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Search for "hydrogen bond" in Full Text gives 435 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.

The activity of indenylidene derivatives in olefin metathesis catalysts

  • Maria Voccia,
  • Steven P. Nolan,
  • Luigi Cavallo and
  • Albert Poater

Beilstein J. Org. Chem. 2018, 14, 2956–2963, doi:10.3762/bjoc.14.275

Graphical Abstract
  • there is a hydrogen bond (Ru···H) that affects the charge on the metal, especially strong when the indenylidene is substituted. The Ru···H distances for 1–6 are 3.110, 3.167, 3.004, 3.036 Å, 2.944, 2.929 Å, respectively (see Figure 2). This interaction is due to the rotation of 90° of the indenylidene
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Published 30 Nov 2018

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

Graphical Abstract
  • has been shown that E-isomers of neutral imines can be stabilised by an intramolecular C=N−H···OMe hydrogen bond with a neighbouring methoxy group. Electron-donating OMe groups dramatically increase the basicity of the imino nitrogen, forcing the latter to abstract a proton from the proton sponge
  • moiety in monoprotonated forms. The participation of the out-inverted and protonated 1-NMe2 group in the Me2N−H···NH=C hydrogen bond is experimentally demonstrated. It was shown that the number and position of OMe groups in the aromatic substituents strongly affects the rate of the internal hindered
  • rotation of the NH2+ fragment in dications. Keywords: hydrogen bond; imine; NMR; proton sponge; superbase; Introduction It is well known that the extremely high basicity of 1,8-bis(dimethylamino)naphthalene (1, DMAN; pKa = 12.1 in H2O [1][2], 18.62 in MeCN [3], 7.5 in DMSO [4]) and its derivatives
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Published 28 Nov 2018

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

Graphical Abstract
  • between H(1) and H(4) in the NOE experiment. The structure contains two carbonyl moieties C(6)–O(2) and C(3)–O(1) with similar distances of 1.222 and 1.218 Å, respectively. The intramolecular hydrogen bond O(1)–H(13) remains strong in the nitrogenated tricycle (2.579 Å) vis-à-vis of the starting hydrazide
  • imino-carboxylic acid form likely evolves to its iminium-carboxylate form B [50]. This last intermediate involves the existence of two possible transition states for the cyclization of the imidazolidinone core of which one of them is favored by an intramolecular hydrogen bond (Scheme 5). This control is
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Published 26 Nov 2018

Non-native autoinducer analogs capable of modulating the SdiA quorum sensing receptor in Salmonella enterica serovar Typhimurium

  • Matthew J. Styles and
  • Helen E. Blackwell

Beilstein J. Org. Chem. 2018, 14, 2651–2664, doi:10.3762/bjoc.14.243

Graphical Abstract
  • ) [21][22]. C) The solid-state structure of the SdiA homodimer (PDB 4Y15; monomers shown in green and grey) bound to OOHL (cyan) [22]. D) Selected residues surrounding OOHL (cyan) in the SdiA ligand binding pocket (from PDB 4Y15 [22]): hydrogen bond acceptors/donors (orange), hydrophobic residues (grey
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Published 17 Oct 2018

Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers

  • Christian Schütz and
  • Martin Empting

Beilstein J. Org. Chem. 2018, 14, 2627–2645, doi:10.3762/bjoc.14.241

Graphical Abstract
  • could prevent activation of the carbonyl group as a CoA-ester. In 2017, Witzgall et al. were able to co-crystallize 6-FABA-AMP within the N-terminal domain of PqsA (Figure 4) [46]. Key interactions involve a water-mediated hydrogen bond between the amino function of the compound and Q162, as in
  • anthraniloyl-AMP. The reason why the fluorinated anthraniloyl-AMP shows good affinity is the formation of a hydrogen bond of the fluorine with the G279 backbone amide hydrogen and furthermore an interaction with the N7 position of the adenine moiety. Additionally a very typical fluorine/main-chain interaction
  • , the chlorine is able to occupy a vacant sub pocket. A hydrogen bond is found between the backbone oxygen of L207 and the 3-NH2 hydrogen atoms. Interestingly, adding the chlorine substituent in 7-position of PQS leads to a 135 times more potent agonist, indicating the importance of the vacant sub
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Published 15 Oct 2018

Synthesis of dihydroquinazolines from 2-aminobenzylamine: N3-aryl derivatives with electron-withdrawing groups

  • Nadia Gruber,
  • Jimena E. Díaz and
  • Liliana R. Orelli

Beilstein J. Org. Chem. 2018, 14, 2510–2519, doi:10.3762/bjoc.14.227

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  • . Such effect would result from an intramolecular hydrogen bond between the ammonium and nitro groups in the reaction intermediate, also known as “built-in solvation” [71] (Figure 2). When 2-ABA was reacted with 2-chloro-3-nitropyridine (CNP) in analogous experimental conditions as 2a, compound 2c was
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Published 26 Sep 2018

Synthesis of eunicellane-type bicycles embedding a 1,3-cyclohexadiene moiety

  • Alex Frichert,
  • Peter G. Jones and
  • Thomas Lindel

Beilstein J. Org. Chem. 2018, 14, 2461–2467, doi:10.3762/bjoc.14.222

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  • appeared as a sharp signal at 5.25 ppm (CDCl3) for 29 and as a broad peak at 3.00 ppm for 30. This can be explained by the presence of an intramolecular hydrogen bond that is possible only in the case of 29. Since the 1H NMR spectrum of cyanohydrin 22 exhibits a sharp hydroxy peak at 5.29 ppm, we derive
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Published 20 Sep 2018

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

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  • -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
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Published 07 Sep 2018

Determining the predominant tautomeric structure of iodine-based group-transfer reagents by 17O NMR spectroscopy

  • Nico Santschi,
  • Cody Ross Pitts,
  • Benson J. Jelier and
  • René Verel

Beilstein J. Org. Chem. 2018, 14, 2289–2294, doi:10.3762/bjoc.14.203

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  • residual value (Table 1). Conceivably, this may be due to intermolecular hydrogen bonding with the solvent or other alcohol molecules in the concentrated solution. In fact, including a methanol solvent molecule as a hydrogen-bond donor in the DFT calculation will shift the δcalc in the right direction for
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Published 30 Aug 2018

Selective formation of a zwitterion adduct and bicarbonate salt in the efficient CO2 fixation by N-benzyl cyclic guanidine under dry and wet conditions

  • Yoshiaki Yoshida,
  • Naoto Aoyagi and
  • Takeshi Endo

Beilstein J. Org. Chem. 2018, 14, 2204–2211, doi:10.3762/bjoc.14.194

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  • structure was fairly stabilized because of the multi hydrogen bond in the intermolecular. Conclusion The efficient CO2 fixation by N-benzyl cyclic guanidine 1 was achieved by bubbling dry CO2 in CH3CN at 25 °C for 2 h. In addition, the zwitterion adduct 2 and bicarbonate salt 3 were selectively prepared
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Published 23 Aug 2018

Synthesis and supramolecular self-assembly of glutamic acid-based squaramides

  • Juan V. Alegre-Requena,
  • Marleen Häring,
  • Isaac G. Sonsona,
  • Alex Abramov,
  • Eugenia Marqués-López,
  • Raquel P. Herrera and
  • David Díaz Díaz

Beilstein J. Org. Chem. 2018, 14, 2065–2073, doi:10.3762/bjoc.14.180

Graphical Abstract
  • conjugated to an aromatic cyclobutenedione ring, can be easily synthesized from different derivatives of squaric acid and amines [1][2][3][4]. The possibility to fabricate chiral squaramide derivatives and their efficient hydrogen bond donor/acceptor ability has driven the pivotal role of these compounds in
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Published 06 Aug 2018

Functionalization of graphene: does the organic chemistry matter?

  • Artur Kasprzak,
  • Agnieszka Zuchowska and
  • Magdalena Poplawska

Beilstein J. Org. Chem. 2018, 14, 2018–2026, doi:10.3762/bjoc.14.177

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  • (above 1700 cm−1) and a new absorption band in the wavenumber range of 1550 cm−1 to 1620 cm−1 can be directly inferred from the formation of either a hydrogen bond between primary amine and the carboxyl groups of GO or an inner salt formation (i.e., COO−NH3+). The presence of the amide bond in the
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Published 02 Aug 2018

Asymmetric Michael addition reactions catalyzed by calix[4]thiourea cyclohexanediamine derivatives

  • Zheng-Yi Li,
  • Hong-Xiao Tong,
  • Yuan Chen,
  • Hong-Kui Su,
  • Tangxin Xiao,
  • Xiao-Qiang Sun and
  • Leyong Wang

Beilstein J. Org. Chem. 2018, 14, 1901–1907, doi:10.3762/bjoc.14.164

Graphical Abstract
  • supramolecular host–guest interaction with the calixarene to form a stable transition state A. Then, another hydrogen bond is formed between the nitrogen atom of the tertiary amine group in A and acetylacetone in its enol form, leading to the formation of a ternary complex B. Finally, nucleophilic attack of
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Published 25 Jul 2018

Preparation and X-ray structure of 2-iodoxybenzenesulfonic acid (IBS) – a powerful hypervalent iodine(V) oxidant

  • Irina A. Mironova,
  • Pavel S. Postnikov,
  • Rosa Y. Yusubova,
  • Akira Yoshimura,
  • Thomas Wirth,
  • Viktor V. Zhdankin,
  • Victor N. Nemykin and
  • Mekhman S. Yusubov

Beilstein J. Org. Chem. 2018, 14, 1854–1858, doi:10.3762/bjoc.14.159

Graphical Abstract
  • (≈1.87–1.88 Å), their short (≈2.59 Å) O(6)···O(12) distance, and a small electron density close to O(6) and O(12). Thus, a proton was added at the small electron density region to the O(6) atom. Such proton positioning results in the formation of an expected strong hydrogen bond (≈1.87 Å ) in the O(6)–H
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Published 20 Jul 2018

First thia-Diels–Alder reactions of thiochalcones with 1,4-quinones

  • Grzegorz Mlostoń,
  • Katarzyna Urbaniak,
  • Paweł Urbaniak,
  • Anna Marko,
  • Anthony Linden and
  • Heinz Heimgartner

Beilstein J. Org. Chem. 2018, 14, 1834–1839, doi:10.3762/bjoc.14.156

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  • centrosymmetric, the compound in the crystal is racemic. The S-atom of the thiophene ring is disordered over two unequally occupied positions as a result of slight but opposite directions of envelope puckering of the ring. The hydroxy group forms an intramolecular hydrogen bond with the adjacent quinoid O-atom
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Published 19 Jul 2018

Host–guest complexes of conformationally flexible C-hexyl-2-bromoresorcinarene and aromatic N-oxides: solid-state, solution and computational studies

  • Rakesh Puttreddy,
  • Ngong Kodiah Beyeh,
  • S. Maryamdokht Taimoory,
  • Daniel Meister,
  • John F. Trant and
  • Kari Rissanen

Beilstein J. Org. Chem. 2018, 14, 1723–1733, doi:10.3762/bjoc.14.146

Graphical Abstract
  • with the observations made from the crystal structures. 1H NMR host–guest solution studies Guest binding studies of the N-oxide guests (1–12) by the receptor BrC6 were investigated in solution via a series of 1H NMR experiments in different hydrogen bond competing solvents and solvent mixtures: acetone
  • bonding (Figures S10–S12, Supporting Information File 1). Due to fast H/D exchange processes on the NMR time scale at 298 K in protic solvents, the hydrogen bond interactions between host and guests were not observed. In CD3OD/CDCl3, complexation-induced chemical shift changes of the guests are observed
  • crystallography and 1H NMR solution studies in three different hydrogen-bond-competitive solvents. In the solid state, BrC6 undergoes large cavity conformational changes to accommodate the N-oxide guests compared to our previously studied host systems, C-ethyl-2-bromoresorcinarene and C-propyl-2
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Published 10 Jul 2018

Design, synthesis and structure of novel G-2 melamine-based dendrimers incorporating 4-(n-octyloxy)aniline as a peripheral unit

  • Cristina Morar,
  • Pedro Lameiras,
  • Attila Bende,
  • Gabriel Katona,
  • Emese Gál and
  • Mircea Darabantu

Beilstein J. Org. Chem. 2018, 14, 1704–1722, doi:10.3762/bjoc.14.145

Graphical Abstract
  • strong hydrogen bond acceptor solvents, such as DMSO-d6 [45], then the NH groups are exposed to the solvent rather than developing intramolecular hydrogen bonds. Conversely, a TG value less negative than −4 ppb K−1 discloses the NH group preference towards intramolecular hydrogen bonds formation, at room
  • temperature, e.g., with s-triazine LPs N-1, -3, -5. If so, the compounds under investigation (Table 3) exhibited TG values denoting significant (peripheral) >N–H···O=SMe2 hydrogen bond interactions. TGs moderately increased, from −5.55 ppb K−1 in G-1 D-N

    NH to about −6.00 ppb K−1 in G-2 dendrimers, together

  • influence on the peripheral (T-0) NH groups/DMSO solvation as they maintained almost the same TG (−6.00 ppb K−1 in 8 vs −6.15 ppb K−1 in 9). In contrast, the inner (T-2) NH groups of 9 appeared “protected” against DMSO (as a hydrogen bond acceptor) because their TG was only −2.00 ppb K−1, (much less
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Published 09 Jul 2018

The phenyl vinyl ether–methanol complex: a model system for quantum chemistry benchmarking

  • Dominic Bernhard,
  • Fabian Dietrich,
  • Mariyam Fatima,
  • Cristóbal Pérez,
  • Hannes C. Gottschalk,
  • Axel Wuttke,
  • Ricardo A. Mata,
  • Martin A. Suhm,
  • Melanie Schnell and
  • Markus Gerhards

Beilstein J. Org. Chem. 2018, 14, 1642–1654, doi:10.3762/bjoc.14.140

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  • -chemical calculations in order to investigate the delicate interplay of noncovalent interactions. The complementary results of vibrational and rotational spectroscopy applied in molecular beam experiments reveal the preference of a hydrogen bond of the methanol towards the ether oxygen (OH∙∙∙O) over the π
  • include the works on benzene–methanol clusters by the Zwier group [11] and on fluorobenzene–methanol clusters by the Brutschy group [12], to mention only two examples. Complexes of aromatic ethers with polar solvent molecules are of special interest due to the presence of different competing hydrogen bond
  • complexes [25] investigated by jet FTIR spectroscopy. The observed OH stretching red-shifts compared to the free alcohols are small, indicating a comparatively weak hydrogen bond, which is also reflected in calculated binding energies [24][25]. With the herein presented work, we now extend our overall multi
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Published 02 Jul 2018

Cobalt-catalyzed C–H cyanations: Insights into the reaction mechanism and the role of London dispersion

  • Eric Detmar,
  • Valentin Müller,
  • Daniel Zell,
  • Lutz Ackermann and
  • Martin Breugst

Beilstein J. Org. Chem. 2018, 14, 1537–1545, doi:10.3762/bjoc.14.130

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  • -coordination. The resulting intermediate 6a is stabilized by an agostic interaction between the C–H bond and the metal atom as well as by an additional weak hydrogen bond between the C–H bond and the acetate oxygen (O…H distance 2.26 Å). A natural population analysis of structure 6a further confirms the
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Published 25 Jun 2018

Enantioselective phase-transfer catalyzed alkylation of 1-methyl-7-methoxy-2-tetralone: an effective route to dezocine

  • Ruipeng Li,
  • Zhenren Liu,
  • Liang Chen,
  • Jing Pan and
  • Weicheng Zhou

Beilstein J. Org. Chem. 2018, 14, 1421–1427, doi:10.3762/bjoc.14.119

Graphical Abstract
  • , then two additional interaction forces in the complex are produced on the same plane, including: 1) the carbonyl of 2 makes a hydrogen bond with the hydroxy group of C7; 2) the phenyl group of 2 forms a face-to-face π-stacking interaction with the benzyl moiety of C7. The complex of 2 with C7 goes to
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Published 11 Jun 2018

Recent applications of chiral calixarenes in asymmetric catalysis

  • Mustafa Durmaz,
  • Erkan Halay and
  • Selahattin Bozkurt

Beilstein J. Org. Chem. 2018, 14, 1389–1412, doi:10.3762/bjoc.14.117

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  • both catalysts gave the Michael adduct in excellent yields, high ees were obtained only when 54b was used as organocatalyst (up to 94% ee, Scheme 16). During the last decade, squaramide catalysts have become a powerful alternative to the urea/thiourea and guanidine catalysts as multiple hydrogen bond
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Published 08 Jun 2018

A three-armed cryptand with triazine and pyridine units: synthesis, structure and complexation with polycyclic aromatic compounds

  • Claudia Lar,
  • Adrian Woiczechowski-Pop,
  • Attila Bende,
  • Ioana Georgeta Grosu,
  • Natalia Miklášová,
  • Elena Bogdan,
  • Niculina Daniela Hădade,
  • Anamaria Terec and
  • Ion Grosu

Beilstein J. Org. Chem. 2018, 14, 1370–1377, doi:10.3762/bjoc.14.115

Graphical Abstract
  • 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
  • , the O–H···N fragment did not preserve its hydrogen-bond arrangement, as the aromatic fragment rather preferred the so-called “antiparallel-displaced” configuration [40][41] (see Figure 6). The intermolecular interaction energy between 1,5-dihydroxynaphthalene and cryptand 2 is −29.28 kcal/mol, while
  • -dihydroxynaphthalene. The higher affinity for anthracene and pyrene than for the dihydroxylated aromatic guest is explained by the influence of the polar solvent (DMSO). Molecular modelling revealed the preference for aryl–aryl stacking instead of a hydrogen bond between the donor OH groups of the guest and the
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Published 06 Jun 2018

Novel unit B cryptophycin analogues as payloads for targeted therapy

  • Eduard Figueras,
  • Adina Borbély,
  • Mohamed Ismail,
  • Marcel Frese and
  • Norbert Sewald

Beilstein J. Org. Chem. 2018, 14, 1281–1286, doi:10.3762/bjoc.14.109

Graphical Abstract
  • the vinca domain (Lys176, Val177 and Tyr210). Other than previously reported [52], the methoxy group of subunit B forms a hydrogen bond with Lys176 (Figure 2). Another binding mode of 2 with high binding affinity and hydrogen bond formation did not involve any interaction of subunit B, yet it was
  • the other derivatives 23 and 24 (Figure 4). Besides hydrogen bond formation and binding affinity of inhibitors 2, 23 and 24, π-interactions and hydrophobic contacts with the binding pocket of the vinca domain were detected that would in turn increase the affinity of the inhibitor and its effect on the
  • magenta. Docking of 22 to the vinca domain of β-tubulin. Surface and backbone of β-tubulin are shown in blue, GDP in yellow. No hydrogen bond formation was detected. The orientation of the azidoethoxy-ethoxyethyl substituent prevents the inhibitor from the correct interaction with the protein. The epoxide
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Published 01 Jun 2018

An overview of recent advances in duplex DNA recognition by small molecules

  • Sayantan Bhaduri,
  • Nihar Ranjan and
  • Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

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  • substituent (3-quinolinyl nitrogen forming a hydrogen bond with a guanine amino group at the base of the minor groove) and a low pKa tail group. This drug was further selected for the treatment of Gram-positive bacteria Clostridium difficile infections and is currently in the phase II clinical trials
  • selectively bind mixed G·C and A·T sequences of DNA. They hypothesized that thiophene (positive electrostatic potential) and the electron-donor nitrogen of N-MeBI should pre-organize the conformation for accepting hydrogen bond from G-NH2, which was validated by replacing the thiophene moiety with other
  • ) were designed and synthesized by Dervan et al. and followed by other groups. It was observed that pyrrole/imidazole polyamides were able to bind side-by-side in the minor groove of DNA with high affinity and in a sequence-specific manner. Crystal structure studies confirmed the existence of a hydrogen
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Published 16 May 2018

Correlation effects and many-body interactions in water clusters

  • Andreas Heßelmann

Beilstein J. Org. Chem. 2018, 14, 979–991, doi:10.3762/bjoc.14.83

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  • explicitly or implicitly influenced by a water environment. An example for this is the hydrogen-bond cooperativity effect that can have a significant impact on the properties of the bare solute molecules [1]. In order to describe such phenomena, computer simulations have become an indispensable tool, since
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Published 02 May 2018
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