Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study

• Ahmet Altun,
• Frank Neese and
• Giovanni Bistoni

Beilstein J. Org. Chem. 2018, 14, 919–929, doi:10.3762/bjoc.14.79

• , and London dispersion terms. Herein, this technique is employed in the study of hydrogen-bonding interactions in a series of conformers of water and hydrogen fluoride dimers. Initially, DLPNO-CCSD(T) dissociation energies for the most stable conformers are computed and compared with available

Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies

• Elias Christoforides,
• Andreas Papaioannou and
• Kostas Bethanis

Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69

• complex bridging the adjacent dimers. The guest phenoxodiol having a length of about 12 Å matches well with the length of the double barrel unit of two β-CDs (≈14.5 Å) and its terminal hydroxy groups make O–H···O hydrogen bonding contacts with water molecules. However, only one C–H···O bond between the

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

• hydrogen bonding to the carbonyl groups of uracil base and the other cyclen serves as an electrophilic catalyst by interacting with the phosphodiester linkage. The tetra- and penta-cations of 2,6-bis(1,4,7,10-tetraazacyclododecan-1-ylmethyl)pyridine (11b) have given similar results. The possible role of

Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides

• Kartik Temburnikar and
• Katherine L. Seley-Radtke

Beilstein J. Org. Chem. 2018, 14, 772–785, doi:10.3762/bjoc.14.65

• modified nucleosides arise from changes in hydrogen bonding motifs, electronic effects, hydrophobic interactions, acid-base properties and chemical reactivity [25][26][27][28][29][30][31][32][33][34][35][36][37]. One such modification is the change in the nature of the glycosidic bond [29][37]. Although

• stability, ii) altered hydrogen bonding motifs, and iii) altered molecular recognition properties [25][29][37][58]. Because of these changes, C-nucleosides have been useful in the study of RNA and DNA processing enzymes, as well as drug design efforts and novel supramolecular structures [12][29][59

Enzyme-free genetic copying of DNA and RNA sequences

• Marilyne Sosson and
• Clemens Richert

Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47

• ' = nucleobase). Interactions attracting the incoming nucleotide to the extension site. Besides base pairing via hydrogen bonding to the templating base, stacking interactions with neighboring bases of primer and a possible downstream-binding helper oligonucleotide, as well as help of solvophobic effects

Investigations towards the stereoselective organocatalyzed Michael addition of dimethyl malonate to a racemic nitroalkene: possible route to the 4-methylpregabalin core structure

• Denisa Vargová,
• Rastislav Baran and
• Radovan Šebesta

Beilstein J. Org. Chem. 2018, 14, 553–559, doi:10.3762/bjoc.14.42

• and pregabalin [9][10]. Later, hydrogen-bonding activation proved to be more general for obtaining Michael adducts via the addition of 1,3-dicarbonyl compounds to nitroalkenes. Chiral thioureas and squaramides, particularly those with the bifunctional mode of action, served as excellent catalysts in

• numerous Michael additions, as well as other reactions [11][12][13][14]. In this way, chiral thioureas, and squaramides were used to synthesize various GABA derivatives [15][16][17][18][19]. Interestingly, hydrogen-bonding activation of this kind of Michael additions worked well also in aqueous media [20

Carbohydrate inhibitors of cholera toxin

• Vajinder Kumar and
• W. Bruce Turnbull

Beilstein J. Org. Chem. 2018, 14, 484–498, doi:10.3762/bjoc.14.34

• pocket. Both of these terminal sugar residues show hydrogen bonding interactions with the protein and associated water molecules. The GM1 oligosaccharide (GM1os) binds very tightly to CTB with a dissociation constant (Kd) of around 40 nM (measured by isothermal titration calorimetry, ITC), while simple

Novel amide-functionalized chloramphenicol base bifunctional organocatalysts for enantioselective alcoholysis of meso-cyclic anhydrides

• Lingjun Xu,
• Shuwen Han,
• Linjie Yan,
• Haifeng Wang,
• Haihui Peng and
• Fener Chen

Beilstein J. Org. Chem. 2018, 14, 309–317, doi:10.3762/bjoc.14.19

• chloramphenicol-derived bifunctional amide organocatalysts and their application for enantioselective alcoholysis of meso-cyclic anhydrides. In the precedented urea- or thiourea-based organocatalytic methanolysis of anhydrides, one big problem is the homo-aggregation of the catalysts via hydrogen bonding, which

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• interactions, it is mainly governed by hydrophobic interactions and hydrogen bonding between nucleobases and the GO surface [132]. Duplex DNA interacts less strongly with GO since the pairing nucleobases are buried inside the duplex in dsDNA. This phenomenon, together with the ability of GO to act as an

• bases). In this section, only those that have been used in combination with PNA will be discussed. More general reviews of fluorescent base analogues in the DNA/RNA context can be found elsewhere [177][178]. Fluorescent nucleobases capable of hydrogen bonding ("base discriminating fluorophores") The

• structures of fluorescent nucleobases with hydrogen-bonding abilities that have been studied in the PNA context are shown in Figure 20. The earliest examples of PNA carrying an intrinsically fluorescent nucleobase 2-aminopurine (2-AP) were reported since 1997 [179]. The 2-AP in aegPNA selectively recognizes

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• conjugation. As an effect of the need for hydrogen bonding properties, size restriction and sterical effects these demands are often conflicting [15][18][19]. However, there is an increasing number of exceptions to this and since the pioneering work of Ward et al. on adenine analogues [20] a whole range of

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

• of HFIP and TFA (3 mol %, Table 3, entries 2 and 3), the reactions were complete in a significantly shorter time, i.e., the initial induction period observed when only HFIP was used [7] disappeared in each case. The ee of entry 2 was lower (19%), showing that the increased hydrogen bonding strength

Aminosugar-based immunomodulator lipid A: synthetic approaches

• Alla Zamyatina

Beilstein J. Org. Chem. 2018, 14, 25–53, doi:10.3762/bjoc.14.3

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

• Susanne Huhmann,
• Anne-Katrin Stegemann,
• Kristin Folmert,
• Damian Klemczak,
• Johann Moschner,
• Michelle Kube and
• Beate Koksch

Beilstein J. Org. Chem. 2017, 13, 2869–2882, doi:10.3762/bjoc.13.279

• strong, short C–F bonds and perturb the acidity and basicity of adjacent functional groups. Moreover, these changes may strongly influence hydrogen bonding and electrostatic interactions that are crucial for binding to receptors or, in context of protease stability, enzymes. Thus, when introduced in the

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

• periodicity may reflect transient intermolecular β-strand contacts involving hydrogen bonding through Val2 and Val4 residues (Figure S16, Supporting Information File 1). However, no long-range HN/HN or Hα/Hα ROEs could be detected in the 8 pentapeptides, indicating that transient intermolecular association

The photodecarboxylative addition of carboxylates to phthalimides as a key-step in the synthesis of biologically active 3-arylmethylene-2,3-dihydro-1H-isoindolin-1-ones

• Ommid Anamimoghadam,
• Saira Mumtaz,
• Anke Nietsch,
• Gaetano Saya,
• Cherie A. Motti,
• Jun Wang,
• Peter C. Junk,
• Ashfaq Mahmood Qureshi and
• Michael Oelgemöller

Beilstein J. Org. Chem. 2017, 13, 2833–2841, doi:10.3762/bjoc.13.275

• photoaddition products 3a and 3b were unambiguously confirmed by X-ray crystallography (Figure 2). In the solid state, molecules of both compounds undergo hydrogen bonding between the newly formed hydroxy group and the intact carbonyl group, resulting in a one-dimensional network (see Supporting Information

CF₃SO₂X (X = Na, Cl) as reagents for trifluoromethylation, trifluoromethylsulfenyl-, -sulfinyl- and -sulfonylation and chlorination. Part 2: Use of CF₃SO₂Cl

• Hélène Chachignon,
• Hélène Guyon and
• Dominique Cahard

Beilstein J. Org. Chem. 2017, 13, 2800–2818, doi:10.3762/bjoc.13.273

• ) species 18. During this step, facial selectivity originated partly from hydrogen-bonding interactions between the chiral phosphate and the N–H bond adjacent to the aryl group. Ion pairing interaction in a concerted transition state probably intervened in this phenomenon as well. The final product was then

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

• that the ancillary chain of 3 is unable to give multiple hydrogen bonding with the host cavity, due to the methyl group placed on the amino N atom. According to literature, this peculiar structural feature is able to enhance largely the outcome of entropy-unfavourable stiffening effects [50][52]. On

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

• (which appear more acidic than expected because of intramolecular hydrogen bonding) was supported by NMR evidences. Owing to solubility issues, we addressed our interest in evaluating the binding abilities of the anionic forms of CAP, namely the mono-, di-, tri- and tetra-anion, which could be obtained

• , a carbonyl band of fair intensity appears at 1727 cm−1, similar to the one expected for an undissociated carboxylic group. In turn, extensive hydrogen bonding affects the flexibility of the macrocycle scaffold, as well as the possible double free rotation of the arene–CH2–proline single bond–single

• bond system. Hydrogen bonding is likely enforced by deprotonation of a phenol group, due to enhanced Coulomb interaction with ammonium groups. Moreover, protonation of the nitrogen atom makes it a further chiral centre, which contributes to the overall optical activity of the system. Then, both 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

• protic solvents. We assumed that the use of the oxygen-free TFPE group would eliminate hydrogen bonding with protic solvents, even water, to avoid attenuation of the fluorescent characteristics of the fluorophore. In this paper, we report the synthesis of a new fluorophore with TFPE groups and its

Metal-mediated base pairs in parallel-stranded DNA

• Jens Müller

Beilstein J. Org. Chem. 2017, 13, 2671–2681, doi:10.3762/bjoc.13.265

• the triplex represents a duplex of its own. Scheme 2a indicates how the A:T and G:CH+ Hoogsteen base pairs are formally derived from the respective base triples. As can be seen, the cytosine residue needs to be protonated to engage in this hydrogen-bonding pattern. Based on the pKa value of a cytosine

• parallel-stranded to antiparallel-stranded (and vice versa) in the above-made correlations. These general considerations on how the type of hydrogen-bonding pattern, the orientation of the glycosidic bonds (syn vs anti) and their relative position (cisoid vs transoid) correlates with the relative strand

• reported in PDB entry 2RVP [25]. Hydrogen-bonding patterns of various reversed Watson–Crick base pairs. a) A:T; b) G:C (steric clash between opposing amino groups indicated by red hemicycles); c) G:C in an alternative geometry; d) iG:C. R, R’ = DNA backbone. Various hydrogen-bonding patterns. a) T:A:T and

Consecutive hydrazino-Ugi-azide reactions: synthesis of acylhydrazines bearing 1,5-disubstituted tetrazoles

• Angélica de Fátima S. Barreto,
• Veronica Alves dos Santos and
• Carlos Kleber Z. Andrade

Beilstein J. Org. Chem. 2017, 13, 2596–2602, doi:10.3762/bjoc.13.256

• presents several advantages. For instance, hydrazinopeptides comprise a class of peptidomimetics with promising biological and conformational activities [18][19][20][21]. It is worth mentioning that in such compounds the so-called "hydrazino-turns" are formed through intramolecular hydrogen bonding between

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

• reporting pyrenyl group and hydrogen-bonding biological nucleobase vector to be tested in DNA recognition and bioimaging applications. Results and Discussion A straightforward, one-pot two-step methodology for aryl–nucleobases has been recently developed in our laboratory and was examined in respect to

• ); C1–C2, 1.428(2); C15–C16, 1.433(2); C12–C13, 1.399(2); C30–Cl31···O28, 2.972(2); C3–H3···O26, 2.879(2); C1–C17–O16, 123.78(15); N22–C23–C24, 114.79(15); O27–C21–N22, 121.79(15); O27–C21–N20, 122.60(15); N20–C21–N22, 115.61(14); C2–C1–C17, 123.28(15). Intermolecular hydrogen bonding (N22–H22···O27

Electron-deficient pyridinium salts/thiourea cooperative catalyzed O-glycosylation via activation of O-glycosyl trichloroacetimidate donors

• Mukta Shaw,
• Yogesh Kumar,
• Rima Thakur and
• Amit Kumar

Beilstein J. Org. Chem. 2017, 13, 2385–2395, doi:10.3762/bjoc.13.236

• thiourea derivative as an hydrogen-bonding cocatalyst. This transformation occurs under mild reaction conditions with a wide range of O-glycosyl trichloroacetimidate donors and glycosyl acceptors to afford the corresponding O-glycosides in moderate to good yields with predictable selectivity. In addition

• amplified in the presence of other cocatalysts known as “cooperative catalysis” [23]. In particular, cooperativity between Brønsted acids and hydrogen-bonding cocatalysts such as thiourea derivatives has attracted much interest [24][25][26][27][28][29]. Despite the broad application of cooperative catalysis

• for the activation of glycals to provide stereoselective 2-deoxyglycosides with high yields [38]. Based on this fact, we anticipated that for electron-deficient pyridinium salts the pKa value would be further diminished in the presence of hydrogen-bonding cocatalysts such as thiourea derivatives. The

Solvent-free copper-catalyzed click chemistry for the synthesis of N-heterocyclic hybrids based on quinoline and 1,2,3-triazole

• Martina Tireli,
• Silvija Maračić,
• Stipe Lukin,
• Marina Juribašić Kulcsár,
• Dijana Žilić,
• Mario Cetina,
• Ivan Halasz,
• Silvana Raić-Malić and
• Krunoslav Užarević

Beilstein J. Org. Chem. 2017, 13, 2352–2363, doi:10.3762/bjoc.13.232

• time, the 1,2,3-triazoles became the heterocycle of choice in drug discovery, due to their favourable pharmacokinetic and safety profiles, hydrogen-bonding capability, moderate dipole moment, rigidity and stability under in vivo conditions [5][6]. Also, the ability of 1,2,3-triazoles to act as amide

Solid-state studies and antioxidant properties of the γ-cyclodextrin·fisetin inclusion compound

• Joana M. Pais,
• Maria João Barroca,
• Maria Paula M. Marques,
• Filipe A. Almeida Paz and
• Susana S. Braga

Beilstein J. Org. Chem. 2017, 13, 2138–2145, doi:10.3762/bjoc.13.212

• and C4 carbons, multiplicity is associated with differences in the conformation about the α(1→4) linkages, while carbons positioned closer to the rims, such as is the case for C6, are more sensitive to ambient changes arising from hydration water molecules and the hydrogen-bonding network [33][34