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

• specialized surface types (e.g., nitrocellulose PATH® slides) which have lower background signals at this wavelength. A decision chart is provided in Figure 2 which can help to decide which surface would be best for a variety of situations. A more detailed discussion of recent glycan linkers and surfaces was

• approach. It is also possible that the results from automated software could be confounding rather than illuminating, if parameters of the experiment or even array fabrication (such as surface chemistry, etc.) are changed. In fact, the various chemical linkers through which glycans are attached to the

Clickable azide-functionalized bromoarylaldehydes – synthesis and photophysical characterization

• Dominik Göbel,
• Marius Friedrich,
• Enno Lork and
• Boris J. Nachtsheim

Beilstein J. Org. Chem. 2020, 16, 1683–1692, doi:10.3762/bjoc.16.139

• alkynes, exhibiting different degrees of steric demand, was performed in high efficiency. Finally, we investigated the photophysical properties of the azide-functionalized arenes and their covalently linked triazole derivatives to gain deeper insight towards the effect of these covalent linkers on the

Pauson–Khand reaction of fluorinated compounds

• Jorge Escorihuela,
• Daniel M. Sedgwick,
• Alberto Llobat,
• Mercedes Medio-Simón,
• Pablo Barrio and
• Santos Fustero

Beilstein J. Org. Chem. 2020, 16, 1662–1682, doi:10.3762/bjoc.16.138

• compounds in the PK reaction started with fluorinated enynes derived from malonates and those containing heteroatoms as linkers. The synthesis of the starting enynes 37 was accomplished following various approaches (Scheme 19). The first of these (via a) was based on a report by Hammond and co-workers, in

• ). Alkyl-substituted derivatives proved to be similarly successful substrates; however, the TMS-substituted derivative was obtained in a significantly lower yield. In terms of linkers, heteroatoms were well-tolerated, although the use of malononitrile resulted exclusively in the elimination product despite

• testing a variety of reaction conditions. More complex biorelevant examples such as isatin derivatives were also suitable substrates, affording the corresponding spirocyclic derivatives, albeit in low yields (Scheme 21) [59]. Unfortunately, thioether and sulfone-based linkers were unsuitable in this

A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA

• Ekaterina A. Bryushkova,
• Erik R. Gandalipov and
• Julia V. Nuzhina

Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100

• strand), that combined the components into a single structure. The T1–T4 strands were connected with the platform by polythymidine or hexaethylene glycol linkers, which provided flexibility of SDFS. All nucleotide sequences are presented in Table S2 of Supporting Information File 1. A calculation of the

• target 60-AR_RNA, and connected with T2 and T3 strands through polythymidine linkers (Figure 1A). The MGA strands can hybridize with each other and attach a molecule of malachite green dye (Figure 1C and D) only in the presence of target mRNA. It provided the high specificity of SDFS. After being

• biological material. SDFS main components and its work model. A) Schematic representation of the SDFS structure. Dotted lines indicate hexaethylene glycol linkers in T1 and T4, and polythymidines linker in T2 and T3; Dz1 and Dz2 – deoxyribozyme sequences. B) The detailed structure of the Dz catalytic core

Towards triptycene functionalization and triptycene-linked porphyrin arrays

• Gemma M. Locke,
• Keith J. Flanagan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2020, 16, 763–777, doi:10.3762/bjoc.16.70

• porphyrin units have been connected in a number of different ways; from phenylene, ethynyl, ethenyl or alkane linkers [5][6][7][8], to meso–β- [9] or β–β-linkages [10] or alternatively by connecting two or more meso–meso-linked porphyrin units via oxidative fusing reactions [11][12][13][14][15]. However

• linked which, theoretically, can cause a significant energy/charge sink. Moreover, the use of π-conjugated linkers in porphyrin arrays results in significantly altered UV–vis spectra, indicating very strong electronic coupling that causes the loss of individual unit characteristics through delocalization

• directly to the periphery of triptycene or via various linkers; arrays with six chromophores 3 have thus far eluded us [26][27]. While much work has been done on the functionalization of the aromatic rings of triptycene as in 2 or 3 [24][25][26][27][28][29][30], the attachment of chromophores at the

Fluorinated maleimide-substituted porphyrins and chlorins: synthesis and characterization

• Valentina A. Ol’shevskaya,
• Elena G. Kononova and
• Andrei V. Zaitsev

Beilstein J. Org. Chem. 2019, 15, 2704–2709, doi:10.3762/bjoc.15.263

• heterocycles have also been used as linkers and for labeling biomolecules in chemical biology [43]. Moreover, this synthetic approach provides high yields, selectivity, mild reaction conditions and simple purification methods. It was demonstrated that the CuAAC reaction of porphyrins 3a and 3b with N

Effect of ring size on photoisomerization properties of stiff stilbene macrocycles

• Sandra Olsson,
• Óscar Benito Pérez,
• Magnus Blom and
• Adolf Gogoll

Beilstein J. Org. Chem. 2019, 15, 2408–2418, doi:10.3762/bjoc.15.233

• diethers into noncyclic diethers (Supporting Information File 1) and the results are visualized in Figure 4. For (E)-1a–d the ring strain decreases with increased linker length. For the less strained (Z)-1a–d the ring strain increases slightly with increased linker length and for the longer linkers (1c,d

Complexation of chiral amines by resorcin[4]arene sulfonic acids in polar media – circular dichroism and diffusion studies of chirality transfer and solvent dependence

• Bartosz Setner and
• Agnieszka Szumna

Beilstein J. Org. Chem. 2019, 15, 1913–1924, doi:10.3762/bjoc.15.187

• capable of forming electrostatic interactions. However, in CSAs polar groups are positioned directly on a macrocyclic scaffold, while for RSAs at conformationally labile methylene linkers. Therefore, we think that RSAs are more adaptable than CSAs and are able to enclose guest molecules more tightly (by

An azobenzene container showing a definite folding – synthesis and structural investigation

• Abdulselam Adam,
• Saber Mehrparvar and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2019, 15, 1534–1544, doi:10.3762/bjoc.15.156

• macrocycles: In the elongated trans,trans-isomer this distance shows a value of 14.1 Å, in the more compact cis,cis-isomer the distance amounts to 11.3 Å. The replace of the isopropyl groups by recognition units and the enlargement of the two linkers, which makes a shielding of a guest from the environment

2,3-Dibutoxynaphthalene-based tetralactam macrocycles for recognizing precious metal chloride complexes

• Li-Li Wang,
• Yi-Kuan Tu,
• Huan Yao and
• Wei Jiang

Beilstein J. Org. Chem. 2019, 15, 1460–1467, doi:10.3762/bjoc.15.146

• File 1). Conclusion In summary, we reported the synthesis of two new tetralactam macrocycles with 2,3-dibutoxynaphthalenes as the sidewalls. The macrocycle with isophthalamide as the linkers is able to bind chloride ions and precious metal chloride complexes in nonpolar solvent, while the macrocycle

Synthesis of dipolar molecular rotors as linkers for metal-organic frameworks

• Sebastian Hamer,
• Fynn Röhricht,
• Marius Jakoby,
• Ian A. Howard,
• Xianghui Zhang,
• Christian Näther and
• Rainer Herges

Beilstein J. Org. Chem. 2019, 15, 1331–1338, doi:10.3762/bjoc.15.132

• linkers in MOFs with potential applications as ferroelectric materials and for optical signal processing. Keywords: benzothiadiazole; dipolar rotor; fluorescence; large dipole moment; metal organic framework linker; Introduction Rotors are among the fundamental functional units in engineering in our

• compromise between the size and dipole moment of the rotor/linker has to be aimed at, and care has to be taken that the rotational barriers are as low as possible. Figure 1 shows the interaction of a pair of dipolar rotors with parallel axes at a distance of 10 Å, which is a typical distance of the linkers

• . We interpret these data as the lower limits of the rotational barriers in a MOF environment. Interactions with other linkers or neighbouring dipoles probably will increase the barriers. The dipole moments of the cyano-substituted rotors are considerably higher than those with fluoride substitution

Insertion of [1.1.1]propellane into aromatic disulfides

• Robin M. Bär,
• Gregor Heinrich,
• Martin Nieger,
• Olaf Fuhr and
• Stefan Bräse

Beilstein J. Org. Chem. 2019, 15, 1172–1180, doi:10.3762/bjoc.15.114

• , 76344 Eggenstein-Leopoldshafen, Germany 10.3762/bjoc.15.114 Abstract Herein we present the synthesis of symmetrically and unsymmetrically substituted 1,3-bissulfanylbicyclo[1.1.1]pentanes from disulfides and [1.1.1]propellane. Bicyclo[1.1.1]pentanes (BCPs) recently gained interest as rigid linkers and

• in most cases. Single crystal X-ray diffraction analysis confirms the rod-like structure of the [2]staffanes that is often required in material applications. Keywords: bicyclo[1.1.1]pentane; bioisosteres; disulfides; linkers; [1.1.1]propellane; Introduction Rigid structures are emerging in both

Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection

• Shahien Shahsavari,
• Dhananjani N. A. M. Eriyagama,
• Bhaskar Halami,
• Vagarshak Begoyan,
• Marina Tanasova,
• Jinsen Chen and
• Shiyue Fang

Beilstein J. Org. Chem. 2019, 15, 1116–1128, doi:10.3762/bjoc.15.108

• linkers for ODN synthesis [40][41]. Due to the low acidity of H-2 (pKa ≈31) in the Dmoc function, these groups and linkers were expected to be stable under ODN synthesis conditions. However, once the dithioketal in the group is oxidized, the acidity of H-2 (pKa ≈12) is drastically increased [42][43

• ]. Considering that the widely used Fmoc protecting group, of which the H-9 has a pKa of ≈22 [42], can be readily removed with a weak base such as piperidine, we hypothesized that the oxidized Dmoc groups and linkers could be cleaved under weakly basic and non-nucleophilic conditions via β-elimination. Indeed

New α- and β-cyclodextrin derivatives with cinchona alkaloids used in asymmetric organocatalytic reactions

• Iveta Chena Tichá,
• Simona Hybelbauerová and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2019, 15, 830–839, doi:10.3762/bjoc.15.80

• as the promoter (not in a catalytic amount) of a Henry reaction and obtained the product with 99% ee. Subsequently, Doyagüez et al. [17] attached L-proline to β-CD via different linkers (including a triazole linker) and used the resulting organocatalysts in an aldol reaction in water, albeit with a

Tuning the stability of alkoxyisopropyl protection groups

• Zehong Liang,
• Henna Koivikko,
• Mikko Oivanen and
• Petri Heinonen

Beilstein J. Org. Chem. 2019, 15, 746–751, doi:10.3762/bjoc.15.70

• applications, where easily cleavable linkers are needed [1]. The stability and properties of acetals/ketals widely varies depending on their structure, which widens the scope of their applicability. The acid lability is increased markedly by attaching electron-donating alkyl groups on the acetal carbon. The

Polyaminoazide mixtures for the synthesis of pH-responsive calixarene nanosponges

• Antonella Di Vincenzo,
• Antonio Palumbo Piccionello,
• Alberto Spinella,
• Delia Chillura Martino,
• Marco Russo and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2019, 15, 633–641, doi:10.3762/bjoc.15.59

• -triazol-1-yl)alkylidene chains as the linkers between the calixarene monomer units. Even these materials were proven effective in sequestrating organic model pollutants, such as p-nitroaniline derivatives or dyes, from aqueous solution. However, their synthesis required much longer times in comparison

Design and synthesis of multivalent α-1,2-trimannose-linked bioerodible microparticles for applications in immune response studies of Leishmania major infection

• Chelsea L. Rintelmann,
• Tara Grinnage-Pulley,
• Kathleen Ross,
• Daniel E. K. Kabotso,
• Angela Toepp,
• Anne Cowell,
• Christine Petersen,
• Balaji Narasimhan and
• Nicola Pohl

Beilstein J. Org. Chem. 2019, 15, 623–632, doi:10.3762/bjoc.15.58

• stable to acidic and basic conditions, but incompatible with reducing conditions. To conserve the relatively expensive TAMRA fluorophore and prevent loss through the synthetic sequence, amino linkers were first conjugated to the dendrimer core. The Nα-Fmoc group of 19 was first removed and coupled to Nε

LCST phase behavior of benzo-21-crown-7 with different alkyl chains

• Yan Deng,
• Xing Li,
• Qiao Zhang,
• Zheng Luo,
• Chengyou Han and
• Shengyi Dong

Beilstein J. Org. Chem. 2019, 15, 437–444, doi:10.3762/bjoc.15.38

• and molecular structures. Results and Discussion Two series of B21C7s, comprising carbamate-based linkers 3a–e and urea-based linkers 5a–e, were designed and synthesized, as shown in Scheme 1 and Scheme 2. All structures were confirmed by NMR spectroscopy and high-resolution mass spectrometry (details

• between the amine groups and isocyanate units (yields, 44.6–76.5%), or between hydroxy groups and isocyanate units (yields, 57.4–84.9%), respectively. We also investigated the role of linkages in LCST behavior by the introduction of urea-based and carbamate-based linkers. The water solubility of the

• ethers with urea-based linkers show higher water solubility (5a–e), compared to crown ethers with carbamate-based linkers (3a–e). As amide groups are more hydrophilic compared with ester groups, it is reasonable that 5a–e show stronger hydration effects and exhibit a larger water-accessible surface area

First synthesis of cryptands with sucrose scaffold

• Patrycja Sokołowska,
• Michał Kowalski and
• Sławomir Jarosz

Beilstein J. Org. Chem. 2019, 15, 210–217, doi:10.3762/bjoc.15.20

• -O-benzyl-sucrose). The latter approach is probably more convenient since it allows preparing cryptands of various size of cavity just by simple elongation of all three terminal positions with linkers of different size. In our model studies we have elongated these positions with the same linker

• . However, since all three terminal positions can be differentiated (as we have proven during our earlier studies see ref. [10]), it is possible to introduce different linkers at the C1’, C6, and C6’ fragments. Thus, our first syntheses of cryptands from ‘sucrose triol’ may open a possibility to prepare

Synthesis of a tubugi-1-toxin conjugate by a modulizable disulfide linker system with a neuropeptide Y analogue showing selectivity for hY1R-overexpressing tumor cells

• Rainer Kufka,
• Robert Rennert,
• Goran N. Kaluđerović,
• Lutz Weber,
• Wolfgang Richter and
• Ludger A. Wessjohann

Beilstein J. Org. Chem. 2019, 15, 96–105, doi:10.3762/bjoc.15.11

• synthesis of suitable linkers is a task of crucial importance and synthetic challenge that still is underestimated by many entering the field. The most promising PDC payloads, often also referred to as ‘warheads’, are toxins of limited molecular size but with outstanding potency in the picomolar or lower

• of linkers are unsuitable, as they rendered the peptide inactive (results not shown). However, disulfide-bonded linkers retained activity, presumably by cleavage in the reductive milieu of cancer cells, if connected via a short ester or amide linkage at the C-terminus. The retrosynthetic analysis

• disulfide linkage was chosen for the tubugi-1 coupling to the peptide moiety due to own promising preliminary work. Several linker chemistries were tested with tubulysin-like peptides – amongst them amide and ester linkers, hydrazone linker, VC linker etc. – the disulfide linker described herein, however

Selective ring-opening metathesis polymerization (ROMP) of cyclobutenes. Unsymmetrical ladderphane containing polycyclobutene and polynorbornene strands

• Yuan-Zhen Ke,
• Shou-Ling Huang,
• Guoqiao Lai and
• Tien-Yau Luh

Beilstein J. Org. Chem. 2019, 15, 44–51, doi:10.3762/bjoc.15.4

• ][8][9][10][11][12][13][14][15] or from biscyclobutene [16] linked with a range of different rigid linkers. When a flexible linker is used, bisnorbornene derivatives undergo cascade metathetical cyclopolymerization giving the corresponding polynorbornenes with hammock-like pendants [17][18

The design and synthesis of an antibacterial phenothiazine–siderophore conjugate

• Abed Tarapdar,
• James K. S. Norris,
• Oliver Sampson,
• Galina Mukamolova and
• James T. Hodgkinson

Beilstein J. Org. Chem. 2018, 14, 2646–2650, doi:10.3762/bjoc.14.242

• -cleavable linker. A polyethylene glycol (PEG) linker was selected as PEG linkers demonstrate enhanced water solubility in comparison to alkyl chain linkers. We then had to make a decision on the position of attachment for the PEG linker to compound 1. For siderophore conjugates, it is crucial that the

Applications of organocatalysed visible-light photoredox reactions for medicinal chemistry

• Michael K. Bogdos,
• Emmanuel Pinard and
• John A. Murphy

Beilstein J. Org. Chem. 2018, 14, 2035–2064, doi:10.3762/bjoc.14.179

• . Naturally occurring amino acids, e.g., glycine, are often used in medicinal chemistry as linkers, structural components of scaffolds or even as precursors to useful building blocks. Wallentin and co-workers have described a method for the reductive decarboxylation of amino acids, using bis(4-chlorophenyl

• identical nature of the substituents on the product. This severely limits its potential applications, and the usefulness of this protocol is likely limited to the creation of linkers or pendant groups. Benzo-fused five-membered heterocycles also find widespread use in medicinal chemistry, with indoles

Coordination-driven self-assembly vs dynamic covalent chemistry: versatile methods for the synthesis of molecular metallarectangles

• Li-Li Ma,
• Jia-Qin Han,
• Wei-Guo Jia and
• Ying-Feng Han

Beilstein J. Org. Chem. 2018, 14, 2027–2034, doi:10.3762/bjoc.14.178

• and metallacages [6][7][8][9]. Following this approach, two self-assembled metallarectangles with different bridging linkers 3a,b were synthesized by utilizing the [Cp*2Rh2(μ-η2-η2-C2O4)Cl2] unit as molecular clips (Scheme 1, method A). Precursor complex 1, which bears two labile triflato ligands was

Chiral bisoxazoline ligands designed to stabilize bimetallic complexes

• Deepankar Das,
• Rudrajit Mal,
• Nisha Mittal,
• Zhengbo Zhu,
• Thomas J. Emge and
• Daniel Seidel

Beilstein J. Org. Chem. 2018, 14, 2002–2011, doi:10.3762/bjoc.14.175

• available. This led to the selection of naphthyridine, pyridazine, pyrazole, and phenol building blocks. We opted to connect these linkers to oxazolines via amide bonds. The reasoning for this was twofold. Firstly, this should provide ligands with significantly improved stabilities over for instance imine

• linkers. In addition, each amide moiety, upon deprotonation (a requirement for complex formation), would provide a formal negative charge on the ligand, thus resulting in increased complex stability while reducing the number of spectator anions associated with the two metals. Different combinations of

• contrast, a distorted square pyramidal binding mode is observed for Zn(2). Phenol-bridged bisoxazoline ligands. Ligands incorporating naphthyridine, pyridazine and pyrazole linkers discussed thus far bridge two metal atoms by attachment to two different nitrogen donor atoms. As a result, metal∙∙∙metal