Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• monosaccharides, substituents and linkages from the list of symbols. However, some wrong combinations of choices can block the interface, resulting in the need to re-start the process (SugarSketcher is on version beta 1.3). Alternatively, SugarSketcher also uses GlycoCT or a native template library as an input. A

• list of pre-built core N- and O-linked carbohydrate moieties, which are usually present in glycoproteins structures, can be used as a template for further modification. A shortlist of glycan epitopes is also included providing templates for drawing more complex molecules. The software uses the Symbol

• glycans and terminals. Also, it provides 80+ monosaccharide (SNFG) symbols and a selection for substituents. The selected template or text string (in CFG linear nomenclature) input directly gets converted into an image in canvas and also appears as text in GlycoCT format. The output can be saved as a .svg

A proposed sustainability index for synthesis plans based on input provenance and output fate: application to academic and industrial synthesis plans for vanillin as a case study

• John Andraos

Beilstein J. Org. Chem. 2020, 16, 2346–2362, doi:10.3762/bjoc.16.196

• matrices and the number of dominances for each plan for each pairwise attribute comparison. Supporting Information File 3 contains an Excel template file that facilitates carrying out the tedious task of pairwise comparisons involved in the poset analysis, particularly when the number of synthesis plans

• synthesis plans on production of 1 kg vanillin, Borda count results, and Poset analysis. Supporting Information File 569: Excel file of sustainability index (SI) calculator. Supporting Information File 570: Excel template file for carrying out poset pairwise dominance analysis. Acknowledgements This paper

Design and synthesis of a bis-macrocyclic host and guests as building blocks for small molecular knots

• Elizabeth A. Margolis,
• Rebecca J. Keyes,
• Stephen D. Lockey IV and
• Edward E. Fenlon

Beilstein J. Org. Chem. 2020, 16, 2314–2321, doi:10.3762/bjoc.16.192

• with 77 backbone atoms (Figure 2a) [15]. More recently, Leigh’s group disclosed the synthesis of the current record holder for the smallest knot, which has 76 backbone atoms (Figure 2b) [16]. Since the metal atom template has been removed, the Leigh compound is a true knot in strict topological terms

Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• intricacies involved at multiple levels. Unlike DNA and proteins, glycans are neither linear nor template driven, making their structures computationally taxing. In addition, the complexity is compounded by the sample and experimental meta data associated with the glycan microarray experiment. The following

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• ]. This heterogeneity can take the form of variable occupancy, also known as macroheterogeneity – the presence or absence of modification at a particular site in a protein, due to inefficient transfer of the initial glycan structure [5]. In addition, the non-template-driven synthesis of glycan structures

A dynamic combinatorial library for biomimetic recognition of dipeptides in water

• Florian Klepel and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2020, 16, 1588–1595, doi:10.3762/bjoc.16.131

• library to be under thermodynamic control. Therefore, the equilibrium responds to stimuli such as addition of a template, which would stabilize a suitable receptor and thus amplifies its formation. This strategy has led to the discovery of many artificial receptors [7][8][9][10], with thiolate disulfide

• by co-elution with the FF template. This is a not an issue for the YY containing sample as the template peak maximum lays between the first and second tripeptide dimer peak. We therefore concluded that the binding affinities of the receptor template pairs should be FF > YY > AA. In order to

• mL vial. Another 100 µL of a template stock solution (90 mM) was added. For a reference sample the template solution was substituted for buffer. Small magnetic stirring bars were added, and the vials were covered by a layer of perforated Parafilm to slow down drying due to fast air exchange. After

Five-component, one-pot synthesis of an electroactive rotaxane comprising a bisferrocene macrocycle

• Natalie Lagesse,
• Luca Pisciottani,
• Maxime Douarre,
• Pascale Godard,
• Brice Kauffmann,
• Vicente Martí-Centelles and
• Nathan D. McClenaghan

Beilstein J. Org. Chem. 2020, 16, 1564–1571, doi:10.3762/bjoc.16.128

• crystal X-ray structure of a doubly ferrocene-decorated [2]rotaxane are further reported. Keywords: ferrocene; macrocycle; rotaxane; single crystal X-ray structure; template; Introduction The development of interlocked molecules with tailored properties allowed the preparation of molecular machines able

• to perform several functions as artificial molecular switches [1]. The template-directed synthesis of such sophisticated catenane and rotaxane molecular architectures allowed the expansion of chemical diversity and properties. Among these architectures, electroactive rotaxanes have been described to

• synthesis of macrocycle 2 was carried out using N,N'-dihexyl-1,4-butanediamide as the template, as represented in Figure 2. While the formation of some macrocyclic product was identified by 1H NMR and MS, it could not be completely separated from impurities (<29% yield after chromatographic purification

Activated carbon as catalyst support: precursors, preparation, modification and characterization

• Melanie Iwanow,
• Tobias Gärtner,
• Volker Sieber and
• Burkhard König

Beilstein J. Org. Chem. 2020, 16, 1188–1202, doi:10.3762/bjoc.16.104

• porosity of the carbon spheres is induced by either aromatization of carbon around an in situ template, in situ chemical activation or gasification of carbon [96]. Xu et al. found that the morphology of the porous carbon materials prepared from propiolate salts with USP are dependent on the choice of

• preparation of these carbon materials (preparation of the solid scaffolds, pyrolysis of the carbon precursors in these templates and finally, the selective removal of the silica template) and the risk of structure and morphology defects by the harsh carbonization and template removal processes, this method is

• aerosol-assisted self-assembly using amphiphilic triblock copolymers as template and low-molecular weight soluble phenol resin as carbon source. The amphiphilic surfactant influences the pore size and mesostructure of the resulting spherical carbons. Finally, the template is removed by calcination [97

Synthesis of esters of diaminotruxillic bis-amino acids by Pd-mediated photocycloaddition of analogs of the Kaede protein chromophore

• Esteban P. Urriolabeitia,
• Pablo Sánchez,
• Alexandra Pop,
• Cristian Silvestru,
• Eduardo Laga,
• Ana I. Jiménez and
• Carlos Cativiela

Beilstein J. Org. Chem. 2020, 16, 1111–1123, doi:10.3762/bjoc.16.98

• of the ε-isomer in 4: (1) the initial (Z)-configuration of the oxazolones 2 is retained during the C–H bond activation step to give 3; (2) the relative transoid arrangement in 3 establishes the 1,3-head-to-tail coupling of the exocyclic C=C bonds; (3) the template effect of the Pd2(O2CCF3)2 moiety

• this lack of reactivity. Release of the 1,3-truxillic derivative by methoxycarbonylation The last step to achieve the synthesis of the 1,3-diaminotruxillic targets was the release of the cyclobutane from the Pd2(O2CCF3)2 template. We previously reported that hydrogenation and halogenation were adequate

• tools to liberate 1,3-diaminotruxillics from the organopalladium template [29][30]. We employed similar reactions in this case with complexes 4, but none of the attempts gave satisfactory results. Therefore, we discarded them and investigated other alternatives. We found that the reaction of ortho

Efficient synthesis of 3,6,13,16-tetrasubstituted-tetrabenzo[a,d,j,m]coronenes by selective C–H/C–O arylations of anthraquinone derivatives

• Seiya Terai,
• Yuki Sato,
• Takuya Kochi and
• Fumitoshi Kakiuchi

Beilstein J. Org. Chem. 2020, 16, 544–550, doi:10.3762/bjoc.16.51

• ]. Anthraquinone was chosen as a convenient template for the PAH syntheses, because various anthraquinone derivatives possessing zero to four oxygen substituents at the ortho-positions are readily available and the regioselective arylation at the positions of either C–H or C–O bonds provided a variety of

• introduction of two different aryl groups at the ortho-positions can be achieved by chemoselective C–O arylation of aromatic ketones possessing both C–H and C–O bonds and subsequent C–H arylation. We envisioned that the application of this strategy to the anthraquinone template would provide its derivatives

Combination of multicomponent KA² and Pauson–Khand reactions: short synthesis of spirocyclic pyrrolocyclopentenones

• Riccardo Innocenti,
• Elena Lenci,
• Gloria Menchi and
• Andrea Trabocchi

Beilstein J. Org. Chem. 2020, 16, 200–211, doi:10.3762/bjoc.16.23

• structure in three single steps (Scheme 1b). This unprecedent molecular scaffold represents a valuable template for medicinal chemistry purpose, as the pyrrolocyclopentenone core is contained in a variety of bioactive molecules [49][50], and can serve as an advanced intermediate for the synthesis of

Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering

• Eric J. N. Helfrich,
• Geng-Min Lin,
• Christopher A. Voigt and
• Jon Clardy

Beilstein J. Org. Chem. 2019, 15, 2889–2906, doi:10.3762/bjoc.15.283

• thiotemplated assembly lines, such as type I polyketide synthases (PKS) and nonribosomal peptide synthetases (NRPS), are modular, with each module contributing a distinct fragment to the final product’s core structure – a short-chain carboxylic acid (PKS) or an amino acid (NRPS). The modularly defined template

Palladium-catalyzed synthesis and nucleotide pyrophosphatase inhibition of benzo[4,5]furo[3,2-b]indoles

• Hoang Huy Do,
• Saif Ullah,
• Alexander Villinger,
• Joanna Lecka,
• Jean Sévigny,
• Peter Ehlers,
• Jamshed Iqbal and
• Peter Langer

Beilstein J. Org. Chem. 2019, 15, 2830–2839, doi:10.3762/bjoc.15.276

• 52% in case of ENPP3, amino acids sequence similarity with template, mouse ENPP1. The RMSD for ENPP1 was 0.613 Å and 1.349 Å for ENPP3, over 816 and 811 residues in comparison to the template, respectively. The Ramachandran plot represented promising stereochemical properties as above 98% amino acids

Formation of alkyne-bridged ferrocenophanes using ring-closing alkyne metathesis on 1,1’-diacetylenic ferrocenes

• Celine Bittner,
• Dirk Bockfeld and
• Matthias Tamm

Beilstein J. Org. Chem. 2019, 15, 2534–2543, doi:10.3762/bjoc.15.246

• can be found in the literature [54][55][56][57], including the formation of olefinic metallocenophanes via ring-closing olefin metathesis [58][59][60][61], and the preparation of supramolecular structures using template synthesis [62][63][64][65][66][67][68][69]. However, only few cases are

In search of visible-light photoresponsive peptide nucleic acids (PNAs) for reversible control of DNA hybridization

• Lei Zhang,
• Greta Linden and
• Olalla Vázquez

Beilstein J. Org. Chem. 2019, 15, 2500–2508, doi:10.3762/bjoc.15.243

• quencher (BHQ)-labelled single-strand (ss) DNA template, a complementary fluorescein (FAM)-labelled ssDNA and the PNA of interest. In this framework, the PNA could bind the BHQ-ssDNA; thus, its addition to the quenched BHQ/FAM-DNA duplex would trigger an exchange reaction and the release of the FAM-ssDNA

Anion-driven encapsulation of cationic guests inside pyridine[4]arene dimers

• Anniina Kiesilä,
• Jani O. Moilanen,
• Anneli Kruve,
• Christoph A. Schalley,
• Perdita Barran and
• Elina Kalenius

Beilstein J. Org. Chem. 2019, 15, 2486–2492, doi:10.3762/bjoc.15.241

• complexes can template the formation of pyridinearene hexameric capsules in the gas phase [6]. Here, we report our novel findings on the ability of dimeric tetraisobutylpyridine[4]arene (compound 1 in Scheme 1) to encapsulate cationic guests. Despite of the obvious structural similarities between the

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

• Ronja Driller,
• Daniel Garbe,
• Norbert Mehlmer,
• Monika Fuchs,
• Keren Raz,
• Dan Thomas Major,
• Thomas Brück and
• Bernhard Loll

Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228

• of the carbocation. Mechanistic aspects of the cyclization reaction and point mutations The floor of the active site is decorated by hydrophobic residues V80, F107, W109, F149, V150, I181, F185, M189, W186, L281, and W288 conferring the overall shape to the cavity that serves as a template for the

1,2,3-Triazolium macrocycles in supramolecular chemistry

• Mastaneh Safarnejad Shad,
• Pulikkal Veettil Santhini and
• Wim Dehaen

Beilstein J. Org. Chem. 2019, 15, 2142–2155, doi:10.3762/bjoc.15.211

• an active metal template strategy. The 1H NMR binding data of 8·Se were studied in organic and aqueous solvent mixtures, revealing that ChB–anion binding affinity can compete with and even outperform hydrogen bonding receptor analogues. Due to the larger degree of covalency with the heavier halides

• template-directed self-assembly procedure via an intramolecular “CuAAC click” reaction in the presence of electron-rich bisnaphtho- or bisbenzo-24-crown-8 ethers. Afterwards, the triazole groups in the catenanes were methylated. The resulting triazolium macrocycle containing catenanes 17a (DN24C8) and 17b

Multiple threading of a triple-calix[6]arene host

• Veronica Iuliano,
• Roberta Ciao,
• Emanuele Vignola,
• Carmen Talotta,
• Patrizia Iannece,
• Margherita De Rosa,
• Annunziata Soriente,
• Carmine Gaeta and
• Placido Neri

Beilstein J. Org. Chem. 2019, 15, 2092–2104, doi:10.3762/bjoc.15.207

• , daisy-chain pseudorotaxanes, olympiadane, Janus rotaxanes [5]) is generally obtained through a template-approach [9] exploiting the threading process between linear (axle) and macrocyclic (wheel) components. In order to synthesize high-order interpenetrated architectures, much attention has been

Halide metathesis in overdrive: mechanochemical synthesis of a heterometallic group 1 allyl complex

• Ross F. Koby,
• Nicholas R. Rightmire,
• Nathan D. Schley,
• Timothy P. Hanusa and
• William W. Brennessel

Beilstein J. Org. Chem. 2019, 15, 1856–1863, doi:10.3762/bjoc.15.181

• ]∞ and [(C6H6)KA']∞ (3.04 Å in the poorer quality [(toluene)KA']∞ structure), and 3.06 Å in [KA'(dme)]∞ [24]. This suggests that the K+…[A'] interaction is a robust one, and its structure potentially capable of serving as a kind of template for inclusion (see below). Formation of the heterometallic allyl

• viewed as a template into which Cs+ are infused during the grinding. There are adjustments in M–C(allyl) bond distances (see above), but another consequence is the generation of multiple intermolecular M…CH3 interactions. Both [KA'] and [CsKA'2] possess K…CH3 contacts at typical distances [32]; in [KA

Nanopatterns of arylene–alkynylene squares on graphite: self-sorting and intercalation

• Tristan J. Keller,
• Joshua Bahr,
• Kristin Gratzfeld,
• Nina Schönfelder,
• Marcin A. Majewski,
• Marcin Stępień,
• Sigurd Höger and
• Stefan-S. Jester

Beilstein J. Org. Chem. 2019, 15, 1848–1855, doi:10.3762/bjoc.15.180

• with different numbers of sides [18], that are scalable to some extent [19]. The long alkoxy side chains mediate sufficient compound solubility and compound adsorption on highly oriented pyrolytic graphite (HOPG) that acts as a template [20][21], and determine the intermolecular interaction [22][23][24

• shown for clarity). Enlarged areas of Figure 3a (shown in Figure 3b and c) show two template macrocycles 1a (of similar orientation), each of which is filled with one molecule of 2 that appears as a bright hexagon – however, with different orientations. The hexagons of the nanographene 2 in Figure 3c

• the procedure described above) a nanopattern of 1a (5 × 10−7 M), and added a 10−4 M solution of 3 in TCB. STM (Figure 4a) shows – again – bright features in the macrocyclic template of 1a. Again, a slight central depression is visible in the STM image which can attributed to the empty center region of

Bambusuril analogs based on alternating glycoluril and xylylene units

• Tomáš Lízal and
• Vladimír Šindelář

Beilstein J. Org. Chem. 2019, 15, 1268–1274, doi:10.3762/bjoc.15.124

• simple example of a chromophoric monomer (Scheme 1). The reaction took place under basic conditions using LiH in dry THF [16]. The LiClO4 salt was used originally as a template in order to drive the reaction towards the three-membered macrocycle (n = 3). Later it was found that the salt does not have a

Self-assembly behaviors of perylene- and naphthalene-crown macrocycle conjugates in aqueous medium

• Xin Shen,
• Bo Li,
• Tiezheng Pan,
• Jianfeng Wu,
• Yangxin Wang,
• Jie Shang,
• Yan Ge,
• Lin Jin and
• Zhenhui Qi

Beilstein J. Org. Chem. 2019, 15, 1203–1209, doi:10.3762/bjoc.15.117

• water-soluble crown macrocycle 3 was synthesized according to reported protocols, by using potassium cations as template [86][87]. The primary amine group in 3 offers diverse reaction pathways to design crown ethers appended LMW gelators, dendrimers and polymers [88][89][90][91][92]. In order to

Design of a double-decker coordination cage revisited to make new cages and exemplify ligand isomerism

• Sagarika Samantray,
• Sreenivasulu Bandi and
• Dillip K. Chand

Beilstein J. Org. Chem. 2019, 15, 1129–1140, doi:10.3762/bjoc.15.109

• OTf−) with the ligand L1 at a 3:4 ratio resulted in the formation of only mononuclear complexes 3b–d (depicted in a later Scheme) and the unutilized proportion of Pd(Y)2 remained in solution. Thus, the counter ion nitrate has a determining role by acting as template for the cavities in the formation

• displayed a template role for the formation of trinuclear complexes, especially for Pd3L4-type complexes. The anions helped to screen the charge repulsion between the palladium(II) ions. The complexation behavior of palladium(II) components with the ligand L2 have been reported earlier [23]. The

Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls

• Dong-Hao Li and
• Bradley D. Smith

Beilstein J. Org. Chem. 2019, 15, 1086–1095, doi:10.3762/bjoc.15.105

• ] macrocycle and a larger amount of the corresponding [2]catenane. Subsequent work found that conducting the reaction in the presence of a dumbbell-shaped template was a general way to make a wide range of [2]rotaxanes [28]. Listed in Scheme 2 are the yields of [2]rotaxane produced using various biscarbonyl

• -based templates [35][36][37][38][39][40][41][42][43]. These reactions are remarkable examples of templated syntheses since they form four covalent bonds and bring together five molecules in a single reaction. The key step is the final amide-bond formation that clips the tetralactam around the template

• (Scheme 3) [35]. The template molecule favors this step over the alternative intermolecular reaction that leads to larger oligomers. The poor solubility of A prevents the traditional host–guest affinity measurements; however, the [2]rotaxane yield is a useful indicator of template affinity for the