Learning from the unexpected in life and DNA self-assembly

• Jennifer M. Heemstra

Beilstein J. Org. Chem. 2015, 11, 2713–2720, doi:10.3762/bjoc.11.292

• research choices throughout my career. Much like a negative judgment about my aptitude for science unexpectedly led me to a career in chemistry, my lab has found that our greatest insights into the molecular recognition and self-assembly properties of DNA have come from unexpected results or failed

• my Ph.D. studies, I had tremendous fun designing and studying organic foldamers, but I also began to be attracted to the especially privileged molecular recognition and self-assembly properties of nucleic acids. I think that Jeff actually recognized this before I did, as he chose the additional

• faculty members on my thesis committee to be Profs. Steve Zimmerman and Scott Silverman, who are both leaders in the field of nucleic acid molecular recognition. As my graduation neared, Jeff, Steve, and Scott all enthusiastically encouraged me to pursue postdoctoral research and then a career in academia

Synthesis of bi- and bis-1,2,3-triazoles by copper-catalyzed Huisgen cycloaddition: A family of valuable products by click chemistry

• Zhan-Jiang Zheng,
• Ding Wang,
• Zheng Xu and
• Li-Wen Xu

Beilstein J. Org. Chem. 2015, 11, 2557–2576, doi:10.3762/bjoc.11.276

• [4]arenes are sulfur-bridged analogs of calix[4]arenes, which have potential application in the molecular recognition of cationic, anionic or neutral molecules. In this regard, Yamato et al. incorporated two urea moieties possessing various aryl groups and two pyrene-appended triazole rings at the

Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

• Giuseppina Raffaini,
• Antonino Mazzaglia and
• Fabio Ganazzoli

Beilstein J. Org. Chem. 2015, 11, 2459–2473, doi:10.3762/bjoc.11.267

• their versatility both as drug carriers [11][14][15] and as self-assembling systems for molecular recognition [16][17][18]. Different research groups investigated the aCD behaviour in solution, elucidating their nanostructures and physicochemical behaviour, including the temperature- and concentration

• or bilayer, or vesicles and nanospheres at appropriate concentrations. In the recent past, some of these structures have been selected to yield versatile and reliable carriers for drug delivery [3][50], and even for molecular recognition of polymers [51]. In this scenario, the proposed study can open

Size-controlled and redox-responsive supramolecular nanoparticles

• Raquel Mejia-Ariza,
• Gavin A. Kronig and
• Jurriaan Huskens

Beilstein J. Org. Chem. 2015, 11, 2388–2399, doi:10.3762/bjoc.11.260

• core of the SNPs. Keywords: host–guest interactions; nanoparticles; self-assembly; stimulus-responsive; supramolecular chemistry; Introduction Self-assembly and molecular recognition are two core concepts underlying supramolecular chemistry. These offer convenient and versatile pathways to

• + guest-stabilizer] = 100 µM (Fc is the number of moieties from Fc8-PAMAM), thus keeping the molecular recognition moieties in a 1:1 stoichiometry ratio. For these experiments, first aqueous solutions of CD-PEI without or with a stabilizer (Ad-PEG, mPEG, Fc-PEG, Ad-TEG; see Scheme 1b) were prepared

Supramolecular chemistry: from aromatic foldamers to solution-phase supramolecular organic frameworks

• Zhan-Ting Li

Beilstein J. Org. Chem. 2015, 11, 2057–2071, doi:10.3762/bjoc.11.222

• : applications for molecular recognition and self-assembly Donor–acceptor interaction and π-stacking for folding. In January 2001, I returned to SIOC again. When I left SIOC for Urbana in 2000, I had built a small research group with two graduates. Thanks to the persistence of Professor Xi-Kui Jiang [19][20

Selected synthetic strategies to cyclophanes

• Sambasivarao Kotha,
• Mukesh E. Shirbhate and
• Gopalkrushna T. Waghule

Beilstein J. Org. Chem. 2015, 11, 1274–1331, doi:10.3762/bjoc.11.142

• to a large number of cations, anions, and neutral molecules. Cyclophanes are widely used in materials science and molecular recognition processes [48][49][50][51][52]. A general classification of cyclophanes is as follows: [n]orthocyclophane, [n]metacyclophane, and [n]paracyclophane (1–3) (Figure 1

Carboxylated dithiafulvenes and tetrathiafulvalene vinylogues: synthesis, electronic properties, and complexation with zinc ions

• Yunfei Wang and
• Yuming Zhao

Beilstein J. Org. Chem. 2015, 11, 957–965, doi:10.3762/bjoc.11.107

• enhance structural and electronic properties as well as to introduce some “intelligent” functions such as conformational switchability and selectivity in terms of molecular recognition and supramolecular interactions. The synthesis of TTFV structures is usually carried out through a facile iodine-promoted

Is organic chemistry science – and does this question make any sense at all?

• Andreas Kirschning and
• Thomas A. C. Reydon

Beilstein J. Org. Chem. 2015, 11, 893–896, doi:10.3762/bjoc.11.100

• conditions (molecular recognition, self-assembly and dynamic combinatorial chemistry) and how their molecular composition would be; the question why nature developed DNA and RNA that utilize ribose and 2-deoxyribose as central nucleotide building blocks instead of the more abundant and readily available

Multivalency as a chemical organization and action principle

• Rainer Haag

Beilstein J. Org. Chem. 2015, 11, 848–849, doi:10.3762/bjoc.11.94

• to establish strong, but also reversible chemical interactions between two units, e.g., a receptor and a ligand, viruses and host cells, or between two cell surfaces. Multivalent binding is based on multiple simultaneous molecular recognition processes and plays an important role in the self

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

• assemblies. Results Design of the model peptides The α-helical coiled-coil folding motif combines the chemical diversity of peptides with the molecular recognition properties and structural stability of DNA, and provides a valuable and variable system for the organisation of functionalized nanoparticles [34

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

• ] 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

Probing multivalency in ligand–receptor-mediated adhesion of soft, biomimetic interfaces

• Stephan Schmidt,
• Hanqing Wang,
• Daniel Pussak,
• Simone Mosca and
• Laura Hartmann

Beilstein J. Org. Chem. 2015, 11, 720–729, doi:10.3762/bjoc.11.82

• simply mediated by the high number of ligand–receptor interactions. Keywords: bio-interfaces; cell mimetic; glycocalyx; glycopolymer; molecular recognition; RICM; specific adhesion; Introduction Vast amounts of biological processes are mediated by interactions between membrane proteins and

NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A–T phosphoramidite building blocks

• Boris Schmidtgall,
• Claudia Höbartner and
• Christian Ducho

Beilstein J. Org. Chem. 2015, 11, 50–60, doi:10.3762/bjoc.11.8

• Oligonucleotides are important agents for a number of biomedical applications [1]. Thus, they are employed to exert antigene [2] or antisense [3] mechanisms as well as to trigger or inhibit RNA interference [4]. The capability of sequence-specific molecular recognition is a striking feature of nucleic acids, but

Inherently chiral calix[4]arenes via oxazoline directed ortholithiation: synthesis and probe of chiral space

• Simon A. Herbert,
• Laura J. van Laeren,
• Dominic C. Castell and
• Gareth E. Arnott

Beilstein J. Org. Chem. 2014, 10, 2751–2755, doi:10.3762/bjoc.10.291

• and applications. These range from their use as molecular receptors [2][3][4][5][6], stationary phase modifiers in separation science [7][8][9], and as molecular storage vessels [10][11][12][13]. In the area of molecular recognition, the importance of chirality in the calixarene receptor has been

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

• create the single-chain stranded, loose-fit structured PPRs. A further investigation focusing on molecular recognition between γ-CD and PHEMA is ongoing in our laboratory. Conclusion A series of γ-CD-based PPRs were prepared via the self-assembly of γ-CDs with a pentablock copolymer PHEMA-PPO-PEO-PPO

• -PHEMA in aqueous solution at room temperature. The resulting PPRs possess a unique single-chain stranded, loose-fit conformation showing no characteristic channel-type crystal structure. This finding highlights a novel model to fulfil molecular recognition between transformable γ-CDs and functional

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

• Michael Kurlemann Bart Jan Ravoo Organic Chemistry Institute, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany 10.3762/bjoc.10.253 Abstract Sequence-specific multivalent molecular recognition has been recognized to play a major role in biological processes

• realize sequence-specific molecular recognition by the use of host–guest chemistry, but the recognition motifs as well as the linkages have to be chosen very carefully. In the case of trivalent systems one adamantane moiety must be included to induce preferred formation of 1:1 adducts. Due to the too weak

• , with non-complementary strands aggregates of higher stoichiometry are generated. Keywords: cooperativity; cyclodextrins; molecular recognition; multivalency; sequence specificity; Introduction Multivalency is the interaction of a receptor and a ligand with at least two recognition motifs on each

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

• in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA–propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure–activity relation

• /AP3am) revealed molecular recognition of AT-DNA by the appearance of an ICD band pattern >300 nm. Significant ICD bands did not appear for other ds-DNA/RNA. A structure–activity relation for the studied series of compounds revealed that the essential structural features for the ICD recognition of AT-DNA

Why a diaminopyrrolic tripodal receptor binds mannosides in acetonitrile but not in water?

• Diogo Vila-Viçosa,
• Oscar Francesconi and
• Miguel Machuqueiro

Beilstein J. Org. Chem. 2014, 10, 1513–1523, doi:10.3762/bjoc.10.156

• over the years [1][2][3][4][5][6]. Most of these were developed for glucose since it is one of the most common sugars in living systems [7] and the preferred monosaccharide for energy storage [8]. However, mannose is essential for various biological functions, such as molecular recognition, being one

Carbohydrate PEGylation, an approach to improve pharmacological potency

• M. Eugenia Giorgi,
• Rosalía Agusti and
• Rosa M. de Lederkremer

Beilstein J. Org. Chem. 2014, 10, 1433–1444, doi:10.3762/bjoc.10.147

• recognized as immunodominant epitopes in antigenic glycoconjugates [14]. Carbohydrates participate in molecular recognition events such as host–pathogen interactions, responsible for mammal infections, and are candidates for chemotherapy [15]. Moreover, synthesis of multivalent carbohydrate ligands provide

Molecular recognition of surface-immobilized carbohydrates by a synthetic lectin

• Melanie Rauschenberg,
• Eva-Corrina Fritz,
• Christian Schulz,
• Tobias Kaufmann and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2014, 10, 1354–1364, doi:10.3762/bjoc.10.138

• Melanie Rauschenberg Eva-Corrina Fritz Christian Schulz Tobias Kaufmann Bart Jan Ravoo Organic Chemistry Institute, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany 10.3762/bjoc.10.138 Abstract The molecular recognition of carbohydrates and proteins mediates a

• agglutinin. It was found that the printed carbohydrates retain their characteristic selectivity towards the synthetic and natural lectins and that the recognition of synthetic and natural lectins is strictly orthogonal. Keywords: carbohydrates; lectins; molecular recognition; microarrays; multivalent

• results obtained from the microarray support our earlier finding that the interaction of HisHis and NANA is 1:2 [39], so that HisHis is likely to bind divalently to the microarray surface. Conclusion In summary, we have investigated the molecular recognition of surface immobilized carbohydrates by a

Design and synthesis of multivalent neoglycoconjugates by click conjugations

• Feiqing Ding,
• Li Ji,
• Ronny William,
• Hua Chai and
• Xue-Wei Liu

Beilstein J. Org. Chem. 2014, 10, 1325–1332, doi:10.3762/bjoc.10.134

• and glycopeptides are the key constituents of the cellular membrane and extracellular matrix, and play a pivotal role in various key cellular events such as cell–cell recognition, host–pathogen or host–symbiont interactions, molecular recognition of antibodies and metastasis [1][2][3][4][5]. The

Tandem Cu-catalyzed ketenimine formation and intramolecular nucleophile capture: Synthesis of 1,2-dihydro-2-iminoquinolines from 1-(o-acetamidophenyl)propargyl alcohols

• Gadi Ranjith Kumar,
• Yalla Kiran Kumar,
• Ruchir Kant and
• Maddi Sridhar Reddy

Beilstein J. Org. Chem. 2014, 10, 1255–1260, doi:10.3762/bjoc.10.125

• constituents in pharmaceutical chemistry [30][31][32][33][34][35][36][37][38][39][40][41][42] and also found to play a crucial role in molecular recognition processes [43][44][45][46]. Due to its vast-spread importance, several methods have been developed to construct this useful framework. Apart from the

Synthesis of a sucrose dimer with enone tether; a study on its functionalization

• Zbigniew Pakulski,
• Norbert Gajda,
• Magdalena Jawiczuk,
• Jadwiga Frelek,
• Piotr Cmoch and
• Sławomir Jarosz

Beilstein J. Org. Chem. 2014, 10, 1246–1254, doi:10.3762/bjoc.10.124

• synthesis; sucrose; Introduction Molecular recognition is one of the most important phenomena in stereoselective processes. Chiral crown ethers (or analogs) are particularly useful in enantioselective reactions [1][2] as well as differentiation of chiral guests [3][4]. From all of the chiral platforms

Olefin cross metathesis based de novo synthesis of a partially protected L-amicetose and a fully protected L-cinerulose derivative

• Bernd Schmidt and
• Sylvia Hauke

Beilstein J. Org. Chem. 2014, 10, 1023–1031, doi:10.3762/bjoc.10.102

• ., through molecular recognition of a preferred binding site [2][3][4][5], thereby ensuring the selectivity of a chemotherapeutic agent. Particularly common are side chains composed of deoxygenated sugars [6]. For example, the kigamicins are bacterial secondary metabolites isolated from Amicolatopsis sp. [7

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

• catalysis, transition metal complexing, molecular recognition, chromatographic separation and analysis of enantiomers [2][3][4][5]. Synthetic modifications of the basic structure, motivated by an improved stereoselectivity potential of quinine, are an issue of ongoing trials [6][7][8][9]. Surprisingly