The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• conjugate Dex-1b in aggregates or nanoparticles. Moreover, it is known that dye conjugation to a polymer even in small percentages can generate a large change in the environment of the chains affecting conformation and chain organization [36]. To assess the influence of hydrophobicity on the formation of

Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups

• Benjamin Jeffries,
• Zhong Wang,
• Robert I. Troup,
• Anaïs Goupille,
• Jean-Yves Le Questel,
• Charlene Fallan,
• James S. Scott,
• Elisabetta Chiarparin,
• Jérôme Graton and
• Bruno Linclau

Beilstein J. Org. Chem. 2020, 16, 2141–2150, doi:10.3762/bjoc.16.182

• activity and conformational profile, which can be very beneficial if this promotes the population of the desired bioactive conformation(s). The introduction or extension of alkyl groups generally leads to an increase in lipophilicity, which is more often than not undesired. Hence, this has led to an

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• this study indicated a clear sequence-to-structure relationship, especially in the context of the dynamics of the (1-6) arm. More specifically, we found that the outstretched (open) conformation of the (1-6) arm gets progressively less populated as the functionalization of the arm grows, i.e., from 85

• differential recognition in glycan arrays [27]. Additionally, the different conformation of the arms explains the known difficulties in sialylating the (1-6) arm by ST6-Gal1, relatively to the (1-3) arm [28]. Also, the different 3D conformational propensity of the arms in function of sequence can have

• fucosylated N-glycans with the same sequence in the (1-6) arm correspond to the same structural ensemble. In this work we discuss how core α(1-3)-Fuc and β(1-2)-Xyl regulate the conformational propensity of the (1-6) arm to push a predominantly outstretched (open) conformation when the arms are functionalized

pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide

• Goutam Ghosh and
• Gustavo Fernández

Beilstein J. Org. Chem. 2020, 16, 2017–2025, doi:10.3762/bjoc.16.168

• ]. The band at 1678 cm−1 was the characteristic feature of an antiparallel conformation of the sheet structure or the β-turn structure [61]. To further confirm the β-sheet formation, we performed a ThT fluorescence spectroscopy assay. ThT is a widely used fluorescent dye that is amyloid-specific and can

• almost similar β-sheet conformation and fractal-like morphology as at pH 7.4. This is evidenced by the negative band at 227 nm in the CD spectrum, and further supported by AFM (Figure S4, Supporting Information File 1). At neutral (pH 7.4) and lower basic (pH 10.3) conditions, the self-assembly occurred

• File 1) and the helical conformation (Figure S6, Supporting Information File 1) as well as a ThT assay for the β-sheet (Figure S7, Supporting Information File 1) to better understand a possible conformational transition over time. However, no changes in the particular conformation were found even after

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• binding is further enhanced by the addition of hydrogen-bonding interactions between the amide NH moiety in position 5 of the pyrrole ring or the pyrrole NH group and the oxoanion (Figure 1, blue part). Thirdly, the rigid and planar conformation of the GCP moiety is beneficial to bind planar anions such

Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines

• Vladimir Kubyshkin

Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151

• the interplay between the substituents and the main chain groups of the amino acid residue. This study aims to showcase the polarity-related effects that arise from the interaction between the functional groups in molecular models. Properties such as conformation, acid–base transition, and amide-bond

• isomerism were examined for diastereomeric 4-fluoroprolines, 4-(trifluoromethyl)prolines, and 1,1-difluoro-5-azaspiro[2.4]heptane-6-carboxylates. The preferred conformation on the proline ring originated from a preferential axial positioning for a single fluorine atom, and an equatorial positioning for a

• C4-exo conformation of the pyrrolidine ring. Keywords: amino acids; cis–trans isomerism; fluorine; polarity; proline; Introduction Polarity is among the key features essential for understanding the behavior of organic molecules of biological origin. In particular, there is a set of polarity-related

Tuneable access to indole, indolone, and cinnoline derivatives from a common 1,4-diketone Michael acceptor

• Dalel El-Marrouki,
• Sabrina Touchet,
• Abderrahmen Abdelli,
• Hédi M’Rabet,
• Mohamed Lotfi Efrit and
• Philippe C. Gros

Beilstein J. Org. Chem. 2020, 16, 1722–1731, doi:10.3762/bjoc.16.144

• achieve the conformation of the proposed intermediate. We next examined the preparation of a set of indolones under the microwave conditions determined in Table 1, entry 13. These conditions were applied to several amines, producing exclusively the corresponding substituted indolones 7d and 7g–k in 48–56

Pauson–Khand reaction of fluorinated compounds

• Jorge Escorihuela,
• Daniel M. Sedgwick,
• Alberto Llobat,
• Mercedes Medio-Simón,
• Pablo Barrio and
• Santos Fustero

Beilstein J. Org. Chem. 2020, 16, 1662–1682, doi:10.3762/bjoc.16.138

• , preferred conformation or hydrogen bond forming ability, among others, may result in a dramatic effect in the therapeutic potential of a drug candidate [5][6]. All these properties may be fine-tuned by the selective incorporation of fluorine into the structure of the molecule [7]. In addition to therapeutic

Models of necessity

• Timothy Clark and
• Martin G. Hicks

Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137

• conformation, reactivity and structure, for example in the determination of the structure of DNA [42]. In inorganic chemistry, the standard Lewis eight-electron picture is complemented by the VSEPR (Valence Shell Electron Pair Repulsion) or Gillespie–Nyholm model [43], which gives rise to a series of standard

• models and descriptions are poorly suited for the more varied interactions involved in, for instance, self-organization in technical systems. Requirement (2) results from the conformation problem. Any technique or model that requires a specific 3D molecular structure must deal with conformational

Rearrangement of o-(pivaloylaminomethyl)benzaldehydes: an experimental and computational study

• Csilla Hargitai,
• Györgyi Koványi-Lax,
• Tamás Nagy,
• Péter Ábrányi-Balogh,
• András Dancsó,
• Gábor Tóth,
• Judit Halász,
• Angéla Pandur,
• Gyula Simig and
• Balázs Volk

Beilstein J. Org. Chem. 2020, 16, 1636–1648, doi:10.3762/bjoc.16.136

• close dielectric constant (ε = 4.7 for CHCl3 and 8.9 for DCM) [28], the similar polarity index (P = 2.7 for CHCl3 and 3.1 for DCM) [29][30][31], and the very close dipole moment (1.15 for CHCl3, 1.14 for DCM) [32], the conformation of the compounds should be almost the same in the NMR solvent and in the

Fluorohydration of alkynes via I(I)/I(III) catalysis

• Jessica Neufeld,
• Constantin G. Daniliuc and
• Ryan Gilmour

Beilstein J. Org. Chem. 2020, 16, 1627–1635, doi:10.3762/bjoc.16.135

• established by single crystal X-ray diffraction (Figure 2). Interestingly, a study by Pattison has established that α-fluoroketones preferentially adopt a cis-conformation in polar solvents [54]. In the solid state, a dihedral angle of φ = −3.7° was observed thereby placing the C–F bond in the same plane as

• . Conformation of the carbonyl group and the fluoride with a torsion angle of φO=C-C-F = −3.7°. CCDC number 2000136. (A) Structure activity relationship of the core scaffold. (B) Exploring the effect of methyl benzoate as an activator. (C) Stoichiometric reaction with p-TolIF2 17 and alkyne 16. Yields refer to

Five-component, one-pot synthesis of an electroactive rotaxane comprising a bisferrocene macrocycle

• Natalie Lagesse,
• Luca Pisciottani,
• Maxime Douarre,
• Pascale Godard,
• Brice Kauffmann,
• Vicente Martí-Centelles and
• Nathan D. McClenaghan

Beilstein J. Org. Chem. 2020, 16, 1564–1571, doi:10.3762/bjoc.16.128

• conformation in the rotaxane placed the two ferrocene groups with a metal centre-to-metal centre distance of 20.7 Å. Conclusion A five-component, one-pot reaction gave rise to an electroactive [2]rotaxane, through four amidination reactions between two ferrocene-grafted isophthalic acid derivatives and two 1,4

Photoredox-catalyzed silyldifluoromethylation of silyl enol ethers

• Vyacheslav I. Supranovich,
• Vitalij V. Levin and
• Alexander D. Dilman

Beilstein J. Org. Chem. 2020, 16, 1550–1553, doi:10.3762/bjoc.16.126

• disfavor the planar conformation needed to stabilize an intermediate benzyl radical. The complete conversions of the enol ethers were usually achieved within 6 hours, though to obtain products 4f,k a longer time of 24 h was needed. Generally, higher yields were observed with substrates containing electron

One-step route to tricyclic fused 1,2,3,4-tetrahydroisoquinoline systems via the Castagnoli–Cushman protocol

• Aleksandar Pashev,
• Nikola Burdzhiev and
• Elena Stanoeva

Beilstein J. Org. Chem. 2020, 16, 1456–1464, doi:10.3762/bjoc.16.121

• ][37][38][39]. As it can be seen from Table 1, the spectra of cis-22–24 displayed 3J1,11b within the narrow interval of 4.0–4.2 Hz, which could be attributed to a relatively more rigid conformation in the cis isomers. The spectra of the trans-22–24 compounds exhibited 3J1,11b in a broader interval of

• stereochemically mobile nitrogen atom [41]. Numbers of studies suggested that the preferred conformation of benzo[a]quinolizidines depended strongly on the type of substituents, the presence of stereocenters and their configuration [36][41][42][43][44][45][46]. As for the 4-oxobenzo[a]quinolizidine derivatives, it

• C-1 acquired a spatial orientation with a smaller steric repulsion with H-11. Based on the data outlaid above the assignment of the preferred conformation of the acids trans- and cis- 21–24 posed significant challenge. Reactions of 1-alkyl-3,4-dihydroisoquinolines 19 and 20 with anhydrides 5–8 The

Photocatalytic trifluoromethoxylation of arenes and heteroarenes in continuous-flow

• Alexander V. Nyuchev,
• Ting Wan,
• Borja Cendón,
• Carlo Sambiagio,
• Job J. C. Struijs,
• Michelle Ho,
• Moisés Gulías,
• Ying Wang and
• Timothy Noël

Beilstein J. Org. Chem. 2020, 16, 1305–1312, doi:10.3762/bjoc.16.111

• conditions, and the latter ensures better solubility and transport across the physiological lipophilic environment (e.g., dissolution in lymph and cell membrane penetration) [5]. In trifluoromethoxylated aryls, the -OCF3 group assumes a peculiar orthogonal conformation relative to the aromatic ring

A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium

• Shun Saito,
• Kota Atsumi,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Naoya Oku,
• Md. Rokon Ul Karim,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97

• C-16/C-17 and C-18/C-19 double bonds in s-trans conformation was determined by the NOESY correlation between H-16 and H-18 and the large vicinal coupling constants (JH-16,H-17 = 15.7 Hz, JH-18,H-19 = 14.9 Hz). The relative configuration of the spiroacetal moiety in 2 was determined by NOESY analysis

• . Correlations between H-23/H-24, H-23/H-25, and H-40/H-22 established the axial positioning of H-23 and H-25 and the placement of H-40 methyl group on the opposite side of the chair-conformation ring. Additional correlations for H-23/H-31 and H-41/H-28ax unequivocally confirmed the chair conformation of another

Fluorinated phenylalanines: synthesis and pharmaceutical applications

• Laila F. Awad and
• Mohammed Salah Ayoup

Beilstein J. Org. Chem. 2020, 16, 1022–1050, doi:10.3762/bjoc.16.91

• , geometry, conformation, reactivity, and moreover the bioavailability of the analogue [1]. Fluorinated amino acids (FAAs) have considerable industrial and pharmaceutical potential [2]. Also, they have played an important role as enzyme inhibitors as well as therapeutic agents [3][4]. Moreover, they modulate

One-pot synthesis of dicyclopenta-fused peropyrene via a fourfold alkyne annulation

• Ji Ma,
• Yubin Fu,
• Junzhi Liu and
• Xinliang Feng

Beilstein J. Org. Chem. 2020, 16, 791–797, doi:10.3762/bjoc.16.72

• 1 were obtained by slow evaporation from a carbon disulfide solution, allowing us to disclose the molecular structure by X-ray crystallography (Figure 2a). As shown in Figure 2a, the crystal structure of 1 clearly displayed a nonplanar conformation, resulting from steric repulsion between the phenyl

Towards triptycene functionalization and triptycene-linked porphyrin arrays

• Gemma M. Locke,
• Keith J. Flanagan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2020, 16, 763–777, doi:10.3762/bjoc.16.70

• , linearly linked triptycene porphyrin complexes could lead to compounds with the required conformation, geometry and spatial arrangement necessary for use in electron transfer studies. For further information on other bridgehead modifications of the triptycene scaffold see the comprehensive review on this

• (iii) of another triptycene molecule. Hydrogen atoms and minor disorder omitted for clarity (thermal displacement 50%). Single crystal X-ray structure of triptycene-linked zinc-nickel porphyrin dimer 16 showing the conformation within the crystal structure; (a) top-view of zinc porphyrin; (b) top-view

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

• Panagiotis S. Gritzapis,
• Panayiotis C. Varras,
• Nikolaos-Panagiotis Andreou,
• Katerina R. Katsani,
• Konstantinos Dafnopoulos,
• George Psomas,
• Zisis V. Peitsinis,
• Alexandros E. Koumbis and
• Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

• new. Compounds 8–13 were produced as a sole product, bearing the Z-conformation [9][43][62]. Their spectroscopic data were in accordance with the proposed structures. In IR spectra all compounds gave 2–3 absorptions above 3200 cm−1 for the NH2 and NH moieties, and the carbonyl absorption at 1700–1720

• cm−1, characteristic of the amide moiety. This low carbonyl absorption probably indicates an intramolecular hydrogen bonding between NH2 and the oxime oxygen, which further verifies the Z-conformation of the amidoxime derivatives. The hydroxylimino structure is verified in 1H NMR spectra from the

• 8.1 to 10.7 ppm and for the benzyl derivative 15 at 6.63 ppm. In the case of aldoxime carbamates three reactions gave mixtures of inseparable Z-stereoisomers ≈10% along with the major E-stereoisomer (products 25–27). It has been noted in the literature the preferable E-conformation for oxime

Formal preparation of regioregular and alternating thiophene–thiophene copolymers bearing different substituents

• Atsunori Mori,
• Keisuke Fujita,
• Chihiro Kubota,
• Toyoko Suzuki,
• Kentaro Okano,
• Takuya Matsumoto,
• Takashi Nishino and
• Masaki Horie

Beilstein J. Org. Chem. 2020, 16, 317–324, doi:10.3762/bjoc.16.31

• copolymer 6c closely corresponded to twice the values, 11.6 × 2 and 2.2 × 2 (Figure 2c), in which the conformation of the carbon–carbon single bond between the thiophene rings was anti. The proposed layer distance of regiorandom poly(3-methylthiophene) of 7.7 Å reported by Yan and co-workers was close to

Ultrasonic-assisted unusual four-component synthesis of 7-azolylamino-4,5,6,7-tetrahydroazolo[1,5-a]pyrimidines

• Yana I. Sakhno,
• Maryna V. Murlykina,
• Oleksandr I. Zbruyev,
• Anton V. Kozyryev,
• Svetlana V. Shishkina,
• Dmytro Sysoiev,
• Vladimir I. Musatov,
• Sergey M. Desenko and
• Valentyn A. Chebanov

Beilstein J. Org. Chem. 2020, 16, 281–289, doi:10.3762/bjoc.16.27

• the structure as ethyl 5-(4-bromophenyl)-3-cyano-7-((4-cyano-1H-pyrazol-5-yl)amino)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-7-carboxylate (Figure 2). Compound 4g existed as a solvate with acetonitrile in the crystal lattice. The tetrahydropyrimidine ring adopted a half-chair conformation (the

Combination of multicomponent KA² and Pauson–Khand reactions: short synthesis of spirocyclic pyrrolocyclopentenones

• Riccardo Innocenti,
• Elena Lenci,
• Gloria Menchi and
• Andrea Trabocchi

Beilstein J. Org. Chem. 2020, 16, 200–211, doi:10.3762/bjoc.16.23

• conformational entropy penalty upon binding to a protein target, and the approach of constraining the ligand conformation with a ring is widely used in drug design [2]. Accordingly, with increasing interest for sp3-rich molecules, spirocyclic compounds are being considered valuable as molecular platforms for the

• compounds 3–39 in the context of chemical space, again with reference to a set of BB drugs. The three principal moments of inertia (Ixx, Iyy, Izz) and the corresponding normalized principal moments of inertia were determined according to Sauer and Schwarz [68] for the lowest energy conformation of all the

• inertia analysis was carried out by calculation of the lowest energy conformation of compounds 3–39 and block buster drugs. The conformation calculation was performed using the built-in AMMP molecular mechanics algorithm with default parameters of the VEGA ZZ molecular modelling software package v.3.0.1

Synthesis of 4-(2-fluorophenyl)-7-methoxycoumarin: experimental and computational evidence for intramolecular and intermolecular C–F···H–C bonds

• Vuyisa Mzozoyana,
• Fanie R. van Heerden and
• Craig Grimmer

Beilstein J. Org. Chem. 2020, 16, 190–199, doi:10.3762/bjoc.16.22

• fluorinated ring is almost coplanar with the coumarin ring, and the molecule is at its least stable conformation due to the electron–electron (e–e) repulsion of H5 and fluorine. The second least stable conformation is found at Φ = 185°, with the fluorine atom and H3 in close proximity (dF···H3 = 2.0 Å

Synthesis, liquid crystalline behaviour and structure–property relationships of 1,3-bis(5-substituted-1,3,4-oxadiazol-2-yl)benzenes

• Afef Mabrouki,
• Malek Fouzai,
• Armand Soldera,
• Abdelkader Kriaa and
• Ahmed Hedhli

Beilstein J. Org. Chem. 2020, 16, 149–158, doi:10.3762/bjoc.16.17

• perfluoroalkyl as terminal chains were synthesized and characterized. Liquid crystal properties of the synthesized compounds have been investigated by polarizing optical microscopy, differential scanning calorimetry and X-ray diffraction techniques. Conformation effects of the synthesized products on the dipole

• high 2θ-region of Figure 4, slightly different values of the d-spacings calculated from these peaks suggest a weakly distorted hexagonal lattice [34]. Structure–conformation relationships Molecular dipole moment Calculated electric dipole moments of compounds 2 and 4 are reported in Table 3. The

• prepared compounds perform three kinds of conformations, A, B and C. The hydrocarbon derivatives exhibit conformation A (Figure 5a–a”), whereas the fluorocarbon analogues adopt, depending on whether they carry linking segment C2H4S or not, the conformation B (Figure 5b–b”) or C (Figure 5c–c”). In Figure 6