Intramolecular glycosylation

• Xiao G. Jia and
• Alexei V. Demchenko

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

• introduced by Kusumoto et al. [46], however, this term was coined by the same group much later [51]. We adopt this term to generally refer to this concept, which in other applications was also named “intramolecular glycosylation of prearranged glycosides” by Ziegler [52][53], “template-directed cyclo

• category was extensively studied and applied to a variety of sugar series and targets [58][73][74]. Phthaloyl and related tethers Phthaloyl tethering was also introduced by Ziegler [53] and practically concomitantly by Valverde et al. [54] as “template-directed cyclo-glycosylation.” In the latter

• 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

A recursive microfluidic platform to explore the emergence of chemical evolution

• David Doran,
• Marc Rodriguez-Garcia,
• Rebecca Turk-MacLeod,
• Geoffrey J. T. Cooper and
• Leroy Cronin

Beilstein J. Org. Chem. 2017, 13, 1702–1709, doi:10.3762/bjoc.13.164

• autocatalytic networks that reproduce, with more or less the same stoichiometry, all functionally active components of their heterogeneous chemical mixtures. Such systems could easily exist outside the boundaries of known biology, and perhaps may not even require a template-driven genetic polymer to reproduce

• conventional, template-directed genetic system. Thus, the first step is to establish a suitable metric for identifying and measuring their capacity for evolution. We propose that, for any given population of discrete living or proto-living units, the average fitness (wi) of the population will be evaluated as

• . Our aim is to design and fabricate a complete device containing a droplet generator, an incubation chamber, a droplet size sorter, a droplet fuser, and a droplet splitter; see Figure 7 for the device template. Microfluidic droplet generators will produce the droplet populations that will then be co

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

• 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

• protocellular „metabolism“. Inspired by the non-enzymatic, template-directed RNA polymerization in bulk aqueous solutions [7] (the synthesis of a RNA using a primer/template system and magnesium ions as catalysts), the Szostak group [21][82] has demonstrated that RNA could be synthesized within mixed vesicles

• composed of several types of “prebiotic” fatty acids and co-surfactants. That is, the vesicles could have retained the primer/template system while activated monomers crossed the vesicle bilayers by passive diffusion. Similarly, amino acids could be dimerized within vesicles [86]. In related experiments

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

• form the desired template [29][30]. A severe disadvantage of both routes is the need of large amounts of solvents, eventually accumulating as waste during the process. Moreover, these approaches require multiple synthesis steps, including template synthesis, calcination, impregnation, pyrolysis, and

• template removal. Therefore, the preparation of porous carbons with a tailored pore structure by conventional templating processes is often time and cost-intensive and environmentally unfavorable. For a more sustainable carbon production, especially in industrial scale, it is necessary to reduce the number

• and the carbochlorination step, we conducted the synthesis under liquid-assisted conditions while adding ethanol as a solvent to see if there is a difference in the polymerization and investigated an alternative template removal approach based on etching with hydrofluoric acid (HF) as well [54]. The

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

• natural products as drugs, for example (Figure 2). Contemporary research aims to elucidate how molecular machines self-assemble, and to discover the mechanisms by which they operate, thereby providing a template for the rational, intentional design of useful molecular machines at the nanoscale [2

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

• below. Mutation involves the emergence of a difference between the parent template and its copies. The accuracy of the replication process of DNA is generally safeguarded by sophisticated enzymes, but systems that lack such machinery are more prone to occasional errors during replication. Mutations

• that of DNA. A DNA molecule consists of two strands of nucleotides that are intertwined to form a double helix. During the replication process of DNA, each of these strands can act as a template for the formation of a complementary strand. In this way an exact copy of the original structure of DNA is

• set of basic building blocks. This fundamental form of a self-replicating system is depicted in Figure 2 and is called a minimal self-replicating system. An essential requirement for a minimal replicating system is that molecules A and B are complementary to template T so that they are able to bind to

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 a template for the daughter, as in nucleic acids, for example. In fact, the entity that is replicated is not a protein complex but an algorithm of construction. Hence, in this particular instance, replication is not a protein-replication system, nor is it directly associated to nucleic acids used

G-Protein coupled receptors: answers from simulations

• Timothy Clark

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

• it has played a major role in the determination of the mechanisms of action of GPCRs [21][22] and was the only structure available, in general, rhodopsin was not considered the ideal template for GPCR drug targets. This was because of both its relatively low similarity to medicinal targets [23] and

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

• possibilities for variation are indeed a requirement for systems to undergo open-ended evolution [66]. The storage of genetic information as a sequence in a polymer associated with template replication through base-pairing constitutes an efficient system to ensure evolvability. It is that evolvability which

• allows selection toward life as we know it on Earth. However, as the proximity from equilibrium has been mentioned above as a limitation, the higher affinity of long strands compared to fragments is the source of another limitation (product inhibition). That limitation, discovered for template

Pd- and Cu-catalyzed approaches in the syntheses of new cholane aminoanthraquinone pincer-like ligands

• Nikolay V. Lukashev,
• Gennadii A. Grabovyi,
• Dmitry A. Erzunov,
• Alexey V. Kazantsev,
• Gennadij V. Latyshev,
• Alexei D. Averin and
• Irina P. Beletskaya.

Beilstein J. Org. Chem. 2017, 13, 564–570, doi:10.3762/bjoc.13.55

• template for design of complex molecules has become increasingly popular in pharmacology, supramolecular chemistry and nanoscience over recent years [4][5]. Many macrocyclic dimeric derivatives of bile acid were described [6][7][8]. As a rule, a route to the majority of macrocyclic structures requires

Synthesis of spiro[isoindole-1,5’-isoxazolidin]-3(2H)-ones as potential inhibitors of the MDM2-p53 interaction

• Salvatore V. Giofrè,
• Santa Cirmi,
• Raffaella Mancuso,
• Francesco Nicolò,
• Giuseppe Lanza,
• Laura Legnani,
• Agata Campisi,
• Maria A. Chiacchio,
• Michele Navarra,
• Bartolo Gabriele and
• Roberto Romeo

Beilstein J. Org. Chem. 2016, 12, 2793–2807, doi:10.3762/bjoc.12.278

• -ethynylbenzamides 1 [35]. The rationale of our choice is based on molecular docking data. Using the published structure of the MDM2–p53 binding site, we have employed computational methods and focused library synthesis based on the isoindolinone template, to develop compounds with inhibitory activity. These studies

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

• generates sequence–template alignments for a query sequence and identifies best structure matches from the PDB [53]. In addition to sequence profile alignments, it also uses multiple structure information as well. DescFold is another webserver which employs SVM-based machine learning algorithms in protein

• fold recognition [54]. Ab initio (de novo) modeling Ab initio or de novo modeling is employed when there is no sufficiently homologous structure to use comparative modeling. De novo protein modeling does not rely on a template structure. It models the target structure solely based on the sequence. Ab

• template free modeling category outperforming the Rosetta server though Rosetta remains to be one of the most popular methods of ab initio structure prediction. Many other ab initio structure prediction software packages have been developed in the last three decades and some of the popular ones are listed

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

• other monocyclic heterocycles The methodology presented in this work can in principle be extended to any monocyclic heterocyclic ring system without restriction. In order to motivate synthetic chemists to further explore opportunities to discover new 3-component coupling reactions, an atlas of template

A detailed view on 1,8-cineol biosynthesis by Streptomyces clavuligerus

• Jan Rinkel,
• Patrick Rabe,
• Laura zur Horst and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2016, 12, 2317–2324, doi:10.3762/bjoc.12.225

• hydrophobic cavity from which water is excluded to enable carbocation chemistry in an aqueous environment. Furthermore, the hydrophobic cavity provides a template that arranges the substrate in a certain conformation to determine the formation of a specific product. Single residues such as phenylalanines are

Diels–Alder reactions in confined spaces: the influence of catalyst structure and the nature of active sites for the retro-Diels–Alder reaction

• Ángel Cantín,
• M. Victoria Gomez and
• Antonio de la Hoz

Beilstein J. Org. Chem. 2016, 12, 2181–2188, doi:10.3762/bjoc.12.208

• )] were prepared according to [31][32][33], using tetraethylammonium hydroxide as template, tetraethyl orthosilicate (TEOS) as silica source and Ti(IV) ethoxide, SnCl4·5H2O and metal Al as sources of heteroatoms. SSZ-53 and SSZ-59 were synthesized according to the procedures described in the literature

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

• template-directed selection of one nucleobase from the reaction mixture with the amine or thiol functional group was investigated [44][45][46][47]. In our studies, dynamic chemistry is applied for post-synthetic functionalization of the threoninol based modified oligonucleotides in a reversible manner

• , we generated the libraries of reversibly interconverting building blocks – dynamic combinatorial libraries (DCL) (Figure 1). The abasic strand and its complementary template strand are spontaneously assembled into a double helix through Watson–Crick base-pairing and the incoming nucleobase monomer

• benefits from the hydrogen bonding recognition by the respective nucleobase in the template strand. The reversible attachment generates a dynamic system that enables the combinatorial screening of the best bound nucleobase by allowing a rapid and continuous exchange between the threoninol site and the set

Bridgehead vicinal diallylation of norbornene derivatives and extension to propellane derivatives via ring-closing metathesis

• Sambasivarao Kotha and
• Rama Gunta

Beilstein J. Org. Chem. 2016, 12, 1877–1883, doi:10.3762/bjoc.12.177

• diallylation; Introduction The norbornene moiety is a useful template and also a versatile synthon in organic synthesis [1]. The double bond present in the norbornene frame is strained and therefore participates in cycloaddition sequences as a C2-synthon [2][3]. It was reported that the norbornene system is

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

• work of Jeremy Sanders and co-workers on dynamic combinatorial chemistry (DCC) while being a graduate student and postdoc (Figure 7) [42][43]. Like folded peptides that self-assemble into their functional state, DCC allows molecules to self-assemble in the presence of a template. Moreover, DCC is

Rearrangements of organic peroxides and related processes

• Ivan A. Yaremenko,
• Vera A. Vil’,
• Dmitry V. Demchuk and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2016, 12, 1647–1748, doi:10.3762/bjoc.12.162

• good 92% yield by using Et3N (Scheme 91) [371]. A sequence consisting of a template-mediated photooxygenation and an acid-catalyzed Kornblum−DeLaMare rearrangement of the intermediate endo-peroxides 310 was used in a one-pot transformation of 3-substituted 2-pyridones

Organic chemistry meets polymers, nanoscience, therapeutics and diagnostics

• Vincent M. Rotello

Beilstein J. Org. Chem. 2016, 12, 1638–1646, doi:10.3762/bjoc.12.161

• one step further, we created a nanoparticle with a mixed monolayer consisting of hydrogen bonding and aromatic staking sidechains. When we incubated this NP with flavin we observed an increase in binding over time, i.e., we were able to template the particle to the guest [22]. We have since

Experimental and theoretical insights in the alkene–arene intramolecular π-stacking interaction

• Valeria Corne,
• Ariel M. Sarotti,
• Carmen Ramirez de Arellano,
• Rolando A. Spanevello and
• Alejandra G. Suárez

Beilstein J. Org. Chem. 2016, 12, 1616–1623, doi:10.3762/bjoc.12.158

• all noncovalent interactions, π-stacking is perhaps the less well understood, although its application in materials sciences, enzyme design and template-directed synthesis have had a dramatic growth, mainly for arene–arene interactions [1][2][3][4][5][6][7][8]. In particular, the use of π–π overlap as

One-pot synthesis of tetracyclic fused imidazo[1,2-a]pyridines via a three-component reaction

• Bo Yang,
• Chuanye Tao,
• Taofeng Shao,
• Jianxian Gong and
• Chao Che

Beilstein J. Org. Chem. 2016, 12, 1487–1492, doi:10.3762/bjoc.12.145

• diverse and biologically relevant heterocycles, and thus have been extensively investigated by organic and medicinal chemists to explore lead compounds in drug discovery efforts [7][8][9][10]. The imidazo[1,2-a]pyridine scaffold is a pharmaceutically important drug template, and its derivatives display a

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

• succeeded to obtain a conjugate of two polyamides by template-directed synthesis on the adjacent sequences of a target DNA fragment using the Huisgen 1,3-cycloaddition reaction even without copper catalysis [39]. The rational for this type of synthesis was to find an optimal orientation of two DNA-binding

• ligands for the synthesis of highly affine conjugates and to provide a favorable approaching and orientation of the two components in order to facilitate the reaction. However, after this publication the use of a Huisgen reaction without copper catalysis in the template-directed synthesis was never

• reproduced. In the present work, we tried to approach and correctly orient two components (TFO and polyamide) by their binding on the target dsDNA sequence as a template. Linkers of different lengths and configurations were used in order to select one that fits better the DNA architecture. Only TINA-TFOs

Conjugate addition–enantioselective protonation reactions

• James P. Phelan and
• Jonathan A. Ellman

Beilstein J. Org. Chem. 2016, 12, 1203–1228, doi:10.3762/bjoc.12.116

• (Scheme 2) [15][16][17]. A Mg-(bis)oxazoline complex serves as both a Lewis acid for the activation of α-substituted acrylates 6 towards radical addition and as a chiral template for an enantioselective hydrogen atom transfer from Bu3SnH to the α-ester radical intermediate. The authors found that the

Superstructures with cyclodextrins: chemistry and applications III

• Gerhard Wenz and
• Eric Monflier

Beilstein J. Org. Chem. 2016, 12, 937–938, doi:10.3762/bjoc.12.91

• of highly active heterogeneous catalysts. Accordingly, the catalytic transformation of bio-oil has been achieved over Cu/MCM-41 and Cu/Kit-6 catalysts obtained by a CD assisted co-impregnation method [12]. Furthermore, the combination of template-directed colloidal self-assembly with a CD-assisted