Towards the sequence-specific multivalent molecular recognition of cyclodextrin oligomers

• Michael Kurlemann and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2014, 10, 2428–2440, doi:10.3762/bjoc.10.253

• preparation of di- and trivalent host sequences and investigated their binding behavior towards complementary and non-complementary di- and trivalent guest sequences which were modified with n-butyl and 1-adamantyl moieties. Such structures can be used for the self-assembly of complicated molecular

• -complementary cyclodextrin trimers host–guest systems of higher stoichiometry are formed. Based on these results further development of the guest strands can be done to create even heteromultivalent systems which show highly selective molecular recognition and can be used for the defined self-assembly of

Synthesis of novel conjugates of a saccharide, amino acids, nucleobase and the evaluation of their cell compatibility

• Dan Yuan,
• Xuewen Du,
• Junfeng Shi,
• Ning Zhou,
• Abdulgader Ahmed Baoum and
• Bing Xu

Beilstein J. Org. Chem. 2014, 10, 2406–2413, doi:10.3762/bjoc.10.250

• evolution, nature selects saccharides, peptides, and nucleobases as the fundamental building blocks for the creation of biomacromolecules, which lay the molecular foundations of life. This simple fact and the self-assembly of small molecules in water have inspired us to explore the conjugates of those three

• fundamental correlation between molecular structure and self-assembly. Here we investigate new molecular conjugates made of basic building blocks by connecting a saccharide segment to amino acids, and nucleobase (i.e., saccharide–amino acids–nucleobase, we term it SAN-type). As shown in Figure 1, in the

• unique types of heteroatom aromatics, not only promote self-assembly [30], but also have the capability for DNA delivery [16]. To examine the role of the saccharide, we also designed and synthesized the respective conjugates of amino acids and nucleobase without the glucuronic moiety (5–8) for comparison

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

• vision, now called “synthetic biology” [13][14][15][16][17], of converting automatically synthesized short DNA molecules (50–100 nucleotides in length) into much longer DNA constructs by autonomous self-assembly, without the cost of manual convergent assembly. In addition to the DARPA Foundries “1,000

• possible interaction, the presence of “strong” and “weak” G:C and A:T pairs makes design challenging. Also complicating self-assembly of single-stranded DNA fragments are folded single-strand structures (such as hairpins) that compete with desired inter-strand hybridization. A rich repertoire of non-Watson

• resistance by autonomous self-assembly, where S:B pairs used to create the clean fragment assembly are later converted via this process to T:A pairs. Figure 4 shows the details of the assembly. Results The OligArch software package and the construct design To support this project, a software package

Molecular ordering at electrified interfaces: Template and potential effects

• Thanh Hai Phan and
• Klaus Wandelt

Beilstein J. Org. Chem. 2014, 10, 2243–2254, doi:10.3762/bjoc.10.233

• mechanism. Comparison of both observed structures with those found earlier at different electrode potentials on a c(2 × 2)Cl-precovered Cu(100) electrode surface enables a clear assessment of the relative importance of adsorbate–substrate and adsorbate–adsorbate interactions, i.e., template vs self-assembly

• effects, in the structure formation process of DBV cations on these modified Cu electrode surfaces. Keywords: cyclic voltammogram; scanning tunneling microscopy; self-assembly; template effect; viologen; Introduction The precise control of the self-organization of molecular layers on either conducting

• the uncharged viologen species DBV0, respectively. The first investigations on the surface redox chemistry as well as the self-assembly of DBV-species on a chloride modified Cu(100) surface, were presented by Safarowsky et al. and Pham et al. [5][6][7]. In the present paper we will describe for the

Supercritical carbon dioxide: a solvent like no other

• Jocelyn Peach and
• Julian Eastoe

Beilstein J. Org. Chem. 2014, 10, 1878–1895, doi:10.3762/bjoc.10.196

• of polar and ionic species and attempts to enhance scCO2 viscosity. Keywords: CO2 chemistry; microemulsion; self-assembly; supercritical CO2; surfactant; viscosity; Introduction In this day and age, sustainability and renewability are watchwords. This includes focus within the scientific community

• . The majority of structures observed with surfactants and polymers in CO2 have been spherical reversed micelles [69], however, other anisotropic surfactant aggregate structures have been observed. Surfactants and polymers that undergo self-assembly and aggregation provide convenient ways to develop

• structure and affect viscosity. Examples of self-assembly structures that are commonly used to enhance viscosity include ellipsoid and rod-like micelles, worm and lamellar structures, bicontinuous phases and also the formation of gels [32][46][49][50][93][94][95]. Polymeric CO2 viscosifiers: Several

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

• DNA, all contribute to this unpredictability. In principle, adding extra nucleotides to the genetic alphabet can improve the predictability and reliability of autonomous DNA self-assembly, simply by increasing the information density of oligonucleotide sequences. These extra nucleotides are now

• a scalable and integrated infrastructure for the rapid and designed engineering of biology. Keywords: AEGIS; bioinformatics; DNA self-assembly; long DNA constructs; software; Introduction Automated synthesis of single stranded DNA fragments has, perhaps more than any other technology, enabled the

• of these fragments. Such engineered L-DNA might encode new and useful functions, including the manufacturing of biofuels, the synthesis of pharmaceuticals, and the development of new materials. As it is taught to non-chemists, DNA appears to be an ideal molecule for such “hands-off” self-assembly. In

Improving the reactivity of phenylacetylene macrocycles toward topochemical polymerization by side chains modification

• Simon Rondeau-Gagné,
• Jules Roméo Néabo,
• Maxime Daigle,
• Katy Cantin and
• Jean-François Morin

Beilstein J. Org. Chem. 2014, 10, 1613–1619, doi:10.3762/bjoc.10.167

• ; phenylacetylene macrocycles; polydiacetylenes; topochemical polymerization; Introduction The self-assembly of molecular building blocks is an increasingly popular method for the preparation of new semiconducting materials. Rational design of building blocks and their assembly using non-covalent interactions can

• . Moreover, subtle changes in the chemical nature of the building blocks can have a dramatic impact on the self-assembly process. This was exemplified in the case of nanotubes obtained from self-assembled butadiyne-containing macrocycles, which stack on top of each other in columnar fashion to give

• topochemical polymerization is necessary. In order to take a step further toward a better comprehension of the self-assembly of PAMs and to increase the polymerization yield, we decided to introduce substituents on the inside of the macrocycles, more precisely a polar 2-hydroxyethoxy group. Such a polar group

The search for new amphiphiles: synthesis of a modular, high-throughput library

• George C. Feast,
• Thomas Lepitre,
• Xavier Mulet,
• Charlotte E. Conn,
• Oliver E. Hutt,
• G. Paul Savage and
• Calum J. Drummond

Beilstein J. Org. Chem. 2014, 10, 1578–1588, doi:10.3762/bjoc.10.163

• amphiphilic species, the synthesis of a combinatorial library of amphiphilic compounds would allow the factors that drive self-assembly and liquid-crystalline phase formation to be analysed. Such studies are critical to the further development and design of new amphiphiles tailored for a specific application

• , and to deepen the understanding of how molecular structure influences the characteristics of self-assembly. Previous amphiphile libraries have been prepared using a thiol–yne reaction [14] and an in situ hydrazone formation between aldehyde tails and hydrazide head groups [15] in order to study gene

• . The interaction of water and the amphiphile was observed with a Nikon Eclipse 80i inverted microscope (Coherent Scientific, Melbourne) without and with an analyser. Images were captured with a Nikon DS-Fi1 camera (Coherent Scientific, Melbourne). Examples of amphiphile applications. Upon self-assembly

Pyrene-modified PNAs: Stacking interactions and selective excimer emission in PNA₂DNA triplexes

• Alex Manicardi,
• Lucia Guidi,
• Alice Ghidini and
• Roberto Corradini

Beilstein J. Org. Chem. 2014, 10, 1495–1503, doi:10.3762/bjoc.10.154

• ][15][16][17][18][19][20]. Furthermore, pyrene has been shown to favour self-assembly processes of supramolecular structures [21][22][23][24][25][26][27][28] and interact with carbon nanostructures such as nanotubes [29] or graphene [30], thus allowing to create composite material with special

Synthesis of the first examples of iminosugar clusters based on cyclopeptoid cores

• Mathieu L. Lepage,
• Alessandra Meli,
• Anne Bodlenner,
• Céline Tarnus,
• Francesco De Riccardis,
• Irene Izzo and
• Philippe Compain

Beilstein J. Org. Chem. 2014, 10, 1406–1412, doi:10.3762/bjoc.10.144

• ], β-cyclodextrin [4][5] and porphyrin [7] cores, and with nanoparticles prepared by self-assembly of iminosugar-based glycopolypetides [6]. So far, the largest multivalent effect (up to 610-fold relative inhibition potency increase on a valency-corrected basis) has been achieved on jack bean α

Biantennary oligoglycines and glyco-oligoglycines self-associating in aqueous medium

• Svetlana V. Tsygankova,
• Alexander A. Chinarev,
• Alexander B. Tuzikov,
• Nikolai Severin,
• Alexey A. Kalachev,
• Juergen P. Rabe,
• Alexandra S. Gambaryan and
• Nicolai V. Bovin

Beilstein J. Org. Chem. 2014, 10, 1372–1382, doi:10.3762/bjoc.10.140

• are cases characterized by the active participation of the surface in accelerating the self-assembly. To discriminate the processes taking place on the surface from similar processes in liquid volume, measurements were carried out immediately after the deprotonation of oligoglycine salts at incubation

Homochiral BINOL-based macrocycles with π-electron-rich, electron-withdrawing or extended spacing units as receptors for C₆₀

• Marco Caricato,
• Silvia Díez González,
• Idoia Arandia Ariño and
• Dario Pasini

Beilstein J. Org. Chem. 2014, 10, 1308–1316, doi:10.3762/bjoc.10.132

• traditionally sought after for enhancing the recognition toward suitable guests [5][6][7][8][9][10], and for the self-assembly, of stable organic nanotubes from the macrocyclic structures as molecular building blocks [11]. Cyclic peptides [12][13][14], phenylacetylene macrocycles [15], amide-containing

• protocol for the preparation of several chiral macrocycles incorporating BINOL (1,1′-bi-2-naphthol) units, through the formation of bridging ester functionalities, which ensure chemical inertness for the purposes of supramolecular sensing, recognition, or self-assembly. We have shown their application in

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

• Holger Busskamp Sascha Keller Marta Robotta Malte Drescher Andreas Marx Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany 10.3762/bjoc.10.104 Abstract The predictability of DNA self-assembly is exploited

• in many nanotechnological approaches. Inspired by naturally existing self-assembled DNA architectures, branched DNA has been developed that allows self-assembly to predesigned architectures with dimensions on the nanometer scale. DNA is an attractive material for generation of nanostructures due to a

• plethora of enzymes which modify DNA with high accuracy, providing a toolbox for many different manipulations to construct nanometer scaled objects. We present a straightforward synthesis of a rigid DNA branching building block successfully used for the generation of DNA networks by self-assembly and

End-group-functionalized poly(N,N-diethylacrylamide) via free-radical chain transfer polymerization: Influence of sulfur oxidation and cyclodextrin on self-organization and cloud points in water

• Sebastian Reinelt,
• Daniel Steinke and
• Helmut Ritter

Beilstein J. Org. Chem. 2014, 10, 680–691, doi:10.3762/bjoc.10.61

• interactions in living systems [3][4]. Since then, the field of self-assembly through molecular recognition has attracted much attention also in the design of smart materials. In this context, cyclodextrins (CD) are of interest as ring shaped host molecules, e.g., for the design of stimuli-responsive hydrogels

Self-assembly of metallosupramolecular rhombi from chiral concave 9,9’-spirobifluorene-derived bis(pyridine) ligands

• Rainer Hovorka,
• Sophie Hytteballe,
• Torsten Piehler,
• Georg Meyer-Eppler,
• Filip Topić,
• Kari Rissanen,
• Marianne Engeser and
• Arne Lützen

Beilstein J. Org. Chem. 2014, 10, 432–441, doi:10.3762/bjoc.10.40

• -protected [(dppp)Pd]2+ and [(dppp)Pt]2+ ions. The self-assembly process of the racemic ligand preferably occurs in a narcissistic self-recognising manner. Hence, a mixture of all three possible stereoisomers [(dppp)2M2{(R)-L}2](OTf)4, [(dppp)2M2{(S)-L}2](OTf)4, and [(dppp)2M2{(R)-L}{(S)-L}](OTf)4 was

• . Keywords: concave templates; metal complexes; self-assembly; self-sorting; 9,9’-spirobifluorene; supramolecular chemistry; Introduction Concave templates are versatile tools to achieve self-sorting behaviour in the self-assembly of defined aggregates from multicomponent mixtures in a social self

• -recognising [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18] or a self-discriminating manner [19][20][21][22][23][24][25][26][27]. As part of our ongoing programme to develop general guidelines for the diastereoselective self-assembly of metallosupramolecular aggregates, we have recently started a

Continuous-flow Heck synthesis of 4-methoxybiphenyl and methyl 4-methoxycinnamate in supercritical carbon dioxide expanded solvent solutions

• Phei Li Lau,
• Ray W. K. Allen and
• Peter Styring

Beilstein J. Org. Chem. 2013, 9, 2886–2897, doi:10.3762/bjoc.9.325

• these cross-coupling methods has undoubtedly revolutionalised the protocols for the construction of natural products, building blocks for supramolecular chemistry, self-assembly of organic materials and polymers, and lead compounds in medicinal chemistry from simpler entities [1]. These include the

Charge-transfer interaction mediated organogels from 18β-glycyrrhetinic acid appended pyrene

• Jun Hu,
• Jindan Wu,
• Qian Wang and
• Yong Ju

Beilstein J. Org. Chem. 2013, 9, 2877–2885, doi:10.3762/bjoc.9.324

• properties. UV–vis, fluorescence, mass spectrometric as well as variable-temperature 1H NMR experiments on these gels suggest that the CT interaction is one of the major driving forces for the formation of these organogels. Keywords: charge transfer; glycyrrhetinic acid; organogel; self-assembly

Self-assembly of 2,3-dihydroxycholestane steroids into supramolecular organogels as a soft template for the in-situ generation of silicate nanomaterials

• Valeria C. Edelsztein,
• Andrea S. Mac Cormack,
• Matías Ciarlantini and
• Pablo H. Di Chenna

Beilstein J. Org. Chem. 2013, 9, 1826–1836, doi:10.3762/bjoc.9.213

• .9.213 Abstract Supramolecular gels are an important and interesting class of soft materials that show great potential for many applications. Most of them have been discovered serendipitously, and understanding the supramolecular self-assembly that leads to the formation of the gel superstructure is the

• model of self-assembly through multiple intermolecular hydrogen bonds between the 1,2-dihydroxy system, which is based on experimental data and computational simulations revealing the importance of the di-axial orientation of the hydroxy groups for the one-dimensional self-assembly. Under controlled

• between the anionic silicate intermediate species and the self-assembled fibrillar network. Keywords: Hansen parameters; nanotube; organogel; self-assembly; supramolecular gel; Introduction Low molecular mass organogelators (LMOGs) have received increasing attention during the last two decades because

Structures of the reaction products of the AZADO radical with TCNQF₄ or thiourea

• Hideto Suzuki,
• Yuta Kawahara,
• Hiroki Akutsu,
• Jun-ichi Yamada and
• Shin’ichi Nakatsuji

Beilstein J. Org. Chem. 2013, 9, 1487–1491, doi:10.3762/bjoc.9.169

• impressively some TEMPO derivatives with appropriate acceptor units such as 1,4-benzoquinone [7] or naphthalenediimide [8] can form single-component CT complexes by self-assembly. Based on previous results, we next intended to see if similar CT complexes would be formed from AZADO (2) with an appropriate

Enhancement of efficiency in organic photovoltaic devices containing self-complementary hydrogen-bonding domains

• Rohan J. Kumar,
• Jegadesan Subbiah and
• Andrew B. Holmes

Beilstein J. Org. Chem. 2013, 9, 1102–1110, doi:10.3762/bjoc.9.122

• . Evidence is presented that the ability of these molecules to form one-dimensional hydrogen-bonded chains and subsequently exhibit hierarchical self-assembly into nanostructured domains can be correlated with improved device efficiency. Keywords: hydrogen-bonding; organic photovoltaics; self-assembly

• masks a known self-complementary hydrogen-bonding domain. The self-assembly properties of this unit have been extensively studied in a variety of systems [21][22][23][24][25][26], but this approach has not yet been applied to improving organic photovoltaic device performance. Solubility could be

• analysis, was reported to be at least 60 KJ mol−1 [29]. Self-assembly of cyanopyridone 2 The hydrogen-bond-mediated self-assembly behaviour of compound 2 was monitored by 1H NMR spectroscopy. The chemical shift of the proton on nitrogen in chloroform was observed to shift downfield in a concentration

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

• -delivery; hydrogel; multifunctional; nanofibers; NSAID; self-assembly; supramolecular; topical use; Introduction This article reports the design, synthesis, and characterization of hydrogelators made of non-steroidal anti-inflammatory drugs (NSAID) and small peptides for the development of multifunctional

• acetylsalicylic acid (aspirin) to connect with dipeptides results in a compound hydrolyzing easily at the ester bond of aspirin, we use salicylic acid (Sal) instead to conjugate with diphenylalanine and dialanine (AA) to make compounds 5a and 5g, respectively. Self-assembly and hydrogelation After the synthesis

• diastereomer of 1a, hydrogelator 1b exhibits quite different behavior in terms of self-assembly and hydrogelation. For example, at a concentration of 0.8 wt %, 1b forms a solution at pH 9.0 and 60 °C, and the solution remains after the conditions have been adjusted to pH 7.0 and room temperature. Further

Spin state switching in iron coordination compounds

• Philipp Gütlich,
• Ana B. Gaspar and
• Yann Garcia

Beilstein J. Org. Chem. 2013, 9, 342–391, doi:10.3762/bjoc.9.39

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

• Jutta Erika Helga Köhler and
• Nicole Grczelschak-Mick

Beilstein J. Org. Chem. 2013, 9, 118–134, doi:10.3762/bjoc.9.15

• chains of proteins [6], to size control of the electrostatic self assembly of nanoparticles [7]. Also a pH-controlled release of many cyclodextrins in long stacks on polymers, such as polyrotaxanes, combined with mesoporous silica particles was observed [8]. Complex formation with solvent molecules can

Self-assembled organic–inorganic magnetic hybrid adsorbent ferrite based on cyclodextrin nanoparticles

• Ângelo M. L. Denadai,
• Frederico B. De Sousa,
• Joel J. Passos,
• Fernando C. Guatimosim,
• Kirla D. Barbosa,
• Ana E. Burgos,
• Fernando Castro de Oliveira,
• Jeann C. da Silva,
• Bernardo R. A. Neves,
• Nelcy D. S. Mohallem and
• Rubén D. Sinisterra

Beilstein J. Org. Chem. 2012, 8, 1867–1876, doi:10.3762/bjoc.8.215

• , suggesting that βCD is able to minimize the ferrite coalescence process in aqueous solution. The ferrite aggregation process may occur in low zeta potential values (−10 mV, see zeta potential data) and is insufficient to avoid van der Waals attraction [30]; however, at pH 7 this self-assembly behavior can

Mannose-decorated cyclodextrin vesicles: The interplay of multivalency and surface density in lectin–carbohydrate recognition

• Ulrike Kauscher and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2012, 8, 1543–1551, doi:10.3762/bjoc.8.175

• functionalized by self-assembly [27]. To this end, cyclodextrins are modified with long alkyl chains (“tails”) and short oligo(ethylene glycol) head groups. These macrocyclic amphiphiles form unilamellar bilayer vesicles in aqueous solution upon hydration of a thin film cast by evaporation from organic solution

• consequence, the density of mannose molecules on the surface of the vesicles is expected to be relatively high, resulting in the formation of an artificial glycocalyx by self-assembly. Therefore, the addition of the lectin ConA should lead to agglutination of the vesicles due to the specific interaction of