(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

Thematic series on supramolecular chemistry

• Christoph A. Schalley

Beilstein J. Org. Chem. 2009, 5, No. 76, doi:10.3762/bjoc.5.76

• successfully transferred to neutral and anionic hosts. Nowadays, multivalent interactions start to play a significant role for host-guest chemistry. But supramolecular chemistry is much more than molecular recognition. Concepts such as templated synthesis, (hierarchical) self-assembly, and self-sorting have

• Christoph A. Schalley Institut für Chemie und Biochemie der Freien Universität Berlin, Takustr. 3, D-14195 Berlin, Germany 10.3762/bjoc.5.76 “Some might say that supramolecular systems rescued physical organic chemistry. The discovery of crown ethers gave the field new recognition: molecular

• recognition.” [1] As the above citation from a paper by Julius Rebek and his coworkers indicates, supramolecular chemistry at its beginning gave new impetus to physical organic chemistry, which at that time had got trapped in ever more detailed kinetic studies. Early on, the nature of non-covalent

Chiral amplification in a cyanobiphenyl nematic liquid crystal doped with helicene-like derivatives

• Alberta Ferrarini,
• Silvia Pieraccini,
• Stefano Masiero and
• Gian Piero Spada

Beilstein J. Org. Chem. 2009, 5, No. 50, doi:10.3762/bjoc.5.50

• (as, for instance, the widely used commercial mixture E7 from BDH) [33][34][35][36][37][38][39][40][41][42][43][44][45] and this has been viewed as a consequence of their structural analogy and molecular recognition via core–core interactions with the host molecules [46][47]. To avoid confusion with

Structural studies on encapsulation of tetrahedral and octahedral anions by a protonated octaaminocryptand cage

• I. Ravikumar,
• P. S. Lakshminarayanan,
• E. Suresh and
• Pradyut Ghosh

Beilstein J. Org. Chem. 2009, 5, No. 41, doi:10.3762/bjoc.5.41

• . Keywords: anion receptor; cryptand; molecular recognition; proton cage; Introduction In recent years considerable efforts have been made in elucidating the coordination chemistry of anions because of their vital roles in biological systems [1], medicine [2], catalysis [3], and environmental issues [4

Quinoline based receptor in fluorometric discrimination of carboxylic acids

• Kumaresh Ghosh,
• Suman Adhikari,
• Asoke P. Chattopadhyay and
• Purnendu Roy Chowdhury

Beilstein J. Org. Chem. 2008, 4, No. 52, doi:10.3762/bjoc.4.52

• ions and molecules by designed synthetic receptors is currently of major interest in the area of molecular recognition [1][2][3]. Among various sensing techniques available for clinical, biological and environmental analyses, fluorescence sensing is unique because of high sensitivity and compatibility

• probes close enough to function as an excimer, are proved to be useful to read out the molecular recognition process more conveniently [8][9]. The recognition and sensing of carboxylic acids has attracted considerable attention owing to their important role in biology [10]. The recognition of both mono

Synthesis of deep- cavity fluorous calix[4]arenes as molecular recognition scaffolds

• Maksim Osipov,
• Qianli Chu,
• Steven J. Geib,
• Dennis P. Curran and
• Stephen G. Weber

Beilstein J. Org. Chem. 2008, 4, No. 36, doi:10.3762/bjoc.4.36

• ; organofluorine; (perfluoroalkyl)alkyl aryl ethers; Introduction Calixarenes [1] are one of the most useful types of macrocyclic scaffolds. Since first reported by Zinke and Ziegler [2], calix[4]arenes have been used for a variety of molecular recognition, nanotechnology, and supramolecular applications. These

• enhance the formation of a single conformer [12]. Of the four possible conformations, the cone is the most desirable for molecular recognition and sensing applications because it has the largest available surface area for host-guest interactions [10]. With appropriate functionality and conformation, the

• extraction of organic substrates into a fluorous liquid phase via hydrogen bonding [21]. Combining the selective nature of fluorous chemistry with the extensive molecular recognition capabilities of calixarenes should generate a scaffold for selective molecular receptors, yet few reports exist that detail

A hydrogen- bonded channel structure formed by a complex of uracil and melamine

• Reji Thomas and
• G. U. Kulkarni

Beilstein J. Org. Chem. 2007, 3, No. 17, doi:10.1186/1860-5397-3-17

• expectation that the structure may involve channels as in the reported structure of the 1:1 molecular complex of cyanuric acid and melamine. In this article, we describe the structure of the hydrogen bonded adduct of uracil and melamine, and bring out the role of uracil in molecular recognition. Rod-shaped

• different, in shape and dimension. This clearly indicates the role of the uracil molecule in directing the shape of the channel structure. In conclusion, we have illustrated the molecular recognition process of melamine with nucleobase uracil. We have also established the presence of channels, in the three

Molecular recognition. 1. Crystal structures of hexaazamacrocyclic amines containing p-xylylene spacers and their adducts with acids

• Teresa Borowiak,
• Grzegorz Dutkiewicz,
• Maciej Kubicki,
• Marek Pietraszkiewicz,
• Agnieszka Gil and
• Rainer Mattes

Beilstein J. Org. Chem. 2005, 1, No. 16, doi:10.1186/1860-5397-1-16

• adduct of; Hydrogen bonding; Molecular recognition; Two-dimensional supramolecular frameworks; Introduction Macrocyclic polyamines are well-known to participate in molecular recognition phenomena with different kinds of substrates such as organic and inorganic anions or neutral molecules[1] that give