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

• the analysis of single crystal X-ray diffraction data and computational studies. First, the crystal structures of polymorphs of Ph3Bi (1) are described emphasizing on the description of London dispersion type bismuth···π arene interactions and other van der Waals interactions in the solid state and

• ), which leads to the formation of zig-zag Bi–arenecentroid ribbons formed as a result of bismuth···π arene interactions and π···π intermolecular contacts. In the crystal structures of the polymorph 2b as well as for 4 bismuth···π arene interactions are not observed, but both compounds revealed C–HPh···π

• interaction as one of the emerging intermolecular interactions that are of particular interest to coordination chemists with regard to supramolecular chemistry [12]. However, most reports on main group metal···π interactions are based on the description of the single crystal structures and lack a profound

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

• , Florida 32611, USA 10.3762/bjoc.14.175 Abstract Chiral bisoxazoline ligands containing naphthyridine, pyridazine, pyrazole, and phenol bridging units were prepared and shown to form bimetallic complexes with various metal salts. X-ray crystal structures of bis-nickel naphthyridine-bridged, bis-zinc

• )∙∙∙Zn(2) distance of 3.857 Å is somewhat long, compared to the M∙∙∙M distances in two of the crystal structures mentioned here, namely, the Ni∙∙∙Ni in 16·Ni2(OAc)2 at 3.338 Å, shorter because of the smaller radius of the bridging μ2-O atom, and the 30·Pd2Br at 3.824 Å, shorter because of both the Pd

Synthesis and characterization of π–extended “earring” subporphyrins

• Haiyan Guan,
• Mingbo Zhou,
• Bangshao Yin,
• Ling Xu and
• Jianxin Song

Beilstein J. Org. Chem. 2018, 14, 1956–1960, doi:10.3762/bjoc.14.170

• single crystal diffraction. The 1H NMR spectra and single crystal structures revealed that aromatic ring current did not extend to the “ear” in both of the two compounds. Their UV–vis/NIR spectra were recorded and the absorption of both compounds is extended to the NIR region and that the absorption of

• further red-shifted and more intense. This work extends the research of “earring” porphyrins to “earring” subporphyrins. Investigations on their photophysical properties and further functionalization are underway. Partial 1H NMR spectrum of 3. X-ray crystal structures of 3: a) top view; b) side view

• . Thermal ellipsoids are drawn at the 50% probability level. All hydrogens on tolyl groups are omitted for clarity. Partial 1H NMR spectrum of 3Pd. X-ray crystal structures of 3Pd: a) top view; b) side view. Thermal ellipsoids are at the 30% probability level. All hydrogens on tolyl are omitted for clarity

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

• force field and 30 different conformers of each ligand were docked into two different X-ray structures of FimH (for details see Supporting Information File 1). These two crystal structures differ in the conformation of the tyrosine gate, formed by Y48 and Y137 positioned at the entrance of the

Synthesis of 9-arylalkynyl- and 9-aryl-substituted benzo[b]quinolizinium derivatives by Palladium-mediated cross-coupling reactions

• Siva Sankar Murthy Bandaru,
• Darinka Dzubiel,
• Heiko Ihmels,
• Mohebodin Karbasiyoun,
• Mohamed M. A. Mahmoud and
• Carola Schulzke

Beilstein J. Org. Chem. 2018, 14, 1871–1884, doi:10.3762/bjoc.14.161

• in the solid state. A preference of such anti-ht arrangement was observed before in the crystal structures of two series of 9-substituted benzo[b]quinolizinium salts with halides or small alkyl substituents [45][46]. Stratford et al. attributed this observation to repulsion forces between the

Synthesis of new tricyclic 5,6-dihydro-4H-benzo[b][1,2,4]triazolo[1,5-d][1,4]diazepine derivatives by [3⁺ + 2]-cycloaddition/rearrangement reactions

• Lin-bo Luan,
• Zi-jie Song,
• Zhi-ming Li and
• Quan-rui Wang

Beilstein J. Org. Chem. 2018, 14, 1826–1833, doi:10.3762/bjoc.14.155

• made on the basis of spectroscopic analysis. To further support our assignment, we were able to acquire X-ray crystal structures of 10k as well as of 13e, which indisputably confirm their structures [51]. For these two compounds, the ORTEP pictures are shown in Figure 2 and Figure 3, respectively

Host–guest complexes of conformationally flexible C-hexyl-2-bromoresorcinarene and aromatic N-oxides: solid-state, solution and computational studies

• Rakesh Puttreddy,
• Ngong Kodiah Beyeh,
• S. Maryamdokht Taimoory,
• Daniel Meister,
• John F. Trant and
• Kari Rissanen

Beilstein J. Org. Chem. 2018, 14, 1723–1733, doi:10.3762/bjoc.14.146

• 1H NMR spectroscopy. In the solid state, of the nine obtained X-ray crystal structures, eight were consistent with the formation of BrC6-N-oxide endo complexes. The lone exception was from the association between 4-phenylpyridine N-oxide and BrC6, in that case the host forms a self-inclusion complex

• Discussion Solid-state X-ray crystallography Nine X-ray crystal structures were obtained from BrC6 in combination with twelve PyNO guest molecules. Several attempts to obtain single crystals of BrC6 by itself, 1+BrC6, 2+BrC6 and 9+BrC6 in methanol were unsuccessful. In the following discussions, for example

• host’s hydroxy groups. To our surprise, our previous X-ray crystal structures of 3@BrC3 and 3@BrC2 complexes obtained from acetone showed interactions with the putative guests (i.e., N-oxide and acetone molecules) by encapsulation within the upper-rim and lower-rim cavity [39][40]. Therefore, in an

Synthesis of diamido-bridged bis-pillar[5]arenes and tris-pillar[5]arenes for construction of unique [1]rotaxanes and bis-[1]rotaxanes

• Ying Han,
• Li-Ming Xu,
• Cui-Yun Nie,
• Shuo Jiang,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2018, 14, 1660–1667, doi:10.3762/bjoc.14.142

• prepared pillar[5]arenes 2a–f and 3a–c were fully characterized by the spectroscopic methods. The single crystal structures of the pillar[5]arenes 2a (Figure 1), 2c, 2d, 2e (Supporting Information File 1, Figure S1–S3) and 2f (Figure 2) were successfully determined by X-ray diffraction. The same structural

A conformationally adaptive macrocycle: conformational complexity and host–guest chemistry of zorb[4]arene

• Liu-Pan Yang,
• Song-Bo Lu,
• Arto Valkonen,
• Fangfang Pan,
• Kari Rissanen and
• Wei Jiang

Beilstein J. Org. Chem. 2018, 14, 1570–1577, doi:10.3762/bjoc.14.134

• based on the information obtained from four representative crystal structures. In addition, heat capacity changes (ΔCp) and enthalpy–entropy compensation phenomena both indicate that solvent reorganization is also involved during the binding. This research further deepens our understanding on the

• 14+@ZB4-III, 16+@ZB4-III, 18+@ZB4-III, and 21+@ZB4-III suitable for X-ray single crystallography, were obtained and their crystal structures are shown in Figure 3. The substituents of these four guests located at three representative positions in Figure 2. Therefore, a closer look at their crystal

• follow a parabolic rather than a linear free energy relationship. A closer look at four representative crystal structures suggested that the parabolic free energy relationship may be caused through influencing the major interactions in the host–guest complexes by tuning the weak C–H∙∙∙O hydrogen bonds

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

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

• the host molecules. The graphic programs used to illustrate the crystal structures are Mercury 3.9 [43] and Olex2 [44]. Selected details of structure refinement along with important statistics are given in Table 1. The data can be obtained from The Cambridge Crystallographic Data Centre under the

Carbohydrate inhibitors of cholera toxin

• Vajinder Kumar and
• W. Bruce Turnbull

Beilstein J. Org. Chem. 2018, 14, 484–498, doi:10.3762/bjoc.14.34

• of the severity of cholera [13][24][27], or it could provide an independent route for cell entry through interactions with cell surface glycoproteins [28]. Structure-based design of inhibitors for cholera toxin The availability of crystal structures for cholera and E. coli heat-labile toxins has

One-pot sequential synthesis of tetrasubstituted thiophenes via sulfur ylide-like intermediates

• Jun Ki Kim,
• Hwan Jung Lim,
• Kyung Chae Jeong and
• Seong Jun Park

Beilstein J. Org. Chem. 2018, 14, 243–252, doi:10.3762/bjoc.14.16

• obtained in a low yield (25%). X-ray crystal structures of thiophenes 8ad and 8an are illustrated in Figure 3 [68]. Mechanistically, our experimental findings may be attributed to the formation of sulfur ylide-like intermediates. To support this reaction pathway, further studies were performed. By changing

• ], 4 [11][12], 5 [33][34], 6 [35][36][37][38]. Metal-free synthesis of thiophene-based heterocycles (A) [54][55], (B) [56]. X-ray crystal structures of 8ad and 8an [68]. The proposed structure of sulfur ylide-like intermediates; resonance contributors (mesomeric structures) [69][70][71][72][78]. One

Aminosugar-based immunomodulator lipid A: synthetic approaches

• Alla Zamyatina

Beilstein J. Org. Chem. 2018, 14, 25–53, doi:10.3762/bjoc.14.3

The photodecarboxylative addition of carboxylates to phthalimides as a key-step in the synthesis of biologically active 3-arylmethylene-2,3-dihydro-1H-isoindolin-1-ones

• Ommid Anamimoghadam,
• Saira Mumtaz,
• Anke Nietsch,
• Gaetano Saya,
• Cherie A. Motti,
• Jun Wang,
• Peter C. Junk,
• Ashfaq Mahmood Qureshi and
• Michael Oelgemöller

Beilstein J. Org. Chem. 2017, 13, 2833–2841, doi:10.3762/bjoc.13.275

• ]. Molecular structures of AL-12, AL-12B and AL-5. Crystal structures of photoaddition products 3a (left) and 3b (right). Crystal structure of (E)-7a. Side view and front view. Crystal structure of (Z)-8a. Side view and front view. Retrosynthetic analysis of AL-12, AL-12B and AL-5 (in their neutral forms) and

What contributes to an effective mannose recognition domain?

• Christoph P. Sager,
• Deniz Eriş,
• Martin Smieško,
• Rachel Hevey and
• Beat Ernst

Beilstein J. Org. Chem. 2017, 13, 2584–2595, doi:10.3762/bjoc.13.255

• ]. Crystal structures of mannose–lectin complexes The X-ray structures of six mannose-binding receptors in complex with either α-D-mannose (1) or methyl α-D-mannopyranoside (2) were analyzed (Figure 1 and Table 1, A–C and G–I). Since for DC-SIGNR (Figure 1, D) and DC-SIGN (Figure 1, E) neither complexes with

• 1 nor 2 were available, we instead modeled the monosaccharide–receptor interactions based on the available oligomannose crystal structures (PDB codes: 1K9J and 1SL4). In addition, because none of the available crystal structures of human MBP met our threshold of a resolution below 2 Å, we used a

• from induced-fit binding, which also correlates to facilitated ligand dissociation: due to increased water exposure, the residence time of flexible ligand–lectin complexes is shortened [51]. A comparison of the apo crystal structures of BDCA-2 (A) and LecB (G) (PDB codes: 3WBP [73] and 1OUX

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

• . Structural and computational data. Crystal structures of fluorous compounds were virtually unknown 20 years ago [51], so opportunities to acquire structural data are usually seized. Crystals of 1,3,5-(Rf6)2C6H3I could be grown as described in the experimental section. X-ray data were collected, and the

Asymmetric synthesis of propargylamines as amino acid surrogates in peptidomimetics

• Matthias Wünsch,
• David Schröder,
• Tanja Fröhr,
• Lisa Teichmann,
• Sebastian Hedwig,
• Nils Janson,
• Clara Belu,
• Jasmin Simon,
• Shari Heidemeyer,
• Philipp Holtkamp,
• Jens Rudlof,
• Lennard Klemme,
• Alessa Hinzmann,
• Beate Neumann,
• Hans-Georg Stammler and
• Norbert Sewald

Beilstein J. Org. Chem. 2017, 13, 2428–2441, doi:10.3762/bjoc.13.240

• N-sulfinylimines, which leads to amines with the same configuration as the proteinogenic (S)-configured amino acids. This stereoselection was confirmed by various X-ray crystal structures of propargylamines obtained during our investigations like 7a, 7c–e, 7s, 7i–k, 7q and triazole 13w (see

• turned brightly yellow when treated with bases like piperidine. The X-ray crystal structures of 11i and 12i confirm unequivocally the structure of the products and thus the postulated two-step rearrangement. Both, the rearrangement of the alkyne to the allene and the subsequent tautomerism to the α,β

• unexpected intramolecular low-temperature Huisgen reaction. Supporting Information Supporting Information File 484: Details about the experiments, methods and materials, the X-ray crystal structures and NMR spectra. Acknowledgements The authors gratefully acknowledge Deutsche Forschungsgemeinschaft for

Solvent-free copper-catalyzed click chemistry for the synthesis of N-heterocyclic hybrids based on quinoline and 1,2,3-triazole

• Martina Tireli,
• Silvija Maračić,
• Stipe Lukin,
• Marina Juribašić Kulcsár,
• Dijana Žilić,
• Mario Cetina,
• Ivan Halasz,
• Silvana Raić-Malić and
• Krunoslav Užarević

Beilstein J. Org. Chem. 2017, 13, 2352–2363, doi:10.3762/bjoc.13.232

• the interactions between the present halogen atoms were not observed. For more detailed description of crystal structures of 5–8 please refer to the section 7 of Supporting Information File 1 and Figures S23–S28 therein. Conclusion In conclusion, mechanochemistry was successfully applied in CuAAC

• halogen bonding observed in their crystal structures. Milling procedures using Cu(II), Cu(I) and Cu(0) catalysts proved to be significantly more efficient than the corresponding solution reactions, with up to 15-fold gain in yield. Both procedures showed the same reactivity trend, resulting in the H < Cl

• = 0.1664, wR = 0.1727, S = 1.320 for 325 parameters and 35 restraints, largest diff. peak and hole 0.426/−0.307 e Å−3. For detailed description of crystal structures for compounds 5–8 please check Supporting Information File 1, Figures S22–S28 and Tables S2–S4. General procedure for the conventional click

One-pot syntheses of blue-luminescent 4-aryl-1H-benzo[f]isoindole-1,3(2H)-diones by T3P^® activation of 3-arylpropiolic acids

• Melanie Denißen,
• Alexander Kraus,
• Guido J. Reiss and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2017, 13, 2340–2351, doi:10.3762/bjoc.13.231

• sterically more biased carbonyl group (Scheme 7). In addition to NMR spectroscopic and mass spectrometric characterization the crystal structures of the imine condensation products 5 and 6 were determined (Figure 2 and Figure 3) [50]. In similarity to 4b the twist angles of the phenyl substituents (rings A

• distance is 3.437(4) Å. Consequently, π–π interactions must be considered for this structure [51][52]. Bond lengths and angles of the reported crystal structures 4b, 5, and 6 are in the expected range. The tricyclic 1H-benzo[f]isoindole-1,3(2H)-dionyl moiety in 4b, 5 and the corresponding 3-imino-1-oxo-2,3

Synthesis and photophysical properties of novel benzophospholo[3,2-b]indole derivatives

• Mio Matsumura,
• Mizuki Yamada,
• Atsuya Muranaka,
• Misae Kanai,
• Naoki Kakusawa,
• Daisuke Hashizume,
• Masanobu Uchiyama and
• Shuji Yasuike

Beilstein J. Org. Chem. 2017, 13, 2304–2309, doi:10.3762/bjoc.13.226

• stretching vibration at 1188 cm−1 was observed. Figure 2 shows the X-ray crystal structures of the benzophospholo[3,2-b]indoles 3 and phosphine oxide 4. Selected bond lengths and angles are listed in Table 1. Figure 2 clearly shows that the tetracyclic skeletons are planar. The mean deviations are 0.022 Å

Mechanochemical synthesis of thioureas, ureas and guanidines

• Vjekoslav Štrukil

Beilstein J. Org. Chem. 2017, 13, 1828–1849, doi:10.3762/bjoc.13.178

• : corrugated chains of head-to-head or head-to-tail aligned molecules and discrete centrosymmetric dimers based on the R22(8) supramolecular synthon in the case of sterically hindered thioureas (Figure 2). The crystal structures of N,N'-diarylthioureas linked in chains via N–H···S hydrogen bonds can further be

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

• 1930, the first crystal structures of organic compounds to be investigated were carbohydrates of low molecular weight. Over the following years, only eight additional crystal structures were reported. The determination of the three dimensional structure of the dehydrated form of sucrose, in 1947, was

• few thousand entries for carbohydrate crystal structures, among which a limited number of molecules are relevant to glycobiology. With the exception of sucrose and cyclic compounds, such as cyclodextrins or cyclo-amyloses, carbohydrates are reluctant to crystallize in form and size suitable for X-ray

• molecular crystals of micrometric dimensions or in the form of polycrystalline materials. Small molecule crystals In the quest to solve the crystal structures of cello-oligosaccharides, as model compounds of cellulose, several attempts to grow crystals of β-D-cellotetraose of a size suitable for X-ray

G-Protein coupled receptors: answers from simulations

• Timothy Clark

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

• simulations often require a simulation induction period of several hundred nanoseconds to a microsecond before they undergo important conformational changes [26]. This is possibly because the starting structures are usually taken from X-ray crystal structures or homology model derived from them. As the force

Expression, purification and structural analysis of functional GABA transporter 1 using the baculovirus expression system

• Jing Hu,
• Chris Weise,
• Christoph Böttcher,
• Hua Fan and
• Jian Yin

Beilstein J. Org. Chem. 2017, 13, 874–882, doi:10.3762/bjoc.13.88

• dependence has also been elucidated by identifying crucial structural elements for chloride binding [15][16]. In addition, a similar core architecture was observed based on several crystal structures of sodium symporters from different families; this observation strongly supports an alternating access