Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

• Marijana Radić Stojković,
• Marko Škugor,
• Łukasz Dudek,
• Jarosław Grolik,
• Julita Eilmes and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2175–2185, doi:10.3762/bjoc.10.225

• . Nevertheless, the dynamic nature of nucleic acids, combined with structural differences between various DNA/RNA sequences, offer numerous highly interesting targets. Within the last two decades, the design of small binding molecules has mostly relied on the three-dimensional recognition of various targeted DNA

Five-membered ring annelation in [2.2]paracyclophanes by aldol condensation

• Henning Hopf,
• Swaminathan Vijay Narayanan and
• Peter G. Jones

Beilstein J. Org. Chem. 2014, 10, 2021–2026, doi:10.3762/bjoc.10.210

• deuteriochloroform) that combine to form a complex three-dimensional pattern (Table 1). Several attempts to obtain crystals of the major isomer 15 suitable for X-ray analysis failed. The anti-orientation of the carbonyl groups of compound 15 was proved by the X-ray structural analysis of the product resulting from a

Chemical templates

• Sigurd Höger

Beilstein J. Org. Chem. 2014, 10, 1670–1671, doi:10.3762/bjoc.10.174

• planar substrate with a specific structure and composition, determines the respective pattern formation on its surface. And three-dimensional templates are a unique and versatile tool for providing well-designed volume structures, often decorated with useful functionality. Not surprisingly, the annual

Synthesis and solvodynamic diameter measurements of closely related mannodendrimers for the study of multivalent carbohydrate–protein interactions

• Yoann M. Chabre,
• Alex Papadopoulos,
• Alexandre A. Arnold and
• René Roy

Beilstein J. Org. Chem. 2014, 10, 1524–1535, doi:10.3762/bjoc.10.157

• moieties and an aromatic central core but the introduction of distinct functionalized linkers may change the overall hydrophobic/hydrophilic balances of the structures. As such, they could engage supplementary intramolecular hydrogen bonding or hydrophobic interactions that could mediate their three

• -dimensional arrangement in aqueous media. Moreover, it is also reported that the relative spatial distribution of the branches around the C=O-centered BTAs strongly depends on the nature of the substituents [40]. This hypothesis can partly explain the discrepancy observed for the calculated diameter of 21

Pd/C-catalyzed aerobic oxidative esterification of alcohols and aldehydes: a highly efficient microwave-assisted green protocol

• Marina Caporaso,
• Giancarlo Cravotto,
• Spyros Georgakopoulos,
• George Heropoulos,
• Katia Martina and
• Silvia Tagliapietra

Beilstein J. Org. Chem. 2014, 10, 1454–1461, doi:10.3762/bjoc.10.149

• different bases on reaction conversion and selectivity when the reaction was catalyzed by Pd(OAc)2, Pd(OAc)2/C, and Pd/C. The three-dimensional array in Figure 1A highlights that high conversion was generally achieved under different conditions. Good results were obtained with Pd (OAc)2 under homogenous and

Stereoselective synthesis of carbocyclic analogues of the nucleoside Q precursor (PreQ₀)

• Sabin Llona-Minguez and
• Simon P. Mackay

Beilstein J. Org. Chem. 2014, 10, 1333–1338, doi:10.3762/bjoc.10.135

• -substituted analogues with interesting three-dimensional character, including chiral cyclopentane-1,2-diol and -1,2,3-triol derivatives. This unusual substitution pattern provides a useful starting point for the discovery of novel bioactive molecules. Keywords: diol synthesis; nucleoside; PreQ0

•  2), an IκB kinase inhibitor with antiviral and anti-inflammatory activity [26][27], we decided to investigate a synthetic route that would allow for the incorporation of carbocyclic systems with interesting three-dimensional character at the 4-position of PreQ0 as part of our fragment-based kinase

Automated solid-phase peptide synthesis to obtain therapeutic peptides

• Veronika Mäde,
• Sylvia Els-Heindl and
• Annette G. Beck-Sickinger

Beilstein J. Org. Chem. 2014, 10, 1197–1212, doi:10.3762/bjoc.10.118

• generally no tertiary, three-dimensional structure compared to proteins [1]. In nature, the oligomers or polymers are assembled at ribosomes by aminoacyl-tRNAs (transfer ribonucleic acid) [2]. Basically, a condensation reaction of a carboxylic acid moiety with a functional amine of trifunctional α-amino

A new building block for DNA network formation by self-assembly and polymerase chain reaction

• Holger Bußkamp,
• Sascha Keller,
• Marta Robotta,
• Malte Drescher and
• Andreas Marx

Beilstein J. Org. Chem. 2014, 10, 1037–1046, doi:10.3762/bjoc.10.104

• , the formed DNA networks are remarkably stabilized (up to 95 °C) compared to the non-branched counterparts. We previously reported an approach to construct three dimensional DNA networks that were generated and amplified by DNA polymerase chain reactions (PCR). In order to construct the network we

• findings correlate well with the decreased mobility of the structures in the agarose gel electrophoresis (Figure 3) demonstrating one covalently connected migrating DNA molecule. The irregular shapes of the DNA networks might result from the collapse of three-dimensional structures forced by ionic

Site-selective covalent functionalization at interior carbon atoms and on the rim of circumtrindene, a C₃₆H₁₂ open geodesic polyarene

• Hee Yeon Cho,
• Ronald B. M. Ansems and
• Lawrence T. Scott

Beilstein J. Org. Chem. 2014, 10, 956–968, doi:10.3762/bjoc.10.94

• ]. Whereas fullerenes comprising complete three-dimensional polyhedra can be classified as “closed” geodesic polyarenes, curved subunits of fullerenes are regarded as “open” geodesic polyarenes [4]. The fullerenes constitute one family of geodesic polyarenes, and bowl-shaped polycyclic aromatic hydrocarbons

Molecular architecture with carbohydrate functionalized β-peptides adopting 3₁₄-helical conformation

• Nitin J. Pawar,
• Navdeep S. Sidhu,
• George M. Sheldrick,
• Dilip D. Dhavale and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2014, 10, 948–955, doi:10.3762/bjoc.10.93

• ; sugar amino acid; Introduction Synthetic biomimetic macromolecules, which are capable to fold into well-defined three-dimensional structures in analogy to natural peptides and proteins, have been extensively studied to increase the understanding of complex biomolecules [1][2][3]. In this respect, β

N-Alkylated dinitrones from isosorbide as cross-linkers for unsaturated bio-based polyesters

• Oliver Goerz and
• Helmut Ritter

Beilstein J. Org. Chem. 2014, 10, 902–909, doi:10.3762/bjoc.10.88

• to dissolve byproducts and catalyst. The pure compounds were obtained by additionally washing with diethyl ether. In order to proof the ability of dinitrones to form three-dimensional networks with itaconate moieties containing polyesters, the bio-based unsaturated polyester 13 was synthesized from

Addition of H-phosphonates to quinine-derived carbonyl compounds. An unexpected C9 phosphonate–phosphate rearrangement and tandem intramolecular piperidine elimination

• Łukasz Górecki,
• Artur Mucha and
• Paweł Kafarski

Beilstein J. Org. Chem. 2014, 10, 883–889, doi:10.3762/bjoc.10.85

• ; Introduction Medicinal, organocatalytic and stereoselective properties of quinine make it the most prominent representative of Cinchona alkaloids [1], a group of natural compounds of a unique three-dimensional structure. The structure involves a particular arrangement of two rigid heterocyclic fragments

Intermediates in monensin biosynthesis: A late step in biosynthesis of the polyether ionophore monensin is crucial for the integrity of cation binding

• Wolfgang Hüttel,
• Jonathan B. Spencer and
• Peter F. Leadlay

Beilstein J. Org. Chem. 2014, 10, 361–368, doi:10.3762/bjoc.10.34

• a decisive effect on the three-dimensional structure of the ionophore-cation complex, as revealed by X-ray crystal structure analysis of both dehydroxymonensin A and demethylmonensin A, each in complex with a sodium ion. Results and Discussion PCR-targetted in-frame deletions using the ReDirect [21

Synthesis of enantiopure sugar-decorated six-armed triptycene derivatives

• Paola Bonaccorsi,
• Maria Luisa Di Gioia,
• Antonella Leggio,
• Lucio Minuti,
• Teresa Papalia,
• Carlo Siciliano,
• Andrea Temperini and
• Anna Barattucci

Beilstein J. Org. Chem. 2013, 9, 2410–2416, doi:10.3762/bjoc.9.278

• geometric features of its skeleton with a D3h symmetry have attracted a lot of attention and its derivatives have been used for applications in supramolecular chemistry, material chemistry, and as molecular machines [1][2]. The interest in this three-dimensional rigid platform is also due to the easy

Crystal design using multipolar electrostatic interactions: A concept study for organic electronics

• Peer Kirsch,
• Qiong Tong and
• Harald Untenecker

Beilstein J. Org. Chem. 2013, 9, 2367–2373, doi:10.3762/bjoc.9.272

• and H∙∙∙O contacts. The calculation of transfer integrals based on the crystal structure indicates that in spite of the brickwall-structure, due to a slight asymmetry of the “layering”, the hole conductivity is rather anisotropic (1D), whereas the electron conductivity is three-dimensional (3D

Cascade radical reaction of substrates with a carbon–carbon triple bond as a radical acceptor

• Hideto Miyabe,
• Ryuta Asada and
• Yoshiji Takemoto

Beilstein J. Org. Chem. 2013, 9, 1148–1155, doi:10.3762/bjoc.9.128

• was assumed by similarity between the present reaction and the previously reported reaction of substrates having the carbon–carbon double bond [39][42]. In these reactions, a ternary complex of ligand, Lewis acid and substrate would control the three-dimensional arrangement of two radical acceptors. A

Camera-enabled techniques for organic synthesis

• Steven V. Ley,
• Richard J. Ingham,
• Matthew O’Brien and
• Duncan L. Browne

Beilstein J. Org. Chem. 2013, 9, 1051–1072, doi:10.3762/bjoc.9.118

• mixing was constant for the required time. Supporting Information File 2 shows the device in operation. Cronin and co-workers have recently reported the use of three-dimensional design software and an open-hardware 3D printing device to produce low-cost bespoke reactionware for applications in both

3D-printed devices for continuous-flow organic chemistry

• Vincenza Dragone,
• Victor Sans,
• Mali H. Rosnes,
• Philip J. Kitson and
• Leroy Cronin

Beilstein J. Org. Chem. 2013, 9, 951–959, doi:10.3762/bjoc.9.109

• reported [4][5]. 3D printing consists of the fabrication of three-dimensional physical objects from a digital model [6]. The 3D printer takes the virtual design from computer-aided design (CAD) software and reproduces it layer-by-layer until the physical definition of the layers gives the designed object

The conjugation of nonsteroidal anti-inflammatory drugs (NSAID) to small peptides for generating multifunctional supramolecular nanofibers/hydrogels

• Jiayang Li,
• Yi Kuang,
• Junfeng Shi,
• Yuan Gao,
• Jie Zhou and
• Bing Xu

Beilstein J. Org. Chem. 2013, 9, 908–917, doi:10.3762/bjoc.9.104

• supramolecular hydrogels. Sharing similar features with the extracellular matrices of tissues (e.g., consisting of three-dimensional networks and a significant amount of water), hydrogels have become an attractive choice for developing biomaterials for a variety of applications. For example, hydrogels have

• and hydrogels. Besides being used for three-dimensional cell cultures [32], supramolecular hydrogels also find applications in typing [33] and against bacteria [34][35][36][37][38], and in enzyme assays [23][39], catalysis [40], and inhibiting cancer cells [41][42][43][44]. These successful examples

Cyclodextrin-based nanosponges as drug carriers

• Francesco Trotta,
• Marco Zanetti and
• Roberta Cavalli

Beilstein J. Org. Chem. 2012, 8, 2091–2099, doi:10.3762/bjoc.8.235

• nanosponges, which are proposed as a new nanosized delivery system, are innovative cross-linked cyclodextrin polymers nanostructured within a three-dimensional network. This type of cyclodextrin polymer can form porous insoluble nanoparticles with a crystalline or amorphous structure and spherical shape or

Design and synthesis of quasi-diastereomeric molecules with unchanging central, regenerating axial and switchable helical chirality via cleavage and formation of Ni(II)–O and Ni(II)–N coordination bonds

• Vadim A. Soloshonok,
• José Luis Aceña,
• Hisanori Ueki and
• Jianlin Han

Beilstein J. Org. Chem. 2012, 8, 1920–1928, doi:10.3762/bjoc.8.223

• ; Introduction The design and synthesis of organic molecules for which the changing of their three-dimensional structure or function can be predicted, is a fast-growing multidisciplinary field of research [1][2][3][4][5][6][7][8][9][10][11][12][13]. In particular, organic compounds that can undergo reversible

Synthetic studies towards bottromycin

• Stefanie Ackermann,
• Hans-Georg Lerchen,
• Dieter Häbich,
• Angelika Ullrich and
• Uli Kazmaier

Beilstein J. Org. Chem. 2012, 8, 1652–1656, doi:10.3762/bjoc.8.189

• by Schipper [20] and Kaneda [21], based on detailed NMR studies. According to them, the bottromycins are cyclic tetrapeptides, connected to a tripeptidic side chain through an amidine structure. The different bottromycins differ only in the substitution pattern of the proline (Figure 1). The three

• -dimensional structure was reported recently by Gouda et al. [22]. This structure is quite unusual, not only because of the amidine moiety but also because most amino acids are found in β-methylated form (tert-leucine can be seen as β-methylvaline). Although a series of synthetic studies towards linear

Synthesis of trifunctional cyclo-β-tripeptide templates

• Frank Stein,
• Tahir Mehmood,
• Tilman Plass,
• Javid H. Zaidi and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2012, 8, 1576–1583, doi:10.3762/bjoc.8.180

• The concept of template-assembled synthetic proteins (TASP) describes a central scaffold that predefines the three dimensional structure for diverse molecules linked to this platform. Cyclic β-tripeptides are interesting candidates for use as templates due to their conformationally defined structure

• such as nucleobases on the template provides a specific hydrogen-bonding network orthogonal to the peptide ring aggregation, which will be of value for aggregate formation and molecular architectures defined by a three-dimensional network of hydrogen bonds. Selective release of the first amino group

• core in order to generate a template that can form a three dimensional network of hydrogen bonds. Experimental General remarks All technical solvents were distilled prior to use. The solvents of analytical and HPLC grade were used as supplied. The solvents used for the synthesis were obtained in

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

Enantioselective supramolecular devices in the gas phase. Resorcin[4]arene as a model system

• Caterina Fraschetti,
• Matthias C. Letzel,
• Antonello Filippi,
• Maurizio Speranza and
• Jochen Mattay

Beilstein J. Org. Chem. 2012, 8, 539–550, doi:10.3762/bjoc.8.62

• +. Furthermore, in all simulations the position of the CO2Me function oscillates between two orientations differing by 180°, except for TH+ in vacuum, while the ethyl group is invariably free to rotate in the three-dimensional space [49]. The computational results indicated that the chair conformation is better