Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• allowed direct detection of double stranded (ds)DNA targets after simple denaturation due to the ability of PNA to bind more strongly to DNA and so effectively compete with the DNA re-association. Another research group from Japan also reported a similar stem-loop non-chimeric PNA beacon carrying two

5-Aminopyrazole as precursor in design and synthesis of fused pyrazoloazines

• Ranjana Aggarwal and
• Suresh Kumar

Beilstein J. Org. Chem. 2018, 14, 203–242, doi:10.3762/bjoc.14.15

The use of 4,4,4-trifluorothreonine to stabilize extended peptide structures and mimic β-strands

• Yaochun Xu,
• Isabelle Correia,
• Tap Ha-Duong,
• Nadjib Kihal,
• Jean-Louis Soulier,
• Julia Kaffy,
• Benoît Crousse,
• Olivier Lequin and
• Sandrine Ongeri

Beilstein J. Org. Chem. 2017, 13, 2842–2853, doi:10.3762/bjoc.13.276

• periodicity may reflect transient intermolecular β-strand contacts involving hydrogen bonding through Val2 and Val4 residues (Figure S16, Supporting Information File 1). However, no long-range HN/HN or Hα/Hα ROEs could be detected in the 8 pentapeptides, indicating that transient intermolecular association

• observed for the central residue upon replacement of Ser by the β-branched Thr residue and the incorporation of a trifluoromethyl group in Thr or allo-Thr further increases the β-propensity of these residues. The presence of self-association involving intermolecular β-sheet formation was not detectable

CF₃SO₂X (X = Na, Cl) as reagents for trifluoromethylation, trifluoromethylsulfenyl-, -sulfinyl- and -sulfonylation and chlorination. Part 2: Use of CF₃SO₂Cl

• Hélène Chachignon,
• Hélène Guyon and
• Dominique Cahard

Beilstein J. Org. Chem. 2017, 13, 2800–2818, doi:10.3762/bjoc.13.273

• single-electron transfer (SET) between CF3SO2Cl and the association CuBr/chiral phosphoric acid. In the process, SO2 and HCl were released, but the latter was scavenged by Ag2CO3, minimising its impact on the reaction process by notably avoiding hydroamination side reactions. The trifluoromethyl radical

CF₃SO₂X (X = Na, Cl) as reagents for trifluoromethylation, trifluoromethylsulfenyl-, -sulfinyl- and -sulfonylation. Part 1: Use of CF₃SO₂Na

• Hélène Guyon,
• Hélène Chachignon and
• Dominique Cahard

Beilstein J. Org. Chem. 2017, 13, 2764–2799, doi:10.3762/bjoc.13.272

• , judicious installation of CF3 group(s) in catalysts or ligands is an effective tool to tune their reactivity and selectivity in synthesis. As a pharmacophore, CF3 substantially improves the catabolic stability, lipophilicity, and transport rate. In association with chalcogens (OCF3, SCF3, SeCF3), the CF3

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

• Marco Russo,
• Daniele La Corte,
• Annalisa Pisciotta,
• Serena Riela,
• Rosa Alduina and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2751–2763, doi:10.3762/bjoc.13.271

• may reasonably hypothesize the occurrence of a loose ion-pairing external association between the cationic pendant groups of the host and the anionic guest (Figure 5). Binding abilities of AmCDs towards Alg Further assessment of a possible out-of-cavity interaction for AmCDs was achieved by studying

• rotation Θ of AmCDs CD1–3 vs pH. Trends of the molar optical rotation Θ of AmCDs vs χH+. Polarimetric data trends for the inclusion of 4 in CD1 at different pH values. Possible association of AmCDs with guests 2–4. Polarimetric data trends for the CD1–Alg interaction (with buffer). nr Values for the AmCD

An efficient synthesis of 1,6-anhydro-N-acetylmuramic acid from N-acetylglucosamine

• Matthew B. Calvert,
• Christoph Mayer and
• Alexander Titz

Beilstein J. Org. Chem. 2017, 13, 2631–2636, doi:10.3762/bjoc.13.261

• : NMR spectra. Acknowledgements The authors thank Dr. Josef Zapp (Saarland University) for recording NMR spectra and Daniel Sauer (Helmholtz Institute for Pharmaceutical Research Saarland, HIPS) for HRMS measurements. We are grateful to the Helmholtz Association (grant no. VH-NG-934) for financial

Synthesis and supramolecular properties of regioisomers of mononaphthylallyl derivatives of γ-cyclodextrin

• Markéta Bláhová,
• Sergey K. Filippov,
• Lubomír Kováčik,
• Jiří Horský,
• Simona Hybelbauerová,
• Zdenka Syrová,
• Tomáš Křížek and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2017, 13, 2509–2520, doi:10.3762/bjoc.13.248

• the shape of peaks, but also in the value of the chemical shifts. For both regioisomers the concentration dependence of chemical shifts in aromatic and allyl areas indicates intermolecular association such as inclusion of the naphthylallyl moiety into the cavity of γ-CD or π stacking of naphthyls. The

• as a ditopic monomer of the AB type with groups A and B undergoing an association of 1:1. However, a number of alternate or competing interactions may occur, as mentioned above, γ-CD is known to form also inclusion complexes of 2:1 stoichiometry and formation of cyclic supramolecular structures my

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

• complex with α-CD and pseudorotaxane inclusion-type complexes with β-, and γ-CDs. UV–vis titrations at pH 7.4 gave association constants for the obtained complexes. The stability of the complexes increases in the series: α-CD/PTX < γ-CD/PTX << β-CD/PTX. The association of PTX with a monomer cyclodextrin

• experiments in phosphate buffered saline (PBS, pH 7.4) were conducted for evaluation of association constants (Kas). Association of PTX with a monomer CD equivalent – methyl α-D-glucopyranoside – was investigated to fully understand the type of interactions between host and guest molecules. Additionally, the

• . Recent results concerning the studies of association modes between FA and CDs clearly showed that, although the overall gas-phase stabilities do not reflect the solution phase association constants, they are helpful in structural differentiation between inclusion and exclusion complexes [16]. The

p-tert-Butylthiacalix[4]arenes functionalized by N-(4’-nitrophenyl)acetamide and N,N-diethylacetamide fragments: synthesis and binding of anionic guests

• Alena A. Vavilova and
• Ivan I. Stoikov

Beilstein J. Org. Chem. 2017, 13, 1940–1949, doi:10.3762/bjoc.13.188

• receptors for F−, CH3CO2− and H2PO4− ions, which based on the synthesized thiacalix[4]arenes, have been obtained. It was shown that p-tert-butylthiacalix[4]arene tetrasubstituted at the lower rim by N-(4’-nitrophenyl)acetamide moieties bonded to the anions studied with association constants within the range

• 335 nm (see Supporting Information File 1, Figure S18). The complexation ability of the compounds 3, 5 and 6 in relation to the anions (F−, Cl−, Br−, I−, СН3СО2−, Н2РО4−, NO3−) was quantitatively evaluated by the stoichiometry and the association constants (Table 2) of the formed complexes. They were

• determined by the isomolar series method, that all the thiacalix[4]arenes studied form in CHСl3 the 1:1 complexes with selected n-Bu4NX (see Supporting Information File 1, Figure S19). The association constants of the complexes studied were estimated by the dilution method (Figure 2). The appropriate

β-Cyclodextrin- and adamantyl-substituted poly(acrylate) self-assembling aqueous networks designed for controlled complexation and release of small molecules

• Liang Yan,
• Duc-Truc Pham,
• Philip Clements,
• Stephen F. Lincoln,
• Jie Wang,
• Xuhong Guo and
• Christopher J. Easton

Beilstein J. Org. Chem. 2017, 13, 1879–1892, doi:10.3762/bjoc.13.183

• attributed to either steric hindrance by the poly(acrylate) backbone, or hydrophobic association of the adamantyl substituents, or both, hindering complexation. The PAAβ-CDen/PAAADddn system contrasts with the other two systems in that N = 1.45 is consistent with one β-CDen substituent complexing the

• dodecyl tether. Ideally, N = 2 should be observed for such a process, but it appears that either the steric hindrance or hydrophobic association of the adamantyl substituents, or both, restrict N to <2. The 2D NOESY 1H NMR spectrum of the PAAβ-CDen/PAAADddn system confirms the complexation of both the

• and ΔH and more positive TΔS [3]. (The N = 0.86 − 0.83 are also consistent with either the steric hindrance by the poly(acrylate) backbone, or the hydrophobic association of the adamantyl substituents, or both, hindering complexation). The greater stabilities of the PAAβ-CDen/PAAADen and PAAβ-CDen

The chemistry and biology of mycolactones

• Matthias Gehringer and
• Karl-Heinz Altmann

Beilstein J. Org. Chem. 2017, 13, 1596–1660, doi:10.3762/bjoc.13.159

• in relation to case reports from Buruli County in Mengo district (today Nakasongola district) in Uganda [20]. Although Bairnsdale ulcer would be the historically more correct denomination, the WHO approved the name Buruli ulcer. Despite the long known association of Buruli ulcer with riverine areas

• specific pathology of M. ulcerans infections [46]. For example, osteomyelitis, a pathology regularly observed in association with M. ulcerans infections in Benin [6] is absent in Australia or Mexico. Likewise, the plaque form of Buruli ulcer which is also found in Benin has not been reported in Australia

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

• . Moreover, trends in enantioselectivity do not follow trends in association constants, i.e., the association constants for the β-CD complexes of both enantiomers of N-acetyltyrosine, N-acetylphenylalanine and N-acetyltryptophan are in decreasing order, whereas their enantioselectivity (ratio of the binding

• . However, as the Job plots suggested, the aliphatic part is influenced by a second host molecule presumably via its secondary side. This implies that in solution, host–guest association is possible through additional orientations and stoichiometry, thus the presence of alternative arrangements in low

• )salicylaldimine complex in ethanol, novel association of β-CD monomers in structures of β-CD complexes, e.g., with 4-pyridinealdazine [30], polyethylene glycol [38] or adamantane [39]. Conclusion This work has been focused on the ability of β-CD to discriminate between the enantiomers of N-acetyltryptophan. NMR

Chemical systems, chemical contiguity and the emergence of life

• Terrence P. Kee and
• Pierre-Alain Monnard

Beilstein J. Org. Chem. 2017, 13, 1551–1563, doi:10.3762/bjoc.13.155

• -surfactants, if available via prebiotic syntheses [20][60][61][62], could have also contributed to the formation of primitive amphiphile-based structures, by allowing structure stabilization under prebiotic conditions, e.g., high ionic strength or temperature or stringent pH values. Selective association of

• /association with the chemical system structure or to the encapsulation of a reaction “machinery” within it. Interface-linked catalysis: The oligomerization of peptides from amino acids with condensing agents has been demonstrated to occur in the presence of phospholipid vesicles [65][66][67]. In these studies

• association with the interface of chemical systems. For instance, the activity of an RNA polymerase ribozyme was improved when the various RNA compounds of the system (the ribozyme, the template/primer) were derivatized with amphiphilic moieties and co-associated within micelle structures [69]. Although no

An improved preparation of phorbol from croton oil

• Alberto Pagani,
• Simone Gaeta,
• Andrei I. Savchenko,
• Craig M. Williams and
• Giovanni Appendino

Beilstein J. Org. Chem. 2017, 13, 1361–1367, doi:10.3762/bjoc.13.133

• once used in human medicine as a topical rubefacient and in veterinarian medicine as a strong laxative [1], but nowadays its only medical use is in rejuvenating esthetic surgery in association to blepharoplasty, a practice that was mastered in the 1960s capitalizing on the potent exfoliating activity

• of the oil, especially in association to phenol [3]. The extraordinarily obnoxious and vesicant properties of croton oil have fostered studies aimed at the identification of its active principles since the very early developments of organic chemistry. Thus, the first chemical study on croton oil was

Biomimetic molecular design tools that learn, evolve, and adapt

• David A Winkler

Beilstein J. Org. Chem. 2017, 13, 1288–1302, doi:10.3762/bjoc.13.125

• biological probes synthesized by automated synthesis by iterative coupling of different building blocks (colors). TBDPSE, tert-butyldiphenylsilylethyl; TMSE, trimethylsilylethyl. Adapted with permission from [37]; copyright 2015 American Association for the Advancement of Science. An example of a composition

Sugar-based micro/mesoporous hypercross-linked polymers with in situ embedded silver nanoparticles for catalytic reduction

• Qing Yin,
• Qi Chen,
• Li-Can Lu and
• Bao-Hang Han

Beilstein J. Org. Chem. 2017, 13, 1212–1221, doi:10.3762/bjoc.13.120

• support of the National Natural Science Foundation of China (Grants 21574031, 21374024, and 21574032), the Ministry of Science and Technology of China (Grant No. 2014CB932200), and CAS Youth Innovation Promotion Association is acknowledged.

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• tool for the investigations of the state of materials in solution at the nanoscale. Many studies have been devoted to polysaccharides, for which structural change have been observed in real time. There exists extensive literature on this subject and the role played by polysaccharide association

From chemical metabolism to life: the origin of the genetic coding process

• Antoine Danchin

Beilstein J. Org. Chem. 2017, 13, 1119–1135, doi:10.3762/bjoc.13.111

• consequence is that this is an abstract way to create an association between matter and information, exactly as the integer “3” can be coded in a variety of languages (e.g., three, trois, τρια, ). The one-to-one correspondence of complementary strands in nucleic acids was a straightforward coding process, but

Correlation of surface pressure and hue of planarizable push–pull chromophores at the air/water interface

• Frederik Neuhaus,
• Fabio Zobi,
• Gerald Brezesinski,
• Marta Dal Molin,
• Stefan Matile and
• Andreas Zumbuehl

Beilstein J. Org. Chem. 2017, 13, 1099–1105, doi:10.3762/bjoc.13.109

• : Surface pressure/area per molecule isotherms, energy minimized structures of the flipper mechanophore, GIXD heightmaps, and IRRAS data. Acknowledgements Parts of this research were carried out at PETRA III at DESY, a member of the Helmholtz Association (HGF). We would like to thank Dr. Uta Ruett and Dr

G-Protein coupled receptors: answers from simulations

• Timothy Clark

Beilstein J. Org. Chem. 2017, 13, 1071–1078, doi:10.3762/bjoc.13.106

• bound. The α-subunit of the G-protein is shown in green, β in yellow and γ in magenta. In this state, the GPCR exhibits basal activity. This figure assumes pre-association of the G-protein to the receptor. (b) Fully activated GPCR. Both an agonist ligand and the G-protein are required for full

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

• species which can interact, leading to macromolecular structures or patterns [18]. The kinetic stability of the organised structures in those cases is associated with energy dissipation from an activating agent able to convert some reactant into transient species able to undergo intermolecular association

• forward by Lynn Margulis [71] half a century ago to explain eukaryotic cell formation is in fact just a particularly striking example of a cooperative association in action. It is also important to emphasise that cooperation may either have involved a physical linkage between different components through

Contribution of microreactor technology and flow chemistry to the development of green and sustainable synthesis

• Flavio Fanelli,
• Giovanna Parisi,
• Leonardo Degennaro and
• Renzo Luisi

Beilstein J. Org. Chem. 2017, 13, 520–542, doi:10.3762/bjoc.13.51

• . (Reproduced with permission from [43], copyright 2016 American Association for the Advancement of Science). Reconfigurable modules and flowcharts for API synthesis. (Reproduced with permission from [85], copyright 2016 American Association for the Advancement of Science). Reconfigurable system for continuous

• production and formulation of APIs. (Reproduced with permission from [85], copyright 2016 American Association for the Advancement of Science). A flow microreactor system for the generation and trapping of highly unstable carbamoyllithium species. Flow synthesis of functionalized α-ketoamides. Reactions of

• microreactor system. Control of anionic Fries rearrangement reactions by using submillisecond residence time. (Adapted with permission [43], copyright 2016 American Association for the Advancement of Science). Flow microreactor system for lithiation, borylation, Suzuki–Miyaura coupling and selected examples of

NMR reaction monitoring in flow synthesis

• M. Victoria Gomez and
• Antonio de la Hoz

Beilstein J. Org. Chem. 2017, 13, 285–300, doi:10.3762/bjoc.13.31

• dispersion of this nucleus. The authors determined the association constant of the complex of NaPF6 with α-cyclodextrin at the picomole level with a detection volume of 50 nL and using non-deuterated solvents [25]. To conclude with the different coil geometries, microslot NMR microprobes and stripline coils

Versatile synthesis of the signaling peptide glorin

• Robert Barnett,
• Daniel Raszkowski,
• Thomas Winckler and
• Pierre Stallforth

Beilstein J. Org. Chem. 2017, 13, 247–250, doi:10.3762/bjoc.13.27

• relationship study. Ultimately, we wish to synthesize chemical probes of glorin for the identification of the unknown glorin receptor. Experimental Quantitative reverse transcription PCR: P. pallidum PN500 cells were cultured in association with Escherichia coli K12 cells. Cells were harvested before first

• for financial support from the Leibniz Association, and the Fonds der Chemischen Industrie (VCI) (P.S.). This work was also supported by the DFG-funded graduate school of excellence Jena School for Microbial Communication (R.B. and D.R.).