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

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