Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

• Marius H. Heddinga and
• Jens Müller

Beilstein J. Org. Chem. 2020, 16, 2870–2879, doi:10.3762/bjoc.16.236

• to release a DNA-bound cargo (in the form of small organic molecules) [10]. Similarly, metal ions can trigger DNA folding into a catalytically active topology [11][12]. Metal-mediated base pairs are artificial base pairs in which hydrogen bonds between the complementary nucleobases are formally

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• electrostatic and (C–H)···O− hydrogen bonds involving the acidic proton at the 2-position of the imidazolium moiety to bind to ATP and other phosphate analytes [46]. A number of cyclophanes and tweezers [53][54][55][56] have been reported possessing the following common structural features: a) the presence of

Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

• Henrik Hupatz,
• Marius Gaedke,
• Hendrik V. Schröder,
• Julia Beerhues,
• Arto Valkonen,
• Fabian Klautzsch,
• Sebastian Müller,
• Felix Witte,
• Kari Rissanen,
• Biprajit Sarkar and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2020, 16, 2576–2588, doi:10.3762/bjoc.16.209

• -8 (DBC8, Figure 1), which bind through noncovalent interactions. In detail, these interactions are strong hydrogen bonds between ether oxygen atoms and ammonium protons. In addition, weaker C–H···O hydrogen bonds with the CH2 groups adjacent to the ammonium nitrogen as well as π–π-interactions

• the experiment. The folded structure observed in the crystal structure hints towards a possible “side-on” complex, where the ammonium axle is not threading through the ring of the macrocycle, yet still forms hydrogen bonds to the crown ether [24][25] (see spectroelectrochemical measurements below

• strength of the hydrogen bonds in the neutral complex and Coulomb repulsion in the oxidized complex [35]. This effect is less pronounced for the complex A2·PF6@exTTFC7 because the TTF unit is more distant to the ammonium unit [37]. The macrocycle bisTTFC8, bearing two TTF units, shows a broadening of the

Water-soluble host–guest complexes between fullerenes and a sugar-functionalized tribenzotriquinacene assembling to microspheres

• Si-Yuan Liu,
• Xin-Rui Wang,
• Man-Ping Li,
• Wen-Rong Xu and
• Dietmar Kuck

Beilstein J. Org. Chem. 2020, 16, 2551–2561, doi:10.3762/bjoc.16.207

• 1505.9611 (Δ = + 5.2 ppm). The surprising presence of six equivalents of water points to the formation of strong hydrogen bonds between the sugar ester bonds of TBTQ-(OAcG)6 and the water molecules as guests. However, the origin of this intriguing observation associated with the attachment of just two

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• analysis to consider how the sugar moiety could interact with the antibody (Tables S1–S7 in Supporting Information File 1). In solution, hydrogen bonds occur within the antigen between Arg5–Asp3 and Arg5–Pro8 (in order donor–acceptor) with occupancies of 31.83% and 14.32% (and 13.67%). For the Tn-antigen

• , the peptide portion has hydrogen bonds between Arg5–Pro8 (26.69% and 26.58%), Arg5–Asp3 (12.45%), an Arg5–Pro2 interaction is observed with an occupancy of 7.13%, and an intramolecular hydrogen bond between the C3 alcohol and the carbonyl of the N-acetyl moiety of the GalNAc has an occupancy of 6.92

• %. A shift in hydrogen-bonding populations on glycosylation and the appearance of the Arg5–Pro2 (7.13%) interaction aligns with the compact structure noted previously for the Tn-antigen. When bound, additional intramolecular hydrogen bonds are observed for the Tn-antigen with interactions between the

Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties

• Anka Utama Putra,
• Deniz Çakmaz,
• Nurgül Seferoğlu,
• Alberto Barsella and
• Zeynel Seferoğlu

Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189

• planar to the dicyanomethylene group. A twist was observed between the dicyanomethylene and aminophenyl groups (salicylidenyl moiety for 8–12) with an angle of about 50°. In addition, the dyes 8–12 exhibited strong intramolecular O–H···N hydrogen bonds with lengths in the range of 2.63–2.64 Å (Figure 1

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• energetically favourable non-covalent interactions, hydrogen bonds, and van der Waals interactions formed between the DNA/RNA and solvent, and between the compound 4 and solvent. The large positive entropy changes suggest solvent release upon binding, which makes a favourable contribution to the reaction Gibbs

Design, synthesis and application of carbazole macrocycles in anion sensors

• Alo Rüütel,
• Ville Yrjänä,
• Sandip A. Kadam,
• Indrek Saar,
• Mihkel Ilisson,
• Astrid Darnell,
• Kristjan Haav,
• Tõiv Haljasorg,
• Lauri Toom,
• Johan Bobacka and
• Ivo Leito

Beilstein J. Org. Chem. 2020, 16, 1901–1914, doi:10.3762/bjoc.16.157

• carboxylates were modelled computationally using COSMO-RS. Several observations were made from the computational structures. Intramolecular hydrogen bonds between the urea carbonyl and the carbazole NH protons were present in macrocycles MC001 and MC003, as indicated in Figure 4. The rings of these macrocycles

• studied anions. Additionally, for MC003, intramolecular hydrogen bonds could be present. For most anions, the champion molecules were MC007 and MC009. According to the computation results, neither benzoate nor pivalate were able to fit into the ring of these receptors because these anions were too large

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• –GlfT2 interactions are depicted as dashed lines (yellow – hydrogen bonds, magenta – salt bridge, green – cation/π interaction). The Mg2+ ion is shown as a purple sphere. TLC analysis of the effects of the target compounds at 500 μM on the production of lower lipid-linked galactan precursors. CON

Models of necessity

• Timothy Clark and
• Martin G. Hicks

Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137

• interaction between halogens and nucleophiles as repulsive; whereas we now know that halogen-bonding attractions can be as strong as hydrogen bonds. There will be more such examples but it is important to identify the encompassing phenomenon, rather than defining a wealth of apparently unique interactions

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

• , indicating the presence of strong hydrogen bonds also in solution. These data suggest that the structures of the predominating conformers should be similar in the solid and liquid phases. Furthermore, we have managed to detect NOE steric proximities between the aldehyde H atom and the H-C(7) (in compounds 3b

Five-component, one-pot synthesis of an electroactive rotaxane comprising a bisferrocene macrocycle

• Natalie Lagesse,
• Luca Pisciottani,
• Maxime Douarre,
• Pascale Godard,
• Brice Kauffmann,
• Vicente Martí-Centelles and
• Nathan D. McClenaghan

Beilstein J. Org. Chem. 2020, 16, 1564–1571, doi:10.3762/bjoc.16.128

• ). The isolated material had low solubility, which is likely due to self-aggregation via complementary amide hydrogen bonds. This prompted us to use a thread with bulky stopper groups to prepare the corresponding rotaxane compounds, which would increase the solubility by the formation of intramolecular

• macrocycle-thread hydrogen bonds, thereby reducing self-aggregation. To this end, a five-component clipping strategy was adopted using different tetrabutylsuccinamide threads (Figure 2) with varying hydrogen-bond basicity (amides > esters) [4][15]. Threads containing an ester group were selected as esters

• macrocycle–thread hydrogen bonds, with the other two macrocycle amides forming hydrogen bonds with the competitive crystallization solvent DMF. In contrast, rotaxane 1a presented four thread–macrocycle hydrogen bonds (Figure 7 and Table 1). The strength of the hydrogen bonds could be estimated by the donor

Synthesis, antiinflammatory activity, and molecular docking studies of bisphosphonic esters as potential MMP-8 and MMP-9 inhibitors

• Abimelek Cortes-Pacheco,
• María Adelina Jiménez-Arellanes,
• Francisco José Palacios-Can,
• José Antonio Valcarcel-Gamiño,
• Rodrigo Said Razo-Hernández,
• María del Carmen Juárez-Vázquez,
• Adolfo López-Torres and
• Oscar Abelardo Ramírez-Marroquín

Beilstein J. Org. Chem. 2020, 16, 1277–1287, doi:10.3762/bjoc.16.108

• kcal/mol; the observed energy values are shown in Table 7. Compound 3 displayed two hydrogen bonds. The first one was formed between a hydrogen atom of His162 with an oxygen atom from the ester moiety (the oxygen atom bound to the ethyl group of the phosphonate unit), with a calculated distance (O–H

• distance and an energy of −2.5 kcal/mol (Figure 4c). Compound 6 showed four hydrogen bonds that varied in force. Two were observed between an oxygen atom from an OEt moiety of a phosphonate group to amide hydrogen atoms localized between Ile159, Leu160, and Ala161 (Figure 4d). These interactions had energy

• values of −1.94 and −2.5 kcal/mol, which is regarded as characteristic for strong hydrogen bonds. The measured O–N distances had values of 3.15 and 2.67 Å. Another hydrogen-bond interaction was seen from an OEt moiety (from the phosphonate group coordinating the zinc ion), with a weak energy of −0.95

The charge-assisted hydrogen-bonded organic framework (CAHOF) self-assembled from the conjugated acid of tetrakis(4-aminophenyl)methane and 2,6-naphthalenedisulfonate as a new class of recyclable Brønsted acid catalysts

• Svetlana A. Kuznetsova,
• Alexander S. Gak,
• Yulia V. Nelyubina,
• Vladimir A. Larionov,
• Han Li,
• Michael North,
• Vladimir P. Zhereb,
• Alexander F. Smol'yakov,
• Artem O. Dmitrienko,
• Michael G. Medvedev,
• Igor S. Gerasimov,
• Ashot S. Saghyan and
• Yuri N. Belokon

Beilstein J. Org. Chem. 2020, 16, 1124–1134, doi:10.3762/bjoc.16.99

• , elemental analysis, and 1H NMR spectroscopy. The framework was supported by hydrogen bonds between the sulfonate anions and the ammonium cations of NDS and protonated TAPM moieties, respectively. The CAHOF material functioned as a new type of catalytically active Brønsted acid in a series of reactions

• developed [25][26][27][28][29][30][31][32][33][34][35][36]. Usually, a HOF is built from multitopic tectons that interact with their neighbors by directional hydrogen bonds, disfavoring close packing, and thus generating significant pore volumes within the crystal [25][26][27][28]. These heterogeneous

• parameters a = 20.6034(8) Å, b = 20.1330(8) Å, c = 22.4357(8) Å, β = 91.989(1)°, and cell volume = 9300.9(6) Å3 at 120 K. An asymmetric part of the unit cell contained two ammonium cations, four sulfonate anions, and nine water molecules, held together by numerous hydrogen bonds (Table S2, Supporting

Efficient synthesis of piperazinyl amides of 18β-glycyrrhetinic acid

• Dong Cai,
• ZhiHua Zhang,
• Yufan Meng,
• KaiLi Zhu,
• LiYi Chen,
• ChangXiang Yu,
• ChangWei Yu,
• ZiYi Fu,
• DianShen Yang and
• YiXia Gong

Beilstein J. Org. Chem. 2020, 16, 798–808, doi:10.3762/bjoc.16.73

• agent [12]. Piperazinyl amide fragments have the ability to form several hydrogen bonds, modulate the acid–base equilibrium constant and change the octanol–water partition coefficient [13]. They are considered as the basic motif for designing many biologically active molecules [14][15]. Some piperazinyl

Synthesis of C₇₀-fragment buckybowls bearing alkoxy substituents

• Yumi Yakiyama,
• Shota Hishikawa and
• Hidehiro Sakurai

Beilstein J. Org. Chem. 2020, 16, 681–690, doi:10.3762/bjoc.16.66

• possessed the same stacking direction (along the a axis) by CH∙∙∙π interactions (C16∙∙∙C23, C16∙∙∙C19, C29∙∙∙C3, C29∙∙∙C15), while connected to the columns with opposite stacking direction via CH∙∙∙O type weak hydrogen bonds (C13∙∙∙O1) along the c axis (Figure 2c). 5b also gave the mixture of the two

• stabilized by CH∙∙∙π interactions (C6∙∙∙C6: 3.77 Å, C9∙∙∙C9: 3.77 Å, C16∙∙∙C17: 3.51 Å) (Figure 4b). These columns were further connected to the neighboring columns by CH∙∙∙O type hydrogen bonds (C9∙∙∙O1: 3.32 Å) along the b axis and CH∙∙∙π interactions (C17∙∙∙C5: 3.60 Å) along the c axis (Figure 4c). In the

• hydrogen bonds (C37∙∙∙O1, C11∙∙∙O2, C40∙∙∙O4) (Figure 5c). Photophysical properties of the dialkoxides were investigated by UV–vis and emission spectroscopies (Figure 6). UV–vis spectra of 5a and 5b well reflected the electric property of 1, showing two strong bands observed at around 280–300 nm and 330

Architecture and synthesis of P,N-heterocyclic phosphine ligands

• Wisdom A. Munzeiwa,
• Bernard Omondi and
• Vincent O. Nyamori

Beilstein J. Org. Chem. 2020, 16, 362–383, doi:10.3762/bjoc.16.35

• applicability of the catalysts in two-phase homogeneous catalysis because it allows easy recycling [85] and separation from the reaction mixture [8]. Carbon–halogen bonds are more activated than carbon–hydrogen bonds and hence the halogen is more labile and preferentially displaced. Brill et al. [86] took

• attributed this to a stabilization of the NH proton by hydrogen bonds to the triazole nitrogen and methoxy oxygen atoms. The initial step in the synthesis of 120 is the enantioselective synthesis of the propargylamine 118 through the reaction of propargyl acetate 117 with the corresponding amine. This

Ultrasonic-assisted unusual four-component synthesis of 7-azolylamino-4,5,6,7-tetrahydroazolo[1,5-a]pyrimidines

• Yana I. Sakhno,
• Maryna V. Murlykina,
• Oleksandr I. Zbruyev,
• Anton V. Kozyryev,
• Svetlana V. Shishkina,
• Dmytro Sysoiev,
• Vladimir I. Musatov,
• Sergey M. Desenko and
• Valentyn A. Chebanov

Beilstein J. Org. Chem. 2020, 16, 281–289, doi:10.3762/bjoc.16.27

• , molecules 4g formed centrosymmetric dimers due to the N1–H···N4 intermolecular hydrogen bonds (1 x, 1 y, 2 z; H···N 2.22 Å, N–H···N 164°). The dimers were bound by a N6–H···O1 intermolecular hydrogen bond (x 1, y, z; H···O 2.16 Å, N–H···O 162°), forming chains along the [100] crystallographic direction

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

• of biologically active compounds as it imparts a variety of properties such as enhanced binding interaction, metabolic stability, and reaction selectivity by changing physical and chemical properties [23][24][25][26]. Hydrogen bonds (HBs) are associated with highly electronegative atoms (oxygen

• activity of a molecule. Oxygen and nitrogen have been proven to be good hydrogen-bond acceptors which form strong intermolecular and intramolecular hydrogen bonds, however, fluorine is still denied hydrogen-bond acceptor status by some scientists. There is evidence of the existence of C–F···H interaction

• aromatic triazole foldmers [37]. In their study, using crystallographic and DFT data, they concluded that their folded conformers are held by C–F···H–C hydrogen bonds. To further these studies, we have synthesized a fluorine-containing phenylcoumarin in order to study the fluorine-hydrogen bond. The

The use of isoxazoline and isoxazole scaffolding in the design of novel thiourea and amide liquid-crystalline compounds

• Itamar L. Gonçalves,
• Rafaela R. da Rosa,
• Vera L. Eifler-Lima and
• Aloir A. Merlo

Beilstein J. Org. Chem. 2020, 16, 175–184, doi:10.3762/bjoc.16.20

• the thiourea moiety, there is only one recent report, in which some derivatives of N-benzoyl-N’-arylthiourea with liquid crystalline properties have been investigated [14]. One aspect that compounds forming hydrogen bonds, such as ureas, thioureas, amides etc. for the use in electronic devices is the

• ability to establish intra- and intermolecular hydrogen bonds [11]. In addition to π–π, dipole–dipole and van der Waals interactions, hydrogen bond interactions are involved in gel formation through self-aggregation of the small gelator molecules. In recent years, there has been increased interest in the

• containing isoxazoline rings 17a–c and isoxazoles 18a–c, as well as LCs amides 19–22 and 24. All compounds listed in Table 1 are capable of self-organization by hydrogen bonds, either in their solid state or in solution. Solubility in protic or aprotic polar solvent is restricted at room temperature. However

The interaction between cucurbit[8]uril and baicalein and the effect on baicalein properties

• Xiaodong Zhang,
• Jun Xie,
• Zhiling Xu,
• Zhu Tao and
• Qianjun Zhang

Beilstein J. Org. Chem. 2020, 16, 71–77, doi:10.3762/bjoc.16.9

• [8] fare forming hydrogen bonds, the cycle B and and a part of cycle C of baicalin inserted into the cavity of the Q[8]. This may be attributed to chrysin containing one hydroxy group less than baicalein, which reduced the hydrophilicity of cycle A, making it enter into the hydrophobic cavity of Q[8

Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides

• Sabrina Müller,
• Jannik Paulus,
• Jochen Mattay,
• Heiko Ihmels,
• Veronica I. Dodero and
• Norbert Sewald

Beilstein J. Org. Chem. 2020, 16, 60–70, doi:10.3762/bjoc.16.8

• acted as a building block inducing a reverse turn, which favored hydrogen bonds between the pyrrole/imidazole amide and the DNA bases. In contrast, the E-configured polyamides did not induce any ICD characteristic for minor groove binding. The incorporation of the photoswitchable azobenzene unit is a

• DNA double strand is stabilized by additional hydrogen bonds between ligand and oligonucleotide, and hence the melting temperature is expected to increase. This effect is of particular interest when considering the sequence selectivity of the polyamides, which should therefore also be reflected in a

• of the DNA duplex in the presence of the corresponding PA. In general, the more energy needed to break the hydrogen bonds between the single strands of the duplex and the stacking interactions of the bases, the higher the melting temperature. Hence, it also increases with higher GC content. The

Influence of the cis/trans configuration on the supramolecular aggregation of aryltriazoles

• Sara Tejera,
• Giada Caniglia,
• Rosa L. Dorta,
• Andrea Favero,
• Javier González-Platas and
• Jesús T. Vázquez

Beilstein J. Org. Chem. 2019, 15, 2881–2888, doi:10.3762/bjoc.15.282

• hydroxymethyl group in position 6 in the gg rotamer, likely linked through hydrogen bonds. Electronic circular dichroism (ECD) is a powerful technique to study supramolecular systems [20][21], since many interactions responsible for the presence of CD Cotton effects occur through space, such as the well-known

• . In addition, compound 10 (cis), with free hydroxy groups, formed hydrogen bonds between the hydroxymethyl groups in position 6 and DMSO molecules while in a gg rotamer conformation. The different types of EDC spectra obtained for compound 10 in solution (exciton) and in gel (non-exciton), using DMSO

Preparation of anthracene-based tetraperimidine hexafluorophosphate and selective recognition of chromium(III) ions

• Qing-Xiang Liu,
• Feng Yang,
• Zhi-Xiang Zhao,
• Shao-Cong Yu and
• Yue Ding

Beilstein J. Org. Chem. 2019, 15, 2847–2855, doi:10.3762/bjoc.15.278

• hydrogen bonds, namely C(3)–H(3A)···F(2) and C(17)–H(17A)···F(2) interactions (Supporting Information File 1, Figure S1b). Chemosensing of cations by 3 Compound 3 was employed as a host to study its ability to detect some cations through fluorescence and UV titrations in CH3CN/DMSO, 9:1, v/v at room

Palladium-catalyzed synthesis and nucleotide pyrophosphatase inhibition of benzo[4,5]furo[3,2-b]indoles

• Hoang Huy Do,
• Saif Ullah,
• Alexander Villinger,
• Joanna Lecka,
• Jean Sévigny,
• Peter Ehlers,
• Jamshed Iqbal and
• Peter Langer

Beilstein J. Org. Chem. 2019, 15, 2830–2839, doi:10.3762/bjoc.15.276

• methoxy group, located on the phenyl ring of compound 5e, were engaged in carbon–hydrogen bonds with Asp225 and Glu400, as depicted in Figure 5b. However, phenyl rings of both indole and benzofuran scaffolds were inclined towards Leu239 and His329, respectively. When compound 5h was taken into account, it