Mechanochemistry of supramolecules

• Anima Bose and
• Prasenjit Mal

Beilstein J. Org. Chem. 2019, 15, 881–900, doi:10.3762/bjoc.15.86

• [7] followed by the lock-and-key concept of Emil Fischer in 1894 [8]. Weak or non-covalent interactions had been used systematically in the early 1960s by Lehn, Cram and Pederson to create targeted supramolecular architectures [9]. Small molecules, anions or cations could be assembled spontaneously

• to form supramolecular structures through self-assembly processes by exploiting the weak or non-covalent interactions [10]. Self-assembly is a kinetically reversible process which is more efficient than traditional stepwise synthesis concerning large molecules. Some recent developments in

• (≈65%). Subcomponent self-assembly and mechano-milling Nature displays innumerable and beautiful creations [67][68] which include highly complex self-assembled structures made from smaller building blocks by using weak or non-covalent interactions [69][70]. Therefore, the supramolecular approach [71

Tetrathiafulvalene – a redox-switchable building block to control motion in mechanically interlocked molecules

• Hendrik V. Schröder and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2018, 14, 2163–2185, doi:10.3762/bjoc.14.190

• to rotaxanes is that the axle does not have bulky stopper groups that prevent the deslipping of the wheel. Thus, a pseudorotaxane forms by non-covalent interactions between host and guest without a mechanical bond. Pseudorotaxanes are important precursors of MIMs from which the construction of

• the [3]rotaxane 23 which bears two cofacially oriented TTF crown ethers on a divalent ammonium axle. The distance between the wheels is convenient for TTF-dimer interactions. In the non-switched neutral state of both TTFs, the wheels adopt a syn co-conformation caused by weak non-covalent interactions

Synthesis and supramolecular self-assembly of glutamic acid-based squaramides

• Juan V. Alegre-Requena,
• Marleen Häring,
• Isaac G. Sonsona,
• Alex Abramov,
• Eugenia Marqués-López,
• Raquel P. Herrera and
• David Díaz Díaz

Beilstein J. Org. Chem. 2018, 14, 2065–2073, doi:10.3762/bjoc.14.180

• gels are typically made of low-molecular-weight (LMW) compounds self-assembled in different solvents via non-covalent interactions. In most cases, this feature enables reversible stimuli-responsive gel-to-sol transitions [31]. Usually, the entanglement of 1D nanofibers of gelator molecules generates a

A pyridinium/anilinium [2]catenane that operates as an acid–base driven optical switch

• Sarah J. Vella and
• Stephen J. Loeb

Beilstein J. Org. Chem. 2018, 14, 1908–1916, doi:10.3762/bjoc.14.165

• easily understood as the neutral benzylaniline site does not allow for appreciable non-covalent interactions and cannot compete for the DB24C8 ring with the dicationic bis(pyridinium)ethane site. However, the addition of one equivalent of triflic acid (CF3SO3H) to a solution of [8DB24C8]6+ results in

Efficient catenane synthesis by cucurbit[6]uril-mediated azide–alkyne cycloaddition

• Antony Wing Hung Ng,
• Chi-Chung Yee,
• Kai Wang and
• Ho Yu Au-Yeung

Beilstein J. Org. Chem. 2018, 14, 1846–1853, doi:10.3762/bjoc.14.158

• yields of the [3]catenanes can serve as an entry point to other high-order [n]catenanes by introducing additional macrocycles through other non-covalent interactions. Results and Discussion Building block design The bis(aminoalkyne) and bis(aminoazide) building blocks used in this study are summarized in

• other topological isomers. The building blocks contain either a central hexaethylene glycol (HEG) unit or are derived from 1,5-dioxynaphthalene (DN), naphthalenediimide (NDI), 2,9-phenanthroline (Phen) or 4,4’-biphenyl (BP) cores which can engage in additional non-covalent interactions, such as metal

• ). Together with our previous demonstration of the compatibility of CBAAC with Cu+-phenanthroline coordination in a [6]catenane assembly, the successful synthesis of Cat-11 shows the feasibility of using CBAAC with a versatile selection of building blocks and non-covalent interactions to construct complex

Host–guest complexes of conformationally flexible C-hexyl-2-bromoresorcinarene and aromatic N-oxides: solid-state, solution and computational studies

• Rakesh Puttreddy,
• Ngong Kodiah Beyeh,
• S. Maryamdokht Taimoory,
• Daniel Meister,
• John F. Trant and
• Kari Rissanen

Beilstein J. Org. Chem. 2018, 14, 1723–1733, doi:10.3762/bjoc.14.146

• understanding of the particular interactions is required. The N-oxide oxygen atoms potential to act as a HB acceptor for multiple simultaneous N–O···(O–H)host interactions raises the molecular complexity. These are the dominant non-covalent interactions, in both the solid and solution state, compared to endo

• , one resides in the upper-rim endo cavity, held in position by C–H···π interactions. The second sits in the lower rim between the hexyl chains and is stabilised through N–O···(H–C)Ar(host) and other weak non-covalent interactions. The remaining final two guests are exo cavity hydrogen bonded to the

• potential regions of the N-oxide oxygen atom in guest 3 (red region in Figure 4a) to establish several intermolecular (C–H)Ar···O–N H-bond interactions at the lower-rim host pocket. In addition, we used Bader’s quantum theory of atoms in molecules (QTAIM) [49] to analyse multiple non-covalent interactions

A conformationally adaptive macrocycle: conformational complexity and host–guest chemistry of zorb[4]arene

• Liu-Pan Yang,
• Song-Bo Lu,
• Arto Valkonen,
• Fangfang Pan,
• Kari Rissanen and
• Wei Jiang

Beilstein J. Org. Chem. 2018, 14, 1570–1577, doi:10.3762/bjoc.14.134

• structures may provide an explanation for their surprising binding behaviors. Multiple non-covalent interactions, including C–H···O hydrogen bonds, cation···π, C–H···π and π···π interactions, are involved in all the cases. Undoubtedly, cation···π interactions between the core quaternary ammonium ions of the

• complexes 16+@ZB4-III and 18+@ZB4-III may be better suited than those of 14+@ZB4-III and 21+@ZB4-III to host the quaternary ammonium and maximize all the non-covalent interactions. Any deviation from these cavity sizes weakens the binding. That is, the secondary C–H···O hydrogen bonds can be tuned through

Cobalt-catalyzed C–H cyanations: Insights into the reaction mechanism and the role of London dispersion

• Eric Detmar,
• Valentin Müller,
• Daniel Zell,
• Lutz Ackermann and
• Martin Breugst

Beilstein J. Org. Chem. 2018, 14, 1537–1545, doi:10.3762/bjoc.14.130

• ORCA 4 [65]. All DFT calculations were performed with Turbomole 7.1 [66][67] and the NCIPLOT code was employed for the visualization non-covalent interactions [48][49]. Experimental Details General remarks: Catalytic reactions were carried out in Schlenk flasks under nitrogen atmosphere using predried

Steric “attraction”: not by dispersion alone

• Ganna Gryn’ova and
• Clémence Corminboeuf

Beilstein J. Org. Chem. 2018, 14, 1482–1490, doi:10.3762/bjoc.14.125

• Ganna Gryn'ova Clemence Corminboeuf Institut des Sciences et Ingénierie Chimiques, École polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland 10.3762/bjoc.14.125 Abstract Non-covalent interactions between neutral, sterically hindered organic molecules generally involve a strong

• recognized in aliphatic systems compared to London dispersion, and are therefore likely to have implications for the development of force fields and methods for crystal structure prediction. Keywords: charge penetration; dispersion; hydrocarbon; non-covalent interactions; steric attraction; Introduction In

• of non-covalent interactions for a range of hydrocarbon dimers featuring both aromatic and aliphatic skeletons and bearing substituents, from methyl all the way to bulky adamantyl (Figure 2). First, we consider the dimers, constructed from the optimized monomers that are kept fixed (frozen) in terms

Spectroelectrochemical studies on the effect of cations in the alkaline glycerol oxidation reaction over carbon nanotube-supported Pd nanoparticles

• Dennis Hiltrop,
• Steffen Cychy,
• Karina Elumeeva,
• Wolfgang Schuhmann and
• Martin Muhler

Beilstein J. Org. Chem. 2018, 14, 1428–1435, doi:10.3762/bjoc.14.120

• voltammetry revealing a lower overpotential of glycerol oxidation for nitrogen-functionalized Pd/NCNTs compared with oxygen-functionalized Pd/OCNTs. Whereas significantly lower current densities were observed for Pd/OCNT in NaOH than in KOH in agreement with stronger non-covalent interactions on the Pd

• observed higher current densities for Pd/NCNT in NaOH compared with KOH considering the non-covalent interactions proposed by Strmcnik et al. [24]. In situ FTIR spectroscopy The reaction products in NaOH and KOH solutions formed over Pd/NCNT were identified by IR spectroscopy (Figure 3, Table 2) using a

• current densities were higher in KOH than in NaOH solution for Pd/OCNT in agreement with the theory of weaker non-covalent interactions on the Pd surface in KOH. Pd/NCNT was electrocatalytically more active as shown by the lower anodic onset potential achieving slightly higher current densities in KOH

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