Synthesis and anion binding properties of phthalimide-containing corona[6]arenes

• Meng-Di Gu,
• Yao Lu and
• Mei-Xiang Wang

Beilstein J. Org. Chem. 2019, 15, 1976–1983, doi:10.3762/bjoc.15.193

• with their adjacent tetrazine rings rather than with the phthalimide units. Most noticeably, the three phthalimide moieties are not cis-configured. The orientation of one phthalimide was just opposite to that of the other two phthalimide segments. It is important to note that corona[3]arene[3

Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

• Silvie Rimpelová,
• Michal Jurášek,
• Lucie Peterková,
• Jiří Bejček,
• Vojtěch Spiwok,
• Miloš Majdl,
• Michal Jirásko,
• Miloš Buděšínský,
• Juraj Harmatha,
• Eva Kmoníčková,
• Pavel Drašar and
• Tomáš Ruml

Beilstein J. Org. Chem. 2019, 15, 1933–1944, doi:10.3762/bjoc.15.189

• , the potent SERCA inhibitors, manual docking of compound 1 into SERCA followed by MD simulation (1–10 ns) was performed. For this simulation, four different complexes of SERCA and SL were chosen: i) compound 1 positioned correspondingly to the orientation of DTB in the SERCA binding cavity (simulation

• 1); ii) compound 1 rotated by 180° (simulation 2); iii) compound 2 (for comparison) used as a ligand with the orientation equal to DTB (simulation 3); iv) SERCA positioned in a phospholipid membrane to reflect the fact that it is a transmembrane protein, with compound 2 as a ligand (simulation 4

• pronounced in the case of compound 1 rotated by 180°. Therefore, we are convinced that especially the orientation and positions of the side chains of compound 1 are very important for its affinity to SERCA or the lack thereof. Winther and co-workers [22] reported that the dissociation constant of

Inherent atomic mobility changes in carbocation intermediates during the sesterterpene cyclization cascade

• Hajime Sato,
• Takaaki Mitsuhashi,
• Mami Yamazaki,
• Ikuro Abe and
• Masanobu Uchiyama

Beilstein J. Org. Chem. 2019, 15, 1890–1897, doi:10.3762/bjoc.15.184

• tightly fixed by the enzyme. As we reported previously, the initial conformation of GFPP, in particular the orientation of six methyl groups (C20–C25), is critical. Therefore, we focused on these methyl groups. While the C20, C21 and C23 methyl groups are quite static in phase I, the other three methyl

Nanopatterns of arylene–alkynylene squares on graphite: self-sorting and intercalation

• Tristan J. Keller,
• Joshua Bahr,
• Kristin Gratzfeld,
• Nina Schönfelder,
• Marcin A. Majewski,
• Marcin Stępień,
• Sigurd Höger and
• Stefan-S. Jester

Beilstein J. Org. Chem. 2019, 15, 1848–1855, doi:10.3762/bjoc.15.180

• oriented relative to the HOPG main axis directions with γ(a,d1) = γ(b,d2) = (7 ± 2)°. The backbones are oriented with γ(c,d1) = (30 ± 4)° relative to the HOPG main axis direction d1. An additional nomenclature describes the orientation of the intermolecularly interdigitating OC16H33 (and OC10H21) side

• ), as expected for an electrically more insulating surface region. Therefore, we assume that the side chains are either aligned along one of the HOPG main axis directions, or, as an effect of lacking an interaction partner, are mobile to some extent. Moreover, the relative orientation of the

• shown for clarity). Enlarged areas of Figure 3a (shown in Figure 3b and c) show two template macrocycles 1a (of similar orientation), each of which is filled with one molecule of 2 that appears as a bright hexagon – however, with different orientations. The hexagons of the nanographene 2 in Figure 3c

Synthesis of a [6]rotaxane with singly threaded γ-cyclodextrins as a single stereoisomer

• Jason Yin Hei Man and
• Ho Yu Au-Yeung

Beilstein J. Org. Chem. 2019, 15, 1829–1837, doi:10.3762/bjoc.15.177

• orientation, possibly due to inter-ring interactions with the CB[6], to give the [6]rotaxane as one single stereoisomer. Considering the ability of γ-CD to form stable 1:2 inclusion complexes, these singly threaded [n]rotaxanes could serve as an entry point to other high order interlocked structures by

• macrocycles in 6R that results in a cooperative interaction so that the formation of 6R is stereoselective. With one less γ-CD in 5R, interactions between the axle and the macrocycles alone are only enough for interlocking the macrocycle, but not sufficient to drive a specific orientation of all the γ-CD

• MHz, D2O, 298 K) of (a) 6R; (b) 5R; and (c) 4R. (a) All the possible sequences of a [6]rotaxane with two CB[6] and three γ-CD interlocked on an axle. Only the sequence on the top left was observed in 6R (with the orientation of the γ-CD disregarded). (b) The four possible relative orientations of the

Norbornadiene-functionalized triazatriangulenium and trioxatriangulenium platforms

• Roland Löw,
• Talina Rusch,
• Tobias Moje,
• Fynn Röhricht,
• Olaf M. Magnussen and
• Rainer Herges

Beilstein J. Org. Chem. 2019, 15, 1815–1821, doi:10.3762/bjoc.15.175

• and enforces an upright orientation of the free standing functional groups [6]. The length and the nature of the spacer is used to tune the distance and electronic coupling of the functional system on top [1]. Preliminary experiments proved that the electronic coupling to the surface is the decisive

Functional panchromatic BODIPY dyes with near-infrared absorption: design, synthesis, characterization and use in dye-sensitized solar cells

• Quentin Huaulmé,
• Cyril Aumaitre,
• Outi Vilhelmiina Kontkanen,
• David Beljonne,
• Alexandra Sutter,
• Gilles Ulrich,
• Renaud Demadrille and
• Nicolas Leclerc

Beilstein J. Org. Chem. 2019, 15, 1758–1768, doi:10.3762/bjoc.15.169

• the close to orthogonal orientation of the anchoring groups induced by steric effects in 2 and 4. As a result, while the LUMO orbital largely extends through the BODIPY unit towards the cyanoacrylic acid anchors in the case of 1 and 3, it is completely confined to the BODIPY-vinylthiophene core in 2

Synthesis, photophysical and electrochemical properties of pyridine, pyrazine and triazine-based (D–π–)₂A fluorescent dyes

• Keiichi Imato,
• Toshiaki Enoki,
• Koji Uenaka and
• Yousuke Ooyama

Beilstein J. Org. Chem. 2019, 15, 1712–1721, doi:10.3762/bjoc.15.167

• , OUK-2 and OUJ-2, respectively, estimated from DFT calculation at the B3LYP/6-31G(d,p) level of theory [47]), Δf is the orientation polarizability, ε is the static dielectric constant, and n is the refractive index of the solvent. The Lippert–Mataga plots (Figure 3) for the three dyes show high

• in various solvents. Correlation of the Stokes shift (νst) and the orientation polarizability (Δf) according to Equation 1 and Equation 2, respectively, for OUY-2, OUK-2 and OUJ-2; solvent (ε, n, Δf): toluene (2.38, 1.4969, 0.0132), 1,4-dioxane (2.21, 1.4224, 0.0205), ethyl acetate (6.02, 1.3724

Water inside β-cyclodextrin cavity: amount, stability and mechanism of binding

• Stiliyana Pereva,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2019, 15, 1592–1600, doi:10.3762/bjoc.15.163

• orientation of the narrow rim hydrogen bonds is CCW; (B) structure with “open” narrow rim; and (C) energy difference between these two configurations at the M062X/6-311++G(d,p)//M062X/6-31G(d,p) level of theory. Schematic representation of β-CD–nH2O complexes (where n = 1–12) with water molecules/clusters

Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP)

• Małgorzata Urbańczyk,
• Michał Jewgiński,
• Joanna Krzciuk-Gula,
• Jerzy Góra,
• Rafał Latajka and
• Norbert Sewald

Beilstein J. Org. Chem. 2019, 15, 1581–1591, doi:10.3762/bjoc.15.162

• peptide 3 (see Table 3 and Figure 4). Such situation is the result of numerous well defined intra- and interresidual NOE signals of sugar moiety protons (see Table S6, Supporting Information File 1). Although the orientation of the galactose ring is highly ordered, as shown the value of the temperature

• coefficient (see Table 1), its arrangement is not stabilized by an intramolecular hydrogen bond formed by the GalNAc amide proton. Instead, as revealed by the results of the structural calculation, the orientation of the galactose ring probably is locked due to interaction of the Ala4 amide proton and the

• side chain oxygen of Thr3. In case of peptide 3, due to weaker intramolecular hydrogen bonds combined with a high flexibility of the peptide main chain, the fixed orientation of the galactose ring is not observed (see Figure 3 and Figure 4). Such conclusion seems to be confirmed by the small value of

Molecular basis for the plasticity of aromatic prenyltransferases in hapalindole biosynthesis

• Takayoshi Awakawa and
• Ikuro Abe

Beilstein J. Org. Chem. 2019, 15, 1545–1551, doi:10.3762/bjoc.15.157

• HU and HA were located at the same position, but their orientations were completely different. These data indicated that the hydrophobic interaction between the enzyme and the terpenoid moiety is important to support the prenyl acceptor, and the orientation can be altered dependently on their steric

• structures. The indole of HU, W117, and Y168 formed a cation shield [27][28], which stabilizes the cation intermediate after the removal of the phosphate from DMAPP in the HU structure, and Y225 was substituted with Y168 in the HA structure (Figure 5). The orientation of W117 changed in accordance with the

• orientation of the indole in HU and HA. As expectedly, W117 was shown to be important for the reaction through a point mutation study, in which W117A and W117F completely lost the catalytic activity. In the HU structure, the distance between C-2 of HU and C-3 of DMSPP (Figure 5A, a: 3.6 Å) is shorter than

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

• the high dispersion energy in the compact cis,cis-isomer. Keywords: azobenzene; macrocycles; molecular switch; Introduction In supramolecular chemistry rigid scaffolds are required to arrange different recognition units in predefined distances and spatial orientation to each other [1]. One example

• for such rigid systems are macrocycles which stem from Lissoclinum cyclopeptide alkaloids (Figure 1) [2][3]. Here, the required recognition units can be introduced via the amino acid side chains or via the side chains of the azole rings. The orientation and the distance between the recognition units

• is the design of artificial Lissoclinum cyclopeptides which can be switched by the incorporation of a suitable switching unit into the scaffold. A switching process would allow to vary the orientation and the distance between the recognition units. Examples for such switching units are photochromic

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

• 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

• parallel orientation. Three of the four NH protons are directed into the cavity, and the fourth one flipped outward and forms a hydrogen bond with the oxygen atom of H2O (H···O distance: 1.97 Å). Two CH3CN molecules were trapped in the cavities by the amide groups through N–H···N hydrogen bonds (H···N

Selenophene-containing heterotriacenes by a C–Se coupling/cyclization reaction

• Pierre-Olivier Schwartz,
• Sebastian Förtsch,
• Astrid Vogt,
• Elena Mena-Osteritz and
• Peter Bäuerle

Beilstein J. Org. Chem. 2019, 15, 1379–1393, doi:10.3762/bjoc.15.138

• Å with S and 3.028 Å with Se) in a face-to-edge orientation (Figure 3c, Table S4a in Supporting Information File 1) [40]. We found as well several non-bonding S–Se contacts (3.644 Å) with four neighboring molecules in all crystallographic axes, which are slightly shorter than the sum of the van der

• formed dimers showed some differences: in DTT 1 the molecules overlap in a parallel orientation whereas in DST 3 an antiparallel orientation of the molecules in the dimer was found. The degree of overlap was determined to 73% and 64% for DTT 1 and DST 3, respectively. Less degree of overlap (43–53% and

Efficient resolution of racemic crown-shaped cyclotriveratrylene derivatives and isolation and characterization of the intermediate saddle isomer

• Sven Götz,
• Andreas Schneider and
• Arne Lützen

Beilstein J. Org. Chem. 2019, 15, 1339–1346, doi:10.3762/bjoc.15.133

• ][51][52][53][54][55][56][57] we were intrigued by the class of chiral CTVs. This is especially true for derivative 1 (Scheme 2) due to its interesting trifold substitution pattern with an almost orthogonal orientation of the functional groups which make it an ideal precursor for the synthesis of other

Synthesis of dipolar molecular rotors as linkers for metal-organic frameworks

• Sebastian Hamer,
• Fynn Röhricht,
• Marius Jakoby,
• Ian A. Howard,
• Xianghui Zhang,
• Christian Näther and
• Rainer Herges

Beilstein J. Org. Chem. 2019, 15, 1331–1338, doi:10.3762/bjoc.15.132

• in a MOF. Five different orientations in C2v, C2h and D2h symmetry are considered. The energy difference between the most favourable and the most unfavourable orientation is 9.7 kcal mol−1. It is important to note that the energy states of 3D ensembles of dipoles assuming periodic boundary conditions

• Müllen et al. [32] without compromising MOF compatibility by 4,5-diamino substitution. Synthesis of dipolar molecular rotor linkers The key step for the synthesis of all reported linkers is the coupling of a substituted aromatic core unit with two ethynyl substituents in para-orientation as spacer units

• orientation of the dipoles. The calculated dipole moment µ of the rotor (chemical structure on top left) is 8.6 D. Structures of molecular dipolar rotors/linker molecules 1–5. General synthetic strategy to prepare the dipolar rotors 1–5. Synthesis of 3,3'-(2,3-difluoro-1,4-phenylene)dipropiolic acid (1

Doebner-type pyrazolopyridine carboxylic acids in an Ugi four-component reaction

• Maryna V. Murlykina,
• Oleksandr V. Kolomiets,
• Maryna M. Kornet,
• Yana I. Sakhno,
• Sergey M. Desenko,
• Victoriya V. Dyakonenko,
• Svetlana V. Shishkina,
• Oleksandr A. Brazhko,
• Vladimir I. Musatov,
• Alexander V. Tsygankov,
• Erik V. Van der Eycken and
• Valentyn A. Chebanov

Beilstein J. Org. Chem. 2019, 15, 1281–1288, doi:10.3762/bjoc.15.126

• diversity and obtaining two types of structures with different orientation of substituents (containing a carboxylic group either at C4 or C6 position of the pyrazolopyridine core). The optimal methodology for the synthesis of target products was elaborated (mixture of methanol and DMF (2:1) and heating to

Bambusuril analogs based on alternating glycoluril and xylylene units

• Tomáš Lízal and
• Vladimír Šindelář

Beilstein J. Org. Chem. 2019, 15, 1268–1274, doi:10.3762/bjoc.15.124

• the orientation of one glycoluril unit were obtained. The building blocks within the macrocycles connected via methylene bridges are flexible giving rise to two preferred conformers for each diastereomer. These conformers were identified by molecular modelling and also by low-temperature NMR

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

• , but with the tetrahydropyrane ring having α orientation. A mixture of epimers at position 4' was also obtained when using the C-5 epimer of substrate 33. Asif et al. [36] developed another 3CR for the synthesis of steroidal thiazole derivatives. As shown in Scheme 11, cholestanic ketone 7 was reacted

Multicomponent reactions (MCRs): a useful access to the synthesis of benzo-fused γ-lactams

• Edorta Martínez de Marigorta,
• Jesús M. de Los Santos,
• Ana M. Ochoa de Retana,
• Javier Vicario and
• Francisco Palacios

Beilstein J. Org. Chem. 2019, 15, 1065–1085, doi:10.3762/bjoc.15.104

• imines 99 to furnish complex spirocyclic γ-lactams 101 (Scheme 29) [107]. These products show a trans orientation of the benzene moiety in the isoindolinone and the substituent in R2, according to NOE experiments and crystal structure analysis. The proposed mechanism involves an initial palladium

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

Mechanistic investigations on multiproduct β-himachalene synthase from Cryptosporangium arvum

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2019, 15, 1008–1019, doi:10.3762/bjoc.15.99

• D, (12-13C)- [43] and enzymatically prepared (13-13C)FPP from (9-13C)GPP [39] and IPP with FPPS were incubated with HcS to follow the fate of the geminal methyl groups for 1 (Figure 6). Combined with the relative orientation of each methyl group deduced by NOESY, these experiments showed an 11Re

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

• The endo-inclusion of guests by NARXs greatly influences the geometry of the system and directly affects the orientation of the upper rim arms. This is particularly true for the NARX derivatives with long chain upper rim substituents. We have previously observed that even with the most suitable

• for interactions with the electropositive methyl groups of either MeCN or MeOH causing the orientation to be similar in both cases. Deformation of the resorcinarene is a result of the small solvent size leading to a decrease in internal cavity volume of the receptor. The calculated space sizes are

• 79.45 Å3 in MeOH@1 and 101.17 Å3 in MeCN@1 (rprobe = 1.2 Å) [34]. The deformation also shifts the relative positions of the N-alkyl “arms” and the halide anions, which additionally change the relative orientation of DIOFB XB donors when directional halogen bonding forms. Two DIOFB linked two MeOH-MeCN@1

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

• of [Cd2L(μ-azo-NMe2)]ClO4·0.5MeOH (6·0.5MeOH). Only one orientation of the disordered azobenzene carboxylato co-ligand is displayed. Hydrogen atoms omitted for clarity. Thermal ellipsoids are drawn at the 50% probability level. Space filling representation of the packing of four [Cd2L(μ-azo-NMe2

• ·8EtOH (7·8EtOH). Only one orientation of the disordered azo-carboxylato co-ligand is displayed. Hydrogen atoms omitted for clarity. Thermal ellipsoids are drawn at the 50% probability level. Left: ORTEP representation of the molecular structure of the [Cd2L(μ-azo-CO2Me)]+ cation in crystals of 8·MeCN

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

• –H (M06-2X/aug-cc-pVDZ) shows that each conformer has three lower-energy rotamers, identified according to the orientation of the nitrogen lone pair as anti (a) and gauche (gX and gH) to H1 (Figure 3). Optimization and frequency calculations were performed for these rotamers at different theory

• equatorial halogen orientation). Previous publications have already reported the C–H bond as slightly better donor than C–C bond [34][35]. Therefore, in the sum of interactions existent in the studied systems the hyperconjugation stands out, explaining the axial halogen and equatorial NH2 (ea) preference in

• ea conformer being the most stable for all series, both in the gas phase and in solution. For the C–N rotation, the most unstable rotamers are gX for the ae conformer and a for ea, due to the orientation of the nitrogen lone pair electrons toward the halogen, which provides greater electrostatic