Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• modification is accommodated in an A'-form duplex [75]. Interestingly, an unconventional C–H···O hydrogen bond was observed between the amide’s carbonyl oxygen and the nearby uracil C6–H6. The thermal stability of this modified duplex was, however, quite similar to native RNA. Typically, there is a decrease of

• suggested the addition of a polarizable group in the longer 2'-O-alkyl chains that could hydrogen bond with nucleobases in the minor groove of the duplex would be well tolerated [114]. This supported the hypothesis that the 2'-O-[2-(methoxy)ethyl] (MOE) modification (Figure 5B) wouldn’t lead to significant

Synthetic reactions driven by electron-donor–acceptor (EDA) complexes

• Zhonglie Yang,
• Yutong Liu,
• Kun Cao,
• Xiaobin Zhang,
• Hezhong Jiang and
• Jiahong Li

Beilstein J. Org. Chem. 2021, 17, 771–799, doi:10.3762/bjoc.17.67

• spectroscopy shows that phosphono radicals could proceed throughout the reaction. A halogen bond (XB) is a noncovalent interaction formed between a halogen atom and a neutral or negatively charged Lewis base. It is a kind of weak intermolecular interaction analogous to a hydrogen bond and basically can be

Amino- and polyaminophthalazin-1(2H)-ones: synthesis, coordination properties, and biological activity

• Zbigniew Malinowski,
• Emilia Fornal,
• Agata Sumara,
• Renata Kontek,
• Karol Bukowski,
• Beata Pasternak,
• Dariusz Sroczyński,
• Joachim Kusz,
• Magdalena Małecka and
• Monika Nowak

Beilstein J. Org. Chem. 2021, 17, 558–568, doi:10.3762/bjoc.17.50

• angles equal to 27.61 and 28.71°, respectively, and moreover, the methyl groups of the methoxy substituents are directed opposite and towards to the pyridin-2-yl substituents, respectively. The crystal structure of complex 17 is stabilized with a 3D intermolecular hydrogen bond network (Figure S1a

Synthesis of (Z)-3-[amino(phenyl)methylidene]-1,3-dihydro-2H-indol-2-ones using an Eschenmoser coupling reaction

• Lukáš Marek,
• Lukáš Kolman,
• Jiří Váňa,
• Jan Svoboda and
• Jiří Hanusek

Beilstein J. Org. Chem. 2021, 17, 527–539, doi:10.3762/bjoc.17.47

• rapidly equilibrating (Z)/(E)-isomers [2], the derivatives containing a secondary nitrogen slightly prefer [2][9][48] the (Z)-configuration due to an intramolecular hydrogen bond. A substitution of hydrogen at the methylidene carbon by an aryl group and a secondary nitrogen, enabling an intramolecular

• hydrogen bond, results in the geometry of a double bond that is locked in a (Z)-configuration [12]. The same (Z)-configuration was observed by us for the primary 3-[amino(aryl)methylidene]oxindoles [33]. The usual method used for the configuration assignment of 3-amino(aryl)methylidene derivatives involves

• solid state by X-ray diffraction. The important role of the intramolecular hydrogen bond fixing the (Z)-configuration has also been observed in the crystal structures of other 3-aminomethylidene derivatives containing a primary or secondary nitrogen [14][49][50][51][52]. The (Z)-configuration of the

1,2,3-Triazoles as leaving groups: S_NAr reactions of 2,6-bistriazolylpurines with O- and C-nucleophiles

• Dace Cīrule,
• Irina Novosjolova,
• Ērika Bizdēna and
• Māris Turks

Beilstein J. Org. Chem. 2021, 17, 410–419, doi:10.3762/bjoc.17.37

• hydrogen bond. This is supported by a smaller deviation of the C(2’’) chemical shift value (61.7 ppm) in comparison to the theoretical shifts for a Csp2 centre. Similar structural analogues are known in the literature [54][83][84][85] but their structural analysis was incomplete. As the aforementioned

Mesoionic tetrazolium-5-aminides: Synthesis, molecular and crystal structures, UV–vis spectra, and DFT calculations

• Vladislav A. Budevich,
• Sergei V. Voitekhovich,
• Alexander V. Zuraev,
• Vadim E. Matulis,
• Vitaly E. Matulis,
• Alexander S. Lyakhov,
• Ludmila S. Ivashkevich and
• Oleg A. Ivashkevich

Beilstein J. Org. Chem. 2021, 17, 385–395, doi:10.3762/bjoc.17.34

• of a hydrogen bond between the exocyclic N5 atom and the solvent is taken into account (model structure in Figure 4b). For the methanol and water solutions, the agreement between the calculated and experimental spectra is observed only when the protonation of the N5 atom is taken into account (model

The preparation and properties of 1,1-difluorocyclopropane derivatives

• Kymbat S. Adekenova,
• Peter B. Wyatt and
• Sergazy M. Adekenov

Beilstein J. Org. Chem. 2021, 17, 245–272, doi:10.3762/bjoc.17.25

Insight into functionalized-macrocycles-guided supramolecular photocatalysis

• Minzan Zuo,
• Krishnasamy Velmurugan,
• Kaiya Wang,
• Xueqi Tian and
• Xiao-Yu Hu

Beilstein J. Org. Chem. 2021, 17, 139–155, doi:10.3762/bjoc.17.15

• resemblance of the pumpkin of the Cucurbitaceae family. The oxygen atoms are located along the edges of the band, which can identify positively charged guests through ion–dipole and hydrogen bond interactions. The internal cavity exhibits a strong hydrophobicity. Depending on the size and shape of the guest

Supramolecular polymers with reversed viscosity/temperature profile for application in motor oils

• Jan-Erik Ostwaldt,
• Christoph Hirschhäuser,
• Stefan K. Maier,
• Carsten Schmuck and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2021, 17, 105–114, doi:10.3762/bjoc.17.11

• -complementary [14] binding units (BU, blue) and a connecting linker unit (LU, green) to connect the BUs. In this case, the BUs are ureidopyrimidone units, which dimerize due to a fourfold hydrogen bond, thus allowing for strong supramolecular interactions [15]. Due to the flexibility of the LUs, the BUs can

Circularly polarized luminescent systems fabricated by Tröger's base derivatives through two different strategies

• Cheng Qian,
• Yuan Chen,
• Qian Zhao,
• Ming Cheng,
• Chen Lin,
• Juli Jiang and
• Leyong Wang

Beilstein J. Org. Chem. 2021, 17, 52–57, doi:10.3762/bjoc.17.6

• DGG. In the CPL-active co-gels, noncovalent weak interactions might be formed between achiral fluorophores and a chiral gelator. So, the CPL emission of co-gels could be adjusted easily by external stimuli. The ᴅ-glutamic acid gelator DGG and its enantiomer LGG possess three hydrogen-bond sites, two

• carboxylic acid groups and one amide, which could be assemblied into the stable spiral structure by hydrogen-bond and other noncovlant interactions. DGG was synthesised by introducing an octadecyl moiety into the glutamic skeleton in 78.6% yield according to the reported route (Supporting Information File 1

Chiral anion recognition using calix[4]arene-based ureido receptors in a 1,3-alternate conformation

• Tereza Horáčková,
• Jan Budka,
• Vaclav Eigner,
• Wen-Sheng Chung,
• Petra Cuřínová and
• Pavel Lhoták

Beilstein J. Org. Chem. 2020, 16, 2999–3007, doi:10.3762/bjoc.16.249

• chain of calixarene molecules joined together by intermolecular hydrogen bonds between the ureido groups (the C=O···H–N distances were 2.293 and 2.048 Å). One of the ureido functions in the macrocycle also held acetone via a C=O···H–N hydrogen bond (2.085 Å) and via a C=O···H–C bond (2.670 Å) from the

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

• weaker hydrogen-bond-acceptor ability of the sulfur atoms incorporated in the TTFC8 crown ether ring [34][54]. NDIC8 also exhibits a comparably low binding energy, likely due to the increased ring size and the consequently weakened hydrogen-bonding pattern (Table 1, entry 11) [44]. However, NDIC8 and

• strong electrostatic interactions to ammonium ions and act as strong, competitive hydrogen-bond acceptors [57]. The high anodic shifts indicate strong attractive interactions between the wheels and axles, which compete with the coordination of the crown ether moiety. Thus, the secondary ammonium axles

• form presumably a non-threaded complex with the reduced NDI crown ethers, where the charged ions are in closer proximity than in the pseudo[2]rotaxane. This assumption was further confirmed by the addition of the hydrogen bond donor (CH3)2NH2PF6 to a solution of the wheel NDIC8, which again leads to

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

• , 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

• %), Tyr37–Pro2 (46.73%), Arg55–Asp3 (37.77%), and Tyr54–Asp3 (31.44%). A hydrogen bond (0.15%) was observed between the hydroxy group of Tyr100 of chain B of the antibody and the 6-hydroxy group of the GalNAc. While seemingly short-lived, it occurs with some frequency throughout the simulation (see Figure

• dispersion interactions would be insufficient to explain a 20-fold increase in affinity. It is unlikely that this hydrogen bond explains a 20-fold increase in affinity yet note that the mobility of the glycan moiety allows the hydrogen-bond interaction to occur. The hydrogen-bonding preferences and

Conformational preferences of fluorine-containing agrochemicals and their implications for lipophilicity prediction

• Daniela Rodrigues Silva,
• Joyce K. Daré and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2020, 16, 2469–2476, doi:10.3762/bjoc.16.200

• Juaristi and Notario [9], and O’Hagan and co-workers [10]. Besides, there is also an interaction between the fluorine electron lone pair nF and the σ*NH orbital of the amine group (of 3.2 kcal mol−1, see Table 1). Iga also experiences this stabilizing hydrogen bond-like intramolecular interaction (nF → σNH

Selective preparation of tetrasubstituted fluoroalkenes by fluorine-directed oxetane ring-opening reactions

• Clément Q. Fontenelle,
• Thibault Thierry,
• Romain Laporte,
• Emmanuel Pfund and
• Thierry Lequeux

Beilstein J. Org. Chem. 2020, 16, 1936–1946, doi:10.3762/bjoc.16.160

• hydrogen-bond accepting capacity with proteins or enzymes would be restored [14]. The synthesis of fluoroalkene precursors of modified acyclonucleosides (VIII) has been explored by Choi, and more recently by us [15][16][17]. Nevertheless, it was reported that no antiviral activity for compounds of series

Regiodivergent synthesis of functionalized pyrimidines and imidazoles through phenacyl azides in deep eutectic solvents

• Paola Vitale,
• Luciana Cicco,
• Ilaria Cellamare,
• Filippo M. Perna,
• Antonio Salomone and
• Vito Capriati

Beilstein J. Org. Chem. 2020, 16, 1915–1923, doi:10.3762/bjoc.16.158

• stability, non-flammability, and low volatility. These are mixtures usually obtained from the combination of 2 or 3 safe, inexpensive and nature-inspired components able to engage in reciprocal hydrogen-bond interactions, and that form fluids at a specified mixing ratio at the desired temperature. Owing to

• by dehydration. The two tautomers 3/3' would most probably originate by two competitive pathways (a and b; Scheme 4) via a [1,5]-hydrogen shift [28][29]. Hydrogen-bond catalysis promoted by DES components may be playing an important role in favoring the loss of nitrogen under mild conditions from a

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

• moiety fulfils several key design requirements. At least four hydrogen bonding sites (N–H groups) are available and positioned in a favourable geometry for carboxylates. Additional hydrogen-bond-donor (HBD) groups can be added with substituents. The solubility of such receptors can be tuned using

• out of the macrocycle plane. It was expected that these macrocycles will have lower affinity constants. MC002 was of sufficient size to accommodate smaller carboxylate ions. However, in the most stable computed structures the hydrogen-bond donor NH fragments directed towards the outside of the ring

• , starting with formate. MC008 was able to fit acetate and lactate. Thus, an additional binding site was available for lactate. In the complexes of lactate with MC006–MC009, a hydrogen bond was present between the oxygen of the hydroxy group of lactate and the NH group of the macrocyclic amide. See Figure 5

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

• C5 hydroxy group very often interacts with the catalytic base aspartate D372 side chain. Moreover, in the poses where this interaction has been found, the C5 hydroxy group creates a hydrogen bond with the ammonium group of the lysine K369 residue. In many docking poses the interaction of the C3

• share the common binding interactions described above. However, the 1bα binding mode slightly differed from the modes of the other compounds. In this case the PO4 and hydroxy group on C5 interacted with a metal ion and the hydroxy groups on C2 and C3 created the hydrogen bond with the tyrosine Y236

Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines

• Vladimir Kubyshkin

Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151

• polarity drops down. The second scenario would occur if there was an N–H…O=C hydrogen bond in the structure. Thus, the presence of proline would leave an unsolvated carbonyl group, and its appearance leads to a polarity rise. Finally, a proline residue usually prefers extended secondary fold and may

One-pot synthesis of isosorbide from cellulose or lignocellulosic biomass: a challenge?

• Isaline Bonnin,
• Raphaël Mereau,
• Thierry Tassaing and
• Karine De Oliveira Vigier

Beilstein J. Org. Chem. 2020, 16, 1713–1721, doi:10.3762/bjoc.16.143

• ; isosorbide; lignocellulosic biomass; Introduction Cellulose, a homopolymer of ᴅ-glucose, is the most abundant component of lignocellulosic biomass. Cellulose is a crystalline polymer due to its intra- and intermolecular hydrogen bond network. The conversion of cellulose to added value chemicals has received

Pauson–Khand reaction of fluorinated compounds

• Jorge Escorihuela,
• Daniel M. Sedgwick,
• Alberto Llobat,
• Mercedes Medio-Simón,
• Pablo Barrio and
• Santos Fustero

Beilstein J. Org. Chem. 2020, 16, 1662–1682, doi:10.3762/bjoc.16.138

• , preferred conformation or hydrogen bond forming ability, among others, may result in a dramatic effect in the therapeutic potential of a drug candidate [5][6]. All these properties may be fine-tuned by the selective incorporation of fluorine into the structure of the molecule [7]. In addition to therapeutic

Models of necessity

• Timothy Clark and
• Martin G. Hicks

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

• parsimonious as possible but at the same time generally applicable [99]. The alternative patchwork of competing bonding models based on non-separable and non-unique interactions cannot provide a stable framework for AI and ML. In this respect, the IUPAC definition of the hydrogen bond [104] serves as an

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

• ). According to the single-crystal X-ray experiments of compounds 3b, 8b, and 23a, the solid-phase structures are stabilized by a hydrogen bond between the amide NH and the carbonyl oxygen atom of the other amide group. The H–C–C–H dihedral angles between the two asymmetric centers are not far from 90° as

• in 23b indicates a weaker hydrogen bond, compared to the value of 9.39 ppm obtained for 23a [27]. The detected 3J(H,H) coupling constant for the hydrogens attached to the two asymmetric centers is 10 Hz in this case, indicating a dihedral angle of ca. 180° in 23b. Moreover, an unexpected extremely

Fluorohydration of alkynes via I(I)/I(III) catalysis

• Jessica Neufeld,
• Constantin G. Daniliuc and
• Ryan Gilmour

Beilstein J. Org. Chem. 2020, 16, 1627–1635, doi:10.3762/bjoc.16.135

• inversion of the local electronic environment, or the precise deletion of hydrogen-bond donors, respectively, with minimal steric variation [7]. The latter aspect is a crucial determinant in enabling fluorinated materials to adopt intriguing conformations which are a manifest representation of stabilising

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

• 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