Synthesis of 2,2-difluoro-1,3-diketone and 2,2-difluoro-1,3-ketoester derivatives using fluorine gas

• Alexander S. Hampton,
• David R. W. Hodgson,
• Graham McDougald,
• Linhua Wang and
• Graham Sandford

Beilstein J. Org. Chem. 2024, 20, 460–469, doi:10.3762/bjoc.20.41

• rotated to maximize the distances between the lone pairs of the electron-rich fluorine and oxygen atoms. Usually, one of the fluorine atoms lies in a syn orientation to an oxygen (e.g., 3f has an F–C–C–O dihedral angle of 15.6°) creating a dipole. This dipole appears to aid crystal packing by forming weak

• -generated N-fluoroammonium ion 7 to form 2-fluoro- and 2,2-difluoro-1,3-dicarbonyl products. Molecular structure of 2,2-difluoro-1,3-diphenylpropane-1,3-dione (3a). Crystal packing structure of 3f as determined by SXRC. Molecular structure and crystal packing of 5e as determined by SXRC. Monofluorination of

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

• between the most stable calculated structure 1 and the crystalline structure is likely due to crystal packing forces, the presence of the counterion, and the inclusion of solvent molecules. The interfacial distances between the nearest neighbor centroid of a paraphenylene unit of [10]CPP and [5]CPP were

• between the Hirshfeld surface and the contacting atoms, most sp2-hybridzed carbon atoms of the [10]CPP host have short contact with the Hirshfeld surface, as shown in green, despite the tilting of [10]CPP and [5]CPP. In the crystal packing, there were two orientations, as highlighted in blue and red in

Facile approach to N,O,S-heteropentacycles via condensation of sterically crowded 3H-phenoxazin-3-one with ortho-substituted anilines

• Eugeny Ivakhnenko,
• Vasily Malay,
• Pavel Knyazev,
• Nikita Merezhko,
• Nadezhda Makarova,
• Oleg Demidov,
• Gennady Borodkin,
• Andrey Starikov and
• Vladimir Minkin

Beilstein J. Org. Chem. 2024, 20, 336–345, doi:10.3762/bjoc.20.34

• (Å) and angles: N(1)–C(11) 1.3061(19), N(1)–C(14) 1.3836(18), O(23)–C(4) 1.2314(19), N(15)–C(3) 1.3765(19), N(15)–C(16) 1.383(2), C(11)–N(1)–C(14) 117.55(12), C(3)–N(15)–C(16) 131.12(14). b) Crystal packing of 4f. Important crystallographic parameters and bond distances are given in Tables S2 and S5

Substitution reactions in the acenaphthene analog of quino[7,8-h]quinoline and an unusual synthesis of the corresponding acenaphthylenes by tele-elimination

• Ekaterina V. Kolupaeva,
• Narek A. Dzhangiryan,
• Alexander F. Pozharskii,
• Oleg P. Demidov and
• Valery A. Ozeryanskii

Beilstein J. Org. Chem. 2024, 20, 243–253, doi:10.3762/bjoc.20.24

• increase in the series 3 → 5 → 8 (“clothespin” effect) [30]. The crystal packing patterns in salts 5·HBF4 and 8·HBF4 are quite similar. The main factor here continues to be the tendency of almost flat disk-shaped heterocyclic cations to π-stacking, leading to the formation of dense columns with anions in

• overlap (с). Again, π-stacking and H-bonding (blue dotted lines) strongly dominate in this structure. Fragment of the crystal packing of neutral dipyridoacenaphthene 5 showing self-association via multiple C–H…N contacts (blue dotted lines) between three independent molecules. Structure of

Photochromic derivatives of indigo: historical overview of development, challenges and applications

• Gökhan Kaplan,
• Zeynel Seferoğlu and
• Daria V. Berdnikova

Beilstein J. Org. Chem. 2024, 20, 228–242, doi:10.3762/bjoc.20.23

• used in the synthesis of indigo [4]. a) Intramolecular (a = 2.26 Å) and intermolecular (b = 2.11 Å) hydrogen bonds in indigo, b) crystal packing of indigo in the solid state obtained from the single-crystal X-ray diffraction data, CCDC 796873 [12], c) photos of indigo in the solid state and solutions

Multi-redox indenofluorene chromophores incorporating dithiafulvene donor and ene/enediyne acceptor units

• Christina Schøttler,
• Kasper Lund-Rasmussen,
• Line Broløs,
• Philip Vinterberg,
• Ema Bazikova,
• Viktor B. R. Pedersen and
• Mogens Brøndsted Nielsen

Beilstein J. Org. Chem. 2024, 20, 59–73, doi:10.3762/bjoc.20.8

• compound 29 is perpendicular with respect to the herringbone pattern and the related structures (see Figure 10, bottom). Compound 25 packs with an intramolecular distance of 3.41 Å between the planes of the π-systems. Neither compound 26 nor 29 shows π–π interactions in the crystal packing. The large

• orbitals), the dianion has an additional 6π-aromatic cyclopentadienyl anion (highlighted in green), while the cation has a 6π-aromatic 1,3-dithiolium ring (highlighted in red). ORTEP plots (50% probability) and crystal packing of compounds a) 25, b) 26, and c) 29. The respective crystal packing of each

Bromination of endo-7-norbornene derivatives revisited: failure of a computational NMR method in elucidating the configuration of an organic structure

• Demet Demirci Gültekin,
• Arif Daştan,
• Yavuz Taşkesenligil,
• Cavit Kazaz,
• Yunus Zorlu and
• Metin Balci

Beilstein J. Org. Chem. 2023, 19, 764–770, doi:10.3762/bjoc.19.56

• ppm). NOE-Diff experiment. Irradiation at the resonance frequency of proton H7 (4.23 ppm). A) Molecular structure of the compound 6 with displacement ellipsoids drawn at the 30% probability level. H-atoms are shown as small spheres of arbitrary radii. B) Perspective view of the crystal packing of

Synthesis, structure, and properties of switchable cross-conjugated 1,4-diaryl-1,3-butadiynes based on 1,8-bis(dimethylamino)naphthalene

• Semyon V. Tsybulin,
• Ekaterina A. Filatova,
• Alexander F. Pozharskii,
• Valery A. Ozeryanskii and
• Anna V. Gulevskaya

Beilstein J. Org. Chem. 2023, 19, 674–686, doi:10.3762/bjoc.19.49

• standard value of 180° by 3–10°. Deviations of bond angles in acetylene bridges are ≈1–7°. The methoxy derivative 5b has the most complex crystal packing with a large number of different nonvalent interactions (see Supporting Information File 1, Figures S62 and S63). The molecule of cyano derivative 5d is

• characterized by the least distortion of the DMAN fragments in the series (twisting Θ = 9.45 and 12.83°, torsions φA = 20.9° and φB = 8.4°, bond angle deviations in both butadiyne and acetylene linkers do not exceed 6°). In the crystal packing of 5d (see Supporting Information File 1, Figures S64 and S65), the

• molecule 5b. In the crystal packing (Figure S66 in Supporting Information File 1), molecules 5e tend to approach π-donor DMAN and π-acceptor p-nitrophenyl fragments, and the shortest distance between the two molecules is 2.810 Å (Figure S67 in Supporting Information File 1). The alternation of the C–C bond

Inclusion complexes of the steroid hormones 17β-estradiol and progesterone with β- and γ-cyclodextrin hosts: syntheses, X-ray structures, thermal analyses and API solubility enhancements

• Alexios I. Vicatos,
• Zakiena Hoossen and
• Mino R. Caira

Beilstein J. Org. Chem. 2022, 18, 1749–1762, doi:10.3762/bjoc.18.184

• to prepare complexes by spray-drying, freeze-drying, co-grinding, kneading and solution-based crystallization; however, this modest type of ‘fingerprinting’ has not generally been pursued further to deduce important features of CD complexes such as the crystal packing of the CD host molecules

Comparison of crystal structure and DFT calculations of triferrocenyl trithiophosphite’s conformance

• Ruslan P. Shekurov,
• Mikhail N. Khrizanforov,
• Ilya A. Bezkishko,
• Tatiana P. Gerasimova,
• Almaz A. Zagidullin,
• Daut R. Islamov and
• Vasili A. Miluykov

Beilstein J. Org. Chem. 2022, 18, 1499–1504, doi:10.3762/bjoc.18.157

• that in these cases crystal packing influences the conformation. A comparison of the crystal packings for the PLEP, P=O, and P=S containing compounds clearly confirms this conclusion experimentally (Figure 4). We compared the crystal packings of three similar compounds: (FcS)3P, (FcS)3PO [19], and (FcS

Experimental and theoretical studies on the synthesis of 1,4,5-trisubstituted pyrrolidine-2,3-diones

• Nguyen Tran Nguyen,
• Vo Viet Dai,
• Nguyen Ngoc Tri,
• Luc Van Meervelt,
• Nguyen Tien Trung and
• Wim Dehaen

Beilstein J. Org. Chem. 2022, 18, 1140–1153, doi:10.3762/bjoc.18.118

• ) Å, N15–H15···O13: 145(3)˚]. The pyrrolidine-2,3-dione ring is planar (rms deviation: 0.003 Å) and makes an angle of 40.39(14)˚ with the phenyl ring C6–C11 and of 82.23(15)˚ with the phenyl ring C26–C31. The dihedral angle between these phenyl rings is 74.87(14)˚. The crystal packing of product 10aa

Thiophene/selenophene-based S-shaped double helicenes: regioselective synthesis and structures

• Mengjie Wang,
• Lanping Dang,
• Wan Xu,
• Zhiying Ma,
• Liuliu Shao,
• Guangxia Wang,
• Chunli Li and
• Hua Wang

Beilstein J. Org. Chem. 2022, 18, 809–817, doi:10.3762/bjoc.18.81

• arrangement in the crystal packing structures of DH-1 and DH-2 indicate that these compounds may be used as supramolecular self-assembly units. Changes in molecular structure may substantially modulate the optical band gap of heteroacenes, and the replacement of heteroatoms from S to Se could fine-tune their

• , and double oxidative photocyclization. The photocyclization was a highly regioselective process. The molecular structures of DH-1 and DH-2 were confirmed by X-ray single-crystal analysis. Multiple intermolecular interactions, such as C–S, C–Se, S–S, S–Se, and Se–Se, were observed in the crystal

• packing structures of these compounds. Spectroscopic results and our previous work showed that the combination of molecular structure change and heteroatom replacement from S to Se could precisely modulate molecular energy levels. Keywords: crystal structure; double helicene; regioselective synthesis

Co-crystallization of an organic solid and a tetraaryladamantane at room temperature

• Fabian Rami,
• Jan Nowak,
• Felix Krupp,
• Wolfgang Frey and
• Clemens Richert

Beilstein J. Org. Chem. 2021, 17, 1476–1480, doi:10.3762/bjoc.17.103

• of the TDA/phenol co-crystal (space group P-1). b) Portion of the asymmetric unit of the TEO/phenol co-crystal (space group Cc). c) Crystal packing in the TDA/phenol system, and d) crystal packing in the TEO/phenol system. Possible states of two organic compounds capable of crystallizing at room

Structural effects of meso-halogenation on porphyrins

• Keith J. Flanagan,
• Maximilian Paradiz Dominguez,
• Zoi Melissari,
• Hans-Georg Eckhardt,
• René M. Williams,
• Dáire Gibbons,
• Caroline Prior,
• Gemma M. Locke,
• Alina Meindl,
• Aoife A. Ryan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88

• alternative substitution types. The labelled displacement ellipsoid plot and packing diagrams for compounds 1 and 2A are available in Supporting Information File 1 (Figures S1–S4). The first feature which is of interest is the crystal packing of each of the 5-halo-substituted compounds which appears to be

• which is not seen in the other two structures (Figure 4B). While this may be difficult to visualize in the crystal packing (Supporting Information File 1, Figure S6), it is clear from the Hirshfeld surface analysis that there are marked decreases in the X···H contacts and an increase in the X···C (where

• porphyrin layers compared to the packing of compounds 13 and 13A (Supporting Information File 1, Figure S37). However, these deviations are in line with crystal packing and minor steric effects to be expected for this class of compounds with little to no deviations seen in the bond lengths, angles, and atom

Synthesis, crystal structures and properties of carbazole-based [6]helicenes fused with an azine ring

• Daria I. Tonkoglazova,
• Anna V. Gulevskaya,
• Konstantin A. Chistyakov and
• Olga I. Askalepova

Beilstein J. Org. Chem. 2021, 17, 11–21, doi:10.3762/bjoc.17.2

• helicene 10b, the enantiomeric molecules are aggregated into pairs differently: the pyrazine ring of one enantiomer is located over the E ring of another enantiomer and the distance between the layers is ca. 3.4 Å (Figure 2c and Figure 2d). The crystal packing of helicene 10c (Figure 2e) is peculiar: the

• [6]helicenes 10a (a), 10b (b) and 10c (c) (X-ray data). Crystal packing of carbazole-based [6]helicenes 10a (a, b), 10b (c,d) and 10c (e). Hydrogen atoms are hidden. Overview of the synthetic methods for the carbazole-based heterohelicenes. i) Pd2dba3, xantphos, K3PO4, xylene, 100 °C, 123 h, 64–88

Ultrasound-assisted Strecker synthesis of novel 2-(hetero)aryl-2-(arylamino)acetonitrile derivatives

• Emese Gal,
• Luiza Gaina,
• Hermina Petkes,
• Alexandra Pop,
• Castelia Cristea,
• Gabriel Barta,
• Dan Cristian Vodnar and
• Luminiţa Silaghi-Dumitrescu

Beilstein J. Org. Chem. 2020, 16, 2929–2936, doi:10.3762/bjoc.16.242

• Crystallographic Data Centre as supplementary publication (CCDC 2018198) (deposit@ccdc.cam.ac.uk). The molecular structure for the representative compound 2a is depicted in Figure 1. As revealed from the crystal packing structure shown in Figure 1, compound 2a forms a single crystalline phase containing both

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• challenging due to their often moderate (µM) binding affinities. If crystal contacts between proteins are favored, this can lead to exclusion of the ligand from the crystal. On the contrary, ligands binding tightly to the protein surface can in some cases compete with crystal packing and thus inhibit

• site is observed by one method but not the other, are likely due to crystal packing effects. If crystal contacts between a ligand and additional copies of the protein are formed, this site might be favored in the crystal but not in solution. Conversely, a site that might be sampled in solution can be

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