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

• Figure 1). The conformation in the solid state is stabilised by intramolecular O–H···S hydrogen bonds (O···S distances 3.2081 (16) and 3.4179 (17) Å) and shows no central void. The formation of the [3 + 3] product is favoured by stronger bases and shorter reaction times. Therefore, in entry 8 of Table 1

• -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

Tetrathiafulvalene – a redox-switchable building block to control motion in mechanically interlocked molecules

• Hendrik V. Schröder and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2018, 14, 2163–2185, doi:10.3762/bjoc.14.190

• TTFs. However, also the type of substituent on the TTF moiety plays a role in terms of weak secondary binding interactions such as hydrogen bonds [63]. For example TTF 5 which is substituted by ethylene glycol chains displays a high association constant of Ka = 50,000 M−1 in acetonitrile. Additionally

• station by hydrogen bonds as shown by the high association constant of a structurally similar pseudorotaxane precursor (Ka = 590,000 M−1). The high association constant is a result of the weakly coordinating anion (WCA) used, i.e., tetrakis(3,5-bis(trifluoromethyl)phenyl)borate. Comparison to a

Synthesis and supramolecular self-assembly of glutamic acid-based squaramides

• Juan V. Alegre-Requena,
• Marleen Häring,
• Isaac G. Sonsona,
• Alex Abramov,
• Eugenia Marqués-López,
• Raquel P. Herrera and
• David Díaz Díaz

Beilstein J. Org. Chem. 2018, 14, 2065–2073, doi:10.3762/bjoc.14.180

• of a self-assembled network in organic solvents is likely driven by the formation of hydrogen bonds between different gelator molecules (polar head) as well as hydrophobic interactions between the long aliphatic chains. Considering our previous results obtained with diacids 1 and 2 [33], we initially

Asymmetric Michael addition reactions catalyzed by calix[4]thiourea cyclohexanediamine derivatives

• Zheng-Yi Li,
• Hong-Xiao Tong,
• Yuan Chen,
• Hong-Kui Su,
• Tangxin Xiao,
• Xiao-Qiang Sun and
• Leyong Wang

Beilstein J. Org. Chem. 2018, 14, 1901–1907, doi:10.3762/bjoc.14.164

• in forming hydrogen bonds with substrates. This may lead to activated forms of the substrates allowing the corresponding reaction to occur [9][10][11]. For example, Jacobsen and co-workers pioneered an effective chiral thiourea catalyst which was employed in an asymmetric Strecker reaction [12][13

A hemicryptophane with a triple-stranded helical structure

• Augustin Long,
• Olivier Perraud,
• Erwann Jeanneau,
• Christophe Aronica,
• Jean-Pierre Dutasta and
• Alexandre Martinez

Beilstein J. Org. Chem. 2018, 14, 1885–1889, doi:10.3762/bjoc.14.162

• helical arrangement of the linkers stabilized by intramolecular hydrogen bonds between amide and amine groups. The chirality of the cyclotriveratrylene unit controls the propeller arrangement of the three aromatic rings in the opposite part of the cage. 1H NMR studies suggest that this structure is

• parallel peptide chains coil about each other in a triple stranded left-handed helical structure. Its high thermal and mechanical stability results mainly from the numerous hydrogen bonds found in the triple helix framework [2]. Bioinspired structures, based on peptide backbones, have been built, allowing

• three imine functions is highly sable [12][13]. Hydrogen bonds between the amide group and the formed imine function could account for the high stability of this intermediate, shifting the equilibrium between the different oligomers and the cage in favor of this latter (vide infra). 1H NMR of cage 1 The

Preparation and X-ray structure of 2-iodoxybenzenesulfonic acid (IBS) – a powerful hypervalent iodine(V) oxidant

• Irina A. Mironova,
• Pavel S. Postnikov,
• Rosa Y. Yusubova,
• Akira Yoshimura,
• Thomas Wirth,
• Viktor V. Zhdankin,
• Victor N. Nemykin and
• Mekhman S. Yusubov

Beilstein J. Org. Chem. 2018, 14, 1854–1858, doi:10.3762/bjoc.14.159

• . In addition, a water molecule was observed in the crystal structure of 6, which forms two strong hydrogen bonds (≈2.05 Å for O(21)–H(2)···O(11) and ≈2.07 Å for O(21)–H(3)···O(5)) with neighbouring oxygen atoms and two short donor–acceptor interactions with K(1) and K(2) potassium ions. Overall, the

Strong binding and fluorescence sensing of bisphosphonates by guanidinium-modified calix[5]arene

• Jie Gao,
• Zhe Zheng,
• Lin Shi,
• Si-Qi Wu,
• Hongwei Sun and
• Dong-Sheng Guo

Beilstein J. Org. Chem. 2018, 14, 1840–1845, doi:10.3762/bjoc.14.157

• was tested as binding receptor. GC5A was prepared according to our previous procedure [26] and the guanidinium groups installed in the upper rim are expected to form multiple salt bridge interactions (charge-assisted hydrogen bonds) with the phosphate groups of BPs (Scheme 1c) [26][29]. To execute IDA

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

• intramolecular O···H–O hydrogen bonds (HBs) [1][2]. The combination of their confined cavity and conformational flexibility has driven the interest in these synthetic receptors [3], a subclass of calixarenes [4], for a wide range of applications in fields such as catalysis [5][6][7][8][9], sensors [10][11

• property usually preferred by resorcinarenes when solvate and guest molecules are absent inside the cavity. Note that the self-inclusion complex of BrC6 has exo methanol solvent hydrogen bonds to host hydroxy groups. This can possibly be explained by the longer lower-rim hexyl chains providing enough

Design, synthesis and structure of novel G-2 melamine-based dendrimers incorporating 4-(n-octyloxy)aniline as a peripheral unit

• Cristina Morar,
• Pedro Lameiras,
• Attila Bende,
• Gabriel Katona,
• Emese Gál and
• Mircea Darabantu

Beilstein J. Org. Chem. 2018, 14, 1704–1722, doi:10.3762/bjoc.14.145

• strong hydrogen bond acceptor solvents, such as DMSO-d6 [45], then the NH groups are exposed to the solvent rather than developing intramolecular hydrogen bonds. Conversely, a TG value less negative than −4 ppb K−1 discloses the NH group preference towards intramolecular hydrogen bonds formation, at room

The phenyl vinyl ether–methanol complex: a model system for quantum chemistry benchmarking

• Dominic Bernhard,
• Fabian Dietrich,
• Mariyam Fatima,
• Cristóbal Pérez,
• Hannes C. Gottschalk,
• Axel Wuttke,
• Ricardo A. Mata,
• Martin A. Suhm,
• Melanie Schnell and
• Markus Gerhards

Beilstein J. Org. Chem. 2018, 14, 1642–1654, doi:10.3762/bjoc.14.140

• hydrogen bonds; Introduction The balance of different noncovalent interactions is crucial for chemical and biochemical processes as it controls molecular recognition and aggregation [1][2][3][4][5][6]. In order to gain a deeper understanding of these processes, knowledge on exact structural arrangements

• the size of the attached alcohol. Torsional balances in solution have been used to probe aromatic OH∙∙∙π interactions and to show that these interactions remain important at room temperature [23]. In such aromatic solute–solvent systems, one frequently encounters hydrogen bonds formed towards oxygen

• . Observing the intermolecular contacts, which may or may not be designated as weak hydrogen bonds but are expected to stabilize the complexes, the main difference between the two structures is a phenyl vs ethenyl CH to methanol O contact (cf. dashed gray lines in Figure 1). Both are separated by only a few

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

• large amplitude conformational responses to the electronic substituents on the guests. Instead of a linear free-energy relationship, ZB4 follows a parabolic free-energy relationship. This is explained by invoking the influence of secondary C–H···O hydrogen bonds on the primary cation···π interactions

• structures may provide an explanation for their surprising binding behaviors. Multiple non-covalent interactions, including C–H···O hydrogen bonds, cation···π, C–H···π and π···π interactions, are involved in all the cases. Undoubtedly, cation···π interactions between the core quaternary ammonium ions of the

• size of the host cavity. As shown in Figure 3 (bottom), the vertical and horizontal distances between the diagonal oxygen atoms are different for all the four complexes. This distance is presumably tuned through the C–H···O hydrogen bonds between the CH2–O–CH2 oxygen atoms and the aromatic protons of

Cobalt-catalyzed C–H cyanations: Insights into the reaction mechanism and the role of London dispersion

• Eric Detmar,
• Valentin Müller,
• Daniel Zell,
• Lutz Ackermann and
• Martin Breugst

Beilstein J. Org. Chem. 2018, 14, 1537–1545, doi:10.3762/bjoc.14.130

• structures, significant interactions can be found between the Cp* ligand and the various phenyl groups of the reagents. In addition, the presence of additional stabilizing interactions such as further hydrogen bonds can also be confirmed by this analysis (e.g., in TS3, see also the Supporting Information

Recent applications of chiral calixarenes in asymmetric catalysis

• Mustafa Durmaz,
• Erkan Halay and
• Selahattin Bozkurt

Beilstein J. Org. Chem. 2018, 14, 1389–1412, doi:10.3762/bjoc.14.117

• ligands based on the same chiral scaffold. It was concluded that free hydroxy groups on the lower rim of the calixarene ligands do not have a beneficial catalytic effect due to the formation of hydrogen bonds with the incoming boronic acids. In the same study, diphosphine ligand (S,S)-29 was used in the

• hydrophilic region via hydrogen bonds between 75 and interfacial water molecules. The catalytic activity of compound 83 as an organocatalyst was evaluated in the enantioselective aldol reaction of 21 and 70 in different amounts of water. In the presence of 10 mol % catalyst, the aldol adduct was obtained in

• results, a plausible reaction mechanism similar to that previously suggested for the L-proline-catalyzed aldol reactions in water which proceeds via an enamine intermediate was proposed. As shown in Figure 10, it is proposed that hydrogen bonds between the OH and NH groups of the calix[4]arene catalyst

A three-armed cryptand with triazine and pyridine units: synthesis, structure and complexation with polycyclic aromatic compounds

• Claudia Lar,
• Adrian Woiczechowski-Pop,
• Attila Bende,
• Ioana Georgeta Grosu,
• Natalia Miklášová,
• Elena Bogdan,
• Niculina Daniela Hădade,
• Anamaria Terec and
• Ion Grosu

Beilstein J. Org. Chem. 2018, 14, 1370–1377, doi:10.3762/bjoc.14.115

• cryptand 2 they were 3.27 Å and 3.21 Å, respectively. Since the 3,5-dicyanopyridine fragment contains hydrogen-bond acceptor nitrogen atoms it might be possible to select a guest system which besides the stacking interaction could establish extra hydrogen bonds to enhance the complex stability. Accordingly

Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• range and its ability to form both intermolecular electrostatic interactions and hydrogen bonds [50]. Letsinger's aminoalkyl phosphoramidate modification was stereogenic at the phosphorus atom, thus leading to complex mixtures of diastereomeric oligomers (with the exception of the aforementioned related

An unusual thionyl chloride-promoted C−C bond formation to obtain 4,4'-bipyrazolones

• Gernot A. Eller,
• Gytė Vilkauskaitė,
• Algirdas Šačkus,
• Vytas Martynaitis,
• Ashenafi Damtew Mamuye,
• Vittorio Pace and
• Wolfgang Holzer

Beilstein J. Org. Chem. 2018, 14, 1287–1292, doi:10.3762/bjoc.14.110

• such a way that mirror enantiomers are interconnected to each other by weak intermolecular hydrogen bonds (C–H···O 2.523 Å, 130.64°, Figure 3). In the following, related 5-hydroxypyrazol-4-carboxylates 1b–i were subjected to the same reaction conditions (refluxing SOCl2) and in all cases the

• two pyrazolone units is 1.544(3) Å. For details see the Supporting Information File 1. Arrangement (4R,4'R)- and (4S,4'S)-3a enantiomers in the crystal unit drawn with 50% displacement ellipsoids. The hydrogen bonds are shown by dashed lines. Supplementary crystallographic data for compound 3a can be

Novel unit B cryptophycin analogues as payloads for targeted therapy

• Eduard Figueras,
• Adina Borbély,
• Mohamed Ismail,
• Marcel Frese and
• Norbert Sewald

Beilstein J. Org. Chem. 2018, 14, 1281–1286, doi:10.3762/bjoc.14.109

• ”, has been proposed [2][52][53]. We performed a docking study to explain the different affinities of the newly synthesized derivatives. The parent compound 2 scored highest with respect to β-tubulin binding (Table 2). Three hydrogen bonds were detected to key residues in the peptide binding pocket of

• activity whereas analogues 23 and 24 showed a reduced activity but were still very cytotoxic. Cryptophycin-1 (1) and -52 (2). Binding mode of 2, showing the interaction to the vinca domain peptide binding pocket (blue). Hydrogen bonds are shown as yellow dots with the interacting amino acid residues in

London dispersion as important factor for the stabilization of (Z)-azobenzenes in the presence of hydrogen bonding

• Andreas H. Heindl,
• Raffael C. Wende and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2018, 14, 1238–1243, doi:10.3762/bjoc.14.106

• important classes of molecular switches is crucial for the design of light-responsive materials using this entity. Herein, we present the stabilization of metastable (Z)-azobenzenes by London dispersion interactions, even in the presence of comparably stronger hydrogen bonds in various solvents. The Z→E

• isomerization rates of several N-substituted 4,4′-bis(4-aminobenzyl)azobenzenes were measured. An intramolecular stabilization was observed and explained by the interplay of intramolecular amide and carbamate hydrogen bonds as well as London dispersion interactions. Whereas in toluene, 1,4-dioxane and tert

• -butyl methyl ether the hydrogen bonds dominate, the variation in stabilization of the different substituted azobenzenes in dimethyl sulfoxide can be rationalized by London dispersion interactions. These findings were supported by conformational analysis and DFT computations and reveal low-energy London

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

• eight Hoogsteen-paired hydrogen bonds to form a tetrad (Figure 1) has further enhanced our understanding of the diversity of DNA shapes and structures. In a parallel tetramolecular quadruplex d(TG4T), the features of nucleotides at each base resemble that of the B-DNA (C2’-endo sugar pucker, anti

• MGBs is their preference for narrow A·T-rich regions compared to G·C regions because (i) they can form hydrogen bonds to N3 of adenine and O2 of thymine in the A·T region; (ii) less steric hindrance in the A·T region in comparison to the G·C region due to the presence of an extra protruding C2-amino

• synthesized in order to investigate the molecular basis of carbohydrate–minor groove DNA interactions by Vicent et al. [95]. NMR spectroscopy and molecular modeling studies further confirmed the existence of directional intramolecular hydrogen bonds and CH–π interactions, which results in stabilizing these

Correlation effects and many-body interactions in water clusters

• Andreas Heßelmann

Beilstein J. Org. Chem. 2018, 14, 979–991, doi:10.3762/bjoc.14.83

• been shown for several structures of the water tetramer that total four-body interactions are in most cases much smaller or even negligible compared to the three-body interactions [27]. The only exception to this was observed for the squared geometry in which the hydrogen bonds act cooperatively to

• by the formation of hydrogen bonds, can be well reproduced already on an uncorrelated level using the Hartree–Fock method. However, electron correlation effects to the interaction energy, including the two-body dispersion interaction, lead to a compression of the cluster sizes relative to the

Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study

• Ahmet Altun,
• Frank Neese and
• Giovanni Bistoni

Beilstein J. Org. Chem. 2018, 14, 919–929, doi:10.3762/bjoc.14.79

• . This information is used to rationalize the trend of stability of various conformers of the water and hydrogen fluoride dimers. Keywords: DLPNO-CCSD(T); hydrogen-bond interaction; interaction energy; local energy decomposition; London dispersion; Introduction Hydrogen bonds are of fundamental

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

• host A and host B) arranged co-axially so that the secondary rim (head) of the one faces the secondary rim of the other forming a head-to-head dimer via intermolecular hydrogen bonds between their O3n-H hydroxy groups. A cholesterol molecule is found fully encapsulated inside the β-CD dimeric cavity

• degree of stability to the inclusion complex. The head–head β-CD dimers formed by units interacting through hydrogen bonds between their secondary hydroxy groups is further stabilized through ion–dipole interactions with a Na+ counterion. This Na+ links the two β-CD’s together and also interacts with

An uracil-linked hydroxyflavone probe for the recognition of ATP

• Márton Bojtár,
• Péter Zoltán Janzsó-Berend,
• Dávid Mester,
• Dóra Hessz,
• Mihály Kállay,
• Miklós Kubinyi and
• István Bitter

Beilstein J. Org. Chem. 2018, 14, 747–755, doi:10.3762/bjoc.14.63

• confirmed our model of complexation [66]. Structures of the studied hydroxyflavone derivatives. Optimized geometries for (a) DEHF∙ATP, (b) UHF∙ATP with the adenine of ATP “sandwiched” between the uracil and flavone units and (c) UHF∙ATP with hydrogen bonds between the uracil and the adenine moieties

Enzyme-free genetic copying of DNA and RNA sequences

• Marilyne Sosson and
• Clemens Richert

Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47

• −1 and k'TCT = 8 310 h−1 M−1 [27]. This was encouraging. As expected, the incorporation of G was most favorable, as this base strongly pairs via three hydrogen bonds and has a large surface area for stacking. Numerically, the t1/2 values for the incorporation of G ranged from 1 min to 15 min, whereas

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17