An azobenzene container showing a definite folding – synthesis and structural investigation

• Abdulselam Adam,
• Saber Mehrparvar and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2019, 15, 1534–1544, doi:10.3762/bjoc.15.156

• possible conformations [cis,trans-(M), cis,trans-(P), cis,cis-(M,M), cis,cis-(M,P) and cis,cis-(P,P)]. However, it turned out that the P conformers represent no minima on the potential energy surface. Furthermore, single point calculations by means of the density functionals B3LYP and B3LYP-D3 were

Diazocine-functionalized TATA platforms

• Roland Löw,
• Talina Rusch,
• Fynn Röhricht,
• Olaf Magnussen and
• Rainer Herges

Beilstein J. Org. Chem. 2019, 15, 1485–1490, doi:10.3762/bjoc.15.150

• to measure kinetics on surfaces [15]. The C–O stretching frequencies proved to be ideal reporter signals to determine the configuration and to measure kinetics in monolayers of azo-TATAs on surfaces. Results and Discussion To obtain information on preferred conformations of 1 and 2 in their cis and

• for both compounds as the thermodynamically most stable isomers. For the corresponding trans-configuration two different conformations were found: the twist and the chair structures. The twist conformation is about 2.5 kcal mol−1 more stable than the chair conformation. Our calculations predict

Synthesis and biological evaluation of truncated derivatives of abyssomicin C as antibacterial agents

• Leticia Monjas,
• Peter Fodran,
• Johanna Kollback,
• Carlo Cassani,
• Thomas Olsson,
• Maja Genheden,
• D. G. Joakim Larsson and
• Carl-Johan Wallentin

Beilstein J. Org. Chem. 2019, 15, 1468–1474, doi:10.3762/bjoc.15.147

• conformations and with expected interaction points in the binding site, providing suitable docking scores (see Supporting Information File 1). The key interactions include a hydrogen bond to the backbone of Arg-45 and lipophilic interactions in the deep pocket defined by Phe-241 and Leu-34 (Figure 2). Our

2,3-Dibutoxynaphthalene-based tetralactam macrocycles for recognizing precious metal chloride complexes

• Li-Li Wang,
• Yi-Kuan Tu,
• Huan Yao and
• Wei Jiang

Beilstein J. Org. Chem. 2019, 15, 1460–1467, doi:10.3762/bjoc.15.146

• interesting new binding properties. During the last six years, our group have developed a series of naphthol-based macrocyclic receptors [24][25][26][27][28][29]. Of them, oxatub[4]arene [30][31] and zorb[4]arene [32][33] show multiple conformations due to the flipping of naphthalenes and thus resulted in a

• rather wide guest scope. Therefore, we wondered whether multiple conformations would be observed by incorporating the 2,3-dialkoxynaphthalene units into tetralactam macrocycles as the sidewalls. How would this affect their binding affinity and selectivity of the resulting macrocycles? Herein, we describe

• pre-organized. In addition, there exist two conformations for both macrocycles 1 and 2 because the two 2,3-dibutoxynaphthalene moieties can be aligned either in parallel or antiparallel orientation (Scheme 1). These two conformations have different cavities defined by the parallel or antiparallel

Anomeric sugar boronic acid analogues as potential agents for boron neutron capture therapy

• Daniela Imperio,
• Erika Del Grosso,
• Silvia Fallarini,
• Grazia Lombardi and
• Luigi Panza

Beilstein J. Org. Chem. 2019, 15, 1355–1359, doi:10.3762/bjoc.15.135

• broadening of the H-2, H-3 and H-4 signals suggest a slow equilibrium between different conformations. After deprotection of the benzylidene group in addition to line broadening, signal superposition is observed, hampering any conclusion on the conformation of compound 11. In order to get more information

Host–guest interactions between p-sulfonatocalix[4]arene and p-sulfonatothiacalix[4]arene and group IA, IIA and f-block metal cations: a DFT/SMD study

• Valya K. Nikolova,
• Cristina V. Kirkova,
• Silvia E. Angelova and
• Todor M. Dudev

Beilstein J. Org. Chem. 2019, 15, 1321–1330, doi:10.3762/bjoc.15.131

• by a hydrophobic mid-region, and adopts different conformations depending on different factors: the solvent, the nature of the guest molecule, the functionalization of the lower (OH) rim [16]. The 3D cavities and the π-electron-rich sulfonate groups endow them with fascinating affinities and

N-doped carbon dots covalently functionalized with pillar[5]arenes for Fe³⁺ sensing

• Jia Gao,
• Ming-Xue Wu,
• Dihua Dai,
• Zhi Cai,
• Yue Wang,
• Wenhui Fang,
• Yan Wang and
• Ying-Wei Yang

Beilstein J. Org. Chem. 2019, 15, 1262–1267, doi:10.3762/bjoc.15.123

• macrocyclic compounds, especially new macrocyclic arenes, have become one of the research hotspots in supramolecular chemistry [11][12][13][14]. Among them pillarenes as a relatively new family of pillar-shaped members discovered a decade ago have played a key role due to their unique conformations

Steroid diversification by multicomponent reactions

• Leslie Reguera,
• Cecilia I. Attorresi,
• Javier A. Ramírez and
• Daniel G. Rivera

Beilstein J. Org. Chem. 2019, 15, 1236–1256, doi:10.3762/bjoc.15.121

• the natural cationic peptide antibiotics [60] or as a way to constrain peptide sequences in protein epitope conformations [61]. In this regard, the groups of Rivera and Wessjohann have pioneered the utilization of MCRs for the conjugation of oligosaccharides [62] and peptides [63][64] to steroids

Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls

• Dong-Hao Li and
• Bradley D. Smith

Beilstein J. Org. Chem. 2019, 15, 1086–1095, doi:10.3762/bjoc.15.105

• macrocyclic structure in a stable conformation with all NH residues directed into the cavity. One way is to use 2,6-pyridine dicarboxamides as the bridging units which permits intramolecular hydrogen bonding within the cavity (Figure 1) [30]. This internal hydrogen bonding stabilizes conformations that have

• conformations is an outward directed NH residue. Solution-state NMR data suggests that the surrounding tetralactam in these [2]rotaxanes undergoes rapid exchange between these different conformations, a dynamic process that has been called macrcocyle breathing, and that there is also simultaneous co

• crystal structures of acene and azaacene guests inside tetralactam B with the surrounding macrocycle in chair or boat conformations [25]. Recent work has shown that water-soluble versions of anthracene tetralactam B can be threaded by water soluble squaraine dyes with very high affinities (Ka ≈ 109 M−1

Stereo- and regioselective hydroboration of 1-exo-methylene pyranoses: discovery of aryltriazolylmethyl C-galactopyranosides as selective galectin-1 inhibitors

• Alexander Dahlqvist,
• Axel Furevi,
• Niklas Warlin,
• Hakon Leffler and
• Ulf J. Nilsson

Beilstein J. Org. Chem. 2019, 15, 1046–1060, doi:10.3762/bjoc.15.102

• C-galactoside aglycons, we performed a 200 ns molecular dynamic simulation of 1b in the complex with galectin-1 and galectin-3. Starting conformations were selected with the galactopyranose of 1b positioned overlapping with the positions of the lactose or N-acetyllactosamine galactopyranoses in

Halogen bonding and host–guest chemistry between N-alkylammonium resorcinarene halides, diiodoperfluorobutane and neutral guests

• Fangfang Pan,
• Mohadeseh Dashti,
• Michael R. Reynolds,
• Kari Rissanen,
• John F. Trant and
• Ngong Kodiah Beyeh

Beilstein J. Org. Chem. 2019, 15, 947–954, doi:10.3762/bjoc.15.91

• incredibly effective tool for observing privileged conformations and structures [15][16][17][18][19]. From the crystallographic information we can extract the polymorphism, high Z’-value, twining, and disorder that provide insight into the dynamics of prenucleation assembly, nucleation, and crystal growth

• , and the resulting empty space, induces disorder for both the hexyl groups on the upper-rim of the cavitand, and the DIOFB molecules. Two preferred conformations of these systems were identified with a ratio of ca. 3:1 (Figure 3, Figures S1 and S3 in Supporting Information File 1). Due to the center of

• inversion, the two conformations show different dimerization modes (Supporting Information File 1, Figure S3). In 1&DIOFB_A, the two hex-NARBrs are linked by two DIOFB molecules via four Br···I halogen bonds with average RXB of 0.86. The two participating bromide anions are on adjacent “arms”; the remaining

Coordination chemistry and photoswitching of dinuclear macrocyclic cadmium-, nickel-, and zinc complexes containing azobenzene carboxylato co-ligands

• Jennifer Klose,
• Tobias Severin,
• Peter Hahn,
• Alexander Jeremies,
• Jens Bergmann,
• Daniel Fuhrmann,
• Jan Griebel,
• Bernd Abel and
• Berthold Kersting

Beilstein J. Org. Chem. 2019, 15, 840–851, doi:10.3762/bjoc.15.81

• drastically alter its structural properties and reactivities. Prominent examples are the cis-bromination of α,β-unsaturated carboxylato ligands [2], regioselective Diels–Alder reactions of encapsulated dienoate ligands [3], and the stabilization of unusual co-ligand conformations, respectively [4]. The

Strong hyperconjugative interactions limit solvent and substituent influence on conformational equilibrium: the case of cis-2-halocyclohexylamines

• Camila B. Francisco,
• Cleverton S. Fernandes,
• Ulisses Z. de Melo,
• Roberto Rittner,
• Gisele F. Gauze and
• Ernani A. Basso

Beilstein J. Org. Chem. 2019, 15, 818–829, doi:10.3762/bjoc.15.79

• most stable rotamer in each conformation (see Supporting Information File 2 for full numerical data). In the PCA (Figure 6), two principal components described 94% of the results. The PC1 is able to differentiate the variables according to the halogens, while the PC2 distinguish the two conformations

• ae. Then, considering all the interactions existent in both conformations, the ones involving the LPX are important for both conformers. However, what differs them are the interactions with the highest weight for ea. It is worth mentioning that the variables corresponding to the N–H bonds and LPN has

• RStudio, version 1.0.153 [45]. Conformations of cis-2-halocyclohexylamines, where X = F, Cl, Br and I. Variable-temperature 1H NMR spectra (500.13 MHz) for cis-2-chlorocyclohexylamine in dichloromethane-d2. Potential energy surfaces (PESs) for cis-2-halocyclohexylamines for the C2–C1–N–H dihedral angle

A diastereoselective approach to axially chiral biaryls via electrochemically enabled cyclization cascade

• Hong Yan,
• Zhong-Yi Mao,
• Zhong-Wei Hou,
• Jinshuai Song and
• Hai-Chao Xu

Beilstein J. Org. Chem. 2019, 15, 795–800, doi:10.3762/bjoc.15.76

• –Hammett scenario (Scheme 4) [42]. Specifically, the equilibrium of the conformations IV and IV′ is much faster than their respectively cyclizations to give V and V′. Since TS2 is relatively lower in energy than TS3, V is formed as the major product. Conclusion In summary, we have developed a

Stereochemical investigations on the biosynthesis of achiral (Z)-γ-bisabolene in Cryptosporangium arvum

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2019, 15, 789–794, doi:10.3762/bjoc.15.75

• enantiomers by BbS, different NPP conformations inside the chiral environment of the active site in BbS have to be assumed (Figure 4B + 4C). The architecture of the active site may stay the same in both cases, so a fixed OPP moiety with binding by the trinuclear Mg2+ cluster and a comparable folding of the

Homo- and hetero-difunctionalized β-cyclodextrins: Short direct synthesis in gram scale and analysis of regiochemistry

• Gábor Benkovics,
• Mihály Bálint,
• Éva Fenyvesi,
• Erzsébet Varga,
• Szabolcs Béni,
• Konstantina Yannakopoulou and
• Milo Malanga

Beilstein J. Org. Chem. 2019, 15, 710–720, doi:10.3762/bjoc.15.66

• staggered conformations about the C5–C6 bond are generally of gt type, except for one case, the gg-oriented H6,6’A-tosyl group in 6A,6D-ditosyl-β-CD. This implies that the group is rotated completely outside its cavity, whereas in all other ditosyl derivatives positioning of the tosyl group partially over

Influence of per-O-sulfation upon the conformational behaviour of common furanosides

• Alexey G. Gerbst,
• Vadim B. Krylov,
• Dmitry A. Argunov,
• Maksim I. Petruk,
• Arsenii S. Solovev,
• Andrey S. Dmitrenok and
• Nikolay E. Nifantiev

Beilstein J. Org. Chem. 2019, 15, 685–694, doi:10.3762/bjoc.15.63

• of sulfates. Keywords: ab initio calculations; conformational analysis; furanosides; NMR; sulfation; Introduction Changes in the conformations of monosaccharides expectedly accompany their modification with different functional groups. Thus, spatial repulsion of silyl groups results in inversion or

• constants significantly differ for non-sulfated and per-O-sulfated furanosides which allows for a conclusion that their conformations are changed after the sulfation. To rationalize these changes, we undertook theoretical conformational analysis of monosaccharides 1–3 and 1s–3s. Conformational analysis of

• -energy conformers which differed from each other by less than 2 kcal/mol. The other conformations found had considerably higher energies. For non-sulfated structures 1–3 sometimes high-energy conformations were obtained with the same puckering state of the furanoside ring (see Tables in Supporting

Conformational signature of Ishikawa´s reagent using NMR information from diastereotopic fluorines

• Laize A. F. Andrade,
• Lucas A. Zeoly,
• Rodrigo A. Cormanich and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2019, 15, 506–512, doi:10.3762/bjoc.15.44

• with the dihedral angle between coupled nuclei [7]. According to this relationship, the SSCC between antiperiplanar nuclei is larger than that observed between gauche nuclei. One-bond SSCCs (1J) can also provide relevant information on the conformations of a molecule. For example, the Perlin effect

• would then be worth to evaluate. It is worth mentioning, however, that the relative and interchangeable orientation of the atoms in a molecule (conformations) is dependent on the medium; while only intramolecular interactions drive the conformational stability of a molecule in the vacuum, the solvent

• polarity plays a significant role in the condensed phase. Thus, it is appropriate to study the conformations of Ishikawa´s reagent in different media, of low and high polarity. This is a challenging task, since the conformational analysis of flexible acyclic organic compounds using NMR SSCCs is more

Systematic synthetic study of four diastereomerically distinct limonene-1,2-diols and their corresponding cyclic carbonates

• Hiroshi Morikawa,
• Jun-ichi Yamaguchi,
• Shun-ichi Sugimura,
• Masato Minamoto,
• Yuuta Gorou,
• Hisatoyo Morinaga and
• Suguru Motokucho

Beilstein J. Org. Chem. 2019, 15, 130–136, doi:10.3762/bjoc.15.13

• accompanied by side reactions. Although the starting material 2b was completely consumed, two major products were detected by thin-layer chromatography. After purification, the desired 1b was obtained in a relatively low yield of 24%. Two conformations (A and B in Scheme 4) are possible for the intermediate

• diastereomers as byproducts except for the reaction of trans-LO with water (Scheme 3, conditions (d)). The reduction under conditions (b) and carbonation under conditions (a) and (c) retain the diastereomeric conformations around the epoxy, 5CC and diol moieties. In all the reactions, the yields for the

• of 2a and 2b were also subjected to 1,1-ADEQUATE (adequate double quantum transfer experiment) analysis. Structures of four LMdiols and four LM5CCs Plausible conformations for the LM5CCs and LMdiols in CDCl3 are proposed in Figure 5. In Figure 3, large coupling constants (J > ca. 10 Hz) for the

Adhesion, forces and the stability of interfaces

• Robin Guttmann,
• Johannes Hoja,
• Christoph Lechner,
• Reinhard J. Maurer and
• Alexander F. Sax

Beilstein J. Org. Chem. 2019, 15, 106–129, doi:10.3762/bjoc.15.12

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• ]. The β-orientation of the fluorine substituent in F-ANA leads to a gauche interaction between O4’–C1’–C2’–F2’ favouring the C2’-endo/O4’-endo conformations of the sugar in solution [16][17]. These DNA-like sugar conformations cause that F–ANA is among the few modifications which can trigger the

• obtained crystal structure of derivative 6 (Table S1, Supporting Information File 1). The reason for that can be attributed to the different conformations of the six-membered rings in these two structures. Apart from that, the two structures were very similar. Synthesis of the modified oligonucleotides and

• intensities were changed, too. Furthermore, the intensity of the 210 nm peak was reduced. RNase H cleavage assay The most important requirement for an antisense oligonucleotide to induce RNase H activity lies in its DNA-like sugar conformations [49]. This is generally fulfilled by the 6’-diF-bc4,3-DNA as well

6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288

• Information File 1) was in the same range (C1’-exo, C2’-endo) as described above for the hybrid duplexes. The backbone torsion angles of the homo-duplex exhibited identical conformations in both strands (Figure S4, Supporting Information File 1). Some variations in the torsion angle ζ (−sc to +ac) and the

Unnatural α-amino ethyl esters from diethyl malonate or ethyl β-bromo-α-hydroxyiminocarboxylate

• Eloi P. Coutant,
• Vincent Hervin,
• Glwadys Gagnot,
• Candice Ford,
• Racha Baatallah and
• Yves L. Janin

Beilstein J. Org. Chem. 2018, 14, 2853–2860, doi:10.3762/bjoc.14.264

• explanation for these average yields could be the occurrence upon the base reaction with compound 47 of cis and trans conformations of the nitrosoacrylate. The cis one would be susceptible to undergo an immediate [2 + 4] cycloaddition with the furan whereas the trans form would not, and since the

Synthesis of 3-aminocoumarin-N-benzylpyridinium conjugates with nanomolar inhibitory activity against acetylcholinesterase

• Nisachon Khunnawutmanotham,
• Cherdchai Laongthipparos,
• Patchreenart Saparpakorn,
• Nitirat Chimnoi and
• Supanna Techasakul

Beilstein J. Org. Chem. 2018, 14, 2545–2552, doi:10.3762/bjoc.14.231

• suitable method for the binding mode of compounds in the rhAChE binding site. The docked conformations of donepezil and the synthesized compounds are shown in Figure 2. All docked compounds were located similar to donepezil in the binding pocket. The benzylpyridinium moiety was bound close to the CT and

• interaction to Trp86 in the CAS. Their conformations were slightly shifted up from Trp86 to form stronger a H-bond interaction between the 2-fluoro-substituent and a hydrogen atom of the β-carbon, thereby causing the slight shift of the remaining parts of the structures. For instance, the methoxy group of the

• -substituents, compound 9a does not form a H-bond interaction to Trp86, which explains the lower activity of compound 9a compared with compound 9h. For compounds 4a (Figure 3a) and 10a (Figure 3g), the docked conformations were partially different from the other compounds. In the case of 4a, having no methoxy

Calixazulenes: azulene-based calixarene analogues – an overview and recent supramolecular complexation studies

• Paris E. Georghiou,
• Shofiur Rahman,
• Abdullah Alodhayb,
• Hidetaka Nishimura,
• Jaehyun Lee,
• Atsushi Wakamiya and
• Lawrence T. Scott

Beilstein J. Org. Chem. 2018, 14, 2488–2494, doi:10.3762/bjoc.14.225

• determinations were made on the possible major conformations, based upon those previously defined in reference [20]. Three distinct conformations (saddle, cone and 1,2-alternate) shown in Figure 2, were generated. Significantly, whereas for 3 which was based upon its X-ray structure, a partial cone conformer

• columnar arrays [17]. In this type of array the host molecules which are in 1,3-alternate conformations align in a “head-to-tail” fashion with the C60 molecules able to be accommodated within the opposite clefts. Furthermore, within such an arrangement, in addition to the “face-to-face” π–π interactions

• for the three different conformations of 5. Supporting Information Supporting Information File 355: Experimental determination of binding constants and DFT calculations. Supporting Information File 356: MOL files. Acknowledgements This project was supported by King Saud University, Deanship of