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

Halogen-bonding-induced diverse aggregation of 4,5-diiodo-1,2,3-triazolium salts with different anions

• Xingyu Xu,
• Shiqing Huang,
• Zengyu Zhang,
• Lei Cao and
• Xiaoyu Yan

Beilstein J. Org. Chem. 2020, 16, 78–87, doi:10.3762/bjoc.16.10

• triazolium salts show diverse aggregation via halogen bonding between C–I bonds and anions. Triazolium with halide anions exists as a tetramer with saddle conformation. Triazolium tetrafluoroborate exists as a trimer with Chinese lantern shape conformation. Triazolium trifluoroacetate and acetate exist as

• dimers, respectively, while the former shows boat conformation and the latter forms rectangle conformation. Triazolium salts form a linear polymer with polyiodide. Keywords: aggregation; 4,5-diiodo-1,2,3-triazolium salts; halogen bond; non-covalent interaction; Introduction The halogen bond (XB) is a

• compounds show XB interactions between the triazolium moiety and anions, and different aggregations are formed. Triazolium with halide anions exists as tetramers with saddle conformation. Triazolium tetrafluoroborate exists as trimer with Chinese lantern shape conformation. Triazolium trifluoroacetate and

Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides

• Sabrina Müller,
• Jannik Paulus,
• Jochen Mattay,
• Heiko Ihmels,
• Veronica I. Dodero and
• Norbert Sewald

Beilstein J. Org. Chem. 2020, 16, 60–70, doi:10.3762/bjoc.16.8

• 4,4'-substituted correlates, as the substituents are not conjugated to the N=N double bond [35][37][38][39]. Moreover, it was demonstrated that in the case of peptides, only the Z-isomer adopts the hairpin conformation. In our setup, this could influence the hydrogen bonding contacts between the

• only the (Z)-azobenzene moiety is able to induce the polyamide hairpin conformation required for binding. We also tested the interaction of the polyamides upon single base mutation in the dsDNA sequences to explore the recognition specificity. Specifically, we tested the sequence 5´-TTGTT-3´ for P1, 5

Understanding the role of active site residues in CotB2 catalysis using a cluster model

• Keren Raz,
• Ronja Driller,
• Thomas Brück,
• Bernhard Loll and
• Dan T. Major

Beilstein J. Org. Chem. 2020, 16, 50–59, doi:10.3762/bjoc.16.7

• conformation of D in the active site model compared to the gas phase. The dihedral angle defined by C3–C2–C6–C7 in D was greater by 53° in the active site model than in the gas phase, and the D dihedral angle C10–C9–C8–C7 in the active site was smaller by 258° than in the gas phase (Figure 4a). Moreover, the

• dihedral angle C2–C1–C11–C10 was greater by 281° in the active site model. The distance between C4 and C13 was significantly greater in the active site model (1.2 Å), indicating a more extended conformation. Figure 4a shows clearly that intermediate D was more folded in the gas phase than in the active

Synthesis and characterization of bis(4-amino-2-bromo-6-methoxy)azobenzene derivatives

• David Martínez-López,
• Amirhossein Babalhavaeji,
• Diego Sampedro and
• G. Andrew Woolley

Beilstein J. Org. Chem. 2019, 15, 3000–3008, doi:10.3762/bjoc.15.296

• methoxy substituents on the same or on the opposite side of the N–N double bond. The conformation where both methoxy groups were on the opposite side was found to be the most stable one, although the conformation where both methoxy groups were on the same side was also predicted to be significantly

• performed for any of the species, the following calculations were performed: To ensure that the conformation shown in Figure 2 was the thermodynamically most stable arrangement around the azo moiety, free energies for two alternative arrangements – conformer 2: with both bromine atoms on the same side of

SnCl₄-catalyzed solvent-free acetolysis of 2,7-anhydrosialic acid derivatives

• Kesatebrhan Haile Asressu and
• Cheng-Chung Wang

Beilstein J. Org. Chem. 2019, 15, 2990–2999, doi:10.3762/bjoc.15.295

• , SnCl4 and Sn(OTf)2 might have formed a coordination bond with the carbonyl oxygen atom of the C-5 NHAc group and the O-6 position of the glucose glucopyranosyl ring. In turn, this retarded the ring-opening reaction. The anchimeric participation of the NHAc group in stabilizing the axial conformation of

Synthesis and optoelectronic properties of benzoquinone-based donor–acceptor compounds

• Daniel R. Sutherland,
• Nidhi Sharma,
• Georgina M. Rosair,
• Ifor D. W. Samuel,
• Ai-Lan Lee and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2019, 15, 2914–2921, doi:10.3762/bjoc.15.285

• donor moieties. The HOMO is more delocalized in 5 and 2 compared to 3 and 4, a function of the more planar conformation of the TPA units despite the stronger donor strength compared to Cz. Time-dependent calculations using the TDA approach predicted ΔEST values of 0.36, 0.22, 0.10, and 0.47 eV for 2, 3

Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering

• Eric J. N. Helfrich,
• Geng-Min Lin,
• Christopher A. Voigt and
• Jon Clardy

Beilstein J. Org. Chem. 2019, 15, 2889–2906, doi:10.3762/bjoc.15.283

• a linear polyene with branching methyl groups that form the core hydrocarbon structure in a single enzyme-catalyzed step [9]. The enzyme, which is called terpene cyclase, holds the linear methyl-branched polyene in a defined conformation that initiates a series of carbocation-driven cyclizations and

• diphosphate (FPP, 9) or geranylgeranyl diphosphate (GGPP, 10, Figure 5a) [11][53]. Upon binding of the precursor, the TC undergoes conformational changes to seal the hydrophobic binding pocket [54]. This induced-fit mechanism locks the acyclic precursor into a defined, preorganized conformation that positions

Influence of the cis/trans configuration on the supramolecular aggregation of aryltriazoles

• Sara Tejera,
• Giada Caniglia,
• Rosa L. Dorta,
• Andrea Favero,
• Javier González-Platas and
• Jesús T. Vázquez

Beilstein J. Org. Chem. 2019, 15, 2881–2888, doi:10.3762/bjoc.15.282

• . In addition, compound 10 (cis), with free hydroxy groups, formed hydrogen bonds between the hydroxymethyl groups in position 6 and DMSO molecules while in a gg rotamer conformation. The different types of EDC spectra obtained for compound 10 in solution (exciton) and in gel (non-exciton), using DMSO