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

• interactions point of view the most efficient association exists in complexes in which all hydrogen bond donors belong to one molecule and all hydrogen bond acceptors to the other. The last condition was tested for quadruple hydrogen bonded associates [14], while the basis of this phenomenon are secondary

• to exist in linear form without any intramolecular HBs and stabilized by four intermolecular ones. In general the dibutyltriuret molecule carrying four hydrogen bond donors (D, red, Figure 2) and three hydrogen bond acceptors (A, blue) can exist in various conformations stabilized by one or two

3-Glucosylated 5-amino-1,2,4-oxadiazoles: synthesis and evaluation as glycogen phosphorylase inhibitors

• Marion Donnier-Maréchal,
• David Goyard,
• Vincent Folliard,
• Tibor Docsa,
• Pal Gergely,
• Jean-Pierre Praly and
• Sébastien Vidal

Beilstein J. Org. Chem. 2015, 11, 499–503, doi:10.3762/bjoc.11.56

• as aryl moieties, with 2-naphthyl identified as the best pharmacophore for the series discussed above (Figure 1, D–I). Nevertheless, hydrogen bonds might also be created in this secondary binding site with other residues. The introduction of hydrogen bond donors and/or acceptors at the 5-position of

Regio- and stereoselective synthesis of new diaminocyclopentanols

• Evgeni A. Larin,
• Valeri S. Kochubei and
• Yuri M. Atroshchenko

Beilstein J. Org. Chem. 2014, 10, 2513–2520, doi:10.3762/bjoc.10.262

• with hydrogen bond donors [25]. Additionally, the synthesis of aminocyclitols from cyclitol epoxides has been described [26][27]. It has been shown that the reaction of cyclitol epoxides with nitrogen-containing nucleophiles in the presence of Lewis acids gave a mixture of C1 and C2 adducts. Both

Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance

• Kristen K. Merritt,
• Kevin M. Bradley,
• Daniel Hutter,
• Mariko F. Matsuura,
• Diane J. Rowold and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 2348–2360, doi:10.3762/bjoc.10.245

• pyrimidines) and (b) hydrogen-bonding complementarity (hydrogen-bond acceptors, A, pair with hydrogen-bond donors, D). Rearranging donor and acceptor groups on the nucleobases, while not changing the geometry of the Watson–Crick pair, creates an artificially expanded genetic information system (AEGIS). AEGIS

OligArch: A software tool to allow artificially expanded genetic information systems (AEGIS) to guide the autonomous self-assembly of long DNA constructs from multiple DNA single strands

• Kevin M. Bradley and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 1826–1833, doi:10.3762/bjoc.10.192

• intermolecular hybridization, especially at low concentrations of oligonucleotide. Watson–Crick pairing rules follow two rules of complementarity: (a) size complementarity (large purines pair with small pyrimidines) and (b) hydrogen bonding complementarity (hydrogen bond acceptors, A, pair with hydrogen bond

• donors D). Rearranging donor and acceptor groups on the nucleobases creates an artificially expanded genetic information system (AEGIS), whose components can independently pair. AEGIS adds information density to the DNA oligonucleotides, thereby diminishing off-target hybridization and other undesired

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

• ][2][3]. They are mechanically interlocked molecules consisting of a macrocycle, called “wheel”, threaded on a linear chain, termed “axle”, see Figure 1 for examples. Typically, the axle has at least one recognition site – often hydrogen bond donors or acceptors [4][5] – for the wheel, because most

Multigramme synthesis and asymmetric dihydroxylation of a 4-fluorobut-2E-enoate

• James A. B. Laurenson,
• John A. Parkinson,
• Jonathan M. Percy,
• Giuseppe Rinaudo and
• Ricard Roig

Beilstein J. Org. Chem. 2013, 9, 2660–2668, doi:10.3762/bjoc.9.301

• molecular properties. Sugar chemistry has proved particularly fertile ground for studies of this type; fluorine atoms can be used to replace hydroxy groups or hydrogen atoms, modifying the arrays of hydrogen bond donors and acceptors, and electron demand at the anomeric centre at minimal steric cost

Synthesis of the reported structure of piperazirum using a nitro-Mannich reaction as the key stereochemical determining step

• James C. Anderson,
• Andreas S. Kalogirou,
• Michael J. Porter and
• Graham J. Tizzard

Beilstein J. Org. Chem. 2013, 9, 1737–1744, doi:10.3762/bjoc.9.200

• . Enantioselective reactions have been controlled by asymmetric metal-centred Lewis acids; chiral hydrogen bond donors, in particular by the use of asymmetric thiourea organocatalysts, chiral Brønsted acids, phase-transfer catalysts and Brønsted base catalysts [3][15][25][26][27][28][29][30][31][32][33][34][35][36

Synthesis of chiral sulfoximine-based thioureas and their application in asymmetric organocatalysis

• Marcus Frings,
• Isabelle Thomé and
• Carsten Bolm

Beilstein J. Org. Chem. 2012, 8, 1443–1451, doi:10.3762/bjoc.8.164

• was known for chiral bifunctional amine-based sulfonamides that two hydrogen bond donors were not strictly required in the enantioselective organocatalytic ring opening of meso-anhydrides [48][54], this particular transformation was chosen as initial test reaction. Cyclic anhydride 4 served as

Synthesis and anion recognition properties of shape-persistent binaphthyl-containing chiral macrocyclic amides

• Marco Caricato,
• Nerea Jordana Leza,
• Claudia Gargiulli,
• Giuseppe Gattuso,
• Daniele Dondi and
• Dario Pasini

Beilstein J. Org. Chem. 2012, 8, 967–976, doi:10.3762/bjoc.8.109

• difunctional carboxylates. We deemed it to be very interesting to increase the availability of hydrogen-bond donors within the macrocycle cavity, and to unlock the hydrogen-bonding capability of the amide NHs to their full potential for anion recognition. The former could in principle be achieved by unmasking

Parallel and four-step synthesis of natural-product-inspired scaffolds through modular assembly and divergent cyclization

• Hiroki Oguri,
• Haruki Mizoguchi,
• Hideaki Oikawa,
• Aki Ishiyama,
• Masato Iwatsuki,
• Kazuhiko Otoguro and
• Satoshi Ōmura

Beilstein J. Org. Chem. 2012, 8, 930–940, doi:10.3762/bjoc.8.105

• groups and hydrogen-bond donors or acceptors. The incorporation of multiple sp3-centers on the scaffold creates a unique three-dimensional shape of the surface, which is responsible for specific molecular recognition with biomacromolecules in the cellular context [1][2][3]. To generate diverse

NMR studies of anion-induced conformational changes in diindolylureas and diindolylthioureas

• Damjan Makuc,
• Jennifer R. Hiscock,
• Mark E. Light,
• Philip A. Gale and
• Janez Plavec

Beilstein J. Org. Chem. 2011, 7, 1205–1214, doi:10.3762/bjoc.7.140

• extensively employed in synthetic anion receptors comprising groups such as amides, pyrroles, indoles, ureas and triazoles, as well as in ammonium, guanidinium and imidazolium moieties used as hydrogen bond donors [16][17][18][19][20][21][22][23]. Amongst neutral anion receptor systems, indole and related

Fluorometric recognition of both dihydrogen phosphate and iodide by a new flexible anthracene linked benzimidazolium-based receptor

• Kumaresh Ghosh and
• Debasis Kar

Beilstein J. Org. Chem. 2011, 7, 254–264, doi:10.3762/bjoc.7.34

• hydrogen bond donors and acceptors are of considerable importance. Among the different binding motifs for anions, the hydrogen bonding properties of NH groups in neutral amines [13], amides [14], ureas/thioureas [15][16], indoles [17][18][19] and pyrroles [20] as well as in guanidinium [21] and imidazolium

Exceptionally small supramolecular hydrogelators based on aromatic–aromatic interactions

• Junfeng Shi,
• Yuan Gao,
• Zhimou Yang and
• Bing Xu

Beilstein J. Org. Chem. 2011, 7, 167–172, doi:10.3762/bjoc.7.23

• complicate the accurate assessment of the aromatic–aromatic interactions and hydrogen bonding since DMSO is prone to form hydrogen bonds with hydrogen bond donors. Therefore, it is necessary to explore small supramolecular hydrogelators for correlating the molecular structure (e.g., numbers of hydrogen bond

• donors and acceptors and aromatic groups) and the capability of self-assembly without the inclusion of DMSO. Recently, Dastidar and Das [33] reported that N-(4-pyridyl)isonicotinamide (MW = 199.21 g/mol) can act as a non-polymeric hydrogelator at the concentration of 0.37 wt %, which further suggests the

Chain stopper engineering for hydrogen bonded supramolecular polymers

• Thomas Pinault,
• Bruno Andrioletti and
• Laurent Bouteiller

Beilstein J. Org. Chem. 2010, 6, 869–875, doi:10.3762/bjoc.6.102

• assemblies as a hydrogen bond donor. For this purpose, we synthesized the bis-thiourea S4, from the corresponding bis-thioisocyanate, because thioureas are known to be strong hydrogen bond donors and weak hydrogen bond acceptors [34][35]. Before evaluating the chain stopper efficiency of these compounds, i.e

Anion receptors containing thiazine-1,1-dioxide heterocycles as hydrogen bond donors

• Hong-Bo Wang,
• James A. Wisner and
• Michael C. Jennings

Beilstein J. Org. Chem. 2010, 6, No. 50, doi:10.3762/bjoc.6.50

Synthesis of indolo[3,2-b]carbazole-based new colorimetric receptor for anions: A unique color change for fluoride ions

• Ajit Kumar Mahapatra,
• Giridhari Hazra and
• Prithidipa Sahoo

Beilstein J. Org. Chem. 2010, 6, No. 12, doi:10.3762/bjoc.6.12

• CH3CN in the presence of I2 for 45 min afforded the desired receptor 1 in 82% yield. To look into the orientation of hydrogen bond donors around the carbazole motif, we optimized the structure by the AM1 method [45] (Figure 2). It is evident from Figure 2 that the two catechol units do not lie in the

The subtle balance of weak supramolecular interactions: The hierarchy of halogen and hydrogen bonds in haloanilinium and halopyridinium salts

• Kari Raatikainen,
• Massimo Cametti and
• Kari Rissanen

Beilstein J. Org. Chem. 2010, 6, No. 4, doi:10.3762/bjoc.6.4

• halides by providing two hydrogen bond donors with different HB strength, thus the ratio [D+–H···] : [C–I···] interaction sites in 13 is 2 : 1. In addition to the disturbance in the HB interactions, the nitro groups were expected to form competing halogen bond acceptor sites as demonstrated in our

Inversion symmetry and local vs. dispersive interactions in the nucleation of hydrogen bonded cyclic n-mer and tape of imidazolecarboxamidines

• Sihui Long,
• Venkatraj Muthusamy,
• Peter G. Willis,
• Sean Parkin and
• Arthur Cammers

Beilstein J. Org. Chem. 2008, 4, No. 23, doi:10.3762/bjoc.4.23

• polymers (tape) [9][10], cyclic n-mers [2][11][12], or dimers. For example, imidazolecarboxamidines 2 and imidazoles 3 have similar hydrogen bonding options offering sp2-NH hydrogen bond donors and sp2-N atom hydrogen bond acceptors. However 3 directs the hydrogen bond donor and acceptor approximately

• carboxamidines from commercial imidazoles and carbodiimides furnished a series of crystalline phases with related hydrogen bonding. The NCNC dihedral angle, θ, between the hydrogen bond donors and acceptors, was assigned values between +180° and −180°. Structures with opposite signs are conformational

A hydrogen- bonded channel structure formed by a complex of uracil and melamine

• Reji Thomas and
• G. U. Kulkarni

Beilstein J. Org. Chem. 2007, 3, No. 17, doi:10.1186/1860-5397-3-17

•  1b (see Table 2). It is clear that the amino groups of the melamine molecule act as hydrogen bond donors and ring nitrogens as acceptors. Unlike with adenine, uracil forms two N-H...O bonds (H9....O2, 2.08Å; H7...O1, 2.03Å) on either side of the N-H...N bond (H2...N6, 1.98Å). All the three hydrogen