Synthetic approaches to bowl-shaped π-conjugated sumanene and its congeners

• Shakeel Alvi and
• Rashid Ali

Beilstein J. Org. Chem. 2020, 16, 2212–2259, doi:10.3762/bjoc.16.186

• , since its first successful synthesis, a variety of functionalized sumanenes as well as heterosumanenes have been developed because of their unique physiochemical properties. For example, bowl-to-bowl inversion, bowl depth, facial selectivity, crystal packing, metal complexes, intermolecular charge

• a tendency of crystal packing [17][18][19][20]. Since these chiral buckybowls contain stable convex or concave faces suitable for the generation of chiral molecular recognition sites which can be used for the construction of helical assemblies and have been used to coordinate the metal atom(s) [21

• the pyrene moiety, an appealing sumanene derivative 93, namely as pyrenylsumanene, was constructed by the groups of Higashibayashi and Sakurai which display both herringbone and columnar crystal packing (Scheme 22) [53]. To synthesize this architecturally interesting molecule, they began with the

Synthesis and highly efficient light-induced rearrangements of diphenylmethylene(2-benzo[b]thienyl)fulgides and fulgimides

• Vladimir P. Rybalkin,
• Sofiya Yu. Zmeeva,
• Lidiya L. Popova,
• Valerii V. Tkachev,
• Andrey N. Utenyshev,
• Olga Yu. Karlutova,
• Alexander D. Dubonosov,
• Vladimir A. Bren,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2020, 16, 1820–1829, doi:10.3762/bjoc.16.149

• bathochromic shift of the 441 nm band accompanied by a typical redistribution of intensity of absorption bands (see Table 1) is detected. At longer irradiation times, the rearrangement processes are reflected by the spectral curves depicted in Figure 3. Crystal packing of the product of the photoinduced

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

• DCM reaction medium. This is further supported by the recent results of Allen et al., who have shown that CHCl3 and DCM molecules exhibited the same interactions also in crystal packing [33]. Conclusion When alkoxy-substituted o-(pivaloylaminomethyl)benzaldehydes 1a,b were kept in solution (DCM or THF

A simple and easy to perform synthetic route to functionalized thienyl bicyclo[3.2.1]octadienes

• Dragana Vuk,
• Irena Škorić,
• Valentina Milašinović,
• Krešimir Molčanov and
• Željko Marinić

Beilstein J. Org. Chem. 2020, 16, 1092–1099, doi:10.3762/bjoc.16.96

• compounds (trans-3–5, trans-7). The structure of trans-6 was also confirmed by X-ray analysis (Figure 7). The compound crystallized in the space group, with the molecular symmetry Ci. The crystal packing is presented in Figure 8. The next synthesis step involved the preparation of the annulated bicyclo

• -isomers of compounds 3–7. Molecular structure of compound trans-6. Displacement ellipsoids are drawn for the probability of 30% and hydrogen atoms are shown as spheres of arbitrary radii. Crystal packing of trans-6. (a) Chain parallel to [100] and (b) chain parallel to [010]. 1H NMR spectra (CDCl3) of

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

• -fused PAHs in large π-systems. High-resolution MALDI-TOF mass spectrum of 1. Inset: isotopic distribution compared to mass spectrum simulated for C84H50. Single-crystal X-ray structure of 1. (a) Top view and (b) side view of the (P,P) isomer. c) Crystal packing of the enantiomer pairs (P,P and M,M) of 1

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

• group of the TIPS at distances of 2.860(1) Å effectively blocking this location from interacting in a similar fashion (Figure 2c). This pattern is also reflected in the crystal packing (Figure S34 in Supporting Information File 1). This motif is similar to other previously reported bridgehead

• molecule. In this structure, it should be noted that there is a high degree of π-stacking between the porphyrin macrocycle. This is highlighted in Figure 4; however, there is a clear preference for the homo-metallic selective interactions between the porphyrin rings. As such, in the crystal packing the Ni

• 3.378(6) Å (Figure 4b). This is further exemplified in the expanded structure view in Figure 5 where it can be clearly seen that the porphyrin rings are aligned in a Zn···Ni···Zn···Ni type pattern throughout the crystal lattice. This pattern is also clearly visible in the crystal packing (Figure S36 in

Synthesis of triphenylene-fused phosphole oxides via C–H functionalizations

• Md. Shafiqur Rahman and
• Naohiko Yoshikai

Beilstein J. Org. Chem. 2020, 16, 524–529, doi:10.3762/bjoc.16.48

• from the side view, the triphenylene moiety slightly deviated from planarity, because the fusion with the phosphole ring caused a subtle steric repulsion between the phosphorus substituents and the triphenylene edge within the phospha[4]helicene moiety. Unlike many triphenylene derivatives, the crystal

• packing of 8a did not involve columnar π–π stacking of the PAH moiety (Figure S1, Supporting Information File 1). This is likely due to the fact that such π-stacking is inhibited by the steric bulk of the phosphole substituents (i.e., the butyl groups, the phenyl group, and the oxygen atom). Upon the

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

• intermolecular interactions to the neighboring molecules (F–H6 and F–H5; different molecules) that play a crucial role in crystal packing (Figure 7). As mentioned above, the structure of coumarin 6 was optimized and the dihedral angle, Φ (C2'–C1'–C4–C4a) was found to be 65.3° (Figure 5), which is comparible

• a manner that brings the fluorine atom closer to H5 than H3. The same orientation was observed in the DFT-optimized (B3LYP/6-311G) structure. The X-ray data also showed the intermolecular C–F···H–C interactions which, together with other interactions, are resposible for the crystal packing

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

• 12 led to single crystals suitable for X-ray crystallography. Its analysis (Figure 3) not only confirmed the structure, but in addition showed a well-organized crystal packing (Figure 4) where the alternate disposition of the molecules displayed a parallelism between the p-bromophenyl groups as well

• ) and its X-ray analysis was not accurate enough to resolve its structure. However, its crystal packing (Figure 5) deserves discussion. As with compound 12, this packing revealed a number of π–bromine interactions [19], together with a high degree of π–π stacking interactions between the aromatic rings

• phenyltriazole substituents in position 2 of this monosaccharide (B) interacted with a corresponding phenyltriazole in position 2 of the vicinal monosaccharide (C, Figure 5, green lines). In addition, it is worth mentioning the presence of a number of DMSO solvate molecules in the crystal packing next to the

Formation of an unexpected 3,3-diphenyl-3H-indazole through a facile intramolecular [2 + 3] cycloaddition of the diazo intermediate

• Andrew T. King,
• Hugh G. Hiscocks,
• Lidia Matesic,
• Mohan Bhadbhade,
• Roger Bishop and
• Alison T. Ung

Beilstein J. Org. Chem. 2019, 15, 1347–1354, doi:10.3762/bjoc.15.134

• . [12] (Scheme 1). Herein, we report the unexpected product derived from 5 under the reaction conditions described in Scheme 1. The unusual crystal packing present in this 3H-indazole product was also analysed. Results and Discussion The one-pot reaction of compound 5 with tert-BuONO and DABSO in the

• Pauling-type hydrogen bonding, and therefore weaker attractions must be used in the crystal packing. Its interaction between the methoxy and diazo functionalities is uncommon, though entirely reasonable in the context of weak hydrogen bonding [14]. The presence of close C–H···H–C contacts in this

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

• signals. X-ray crystal structure of 1b-1 (left), layered structure of crystal packing (right). Reaction of 2,4-dimethylglycoluril and m-xylylene dibromide. Supporting Information Supporting Information File 273: MS and NMR spectra, computational details and crystallographic data for macrocycles 1a and 1b

Catalytic asymmetric oxo-Diels–Alder reactions with chiral atropisomeric biphenyl diols

• Chi-Tung Yeung,
• Wesley Ting Kwok Chan,
• Wai-Sum Lo,
• Ga-Lai Law and
• Wing-Tak Wong

Beilstein J. Org. Chem. 2019, 15, 955–962, doi:10.3762/bjoc.15.92

• is 76.25(35)–78.27(35)°; axial configuration is M. (b) Crystal packing of 3 shows one strand of supramolecular left-handed helixes (hydrogens that are not involved in interactions are omitted for clarity). X-ray crystal structure of (P)-(S,S)-6 at two different orientations to show (a) P

Mechanochemistry of supramolecules

• Anima Bose and
• Prasenjit Mal

Beilstein J. Org. Chem. 2019, 15, 881–900, doi:10.3762/bjoc.15.86

• differences in the crystal packing in the solid state. The products 32 were obtained via thermodynamic control (Figure 18) from a dynamic combinatorial library [53][88]. In 2010, Otto and co-workers observed unprecedented product selectivity for the formation of disulfide macromolecules based on mechanical

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

• ellipsoids are drawn at the 50% probability level and H-atoms are shown as small spheres of arbitrary size. Hydrogen bonds are shown as dashed lines. The crystal packing of 8 shows the intramolecular hydrogen-bonding network (projection parallel to the x-axis). N- and S-conformation for cyclonucleoside 8. B

Evaluation of dispersion type metal···π arene interaction in arylbismuth compounds – an experimental and theoretical study

• Ana-Maria Preda,
• Małgorzata Krasowska,
• Lydia Wrobel,
• Philipp Kitschke,
• Phil C. Andrews,
• Jonathan G. MacLellan,
• Lutz Mertens,
• Marcus Korb,
• Tobias Rüffer,
• Heinrich Lang,
• Alexander A. Auer and
• Michael Mehring

Beilstein J. Org. Chem. 2018, 14, 2125–2145, doi:10.3762/bjoc.14.187

• (geometry preparation; denoted as Eprep in Figures 11, 13, and 15) were computed in order to gain knowledge on crystal packing effects. The distortion energy is obtained as the difference between the energy of a single relaxed molecule and the energy of an unrelaxed molecule in the crystal structure

• and amounts to −15 kJ mol−1. The distortion energies (Eprep) of the monomers in polymorph 1a are quite large and amount to almost 17 kJ mol−1. This indicates that, although the interactions between specific monomers to form dimeric structures by Bi···π arene are strong, the crystal packing effects are

• −40 kJ mol−1. The distortion energies of monomers (17 kJ mol−1) suggest that crystal packing effects are large in polymorph 1a. Polymorph 1b In case of polymorph 1b four tetrameric units were identified and are depicted in Figure 13. Tetramers 1b-1 and 1b-2 consist of zig-zag chains formed by Bi···π

Chiral bisoxazoline ligands designed to stabilize bimetallic complexes

• Deepankar Das,
• Rudrajit Mal,
• Nisha Mittal,
• Zhengbo Zhu,
• Thomas J. Emge and
• Daniel Seidel

Beilstein J. Org. Chem. 2018, 14, 2002–2011, doi:10.3762/bjoc.14.175

• oxygen of a second molecule of the complex (not shown in the figure for clarity). Apparently, the coordination environment involving three O-atoms from acetate groups (the Ni(1) situation) for one of the two metals is preferred in 16·Ni2(OAc)2, presumably for steric reasons, as crystal packing

Polysubstituted ferrocenes as tunable redox mediators

• Sven D. Waniek,
• Jan Klett,
• Christoph Förster and
• Katja Heinze

Beilstein J. Org. Chem. 2018, 14, 1004–1015, doi:10.3762/bjoc.14.86

• tetraesters 2–4 suggest an intramolecular coupling of the C=O vibrations of the ester moieties substantiating the number of observed bands (Table S1, Supporting Information File 1). Furthermore, crystal packing effects with intermolecular C=O∙∙∙H–C interactions, differing in strengths, can be responsible for

Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies

• Elias Christoforides,
• Andreas Papaioannou and
• Kostas Bethanis

Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69

• ), hydrogen bonded with primary hydroxy groups of vicinal β-CD dimers (O1···O63B(1+x, y, z) = 2.688(4) Å, and O1···O66B(x, −1+y, z) = 2.721(5) Å,) aiding the crystal packing and also affecting the inclusion depth of the guest in the crystalline state (Figure 2c). The inclusion complex gains stability from

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• distance = 2.882(2) Å) and halogen bonding (C30–Cl31···O28 distance = 2.972(2) Å) observed in the crystal packing of 2. UV–vis absorption and fluorescence spectra of pyrene–adenines 5 (a) and 3 (b) in diluted (c ≈ 10−5 M) dichloromethane solutions at ambient temperature. Absorption changes during titration

Complexation of molecular clips containing fragments of diphenylglycoluril and benzocrown ethers with paraquat and its derivatives

• Leonid S. Kikot',
• Catherine Yu. Kulygina,
• Alexander Yu. Lyapunov,
• Svetlana V. Shishkina,
• Roman I. Zubatyuk,
• Tatiana Yu. Bogaschenko and
• Tatiana I. Kirichenko

Beilstein J. Org. Chem. 2017, 13, 2056–2067, doi:10.3762/bjoc.13.203

• °). The oxygen atom of the second hydroxy group acts as proton acceptor and forms the weak C–H···О hydrogen bonds with CH2 and Hα hydrogen atoms of 10 belonging to the neighboring complex (C–H···O, C···O, C–H···O, 2.59, 3.27 Å, 126.3°; 2.67, 3.30 Å, 124.5°). The crystal packing is similar to the one

• 10 participate in the intermolecular interactions with the carbonyl oxygen atoms of neighboring molecules only forming two hydrogen bonds (О–H···O, O···O, О–H···O, 2.51, 2.77 Å, 99.1° and 1.98, 2.80 Å, 174.1°). As a result, the crystal packing of this complex differs from the described above. The

• for the complexes (lgK) of molecular clips 1–5 with guests 7–10 on the size of crown ether cycles in acetonitrile at 20 °C. Molecular structures of complexes of clips 3, 2 and 5 with paraquat (7). Anions and solvate molecules are omitted for clarity. Crystal packing of molecules in complexes of clips

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• surface entropy and hinder crystal packing. For this reason, it is sometime necessary to manipulate the glycoform to facilitate the crystallization. In the case of the human IgE-FcεRIα [31], Man5-GlcNAc-GlcNAc-Asp-linked glycoforms produced better crystals than in the case where only the Man-GlcNAc-GlcNAc

G-Protein coupled receptors: answers from simulations

• Timothy Clark

Beilstein J. Org. Chem. 2017, 13, 1071–1078, doi:10.3762/bjoc.13.106

• structures in which the allosteric rearrangement was overlaid by crystal-packing effects. Today’s combinations of hard- and software allow routine simulations of several μs, which means that homology models can be equilibrated long enough for them to adopt what is probably a biologically relevant structure

• crystal-packing forces are large enough to change the induction state of the tetracycline repressor [26]. GPCR simulations often also show geometric rearrangements after several hundred nanoseconds, which suggests that the simulation is perhaps switching to a conformation closer to the biologically

Fluorinated cyclohexanes: Synthesis of amine building blocks of the all-cis 2,3,5,6-tetrafluorocyclohexylamine motif

• Tetiana Bykova,
• Nawaf Al-Maharik,
• Alexandra M. Z. Slawin and
• David O'Hagan

Beilstein J. Org. Chem. 2017, 13, 728–733, doi:10.3762/bjoc.13.72

• of the cyclohexane rings. These polarized cyclohexyl derivatives should prove valuable as potential building blocks in drug discovery and agrochemistry research programs [3][25]. The derivatives of all-cis-2,3,5,6-tetrafluorocyclohexane. X-ray structures and crystal packing of compounds 13, 14 and 15

Synthesis of spiro[isoindole-1,5’-isoxazolidin]-3(2H)-ones as potential inhibitors of the MDM2-p53 interaction

• Salvatore V. Giofrè,
• Santa Cirmi,
• Raffaella Mancuso,
• Francesco Nicolò,
• Giuseppe Lanza,
• Laura Legnani,
• Agata Campisi,
• Maria A. Chiacchio,
• Michele Navarra,
• Bartolo Gabriele and
• Roberto Romeo

Beilstein J. Org. Chem. 2016, 12, 2793–2807, doi:10.3762/bjoc.12.278

• ’, respectively). Crystal packing is a racemate due to the centrosymmetric symmetry and in the picture the choice of the enantiomer is arbitrary. C: light blue, H: white, O: red, N: magenta. Probability of the ORTEP ellipsoids is set to 50%, whereas H size is arbitrary. Three-dimensional plots of TSs of reaction

Synthesis and properties of fluorescent 4′-azulenyl-functionalized 2,2′:6′,2″-terpyridines

• Adrian E. Ion,
• Liliana Cristian,
• Mariana Voicescu,
• Masroor Bangesh,
• Augustin M. Madalan,
• Daniela Bala,
• Constantin Mihailciuc and
• Simona Nica

Beilstein J. Org. Chem. 2016, 12, 1812–1825, doi:10.3762/bjoc.12.171

• supramolecular interactions are observed in the crystal packing, via the azulene moieties and the terpyridine groups. In the crystal of 4a, the molecules are organized in columns running along the crystallographic a axis by π–π stacking interactions (3.39–3.64 Å). In the neighboring columns the molecular units

• structures, different twisting was observed that might be responsible for the observed fluorescent profile. The solid-state crystal packing showed π–π stacking interactions between the pyridine rings in face-to-face or T-shape orientation, completed by slipped-off π–π stacked azulenyl moieties according to