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

Stereochemical outcomes of C–F activation reactions of benzyl fluoride

• Neil S. Keddie,
• Pier Alexandre Champagne,
• Justine Desroches,
• Jean-François Paquin and
• David O'Hagan

Beilstein J. Org. Chem. 2018, 14, 106–113, doi:10.3762/bjoc.14.6

• synthesis by capitalizing on the low reactivity of the C–F bond. Paquin et al. have published extensively on non-metal based methods for benzylic C–F bond activation [3][4][5][6][7]. The reactivity relies on protic activation driven by the capacity of organic fluoride to form hydrogen bonds [8][9

The use of 4,4,4-trifluorothreonine to stabilize extended peptide structures and mimic β-strands

• Yaochun Xu,
• Isabelle Correia,
• Tap Ha-Duong,
• Nadjib Kihal,
• Jean-Louis Soulier,
• Julia Kaffy,
• Benoît Crousse,
• Olivier Lequin and
• Sandrine Ongeri

Beilstein J. Org. Chem. 2017, 13, 2842–2853, doi:10.3762/bjoc.13.276

• temperature dependence [35][36] which can be used to get information on the presence and the stability of hydrogen bonds [37]. In aqueous and alcoholic solvents, small negative temperature coefficients (ΔδHN/ΔT > –4.5 ppb K−1) usually characterize amide protons that are engaged in intramolecular hydrogen

• not engaged in stable intra- (or inter-)molecular hydrogen bonds with carbonyl groups (Table 5). Interestingly, residue Val4 displays the smallest temperature coefficient (around –4.5 ppb K−1) in pentapeptides 4a and 4b while residue Val2 shows intermediate values of −5.5 and −5.9 ppb K−1. This i/i+2

• bonds, while more negative values (ΔδHN/ΔT < –6 ppb K−1) rather indicate that they are exposed to solvent. The analysis of the temperature coefficient of the amide bond NH protons (ΔδHN/ΔT) reveals negative values in the range of −9.0 ppb/K to −5.0 ppb/K for most protons, which indicates that they are

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

• Marco Russo,
• Daniele La Corte,
• Annalisa Pisciotta,
• Serena Riela,
• Rosa Alduina and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2751–2763, doi:10.3762/bjoc.13.271

• occurrence of a significant interaction between the cationic polyamine pendant chains and the counter-anions of the buffer, probably by either ion pairing or formation of multiple hydrogen bonds. Consequently, the mobility of the chains and, in turn, the conformational dynamics of the entire CD scaffold, are

Binding abilities of a chiral calix[4]resorcinarene: a polarimetric investigation on a complex case of study

• Marco Russo and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2698–2709, doi:10.3762/bjoc.13.268

• [32]. Trivial molecular models (Figure 4) easily show that both the nitrogen atom and the carboxylate group of the proline units can participate in this network by donating or accepting hydrogen bonds. This hypothesis is supported by analysis of FTIR spectra (Figure 5). In fact, preCA shows the

Development of a fluorogenic small substrate for dipeptidyl peptidase-4

• Futa Ogawa,
• Masanori Takeda,
• Kanae Miyanaga,
• Keita Tani,
• Ryuji Yamazawa,
• Kiyoshi Ito,
• Atsushi Tarui,
• Kazuyuki Sato and
• Masaaki Omote

Beilstein J. Org. Chem. 2017, 13, 2690–2697, doi:10.3762/bjoc.13.267

• push–pull system, which has a single benzene ring substituted by both electron-donating and electron-withdrawing groups [15][16][17]. We focused on the 3,3,3-trifluoropropenyl (TFPE) group, which is an electron-withdrawing substituent that is free of oxygen atoms, which would form hydrogen bonds in

• from THF to H2O/DMSO (9:1) as shown in Figure 2 and Table 3. The fluorescence quantum yield of a fluorophore generally decreases significantly in an aqueous solvent because of release of energy in the excited state of the fluorophore by forming hydrogen bonds with water. However, in the cases of 1 and

• 3, the decreases in the fluorescence quantum yield were small, namely 0.27 and 0.20, respectively. This is reasonable for 1 and 3 because the oxygen-free TFPE group is less likely to form hydrogen bonds, even in aqueous solution. Additionally, the emission peak of 1 is red-shifted from 436 to 461 nm

Metal-mediated base pairs in parallel-stranded DNA

• Jens Müller

Beilstein J. Org. Chem. 2017, 13, 2671–2681, doi:10.3762/bjoc.13.265

• metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by

• metal-mediated base pair, the complementary nucleobases are pairing via coordinate bonds rather than hydrogen bonds (Figure 1). Metal-mediated base pairs can be obtained from natural nucleobases such as cytosine or thymine [5]. In addition, many artificial nucleobases have been developed for an

• –Crick base pairs [35][36][37]. As can be seen in Scheme 1a, the resulting A:T base pair contains two hydrogen bonds and hence can be expected to be of similar stability as is canonical counterpart. In contrast, application of the above-mentioned formalism to a Watson–Crick G:C pair leads to a base pair

Recent progress in the racemic and enantioselective synthesis of monofluoroalkene-based dipeptide isosteres

• Myriam Drouin and
• Jean-François Paquin

Beilstein J. Org. Chem. 2017, 13, 2637–2658, doi:10.3762/bjoc.13.262

• located on the oxygen atom and the dipole moment of the amide bond is 3.6 D [7]. The amide bond can also perform hydrogen bonds, with the oxygen atom as the hydrogen bond acceptor and N–H as hydrogen bond donor. This characteristic is important for the formation of secondary structures and folding into