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

Synthesis of eunicellane-type bicycles embedding a 1,3-cyclohexadiene moiety

• Alex Frichert,
• Peter G. Jones and
• Thomas Lindel

Beilstein J. Org. Chem. 2018, 14, 2461–2467, doi:10.3762/bjoc.14.222

• , those conformations are within 10 kJ/mol range of each other. However, only one of those conformations shows the required short distance between 14-H and 3-CH3, making the configuration (2R,3S,14R) probable for diastereomer 18. In the preferred conformation of 18, all non-sp3-hybridized carbon atoms of

• -containing 8 adopts two distinct major conformations in CDCl3, whereas diastereomeric diols 18 and 19 prefer only one, which were elucidated by NOESY spectroscopy. In upcoming studies we will address the synthesis of systems that contain a cyclohexene ring keeping the sp2–sp2 bridge of the product from the

• benzene partial structure. Preferred conformations of diastereomeric diols 18 and 19 including decisive NOESY correlations. Access to ketoester 14 that did not cyclize to the ethyl vinyl ether under McMurry conditions. Synthesis of the 1,3-cyclohexadiene-containing eunicellane-type [8.4.0]bicycle 18 by

Nucleoside macrocycles formed by intramolecular click reaction: efficient cyclization of pyrimidine nucleosides decorated with 5'-azido residues and 5-octadiynyl side chains

• Jiang Liu,
• Peter Leonard,
• Sebastian L. Müller,
• Constantin Daniliuc and
• Frank Seela

Beilstein J. Org. Chem. 2018, 14, 2404–2410, doi:10.3762/bjoc.14.217

• conformations of the 5’-azido compounds 7 and 2 as well as dC macrocycle 4 were investigated in solution. To this end, high resolution spectra (600 MHz NMR) were measured in DMSO-d6 and the population of S vs N conformers (Supporting Information File 1, Table S2) were calculated using the program PSEUROT

Tetrathiafulvalene – a redox-switchable building block to control motion in mechanically interlocked molecules

• Hendrik V. Schröder and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2018, 14, 2163–2185, doi:10.3762/bjoc.14.190

• arrangement. Starting from the pre-assembled catenane, the axle molecule is threaded through the wheel and end-capped by a copper-catalyzed click reaction. A variety of different spectroscopic and electrochemical methods was applied to reveal the switching behavior of 24 and its stable co-conformations in

• motion, a circumrotation and a translational motion, must occur. The equilibrium between these two co-conformations of 242(●+) was determined to be approximately 1:1. Further oxidation drives the equilibrium completely to the side of the co-conformation in which both dihydroxynaphthalene units are

• ′-bipyridinium radical cation which forms a purple trisradical complex with the doubly reduced cyclobis(paraquat-p-phenylene). Electrochemical and several spectroscopic techniques showed that, overall, six stable oxidation states – each of them with a unique color – and three co-conformations are accessible in

Calix[6]arene-based atropoisomeric pseudo[2]rotaxanes

• Carmine Gaeta,
• Carmen Talotta and
• Placido Neri

Beilstein J. Org. Chem. 2018, 14, 2112–2124, doi:10.3762/bjoc.14.186

• different conformations adopted by the wheel are reported here. Upon threading hexahexyloxycalix[6]arene 1 with ammonium axles 2+ or 3+, bearing biphenyl or trifluoromethylbenzyl moieties, respectively, two atropoisomeric pseudorotaxanes were formed in which the calix[6]-wheel 1 adopts the 1,2,3-alternate

• and cone conformations. The interconversion between them cannot be obtained by simple rotation around the ArCH2Ar bonds of the calixarene wheel, which is blocked by the presence of the axle inside its cavity. Therefore, it can only be obtained through a mechanism of de-threading/re-threading of the

• catalysis [24]. The widespread use of the calixarene derivatives is due to their convenient synthesis and to their chemical and conformational versatility [25]. In fact, calixarene macrocycles present a conformational isomerism that in the case of calix[6]arenes gives rise to eight discrete conformations

A pyridinium/anilinium [2]catenane that operates as an acid–base driven optical switch

• Sarah J. Vella and
• Stephen J. Loeb

Beilstein J. Org. Chem. 2018, 14, 1908–1916, doi:10.3762/bjoc.14.165

• sites and these two possible co-conformations are designated A and B in Figure 4a. The ethylene protons at the core of the bis(pyridinium)ethane motif, labelled s and t in A and s’ and t’ in B are clearly distinguishable and show that there is a 4:1 ratio of A:B indicating that the smaller DB24C8 ring

• crown resides solely on the bis(pyridinium)ethane site for [8DB24C8]6+ but, when the [2]catenane does not absorb in the UV–visible region yielding a colorless solution this means the crown ether must be shuttling (i.e., circumrotating) back and forth between the two co-conformations, A and B, of [8

• + can be protonated to yield [8-HDB24C8]7+ in two different co-conformations A and B. b) The partial 1H NMR spectrum (500 MHz, 298 K, CD3CN) of [8-HDB24C8]7+ shows key resonances for both co-conformations A (red) and B (blue). See Scheme 1 for labelling; atoms of co-conformer B are labelled with a prime

Diazirine-functionalized mannosides for photoaffinity labeling: trouble with FimH

• Femke Beiroth,
• Tomas Koudelka,
• Thorsten Overath,
• Stefan D. Knight,
• Andreas Tholey and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2018, 14, 1890–1900, doi:10.3762/bjoc.14.163

• carbohydrate binding site. They are flexible and can be more distant to one another (“open gate”) or closer together (“closed gate”) [20]. Both conformations were considered for the docking studies. For each docked conformation, a scoring value is obtained that correlates with the affinity of the ligand to the

• carbohydrate binding site. A more negative value predicts better binding. Scores obtained for mannosides 3 and 4 suggest a high affinity for FimH, surpassing that of pNPMan 1 for both protein conformations tested (Table 1). (Diazirines cannot be tested in bacterial adhesion–inhibition assays due to their light