In-depth characterization of self-healing polymers based on π–π interactions

• Josefine Meurer,
• Julian Hniopek,
• Johannes Ahner,
• Michael Schmitt,
• Jürgen Popp,
• Stefan Zechel,
• Kalina Peneva and
• Martin D. Hager

Beilstein J. Org. Chem. 2021, 17, 2496–2504, doi:10.3762/bjoc.17.166

• previous studies, several of these interactions were already applied such as metal–ligand interactions [13][14], hydrogen bonds [15][16] or halogen bonds [17]. Furthermore, π–π interactions also feature a reversible behavior and were therefore utilized for the design of different self-healing polymers [18

Targeting active site residues and structural anchoring positions in terpene synthases

• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2021, 17, 2441–2449, doi:10.3762/bjoc.17.161

• hydrogen bonds to the substrate’s diphosphate and to the second Asp of the Asp-rich motif (Figure 1), is also not observed in SmTS1, but here a Phe residue (F307) is found. Site-directed mutagenesis and sesterterpene synthase activity To investigate possible functions of the unusual residues in SmTS1

• sensor R178 (Figure 1). As SmTS1 does not contain this Arg residue, but a Gly instead, the opened space in this region could allow for direct hydrogen bonds between Q227 and the substrate’s diphosphate, which may become even stronger in the Q227D variant, explaining its higher catalytic efficiency

Halides as versatile anions in asymmetric anion-binding organocatalysis

• Lukas Schifferer,
• Martin Stinglhamer,
• Kirandeep Kaur and
• Olga García Macheño

Beilstein J. Org. Chem. 2021, 17, 2270–2286, doi:10.3762/bjoc.17.145

• halogens are often regarded as surrogates for further functionalization, their role in natural and physiological processes is much more diverse. One of these processes is the ability of large complex molecules and enzymes to recognize halide anions via hydrogen bonds in aqueous media [5]. Amongst others

• ) [76]. Due to the linkage of the two molecules, the participating hydrogen bonds are aligned such that a 4H-abstraction mode is achieved, which is more likely to ensure higher catalyst activity in the activation step than the competing 2H-abstraction pathway. Indeed, with multidentate bis-thiourea

(Phenylamino)pyrimidine-1,2,3-triazole derivatives as analogs of imatinib: searching for novel compounds against chronic myeloid leukemia

• Luiz Claudio Ferreira Pimentel,
• Lucas Villas Boas Hoelz,
• Henayle Fernandes Canzian,
• Frederico Silva Castelo Branco,
• Andressa Paula de Oliveira,
• Vinicius Rangel Campos,
• Floriano Paes Silva Júnior,
• Rafael Ferreira Dantas,
• Jackson Antônio Lamounier Camargos Resende,
• Anna Claudia Cunha,
• Nubia Boechat and
• Mônica Macedo Bastos

Beilstein J. Org. Chem. 2021, 17, 2260–2269, doi:10.3762/bjoc.17.144

• original work that led to compound 3, and, additionally, they are able to act as acceptors and donors in hydrogen bonds and thus were expected to increase the aqueous solubility of the compounds. Additionally, Kalesh and co-workers demonstrated good results with derivative 4 which contains the amide group

• ). Additionally, the analysis of the interactions between IMT and the enzyme BCR-Abl-1 shows hydrogen bonds with Glu305, Thr334, Met337, and Asp400 (hydrogen bonding energy = −8.97 a.u.) and steric interactions with Glu305, Thr334, Met337, Ile379, and Asp400 (steric binding energy = −193,658 a.u.), in agreement

• , 2c, 2d, and 2g with the BCR-Abl-1 structure (PDB code: 3PYY), showing steric interactions (red dotted lines) and hydrogen bonds (blue dotted lines). Synthetic route of the triazole derivatives 1a,b, and 2a–j. Cytotoxic activity, confidence interval, and selectivity index of imatinib and derivatives

Constrained thermoresponsive polymers – new insights into fundamentals and applications

• Patricia Flemming,
• Alexander S. Münch,
• Andreas Fery and
• Petra Uhlmann

Beilstein J. Org. Chem. 2021, 17, 2123–2163, doi:10.3762/bjoc.17.138

• and ∆mG becomes negative and the polymer dissolves. This phenomenon occurs for polymers whose interactions with the solvent or between the chains are characterized by strong dipol–dipol interactions, such as Coulomb forces, or by hydrogen bonds. Hence, on the one hand, strongly charged zwitterionic

• entropic effect characterized by negative ∆mH and ∆mS values. The essential structural feature of such polymers is their amphiphilic structure of hydrophobic domains and hydrophilic groups, which can form hydrogen bonds with water. These interactions result in a highly ordered hydration shell when the

• macromolecule is in solution. The best known example of a phase transition with an LCST is PNIPAAm with its hydrophilic isopropyl groups interacting with water molecules [48][97][98][99]. From a thermodynamic point of view, the hydrogen bonds between the polymer and the water molecules lead to a negative value

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

• orientation of the individual chains and in the number of hydrogen bonds in the crystalline structures [42][43]. In Cellulose I, the chains are oriented parallel, whereas in Cellulose II antiparallel. Natural cellulose is produced by cellulose synthases [44][45][46]. As the chain gets elongated, microfibrils

• pattern by chemical synthesis, albeit in low yields. Selective disruption of intra- and intermolecular hydrogen bonds suggested that modifications can be designed to prevent precipitation and guide cellulose assembly. Xyloglucans Xyloglucans (XGs) are based on a β(1–4)-Glc backbone decorated with

Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides

• Mathias B. Danielsen and
• Jesper Wengel

Beilstein J. Org. Chem. 2021, 17, 1828–1848, doi:10.3762/bjoc.17.125

•  3A) [57]. The G-clamp modification was later observed to have antisense inhibition activity involving RNase H cleavage with a single incorporation into a PS-ON [58]. Afterwards, a guanidino-G-clamp (modification 24) was synthesized to increase the number of hydrogen bonds that could be established

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

• Hoogsteen triplets in Figure 6 are stabilized by two hydrogen bonds, because of the positive charge, M forms a significantly more stable M+•G–C triplet compared to either J•G–C or T•A–U in dsRNA [28][30]. In a recent study, replacement of six Js with Ms increased the binding affinity of a PNA 9-mer ≈100

• recognition of dsDNA and dsRNA. However, the triple helical recognition has a severe sequence limitation – the requirement of polypurine tracts in target nucleic acids. Natural triple helices allow only T•A–T (or U•A–U) and C+•G–C triplets stabilized by two Hoogsteen hydrogen bonds (Figure 6) [94]. Analogous

Co-crystallization of an organic solid and a tetraaryladamantane at room temperature

• Fabian Rami,
• Jan Nowak,
• Felix Krupp,
• Wolfgang Frey and
• Clemens Richert

Beilstein J. Org. Chem. 2021, 17, 1476–1480, doi:10.3762/bjoc.17.103

• methyl substituent of the chaperone was found to be disordered, but otherwise well resolved structures were obtained, with hydrogen bonds between phenol hydroxy groups and ether groups of the chaperone (see Table S1 in Supporting Information File 1). For TEO, the crystal system of the co-crystals is

• group. But again, hydrogen bonds between phenol hydroxy groups and the alkoxy substituent of the crystallization chaperone can be resolved. So, in both co-crystal lattices, hydrogen bonding stabilizes the packing arrangement. For TDA/phenol, the host builds the crystal lattice with TDA molecules in

Structural effects of meso-halogenation on porphyrins

• Keith J. Flanagan,
• Maximilian Paradiz Dominguez,
• Zoi Melissari,
• Hans-Georg Eckhardt,
• René M. Williams,
• Dáire Gibbons,
• Caroline Prior,
• Gemma M. Locke,
• Alina Meindl,
• Aoife A. Ryan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88

• ‘guests’ within the crystal lattice, through hydrogen-bonding and van der Waals forces. Thereafter, research over the crystal engineering of porphyrins has focused on the noncovalent interactions, such as hydrogen bonds and halogen bonds, or metal coordination interactions [2][3][4][5][6][7][8][9][10][11

Synthesis of multiply fluorinated N-acetyl-D-glucosamine and D-galactosamine analogs via the corresponding deoxyfluorinated glucosazide and galactosazide phenyl thioglycosides

• Vojtěch Hamala,
• Lucie Červenková Šťastná,
• Martin Kurfiřt,
• Petra Cuřínová,
• Martin Dračínský and
• Jindřich Karban

Beilstein J. Org. Chem. 2021, 17, 1086–1095, doi:10.3762/bjoc.17.85

• desolvation penalty associated with binding of hydrophilic natural carbohydrates [8], and (2) create additional contacts with the binding cavity via electrostatic and dipolar interactions with C–F bonds [9][10], new intermolecular hydrogen bonds [11], or rearrangement of hydrogen bond-mediating water

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• ]. Compared to the native complex, conformational changes in the RNA and protein were only observed around the site of the AM1 modification. Not only was the amide an ideal structural mimic of phosphate, it also possessed stabilizing hydrogen bonds between the amide N–H and the main chain oxygen and side

• revealed that thermal stabilization may be attributed to nonconventional hydrogen bonds in the backbone [195][196][197]. Gene silencing by RNAi has also been explored with siRNA containing FANA residues [198]. These studies have shown that FANA is accommodated in the sense strand and 5'-end and 3'-termini

DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

• Yongdong Su,
• Maitsetseg Bayarjargal,
• Tracy K. Hale and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65

• hydrophobicity of Ts results in less water molecules involved in the formation of hydrogen bonds with dsDNA. However, it does not improve the interaction between two DNA strands, possibly due to the large size of the Ts moiety. For duplexes of the N+ and Ts-ONs formed with complementary RNA, both ΔH and TΔS

• cell-based applications. Illustration of H-bonding in a DNA duplex and a parallel triplex. A) Depiction of Watson–Crick base-paring (left: T-A and right: C-G); B) parallel triple helices: pyrimidine-rich third strand interactions are stabilised by Hoogsteen hydrogen bonds (the duplex is in black, TFO

[2 + 1] Cycloaddition reactions of fullerene C₆₀ based on diazo compounds

• Yuliya N. Biglova

Beilstein J. Org. Chem. 2021, 17, 630–670, doi:10.3762/bjoc.17.55

• butyric acid 209. Based on this, fullerene dimer 210 with four hydrogen bonds having a very high dimerization constant was obtained (Scheme 43). Diethyl 4-oxopimelate was used as the precursor of polymer 213. The former was converted via diacid 211 to the target methanofullerene 212, the solution of which

Mesoionic tetrazolium-5-aminides: Synthesis, molecular and crystal structures, UV–vis spectra, and DFT calculations

• Vladislav A. Budevich,
• Sergei V. Voitekhovich,
• Alexander V. Zuraev,
• Vadim E. Matulis,
• Vitaly E. Matulis,
• Alexander S. Lyakhov,
• Ludmila S. Ivashkevich and
• Oleg A. Ivashkevich

Beilstein J. Org. Chem. 2021, 17, 385–395, doi:10.3762/bjoc.17.34

• show no hydrogen bonds in their crystal structures and only van der Waals interactions take place between the molecules. The bistetrazolium salt 9 (bromide salt of mesoionic compound 10) crystallizes in the trigonal space group , with 18 formula units in the unit cell. The asymmetric unit includes one

• their complexation. In salt 9, the bromide ions are held in the crystal structure by hydrogen bonds N15–H15···Br1b [D···A = 3.2774(17) Å, D–H···A = 142°; symmetry code: (b) –x + y + 1/3, −x + 2/3, z + 2/3] and N25–H25···Br2 (D···A = 3.2654(17) Å, D–H···A = 144°). There are also intramolecular hydrogen

• following reasons: in case of chloroform, the solvent can form hydrogen bonds with the nitrogen atoms of the 8a molecule, whereas for methanol and water solutions, the solvent can act as a proton donor, and as a result, compound 8a may exist in the 1,3-di-tert-butyl-5-aminotetrazolium cationic form. To

Multiswitchable photoacid–hydroxyflavylium–polyelectrolyte nano-assemblies

• Alexander Zika and
• Franziska Gröhn

Beilstein J. Org. Chem. 2021, 17, 166–185, doi:10.3762/bjoc.17.17

• change of the pH value from pH 7.0 to pH 5.0 leads to an addition of one hydroxy group. This means that the number of possible hydrogen bonds increases from four at pH 7.0 to five at pH 5.0. Yet, the added hydroxy group is in a position where steric hindrance can play a major role. Furthermore, Flavy and

• the photoacid also form nano-assemblies on their own, which are also dependent on the pH value (see Supporting Information File 1). The assemblies are expected to form due to hydrogen bonds and ionic-dipole interaction. Already the raw data (Figure 8) clearly show an exothermic, an endothermic, and

• and one charge plus four hydrogen bonds, which corresponds to one Flavy for example. In difference, the second and fourth binding step are endothermic with ΔH2 = 64.5 kJ/mol and ΔH4 = 75.5 kJ/mol. Here, the association is entropically driven with ΔS2 = 0.22 kJ/mol/K and ΔS4 = 0.22 kJ/mol/K, indicating

Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders

• David Straßburger,
• Svenja Herziger,
• Katharina Huth,
• Moritz Urschbach,
• Rainer Haag and
• Pol Besenius

Beilstein J. Org. Chem. 2021, 17, 97–104, doi:10.3762/bjoc.17.10

• interactions [17][18]. By a careful design of the corresponding building blocks, extensive multilateral hydrogen bonds between the amino acid sequences of the oligopeptide backbone lead to secondary structures that direct the equilibrium to polymeric nano-scaled assemblies. A well-studied receptor making use

Circularly polarized luminescent systems fabricated by Tröger's base derivatives through two different strategies

• Cheng Qian,
• Yuan Chen,
• Qian Zhao,
• Ming Cheng,
• Chen Lin,
• Juli Jiang and
• Leyong Wang

Beilstein J. Org. Chem. 2021, 17, 52–57, doi:10.3762/bjoc.17.6

• rac-TBPP/DGG = 1:80, a mirror symmetry was observed in the CPL spectra of the co-gel at the molar ratio of rac-TBPP/LGG = 1:80 (Figure 2d). rac-TBPP contains pyridine units, and the gelator DGG has the carboxyl groups. Therefore, hydrogen bonds might be formed between pyridine in rac-TBPP and the

• could be involved in the formation of various hydrogen bonds (Figure 3b, Figure S7, Supporting Information File 1). At the molar ratio of rac-TBPP/DGG = 1:16, the intensity of the peak at 1691 cm−1 decreases, and the peak at 1729 cm−1 brodens. A new peak adjacent to 1645 cm−1 appears at 1627 cm−1. The

• results demonstrate that some of the acid–acid hydrogen bonds between DGG molecules might be replaced by acid–pyridine hydrogen bonds between DGG and rac-TBPP [27]. In addition, the possible influence of the stoichiometric ratios to the morphologies of rac-TBPP/DGG co-gels was investigated using a

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• . In obligate complexes, the interface is characterised by hydrophobic and aromatic residues while in non-obligate, the residues are more polar and charged, with the interface area being smaller [55] and containing more hydrogen bonds [56]. PPIs can also be differentiated by either being transient

Chiral anion recognition using calix[4]arene-based ureido receptors in a 1,3-alternate conformation

• Tereza Horáčková,
• Jan Budka,
• Vaclav Eigner,
• Wen-Sheng Chung,
• Petra Cuřínová and
• Pavel Lhoták

Beilstein J. Org. Chem. 2020, 16, 2999–3007, doi:10.3762/bjoc.16.249

• . The shapes and geometries of anions are widely different, and therefore the design of corresponding tailor-made receptors is based mostly on more directional interactions, such as hydrogen bonds. Indeed, an incredible number of neutral receptors bearing amide, sulfonamide, urea, thiourea, pyrrole, or

• chain of calixarene molecules joined together by intermolecular hydrogen bonds between the ureido groups (the C=O···H–N distances were 2.293 and 2.048 Å). One of the ureido functions in the macrocycle also held acetone via a C=O···H–N hydrogen bond (2.085 Å) and via a C=O···H–C bond (2.670 Å) from the

• the dimeric motif. X-ray structure of 7d, showing hydrogen bonds between the ureido units (green) and hydrogen bonding of acetone molecules (black). One alkyl group in each calixarene was removed for better clarity. 1H NMR titration of 7c with N-acetyl-ᴅ-phenylalaninate and N-acetyl-ʟ-phenylalaninate

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• ). The inhibition by peptide 9 is found to be in a reversible and noncompetitive way. Molecular modeling shows four cationic ammonium groups forming ion pairs and hydrogen bonds with negatively charged residues, such as Glu217, Asp60B, Asp147 and Glu217, respectively and completely block the central pore

Naphthalonitriles featuring efficient emission in solution and in the solid state

• Sidharth Thulaseedharan Nair Sailaja,
• Iván Maisuls,
• Jutta Kösters,
• Alexander Hepp,
• Andreas Faust,
• Jens Voskuhl and
• Cristian A. Strassert

Beilstein J. Org. Chem. 2020, 16, 2960–2970, doi:10.3762/bjoc.16.246

• together by C–H…N intermolecular hydrogen bonds with distances of 3.006 Å for C–H(2e)/N(6) and 3.083 Å for C–H(2d)/N(6) while involving hydrogen atoms of the tolyl moieties and the nitrogen atoms of nitrile groups. Then, these dimeric substructures are linked by C–H…N intermolecular interactions to

Construction of pillar[4]arene[1]quinone–1,10-dibromodecane pseudorotaxanes in solution and in the solid state

• Xinru Sheng,
• Errui Li and
• Feihe Huang

Beilstein J. Org. Chem. 2020, 16, 2954–2959, doi:10.3762/bjoc.16.245

• in the solid state. From single crystal X-ray diffraction, the linear guest molecules thread into cyclic pillar[4]arene[1]quinone host molecules in the solid state, stabilized by CH∙∙∙π interactions and hydrogen bonds. The bromine atoms at the periphery of the guest molecule provide convenience for

• bonds. Specifically, there are four hydrogen atoms on the guest molecule to form multiple CH∙∙∙π interactions with the 1,4-diethoxybenzene subunits of the host. In addition, the two bromine atoms at the periphery of the guest molecule are outside the host cavities and form moderate hydrogen bonds with

• crystallography revealed that two host molecules complex one guest molecule, forming a [3]pseudorotaxane in the solid state (Figure 1). In the crystal structure, the alkyl chain of the guest is threaded through the cavities of two host molecules, which is stabilized by multiple CH∙∙∙π interactions and hydrogen

Controlled decomposition of SF₆ by electrochemical reduction

• Sébastien Bouvet,
• Bruce Pégot,
• Stéphane Sengmany,
• Erwan Le Gall,
• Eric Léonel,
• Anne-Marie Goncalves and
• Emmanuel Magnier

Beilstein J. Org. Chem. 2020, 16, 2948–2953, doi:10.3762/bjoc.16.244

• supporting electrolytes based on tetrabutylammonium (TBA) structures after anion exchange. This poor resolved signal is quite classical for such species due to hydrogen bonds. Another important point is the production of H+ ions at the counter electrode because of the oxidation of acetonitrile [31][32

UV resonance Raman spectroscopy of the supramolecular ligand guanidiniocarbonyl indole (GCI) with 244 nm laser excitation

• Tim Holtum,
• Vikas Kumar,
• Daniel Sebena,
• Jens Voskuhl and
• Sebastian Schlücker

Beilstein J. Org. Chem. 2020, 16, 2911–2919, doi:10.3762/bjoc.16.240

• -covalent interactions namely hydrogen bonds, van der Waals, and/or hydrophobic interactions [1][2][3][4][5]. In this context, Schmuck and co-workers have introduced a class of synthetic receptors based on the guanidiniocarbonyl pyrrole (GCP) moiety (cf. Figure 1 top right) as a carboxylate binding site