Efficient catenane synthesis by cucurbit[6]uril-mediated azide–alkyne cycloaddition

• Antony Wing Hung Ng,
• Chi-Chung Yee,
• Kai Wang and
• Ho Yu Au-Yeung

Beilstein J. Org. Chem. 2018, 14, 1846–1853, doi:10.3762/bjoc.14.158

• mechanically interlocked macrocycles. The flexible but strong mechanical bond between the interlocked macrocycles offers a unique opportunity for exploiting catenanes as molecular machines or new materials with unusual mechanical properties [1][2][3][4][5][6][7][8][9]. Over the years, different templates and

• . Further extending the reaction time to 3, 5 or 8 hours resulted in similar chromatograms with no significant improvement of the yield of Cat-1. A similar observation has been reported in a CBAAC-mediated rotaxane synthesis and additional templates have been used to positively cooperate with the CB[6

Natural and redesigned wasp venom peptides with selective antitumoral activity

• Marcelo D. T. Torres,
• Gislaine P. Andrade,
• Roseli H. Sato,
• Cibele N. Pedron,
• Tania M. Manieri,
• Giselle Cerchiaro,
• Anderson O. Ribeiro,
• Cesar de la Fuente-Nunez and
• Vani X. Oliveira Jr.

Beilstein J. Org. Chem. 2018, 14, 1693–1703, doi:10.3762/bjoc.14.144

• conformational propensity led to peptide inactivation, whereas increasing the net positive charge of peptides enhanced their activity. We present peptide templates with selective activity towards breast cancer cells that leave normal cells unaffected. These templates represent excellent scaffolds for the design

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

• examples can also be found in the literature of the 1960s [12]. The early monomer-based work on copying RNA focused on oligomerization of nucleotides on homosequences as templates [13][14]. The best results were observed for poly(C) as template, the 2-methylimidazolide of guanosine as activated monomer

• arrangement became the most common way of performing the reaction [17][18][19][20]. In this brief account we will focus on primer extension reactions on DNA and RNA templates. The copying of DNA sequences is usually performed with primers terminating in a 3'-amino-2',3'-dideoxynucleoside. The amino group is

• homopolymer templates, Joyce and Orgel concluded that the structure and hybridization status of templates was important for high-yielding copying reactions [26]. In a later series of papers with specific, synthetic sequences, Wu and Orgel reported that primer extension proceeds poorly if too many weakly

Fluorogenic PNA probes

• Tirayut Vilaivan

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

• for matched over mismatched templates for these short PNA probes (>100:1) is higher than in the case of molecular beacons or other DNA-based probes that are typically much longer [92]. Examples of fluorogenic non-ligated templated reactions are summarized in Table 2. Many of these reactions feature

• synthetic oligonucleotide templates, and applications for intracellular nucleic acid detection are also emerging [90][100]. The unmasking by template-catalyzed hydrolysis or thiolysis is susceptible to other non-selective pathways, such as enzymatic hydrolysis, giving rise to false positive signals or a

Acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicyclo[2.2.1]hept-5-ene with alcohols

• Katrina Tait,
• Alysia Horvath,
• Nicolas Blanchard and
• William Tam

Beilstein J. Org. Chem. 2017, 13, 2888–2894, doi:10.3762/bjoc.13.281

• ; alcohol nucleophiles; cyclopropanation; heterobicyclic compounds; ring-opening reactions; Introduction Heterobicyclic alkenes are useful templates to generate complex cyclic and acyclic systems [1][2]. 3-Aza-2-oxabicyclic alkenes are particularly interesting due to their asymmetric nature and the ability

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• detecting markers [14], as fluorescent DNA probes [15], non-covalent binders to canonical oligonucleotide templates [16], and antiviral agents [17][18]. Notably, pyrene excimer formation in DNA template assemblies is much less efficient than in normal pyrene conjugates due to the helical twist between

• investigated towards application as fluorescent cell imaging bioprobes so far. Furthermore, self-assembly studies of pyrene–nucleobases on oligonucleotide templates have not been reported as well. The work presented herein addresses these two problems. Accordingly, in this contribution we report on the

• was prehybridized, so that canonical base pairing of the chromophore–nucleoside conjugates with the template could be excluded. After centrifugation, compound 3 shows no effective self-assembly to single or double-stranded templates in buffer; only in water an assembly occurring to both single

Main group mechanochemistry

• Agota A. Gečiauskaitė and
• Felipe García

Beilstein J. Org. Chem. 2017, 13, 2068–2077, doi:10.3762/bjoc.13.204

• by condensation reactions between acenaphthoquinone and the corresponding aniline derivative under acidic conditions, involving the use of transition-metal templates [85]. The acid-catalysed ball-milling of acenaphthoquinone with aniline derivatives in the presence of an organic catalyst was able to

Intramolecular glycosylation

• Xiao G. Jia and
• Alexei V. Demchenko

Beilstein J. Org. Chem. 2017, 13, 2028–2048, doi:10.3762/bjoc.13.201

• that affected the removal of the template and all benzyl protecting groups followed by acetylation of the resulting hydroxy groups. Peptide tether/template Short peptide chains have also been investigated as templates for glycosylation. The general underpinning idea is to streamline the oligosaccharide

• synthesis and purification by using well developed peptide coupling reactions with or without the use of solid phase methods. To execute this concept, Fairbanks et al. investigated a number of peptide chains with various amino acids as templates (Scheme 9) [76][77]. Using DCC-mediated coupling reactions

• ) linkages. The stereoselectivity of these linkages can vary, but it was typically very relaxed perhaps due to a fairly low rigidity of this type of a template. Hence, further development of this methodology focused on solid-supported peptide templates [78]. For instance, Warriner and co-workers investigated

New bio-nanocomposites based on iron oxides and polysaccharides applied to oxidation and alkylation reactions

• Daily Rodríguez-Padrón,
• Alina M. Balu,
• Antonio A. Romero and
• Rafael Luque

Beilstein J. Org. Chem. 2017, 13, 1982–1993, doi:10.3762/bjoc.13.194

• been an attractive option to imitate based on a fundamental and rational understanding [28][32]. In that sense, polysaccharides extracted from fungal organisms can be used both as nanoparticle carriers and sacrificial templates due to their highly functionalized structure. Although such carbohydrates

Accessing simply-substituted 4-hydroxytetrahydroisoquinolines via Pomeranz–Fritsch–Bobbitt reaction with non-activated and moderately-activated systems

• Marco Mottinelli,
• Mathew P. Leese and
• Barry V. L. Potter

Beilstein J. Org. Chem. 2017, 13, 1871–1878, doi:10.3762/bjoc.13.182

• to access libraries of regioisomeric N-aryl-1,2,3,4-tetrahydroisoquinoline derivatives that might facilitate the design of new structural templates for steroid-binding receptors. We thus evaluated the robustness and flexibility of this approach to the THIQ system and considered, in particular, the

• + H)+ calcd. for C15H16NO, 226.1226; found, 226.1234. Non-steroidal templates from estradiol. Pomeranz–Fritsch and Pomeranz–Fritsch–Bobbitt reactions. Conditions: (a) conc. H2SO4; (b) benzene, ∆, Dean–Stark then Raney Ni, H2, 50 psi, EtOH; (c) conc. HCl, Δ. Designed synthesis of THIQ. Conditions: (a

Grip on complexity in chemical reaction networks

• Albert S. Y. Wong and
• Wilhelm T. S. Huck

Beilstein J. Org. Chem. 2017, 13, 1486–1497, doi:10.3762/bjoc.13.147

• networks exhibiting oscillatory behavior. Within this framework, Figure 4b shows an in vitro implementation of an oscillator comprising a positive and a delayed negative feedback loop [90]. The canonical gene regulation pathway uses the information encoded in DNA templates T1−T3. Similarly, a genetic

Mechanochemistry-assisted synthesis of hierarchical porous carbons applied as supercapacitors

• Desirée Leistenschneider,
• Nicolas Jäckel,
• Felix Hippauf,
• Volker Presser and
• Lars Borchardt

Beilstein J. Org. Chem. 2017, 13, 1332–1341, doi:10.3762/bjoc.13.130

• designing the porosity of carbon materials involves hard or soft templates [22][23][24]. Hard-templating utilizes metal oxide nanoparticles [25] and salts [26][27][28], which have to be synthesized in advance. Soft-templating employs surfactants or other structure-directing molecules, which self-assemble to

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

• only sub exponential growth. In many cases r = 1/2 and the system is said to obey the square root law of autocatalytic systems [28]. By seeding mixtures with different amounts of preformed templates T and measuring the initial rate of template formation, a plot of log(d[T]/dt) versus log[T] can be

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

• as templates. The algorithm that drives duplication of the centriole is a piece of information with delayed implementation, associated to a specific set of genes that are replicated when the cell reproduces. Protein-network replication might have predated replication mediated by nucleic acids, via

• information into the formation of the first living organisms. From substrates to templates, RNAs at the origin of the genetic code Among the many codes still to be discovered, the genetic code is at the heart of life. Having set the stage, we now can try to understand how such an abstract operation as that of

• carrying amino acids created a positive interference in this process that improved the formation of peptides. This class of RNAs behaved as templates to order the amino acid residues of the peptides into a well-defined sequence. The RNA-genome world Accumulation of these latter “peptide sequence-specifying

Biosynthetic origin of butyrolactol A, an antifungal polyketide produced by a marine-derived Streptomyces

• Enjuro Harunari,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2017, 13, 441–450, doi:10.3762/bjoc.13.47

• templates for new pharmacophores [3]. While the frequency of discovering new skeletons from actinomycetes seems declining, biosynthetic analysis of structurally unique known compounds and the following bioengineering of biosynthetic genes are currently becoming an essential part of the creation of new drug

Efficient access to β-vinylporphyrin derivatives via palladium cross coupling of β-bromoporphyrins with N-tosylhydrazones

• Vinicius R. Campos,
• Ana T. P. C. Gomes,
• Anna C. Cunha,
• Maria da Graça P. M. S. Neves,
• Vitor F. Ferreira and
• José A. S. Cavaleiro

Beilstein J. Org. Chem. 2017, 13, 195–202, doi:10.3762/bjoc.13.22

• biological properties or might become important templates for further functionalization procedures (Scheme 2). Results and Discussion For this work 2-bromo-5,10,15,20-tetraphenylporphyrinatozinc(II) (1) was used as the aryl halide and also the easily accessible N-tosylhydrazones 2a–c (Scheme 3). Both

• approach can be excellent templates for further functionalization and also might became compounds with potential important biological activities. This new methodology can be used to have access to a significant number of new porphyrin derivatives and certainly future work will demonstrate this fact

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• templates for the generation of a wide range of molecular hosts through chemical modifications. ii) Modified cyclodextrins In order to meet specific requirements in the host–guest complex, chemical modifications make it possible to tailor CDs to a particular guest. The hydroxy groups serve as scaffolds on

Facile synthesis of indolo[3,2-a]carbazoles via Pd-catalyzed twofold oxidative cyclization

• Chao Yang,
• Kai Lin,
• Lan Huang,
• Wei-dong Pan and
• Sheng Liu

Beilstein J. Org. Chem. 2016, 12, 2490–2494, doi:10.3762/bjoc.12.243

• : cyclization; indolo[3,2-a]carbazole; N-arylation; oxidative biaryl coupling; palladium catalysis; Introduction Many biologically active carbazole derivatives are of interest as drug-like templates. The indolo[3,2-a]carbazole skeleton, one of the isomeric indolocarbazoles, was firstly identified from nature

Inhibition of peptide aggregation by means of enzymatic phosphorylation

• Kristin Folmert,
• Malgorzata Broncel,
• Hans v. Berlepsch,
• Christopher H. Ullrich,
• Mary-Ann Siegert and
• Beate Koksch

Beilstein J. Org. Chem. 2016, 12, 2462–2470, doi:10.3762/bjoc.12.240

• functional templates like conductive nanowires [7], water-filled nanotubes [8] or biocompatible hydrogels [9]. Likewise, nature uses amyloid-like cross-β-sheet-rich conformations to store peptide hormones in secretory granules of the endocrine system [10]. As another example it was found that mammalian

• Pmel17 amyloid templates and accelerates the covalent polymerization of reactive small molecules into melanin, an important biopolymer that protects against a broad range of cytotoxic insults, including UV and oxidative damage [11]. While amyloid morphologies and events which induce amyloid formation are

A new paradigm for designing ring construction strategies for green organic synthesis: implications for the discovery of multicomponent reactions to build molecules containing a single ring

• John Andraos

Beilstein J. Org. Chem. 2016, 12, 2420–2442, doi:10.3762/bjoc.12.236

• bolded bonds. Permutations of two-component coupling patterns for synthesizing the cyclohexanone ring overlayed with nucleophilic (n) and electrophilic (e) labels at the termini of partition fragments. Synthesis bonds are shown as bolded bonds. Red structures correspond to target templates that form the

• - and 3-partition fragment possibilities for pyrrolidine; Schemes S4 and S5 showing new [3 + 2 + 1] and [4 + 1 + 1] strategies to synthesize the Biginelli adduct; Schemes S6 to S32 showing superposition of 3-partition templates for various heterocycles. Supporting Information File 366: Application of

Experimental and theoretical investigations into the stability of cyclic aminals

• Edgar Sawatzky,
• Antonios Drakopoulos,
• Martin Rölz,
• Christoph Sotriffer,
• Bernd Engels and
• Michael Decker

Beilstein J. Org. Chem. 2016, 12, 2280–2292, doi:10.3762/bjoc.12.221

• with aldehydes or ketones yielding bicyclic structures [25][26][27], or by the reduction of the corresponding dihydroquinazolinones [15][16][17] (Scheme 1). The aminal templates obtained can be used as starting materials for the synthesis of a broad spectrum of diverse structures. Oxidation reactions

DNA functionalization by dynamic chemistry

• Zeynep Kanlidere,
• Oleg Jochim,
• Marta Cal and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2016, 12, 2136–2144, doi:10.3762/bjoc.12.203

• oligonucleotides. The amino group containing phosphoramidite was used together with complementary single-strand DNA templates that influenced the Watson–Crick base-pairing equilibrium in the mixture with a set of aldehyde modified nucleobases. A significant fraction of all possible base-pair mismatches was

• analogue. Keywords: base-pairing; base-pair mismatch; DNA functionalization; DNA templates; dynamic combinatorial chemistry; D-threoninol based scaffolds; Introduction The well-defined duplex structure, self-assembling by base-pair recognition, and the accessibility by solid-phase synthesis make DNA

• . Here we synthesized the phosphoramidite building blocks derived from D-threoninol which contain protected amine or thiol groups. These building blocks are used for later incorporation into oligonucleotides via solid-phase synthesis. Using these modified oligonucleotides and single strand DNA templates

Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides

• Franziska Hemmerling and
• Frank Hahn

Beilstein J. Org. Chem. 2016, 12, 1512–1550, doi:10.3762/bjoc.12.148

• templates particular cyclisation patterns. The fact that PieC was dispensable for piericidin A1 (221) biosynthesis was explained by that it could either be complemented by other endogenous cyclases in S. piomogeues or that the thermodynamically favoured formation of the six-membered heterocycle occurs

Application of Cu(I)-catalyzed azide–alkyne cycloaddition for the design and synthesis of sequence specific probes targeting double-stranded DNA

• Svetlana V. Vasilyeva,
• Vyacheslav V. Filichev and
• Alexandre S. Boutorine

Beilstein J. Org. Chem. 2016, 12, 1348–1360, doi:10.3762/bjoc.12.128

• was used for their final purification. DNA-templated synthesis of TFO-MGB conjugates It has been shown that the presence of copper ions does not prevent duplex and triplex formation and the DNA-directed cycloaddition reaction proceed smoothly on these templates [38]. In 2003, the team of P. Dervan

1H-Imidazol-4(5H)-ones and thiazol-4(5H)-ones as emerging pronucleophiles in asymmetric catalysis

• Antonia Mielgo and
• Claudio Palomo

Beilstein J. Org. Chem. 2016, 12, 918–936, doi:10.3762/bjoc.12.90

• = S) analogues of these oxazol-4(5H)-ones have been demonstrated to be very interesting templates in asymmetric catalysis. In these cases the hydrolysis of the adducts coming from an asymmetric reaction can provide enantioenriched α-hydroxy acids (X = O), N-substituted α-amino acids (X = NR’) or α

• ]. The main advantages of these pronucleophiles over the previous known templates are: i) the NR group can be installed in the heterocycle previous to the asymmetric reaction, ii) they are easily deprotonated under soft enolization conditions (aromatic enolate formation), and iii) unlike azlactones and

• the reactions with the α’-hydroxyenone provided the adducts in very poor enantioselectivity. This is a particular and interesting characteristic of these templates because the α-hydroxy group can be transformed into other oxy derivatives to better adapt to the most suitable substrate/catalyst