Impact of multivalent charge presentation on peptide–nanoparticle aggregation

• Daniel Schöne,
• Boris Schade,
• Christoph Böttcher and
• Beate Koksch

Beilstein J. Org. Chem. 2015, 11, 792–803, doi:10.3762/bjoc.11.89

• increasing demand for smaller, more complex, but even cheaper materials, the commonly used “top-down” methods are not available. Thus, new strategies like the “bottom-up” approach have been developed to achieve materials in the nanometer range [11][12]. This technique is based on the self-assembly of small

• switching [15] applications, a variety of specific and site selective binding properties are available [16]. In particular, the specificity of Watson–Crick base pairing of DNA nucleotides can be used for the directed and predictable self-assembly of nanoparticles [17]. The DNA mediated assembly of

Discrete multiporphyrin pseudorotaxane assemblies from di- and tetravalent porphyrin building blocks

• Mirko Lohse,
• Larissa K. S. von Krbek,
• Sebastian Radunz,
• Suresh Moorthy,
• Christoph A. Schalley and
• Stefan Hecht

Beilstein J. Org. Chem. 2015, 11, 748–762, doi:10.3762/bjoc.11.85

• stoichiometry, while the amount of alternative structures can be neglected. Our results illustrate the power of multivalency to program the multicomponent self-assembly of specific entities into discrete functional nanostructures. Keywords: crown ethers; multicomponent assembly; multivalency; porphyrins

• ] to life science [13][14][15][16][17] have benefited from the development of the basic concepts of molecular recognition, templation [18], self-assembly [19], or self-sorting [20][21], just to name a few. More recently, multivalent binding [22][23][24] and cooperativity [25][26] have attracted

• functional building blocks, the formation of specific multiply threaded pseudorotaxanes was achieved, thereby demonstrating the ability to program complex multicomponent self-assembly [74][75]. Results and Discussion Synthesis The synthesis of the two ammonium-substituted porphyrins A2 and A4 was performed

DNA display of glycoconjugates to emulate oligomeric interactions of glycans

• Alexandre Novoa and
• Nicolas Winssinger

Beilstein J. Org. Chem. 2015, 11, 707–719, doi:10.3762/bjoc.11.81

• sugar-core glycoconjugate DNA. Combinatorial self-assembly of PNA glycoconjugates on a DNA microarray. General scheme of the 10,000 member PNA-encoded glycoconjugate library. Oligomeric interaction with arrayed mono- and divalent ligands (represented as the black spheres) as a function of surface

Self-assembly of heteroleptic dinuclear metallosupramolecular kites from multivalent ligands via social self-sorting

• Christian Benkhäuser and
• Arne Lützen

Beilstein J. Org. Chem. 2015, 11, 693–700, doi:10.3762/bjoc.11.79

• central 1,3-diethynylbenzene unit 2 were synthesized. Each of these ligands acts as a multivalent entity for the binding of two copper(I) ions. Upon coordination to the metal ions these two ligands undergo selective self-assembly into heteroleptic dinuclear metallosupramolecular kites in a high-fidelity

• social self-sorting manner as evidenced by NMR spectroscopy and mass spectrometry. Keywords: metal complexes; multivalency; self-assembly; self-sorting; supramolecular chemistry; Tröger's base; Introduction Self-assembly of defined aggregates from multicomponent mixtures through self-sorting effects

• strategy has proven to be very successful for the formation of homoleptic complexes through self-recognition [1][2][3][4]. However, self-assembly processes of metallosupramolecular aggregates that integrate more than one type of bridging ligand and/or one type of metal ion into an assembly are even more

Potential of acylated peptides to target the influenza A virus

• Daniel Lauster,
• Damian Pawolski,
• Julian Storm,
• Kai Ludwig,
• Rudolf Volkmer,
• Henry Memczak,
• Andreas Herrmann and
• Sumati Bhatia

Beilstein J. Org. Chem. 2015, 11, 589–595, doi:10.3762/bjoc.11.65

• has not been explored much in the context of virus inhibition. There are only a few reports on using peptide based self-assembly for influenza virus inhibition [12][13][14]. The entry blocker (EB) which is a peptide fragment derived from the fibroblast growth factor signal sequence 4 (FGF) has a

Properties of cationic monosubstituted tetraalkylammonium cyclodextrin derivatives – their stability, complexation ability in solution or when deposited on solid anionic surface

• Martin Popr,
• Sergey K. Filippov,
• Nikolai Matushkin,
• Juraj Dian and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2015, 11, 192–199, doi:10.3762/bjoc.11.20

• acid [26]. Similar approaches of ionic self-assembly with CDs were used for the preparation of nanoparticles with external CD trigger [27], new material nanostructures [28], polyelectrolyte-surfactant complexes which yield new types of solid mesomorphous materials [29], or membranes with size-selective

• (PErMethylated EthyleneDiAmine substituted). Its binding ability toward selected aromatic guests is compared to the native β-CD at different pH. Deposition of PEMPDA-β-CD on the surface of an anionic Nafion® 117 membrane via ionic self-assembly was also studied along with the determination of sorption kinetics

• SAL and MEQ at acidic and neutral pH, whose stabilities are superior to those of the native β-CD. Immobilization of PEMPDA-β-CD on anionic surface via ionic self-assembly In the next part of our research, we focused on the possibility of deposition of the permanently charged PEMPDA-β-CD onto the solid

Articulated rods – a novel class of molecular rods based on oligospiroketals (OSK)

• Pablo Wessig,
• Roswitha Merkel and
• Peter Müller

Beilstein J. Org. Chem. 2015, 11, 74–84, doi:10.3762/bjoc.11.11

• hydrophobic backbone of the ARs and the markedly smaller surface of the FOL conformation. This behavior resembles folding of peptides and self-assembly of lipids. It is well known that cyclodextrines (CDs), bearing a hydrophobic cavity and a hydrophilic exterior, are able to encapsulate small hydrophobic

Release of β-galactosidase from poloxamine/α-cyclodextrin hydrogels

• César A. Estévez,
• José Ramón Isasi,
• Eneko Larrañeta and
• Itziar Vélaz

Beilstein J. Org. Chem. 2014, 10, 3127–3135, doi:10.3762/bjoc.10.330

• kinetics [6]. The hydrophilic nature of the hydrogels is due to the presence of groups along the polymer chains such as hydroxy, carboxy, amide and sulfonic acid [7]. The cross-linking may be either physical or chemical (covalent). According to the reversible and tunable nature of self-assembly, the

• change, making the self-assembly process feasible. In addition, X-ray diffraction showed that some degree of order can be found in the gel structure, attributable to the formation of EO/α-CD complexes that become aggregated into ordered domains. As can be seen in Figure 3, the FTIR spectrum of T25a10

Synthesis and characterization of pH responsive D-glucosamine based molecular gelators

• Navneet Goyal,
• Hari P. R. Mangunuru,
• Bargav Parikh,
• Sonu Shrestha and
• Guijun Wang

Beilstein J. Org. Chem. 2014, 10, 3111–3121, doi:10.3762/bjoc.10.328

• ; naproxen; organogelator; pH responsive; self-assembly; Introduction Low molecular weight gelators (LMWGs) have drawn great attention over the past few decades due to the formation of supramolecular structures and their potential applications as advanced materials [1][2][3][4][5][6][7]. LMWGs are also

Mono- and multilayers of molecular spoked carbazole wheels on graphite

• Stefan-S. Jester,
• A. Vikas Aggarwal,
• Daniel Kalle and
• Sigurd Höger

Beilstein J. Org. Chem. 2014, 10, 2783–2788, doi:10.3762/bjoc.10.295

• the single bonds of two corner units) in the presence of molecular squares [8]. Consequently, an increased understanding of the 2D self-assembly of MSWs on HOPG should nominally pave the way towards a suitable molecular design for (stiffened) hexagons that is compatible with our previous series and

Self-assembled monolayers of shape-persistent macrocycles on graphite: interior design and conformational polymorphism

• Joscha Vollmeyer,
• Friederike Eberhagen,
• Sigurd Höger and
• Stefan-S. Jester

Beilstein J. Org. Chem. 2014, 10, 2774–2782, doi:10.3762/bjoc.10.294

• supramolecular surface patterning is highly oriented pyrolytic graphite (HOPG) which provides large atomically flat terraces between step edges and a sufficient adsorbate mobility, required for the self-assembly process that leads to the 2D crystal formation. For a more detailed understanding of the macrocycle

• unit is varied. The driving forces for their 2D self-assembly are most probably independent from the presence of additional functional groups pointing into the third dimension or located inside the cavity interior. To the best of our knowledge, only little effort has been spent so far on investigating

• the intraannular substitution on the 2D supramolecular self-assembly of macrocycles. Compounds 1–3 (Figure 3) have the same macrocyclic rigid backbone and flexible octadecyloxy periphery and differ only in their intraannular substitution. While 1 has an empty interior, 2 contains an alkyl chain

Removal of volatile organic compounds using amphiphilic cyclodextrin-coated polypropylene

• Ludmilla Lumholdt,
• Sophie Fourmentin,
• Thorbjørn T. Nielsen and
• Kim L. Larsen

Beilstein J. Org. Chem. 2014, 10, 2743–2750, doi:10.3762/bjoc.10.290

• surfaces, including polyethylene, polyvinyl chloride and polyurethane, was previously reported [21]. This method relies on the self-assembly properties of amphiphilic CDs (ACDs), which are CDs with some of the hydroxy groups substituted by alkyl chains. This can be performed in situ by, for example, simply

Linear-g-hyperbranched and cyclodextrin-based amphiphilic block copolymer as a multifunctional nanocarrier

• Yamei Zhao,
• Wei Tian,
• Guang Yang and
• Xiaodong Fan

Beilstein J. Org. Chem. 2014, 10, 2696–2703, doi:10.3762/bjoc.10.284

• ) (PDMAEMA) block (Scheme 1A, P1), allows for the self-assembly and controlled release by taking advantage of the amphiphilic structure and the stimuli-responsive property of PDMAEMA block, respectively. When the hyperbranched polycarbonsilane (HBPCSi) is grafted onto the side chain of PHEMA blocks (Scheme

• in the micellization process. Self-assembly behaviour of P3 in aqueous solution After the synthesis of P3 with amphiphilic characteristics, the corresponding micelle system with a core–shell structure can be formed in aqueous solution by self-assembly. This is driven by the strong hydrophobic

• employed to obtain a deeper insight into the self-assembly morphology and size of P3 in aqueous solution. Figure 1 presents the diameter distributions of P1, P2 and P3 micelles (denoted as MP1, MP2, and MP3) in aqueous solution at 25 ºC. Compared with the Z–average diameter values of P1 (242 nm) and P2

A green approach to the synthesis of novel phytosphingolipidyl β-cyclodextrin designed to interact with membranes

• Yong Miao,
• Florence Djedaïni-Pilard and
• Véronique Bonnet

Beilstein J. Org. Chem. 2014, 10, 2654–2657, doi:10.3762/bjoc.10.278

• order to have good water solubility, selectively modified (methylated) CDs are mostly desired [3]. Among the selectively modified CDs, mono-substituded CD derivatives do not only have self-assembly properties, but also have a good water solubility, allowing passive diffusion across a membrane through

Loose-fit polypseudorotaxanes constructed from γ-CDs and PHEMA-PPG-PEG-PPG-PHEMA

• Tao Kong,
• Lin Ye,
• Ai-ying Zhang and
• Zeng-guo Feng

Beilstein J. Org. Chem. 2014, 10, 2461–2469, doi:10.3762/bjoc.10.257

• ) initiated by 2-bromoisobutyryl end-capped PPO-PEO-PPO as a macroinitiator in DMF. Attaching PHEMA blocks altered the self-assembly process of the pentablock copolymer with γ-CDs in aqueous solution. Before attaching the PHEMA, the macroinitiator was preferentially bent to pass through the inner cavity of γ

• instead of PEG, and γ-CDs accommodate either single-chain PPG or double-chain PEG [1]. The driving force behind the self-assembly is mostly ascribed to a suitable fit between the cross-sectional area of the incoming polymer chain and the cavity size of the CDs [2]. However, the cavity shape and size of

• with γ-CDs in aqueous solution to form PPRs. The results of 1H NMR, WXRD, DSC, TGA, 13C CP/MAS NMR and FTIR analyses indicate that the attachment of PHEMA clearly changes the self-assembly direction of γ-CDs with PHEMA-PPO-PEO-PPO-PHEMA. This results in unique, single-chain stranded, loose-fit PPRs

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