Enhanced host–guest interaction between [10]cycloparaphenylene ([10]CPP) and [5]CPP by cationic charges

• Eiichi Kayahara,
• Yoshiyuki Mizuhata and
• Shigeru Yamago

Beilstein J. Org. Chem. 2024, 20, 436–444, doi:10.3762/bjoc.20.38

• hot (red, 1.0 Å) as de decreases. e) Space-filling view of packing structure containing four crystalline unit lattices viewed from the b-axis. Wire-flame view of the packing structure of crystalline unit lattices viewed from f) the a-axis and g) the b-axis. Supporting Information Supporting

Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups

• Benjamin Jeffries,
• Zhong Wang,
• Robert I. Troup,
• Anaïs Goupille,
• Jean-Yves Le Questel,
• Charlene Fallan,
• James S. Scott,
• Elisabetta Chiarparin,
• Jérôme Graton and
• Bruno Linclau

Beilstein J. Org. Chem. 2020, 16, 2141–2150, doi:10.3762/bjoc.16.182

• isopropyl substituent led to larger lipophilicity modulation compared to fluorination of the cyclopropyl substituent. Keywords: aliphatic fluorination; cyclopropane; isopropyl; isostere; lipophilicity; oxetane; Introduction The introduction of small alkyl groups onto bioactive compounds as space filling

Fluorinated azobenzenes as supramolecular halogen-bonding building blocks

• Esther Nieland,
• Oliver Weingart and
• Bernd M. Schmidt

Beilstein J. Org. Chem. 2019, 15, 2013–2019, doi:10.3762/bjoc.15.197

• to facilitate readability. a) Space-filling model of U1···A2. The kinked alignment of both the lutidine units of U1 and the azobenzenes A2 can be seen. b) Part of the X-ray crystal structure showing the halogen bonding azobenzene A2 in detail. Selected bond lengths: N3–I1 2.7810(2), I2–N4 2.816(2) Å

Self-assembly behaviors of perylene- and naphthalene-crown macrocycle conjugates in aqueous medium

• Xin Shen,
• Bo Li,
• Tiezheng Pan,
• Jianfeng Wu,
• Yangxin Wang,
• Jie Shang,
• Yan Ge,
• Lin Jin and
• Zhenhui Qi

Beilstein J. Org. Chem. 2019, 15, 1203–1209, doi:10.3762/bjoc.15.117

• temperature. TEM images of 1 aggregates in (a) CHCl3, (b) MeCN, and (c) H2O/MeCN (v/v = 10:1) (inset: schematic space-filling models illustrating the self-assembly of 1); TEM images of 2 aggregates in (d) CHCl3, (e) MeCN, and (f) H2O/MeCN (v/v = 10:1). Concentration of solutions for all the TEM analysis is 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

• blue, O red, S yellow, metals flesh (Zn, Cd) or green (Ni)). Space filling representation of the packing of two symmetry-related [Zn2L(μ-azo-NMe2)]+ cations in crystals of 5·1.5MeCN. The ClO4− anions and solvate molecules are omitted for clarity. Structure of the [Cd2L(μ-azo-NMe2)]+ cation in crystals

• 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

• . Right: Space filling representation of the packing of two [Cd2L(μ-azo-CO2Me)]+ cations in crystals of 8·MeCN. H atoms, BPh4− anions and solvate molecules are omitted for clarity. Plots of the effective magnetic moment μeff for 2 (open circles), 4 (open squares), and 7 (open triangles) at H = 0.5 T (2, 7

Synthesis and post-functionalization of alternate-linked-meta-para-[2ⁿ.1ⁿ]thiacyclophanes

• Wout De Leger,
• Koen Adriaensen,
• Koen Robeyns,
• Luc Van Meervelt,
• Joice Thomas,
• Björn Meijers,
• Mario Smet and
• Wim Dehaen

Beilstein J. Org. Chem. 2018, 14, 2190–2197, doi:10.3762/bjoc.14.192

• -thiacyclophane 6: (a) ball-and-stick representation, with O–H···S hydrogen bonds shown as green dashed lines, (b) space-filling representation viewed along the pseudo twofold axis. Macrocyclization towards homothiacalixarenes 3a and 3b [12]. Cyclocondensation reaction of 4 and 5 towards [2 + 2] and [3 + 3

Syntheses, structures, and stabilities of aliphatic and aromatic fluorous iodine(I) and iodine(III) compounds: the role of iodine Lewis basicity

• Tathagata Mukherjee,
• Soumik Biswas,
• Andreas Ehnbom,
• Subrata K. Ghosh,
• Ibrahim El-Zoghbi,
• Nattamai Bhuvanesh,
• Hassan S. Bazzi and
• John A. Gladysz

Beilstein J. Org. Chem. 2017, 13, 2486–2501, doi:10.3762/bjoc.13.246

• 119.6(2), C6–C5–C13 119.3(2), average of 8 CF–CF–CF 115.0(10). Ball-and-stick and space filling representations of the unit cell of 1,3,5-(Rf6)2C6H3I. Free energies of chlorination of relevant aryl and alkyl iodides to the corresponding iodine(III) dichlorides in the gas phase (kcal/mol), presented in a

Exploring mechanochemistry to turn organic bio-relevant molecules into metal-organic frameworks: a short review

• Vânia André,
• Sílvia Quaresma,
• João Luís Ferreira da Silva and
• M. Teresa Duarte

Beilstein J. Org. Chem. 2017, 13, 2416–2427, doi:10.3762/bjoc.13.239

• to incorporate APIs as a guest. Indeed, they synthesized two BioMOFs by grinding together zinc, fumaric acid and 4,4’-bipyridyl (bipy) or trans-1,2-di(4-pyridyl)ethylene (bpe) as ligands in the presence of a space-filling liquid agent (N,N-dimethylformamide, DMF). This synthesis also proceeded when

• , they used LAG with ZnO and the previous imidazole ligands in the presence of DMF as a space-filling liquid. However, this method only partially succeeded: with HIm the quantitative formation of ZIF-4 was obtained after 60 min, whereas with HMeIm only partial formation of ZIF-8 was achieved and with

Novel approach to hydroxy-group-containing porous organic polymers from bisphenol A

• Tao Wang,
• Yan-Chao Zhao,
• Li-Min Zhang,
• Yi Cui,
• Chang-Shan Zhang and
• Bao-Hang Han

Beilstein J. Org. Chem. 2017, 13, 2131–2137, doi:10.3762/bjoc.13.211

• PPOPs are microporous. The pore size for PPOPs and the total pore volume for PPOP-2 and PPOP-3 do not show any obvious difference with increasing monomer strut length, which may be attributed to the random penetration and space-filling within the fragments of the extended repeating units [16]. The gas

Self-optimisation and model-based design of experiments for developing a C–H activation flow process

• Alexander Echtermeyer,
• Yehia Amar,
• Jacek Zakrzewski and
• Alexei Lapkin

Beilstein J. Org. Chem. 2017, 13, 150–163, doi:10.3762/bjoc.13.18

• optimisation. For this approach five experiments were used as a training set, using Latin Hypercube space filling algorithm; the results are shown in Supporting Information File 1, Table S7 (Expt. 1–5). Figure 5 shows results of the initial set of experiments on the left side of the plot. It is noted that two

• that the self-optimisation works well when trained on a space-filling method to avoid many necessary experiments for model generation. This results in a set of experiments that reach the pre-defined targets in six iterations, although it does not provide any process knowledge. Hence, a combined

Radical polymerization by a supramolecular catalyst: cyclodextrin with a RAFT reagent

• Kohei Koyanagi,
• Yoshinori Takashima,
• Takashi Nakamura,
• Hiroyasu Yamaguchi and
• Akira Harada

Beilstein J. Org. Chem. 2016, 12, 2495–2502, doi:10.3762/bjoc.12.244

• . DMA molecules outside the α-CD, hydrogen atoms, and water molecules are omitted for clarity. Colors of the atoms are based on CPK coloring. DMA, space-filling model; CD, stick model. (b) A schematic diagram of the inclusion complex of α-CD/DMA. Time-conversion curves (a), kinetic plots (b) and plots

From steroids to aqueous supramolecular chemistry: an autobiographical career review

• Bruce C. Gibb

Beilstein J. Org. Chem. 2016, 12, 684–701, doi:10.3762/bjoc.12.69

Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career

• Eric V. Anslyn

Beilstein J. Org. Chem. 2016, 12, 362–376, doi:10.3762/bjoc.12.40

• Atwood’s clusters [8][9], our field is associated with creating complex structures, often of very high symmetry. This makes ChemDraw structures, space-filling models, or ball and stick renderings very akin to objects found in modern art [10]. Can one look at an Atwood cluster without thinking of Geometric

Inclusion complexes of 2-methoxyestradiol with dimethylated and permethylated β-cyclodextrins: models for cyclodextrin–steroid interaction

• Mino R. Caira,
• Susan A. Bourne,
• Halima Samsodien and
• Vincent J. Smith

Beilstein J. Org. Chem. 2015, 11, 2616–2630, doi:10.3762/bjoc.11.281

• 3.280(7) Å and angle C–H···O 143°). A side-view of the complex unit (Figure 2b) in space-filling representation reveals that essentially only the A-ring of the 2ME molecule protrudes significantly from the host secondary side, while the sectioned view (Figure 2c) indicates that the steroid molecule

• A, and 3.186(6) Å and 170° for unit B. Figure 4a, featuring complex unit A as representative, illustrates in space-filling mode the nature of the common guest inclusion mode in complex units A and B. This involves encapsulation of the C- and D-rings of 2ME within the host cavity while the A- and B

• Information File 1), which result in a RMSD of 0.819 Å and a maximum deviation of 3.417 Å between two terminal methoxy carbon atoms. Figure 4b illustrates in space-filling mode the inclusion of 2ME in host molecule C as representative. Guest inclusion again involves hydrogen bonding between the phenolic group

Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

• Giuseppina Raffaini,
• Antonino Mazzaglia and
• Fabio Ganazzoli

Beilstein J. Org. Chem. 2015, 11, 2459–2473, doi:10.3762/bjoc.11.267

• distances (in Å, at right) between the centres of mass of the four macrocycles is shown (see Figure 7 for more details). a) The initial random arrangement of eight molecules of the model aCD in a space-filling representation within the simulation box (note that the overlap of the molecules is only apparent

• aCD, cluster A (at left) and cluster B (at right) in a space-filling representation. The hydrogen atoms were omitted for clarity, while the atoms colour code is the same as in the line drawings of Figure 1. The PDF of the S atoms of the H groups at the primary rim (black symbols) and of the oxygen

Cathodic hydrodimerization of nitroolefins

• Michael Weßling and
• Hans J. Schäfer

Beilstein J. Org. Chem. 2015, 11, 1163–1174, doi:10.3762/bjoc.11.131

• reasons, which can explain the absence of the dimer. This can favour the further reaction of the radical anion of 14 to the oxime 24 and the Michael addition of hydroxy ions to form the nitro alcohol 25. The smaller space filling of the fluorine atom compared to the chlorine atom should lead to a

Quarternization of 3-azido-1-propyne oligomers obtained by copper(I)-catalyzed azide–alkyne cycloaddition polymerization

• Shun Nakano,
• Akihito Hashidzume and
• Takahiro Sato

Beilstein J. Org. Chem. 2015, 11, 1037–1042, doi:10.3762/bjoc.11.116

• are attached onto the 3-position for simplicity. From this space-filling model, the contour length of the oligoAPMe was estimated to be 5.6 nm. When this oligomer model is viewed as a rodlike touched bead model with a bead diameter (d) of 0.7 nm (Figure 3b), RH is calculated to be 1.03 nm [45]. This

Inclusion of trans-resveratrol in methylated cyclodextrins: synthesis and solid-state structures

• Lee Trollope,
• Dyanne L. Cruickshank,
• Terence Noonan,
• Susan A. Bourne,
• Milena Sorrenti,
• Laura Catenacci and
• Mino R. Caira

Beilstein J. Org. Chem. 2014, 10, 3136–3151, doi:10.3762/bjoc.10.331

• the ordered RSV molecule A (blue) present in host A and the two disorder components B (orange, s.o.f. = 0.56) and C (green, s.o.f. = 0.44) of the RSV molecule included in host molecule B. Space-filling representations of the two independent complex units A (a) and B (b) of the complex TMA·RSV·6.25H2O

• the host TMB (b). Only the major RSV disorder component is shown in (a) for clarity. Space-filling model of the inclusion complex TMB·RSV·5.6H2O showing the inclusion of the RSV molecule in the host TMB (left) and a cutaway view (right) emphasising the shallow inclination of the guest molecule in the

• complex DMB·RSV·4.0H2O (a), ring and atomic nomenclature for the host molecule DMB (b), and structure and atomic numbering of the included RSV molecule (c). Space-filling model of the inclusion complex DMB·RSV·4.0H2O showing the encapsulation of part of the RSV molecule by the host DMB (left) and a

Synthesis of uniform cyclodextrin thioethers to transport hydrophobic drugs

• Lisa F. Becker,
• Dennis H. Schwarz and
• Gerhard Wenz

Beilstein J. Org. Chem. 2014, 10, 2920–2927, doi:10.3762/bjoc.10.310

• available native CDs and β-CD derivatives showed rather poor affinities to sevoflurane, as shown in Table 2. Among the native CDs β-CD had far the highest binding constant which was attributed to the best space filling of this host by sevoflurane. We recently demonstrated also for other guests that space

• β-CD derivatives 3b1 and 4b1 which can be again rationalized by the better space filling of the seven membered rings by sevoflurane. The binding constant decreased with increasing lengths of the alkyl substituents at the sulfur atoms as well as with the lengths of the oligoethylene oxide chains

• filling has a very significant influence on the binding constants [30]. We found indeed an even higher binding constant for heptakis-2,6-di-O-methyl-β-CD (DIMEB), but medical applications remain questionable for this host because of its known high toxicity [6]. On the other hand, heptakis-2,3,6-tri-O

Mono- and multilayers of molecular spoked carbazole wheels on graphite

• Stefan-S. Jester,
• A. Vikas Aggarwal,
• Daniel Kalle and
• Sigurd Höger

Beilstein J. Org. Chem. 2014, 10, 2783–2788, doi:10.3762/bjoc.10.295

• ). Moreover, the six kinks that are seen in the STM images (one of which is marked by the white circle in Figure 2c and d) correspond (not to the carbazole units but) to the intersections of the terminal acetylenes of the rim segments. According to the space-filling model, only three of the four pseudo

Effect of cyclodextrin complexation on phenylpropanoids’ solubility and antioxidant activity

• Miriana Kfoury,
• David Landy,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2014, 10, 2322–2331, doi:10.3762/bjoc.10.241

• either in solution or in solid state [14]. The relative stabilities of inclusion complexes are governed by different factors such as hydrogen bonding, hydrophobic interactions, solvation effects as well as the guest molecule's space filling ability [15][16]. CD derivatives are also of great importance

Macrocyclic bis(ureas) as ligands for anion complexation

• Claudia Kretschmer,
• Gertrud Dittmann and
• Johannes Beck

Beilstein J. Org. Chem. 2014, 10, 1834–1839, doi:10.3762/bjoc.10.193

• the cavity of the macrocycle (Figure 2). The ligand is strongly tilted. The four N−H∙∙∙Br bonds, however, show uniform lengths (H1−Br, 2.72; H2−Br, 2.74; H3−Br, 2.75; H4−Br, 2.71 Å; N−H∙∙∙O angles 149–169°). The representation with space filling radii shows that the halide anion fits well into the bis

• different representations are given, on top with thermal ellipsoids scaled at the 50% probability level, on bottom in a space filling representation showing the strong twist of the macrocyclic bis(urea) ligand. 1H NMR spectra of 2 in THF-d8 after addition of several different tetrabutylammonium salts. The N

Molecular assembly of amino acid interlinked, topologically symmetric, π-complementary donor–acceptor–donor triads

• M. B. Avinash,
• K. V. Sandeepa and
• T. Govindaraju

Beilstein J. Org. Chem. 2013, 9, 1565–1571, doi:10.3762/bjoc.9.178

• e) and aqueous NMP (b, d and f). Concentration of 1, 2 and 3 used was 400 μM. FESEM image of (a) 1 obtained from 40% aqueous NMP, (b) 2 obtained from 80% aqueous NMP. Energy-minimized structures of (a) 1 and (b) 2. Proposed molecular stacking (Chem3D; space filling model) of topologically symmetric

Space filling of β-cyclodextrin and β-cyclodextrin derivatives by volatile hydrophobic guests

• Sophie Fourmentin,
• Anca Ciobanu,
• David Landy and
• Gerhard Wenz

Beilstein J. Org. Chem. 2013, 9, 1185–1191, doi:10.3762/bjoc.9.133

• constants strongly increase with the amount of space filling of the CD cavity and the salt concentration. β-CD thioethers show a 3–10 times higher binding potential than native β-CD. Keywords: cyclodextrins; inclusion compound; molecular modelling; space filling; static headspace gas chromatography; vapor

• ]. Generally, the binding constant K increases with the degree of space filling of the β-CD cavity. The volume of the guest is often expressed by the number of carbon atoms n of its hydrophobic part. The Gibbs free enthalpy ΔG° of binding decreases nearly linearly with n by δΔG0/δn = −3.1 kJ mol−1 for linear

• molecular origin of hydrophobic interactions in general was already discussed controversially for many years [10][11][12][13]. Reliable quantitative predictive models are still missing [14]. Expulsion of “high energy water” from a cavity during space filling by a hydrophobic guest appears to be the main

Inclusion of the insecticide fenitrothion in dimethylated-β-cyclodextrin: unusual guest disorder in the solid state and efficient retardation of the hydrolysis rate of the complexed guest in alkaline solution

• Dyanne L. Cruickshank,
• Natalia M. Rougier,
• Raquel V. Vico,
• Susan A. Bourne,
• Elba I. Buján,
• Mino R. Caira and
• Rita H. de Rossi

Beilstein J. Org. Chem. 2013, 9, 106–117, doi:10.3762/bjoc.9.14

• molecules and there are no close contacts between the disordered guest molecules and host molecules. Figure 7 shows space-filling diagrams that illustrate representative modes of guest inclusion. Crystal packing is shown in Figure 8. The complex units stack head-to-tail in infinite columns parallel to the x

• ) have site occupancies 0.70 and 0.30, respectively. Stereoview of the three disordered guest components that occupy the cavity of host molecule B. Guest components B (green) and C (blue) have similar orientations while component E (pink) adopts the opposite orientation. Space-filling diagrams showing