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Search for "hydrogen bonds" in Full Text gives 438 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
A conformationally adaptive macrocycle: conformational complexity and host–guest chemistry of zorb[4]arene
Beilstein J. Org. Chem. 2018, 14, 1570–1577, doi:10.3762/bjoc.14.134
- large amplitude conformational responses to the electronic substituents on the guests. Instead of a linear free-energy relationship, ZB4 follows a parabolic free-energy relationship. This is explained by invoking the influence of secondary C–H···O hydrogen bonds on the primary cation···π interactions
- structures may provide an explanation for their surprising binding behaviors. Multiple non-covalent interactions, including C–H···O hydrogen bonds, cation···π, C–H···π and π···π interactions, are involved in all the cases. Undoubtedly, cation···π interactions between the core quaternary ammonium ions of the
- size of the host cavity. As shown in Figure 3 (bottom), the vertical and horizontal distances between the diagonal oxygen atoms are different for all the four complexes. This distance is presumably tuned through the C–H···O hydrogen bonds between the CH2–O–CH2 oxygen atoms and the aromatic protons of
Cobalt-catalyzed C–H cyanations: Insights into the reaction mechanism and the role of London dispersion
Beilstein J. Org. Chem. 2018, 14, 1537–1545, doi:10.3762/bjoc.14.130
- structures, significant interactions can be found between the Cp* ligand and the various phenyl groups of the reagents. In addition, the presence of additional stabilizing interactions such as further hydrogen bonds can also be confirmed by this analysis (e.g., in TS3, see also the Supporting Information
Recent applications of chiral calixarenes in asymmetric catalysis
Beilstein J. Org. Chem. 2018, 14, 1389–1412, doi:10.3762/bjoc.14.117
- ligands based on the same chiral scaffold. It was concluded that free hydroxy groups on the lower rim of the calixarene ligands do not have a beneficial catalytic effect due to the formation of hydrogen bonds with the incoming boronic acids. In the same study, diphosphine ligand (S,S)-29 was used in the
- hydrophilic region via hydrogen bonds between 75 and interfacial water molecules. The catalytic activity of compound 83 as an organocatalyst was evaluated in the enantioselective aldol reaction of 21 and 70 in different amounts of water. In the presence of 10 mol % catalyst, the aldol adduct was obtained in
- results, a plausible reaction mechanism similar to that previously suggested for the L-proline-catalyzed aldol reactions in water which proceeds via an enamine intermediate was proposed. As shown in Figure 10, it is proposed that hydrogen bonds between the OH and NH groups of the calix[4]arene catalyst
A three-armed cryptand with triazine and pyridine units: synthesis, structure and complexation with polycyclic aromatic compounds
Beilstein J. Org. Chem. 2018, 14, 1370–1377, doi:10.3762/bjoc.14.115
- cryptand 2 they were 3.27 Å and 3.21 Å, respectively. Since the 3,5-dicyanopyridine fragment contains hydrogen-bond acceptor nitrogen atoms it might be possible to select a guest system which besides the stacking interaction could establish extra hydrogen bonds to enhance the complex stability. Accordingly
Oligonucleotide analogues with cationic backbone linkages
Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111
- range and its ability to form both intermolecular electrostatic interactions and hydrogen bonds [50]. Letsinger's aminoalkyl phosphoramidate modification was stereogenic at the phosphorus atom, thus leading to complex mixtures of diastereomeric oligomers (with the exception of the aforementioned related
An unusual thionyl chloride-promoted C−C bond formation to obtain 4,4'-bipyrazolones
Beilstein J. Org. Chem. 2018, 14, 1287–1292, doi:10.3762/bjoc.14.110
- such a way that mirror enantiomers are interconnected to each other by weak intermolecular hydrogen bonds (C–H···O 2.523 Å, 130.64°, Figure 3). In the following, related 5-hydroxypyrazol-4-carboxylates 1b–i were subjected to the same reaction conditions (refluxing SOCl2) and in all cases the
- two pyrazolone units is 1.544(3) Å. For details see the Supporting Information File 1. Arrangement (4R,4'R)- and (4S,4'S)-3a enantiomers in the crystal unit drawn with 50% displacement ellipsoids. The hydrogen bonds are shown by dashed lines. Supplementary crystallographic data for compound 3a can be
Novel unit B cryptophycin analogues as payloads for targeted therapy
Beilstein J. Org. Chem. 2018, 14, 1281–1286, doi:10.3762/bjoc.14.109
- ”, has been proposed [2][52][53]. We performed a docking study to explain the different affinities of the newly synthesized derivatives. The parent compound 2 scored highest with respect to β-tubulin binding (Table 2). Three hydrogen bonds were detected to key residues in the peptide binding pocket of
- activity whereas analogues 23 and 24 showed a reduced activity but were still very cytotoxic. Cryptophycin-1 (1) and -52 (2). Binding mode of 2, showing the interaction to the vinca domain peptide binding pocket (blue). Hydrogen bonds are shown as yellow dots with the interacting amino acid residues in
London dispersion as important factor for the stabilization of (Z)-azobenzenes in the presence of hydrogen bonding
Beilstein J. Org. Chem. 2018, 14, 1238–1243, doi:10.3762/bjoc.14.106
- important classes of molecular switches is crucial for the design of light-responsive materials using this entity. Herein, we present the stabilization of metastable (Z)-azobenzenes by London dispersion interactions, even in the presence of comparably stronger hydrogen bonds in various solvents. The Z→E
- isomerization rates of several N-substituted 4,4′-bis(4-aminobenzyl)azobenzenes were measured. An intramolecular stabilization was observed and explained by the interplay of intramolecular amide and carbamate hydrogen bonds as well as London dispersion interactions. Whereas in toluene, 1,4-dioxane and tert
- -butyl methyl ether the hydrogen bonds dominate, the variation in stabilization of the different substituted azobenzenes in dimethyl sulfoxide can be rationalized by London dispersion interactions. These findings were supported by conformational analysis and DFT computations and reveal low-energy London
An overview of recent advances in duplex DNA recognition by small molecules
Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93
- eight Hoogsteen-paired hydrogen bonds to form a tetrad (Figure 1) has further enhanced our understanding of the diversity of DNA shapes and structures. In a parallel tetramolecular quadruplex d(TG4T), the features of nucleotides at each base resemble that of the B-DNA (C2’-endo sugar pucker, anti
- MGBs is their preference for narrow A·T-rich regions compared to G·C regions because (i) they can form hydrogen bonds to N3 of adenine and O2 of thymine in the A·T region; (ii) less steric hindrance in the A·T region in comparison to the G·C region due to the presence of an extra protruding C2-amino
- synthesized in order to investigate the molecular basis of carbohydrate–minor groove DNA interactions by Vicent et al. [95]. NMR spectroscopy and molecular modeling studies further confirmed the existence of directional intramolecular hydrogen bonds and CH–π interactions, which results in stabilizing these
Correlation effects and many-body interactions in water clusters
Beilstein J. Org. Chem. 2018, 14, 979–991, doi:10.3762/bjoc.14.83
- been shown for several structures of the water tetramer that total four-body interactions are in most cases much smaller or even negligible compared to the three-body interactions [27]. The only exception to this was observed for the squared geometry in which the hydrogen bonds act cooperatively to
- by the formation of hydrogen bonds, can be well reproduced already on an uncorrelated level using the Hartree–Fock method. However, electron correlation effects to the interaction energy, including the two-body dispersion interaction, lead to a compression of the cluster sizes relative to the
Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study
Beilstein J. Org. Chem. 2018, 14, 919–929, doi:10.3762/bjoc.14.79
- . This information is used to rationalize the trend of stability of various conformers of the water and hydrogen fluoride dimers. Keywords: DLPNO-CCSD(T); hydrogen-bond interaction; interaction energy; local energy decomposition; London dispersion; Introduction Hydrogen bonds are of fundamental
Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies
Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69
- host A and host B) arranged co-axially so that the secondary rim (head) of the one faces the secondary rim of the other forming a head-to-head dimer via intermolecular hydrogen bonds between their O3n-H hydroxy groups. A cholesterol molecule is found fully encapsulated inside the β-CD dimeric cavity
- degree of stability to the inclusion complex. The head–head β-CD dimers formed by units interacting through hydrogen bonds between their secondary hydroxy groups is further stabilized through ion–dipole interactions with a Na+ counterion. This Na+ links the two β-CD’s together and also interacts with
An uracil-linked hydroxyflavone probe for the recognition of ATP
Beilstein J. Org. Chem. 2018, 14, 747–755, doi:10.3762/bjoc.14.63
- confirmed our model of complexation [66]. Structures of the studied hydroxyflavone derivatives. Optimized geometries for (a) DEHF∙ATP, (b) UHF∙ATP with the adenine of ATP “sandwiched” between the uracil and flavone units and (c) UHF∙ATP with hydrogen bonds between the uracil and the adenine moieties
Enzyme-free genetic copying of DNA and RNA sequences
Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47
- −1 and k'TCT = 8 310 h−1 M−1 [27]. This was encouraging. As expected, the incorporation of G was most favorable, as this base strongly pairs via three hydrogen bonds and has a large surface area for stacking. Numerically, the t1/2 values for the incorporation of G ranged from 1 min to 15 min, whereas
Stereochemical outcomes of C–F activation reactions of benzyl fluoride
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
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
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
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
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
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
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
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?
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
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
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