Interaction of cyclodextrins with pyrene-modified polyacrylamide in a mixed solvent of water and dimethyl sulfoxide as studied by steady-state fluorescence

• Akihito Hashidzume,
• Yongtai Zheng and
• Akira Harada

Beilstein J. Org. Chem. 2012, 8, 1312–1317, doi:10.3762/bjoc.8.150

• hydrogels [22][23][24][25][26][27] and macroscopic assemblies based on molecular recognition [28][29][30][31]. Aromatic residues absorb light to become excited, and subsequently they can transfer energy and electrons. The interaction of CDs with water-soluble polymers carrying aromatic residues may allow

• one to construct functional systems that convert photo energy based on molecular recognition. Among aromatic compounds, pyrene is the most examined as a fluorescence probe or label because it shows a relatively high fluorescence quantum yield and a relatively long fluorescence lifetime in both monomer

• ][36]. Recently, we have demonstrated this selectivity switching on macroscopic molecular recognition for polyacrylamide-based gels carrying pyrenyl (Py) and CD residues, by changing the composition of a mixed solvent of water and dimethyl sulfoxide (DMSO) [37]. In the present study, the interaction of

The effect of the formyl group position upon asymmetric isomeric diarylethenes bearing a naphthalene moiety

• Renjie Wang,
• Shouzhi Pu,
• Gang Liu and
• Shiqiang Cui

Beilstein J. Org. Chem. 2012, 8, 1018–1026, doi:10.3762/bjoc.8.114

• nucleosides and molecular recognition properties of nucleic acids with the light sensitivity of diarylethenes [34]. Recently, Wu et al. designed and synthesized a novel diarylethene-containing dithiazolethene, which exhibited a gated photochromic reactivity controlled by complexation/dissociation with BF3 [35

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

Investigation of the network of preferred interactions in an artificial coiled-coil association using the peptide array technique

• Raheleh Rezaei Araghi,
• Carsten C. Mahrenholz,
• Rudolf Volkmer and
• Beate Koksch

Beilstein J. Org. Chem. 2012, 8, 640–649, doi:10.3762/bjoc.8.71

• close to and within the interhelical core (a,d,e,g), which are most important for molecular recognition, were mutated. More specifically, hydrophobic (a15,d18) and electrostatic (e19,g21) positions were mutated simultaneously (Figure 2). The 35mer mutants on the membrane only differ in the positions

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

• life's supramolecular systems in which the guest molecule (e.g., amino acids, neurotransmitters, drugs) is selectively captured into the host macromolecular structure (molecular recognition) and transformed catalytically at a specific “active site” (enzyme catalysis) [1][2][3]. Furthermore, the

• the effective probability that the necessary proton transfer from T to B occurs. Rigid resorcin[4]arenes as chiral selectors of amino acids and neurotransmitters. Further insights into the molecular recognition of basket resorcin[4]arene V towards representative chiral molecules were gathered. For

Synthesis of multivalent host and guest molecules for the construction of multithreaded diamide pseudorotaxanes

• Nora L. Löw,
• Egor V. Dzyuba,
• Boris Brusilowskij,
• Lena Kaufmann,
• Elisa Franzmann,
• Wolfgang Maison,
• Emily Brandt,
• Daniel Aicher,
• Arno Wiehe and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2012, 8, 234–245, doi:10.3762/bjoc.8.24

• these concepts are not only molecular recognition and the noncovalent bonds themselves, but also self-assembly, self-sorting, templation and multivalent binding [1][2][3][4][5][6][7][8]. Consequently, the reductionist investigation of synthetic supramolecules can help us to understand biological systems

Fifty years of oxacalix[3]arenes: A review

• Kevin Cottet,
• Paula M. Marcos and
• Peter J. Cragg

Beilstein J. Org. Chem. 2012, 8, 201–226, doi:10.3762/bjoc.8.22

• -substituted phenol; however, in host–guest chemistry an asymmetric macrocycle can provide a site for enantioselective molecular recognition. In the case of p-tert-butylcalix[n]arenes the tert-butyl substituent can be removed, as mentioned previously, through a retro-Friedel–Crafts acylation, and replaced by

• function as a molecular recognition centre. The cavity created by the lipophilic phenolic units, particularly when held in place through allosteric effects of lower-rim substituents bound to metals, can accommodate a number of quaternary ammonium ions or buckminsterfullerene, C60. Consequently, the ability

Binding of group 15 and group 16 oxides by a concave host containing an isophthalamide unit

• Jens Eckelmann,
• Vittorio Saggiomo,
• Svenja Fischmann and
• Ulrich Lüning

Beilstein J. Org. Chem. 2012, 8, 11–17, doi:10.3762/bjoc.8.2

• ; macrocycle; molecular recognition; Introduction In the last decade, isophthalamide derivatives have become attractive neutral hosts as anion receptors [1][2]. Some of these derivatives show a high selectivity for one anion over others [3]. Isophthalamide units have also been incorporated into macrocycles [4

(How) does 1,3,5-triethylbenzene scaffolding work? Analyzing the abilities of 1,3,5-triethylbenzene- and 1,3,5-trimethylbenzene-based scaffolds to preorganize the binding elements of supramolecular hosts and to improve binding of targets

• Xing Wang and
• Fraser Hof

Beilstein J. Org. Chem. 2012, 8, 1–10, doi:10.3762/bjoc.8.1

• Xing Wang Fraser Hof University of Victoria, Department of Chemistry, Victoria, BC, V8W 3V6, Canada 10.3762/bjoc.8.1 Abstract 1,3,5-triethylbenzenes have been widely used as supramolecular templates to organize molecular-recognition elements. It is believed that the steric-gearing effect of the

• methyl groups, but the size of this advantage can be small and is dependent on the groups involved. Keywords: binding affinity; entropy; molecular recognition; scaffolds; supramolecular hosts; triethylbenzene; trimethylbenzene; Introduction Supramolecular hosts use arrays of multiple weak interactions

• of preorganization [3][4]. As a nonmacrocyclic alternative, 1,3,5-triethylbenzenes are widely used as an easy-to-synthesize and general scaffold for presenting molecular-recognition elements in a convergent manner (Figure 1) [1][5]. These systems were spawned by the work of Mislow, who studied the

Highly efficient cyclosarin degradation mediated by a β-cyclodextrin derivative containing an oxime-derived substituent

• Michael Zengerle,
• Florian Brandhuber,
• Christian Schneider,
• Franz Worek,
• Georg Reiter and
• Stefan Kubik

Beilstein J. Org. Chem. 2011, 7, 1543–1554, doi:10.3762/bjoc.7.182

• cyclodextrins goes beyond molecular recognition since the recognition event can in some cases be coupled with the chemical transformation of a substrate. This property was already realized in 1959 when it was shown that native cyclodextrins accelerate the cleavage of some acetic acid esters [12]. Subsequent

Supramolecular chemistry II

• Christoph A. Schalley

Beilstein J. Org. Chem. 2011, 7, 1541–1542, doi:10.3762/bjoc.7.181

• cell. But the same concepts are useful for generating materials with function, when for example the building blocks are programmed appropriately to find their places in a larger, noncovalent architecture. The basis for all these concepts is molecular recognition. Recently, many studies have been

Chiral recognition of ephedrine: Hydrophilic polymers bearing β-cyclodextrin moieties as chiral sensitive host molecules

• Sabrina Gingter and
• Helmut Ritter

Beilstein J. Org. Chem. 2011, 7, 1516–1519, doi:10.3762/bjoc.7.177

• ; stimuli-responsive polymer; Findings Chiral recognition is an important topic in medical and pharmaceutical applications. The sheer number of publications dealing with chiral and molecular recognition systems underlines the importance of finding reliable recognition systems [1][2][3][4][5]. Particularly

pH-Responsive chromogenic-sensing molecule based on bis(indolyl)methene for the highly selective recognition of aspartate and glutamate

• Litao Wang,
• Xiaoming He,
• Yong Guo,
• Jian Xu and
• Shijun Shao

Beilstein J. Org. Chem. 2011, 7, 218–221, doi:10.3762/bjoc.7.29

• )methene; colorimetric sensor; molecular recognition; proton transfer; Introduction The development of artificial receptors for the selective recognition of biologically important species has attracted much attention [1][2]. However, compared to the large number of chromo/fluororeceptors for cations or

• anions [3][4][5][6][7], the development of artificial receptors for amino acids is quite limited. The effective and selective molecular recognition or sensing of unprotected amino acids in aqueous solution is still a challenging problem due to their highly hydrophilic character [8]. Several studies have

An easy assembled fluorescent sensor for dicarboxylates and acidic amino acids

• Xiao-bo Zhou,
• Yuk-Wang Yip,
• Wing-Hong Chan and
• Albert W. M. Lee

Beilstein J. Org. Chem. 2011, 7, 75–81, doi:10.3762/bjoc.7.11

• developed fluorescent probes for detecting dicarboxylates and trifunctional aminoacids [17][18]. To continue our interest in this research direction, we report here the facile synthesis and molecular recognition properties of two new sensing probes 1 and 2. Trimethyl- or triethylbenzene have been widely

• used building blocks to prepare both tripodal or ditopic supramolecular systems for molecular recognition [19][20][21][22][23][24]. An obvious incentive for the use of the mesitylyl moiety is that the required 1,3,5-trimethyl-2,4-bis(bromomethyl)benzene and 1,3,5-trimethyl-2,4,6-tri(bromomethyl)benzene

Gelation or molecular recognition; is the bis-(α,β-dihydroxy ester)s motif an omnigelator?

• Peter C. Griffiths,
• David W. Knight,
• Ian R. Morgan,
• Amy Ford,
• James Brown,
• Ben Davies,
• Richard K. Heenan,
• Stephen M. King,
• Robert M. Dalgliesh,
• John Tomkinson,
• Stuart Prescott,
• Ralf Schweins and
• Alison Paul

Beilstein J. Org. Chem. 2010, 6, 1079–1088, doi:10.3762/bjoc.6.123

• gelation of liquids by low molecular weight solutes at low concentrations gives an insight into many molecular recognition phenomena and also offers a simple route to modifying the physical properties of the liquid. Bis-(α,β-dihydroxy ester)s are shown here to gel thermoreversibly a wide range of solvents

• based on hydrogen bonding of the end-group was confirmed by IR and circular dichroism (CD) spectroscopic characterisation. The specific stereochemistry of the gelator end-groups is a crucial factor, providing an obvious analogy to molecular recognition phenomena. Small-angle neutron scattering provided

• universality of the radius would seem to be a feature of the gelator structure rather than the solvent, i.e., self-association driven by a molecular recognition process, as opposed to a classical aggregation such as that observed in surfactants. There is a negligible variation in the scattering behavior with

Catalysis: transition-state molecular recognition?

• Ian H. Williams

Beilstein J. Org. Chem. 2010, 6, 1026–1034, doi:10.3762/bjoc.6.117

• Ian H. Williams Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom 10.3762/bjoc.6.117 Abstract The key to understanding the fundamental processes of catalysis is the transition state (TS): indeed, catalysis is a transition-state molecular recognition event. Practical

• transferase are described and compared with those for a model reaction in water, as computed by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulations. The case is discussed of molecular recognition in a xylanase enzyme that stabilises its sugar substrate in a (normally unfavourable

• ) boat conformation and in which a single-atom mutation affects the free-energy of activation dramatically. Keywords: catalysis; computational simulation; enzymes; molecular recognition; transition state; Introduction “Molecular recognition of transition states” was the title of a paper presented by

RAFT polymers for protein recognition

• Alan F. Tominey,
• Julia Liese,
• Sun Wei,
• Klaus Kowski,
• Thomas Schrader and
• Arno Kraft

Beilstein J. Org. Chem. 2010, 6, No. 66, doi:10.3762/bjoc.6.66

• where antibodies are generated in response to minute amounts of foreign antigens. A continual challenge in nanoscale chemistry is to mimic the biological molecular recognition functions by synthetic chemistry with the aim of producing systems of lower complexity. When successful, this will enable the

• , with tunable stoichiometries close to the ideal 1:1 ratio. Although molecular recognition is based on unspecific electrostatic attraction and hydrophobic forces, those proteins which feature a high density of positive charges on their surfaces are bound especially well by the bisphosphonate site, in

New amphiphilic glycopolymers by click functionalization of random copolymers – application to the colloidal stabilisation of polymer nanoparticles and their interaction with concanavalin A lectin

• Otman Otman,
• Paul Boullanger,
• Eric Drockenmuller and
• Thierry Hamaide

Beilstein J. Org. Chem. 2010, 6, No. 58, doi:10.3762/bjoc.6.58

• Pluronic® F-68. The mannose moieties are accessible at the surface of nanoparticles and available for molecular recognition by concanavalin A lectin. Interaction of mannose units with the lectin were evaluated by measuring the changes in nanoparticles size by dynamic light scattering in dilute media

• addition to the hydrophilicity conferred by the carbohydrate moiety, specific targeting may be result from coating nanoparticles with oligo- or polysaccharide chains since the carbohydrate moieties play an essential role in molecular recognition processes. Although the carbohydrate ligands occur naturally

• copolymer in order to obtain glycosylated polycaprolactone nanoparticles stable over a long period of storage. The carbohydrates covalently bound to the copolymers are accessible at the surface of the nanoparticles and are available for molecular recognition. The recognition of α-D-mannose at the surface of

Preparation, structures and preliminary host–guest studies of fluorinated syn-bis-quinoxaline molecular tweezers

• Markus Etzkorn,
• Jacob C. Timmerman,
• Matthew D. Brooker,
• Xin Yu and
• Michael Gerken

Beilstein J. Org. Chem. 2010, 6, No. 39, doi:10.3762/bjoc.6.39

• structurally diverse molecular tweezers, i.e., scaffolds in which a tether unit connects two syn-oriented aromatic pincers, are well-established as devices for the molecular recognition of mostly electron-deficient guest compounds [1][2][3][4][5][6][7][8][9][10]. Conversely, molecular tweezers with a binding

Molecular recognition of organic ammonium ions in solution using synthetic receptors

• Andreas Späth and
• Burkhard König

Beilstein J. Org. Chem. 2010, 6, No. 32, doi:10.3762/bjoc.6.32

• develop synthetic receptors for their selective molecular recognition. The type of host compounds for organic ammonium ion binding span a wide range from crown ethers to calixarenes to metal complexes. Typical intermolecular interactions are hydrogen bonds, electrostatic and cation–π interactions

• , hydrophobic interactions or reversible covalent bond formation. In this review we discuss the different classes of synthetic receptors for organic ammonium ion recognition and illustrate the scope and limitations of each class with selected examples from the recent literature. The molecular recognition of

• applications. Keywords: amino acids; ammonium ion; molecular recognition; synthetic receptors; Introduction The amino group is one of the most important functional groups in molecules of biological relevance. Examples of physiologically active amines (Figure 1) are histamine (1), dopamine (2) and quaternary

(Pseudo)amide-linked oligosaccharide mimetics: molecular recognition and supramolecular properties

• José L. Jiménez Blanco,
• Fernando Ortega-Caballero,
• Carmen Ortiz Mellet and
• José M. García Fernández

Beilstein J. Org. Chem. 2010, 6, No. 20, doi:10.3762/bjoc.6.20

• tried to highlight the recent advances in the synthesis of oligosaccharide mimetics. We have focussed on amide and pseudoamide-linked oligosaccharides, and their molecular recognition properties. We intend this survey to be wide-ranging and cover the most recent trends in the field. Amide-linked sugars

• can give rise to defined secondary structures or be exploited in molecular recognition. Conformational studies by temperature coefficient measurements and ROESY experiments showed that thioureidodisaccharides adopt the Z,E conformation at N–(C=S) bonds, which is stabilised by intramolecular hydrogen

• monosaccharide units in glycooligomers is particularly attractive with regard to molecular recognition processes. Like thioureas and ureas, guanidines can also form bidentate hydrogen bonds. In addition, because of their positively charged character, guanidines can exert strong electrostatic interactions with

Size selective recognition of small esters by a negative allosteric hemicarcerand

• Holger Staats and
• Arne Lützen

Beilstein J. Org. Chem. 2010, 6, No. 10, doi:10.3762/bjoc.6.10

• bulky esters were not recognized by this hemicarcerand. This size selective molecular recognition could be controlled by a negative cooperative allosteric effect: coordination of a triscarbonyl rhenium chloride fragment to the bipyridine causes a conformational rearrangement that orientates the

• resorcinarene moieties in different directions so that they cannot act cooperatively in the binding of the substrate. Keywords: allosteric receptors; 2,2′-bipyridine; hemicarcerand; molecular recognition; resorcin[4]arene; Introduction Nature uses allosteric effects in a very elegant manner to control

Recognition properties of receptors consisting of imidazole and indole recognition units towards carbohydrates

• Monika Mazik and
• André Hartmann

Beilstein J. Org. Chem. 2010, 6, No. 9, doi:10.3762/bjoc.6.9

• selected carbohydrates are described and compared with those of the previously described receptors. Keywords: carbohydrates; hydrogen bonds; molecular recognition; receptors; supramolecular chemistry; Introduction Analysis of the binding motifs found in the crystal structures of protein–carbohydrate

• carbohydrate-based molecular recognition processes and might serve as a basis for the development of new therapeutic agents (for example, anti-infective agents) or saccharide sensors [19][20][21][22][23][24][25][26]. Our previous studies showed that mimicking the binding motifs observed in the crystal

Synthesis and binding studies of two new macrocyclic receptors for the stereoselective recognition of dipeptides

• Ana Maria Castilla,
• M. Morgan Conn and
• Pablo Ballester

Beilstein J. Org. Chem. 2010, 6, No. 5, doi:10.3762/bjoc.6.5

• experiments are used to quantify the dimerization constants, as well as the association constant values of the 1:1 complexes formed between the receptors and a series of diamides and dipeptides. The receptors show moderate levels of selectivity in the molecular recognition of the hydrogen-bonding pattern

• -DL) = −1.08 kcal/mol and ΔΔG01 (DD-LD) = −0.89 kcal/mol). Surprisingly, the linear synthetic precursors show higher levels of stereoselectivity than their cyclic counterparts. Keywords: dipeptides; host–guest; macrocyclic; molecular recognition; receptors; stereoselective; Introduction Manipulation

• for the selective recognition of D-Ala-D-Ala. We also report on the studies performed using these two macrocyclic receptors, as well as their linear precursors, in the molecular recognition of a series of dipeptides and diamides with diverse hydrogen-bonding patterns. We rationalize the observed

Self-association of an indole based guanidinium-carboxylate-zwitterion: formation of stable dimers in solution and the solid state

• Carolin Rether,
• Wilhelm Sicking,
• Roland Boese and
• Carsten Schmuck

Beilstein J. Org. Chem. 2010, 6, No. 3, doi:10.3762/bjoc.6.3

• planarity from the rest of the molecule forcing the two monomers in dimer 2·2 to interact in a non-ideal orientation. Furthermore, the acidity of the NHs is lower than in 1 (as determined by UV-pH-titration) also leading to less efficient binding interactions. Keywords: dimerisation; molecular recognition