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

Regioselective decarboxylative addition of malonic acid and its mono(thio)esters to 4-trifluoromethylpyrimidin-2(1H)-ones

• Sergii V. Melnykov,
• Andrii S. Pataman,
• Yurii V. Dmytriv,
• Svitlana V. Shishkina,
• Mykhailo V. Vovk and
• Volodymyr A. Sukach

Beilstein J. Org. Chem. 2017, 13, 2617–2625, doi:10.3762/bjoc.13.259

• heterochiral dimer in the crystal state. Intermolecular hydrogen bonds in the dimer are shown as dashed lines. Thermal ellipsoids are defined at 50% probability. Hydrogenation of compounds 4–6 and preparation of N1(3)-unsubstituted compounds 9–11d. Screening of the reaction conditions for organic base

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

• lectins and of three bacterial adhesins were analyzed. One important finding is that the high enthalpic penalties caused by desolvation can only be compensated for by the number and quality of hydrogen bonds formed by each of the polar hydroxy groups engaged in the binding process. In addition, since

• ) forms a complex network of eight hydrogen bonds with ligand 2, one of them mediated by a conserved water [37]. Various approaches to realize binding affinity The immense variability of binding affinities among mannose-binding receptors is remarkable, albeit not surprising. While CRDs involved in the

• calcium ions. During MD simulations, the number of ligand–protein hydrogen-bond interactions for lectins A–F varied from 1.5 to 3.5, and subsequently increased to 4.5 and 5.4 for LecB (G) and BC2L-A (H), respectively. Lastly, FimH (I) forms on average 7.9 hydrogen bonds with methyl α-D-mannopyranoside (2

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• characterized. X-ray single-crystal structure analysis performed for the pyrene–C(O)CH2CH2–thymine (2) conjugate reveals dimers of molecules 2 stabilized by hydrogen bonds between the thymine moieties. The photochemical characterization showed structure-dependent fluorescence properties of the investigated

• independent molecule of compound 2 forms a dimeric structure stabilized through hydrogen bonds between the N22–H22 amido and the C21=O27 carbonyl function of the thymine moieties (Figure 3). The N22···O27 distance is 2.882(2) Å while the N22–H22···O27 angle is 174(3)°. Similar dimeric systems have been

• are characterized by structural features originated from their components: a planar pyrenyl group and the heterocyclic nucleobase unit. While the pyrenyl group is known to act as intercalator [8][9], the nucleobases are known to self-assemble via a network of hydrogen bonds [16][34]. Our aim was to

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

• starting material. Attempted syntheses of RfnICl2. Prior to the efforts described in the previous sections, iodine(III) dichlorides derived from perfluoroalkyl iodides RfnI were considered as targets. Since these lack sp3 carbon–hydrogen bonds, they are not susceptible to possible chlorination or other

• species have never been described in the literature. Silicon has been used as a locus for branching, as exemplified by a variety of highly fluorophilic compounds of the formula (RfnCH2CH2)3SiZ (see XI in Scheme 7, Z = 4-C6H5X [53][54]). However, these feature silicon–carbon and sp3 carbon–hydrogen bonds

A permutation approach to the assignment of the configuration to diastereomeric tetrads by comparison of experimental and ab initio calculated differences in NMR data

• Przemysław J. Boratyński

Beilstein J. Org. Chem. 2017, 13, 2478–2485, doi:10.3762/bjoc.13.245

• emphasized that the 1H NMR data for tetrads 1 and 4 were very predictive of configuration, as demonstrated by higher correlation coefficients than for 13C NMR data. These two compounds are less likely to form hydrogen bonds and specific interactions with the solvent, therefore their conformational equilibria

Structural diversity in the host–guest complexes of the antifolate pemetrexed with native cyclodextrins: gas phase, solution and solid state studies

• Magdalena Ceborska,
• Magdalena Zimnicka,
• Aneta Aniela Kowalska,
• Kajetan Dąbrowa and
• Barbara Repeć

Beilstein J. Org. Chem. 2017, 13, 2252–2263, doi:10.3762/bjoc.13.222

• (FA) with β-CD and γ-CD are far more stable than exclusion associate of FA and α-CD [16]. From collisional experiments we have also learnt that augmented stability of both inclusion complexes is mainly due to the increase of electrostatic forces and hydrogen bonds between FA and β- or γ-CD in the gas

• directed inside the cavity are responsible for the formation of favorable hydrophobic interactions with the guest molecule. Similarly, H2 and H4 protons which are directed outwards the cavity may also interact, plausibly indirectly via OH hydrogen bonds, with guest molecules located outside the cavity. The

• with α- and β-CDs, there are significant changes for the protons belonging to the PTX molecule, which further supports that PTX is engaged in hydrogen bonds with CD’s hydroxy groups (Table S4 and Figures S9, S12 and S13, Supporting Information File 1). In order to establish the type of interactions

Phosphonic acid: preparation and applications

• Charlotte M. Sevrain,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2017, 13, 2186–2213, doi:10.3762/bjoc.13.219

• activator of Vγ9Vδ2 T cells [53][54] (Figure 3D). Phosphonic acid is a function that is readily involved in hydrogen bonds thus generating auto-assembling supramolecular structures [55] or, when a second organic partner possessing basic groups is present (e.g., amine), mixt supramolecular materials [56][57

• in aqueous solution, the phosphonic acid can co-crystallize with water due to the presence of hydrogen bonds between the phosphonic acid moiety and H2O [119]. As depicted on Figure 6, the selected phosphonic acids prepared by the hydrolysis of phosphonate with concentrated HCl water solution present

Novel approach to hydroxy-group-containing porous organic polymers from bisphenol A

• Tao Wang,
• Yan-Chao Zhao,
• Li-Min Zhang,
• Yi Cui,
• Chang-Shan Zhang and
• Bao-Hang Han

Beilstein J. Org. Chem. 2017, 13, 2131–2137, doi:10.3762/bjoc.13.211

• located at 0.68 nm that is different from the other two polymers in Figure 3b is probably the best candidate for CO2 capture. The high carbon dioxide uptake capacity for PPOPs may correspond to the large amount of the hydroxy groups in the PPOPs through the formation of O=C=O(δ–)…H(δ+)–O hydrogen bonds

Complexation of molecular clips containing fragments of diphenylglycoluril and benzocrown ethers with paraquat and its derivatives

• Leonid S. Kikot',
• Catherine Yu. Kulygina,
• Alexander Yu. Lyapunov,
• Svetlana V. Shishkina,
• Roman I. Zubatyuk,
• Tatiana Yu. Bogaschenko and
• Tatiana I. Kirichenko

Beilstein J. Org. Chem. 2017, 13, 2056–2067, doi:10.3762/bjoc.13.203

• paraquat, the following moieties may be involved: the glycoluril fragment (hydrogen bonds involving the oxygen atoms of the carbonyl groups), the catechol part of the crown ether fragments (π–π stacking interactions) and the polyether chains of benzocrown ethers (C–H···О interactions). The first two

• clips, as well as through hydrogen bonds between the Hα, Hβ, and CH3 protons of paraquat with oxygen atoms of carbonyl groups in glycoluril fragment. The contribution of the polyether chains to the stabilization of the complex with 1:1 composition, in the first approximation, may be considered as the

• by weakening of π–π stacking and C–H···O interactions [36]. At the same time, the presence of terminal hydroxy groups in compounds 8–10 may increase the stability of complexes by forming additional hydrogen bonds between molecular clips and hydroxy groups of the substituted dipyridinium salts [37][38

Mechanochemical Knoevenagel condensation investigated in situ

• Sebastian Haferkamp,
• Franziska Fischer,
• Werner Kraus and
• Franziska Emmerling

Beilstein J. Org. Chem. 2017, 13, 2010–2014, doi:10.3762/bjoc.13.197

• interactions such as hydrogen bonds, halogen bonds, and π∙∙∙π interactions [16][17][18][19]. For example, Toda et al. reported yields of 97% for Aldol condensations in the absence of any solvents [20]. Kaupp et al. described the first Knoevenagel condensation in a ball mill [21]. Compared to conventional

p-tert-Butylthiacalix[4]arenes functionalized by N-(4’-nitrophenyl)acetamide and N,N-diethylacetamide fragments: synthesis and binding of anionic guests

• Alena A. Vavilova and
• Ivan I. Stoikov

Beilstein J. Org. Chem. 2017, 13, 1940–1949, doi:10.3762/bjoc.13.188

• lower rim are also valuable precursors for a further functionalization of the macrocycle. However, their preparation is significantly more difficult than the synthesis of 1,3-disubstituted thiacalix[4]arenes. Bulky functional groups able to form hydrogen bonds with free phenolic hydroxy groups and

• therefore block three residual hydroxy groups are usually applied in the synthesis of the monosubstituted derivatives of p-tert-butylthiacalix[4]arene [43]. For the synthesis of the monosubstituted derivative, the bulky N,N-diethylacetamide group able to participate in the formation of hydrogen bonds was

• negatively charged substrates. Usually, receptors for anions are charged systems capable of electrostatic interaction with anions [1][44][45] or neutral systems using other types of interactions, such as donor–acceptor interactions, hydrogen bonds, hydrophobic effects, etc. [46][47][48][49][50][51][52][53

Mechanochemical synthesis of small organic molecules

• Tapas Kumar Achar,
• Anima Bose and
• Prasenjit Mal

Beilstein J. Org. Chem. 2017, 13, 1907–1931, doi:10.3762/bjoc.13.186

• ], carbon–heteroatom [41][42], metal–ligand coordination bonds [43], non-covalent interactions such as hydrogen bonds or π–π arene stacking interactions [44], etc. are popularly known in literature. In this review the efforts are given towards documentation of various mechanochemical reactions like organic

Mechanochemical synthesis of thioureas, ureas and guanidines

• Vjekoslav Štrukil

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

• laboratory, where all the steps from synthesis to structural characterization are carried out without using bulk solvents. The systematic PXRD analyses of 49 thioureas revealed that thioureas, on a supramolecular level, organize into three types of self-assembly motifs based on N–H···S hydrogen bonds

• : 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

18-Hydroxydolabella-3,7-diene synthase – a diterpene synthase from Chitinophaga pinensis

• Jeroen S. Dickschat,
• Jan Rinkel,
• Patrick Rabe,
• Arman Beyraghdar Kashkooli and
• Harro J. Bouwmeester

Beilstein J. Org. Chem. 2017, 13, 1770–1780, doi:10.3762/bjoc.13.171

• ) and the NSE triad NDXXSXX(R,K)(E,D), modified to a DTE triad in plants, for binding of the Mg2+ cofactor that forms a trinuclear (Mg2+)3 cluster to which the diphosphate portion of the substrate binds. Upon substrate binding the active site closes, resulting in hydrogen bonds between the substrate’s

Molecular recognition of N-acetyltryptophan enantiomers by β-cyclodextrin

• Spyros D. Chatziefthimiou,
• Mario Inclán,
• Petros Giastas,
• Athanasios Papakyriakou,
• Konstantina Yannakopoulou and
• Irene M. Mavridis

Beilstein J. Org. Chem. 2017, 13, 1572–1582, doi:10.3762/bjoc.13.157

• towards their 7-fold axis are small and close to their average values (7.1 and 7.7°, respectively). As in all β-CD dimeric complexes [28], the macrocycles’ conformation is stabilized by hydrogen bonds connecting (i) intramolecularly, the O-3n and O-2(n+1) atoms of neighboring glucopyranose units (mean

Synthesis and metal binding properties of N-alkylcarboxyspiropyrans

• Alexis Perry and
• Christina J. Kousseff

Beilstein J. Org. Chem. 2017, 13, 1542–1550, doi:10.3762/bjoc.13.154

• similar tether do not. To probe involvement of the carboxylate/carboxylic acid moiety (e.g., in forming inter- or intramolecular hydrogen bonds) we prepared C6 ester derivative 10 (Figure 7) as a direct point of comparison with C6SP. In the absence of a hydrogen bond donor group, the concentration of 10MC

Construction of highly enantioenriched spirocyclopentaneoxindoles containing four consecutive stereocenters via thiourea-catalyzed asymmetric Michael–Henry cascade reactions

• Yonglei Du,
• Jian Li,
• Kerong Chen,
• Chenglin Wu,
• Yu Zhou and
• Hong Liu

Beilstein J. Org. Chem. 2017, 13, 1342–1349, doi:10.3762/bjoc.13.131

• mechanism was proposed in Scheme 3. The multifunctional organocatalyst d has a chiral scaffold including a thiourea moiety and an amino group. Both the 3-substituted oxindoles 1 and nitrovinylacetamide (2a) that participate in this reaction are activated simultaneously via multiple hydrogen bonds. In

One-pot synthesis of block-copolyrotaxanes through controlled rotaxa-polymerization

• Jessica Hilschmann,
• Gerhard Wenz and
• Gergely Kali

Beilstein J. Org. Chem. 2017, 13, 1310–1315, doi:10.3762/bjoc.13.127

• hydrophobic interaction, as the driving force of complex formation, the threading of the CDs is only achievable in aqueous solution, but the hydrogen bonds between the hydroxy groups impede the water solubility of the products. Thus, the stoppering reaction is mostly limited to organic solutes, in which