Recent applications of chiral calixarenes in asymmetric catalysis

• Mustafa Durmaz,
• Erkan Halay and
• Selahattin Bozkurt

Beilstein J. Org. Chem. 2018, 14, 1389–1412, doi:10.3762/bjoc.14.117

• upper and/or lower rims of the molecular skeleton, they have been widely used for construction of artificial host molecules and found applications in various fields like molecular recognition, sensing, self-assembly, catalysis, nanoscience, drug delivery and separation science [7][8][9][10][11][12][13

Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• biological mechanisms via sequence-specific molecular recognition makes them highly attractive candidates for drug development. However, their pharmacokinetic properties are problematic and represent a significant hurdle for their therapeutic application. First, the high polarity of ONs, mainly caused by

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• study their solution-phase self-association characteristics and DNA molecular-recognition properties [17]. The authors showed a measurable difference in solution-phase self-assembly character with enhanced DNA association characteristics by replacing the formamide head group in thiazotropsin A with

Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides

• Kartik Temburnikar and
• Katherine L. Seley-Radtke

Beilstein J. Org. Chem. 2018, 14, 772–785, doi:10.3762/bjoc.14.65

• stability, ii) altered hydrogen bonding motifs, and iii) altered molecular recognition properties [25][29][37][58]. Because of these changes, C-nucleosides have been useful in the study of RNA and DNA processing enzymes, as well as drug design efforts and novel supramolecular structures [12][29][59

• acids. Shown is the monomeric building block of nucleic acids. Changes to the nucleotide structure can affect molecular recognition, as well as structure and function. Formation of oxocarbenium ion during glycosidic bond cleavage in nucleosides [31]. The extent of leaving group stabilization and

An uracil-linked hydroxyflavone probe for the recognition of ATP

• Márton Bojtár,
• Péter Zoltán Janzsó-Berend,
• Dávid Mester,
• Dóra Hessz,
• Mihály Kállay,
• Miklós Kubinyi and
• István Bitter

Beilstein J. Org. Chem. 2018, 14, 747–755, doi:10.3762/bjoc.14.63

• -5’-triphosphate, GTP) and the strong solvation of the chemosensor and the analyte in aqueous media, reducing the association constant of their complex, and through that the sensitivity of the sensor [31][32]. The molecular recognition of nucleotides in most chemosensors is achieved by charged

Enzyme-free genetic copying of DNA and RNA sequences

• Marilyne Sosson and
• Clemens Richert

Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47

• enzymes and ribozymes, relying on solely on base pairing for molecular recognition and chemical reactivity to drive the formation of phosphodiester bonds in aqueous media. This is what is usually referred to as "enzyme-free copying" (Figure 1). Studies on enzyme-free copying of genetic polymers date back

Structural diversity in the host–guest complexes of the antifolate pemetrexed with native cyclodextrins: gas phase, solution and solid state studies

• Magdalena Ceborska,
• Magdalena Zimnicka,
• Aneta Aniela Kowalska,
• Kajetan Dąbrowa and
• Barbara Repeć

Beilstein J. Org. Chem. 2017, 13, 2252–2263, doi:10.3762/bjoc.13.222

• techniques (NMR, CID-MS, FTIR–ATR and Raman spectroscopy) allows for a deeper and clearer understanding of the molecular recognition of native CDs. Experimental Materials FA (≥97%) was obtained from Sigma-Aldrich and used as disodium salt. PTX-Na2 (≥98%) was obtained from ChemScene (USA). α-, β-, and γ-CDs

Dialkyl dicyanofumarates and dicyanomaleates as versatile building blocks for synthetic organic chemistry and mechanistic studies

• Grzegorz Mlostoń and
• Heinz Heimgartner

Beilstein J. Org. Chem. 2017, 13, 2235–2251, doi:10.3762/bjoc.13.221

• observed by 1H NMR spectroscopy [8]. Similar systems were prepared on solid phase and used as a new molecular recognition system [44]. The [4 + 2]-cycloaddition reactions of E- and Z-1b with electron-rich 1,3-dienes have been studied extensively by Sustmann and collaborators. Thus, 1-methoxybuta-1,3-diene

Superstructures with cyclodextrins: Chemistry and applications IV

• Gerhard Wenz

Beilstein J. Org. Chem. 2017, 13, 2157–2159, doi:10.3762/bjoc.13.215

• Beilstein Journal of Organic Chemistry also provides further insights into the synthesis and properties of CD superstructures, covering many aspects such as catalysis, molecular recognition, colloids, polyrotaxanes, drug delivery and more. Gerhard Wenz Saarbrücken, September 2017

Molecular recognition of N-acetyltryptophan enantiomers by β-cyclodextrin

• Spyros D. Chatziefthimiou,
• Mario Inclán,
• Petros Giastas,
• Athanasios Papakyriakou,
• Konstantina Yannakopoulou and
• Irene M. Mavridis

Beilstein J. Org. Chem. 2017, 13, 1572–1582, doi:10.3762/bjoc.13.157

Towards open-ended evolution in self-replicating molecular systems

• Herman Duim and
• Sijbren Otto

Beilstein J. Org. Chem. 2017, 13, 1189–1203, doi:10.3762/bjoc.13.118

• means of molecular recognition. The peptide building blocks again are ligated, resulting in the formation of a template duplex with a coiled-coil motif. When separated from the original template, a copy of the template is obtained. Initially these replicating systems were reported to show only parabolic

Interactions between shape-persistent macromolecules as probed by AFM

• Johanna Blass,
• Jessica Brunke,
• Franziska Emmerich,
• Cédric Przybylski,
• Vasil M. Garamus,
• Artem Feoktystov,
• Roland Bennewitz,
• Gerhard Wenz and
• Marcel Albrecht

Beilstein J. Org. Chem. 2017, 13, 938–951, doi:10.3762/bjoc.13.95

• configuration of the CD moieties. Depending on the geometrical configuration of attachment anisotropic adhesion characteristics of the polymer system can be distinguished between a peeling and a shearing mechanism. Keywords: AFM; cyclodextrin; inclusion complexes; molecular recognition; polyconjugated polymers

How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution

• Addy Pross and
• Robert Pascal

Beilstein J. Org. Chem. 2017, 13, 665–674, doi:10.3762/bjoc.13.66

• required by the Second Law (Figure 1A). With regard to living organisms, the situation is more complex. On the one hand, association processes directly driven by the Second Law are common in living organisms (e.g., protein folding, the assembly of protein sub-units through molecular recognition, assembly

Radical polymerization by a supramolecular catalyst: cyclodextrin with a RAFT reagent

• Kohei Koyanagi,
• Yoshinori Takashima,
• Takashi Nakamura,
• Hiroyasu Yamaguchi and
• Akira Harada

Beilstein J. Org. Chem. 2016, 12, 2495–2502, doi:10.3762/bjoc.12.244

• β-CD cavity of β-CD-CTA was capped by the CTA unit, inhibiting the molecular recognition property. Crystal structure of the α-CD-DMA and β-CD-DMA complexes We chose N,N-dimethylacrylamide (DMA), acrylic acid (AA), and acrylamide (AAm) as water-soluble vinyl monomers for radical polymerization. Prior

• result in a precipitate, indicating that the affinities of the CDs for AAm were low. Polymerization of vinyl monomers mediated by α-CD-CTA α-CD-CTA-mediated polymerizations of water-soluble vinyl monomers were performed in aqueous media, where the strong molecular recognition property of α-CD is expected

• inhibiting the molecular recognition of α-CD, the inclusion complexation ratio between the monomer and α-CD-CTA was decreased, which lead to lower yields and higher molecular weight of the resulting polymers due to preceding free radical polymerization. In the reaction of AAm monomer, which has a low

A chiral analog of the bicyclic guanidine TBD: synthesis, structure and Brønsted base catalysis

• Mariano Goldberg,
• Denis Sartakov,
• Jan W. Bats,
• Michael Bolte and
• Michael W. Göbel

Beilstein J. Org. Chem. 2016, 12, 1870–1876, doi:10.3762/bjoc.12.176

• in the field of molecular recognition, however, without being tested as catalysts [5][6][7][8][9][10]. A first example of enantioselective Michael addition has been reported for guanidine 3, albeit with low selectivity [11]. Compounds 4 and 5, inspired by the structure of ptilomycalin A and related

From supramolecular chemistry to the nucleosome: studies in biomolecular recognition

• Marcey L. Waters

Beilstein J. Org. Chem. 2016, 12, 1863–1869, doi:10.3762/bjoc.12.175

• -helices; aromatic interactions; β-hairpin peptides; cation–π interactions; dynamic combinatorial chemistry; histone; molecular recognition in water; nucleosome; π–π-stacking; post-translational modification; supramolecular chemistry; Review Childhood influences When thinking about how to start writing

• genetics, but at that point I found biology too vague for me; molecular level detail was what satisfied my curiosity. Indeed, it was only later once I felt I had a strong molecular understanding of molecular recognition principles that underpinned all of the cartoons of protein complexes that I turned back

• when I was an undergraduate. I took a graduate physical organic chemistry class from Jay Siegel, who was an assistant professor at the time. In his class, in addition to presenting the usual material, he covered recent published literature on molecular recognition that caught my attention, such as

Mutagenic activity of quaternary ammonium salt derivatives of carbohydrates

• Barbara Dmochowska,
• Karol Sikora,
• Anna Woziwodzka,
• Jacek Piosik and
• Beata Podgórska

Beilstein J. Org. Chem. 2016, 12, 1434–1439, doi:10.3762/bjoc.12.138

• RNA and DNA, respectively. The mechanisms of molecular recognition and cell interaction are mostly explained by the interaction of carbohydrates with proteins, called lectins, exposed at the cell surface. This process, on the one hand, allows bacteria to interact with other cells during infection, but

Supramolecular chemistry at the interface of biology, materials and medicine

• Eric V. Anslyn and
• Steven C. Zimmerman

Beilstein J. Org. Chem. 2016, 12, 1101–1102, doi:10.3762/bjoc.12.105

• ; molecular recognition; molecular sensors; What do art, auto-mechanics, a rural Australian and Chinese village, two civil wars, and house building have to do with supramolecular chemistry? Unless you are an avid cover-to-cover reader of the Thematic Series of the Beilstein Journal of Organic Chemistry and

Correction: Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 608–610, doi:10.3762/bjoc.12.59

• ; computational chemistry; drug design; molecular recognition; relaxed force constants; Our original publication contains an erratic number of predicted antibiotic structures in Scheme 2. With this Erratum we provide the corrected Scheme 2. Scheme 2 in the original article: Predicted new linezolid-like

New synthetic strategies for xanthene-dye-appended cyclodextrins

• Milo Malanga,
• Andras Darcsi,
• Mihaly Balint,
• Gabor Benkovics,
• Tamas Sohajda and
• Szabolcs Beni

Beilstein J. Org. Chem. 2016, 12, 537–548, doi:10.3762/bjoc.12.53

• spectroscopically inert molecules by guest-induced spectroscopic changes associated with the formation of inclusion complexes. These fluorescent CDs exhibit remarkable molecular recognition abilities, discriminating shape, bulkiness and polarity of the guests [1][2]. Furthermore, CDs can be directly modified with

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 415–428, doi:10.3762/bjoc.12.45

• : compliance constants; computational chemistry; drug design; molecular recognition; relaxed force constants; Introduction Antibiotic resistance is one of the major health problems in modern societies, causing millions of deaths per year [1][2][3]. Although Alexander Fleming recognized the importance of the

• force field method evaluation is therefore a prerequisite for any meaningful in silico study, especially of processes that involve molecular recognition by DNA/RNA hosts [26]. Though there are many success stories in the literature, it is not all it's cracked up to be in the euphoric 1990s, when

• complex between the ribosome and linezolid (Eribo-lzd), 3) the solvated linezolid analog (Eguest) and finally 4) the solvated linezolid (Elzd). Force field evaluation: bioactive conformation of linezolid Since the description of any molecular recognition process relies, first and foremost, on an

Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career

• Eric V. Anslyn

Beilstein J. Org. Chem. 2016, 12, 362–376, doi:10.3762/bjoc.12.40

• organic reactions, molecular recognition, and photophysical techniques. In each study, we’ll be driven to create imaginative new approaches and complex physical entities of beauty that perform functions and tasks. As discussed above, we’ll continue to create differential sensing arrays for new, ever

• survive and thrive, supramolecular analytical chemistry must create results that are widely recognized by the chemical community. Our field has to have broad impact, not only advancing the basic science of molecular recognition and chemical reactivity, but also using this information to influence how

• cascade reactions, for signal amplification purposes. Given their advances, we are currently using our own physical organic chemistry insights to amplify the responses of molecular recognition in single analyte or array sensing. This is an area where supramolecular and physical organic chemists can create

Enabling technologies and green processes in cyclodextrin chemistry

• Giancarlo Cravotto,
• Marina Caporaso,
• Laszlo Jicsinszky and
• Katia Martina

Beilstein J. Org. Chem. 2016, 12, 278–294, doi:10.3762/bjoc.12.30

• versatile receptors for molecular recognition and building blocks for functional materials. Due to the binding of two adjacent CD units, bridged bis-CDs display high binding abilities and molecular selectivities compared to native and monosubstituted CDs. A well-organized pseudo-cavity may be provided by

A journey in bioinspired supramolecular chemistry: from molecular tweezers to small molecules that target myotonic dystrophy

• Steven C. Zimmerman

Beilstein J. Org. Chem. 2016, 12, 125–138, doi:10.3762/bjoc.12.14

• early career efforts in molecular recognition, especially molecular tweezers. Although designed to complex DNA, these hosts proved more applicable to the field of host–guest chemistry. This early experience and interest in intercalation ultimately led to the current efforts to develop small molecule

• to molecular recognition, and analogously the cleft approach pioneered by Rebek, Hamilton, and others (vide supra), is the ability to recognize large guests, for example, part of the surface of a large macromolecule or biomolecule. Indeed, our original goal of challenging the NEP was guided by the

• reports on molecular-recognition-driven self-assembly. The grand challenge was to design small subunits that would spontaneously form complex structures noncovalently, ultimately with some particular function. So we began in earnest to develop such systems, focusing primarily on hydrogen bonding. This

Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies

• Giuseppina Raffaini,
• Fabio Ganazzoli and
• Antonino Mazzaglia

Beilstein J. Org. Chem. 2016, 12, 73–80, doi:10.3762/bjoc.12.8

• molecular recognition [3] or nanocarriers for drug delivery [4]. In the recent past, the aggregation behavior of aCD was investigated in water, getting insights on the structures of free nanoassemblies [5][6] or in combination with therapeutic agents [7]. However, in some stages of preparation and