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

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

• via physisorption. However, functionalised molecules and ions can strongly bind through chemisorption by covalent bonds, hydrogen bonding, or electrostatic attraction and have been shown to influence the photophysical properties of TiO2, generally causing a bathochromic shift of the absorption

Highly selective Diels–Alder and Heck arylation reactions in a divergent synthesis of isoindolo- and pyrrolo-fused polycyclic indoles from 2-formylpyrrole

• Carlos H. Escalante,
• Eder I. Martínez-Mora,
• Carlos Espinoza-Hicks,
• Alejandro A. Camacho-Dávila,
• Fernando R. Ramos-Morales,
• Francisco Delgado and
• Joaquín Tamariz

Beilstein J. Org. Chem. 2020, 16, 1320–1334, doi:10.3762/bjoc.16.113

• hydrogen bonding, which was found for these and the other cycloaddends between a proton of the benzene ring of the diene and an oxygen atom of the dienophile (Table 7), also stabilize the endo TS. Therefore, this theoretical study indicated that the non-covalent π···π and C–H···π interactions control the

Synthesis, antiinflammatory activity, and molecular docking studies of bisphosphonic esters as potential MMP-8 and MMP-9 inhibitors

• Abimelek Cortes-Pacheco,
• María Adelina Jiménez-Arellanes,
• Francisco José Palacios-Can,
• José Antonio Valcarcel-Gamiño,
• Rodrigo Said Razo-Hernández,
• María del Carmen Juárez-Vázquez,
• Adolfo López-Torres and
• Oscar Abelardo Ramírez-Marroquín

Beilstein J. Org. Chem. 2020, 16, 1277–1287, doi:10.3762/bjoc.16.108

• ligand to the zinc ion, with the same applying to 5. This could explain why no predicted hydrogen bonding was present in 6 and just very weak ones in 5. For MMP-9, the hydrophobic zones were formed by Ile159, Leu160, and Ala161, as was the case for Gly158 and Val194. As stated before, π–π interactions

Aldehydes as powerful initiators for photochemical transformations

• Maria A. Theodoropoulou,
• Nikolaos F. Nikitas and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2020, 16, 833–857, doi:10.3762/bjoc.16.76

• then kept constant or slightly decreased. The possible initiation of the polymerization is presented in Scheme 11, where hydrogen bonding of 36 with water is crucial. In 2013, Wang and co-workers also reported the use of aliphatic ketones and aldehydes as photoinitiators for the photopolymerization of

• when they were alone present in an aqueous solution, they tended to form hydrates 45 with water via hydrogen bonding. The hydrogen bonding increased the energy levels of the excited states of 45, permitting the formation of radicals after UV light absorption [48]. These radicals either dissociated via

Combining enyne metathesis with long-established organic transformations: a powerful strategy for the sustainable synthesis of bioactive molecules

• Valerian Dragutan,
• Ileana Dragutan,
• Albert Demonceau and
• Lionel Delaude

Beilstein J. Org. Chem. 2020, 16, 738–755, doi:10.3762/bjoc.16.68

• evidenced the hydrogen-bonding network of amphidinolide N (6a, Scheme 10). Furthermore, a rigorous evaluation of the 13C NMR chemical shift differences suggested that amphidinolide N and its analog, carbenolide I, are identical chemical compounds [72]. In the course of their comprehensive studies on the

Exploring the scope of DBU-promoted amidations of 7-methoxycarbonylpterin

• Anna R. Bockman and
• Jeffrey M. Pruet

Beilstein J. Org. Chem. 2020, 16, 509–514, doi:10.3762/bjoc.16.46

• attractive scaffold in the field of supramolecular chemistry, due to their well-defined donor/acceptor hydrogen-bonding arrays [10][11]. One limitation often encountered with the synthesis of structurally diverse pterins is the notorious insolubility in most solvents. This can be dealt with by preemptive

• (product 5). For β-hydroxyamines it is expected the hydroxy group expedites the amidation via hydrogen bonding to the 7-CMP carbonyl group, to assist in bringing the amine nucleophile into place (Figure 2). Quite unsurprisingly, secondary amines were less reactive, with N-methylbenzylamine (for 16) being

• insolubility of pterins in most solvents. We have shown that this reaction also benefits in its ease and often rapid reaction times (typically 5–10 min). While this amidation reaction can be hindered by typical steric effects, we have shown these issues are largely overcome in amines with additional hydrogen

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

• Panagiotis S. Gritzapis,
• Panayiotis C. Varras,
• Nikolaos-Panagiotis Andreou,
• Katerina R. Katsani,
• Konstantinos Dafnopoulos,
• George Psomas,
• Zisis V. Peitsinis,
• Alexandros E. Koumbis and
• Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

• cm−1, characteristic of the amide moiety. This low carbonyl absorption probably indicates an intramolecular hydrogen bonding between NH2 and the oxime oxygen, which further verifies the Z-conformation of the amidoxime derivatives. The hydroxylimino structure is verified in 1H NMR spectra from the

Synthesis of 4-(2-fluorophenyl)-7-methoxycoumarin: experimental and computational evidence for intramolecular and intermolecular C–F···H–C bonds

• Vuyisa Mzozoyana,
• Fanie R. van Heerden and
• Craig Grimmer

Beilstein J. Org. Chem. 2020, 16, 190–199, doi:10.3762/bjoc.16.22

• amongst the weakest of hydrogen bonding phenomena because a carbon acid (C–H) is weak, therefore is a weak donor, and the acceptor is non-polarizable, therefore is a poor acceptor [34][35][36]. Wang and co-workers reported the existence of the C–F···H–C intramolecular hydrogen bond in the structure of

The use of isoxazoline and isoxazole scaffolding in the design of novel thiourea and amide liquid-crystalline compounds

• Itamar L. Gonçalves,
• Rafaela R. da Rosa,
• Vera L. Eifler-Lima and
• Aloir A. Merlo

Beilstein J. Org. Chem. 2020, 16, 175–184, doi:10.3762/bjoc.16.20

• thioureas is the reaction of carbon disulfide with either one or two different amines [9]. Due to their self-assembly and self-organization through intermolecular hydrogen bonding, thioureas display interesting technological applications to this group of molecules, one of which explores its application in

• crystals containing hydrogen bonds may exhibit a wide variety of phase polymorphism depending on the length of the chain, type of bonding and the functional groups involved [12][28][29][30]. Many liquid crystalline compounds have been developed exploring the ability of hydrogen bonding formation between

Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides

• Sabrina Müller,
• Jannik Paulus,
• Jochen Mattay,
• Heiko Ihmels,
• Veronica I. Dodero and
• Norbert Sewald

Beilstein J. Org. Chem. 2020, 16, 60–70, doi:10.3762/bjoc.16.8

• 4,4'-substituted correlates, as the substituents are not conjugated to the N=N double bond [35][37][38][39]. Moreover, it was demonstrated that in the case of peptides, only the Z-isomer adopts the hairpin conformation. In our setup, this could influence the hydrogen bonding contacts between the

• required because this allowed for an alignment between hydrogen-bonding groups in long polyamides and in the minor groove of DNA [41]. The Fmoc-protected heterocyclic amino acids 2 were obtained from N-methylpyrrole and N-methylimidazole, respectively (Scheme 2A). The N-terminal N-methylpyrrole and N

SnCl₄-catalyzed solvent-free acetolysis of 2,7-anhydrosialic acid derivatives

• Kesatebrhan Haile Asressu and
• Cheng-Chung Wang

Beilstein J. Org. Chem. 2019, 15, 2990–2999, doi:10.3762/bjoc.15.295

• 2,7-anhydro backbone formation, which resulted in alleviation of hydrogen bonding, and thus enhancing the reactivity of the OH-4 group as an acceptor (Figure 1) [6]. Several chemical and enzymatic syntheses of 2,7-anhydro-Neu5Ac are currently being developed [6][25][26][27][28]. However, only few

• clearly showed that the NHAc group in position C-5 and the OH-4 group were oriented in a trans-diaxial configuration (Figure 2a). This enhanced the nucleophilicity of the OH-4 group due to the absence of hydrogen bonding between these moieties. After confirming the structure of 4 by single crystal X-ray

Regioselectivity of glycosylation reactions of galactose acceptors: an experimental and theoretical study

• Enrique A. Del Vigo,
• Carlos A. Stortz and
• Carla Marino

Beilstein J. Org. Chem. 2019, 15, 2982–2989, doi:10.3762/bjoc.15.294

• accurate prediction of the trends in selectivity could not be achieved. We have tried to explain the reduced regioselectivity of the β-anomers through hydrogen bonding interactions of the OH-3 and OH-4 groups of the model acceptors. Doutheau and co-workers proposed that such a reduced regioselectivity