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

• . This review presents the latest findings in the pursuit of novel synthetic DNA binders. This article provides recent coverage of major strategies (such as groove recognition, intercalation and cross-linking) adopted in the duplex DNA recognition by small molecules, with an emphasis on major works of

• all DNA binding agents, this review article intends to provide a substantial coverage of new advancements made in the discovery of major leads in three most visited areas (groove recognition, intercalation and cross linking agents) of DNA recognition. 2. Minor groove binders (MGBs) DNA groove binding

Nanoreactors for green catalysis

• M. Teresa De Martino,
• Loai K. E. A. Abdelmohsen,
• Floris P. J. T. Rutjes and
• Jan C. M. van Hest

Beilstein J. Org. Chem. 2018, 14, 716–733, doi:10.3762/bjoc.14.61

• -aminophenol in water. The activity of these nanoreactors was tuned by varying the Ag NPs loading and the cross-linking density; higher activities were achieved by increasing the amount of Ag NPs loaded and decreasing the degree of polymer cross-linking. Such conditions facilitated the diffusion of water and

Mannich base-connected syntheses mediated by ortho-quinone methides

• Petra Barta,
• Ferenc Fülöp and
• István Szatmári

Beilstein J. Org. Chem. 2018, 14, 560–575, doi:10.3762/bjoc.14.43

• ). Rokita et al. focused on generating o-QMs and used them as cross-linking and DNA alkylating agents. Starting from Mannich base 56 and transforming it by a number of synthetic steps, they were managed to elaborate a process that provides easy access to o-QM precursors containing a broad array of linkers

• phenolic Mannich bases bearing functional groups that are suitable for cross-linking DNA; therefore, their antitumor effects could also be confirmed [96]. The formation of o-QMs and their biological properties were also illustrated by kinetic studies. Rokita et al. using laser flash photolysis showed that

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

• , the polymer self-optimised its binding affinity for the protein by increasing the proportion of galactosyl residues in the backbone. In the presence of low concentrations of a dihydrazide cross-linking agent, these polymers can also be used to make crosslinked films on surfaces coated with bacterial

Fluorogenic PNA probes

• Tirayut Vilaivan

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

• extended backbone at the ligation site [91]. Examples of the fluorogenic templated ligation of PNA are given in Table 1 which include the simple native chemical ligation of two fluorophore-labeled probes [92], formation of cyanine dyes [93][94], fluorogenic Michael addition [95][96] and cross-linking of

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• tetrazoles. Even photo-crosslinking moieties were enzymatically transferred to the N7-position of the mRNA cap from suitable AdoMet analogues. Notably, quantitative modification at the N7-position was achieved [96]. Diazirine and aryl–azide photo-crosslinker moieties were functional showing cross-linking to

Novel approach to hydroxy-group-containing porous organic polymers from bisphenol A

• Tao Wang,
• Yan-Chao Zhao,
• Li-Min Zhang,
• Yi Cui,
• Chang-Shan Zhang and
• Bao-Hang Han

Beilstein J. Org. Chem. 2017, 13, 2131–2137, doi:10.3762/bjoc.13.211

• connecting phenolic molecules with formaldehyde or other aromatic aldehydes to form cross-linking structures through the simple Bakelite-type chemistry to obtain great number of polymers with different functionalities. Phloroglucinol has been utilized as a monomer by Kanatzidis and Katsoulidis [23][24] to

The chemistry and biology of mycolactones

• Matthias Gehringer and
• Karl-Heinz Altmann

Beilstein J. Org. Chem. 2017, 13, 1596–1660, doi:10.3762/bjoc.13.159

• , ribosome-independent translocation of short secretory proteins (SSPs) is only partially affected. Together with the results of cross-linking experiments, these data indicate that mycolactone interferes with the ribosome–nascent chain (RNC)-Sec61 complex. Similar conclusions were recently derived from an

One-pot synthesis of block-copolyrotaxanes through controlled rotaxa-polymerization

• Jessica Hilschmann,
• Gerhard Wenz and
• Gergely Kali

Beilstein J. Org. Chem. 2017, 13, 1310–1315, doi:10.3762/bjoc.13.127

• polymers without chemical modification of the backbone. Through polyrotaxane formation solubility [2][3][4][5], as well as mechanical [1][2][3][6][7][8][9] and electrical properties [10], can be improved. Cross-linking of threaded macrocycles gives rise to so-called slide-ring gels with unique mechanical

Strategies toward protecting group-free glycosylation through selective activation of the anomeric center

• A. Michael Downey and
• Michal Hocek

Beilstein J. Org. Chem. 2017, 13, 1239–1279, doi:10.3762/bjoc.13.123

• debenzoylated or deacetylated using standard conditions (NaOMe/MeOH) nearly quantitatively and then covalently linked to several electrophiles, including proteins. Shown in Scheme 26 is the cross-linking of 1-thiohexahyaluronane (HA-6-SH) to a protein, the engineered thermostable lipase TTL from

• Thermoanaerobacter thermohydrosulfuricus, which contained an unnatural N-pentenoyllysine residue at position 221. They incorporated this N-pentenoyllysine amino acid into the protein using stop-codon suppression [81][82]. The subsequent thio–ene ligation resulted in quantitative cross-linking to the protein (as

Sugar-based micro/mesoporous hypercross-linked polymers with in situ embedded silver nanoparticles for catalytic reduction

• Qing Yin,
• Qi Chen,
• Li-Can Lu and
• Bao-Hang Han

Beilstein J. Org. Chem. 2017, 13, 1212–1221, doi:10.3762/bjoc.13.120

• -linkers [4], and self-polycondensation of small molecular monomers [5]. Since the Tan group proposed the new synthetic strategy that "knits" low functionality rigid aromatic compounds with formaldehyde dimethyl acetal (FDA) as an external cross-linking agent through a Friedel–Crafts reaction to synthesize

• -linker, the Friedel–Crafts cross-linking polymerization is promoted smoothly by anhydrous FeCl3 in dry 1,2-dichloroethane (DCE). The monomers were either commercially available (Sug-1) or prepared (Sug-2 and Sug-3) by benzylation of free sugars with benzyl bromide and sodium hydride. The chemical

Kinetic analysis of mechanoradical formation during the mechanolysis of dextran and glycogen

• Naoki Doi,
• Yasushi Sasai,
• Yukinori Yamauchi,
• Tetsuo Adachi,
• Masayuki Kuzuya and
• Shin-ichi Kondo

Beilstein J. Org. Chem. 2017, 13, 1174–1183, doi:10.3762/bjoc.13.116

• a cross-linking region without defined structure (structureless). We compared the spectral intensities of the singlet (II) in Dx and Gly. In Dx the spectral intensity of II reached the maximum value at 60 min of vibratory milling, and then tended to decrease gradually. On the other hand, the

• DBS of Gly might be more stabilized than that of Dx due to higher cross-linking in the hyper-branched structure of Gly. As mechanoradicals are formed by polymer main-chain scission [3][4][5], the quantity of mechanoradicals formed in the course of mechanolysis is associated with a change in molecular

• chains, different from amylose. Figure 7 also shows that the DBS in Gly was considerably more stable than that in Dx due to the higher cross-linking present in the hyper-branched structure of Gly. Conclusion We discussed here the nature of mechanoradical formation during mechanolysis of Dx and Gly, based

Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy

• Monica Ferro,
• Franca Castiglione,
• Nadia Pastori,
• Carlo Punta,
• Lucio Melone,
• Walter Panzeri,
• Barbara Rossi,
• Francesco Trotta and
• Andrea Mele

Beilstein J. Org. Chem. 2017, 13, 182–194, doi:10.3762/bjoc.13.21

• interest as drug carriers, since these materials are able to accommodate small drug molecules within their porous network made of CD lipophilic cavities and more hydrophilic polymer channels originated during the cross-linking process with suitable cross-linking agents (CL). The polymer is obtained by

• condensation reaction of the OH groups of the glucopyranose units of cyclodextrins (CD) with a poly-functional cross-linking agent [3]. CDNS have been characterized, in the solid state, by a repertoire of physical methods such as solid-state 13C CP-MAS NMR, FTIR and Raman spectroscopy [4][5][6]. Moreover, in

• ) was encapsulated in cyclodextrin nanosponges (CDNS) obtained by cross-linking of β-cyclodextrin with ethylenediaminetetraacetic acid dianhydride (EDTAn) in two different preparations: CDNS(1:4) and CDNS(1:8), where the 1:n notation indicates the CD to EDTAn molar ratio used for the synthesis. The

Supramolecular frameworks based on [60]fullerene hexakisadducts

• Andreas Kraft,
• Johannes Stangl,
• Ana-Maria Krause,
• Klaus Müller-Buschbaum and
• Florian Beuerle

Beilstein J. Org. Chem. 2017, 13, 1–9, doi:10.3762/bjoc.13.1

• materials with the prospect of applications in gas storage [2][3], catalysis [4][5], luminescence [6][7][8][9] and sensing [10][11][12][13] or optoelectronics [14][15][16]. Owing to a modular approach, building blocks and cross-linking interactions can be varied over a wide range resulting in metal-organic

• distances between the molecules depending on the spacer length and the mode of cross-linking. For HFF-1 (hydrogen-bonded fullerene framework) derived from C2, a densely packed structure is observed possessing only very small cavities within the octahedral sites of the fcc packing filled with one CH2Cl2

• indicated in grey); images are created with PyMOL [58]. Interpenetration of two distinct hydrogen bonding networks for HFF-3: a) side view indicating the spiral staircase-like cross-linking of individual molecules of C4, b) top view and c) side view highlighting the interpenetration of two networks colored

Hydroxy-functionalized hyper-cross-linked ultra-microporous organic polymers for selective CO₂ capture at room temperature

• Partha Samanta,
• Priyanshu Chandra and
• Sujit K. Ghosh

Beilstein J. Org. Chem. 2016, 12, 1981–1986, doi:10.3762/bjoc.12.185

• polymers (HCPs) are a subclass of this type of porous materials. Recently, hyper-cross-linked MOPs are emerged as a new subclass, synthesized by hyper-cross linking of basic small organic building blocks by Friedel–Crafts reaction in the presence of the Lewis acid FeCl3 (as catalyst) and formaldehyde

• synthesis, the cost-effective formaldehyde dimethyl acetal (FDA), FeCl3 and that organic small molecules can produce very low cost materials with high yield [28]. Hyper-cross-linking prevents the close packing of polymeric chains in this type of material to impart the intrinsic porosity. Hyper-cross-linked

Cross-linked cyclodextrin-based material for treatment of metals and organic substances present in industrial discharge waters

• Élise Euvrard,
• Nadia Morin-Crini,
• Coline Druart,
• Justine Bugnet,
• Bernard Martel,
• Cesare Cosentino,
• Virginie Moutarlier and
• Grégorio Crini

Beilstein J. Org. Chem. 2016, 12, 1826–1838, doi:10.3762/bjoc.12.172

• for the use of carboxylic acids and pyromellitic dianhydride, respectively, as agents to cross-linking CDs. Other cross-linking agents such as epichlorohydrin, ethylene glycol diglycidyl ether, glutaraldehyde, benzoquinone or isocyanates can be also used [1][12]. The main objective of the study was to

• C-6’, C-6 and C-7, respectively. These attributions were confirmed using cross-polarization with a polarization inversion sequence (CPPI spectrum not shown), which revealed three CH2 signals due to the CD and also a peak at 30.15 ppm corresponding to CH2 groups introduced by the cross-linking agent

• detail by Martel et al. [10][30]. Based from their methodology, the typical cross-linking reaction was carried out as follows: in a reactor, 0.37 mol·L−1 of sodium dihydrogenophosphate (Na2H2PO2·H2O, catalyst), 0.85 mol·L−1 of BTCA and 0.18 mol·L−1 of HPβCD were dissolved; the resulting solution was then

Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides

• Andrew W. Truman

Beilstein J. Org. Chem. 2016, 12, 1250–1268, doi:10.3762/bjoc.12.120

• thioester acyl–enzyme intermediate that is then attacked by Cys28 of AgrD to generate a 16-membered thiolactone [120] (Figure 9). Radical SAM-catalysed oxidative cross-linking The majority of characterised cyclic RiPPs are generated by standard ionic reactions. In contrast, radical mechanisms permit

• –4S] cluster along with simultaneous loss of a proton to rearomatise. An analogous reaction takes place in the biosynthesis of the bacterial cofactor pyrroloquinoline quinone (PQQ), where the SPASM protein PqqE was proposed to catalyse the oxidative cross-linking of carbon bonds on glutamate and

• PqqE, which then catalyses cross-linking. A number of SPASM proteins actually have a PqqD-like domain at their N-terminus, including AlbA and ThnB [130]. ThnB catalyses thioether bridge formation in thurincin H biosynthesis, and in vitro analysis demonstrated that its PqqD-like domain is essential for

Muraymycin nucleoside-peptide antibiotics: uridine-derived natural products as lead structures for the development of novel antibacterial agents

• Daniel Wiegmann,
• Stefan Koppermann,
• Marius Wirth,
• Giuliana Niro,
• Kristin Leyerer and
• Christian Ducho

Beilstein J. Org. Chem. 2016, 12, 769–795, doi:10.3762/bjoc.12.77

• , transformation to a disaccharide and transport to the extracellular side of the membrane (Figure 4, steps B, C); finally, polymerisation to long oligosaccharide chains and cross-linking occur (Figure 4, steps D, F). In the cytosol, uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), that is formed from

New synthetic strategies for xanthene-dye-appended cyclodextrins

• Milo Malanga,
• Andras Darcsi,
• Mihaly Balint,
• Gabor Benkovics,
• Tamas Sohajda and
• Szabolcs Beni

Beilstein J. Org. Chem. 2016, 12, 537–548, doi:10.3762/bjoc.12.53

• Supporting Information File 1, Figure S1) and the cross-linking with the data obtained by the COSY and DEPT-ed-HSQC spectra (see Supporting Information File 1, Figures S2 and S3, respectively) allowed for the complete assignment (the data are in agreement with the literature [22]). The multiplicity of the

• Information File 1, Figure S19) and the analysis of H–H J coupling and the cross-linking with the data obtained by the COSY and DEPT-ed HSQC spectra (Supporting Information File 1, Figures S21, S22 and Supporting Information File 1, Figure S24, respectively) allowed for a complete assignment of the resonance

Simple activation by acid of latent Ru-NHC-based metathesis initiators bearing 8-quinolinolate co-ligands

• Julia Wappel,
• Roland C. Fischer,
• Luigi Cavallo,
• Christian Slugovc and
• Albert Poater

Beilstein J. Org. Chem. 2016, 12, 154–165, doi:10.3762/bjoc.12.17

• Test. Tensile strength values (Rm) and the Young’s modulus (ε) were determined and used for comparison with literature data. The most reactive complexes 2b and 4 exhibit the highest Rm and Young’s Modulus values (see Table 2), which exceed data taken from literature. This indicates a higher cross

• linking density of the test specimens. Conclusion In conclusion we were able to synthesize a new family of N,O-chelating initiators bearing 5,7-dihalide-hydroxyquinoline co-ligands. We showed that it is possible to synthesize these initiators using starting complexes bearing different carbene- and

Supramolecular structures based on regioisomers of cinnamyl-α-cyclodextrins – new media for capillary separation techniques

• Gabor Benkovics,
• Ondrej Hodek,
• Martina Havlikova,
• Zuzana Bosakova,
• Pavel Coufal,
• Milo Malanga,
• Eva Fenyvesi,
• Andras Darcsi,
• Szabolcs Beni and
• Jindrich Jindrich

Beilstein J. Org. Chem. 2016, 12, 97–109, doi:10.3762/bjoc.12.11

• . The two regioisomers could be unambiguously distinguished and characterized by cross-linking the data of 1H NMR, 13C NMR, COSY, TOCSY, DEPT-ed-HSQC and HMBC. As an example, the elucidation of the regioisomer 2 is discussed here. The allylic proton signals can be detected in a separated region of the

Recent advances in metathesis-derived polymers containing transition metals in the side chain

• Ileana Dragutan,
• Valerian Dragutan,
• Bogdan C. Simionescu,
• Albert Demonceau and
• Helmut Fischer

Beilstein J. Org. Chem. 2015, 11, 2747–2762, doi:10.3762/bjoc.11.296

• norbornene monomer (27) functionalized with a water-soluble bis(terpyridine)ruthenium(II) complex, with dicyclopentadiene as a cross-linking agent (Scheme 12). In the resulted copolymer 28 each Ru complex is associated with two counteranions (chloride), which represents a novelty versus most cation-based

• membranes provided with single cation–anion pairs. Cross-linking with dicyclopentadiene ensured a high mechanical stability of the copolymer. The film cast from 28 displayed an anion conductivity and mechanical properties similar to those of the traditional quaternary ammonium-based anion exchange membranes

Synthesis, structure, and mechanical properties of silica nanocomposite polyrotaxane gels

• Kazuaki Kato,
• Daisuke Matsui,
• Koichi Mayumi and
• Kohzo Ito

Beilstein J. Org. Chem. 2015, 11, 2194–2201, doi:10.3762/bjoc.11.238

• polymers and surfaces, so that the mobility of the polymers can be maintained at the cross-linking points or the interface. We demonstrate here that the indirect connection between the backbone polymers and nanoparticles can be applied also for soft nanocomposite materials. As illustrated in Figure 1

• gelation occurred without silica. Thus, the modulus tends to increase with the concentration of silica, though the incremental increase of modulus is not proportional to silica concentration but stepwise. This suggests that the cross-linking density becomes higher with increasing silica concentration

• the significantly low modulus. Recent research in polyrotaxane gels, which were obtained by the simple cross-linking of polyrotaxanes via intermolecular covalent bonds between CDs, indicated a new origin of the elasticity experimentally and theoretically [12][14][16][18]. Since the polymer chains can

Dicarboxylic esters: Useful tools for the biocatalyzed synthesis of hybrid compounds and polymers

• Ivan Bassanini,
• Karl Hult and
• Sergio Riva

Beilstein J. Org. Chem. 2015, 11, 1583–1595, doi:10.3762/bjoc.11.174

• diacid derivative of oleic acid catalyzed by dibutyltin oxide and Novozyme 435 (Figure 10) [59]. Dibutyltin oxide catalysis resulted in cross-linking and gel formation. This was not observed by enzyme catalysis, presumably due to steric hindrance which may be imposed by the active site of the enzyme

Glycodendrimers: tools to explore multivalent galectin-1 interactions

• Jonathan M. Cousin and
• Mary J. Cloninger

Beilstein J. Org. Chem. 2015, 11, 739–747, doi:10.3762/bjoc.11.84

• exogenous galectin-1, extensive cellular aggregation was observed. Inducement of aggregation by exogenous galectin-1 comports with literature reporting pro-adhesive activity with galectin-1 [38][39][40][41]. There are two likely mechanism for galectin-1 mediation of cellular aggregation: (i) cross-linking

• glycodendrimers inhibited galectin-1 mediated cellular aggregation of the DU145 cells, which indicates that glycodendrimers mediate inhibition of cellular aggregation by competitively binding galectin-1, thereby altering its presentation to cells and preventing cellular cross-linking. Lactose functionalized G(2

• were added to cancer cells to modulate galectin-1 mediated cellular aggregation. The glycodendrimers inhibited cellular aggregation by providing competitive binding sites for the galectin-1 and diverting the galectin-1 from its native role in cellular cross-linking, which leads to cellular aggregation