select representative conformations of the guest molecule in all types of cyclodextrins (Figure 5) using the spatial densities gained from classical MD simulations. Compounds 1–8 (as hydrochloride salts or free bases), were attempted to co-crystallize with α-, β- and γ

• to compare the solid-state structure of the guest 2–α-CD host complex with its proposed solution state conformations (Figure 6). Conclusion We have demonstrated that simple 13C NMR analyses of properly chosen Cs symmetric compounds varying in size can be used to estimate the host–guest spatial

Aromatic systems with two and three pyridine-2,6-dicarbazolyl-3,5-dicarbonitrile fragments as electron-transporting organic semiconductors exhibiting long-lived emissions

• Karolis Leitonas,
• Brigita Vigante,
• Dmytro Volyniuk,
• Audrius Bucinskas,
• Pavels Dimitrijevs,
• Sindija Lapcinska,
• Pavel Arsenyan and
• Juozas Vidas Grazulevicius

Beilstein J. Org. Chem. 2023, 19, 1867–1880, doi:10.3762/bjoc.19.139

• conformations that contain dimethylacridan substituents [8]. OLEDs based on phenyl-substituted pyridine-3,5-dicarbonitrile showed very high EQEmax of 29.1% due to a high PLQY of 89% ascribed to the rigid acceptor geometry. In addition to the utilization of pyridine-3,5-dicarbonitriles in OLEDs, an example of

• bands and high-intensity low-energy bands. The presence of two distinct fluorescence bands is an indication of the existence of molecular conformations separated by a barrier. This is a characteristic of twisted internal charge transfer (TICT) states. It is worth of noting that the PL intensity of

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

• ability to undergo E/Z isomerization in a stimuli-responsive imine bond is what makes this class useful for applications in the field of molecular electronics, as switchers [5][6]. In addition, these compounds can also adopt syn- or antiperiplanar conformations, due to the constriction of the rotation

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

• broadening and then coalescence of some of these peaks on increasing the temperature, consistent with the room-temperature spectrum being affected by restricted rotation; interestingly the crystal structure of 1b2 contains molecules with two very different conformations (see below). The 12 dimers 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

• (II) compounds 16-Pd–19-Pd exhibited conformations with the characteristic Pacman clefts, resembling their postulated solution structures and typical square-planar geometry around the palladium(II) centres. Titanium(III), vanadium(III), and chromium(III) complexes were synthesised through salt