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

• to the edges of the base pairs of the DNA duplex (usually G·C sites in the major groove, A·T sites in the minor groove) via reversible non-covalent interactions. These binding interactions reduce the conformational freedom of the small molecules and usually are opposed by an unfavorable entropic cost

Mechanochemistry of nucleosides, nucleotides and related materials

• Olga Eguaogie,
• Joseph S. Vyle,
• Patrick F. Conlon,
• Manuela A. Gîlea and
• Yipei Liang

Beilstein J. Org. Chem. 2018, 14, 955–970, doi:10.3762/bjoc.14.81

• . Mechanochemistry has also found recent attention in materials chemistry and API formulation during which rearrangement of non-covalent interactions give rise to functional products. However, this has been known to nucleic acids science almost since its inception in the late nineteenth century when Miescher

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

• substrate binding sites in their basic and acidic forms, respectively. 3.2. Nanogels Nanogels are hydrophilic polymer networks which can swell in the presence of water [109]. They can be crosslinked by either chemical bonds or physical methods, such as non-covalent interactions, entanglements and

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• nucleic acids, whose helices are normally elongated in a single direction [2]. In this context one of the most common approaches is to monitor the changes in the ECD or LD spectrum upon binding of a ligand to DNA or RNA [6]. Non-covalent interactions of small molecules (ligands) with DNA and RNA are of

• between nucleic acids and small ligands. This tutorial aims to help researchers entering the research field to organize experiments accurately and to interpret the obtained data reliably. Keywords: circular dichroism; emission-based dichroism; groove binding; intercalation; linear dichroism; non-covalent

• interactions; nucleic acids recognition; vibrational circular dichroism; Review 1. Introduction Many biological molecules are chiral and chromophoric among which the most important examples include proteins and nucleic acids. Moreover, the chiral constituents of natural biopolymers are homochiral, e.g

Synthesis and supramolecular properties of regioisomers of mononaphthylallyl derivatives of γ-cyclodextrin

• Markéta Bláhová,
• Sergey K. Filippov,
• Lubomír Kováčik,
• Jiří Horský,
• Simona Hybelbauerová,
• Zdenka Syrová,
• Tomáš Křížek and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2017, 13, 2509–2520, doi:10.3762/bjoc.13.248

• CDs are attractive building blocks for various types of supramolecular structures [6][7]. Necessary non-covalent interactions depend on the type and derivatization of CD, on lipophilicity, shape, and size of the guest molecule, and on conditions such as temperature, pH, or solvent used [8]. In

Structural diversity in the host–guest complexes of the antifolate pemetrexed with native cyclodextrins: gas phase, solution and solid state studies

• Magdalena Ceborska,
• Magdalena Zimnicka,
• Aneta Aniela Kowalska,
• Kajetan Dąbrowa and
• Barbara Repeć

Beilstein J. Org. Chem. 2017, 13, 2252–2263, doi:10.3762/bjoc.13.222

• comparison of the data obtained from the gas phase (without the influence of the environment) with the data obtained for solution and solid state (strongly influenced by the molecule’s environment) for deeper understanding of the non-covalent interactions responsible for the formation and stabilization of

Superstructures with cyclodextrins: Chemistry and applications IV

• Gerhard Wenz

Beilstein J. Org. Chem. 2017, 13, 2157–2159, doi:10.3762/bjoc.13.215

• Gerhard Wenz Saarland University, Organic Macromolecular Chemistry, Campus C4 2, 66123 Saarbrücken, Germany 10.3762/bjoc.13.215 Keywords: cyclodextrins; superstructures; Superstructures are generally formed from molecules through non-covalent interactions, which can be either attractive or

Mechanochemical Knoevenagel condensation investigated in situ

• Sebastian Haferkamp,
• Franziska Fischer,
• Werner Kraus and
• Franziska Emmerling

Beilstein J. Org. Chem. 2017, 13, 2010–2014, doi:10.3762/bjoc.13.197

• reactions with quantitative yields of the final product are possible, rendering the use of solvents and work-up procedures unnecessary [3][15]. The mechanochemical synthesis can effect carbon–carbon and carbon–heteroatom covalent bonds, coordinating bonds between metal and ligands, and non-covalent

• interactions such as hydrogen bonds, halogen bonds, and π∙∙∙π interactions [16][17][18][19]. For example, Toda et al. reported yields of 97% for Aldol condensations in the absence of any solvents [20]. Kaupp et al. described the first Knoevenagel condensation in a ball mill [21]. Compared to conventional

Mechanochemical synthesis of small organic molecules

• Tapas Kumar Achar,
• Anima Bose and
• Prasenjit Mal

Beilstein J. Org. Chem. 2017, 13, 1907–1931, doi:10.3762/bjoc.13.186

• ], carbon–heteroatom [41][42], metal–ligand coordination bonds [43], non-covalent interactions such as hydrogen bonds or π–π arene stacking interactions [44], etc. are popularly known in literature. In this review the efforts are given towards documentation of various mechanochemical reactions like organic

A new class of organogelators based on triphenylmethyl derivatives of primary alcohols: hydrophobic interactions alone can mediate gelation

• Wangkhem P. Singh and
• Rajkumar S. Singh

Beilstein J. Org. Chem. 2017, 13, 138–149, doi:10.3762/bjoc.13.17

• prediction of the gel forming ability of a given molecule is still a formidable challenge, if not altogether impossible [7][8]. Often, the discovery of new gelators relies on an empirical approach wherein structural components capable of forming non-covalent interactions are incorporated into different

• ][21][22]. As mentioned above, developing a new gelator is still largely a trial and error method. The most widely used design strategy involves the inclusion of structural components favouring intermolecular non-covalent interactions (like H-bonding, π-stacking, donor–acceptor interaction, metal

• ][24]. Similar is the case for π-stacking interaction (seen in naphthalene, anthracene, pyrene, perylene, etc.) which has been mostly used in combination with other types of secondary interactions in the discovery of many gelators [25][26]. This holds true for many other non-covalent interactions as

Phosphated cyclodextrins as water-soluble chiral NMR solvating agents for cationic compounds

• Cira Mollings Puentes and
• Thomas J. Wenzel

Beilstein J. Org. Chem. 2017, 13, 43–53, doi:10.3762/bjoc.13.6

• chemical shifts that can be used in the assignment of the absolute stereochemistry [1][2][3][4][5][6][7]. Since chiral solvating agents associate with the compound being studied through non-covalent interactions, they are easy to use and involve merely mixing the reagent with the compound in an NMR tube

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

• strengthen the non-covalent interactions in a cooperative manner. In this regard, [60]fullerene hexakisadducts [47], which can arrange up to twelve functional sites with icosahedral symmetry, exhibit one of the highest degrees of functionalization for organic molecules (see Figure 1). In recent years, a

New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

• Pavel Nagorny and
• Zhankui Sun

Beilstein J. Org. Chem. 2016, 12, 2834–2848, doi:10.3762/bjoc.12.283

• of organocatalysis. While traditional hydrogen bond donors containing N–H and O–H moieties have been effectively used for electrophile activation, activation based on other types of non-covalent interactions is less common. This mini review highlights recent progress in developing and exploring new

• have gathered great amounts of information about the factors governing enzymatic reactions. These studies have helped to realize the importance of non-covalent interactions within the receptor, and many subsequent efforts have been focused on adopting the knowledge learned from nature to the rational

• design of small molecule-based catalysts mimicking enzymatic function. A significant number of such efforts has been dedicated to designing new catalysts to enhance the electrophilicity of organic molecules through non-covalent interactions, and many important areas of organocatalysis have emerged from

Stereodynamic tetrahydrobiisoindole “NU-BIPHEP(O)”s: functionalization, rotational barriers and non-covalent interactions

• Golo Storch,
• Sebastian Pallmann,
• Frank Rominger and
• Oliver Trapp

Beilstein J. Org. Chem. 2016, 12, 1453–1458, doi:10.3762/bjoc.12.141

• basis of non-covalent interactions. Enantioselective dynamic HPLC (DHPLC) allowed for the determination of rotational barriers of ΔG‡298K = 92.2 ± 0.3 kJ mol−1 and 99.5 ± 0.1 kJ mol−1 underlining the stereodynamic properties of “NU-BIPHEPs” and “NU-BIPHEP(O)s”, respectively. These results make the

• preparation of tailor-made functionalized stereodynamic ligands possible and give an outline for possible applications in enantioselective catalysis. Keywords: atropisomer; enantioselective DHPLC; ligand design; non-covalent interactions; Okamoto phases; phosphine ligand; stereodynamic ligands; Introduction

• paper, we describe the application of Doherty’s synthetic strategy for the synthesis of stereodynamic tetrahydrobiisoindole “NU-BIPHEP(O)” compounds bearing secondary amino groups for functionalization. The attachment of a 3,5-dichlorobenzoyl binding site is reported and non-covalent interactions as

Indenopyrans – synthesis and photoluminescence properties

• Andreea Petronela Diac,
• Ana-Maria Ţepeş,
• Albert Soran,
• Ion Grosu,
• Anamaria Terec,
• Jean Roncali and
• Elena Bogdan

Beilstein J. Org. Chem. 2016, 12, 825–834, doi:10.3762/bjoc.12.81

• bathochromic shift together with an emission-band broadening in contrast to their emission spectra recorded in solution. The supramolecular arrangement in the solid state of indenopyrone 6a is ensured by a number of non-covalent interactions such as intermolecular H-bonding, C–H···π and π···π contacts

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