Insight into functionalized-macrocycles-guided supramolecular photocatalysis

• Minzan Zuo,
• Krishnasamy Velmurugan,
• Kaiya Wang,
• Xueqi Tian and
• Xiao-Yu Hu

Beilstein J. Org. Chem. 2021, 17, 139–155, doi:10.3762/bjoc.17.15

• photocatalytic reaction with a rate acceleration facilitated by supramolecular host–guest interactions and hybrid materials are typically assisted by noncovalent forces, including Coulomb and van der Waals forces, hydrogen bonding, and π–π interactions. For potential supramolecular photocatalysts, they should

• of two different crown ether-substituted molecules, styrylbenzothiazole and cinnamic acid [18]. In this system, the Ba2+ cation can preorganize the two crown ether-substituted molecules into a supramolecular complex (Figure 2), which was further stabilized by hydrogen bonding and π–π interactions

Tuning the solid-state emission of liquid crystalline nitro-cyanostilbene by halogen bonding

• Subrata Nath,
• Alexander Kappelt,
• Matthias Spengler,
• Bibhisan Roy,
• Jens Voskuhl and
• Michael Giese

Beilstein J. Org. Chem. 2021, 17, 124–131, doi:10.3762/bjoc.17.13

• supramolecular liquid crystals, especially hydrogen bonding and halogen bonding have gained considerable attention [3][4][5][6][7]. In 2004, Bruce and co-workers reported the first example of a halogen-bonded liquid crystal based on pentafluoroiodobenzene and 4-alkoxystilbazole [5]. Ever since, several other

Supramolecular polymers with reversed viscosity/temperature profile for application in motor oils

• Jan-Erik Ostwaldt,
• Christoph Hirschhäuser,
• Stefan K. Maier,
• Carsten Schmuck and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2021, 17, 105–114, doi:10.3762/bjoc.17.11

• constants, based on a sixfold hydrogen-bonding interaction, strengthened by coulombic interactions (see Figure 2a) [20][21]. The GCP motif has successfully been applied for the formation of supramolecular polymers in earlier works [22][23][24][25]. The ionic nature of the GCP motif allows self-pairing even

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

• the co-assembly strategy. The cogels show significant CPL emission and stoichiometry-controlled inversion of chirality due to the hydrogen bonding interactions and packing modes in the supramolecular co-assemblies. Owing to TB special V-shaped structure, rigid conformation, and nitrogen stereogenic

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

• discussed here can be employed to detect PPIs. Miura [41] and Carter et al. [11] provided a detailed explanation and comparison of such methodologies. Molecular interactions involved in PPIs There are different forces and mechanisms that affect PPIs and their formation, including hydrogen bonding [42][43

Synthesis of tetrafluorinated piperidines from nitrones via a visible-light-promoted annelation reaction

• Vyacheslav I. Supranovich,
• Igor A. Dmitriev and
• Alexander D. Dilman

Beilstein J. Org. Chem. 2020, 16, 3104–3108, doi:10.3762/bjoc.16.260

• modify basicity, lipophilicity, as well as the hydrogen-bonding properties of amines [4][5] makes fluorinated piperidines [6][7] attractive targets in medicinal chemistry [8][9]. Previous efforts were mainly focused on the synthesis of mono- and difluorinated compounds. A single fluorine atom is

Deoxyfluorination of acyl fluorides to trifluoromethyl compounds by FLUOLEAD^®/Olah’s reagent under solvent-free conditions

• Yumeng Liang,
• Akihito Taya,
• Zhengyu Zhao,
• Norimichi Saito and
• Norio Shibata

Beilstein J. Org. Chem. 2020, 16, 3052–3058, doi:10.3762/bjoc.16.254

• the products 2. A mechanism of the deoxyfluorination of the acyl fluorides with FLUOLEAD®/nHF·pyridine is proposed in Scheme 3. First, FLUOLEAD® is activated with (HF)n via hydrogen bonding to provide an activated form I, which induces a nucleophilic attack from the carbonyl oxygen of 1 to I providing

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

• Å, respectively. Every ureido group held one molecule of DMSO via synchronous hydrogen bonding interactions between the two NH protons and a sulfoxide oxygen atom (Figure 3a). The S=O···H–N distances were 1.995, 2.285, 2.033, and 2.328 Å, indicating strong interactions in the solid state. At the

• -acetylphenylalaninate. Design of chiral calix[4]arene-based receptors for anions. X-ray structure of 4a: (a) Top view into the cavity. (b) Side view of the same cavity. X-ray structure of 7a: (a) Hydrogen bonding interactions (black) in a dimeric motif, chalcogen interactions are shown in green. (b) π–π interactions in

• 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

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

• considerations: (1) the p-phenyl substituents act as electron-donor units and as AIE activators; (2) the nitrile groups provide a significant π-acceptor strength, and also promote hydrogen bonding in the aggregates [39][40][41][42]. By varying the substituents at the phenyl groups ranging from mild π-donors

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

• (CBS) [6][7][8][9]. The GCP takes part selectively and efficiently in the complexation of carboxylates based on the electrostatic interaction between the positively charged CBS and the negatively charged carboxylate in the combination with hydrogen bonding, enabling molecular recognition even in the

• vibrational modes of the molecule. Especially for non-covalent interactions such as hydrogen bonding, vibrational spectroscopy has been shown to be very sensitive [10][11]. In the context of supramolecular recognition, for example, IR spectroscopy has been applied to monitor the binding of tetrapeptides by

• -covalent, i.e., only weak intermolecular interactions present, one would expect a peak shift for the isolated supramolecular ligand. However, the GCI is dissolved in water and therefore already involved in hydrogen bonding to water molecules. Upon the addition of the RGD binding partner, the water

Using multiple self-sorting for switching functions in discrete multicomponent systems

• Amit Ghosh and
• Michael Schmittel

Beilstein J. Org. Chem. 2020, 16, 2831–2853, doi:10.3762/bjoc.16.233

• derivative is the main reason behind this unusual social self-sorting phenomenon. Wärnmark and Orentas reported on a guest- and solvent-induced 2-fold self-sorting through hydrogen-bonding [49]. When the C2-symmetric monomers 5 and 6, both exhibiting similar shapes except for different solubility-enhancing

• of various similar molecules. Similarly, Shi controlled a conversion between helicates and a tetrahedral cage by varying the radius of the metal ion (Hg2+ vs Fe2+) [55]. They reported on the self-assembly of the monomer 20, encompassing the quadruple DDAA hydrogen-bonding arrays and 2,2’-bipyridine

• +. In contrast, metal ions (Hg2+) with a larger radius provided enough space for the hydrogen-bonding motif to set up different supramolecular architectures, such as the helicate [Hg2(20)6]4+ (SelfSORT-I). Furthermore, upon adding stoichiometric amounts of Fe(OTf)2 into the solution of the helicate, the

Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• terminated with an N-benzylamide functionality to establish the attractive hydrogen bonding and π stacking with the thymidine residues in the loops in G4-DNA, so that this ligand binds with very high selectivity to the particular quadruplex-forming oligonucleotide J19 [49]. Overall, the above-mentioned

Synthesis of purines and adenines containing the hexafluoroisopropyl group

• Viacheslav Petrov,
• Rebecca J. Dooley,
• Alexander A. Marchione,
• Elizabeth L. Diaz,
• Brittany S. Clem and
• William Marshall

Beilstein J. Org. Chem. 2020, 16, 2739–2748, doi:10.3762/bjoc.16.224

• (with minimal contribution from such forces as hydrogen bonding or solvent interactions), and the relative enthalpy of activation for each compound (major to minor vs minor to major) are roughly similar to the difference in total enthalpy for the two rotamers for each compound. Experimental GC and GC–MS

Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

• Henrik Hupatz,
• Marius Gaedke,
• Hendrik V. Schröder,
• Julia Beerhues,
• Arto Valkonen,
• Fabian Klautzsch,
• Sebastian Müller,
• Felix Witte,
• Kari Rissanen,
• Biprajit Sarkar and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2020, 16, 2576–2588, doi:10.3762/bjoc.16.209

• weaker hydrogen-bond-acceptor ability of the sulfur atoms incorporated in the TTFC8 crown ether ring [34][54]. NDIC8 also exhibits a comparably low binding energy, likely due to the increased ring size and the consequently weakened hydrogen-bonding pattern (Table 1, entry 11) [44]. However, NDIC8 and

• TTFC8 differ significantly in the entropic and enthalpic contributions to the binding energy (Table 1, entries 11 and 12). The comparably rigid structure of NDIC8 is unable to adjust the conformation in the complex to achieve an optimal hydrogen-bonding pattern with the ammonium axle, and simultaneously

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• tools are applied to each of the simulation trajectories and this process was streamlined by using Galaxy workflows. The conformations of the antigens were analyzed using root-mean-square deviation, end-to-end distance, Ramachandran plots, and hydrogen bonding analysis. Additionally, RMSF and clustering

• a time step of 0.001 ps. The particle mesh Ewald (PME) method was used. Nonbonded interactions were cut-off using the force-switching method from 10 Å to 12 Å, and hydrogen bonding constraints applied. During equilibration, the protein backbone and side chains were restrained (force constants of

• solution and bound to antibody) were also measured. A standard hydrogen-bonding analysis using MDAnalysis and VMD was carried out with the default angle cut-off and distance cut-off. A cluster analysis of the peptide portion of the antigen was carried out (Figure 5) using TTClust [42]. The clusters were

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• guanidinocarbonylpyrrole (GCP)-based ligands [41]. GCP mimics the natural amino acid arginine binding to the carboxylate side chains of aspartate (Asp) and glutamate (Glu). The GCP unit provides an extended hydrogen bonding/salt bridge interface, which leads to better binding compared to its natural counterpart. The

Recent developments in enantioselective photocatalysis

• Callum Prentice,
• James Morrisson,
• Andrew D. Smith and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2020, 16, 2363–2441, doi:10.3762/bjoc.16.197

• are promising for this mode of catalysis, more work is required to address the limited substrate scope. Hydrogen bonding Krische et al. were the first to develop a bifunctional hydrogen bonding photocatalyst 169 (Scheme 25) [78] that was used in an intramolecular enantioselective [2 + 2

• enantioselectivity (60:40 er). While the enantioselectivity was low, this reaction represented an interesting proof of concept that would be later expanded by others. Later, Bach et al. developed a similar bifunctional hydrogen bonding photocatalyst 174. Reactions using catalysts of this type are well covered in

• Bach’s recent review on the subject [13]. Photocatalyst 174 was first used in a cyclisation reaction where the putative mechanism involves a hydrogen bonding complex 175 between the catalyst and quinolone substrate 176 (Scheme 26) [2]. Subsequent photoexcitation promotes a photoinduced electron transfer

Host–guest interaction of cucurbit[8]uril with oroxin A and its effect on the properties of oroxin A

• Zhishu Zeng,
• Jun Xie,
• Guangyan Luo,
• Zhu Tao and
• Qianjun Zhang

Beilstein J. Org. Chem. 2020, 16, 2332–2337, doi:10.3762/bjoc.16.194

• involve three main intermolecular forces: a hydrophobic effect, hydrogen bonding and ion–dipole interactions at the carbonyl portals [7][8][9]. The high thermal stability [10], ease of synthesis [11], general absence of cytotoxicity or toxicity [12][13] and their good molecular recognition and binding

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• interesting feature, through the cumulative 3 μs MD sampling, the xylose ring repeatedly inverts its conformation from the all equatorial 4C1 chair, to the 1C4 chair, where all hydroxy groups are axial, see Figure 3. This transition may be energetically facilitated by the hydrogen bonding interaction xylose

• synergistic effect as this conformation is stabilized by a hydrogen bonding network involving the core fucose, the GlcNAc on the (1-6) arm and the xylose, as shown in Figure S1, Supporting Information File 1. Such folding event has been observed as a stable conformation in two independent simulations. To note

• arms, which is not observed when the arms are linear, neither here for plants N-glycans, nor for mammalian IgG-type complex biantennary N-glycans [24]. The interaction between the arms is promoted by the ability to form complex hydrogen bonding networks, which in this specific case, may also involve

pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide

• Goutam Ghosh and
• Gustavo Fernández

Beilstein J. Org. Chem. 2020, 16, 2017–2025, doi:10.3762/bjoc.16.168

• secondary structures, which lead to nanostructured materials [16][17]. Noncovalent interactions, such as hydrogen bonding, van der Waals interactions, hydrophobic interactions, electrostatic interactions, and π–π interactions [18][19][20][21][22] are common driving forces in peptide self-assembly. These

• ability to undergo significant changes in their morphologies and secondary structures in response to pH stimuli. For instance, hydrogen bonding interactions are strongly influenced by the pH value, leading to a collapse of the supramolecular aggregates when an acid or base is added [4]. The pH

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• binding is further enhanced by the addition of hydrogen-bonding interactions between the amide NH moiety in position 5 of the pyrrole ring or the pyrrole NH group and the oxoanion (Figure 1, blue part). Thirdly, the rigid and planar conformation of the GCP moiety is beneficial to bind planar anions such

Selective preparation of tetrasubstituted fluoroalkenes by fluorine-directed oxetane ring-opening reactions

• Clément Q. Fontenelle,
• Thibault Thierry,
• Romain Laporte,
• Emmanuel Pfund and
• Thierry Lequeux

Beilstein J. Org. Chem. 2020, 16, 1936–1946, doi:10.3762/bjoc.16.160

• nucleotides such as the antiviral agent FPMPA (IV) [7][8][9]. Other main structural modifications of ACN relied on the introduction of a hydroxy group into the aliphatic chain to improve hydrogen bonding with enzymes [10], or of a carbon–carbon double bond to constrain the aliphatic chain and to limit

Design, synthesis and application of carbazole macrocycles in anion sensors

• Alo Rüütel,
• Ville Yrjänä,
• Sandip A. Kadam,
• Indrek Saar,
• Mihkel Ilisson,
• Astrid Darnell,
• Kristjan Haav,
• Tõiv Haljasorg,
• Lauri Toom,
• Johan Bobacka and
• Ivo Leito

Beilstein J. Org. Chem. 2020, 16, 1901–1914, doi:10.3762/bjoc.16.157

• hydrogen bonding. The primary site of interaction is the X-COO− group. The geometry of the carboxylate group (and to a large extent also its charge distribution) is the same for all carboxylate anions. Therefore, high affinity towards carboxylates is easily achievable, but selectivity towards a specific

• moiety fulfils several key design requirements. At least four hydrogen bonding sites (N–H groups) are available and positioned in a favourable geometry for carboxylates. Additional hydrogen-bond-donor (HBD) groups can be added with substituents. The solubility of such receptors can be tuned using

Natural dolomitic limestone-catalyzed synthesis of benzimidazoles, dihydropyrimidinones, and highly substituted pyridines under ultrasound irradiation

• Kumar Godugu,
• Venkata Divya Sri Yadala,
• Mohammad Khaja Mohinuddin Pinjari,
• Trivikram Reddy Gundala,
• Lakshmi Reddy Sanapareddy and
• Chinna Gangi Reddy Nallagondu

Beilstein J. Org. Chem. 2020, 16, 1881–1900, doi:10.3762/bjoc.16.156

• confirmed that the reaction stopped at the bisimine I stage. This was due to the intramolecular hydrogen bonding between the hydrogen atom of the ortho-hydroxy group and the nitrogen atom of the imine group in a six-membered ring transition state [87]. Similarly, the reaction between 3-ethoxysalicylaldehyde

Five-component, one-pot synthesis of an electroactive rotaxane comprising a bisferrocene macrocycle

• Natalie Lagesse,
• Luca Pisciottani,
• Maxime Douarre,
• Pascale Godard,
• Brice Kauffmann,
• Vicente Martí-Centelles and
• Nathan D. McClenaghan

Beilstein J. Org. Chem. 2020, 16, 1564–1571, doi:10.3762/bjoc.16.128

• of Bordeaux, Pessac, France 10.3762/bjoc.16.128 Abstract The templated clipping of a ferrocene-grafted isophthalic acid derivative to encircle a hydrogen-bonding axle through the reaction with 1,4-bis(aminomethyl)benzene is described. The constituent electroactive macrocycle of the resultant [2

• ]rotaxane is a homologue of the versatile benchmark tetraamide variant developed by Leigh and co-workers. The relative templating effect of different hydrogen-bonding motifs in rotaxane and pseudorotaxane generation is compared, with yields varying from 0 to 41%. The electrochemical properties and single

• free ferrocene macrocycle, the ferrocene rotaxane 1a was soluble in CDCl3 suggesting a complementary macrocycle-thread hydrogen-bonding interaction. While the rotaxane 1a was insoluble at room temperature in DMSO-d6, heating at 160 °C dissolved the rotaxane. Macrocycle dethreading in DMSO-d6 at 160 °C