Water inside β-cyclodextrin cavity: amount, stability and mechanism of binding

• Stiliyana Pereva,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2019, 15, 1592–1600, doi:10.3762/bjoc.15.163

• “open” configuration the primary hydroxy groups do not participate in intramolecular hydrogen bond interactions. Relatively weak hydrogen bonds are formed between the secondary hydroxy groups in the wider/lower rim of the molecule. The calculations reveal that the “head–tail” arrangement of the narrow

• efficiency of the hydration process. For example, the β-CD dihydrate (Figure 3) containing two water molecules bridging the oppositely placed hydroxy groups from the upper belt thus increasing the number of hydrogen bonds, is characterized with a lower (i.e., more favorable) enthalpy of formation than other

• location. Inside the β-CD cavern a water cluster is formed by a stepwise consecutive coordination of water guests. The cluster is stabilized by a network of hydrogen bonds mostly between the water molecules themselves and interactions between water ligands and cyclodextrin walls. The general trends

Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP)

• Małgorzata Urbańczyk,
• Michał Jewgiński,
• Joanna Krzciuk-Gula,
• Jerzy Góra,
• Rafał Latajka and
• Norbert Sewald

Beilstein J. Org. Chem. 2019, 15, 1581–1591, doi:10.3762/bjoc.15.162

• antifreeze activity, as well as to clarify the influence of hydrogen bonds on the preferred conformation of the molecule. Model AFGP analogues were investigated by NMR in order to elucidate the stereochemical influence of the amino acid configuration on the three-dimensional structure of the glycopeptides. A

• , simplified AFGP analogues avoided overlapping of signals. Temperature coefficient of the amide protons The temperature coefficient factor of amide protons dδ/dT [ppb/K] is one of the parameters, which can be used to determine the existence of hydrogen bonds in peptide chains. The amide protons involved in

• side chain oxygen of Thr3. In case of peptide 3, due to weaker intramolecular hydrogen bonds combined with a high flexibility of the peptide main chain, the fixed orientation of the galactose ring is not observed (see Figure 3 and Figure 4). Such conclusion seems to be confirmed by the small value of

2,3-Dibutoxynaphthalene-based tetralactam macrocycles for recognizing precious metal chloride complexes

• Li-Li Wang,
• Yi-Kuan Tu,
• Huan Yao and
• Wei Jiang

Beilstein J. Org. Chem. 2019, 15, 1460–1467, doi:10.3762/bjoc.15.146

• the shrunken cavity caused by intramolecular hydrogen bonds in the latter tetralactam macrocycle. The binding of the isophthalamide-based macrocycle is mainly driven by hydrogen bonds and electrostatic interactions. This naphthalene-based macrocycle has similar binding affinities to all the three

• in the 1H NMR spectra of the two macrocycles. In particular, the NH protons of 2 (7.51 ppm) are located more downfield than that of 1 (6.08 ppm). This should be caused by the intramolecular hydrogen bonds with pyridine nitrogen atoms in 2 [35][36][37][38]. These hydrogen bonds make macrocycles 2 more

• , which may be caused by intramolecular hydrogen bonds, but the conformational interconversion should be fast as well for macrocycle 2 at room temperature, which is supported by only one set of sharp signals for the aromatic protons and the non-split and sharp signals of diastereotopic protons at the

Host–guest interactions between p-sulfonatocalix[4]arene and p-sulfonatothiacalix[4]arene and group IA, IIA and f-block metal cations: a DFT/SMD study

• Valya K. Nikolova,
• Cristina V. Kirkova,
• Silvia E. Angelova and
• Todor M. Dudev

Beilstein J. Org. Chem. 2019, 15, 1321–1330, doi:10.3762/bjoc.15.131

• with sulfonate groups. The optimized C[4]A and TC[4]A systems possess four-fold symmetry (Figure 1B). The four hydroxy groups surrounding the narrow rim (OH rim) are linked via hydrogen bonds in a tail–head arrangement. C[4]A and TC[4]A as first-shell ligands for IA/IIA/f-block metal cations The

Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls

• Dong-Hao Li and
• Bradley D. Smith

Beilstein J. Org. Chem. 2019, 15, 1086–1095, doi:10.3762/bjoc.15.105

• acene guests Rotaxane template 18 in Scheme 2 is a squaraine dye whose central core has two oxygen atoms that can form hydrogen bonds with the tetralactam NH residues. Squaraine rotaxanes were first prepared by the Smith group in 2005 using the Leigh-type clipping method [44]. As a general trend the

Novel (2-amino-4-arylimidazolyl)propanoic acids and pyrrolo[1,2-c]imidazoles via the domino reactions of 2-amino-4-arylimidazoles with carbonyl and methylene active compounds

• Victoria V. Lipson,
• Tetiana L. Pavlovska,
• Nataliya V. Svetlichnaya,
• Anna A. Poryvai,
• Nikolay Yu. Gorobets,
• Erik V. Van der Eycken,
• Irina S. Konovalova,
• Svetlana V. Shiskina,
• Alexander V. Borisov,
• Vladimir I. Musatov and
• Alexander V. Mazepa

Beilstein J. Org. Chem. 2019, 15, 1032–1045, doi:10.3762/bjoc.15.101

• take part in the formation of the hydrogen bonds were refined using the isotropic approximation as well as all hydrogen atoms in the structure 9i. Full-matrix least-squares refinement of the structures against F2 in anisotropic approximation for non-hydrogen atoms using 3879 (9i), 5051 (11b), 3968 (16a

Catalytic asymmetric oxo-Diels–Alder reactions with chiral atropisomeric biphenyl diols

• Chi-Tung Yeung,
• Wesley Ting Kwok Chan,
• Wai-Sum Lo,
• Ga-Lai Law and
• Wing-Tak Wong

Beilstein J. Org. Chem. 2019, 15, 955–962, doi:10.3762/bjoc.15.92

• hydroxy and NH units for hydrogen bonding activation, % ee and yields in oxo-DA reactions were found to be enhanced with increasing NH acidity, leading to stronger hydrogen bonds [32]. So, there is much room for further investigation and improvement with other hydrogen bonding organocatalysts. An earlier

• form strong hydrogen bonds could perform the same catalytic role in oxo-DA reactions as reported in the literature. Inspired by Rawal’s work on TADDOL and BAMOL organocatalysts, we, in this work, have adopted a similar reaction of Rawal’s diene with benzaldehyde as a starting point of our study and

• formation of the other atropisomer (P)-(S,S)-3 as a higher steric repulsion is generated during the close approach of two bulky phenyl peripheral substituents. The X-ray crystal structure also reveals that an alternative formation of intra- and intermolecular hydrogen bonds [intra- D(OH···O): 1.951(3) Å

Halogen bonding and host–guest chemistry between N-alkylammonium resorcinarene halides, diiodoperfluorobutane and neutral guests

• Fangfang Pan,
• Mohadeseh Dashti,
• Michael R. Reynolds,
• Kari Rissanen,
• John F. Trant and
• Ngong Kodiah Beyeh

Beilstein J. Org. Chem. 2019, 15, 947–954, doi:10.3762/bjoc.15.91

• Br− counterion with an RNB of 0.96 (Supporting Information File 1, Figure S2). MeOH-stabilized systems instead employ weak NH···O and OH···N hydrogen bonds (Supporting Information File 1, Figure S2). In both cases, the electron-rich environment of the cavity provides a negative electrostatic surface

• were positioned at the same level as the (HNH···Cl−)4 HB circle. The O···Cl− distances of 3.13(3) and 3.22(4) Å suggest OH···Cl− hydrogen bonds. Meanwhile, an OH···O hydrogen bond should also exist between the two water molecules with the O···O distance of 3.01(5) Å. It is surprising to find that the

• resorcinarene cavity below these water molecules is empty. It seems the electronegative surface of the cavity repels the water molecules and pushes them up (Figure 4). Besides the hydrogen bonds, each Cl− anion also donates electron density to one DIOFB molecule via a halogen bond with an average RXB of 0.88

An anomalous addition of chlorosulfonyl isocyanate to a carbonyl group: the synthesis of ((3aS,7aR,E)-2-ethyl-3-oxo-2,3,3a,4,7,7a-hexahydro-1H-isoindol-1-ylidene)sulfamoyl chloride

• Aytekin Köse,
• Aslı Ünal,
• Ertan Şahin,
• Uğur Bozkaya and
• Yunus Kara

Beilstein J. Org. Chem. 2019, 15, 931–936, doi:10.3762/bjoc.15.89

• for C10H13ClN2O3S, 276.7350; found, 277.0434. The dipolar intermediate formed in the reaction of CSI with olefins. (a) Molecular structure of racemic molecule 10 (asymmetric unit). Thermal ellipsoids are drawn at the 30% probability level. (b) Geometric parameter with H-bonded geometry. Hydrogen bonds

Mechanochemistry of supramolecules

• Anima Bose and
• Prasenjit Mal

Beilstein J. Org. Chem. 2019, 15, 881–900, doi:10.3762/bjoc.15.86

• the amides 47 (Figure 26). The development of sustainable methods for the activation of less-reactive undirected C(sp3)–H bonds is challenging however, highly desired in organic synthesis. Mal and co-workers also demonstrated that acidic C(sp3)–hydrogen bonds within a molecule could be used to control

Synthesis of 2H-furo[2,3-c]pyrazole ring systems through silver(I) ion-mediated ring-closure reaction

• Vaida Milišiūnaitė,
• Rūta Paulavičiūtė,
• Eglė Arbačiauskienė,
• Vytas Martynaitis,
• Wolfgang Holzer and
• Algirdas Šačkus

Beilstein J. Org. Chem. 2019, 15, 679–684, doi:10.3762/bjoc.15.62

• −127.5 to −128.0 ppm for N-1. The structure of 4d was investigated additionally by single crystal X-ray analysis (Figure 1) [39]. The asymmetric unit of the crystal consists of two molecules 4d(A) and 4d(B) held together by the weak CH···N type hydrogen bonds C19–H···N51 (C···N = 3.470(11) Å, H···N

• one plane, but the phenyl substituents are slightly turned in relation to this plane (Table 3). The molecules in the crystal are located in columns made up of asymmetric units held by hydrogen bonds (Figure 1b). Conclusion In conclusion, we have demonstrated a new, three-step synthetic route to 2H

Synthesis and fluorescent properties of N(9)-alkylated 2-amino-6-triazolylpurines and 7-deazapurines

• Andrejs Šišuļins,
• Jonas Bucevičius,
• Yu-Ting Tseng,
• Irina Novosjolova,
• Kaspars Traskovskis,
• Ērika Bizdēna,
• Huan-Tsung Chang,
• Sigitas Tumkevičius and
• Māris Turks

Beilstein J. Org. Chem. 2019, 15, 474–489, doi:10.3762/bjoc.15.41

• as cell imaging tools [31][32], biosensors and sensors for detection of heavy metals [33]. The tendency of these structures to form hydrogen bonds, to respond to medium effects (solvatochromism) [34] and to certain impurities (e.g., coordination complexes with metal ions) make these compound classes

Synthesis of nonracemic hydroxyglutamic acids

• Dorota G. Piotrowska,
• Iwona E. Głowacka,
• Andrzej E. Wróblewski and
• Liwia Lubowiecka

Beilstein J. Org. Chem. 2019, 15, 236–255, doi:10.3762/bjoc.15.22

• groups capable for the formation of additional hydrogen bonds, both as donors and acceptors. The majority of synthetic strategies starts from natural products and relies on application of chirons having the required configuration at the carbon atom bonded to nitrogen (e.g., serine, glutamic and

• additional substituents, tuning the conformational flexibility of analogues and introducing groups capable of hydrogen bonding. Crystallographic data obtained for glutamate receptors [13][14][15] showed complex set of atoms interacting electrostatically and through hydrogen bonds and the conclusions from

Silanediol versus chlorosilanol: hydrolyses and hydrogen-bonding catalyses with fenchole-based silanes

• Falco Fox,
• Jörg M. Neudörfl and
• Bernd Goldfuss

Beilstein J. Org. Chem. 2019, 15, 167–186, doi:10.3762/bjoc.15.17

• kcal mol−1) and BIFOXSiCl(OH) (8) to BIFOXSi(OH)2 (9, Ea = 31.4 kcal mol−1) with high activation barriers, enforced by endo fenchone units. Crystal structure analyses of silanediol 9 with acetone show shorter hydrogen bonds between the Si–OH groups and the oxygen of the bound acetone (OH···O 1.88(3

• % ee), reaction of 1-chloroisochroman (18) and silyl ketene acetals 11 (up to 85% yield and 5% ee), reaction of chromen-4-one (20) and silyl ketene acetals 11 (up to 98% yield and 4% ee). Keywords: hydrogen bonds; hydrolysis; ion pairs; organocatalysis; silanediol; Introduction Silanediols are

• alcohol group for single hydrogen bonds (CH3OH (11.88 kcal mol−1) vs SiH3OH (16.43 kcal mol−1), Table 4, entries 1 and 2), which is more acidic and inconsistent with the results of West et al. [73]. In case of double hydrogen bonds in the glyoxal based system, both are equally strong, because of a third

Ammonium-tagged ruthenium-based catalysts for olefin metathesis in aqueous media under ultrasound and microwave irradiation

• Łukasz Gułajski,
• Andrzej Tracz,
• Katarzyna Urbaniak,
• Stefan J. Czarnocki,
• Michał Bieniek and
• Tomasz K. Olszewski

Beilstein J. Org. Chem. 2019, 15, 160–166, doi:10.3762/bjoc.15.16

• surface area involved or on the electrostatic nature of the surface itself [81]. Additionally, the packing density of supramolecular clusters of water created by strong intermolecular hydrogen bonds may also play a key role. Indeed, various effects may be depending on the solubility of the reactants in

Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

• Ferran Planas,
• Michael J. McLeish and
• Fahmi Himo

Beilstein J. Org. Chem. 2019, 15, 145–159, doi:10.3762/bjoc.15.15

• the crystallographic water in model C, the presence of the substrate pushes the thiazolium ring somewhat towards the interior of the cavity. In all ThDP states the carboxylate of BF forms hydrogen bonds to the side chain hydroxy group and the backbone NH of Ser26, and to the Nε of His281 (Figure 5

• a source of additional interactions. In the AP and APH+ states, the hydroxy group forms hydrogen bonds with His70 and the exocyclic NH2. Support was lent to the validity of model E when superposition of the structure of the APH+ form on the structure of BFDC:(R)-mandelate complex (PDB 1MCZ) showed

Adhesion, forces and the stability of interfaces

• Robin Guttmann,
• Johannes Hoja,
• Christoph Lechner,
• Reinhard J. Maurer and
• Alexander F. Sax

Beilstein J. Org. Chem. 2019, 15, 106–129, doi:10.3762/bjoc.15.12

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• . The reason for the stabilization is an increased strength of the Watson–Crick base pairing and base stacking interactions due to the electronic effects of the axially oriented 2’-fluorine atom [11][12]. Additionally, FC–H···O hydrogen bonds between the 2’-fluorine and the 4’-oxygen or 5’-oxygen of the

1,8-Bis(dimethylamino)naphthyl-2-ketimines: Inside vs outside protonation

• A. S. Antonov,
• A. F. Pozharskii,
• P. M. Tolstoy,
• A. Filarowski and
• O. V. Khoroshilova

Beilstein J. Org. Chem. 2018, 14, 2940–2948, doi:10.3762/bjoc.14.273

• function are additionally stabilised by hydrogen bonds with solvent molecules and thus the amount of b’ forms correlates with the proton accepting ability of the medium [11]. The gas phase calculations show that without any additional interaction with the medium, the forms protonated at the imino group are

Green synthesis of new chiral 1-(arylamino)imidazo[2,1-a]isoindole-2,5-diones from the corresponding α-amino acid arylhydrazides in aqueous medium

• Nadia Bouzayani,
• Jamil Kraїem,
• Sylvain Marque,
• Yakdhane Kacem,
• Abel Carlin-Sinclair,
• Jérôme Marrot and
• Béchir Ben Hassine

Beilstein J. Org. Chem. 2018, 14, 2923–2930, doi:10.3762/bjoc.14.271

• observed with a total trans-diastereoselectivity controlled by intramolecular hydrogen bonds. Chemical structures of analogues. NOEs correlation showing the stereochemistry of the compound 5a. X-ray crystal structure of 5f shown at the 30% probability level. Strategy for the formation of 1-(arylamino)-1H

Olefin metathesis catalysts embedded in β-barrel proteins: creating artificial metalloproteins for olefin metathesis

• Daniel F. Sauer,
• Johannes Schiffels,
• Takashi Hayashi,
• Ulrich Schwaneberg and
• Jun Okuda

Beilstein J. Org. Chem. 2018, 14, 2861–2871, doi:10.3762/bjoc.14.265

• are generally regarded to be more rigid than disordered or α-helix structures [30][31]. β-Barrels are structural motifs found in numerous proteins in which (mostly) antiparallel β-strands twist and coil to form closed, quasi-cylindrical structures held together by a network of hydrogen bonds [32

An overview on recent advances in the synthesis of sulfonated organic materials, sulfonated silica materials, and sulfonated carbon materials and their catalytic applications in chemical processes

• Hashem Sharghi,
• Pezhman Shiri and
• Mahdi Aberi

Beilstein J. Org. Chem. 2018, 14, 2745–2770, doi:10.3762/bjoc.14.253

• substance and chlorosulfonic acid for the first time. The authors proposed that the high Brønsted acidity of the catalyst arises mainly from hydrogen bonds between the two -SO3H groups. The catalyst 53 was studied by different analyses including FTIR, 1H NMR, 13C NMR, UV–vis, and fluorescence spectra. Then

Pathoblockers or antivirulence drugs as a new option for the treatment of bacterial infections

• Matthew B. Calvert,
• Varsha R. Jumde and
• Alexander Titz

Beilstein J. Org. Chem. 2018, 14, 2607–2617, doi:10.3762/bjoc.14.239

• interact with the tyrosine gate formed by Tyr48 and Tyr137 [15][16], as well as form hydrogen bonds and electrostatic interactions with the Arg98/Glu50 salt bridge of the protein. Taking this coordination geometry into consideration for further ligand optimization, it was found important to focus on the

Nucleoside macrocycles formed by intramolecular click reaction: efficient cyclization of pyrimidine nucleosides decorated with 5'-azido residues and 5-octadiynyl side chains

• Jiang Liu,
• Peter Leonard,
• Sebastian L. Müller,
• Constantin Daniliuc and
• Frank Seela

Beilstein J. Org. Chem. 2018, 14, 2404–2410, doi:10.3762/bjoc.14.217

• -dimensional network consisting of a linear unit connected by hydrogen bonds between N3–H and the triazole N3’’ of a second molecule (Figure 3, Supporting Information File 1, Figures S3 and S4). Additionally, the molecules are bridged by water molecules connecting O2 of the base moiety and N2’’ of the triazole

• ring with 3’-OH of the next unit. The second layer is twisted by ≈54° to the first layer and both layers are hold together by weak hydrogen bonds between O4 and methylene groups C9 and C11. In a particular layer the triazole rings are stacked. The same is true for the base moieties. For comparison, the

• ellipsoids are drawn at the 50% probability level and H-atoms are shown as small spheres of arbitrary size. Hydrogen bonds are shown as dashed lines. The crystal packing of 8 shows the intramolecular hydrogen-bonding network (projection parallel to the x-axis). N- and S-conformation for cyclonucleoside 8. B

Catalyst-free synthesis of 4-acyl-NH-1,2,3-triazoles by water-mediated cycloaddition reactions of enaminones and tosyl azide

• Lu Yang,
• Yuwei Wu,
• Yiming Yang,
• Chengping Wen and
• Jie-Ping Wan

Beilstein J. Org. Chem. 2018, 14, 2348–2353, doi:10.3762/bjoc.14.210

• -triazoline 4 which couples to water by strong hydrogen bond effect [51]. The presence of the hydrogen bonds may promote the elimination of the amino group and the acidic C–H bond at the α-position of the acyl group, which affords N-tosyl-1,2,3-triazole 5. Under the present reaction conditions, the