Interactions between 4-thiothymidine and water-soluble cyclodextrins: Evidence for supramolecular structures in aqueous solutions

• Vito Rizzi,
• Sergio Matera,
• Paola Semeraro,
• Paola Fini and
• Pinalysa Cosma

Beilstein J. Org. Chem. 2016, 12, 549–563, doi:10.3762/bjoc.12.54

• development requires the use of all resources of molecular chemistry combined with the designed manipulation of non-covalent interactions so as to form supramolecular entities, supermolecules possessing features as well defined as those of molecules themselves” [1]. Starting from this definition, it is worth

• mentioning that among different kinds of non-covalent interactions, the host–guest type is extensively discussed in literature covering a large field of applications [4]. For example, cyclodextrins (CDs), among host molecules, are reported to occupy an important place in the field of inclusion phenomena [5

The aminoindanol core as a key scaffold in bifunctional organocatalysts

• Isaac G. Sonsona,
• Eugenia Marqués-López and
• Raquel P. Herrera

Beilstein J. Org. Chem. 2016, 12, 505–523, doi:10.3762/bjoc.12.50

• covalent and non-covalent interactions in an interesting bifunctional activation mode. Conclusion The design, synthesis and application of catalysts acting in a bifunctional manner is a hot topic in the field of organocatalysis and thus widely investigated. Generally, this particular mode of activation

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 415–428, doi:10.3762/bjoc.12.45

• linezolid in its bioactive conformation and 2) the existence of all non-covalent interactions known from the crystal structure, was finally the starting point for our conformational scan. All Mg2+ and Sr2+ ions of the mother-shell were replaced by Ca2+, the partially cut residues were completed. In order to

Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career

• Eric V. Anslyn

Beilstein J. Org. Chem. 2016, 12, 362–376, doi:10.3762/bjoc.12.40

• Eric V. Anslyn Department of Chemistry, University of Texas, Austin, TX 78712, USA 10.3762/bjoc.12.40 Abstract While the strict definition of supramolecular chemistry is “chemistry beyond the molecule”, meaning having a focus on non-covalent interactions, the field is primarily associated with

Interactions of cyclodextrins and their derivatives with toxic organophosphorus compounds

• Sophie Letort,
• Sébastien Balieu,
• William Erb,
• Géraldine Gouhier and
• François Estour

Beilstein J. Org. Chem. 2016, 12, 204–228, doi:10.3762/bjoc.12.23

• detect and to degrade organophosphate nerve agents [27]. In this respect, cyclodextrins (CDs) are interesting scaffolds because of their macrocyclic structure able to bind more or less selectively some organic substrates via non covalent interactions [28][29][30]. Due to their affinity for

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

• held together by non-covalent interactions, such as electrostatic interactions, coordination bonds, hydrogen bonds, hydrophobic interactions and host–guest interactions [1]. Their formation is spontaneous and reversible by self-assembly of the monomer units. Because of this special non-covalent

Assembly of synthetic Aβ miniamyloids on polyol templates

• Sebastian Nils Fischer and
• Armin Geyer

Beilstein J. Org. Chem. 2015, 11, 2646–2653, doi:10.3762/bjoc.11.284

• the template limits the aggregation degree. a) Peptide boronic acids 1 and 2 are schematically shown as green sticks (peptide) with a red gripper (boronic acid) and the template is blue. The peptide must be short enough to prevent the fibrillation shown on the right. b) Non-covalent interactions

Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

• Giuseppina Raffaini,
• Antonino Mazzaglia and
• Fabio Ganazzoli

Beilstein J. Org. Chem. 2015, 11, 2459–2473, doi:10.3762/bjoc.11.267

• place both in apolar solvent and in water in terms of the geometry of the aggregates and of their interaction energy in a given solvent. In the proposed approach the different shapes assumed by aCD and the non-covalent interactions with the solvent may lead to different macro-aggregates, either micelles

Size-controlled and redox-responsive supramolecular nanoparticles

• Raquel Mejia-Ariza,
• Gavin A. Kronig and
• Jurriaan Huskens

Beilstein J. Org. Chem. 2015, 11, 2388–2399, doi:10.3762/bjoc.11.260

• nanostructured materials composed of molecular building blocks [1]. This fabrication strategy has been used to form supramolecular nanoparticles (SNPs) in which multiple copies of different building blocks interact via specific, non-covalent interactions [2]. They have the potential to be used in biomedical

Conformational equilibrium in supramolecular chemistry: Dibutyltriuret case

• Karina Mroczyńska,
• Małgorzata Kaczorowska,
• Erkki Kolehmainen,
• Ireneusz Grubecki,
• Marek Pietrzak and
• Borys Ośmiałowski

Beilstein J. Org. Chem. 2015, 11, 2105–2116, doi:10.3762/bjoc.11.227

• ; hydrogen bonding; NMR; rotamerism; supramolecular chemistry; Introduction The hydrogen bond (HB) is one of the most common non-covalent interactions. Since it stabilizes, for example, the double helix of DNA and influences peptide folding it is quite reasonable to assume that HBing is crucial for

• [62][63] model of solvation (chloroform). The M05 functional suggested for non-covalent interactions [64][65] was used to sustain the methodology from our previous publications [9][10][50][66]. The Synchronous Transit-Guided Quasi-Newton method [67][68] has been used for optimization of the transition

Ru complexes of Hoveyda–Grubbs type immobilized on lamellar zeolites: activity in olefin metathesis reactions

• Hynek Balcar,
• Naděžda Žilková,
• Martin Kubů,
• Michal Mazur,
• Zdeněk Bastl and
• Jiří Čejka

Beilstein J. Org. Chem. 2015, 11, 2087–2096, doi:10.3762/bjoc.11.225

• developed [1][5][13]; most of them are based on surface modification by specially designed linkers providing covalent bond linkage between the support and Ru complex. Hoveyda–Grubbs type catalysts are also capable of direct (linker-free) immobilization by means of non-covalent interactions [8][14][15][16

• −) and their immobilization on silica, and mesoporous molecular sieves MCM-41 and SBA-15 [21]. XPS analysis revealed that complexes were attached to the surface by non-covalent interactions and both cationic and anionic parts were present on the surface. The hybrid catalysts prepared were active in RCM

Polythiophene and oligothiophene systems modified by TTF electroactive units for organic electronics

• Alexander L. Kanibolotsky,
• Neil J. Findlay and
• Peter J. Skabara

Beilstein J. Org. Chem. 2015, 11, 1749–1766, doi:10.3762/bjoc.11.191

• system to 2D with a significant contribution from S···S non-covalent interactions [26]. This gave a record transition temperature among TTF mixed valence ambient pressure superconductors in the salt κ-(BEDT-TTF)2Cu[N(CN)2]Br [27]. In an attempt to create macromolecular compounds with multi-electron redox

• between thiophenes C and G is higher (18.36°) but the two S-atoms are involved in a weak non-covalent interaction with a distance of 3.81 Å between them. The strong π–π stacking interaction and the presence of multiple S–S non-covalent interactions in the H-shaped TTF-oligothiophene system 54 (n = 2) made

Thiazole-induced rigidification in substituted dithieno-tetrathiafulvalene: the effect of planarisation on charge transport properties

• Rupert G. D. Taylor,
• Joseph Cameron,
• Iain A. Wright,
• Neil Thomson,
• Olena Avramchenko,
• Alexander L. Kanibolotsky,
• Anto R. Inigo,
• Tell Tuttle and
• Peter J. Skabara

Beilstein J. Org. Chem. 2015, 11, 1148–1154, doi:10.3762/bjoc.11.129

• demonstrated that the substitution of thiophene units for thiazoles was found to increase the observed charge transport, which is attributed to induced planarity through S–N interactions of adjacent thiazole nitrogen atoms and TTF sulfur atoms and better packing in the bulk. Keywords: non-covalent

• interactions; organic field effect transistor (OFET); organic semiconductors; tetrathiafulvalene; thiazole; Introduction The TTF moiety has received much attention in the field of organic electronics owing to its reliable redox behaviour [1], good charge transport properties [2] and scope for

Synthesis of photoresponsive cholesterol-based azobenzene organogels: dependence on different spacer lengths

• Yuchun Ren,
• Bin Wang and
• Xiuqing Zhang

Beilstein J. Org. Chem. 2015, 11, 1089–1095, doi:10.3762/bjoc.11.122

• ], etc. The driving force for the spontaneous formation of gel could be relatively non-covalent interactions such as π–π stacking [4][5][6][7], hydrogen bonding [7][8][9], dipole–dipole [10], and van der Waals interactions [11][12]. A series of cholesterol-based gelators were reported [13][14][15]. These

Mechanical stability of bivalent transition metal complexes analyzed by single-molecule force spectroscopy

• Manuel Gensler,
• Christian Eidamshaus,
• Maurice Taszarek,
• Hans-Ulrich Reissig and
• Jürgen P. Rabe

Beilstein J. Org. Chem. 2015, 11, 817–827, doi:10.3762/bjoc.11.91

• important in biochemistry [1] and supramolecular chemistry [2], but still not fully understood on the level of individual non-covalent interactions [3]. Synthetic supramolecular systems are ideal for a quantitative analysis of multivalency on the level of single molecules, because specific ligand design can

• clamp motifs, as suggested by Sikora et al. [19]. For example, zipper-type unfolding requires less force than shear-type denaturation. However due to the high complexity of biological multivalent interactions less is known about the influence from individual non-covalent interactions. Here, well defined

Regulation of integrin and growth factor signaling in biomaterials for osteodifferentiation

• Qiang Wei,
• Theresa L. M. Pohl,
• Anja Seckinger,
• Joachim P. Spatz and
• Elisabetta A. Cavalcanti-Adam

Beilstein J. Org. Chem. 2015, 11, 773–783, doi:10.3762/bjoc.11.87

• , which can stimulate cell growth and differentiation, have also been employed for bone treatment [8][9]. Growth factors are water soluble proteins embedded in the ECM network mainly via non-covalent interactions with glycosaminoglycanes (GAG) [10]. Therefore, the ECM serves as a reservoir by establishing

Diastereoselective and enantioselective conjugate addition reactions utilizing α,β-unsaturated amides and lactams

• Katherine M. Byrd

Beilstein J. Org. Chem. 2015, 11, 530–562, doi:10.3762/bjoc.11.60

• available materials. Organocatalysts can be placed into two catagories: 1) catalysts that covalently attach themselves to the starting materials (e.g., enamine [269] and iminium [270] catalysis) and 2) catalysts that interact with the starting materials through non-covalent interactions (e.g., hydrogen

Release of β-galactosidase from poloxamine/α-cyclodextrin hydrogels

• César A. Estévez,
• José Ramón Isasi,
• Eneko Larrañeta and
• Itziar Vélaz

Beilstein J. Org. Chem. 2014, 10, 3127–3135, doi:10.3762/bjoc.10.330

• are able to form host–guest complexes by the inclusion of hydrophobic molecules. Cyclodextrins also act as hosts in the formation of inclusion compounds with polymer chains through non-covalent interactions [10]. For instance, incorporation of 5% α-CD transforms dilute Tetronic solutions into gels

A one-pot multistep cyclization yielding thiadiazoloimidazole derivatives

• Debabrata Samanta,
• Anup Rana,
• Jan W. Bats and
• Michael Schmittel

Beilstein J. Org. Chem. 2014, 10, 2989–2996, doi:10.3762/bjoc.10.317

• with a 6-31G(d,p) basis set for hydrogen to include polarization on hydrogen and the 6-31G(d) basis set for the other main group elements using NWChem 6.3 [15]. During optimization, we utilized Grimme’s D3 dispersion [16] for a better description of non-covalent interactions like hydrogen bonding and π

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

• shape, whereas the high polarizability (and permanent positive charge of N-5 alkylated derivatives) also plays an important role in aromatic and electrostatic interactions with polynucleotides. Moreover, non-covalent interactions with DNA and RNA can be reversibly controlled by a pH-induced positive

• allows the incorporation of considerably long substituents at 3,8- positions available for attachment to DNA and RNA and/or various additional non-covalent interactions with the polynucleotide backbone. The ethidium bromide incorporated as an artificial DNA base (18, Figure 9) at specific sites in duplex

Synthesis and biological evaluation of novel N-α-haloacylated homoserine lactones as quorum sensing modulators

• Michail Syrpas,
• Ewout Ruysbergh,
• Christian V. Stevens,
• Norbert De Kimpe and
• Sven Mangelinckx

Beilstein J. Org. Chem. 2014, 10, 2539–2549, doi:10.3762/bjoc.10.265

• with high structural deviation from the parent autoinducer [15]. In biological processes, covalent binding and non-covalent interactions are encountered in many protein-ligand interactions as well as in protein secondary structures and are of great significance. In the past years, it was shown that the

Towards the sequence-specific multivalent molecular recognition of cyclodextrin oligomers

• Michael Kurlemann and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2014, 10, 2428–2440, doi:10.3762/bjoc.10.253

• -covalent interactions stable yet reversible systems are generated, which are responsive to external stimuli. These advantages have made synthetic multivalent systems interesting for a broad field of applications. In the case of medicinal applications multivalent molecules have been used as inhibitors of

• binding partner [1]. In recent years multivalency has been recognized to play a major role in almost all biological processes, e.g., the recognition of cells by other cells, bacteria or viruses, the adhesion of cells or signal transduction pathways [2]. By the combination of multiple, rather weak non

Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

• Marijana Radić Stojković,
• Marko Škugor,
• Łukasz Dudek,
• Jarosław Grolik,
• Julita Eilmes and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2175–2185, doi:10.3762/bjoc.10.225

• /RNA intercalation, minor or major groove binding, and external electrostatic binding [1]. However, non-covalent interactions involving small molecules (Mw < 600) can only rely on a small number of interacting groups, while the steric parameters of DNA/RNA binding sites are also quite limited

Improving the reactivity of phenylacetylene macrocycles toward topochemical polymerization by side chains modification

• Simon Rondeau-Gagné,
• Jules Roméo Néabo,
• Maxime Daigle,
• Katy Cantin and
• Jean-François Morin

Beilstein J. Org. Chem. 2014, 10, 1613–1619, doi:10.3762/bjoc.10.167

• ; phenylacetylene macrocycles; polydiacetylenes; topochemical polymerization; Introduction The self-assembly of molecular building blocks is an increasingly popular method for the preparation of new semiconducting materials. Rational design of building blocks and their assembly using non-covalent interactions can

Substitution effect and effect of axle’s flexibility at (pseudo-)rotaxanes

• Friedrich Malberg,
• Jan Gerit Brandenburg,
• Werner Reckien,
• Oldamur Hollóczki,
• Stefan Grimme and
• Barbara Kirchner

Beilstein J. Org. Chem. 2014, 10, 1299–1307, doi:10.3762/bjoc.10.131

• non-covalent interactions between the axle and the wheel. Therefore, the understanding of these (mostly) attractive forces is crucial for the development of the field. Also, by understanding how one can modify or even tune the axle–wheel interplay, rotaxanes for different purposes can be designed

• enhancing the applicability of such materials. This study aims to understand rotaxanes with respect to its non-covalent interactions on the molecular level and to contribute to a more rational design of new molecular machines. Therefore, we investigated the energetics by substitution the rotaxanes with

• of non-covalent interactions. The distances R1, R2, and R3 are significantly smaller in the crystal compared to the gas phase structure. The torsion angles φ1 and φ2 describe the relative tilting between the flexible phenyl rings, which differs by more than 10° between crystal and gas phase. All