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

Anion-driven encapsulation of cationic guests inside pyridine[4]arene dimers

• Anniina Kiesilä,
• Jani O. Moilanen,
• Anneli Kruve,
• Christoph A. Schalley,
• Perdita Barran and
• Elina Kalenius

Beilstein J. Org. Chem. 2019, 15, 2486–2492, doi:10.3762/bjoc.15.241

• "through-wall" electrostatic interactions. Results and Discussion We have previously shown that tetraisobutylpyridine[4]arene forms hydrogen-bonded dimers with eight intermolecular N–H···O(amide) hydrogen bonds in the solid state, in solution and in the gas phase [11]. Resorcinarene capsules of similar

• intermolecular hydrogen bonds of the dimer. Smaller quaternary cations Me4N+ and Et4N+ were observed to form 1:1 and 2:1 host–guest complexes. With Me4N+, [12 + Me4N]+ was observed in the positive mode, and ions [1 − 2H + Me4N]− and [12 − 2H + Me4N]− in the negative mode (Figure 1). Complexation of Et4N+ was

• dispersion correction (hydrogen bond lengths are listed in Table S2, Supporting Information File 1). This is expected, because the standard hybrid functionals are able to describe strong hydrogen bonds such as NH···O and OH···O in a reasonable manner [31][32]. Due to the encapsulated guest molecule, the [12

Ultrafast processes triggered by one- and two-photon excitation of a photochromic and luminescent hydrazone

• Alessandro Iagatti,
• Baihao Shao,
• Alberto Credi,
• Barbara Ventura,
• Ivan Aprahamian and
• Mariangela Di Donato

Beilstein J. Org. Chem. 2019, 15, 2438–2446, doi:10.3762/bjoc.15.236

• the competition between the intramolecular hydrogen bond between the N–H and C=O groups in the Z-form and hydrogen bonds formed by these functional groups with solvent molecules. The conformational distortion and the increased conformational disorder arising from hydrogen bonding with the solvent can

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

• Ronja Driller,
• Daniel Garbe,
• Norbert Mehlmer,
• Monika Fuchs,
• Keren Raz,
• Dan Thomas Major,
• Thomas Brück and
• Bernhard Loll

Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228

• bidentate salt bridge with D111 of the aspartate-rich motif, and two salt bridges to the diphosphate moiety derived from FGGDP (Figure 3 and Figure 5). Y295 establishes hydrogen bonds to the diphosphate moiety as well as to N220 of the NSE motif (Figure 5). In the closed conformation of the labdane-related

• . Residues of the DDXD motif are shown in red and residues of the NSE motif in yellow. The conserved residues of the WXXXXXRY motif are drawn in light green and the R227 that interacts with diphosphate moiety in light brown. The cleaved diphosphate is shown in orange. Hydrogen bonds and salt bridges are

Perspective isomorphs – a new classification of molecular structures based on artistic and chemical concepts

• Jannis Neumann,
• Ansgar Schnurr and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2019, 15, 2319–2326, doi:10.3762/bjoc.15.224

• Contextualization The understanding of space in chemistry is highly linked to the three-dimensional extensions of molecules and their directionality in chemical bonds, reactions, and processes. In this context, interactions, such as hydrogen-bonds [3], metal-coordination [4] or quadrupole interactions [5][6

• possibility of specific orientation and space-depended interactions, such as hydrogen-bonds, etc., which is of utmost importance for instance in any biological process [15]. Proposal of perspective isomorphs When applying the principle of the central perspective to the view on molecules, their representation

• molecules included by a PI code. This gives the option of not only providing information about a whole group of perspective isomorphs, but also about certain molecules belonging to this group. The layer x, for instance, defines the atoms of the substitutes X1-Xn, layer hx indicates the hydrogen bonds of the

Small anion-assisted electrochemical potential splitting in a new series of bistriarylamine derivatives: organic mixed valency across a urea bridge and zwitterionization

• Keishiro Tahara,
• Tetsufumi Nakakita,
• Alyona A. Starikova,
• Takashi Ikeda,
• Masaaki Abe and
• Jun-ichi Kikuchi

Beilstein J. Org. Chem. 2019, 15, 2277–2286, doi:10.3762/bjoc.15.220

• promising trigger to directly change the charge distributions of molecules and assemblies, potentially allowing tuning of the strength of non-covalent interactions, including hydrogen bonds (H-bonds) [23][24][25][26]. In this context, a number of redox-active compounds bearing H-bond donors and acceptors

1,2,3,4-Tetrahydro-1,4,5,8-tetraazaanthracene revisited: properties and structural evidence of aromaticity loss

• Arnault Heynderickx,
• Sébastien Nénon,
• Olivier Siri,
• Vladimir Lokshin and
• Vladimir Khodorkovsky

Beilstein J. Org. Chem. 2019, 15, 2059–2068, doi:10.3762/bjoc.15.203

• level optimized and experimental geometry of THTAA and its derivatives show considerable loss of aromaticity within the quinoxaline moiety. Keywords: aromaticity; density functional calculations; heterocycles; hydrogen bonds; X-ray structures; Introduction Quinoxaline derivatives 1 – also called

• the formation of hydrogen bonds, an approach known as ‘crystal engineering’ (see, for instance, [13][14] and references therein). Indeed, whereas several two-component molecular systems cocrystallizing in a special layered way involving pyrazine, quinoline and phenazine as the H-bond acceptor and

• bond lengths. The dominant motive seen for 3 in the solid state is the formation of infinite chains based on N–H···N=C hydrogen bonds (N···N distances 3.011–3.047 Å, Figure 9). The crystal lattice of 6a (Figure 10) also exhibits the presence of the infinite chains >N–H···Cl−···H–N+: the Cl−···N and Cl

Synthesis of 1-azaspiro[4.4]nonan-1-oxyls via intramolecular 1,3-dipolar cycloaddition

• Yulia V. Khoroshunova,
• Denis A. Morozov,
• Andrey I. Taratayko,
• Polina D. Gladkikh,
• Yuri I. Glazachev and
• Igor A. Kirilyuk

Beilstein J. Org. Chem. 2019, 15, 2036–2042, doi:10.3762/bjoc.15.200

• one order of magnitude lower for EPR spectra in water (0.005–0.006 mT), obviously because strong intermolecular hydrogen bonds are formed due to solvation. The initial rates of the EPR signal decay were used to obtain the rate constants of the nitroxide reduction by ascorbic acid (see Figure 2 and

Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

• Silvie Rimpelová,
• Michal Jurášek,
• Lucie Peterková,
• Jiří Bejček,
• Vojtěch Spiwok,
• Miloš Majdl,
• Michal Jirásko,
• Miloš Buděšínský,
• Juraj Harmatha,
• Eva Kmoníčková,
• Pavel Drašar and
• Tomáš Ruml

Beilstein J. Org. Chem. 2019, 15, 1933–1944, doi:10.3762/bjoc.15.189

• domain between the helices 3, 5 and 7 [7][21]. Comparing the polarity of these compounds with compound 1 based on the formation of hydrogen bonds, the most polar compound capable of forming the highest number of hydrogen bonds is thapsigargin, the least polar is compound 1 (for details, see Supporting

• Information File 1, Table S4). Nevertheless, the complex of SERCA with thapsigargin is preferentially stabilized by hydrophobic interactions, [21] and all three mentioned SLs are strongly hydrophobic molecules. We therefore assumed that compounds 1 and 2, which can form even fewer hydrogen bonds than

• parts of Glu255 and Gln259 were detected. When the simulation was performed without constrained positions, compound 1 escaped from the SERCA protein cavity. After the first simulation of compound 2 (simulation 3) in non-water environment, hydrogen bonds of compound 2 with Glu255 and Gln259 residues, and

Complexation of chiral amines by resorcin[4]arene sulfonic acids in polar media – circular dichroism and diffusion studies of chirality transfer and solvent dependence

• Bartosz Setner and
• Agnieszka Szumna

Beilstein J. Org. Chem. 2019, 15, 1913–1924, doi:10.3762/bjoc.15.187

• nondirectional, while directional interactions (charged/neutral hydrogen bonds) are diminished by solvent competition. Numerous studies show that the most promising strategy for the formation of ordered complexes in polar media involves a combination of at least two types of interactions, one of which is usually

• conclusion comes from a comparison of complexes in methanol and DMSO. One would expect that due to the dual hydrogen bond donor/acceptor character of methanol this solvent should be more destructive to ion-pair complexes based on charged hydrogen bonds than DMSO that can only serve as a hydrogen bond

Tautomerism as primary signaling mechanism in metal sensing: the case of amide group

• Vera Deneva,
• Georgi Dobrikov,
• Aurelien Crochet,
• Daniela Nedeltcheva,
• Katharina M. Fromm and
• Liudmil Antonov

Beilstein J. Org. Chem. 2019, 15, 1898–1906, doi:10.3762/bjoc.15.185

• exchange was especially developed to describe main-group thermochemistry and noncovalent interactions. It shows very good results in predicting the position of the tautomeric equilibria for compounds with intramolecular hydrogen bonds as well as describing the ground and excited state proton transfer

Halide metathesis in overdrive: mechanochemical synthesis of a heterometallic group 1 allyl complex

• Ross F. Koby,
• Nicholas R. Rightmire,
• Nathan D. Schley,
• Timothy P. Hanusa and
• William W. Brennessel

Beilstein J. Org. Chem. 2019, 15, 1856–1863, doi:10.3762/bjoc.15.181

• Information File 1, Figure S3). Despite the gas-phase environment of the calculations, the distance between K+ and CH4 is 3.22 Å, a typical value for potassium–methyl interactions in the solid state, as is the ∆H° of almost 12 kJ mol−1, in the range of hydrogen bonds (Table 3, entries 1 and 2) [32]. The

Synthesis of a [6]rotaxane with singly threaded γ-cyclodextrins as a single stereoisomer

• Jason Yin Hei Man and
• Ho Yu Au-Yeung

Beilstein J. Org. Chem. 2019, 15, 1829–1837, doi:10.3762/bjoc.15.177

• between CB[6] and cyclodextrins via hydrogen bonds in rigid (pseudo)rotaxane systems has been previously reported [43][44][45][46][47][48]. The full occupancy of the axle by five macrocycles and the resulting close proximity of the macrocycles in 6R may hence resulted in similar interactions that

Complexation of 2,6-helic[6]arene and its derivatives with 1,1′-dimethyl-4,4′-bipyridinium salts and protonated 4,4'-bipyridinium salts: an acid–base controllable complexation

• Jing Li,
• Qiang Shi,
• Ying Han and
• Chuan-Feng Chen

Beilstein J. Org. Chem. 2019, 15, 1795–1804, doi:10.3762/bjoc.15.173

• between the proton of G1 and oxygen of H1 in the distance of 2.683 Å for G. Moreover, C-H···F hydrogen bonds between the two adjacent guests with the distances of 2.670 (H), 2.570 (I), 2.594 (J) and 1.981 Å (K), respectively, were observed. These multiple interactions play an important role in the

• H5 in the distance of 1.989 Å (R). In addition, C-H···F hydrogen bonds between the two adjacent guests with the distance of 2.420 (S), 2.474 (T) and 2.187 Å (U), respectively, are observed as well. These multiple intermolecular hydrogen-bonding interactions between the host and the guest might be the

• Information File 1, Figure S92). The calculation results revealed the C–H···π interactions between the protons on the pyridinium ring of G1 and the benzene ring units of the host H4 and C–H···O hydrogen bonds between the protons of the methyl group and pyridinium rings of G1 and the oxygen atom of H4 with

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

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