Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• intensities of absorption or emission at two wavelengths minimizes the error from the physical or chemical fluctuations in the sample. Conventional peptide probes based on environment-sensitive fluorophores [20][21][22], fluorescence resonance energy transfer (FRET) pairs [13] and pyrene excimer/monomer [23

• ]. The attachment of pyrenes to the termini of a flexible peptide linker results in a ratiometric fluorescent probe (Figure 1C). Upon interaction with a biomolecule, the distance between the pyrenes changes, subsequently their monomer to excimer and vice versa fluorescence signal changes. However, the

• excimer (490 nm) to monomer emission (406 nm, Figure 3B). Thus, monitoring the relative fluorescence intensities at two wavelengths (F406/F490) allowed the ratiometric detection of nucleic acids. Schmuck et al. reported a similar cationic peptide beacon 3 coupled with a FRET pair, a naphthalene donor and

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

• Jennifer Frommer and
• Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

• , functionalized phosphoramidite building blocks of all four nucleosides are highly desired. The number of commercially available RNA phosphoramidites that carry a suitable functionality for post-synthetic attachment of dyes, reporter groups or other conjugates is still rather limited. In particular, monomer

• charge transfer [23][24]. In the course of monomer synthesis, we encountered unexpected results regarding the reactivity and selectivity of the two secondary hydroxy groups of the adenosine derivative 7 (Scheme 1) in the silylation step, leading to non-satisfactory overall reaction yields. Therefore, the

Using multiple self-sorting for switching functions in discrete multicomponent systems

• Amit Ghosh and
• Michael Schmittel

Beilstein J. Org. Chem. 2020, 16, 2831–2853, doi:10.3762/bjoc.16.233

• of various similar molecules. Similarly, Shi controlled a conversion between helicates and a tetrahedral cage by varying the radius of the metal ion (Hg2+ vs Fe2+) [55]. They reported on the self-assembly of the monomer 20, encompassing the quadruple DDAA hydrogen-bonding arrays and 2,2’-bipyridine

• hydrogen-bonded octameric and tetrameric tubes. (c) A representation of the complex mixture after combining the monomers 5 and 6 in CDCl3. (d) The partial separation of the mixture upon the selective C60 complexation by monomer 5. The guest-induced rearrangement results in an incomplete self-sorted mixture

• four-component sandwich complex [Cu2(16)(17)(18)]2+. a) Chemical structure of the monomer 20 with its quadruple hydrogen-bonding array and a metal-affine 2,2’-bipyridine unit. b) Conversion of the helicate [Hg2(20)6]4+ to the S4-cage [Fe4(20)12]8+ and [Hg2(20)2]4+ based on double self-sorting

Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

• Henrik Hupatz,
• Marius Gaedke,
• Hendrik V. Schröder,
• Julia Beerhues,
• Arto Valkonen,
• Fabian Klautzsch,
• Sebastian Müller,
• Felix Witte,
• Kari Rissanen,
• Biprajit Sarkar and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2020, 16, 2576–2588, doi:10.3762/bjoc.16.209

• NDI monomer between 300 and 380 nm (Figure 4a–c, black) [59]. A weak charge-transfer band at ≈450 nm is observed for the free macrocycle NDIC7 (Figure 4a, black), which is most likely caused by an intramolecularly folded naphthalene–NDI complex in solution, similar to the crystal structure. In

A new method for the synthesis of diamantane by hydroisomerization of binor-S on treatment with sulfuric acid

• Rishat I. Aminov and
• Ravil I. Khusnutdinov

Beilstein J. Org. Chem. 2020, 16, 2534–2539, doi:10.3762/bjoc.16.205

• diamondoid homologous series, which is produced on an industrial scale (prepared by AlBr3 or AlCl3-induced skeletal isomerization of a petrochemical monomer, hydrogenated dicyclopentadiene) [1], have been studied rather extensively, the chemical behavior of diamantane, the second member of the diamandoid

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• manually compiled dictionary that translates the PDB Chemical Component Dictionary [62] three-letter codes of carbohydrate monomer definitions found in the structure files into WURCS definitions of unique monomers (described as “UniqueRES” [52]). The WURCS notations are generated for all detected glycans

• model by renaming one of the fucose residues from FUL to FUC due to an anomer mismatch between the three letter code and the actual coordinates of the monomer. The new model thus generated the GlyTouCan ID G21290RB, which in turn could be matched to the GlyConnect ID 54. Under further manual review of

Dawn of a new era in industrial photochemistry: the scale-up of micro- and mesostructured photoreactors

• Emine Kayahan,
• Mathias Jacobs,
• Leen Braeken,
• Leen C.J. Thomassen,
• Simon Kuhn,
• Tom van Gerven and
• M. Enis Leblebici

Beilstein J. Org. Chem. 2020, 16, 2484–2504, doi:10.3762/bjoc.16.202

Hierarchically assembled helicates as reaction platform – from stoichiometric Diels–Alder reactions to enamine catalysis

• David Van Craen,
• Jenny Begall,
• Johannes Großkurth,
• Leonard Himmel,
• Oliver Linnenberg,
• Elisabeth Isaak and
• Markus Albrecht

Beilstein J. Org. Chem. 2020, 16, 2338–2345, doi:10.3762/bjoc.16.195

• of the stereoselectivity of the Diels–Alder reaction. In THF the stereochemically locked dimer of the hierarchical helicate was present. Here stereoselectivity was turned on. On the other hand, the highly dynamic and fast diastereomerizing/epimerizing monomer was the major species in DMF switching

• or rigid chiral ligands. In addition, a solvent screening was performed in which solvents were used which favor the dimer. This is imminent for good enantioselectivities because the presence of a high amount of stereolabile monomer switches off the selectivity [13]. Solvent dependence Initially the

• capability of the solvent resulting in a higher proportion of the monomer and thus in lower stereoselectivities. In contrast to this, less polar solvents such as dichloromethane and chloroform resulted in increasing stereoselectivities in the Diels–Alder reaction due to their poor ability to stabilize

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• chromophores, the intrinsic CD spectrum of compound 4 at the 220–400 nm range is negligible. Further, for the analysis of the CD results we compared our data with those published for a close NDI-monomer analogue [26][27], whereby the strong positive ICD band at 270–280 nm was attributed to the intercalation of

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• offsetting a charge repulsion of the extra lysine residues, and thus allowing the formation of stable cationic nanofibers. These nanoaggregates, assembled from the monomer 16, are efficient gene transfection vectors. However, the control peptide 17, which cannot self-assemble into nanotubes, shows negative

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• galactofuranose (Galf) residues linked by alternating β-(1→5)- and β-(1→6)-glycosidic bonds [4]. The Galf monomer is restricted to some bacteria, fungi and a few protozoan species, and it seems to be absent in humans [5]. The enzymes participating in the galactan build-up could thus be considered as potential

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

• cysteines are converted quantitively to disulfides by oxidation with oxygen. Until fully oxidized library members can exchange building blocks in a thiol–disulfide exchange reaction. While a closed monomer can be observed in the beginning (Figure S1, Supporting Information File 1), exclusively cyclic

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

• in the review (see Section 4). Some example methods of immobilising catalysts include covalently bonding the catalyst to a polymer support either by incorporating a monomer with a photocatalytic moiety or post synthetically coupling a photocatalyst to a polymer via direct synthesis. Examples of this

• from our own group include the synthesis of a polystyrene gel with a photocatalytic cross-linking monomer, 4,7-bis(4-vinylphenyl)benzo[c][1,2,5]thiadiazole (St-BTZ) [47]. Additionally, we showed the direct synthesis of a BODIPY photocatalyst as a postsynthetic modification to an aldehyde-functionalised

• solubilising monomers with the same St-BTZ photocatalyst monomer previously reported by Vilela and co-workers [47][139]. They showed that the supported photocatalyst material was an effective HPCat for pharmaceutically relevant transformations in the optimal solvent for the reaction, despite the native

Recent applications of porphyrins as photocatalysts in organic synthesis: batch and continuous flow approaches

• Rodrigo Costa e Silva,
• Luely Oliveira da Silva,
• Aloisio de Andrade Bartolomeu,
• Timothy John Brocksom and
• Kleber Thiago de Oliveira

Beilstein J. Org. Chem. 2020, 16, 917–955, doi:10.3762/bjoc.16.83

• brominated tin porphyrin (SnTBPP) as monomer (Scheme 47). The irradiation of this material in the presence of both sulfides and molecular oxygen furnished a variety of sulfoxides in 70–97% yields. The SnPor@PAF presented the same photocatalytic activity of its monomer (SnTBPP) with the advantage of its easy

Aldehydes as powerful initiators for photochemical transformations

• Maria A. Theodoropoulou,
• Nikolaos F. Nikitas and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2020, 16, 833–857, doi:10.3762/bjoc.16.76

• acetone (4) and formaldehyde (35) in initiating the photografting in an aqueous solution. The maximum extent of grafting was observed for 10 wt % of 36. The concentration of 42 also affected the extent of photografting. The extent of grafting increased with the increase of the monomer up to 2 mol/L and

• carried out, indicating that the polymerization of MAA (42) was mainly induced by photoinitiation by the aliphatic ketones 44 or formaldehyde (35), rather than by self-initiation of the monomer. Furthermore, oxygen was shown to strongly inhibit the photopolymerization, and an increase in the UV intensity

• increased the percentage of conversion and the polymerization rate. Finally, the percentage of conversion decreased, whereas the polymerization rate increased with an increase of the initial monomer concentration since an increase in the concentration of the monomer led to MAA (42) absorbing more energy

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

• band positions were seen for the symmetric zinc dimer 9, the unsymmetrical dimer 16 and the zinc monomer 14 at 431 (23202), 432 (23149) and 433 (23095) nm (cm−1) in CHCl3, respectively (Figure 6). A similar Soret band for both the dimer and monomer 9 and 14 suggested that the two subunits in the dimer

• bands observed for the zinc dimer and monomer had low full-width at half-maxima (FWHM) of ≈26 nm (3.85 × 105 cm−1), i.e., a narrow band, the zinc-nickel dimer 16 exhibited a high FWHM of ≈50 nm (2 × 105 cm−1), potentially caused by overlapping of the nickel and zinc porphyrin Q bands which could be due

• dimers and 8 nm (1.25 × 106 cm−1) for the monomer. The difference in properties of the unsymmetric zinc-nickel dimer 16 is observed significantly more in the corresponding fluorescence emission spectrum (Figure 7). The emission observed for the zinc monomer and dimer, 14 and 9, respectively, was

KOt-Bu-promoted selective ring-opening N-alkylation of 2-oxazolines to access 2-aminoethyl acetates and N-substituted thiazolidinones

• Qiao Lin,
• Shiling Zhang and
• Bin Li

Beilstein J. Org. Chem. 2020, 16, 492–501, doi:10.3762/bjoc.16.44

• proceeded well with heterocycle-containing chlorides such as 2-chloro-5-(chloromethyl)thiophene (4e), leading to 2-aminoethyl acetate product 3k in 66% yield which has potential as bifunctional monomer for polymerization. Furthermore, oxazole derivative 2,4,4-trimethyl-4,5-dihydrooxazole (2b) was also

Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0

• Bernd Strehmel,
• Christian Schmitz,
• Ceren Kütahya,
• Yulian Pang,
• Anke Drewitz and
• Heinz Mustroph

Beilstein J. Org. Chem. 2020, 16, 415–444, doi:10.3762/bjoc.16.40

• molar masses and narrow molecular weight distributions. These techniques allow linear increase of molar mass by time and monomer conversion and low dispersity (principally between 1.2 to 1.5). The most common methods of controlled radical polymerization are namely the nitroxide-mediated radical

• metal ions. In this process, basically, in the presence of photoactive materials (PAs) such as photoinitiators, photosensitizers or photoredox catalysts, the photoexcitation of a photoredox system results in formation of reactive radicals. Those reactive radicals add monomer and the polymerization

• presented for in situ generation of Cu(I) to initiate the polymerization with the alkyl bromide. In this system, the Cu(II) complex was exposed to UV light to form Cu(I) which can react with alkyl halide resulting in generation of reactive radicals and Cu(II), Scheme 9. Those reactive radicals add monomer

Room-temperature Pd/Ag direct arylation enabled by a radical pathway

• Amy L. Mayhugh and
• Christine K. Luscombe

Beilstein J. Org. Chem. 2020, 16, 384–390, doi:10.3762/bjoc.16.36

• . Results and Discussion Initial attempts to polymerize iodoindole monomer 1 using the reported conditions (Scheme 1) produced oligomers with an unanticipated coupling pattern in good yield (87%, Figure 1, Supporting Information File 1, Figure S3). The 1H NMR signals from the C2-H, C3-H on the pyrrole ring

• for a radical mechanism. Moreover, the observed behavior appears to be common between the iodoindole monomer and iodobenzene/indole system, rather than a phenomenon unique to an electron-rich iodoindole. The growing evidence for a phenyl radical in the catalytic cycle is in contrast to the typically

• that proceed under mild conditions, improving energy requirements and scalability. Work is ongoing to leverage this insight into new direct arylation methods utilizing palladium-involved radicals. 1H NMR (500 MHz, CDCl3) of (a) 5-iodo-1-octylindole monomer (b) PIn prepared according to conditions in

Formal preparation of regioregular and alternating thiophene–thiophene copolymers bearing different substituents

• Atsunori Mori,
• Keisuke Fujita,
• Chihiro Kubota,
• Toyoko Suzuki,
• Kentaro Okano,
• Takuya Matsumoto,
• Takashi Nishino and
• Masaki Horie

Beilstein J. Org. Chem. 2020, 16, 317–324, doi:10.3762/bjoc.16.31

• a monomer. Nickel-catalyzed polymerization of bithiophene with substituents at the 3-position, including alkyl-, fluoroalkyl-, or oligosiloxane-containing groups, afforded the corresponding copolymers in good to excellent yield. The solubility test in organic solvents was performed to reveal that

• to afford the regioregular polythiophene in which 2,5-dihalo-3-substituted thiophene 1 is employed as a monomer precursor, converting to the corresponding organometallic monomer by a halogen−magnesium exchange reaction with a Grignard reagent. The employment of 1 leading to polythiophene has been

• shown to proceed in a dehalogenative manner [3]. We have recently shown that the generation of the organometallic monomer species can alternatively also be achieved by deprotonation, using 2-halo-3-substituted thiophene 2 or 3 with a bulky magnesium amide Knochel–Hauser base (TMPMgCl⋅LiCl) [7], followed

Copper-promoted/copper-catalyzed trifluoromethylselenolation reactions

• Clément Ghiazza and
• Anis Tlili

Beilstein J. Org. Chem. 2020, 16, 305–316, doi:10.3762/bjoc.16.30

• ]. Noteworthy, depending on the nature of the bidentate ligand used, the corresponding copper complex could be isolated as monomer or dimer, and both were air-stable. Among the new complexes, the reactivity of [(bpy)CuSeCF3]2 in trifluoromethylselenolations was thoroughly investigated using a large panel of

Reversible photoswitching of the DNA-binding properties of styrylquinolizinium derivatives through photochromic [2 + 2] cycloaddition and cycloreversion

• Sarah Kölsch,
• Heiko Ihmels,
• Jochen Mattay,
• Norbert Sewald and
• Brian O. Patrick

Beilstein J. Org. Chem. 2020, 16, 111–124, doi:10.3762/bjoc.16.13

• identify possible primary photoprocesses (Figure 7A). The initial maximum of the monomer 3b decreased substantially by approximately half within a second, whereas further reaction was indicated by the appearance of the absorption maximum of 4b at 317–331 nm. Notably, no additional intermediate absorption

• cyclobutane 4b at 315 nm in H2O, the monomer 3b formed, as indicated by the development of its characteristic absorption band (Figure 7B). After 30 min, the reaction was almost complete, however, dimer 4b still remained in solution in the photostationary state. Interactions of the photodimer 4b with DNA The

• absorption and CD spectroscopy (Figure 10). In the course of the photoreaction, the formation of 3b was indicated by the emergence of its characteristic long-wavelength absorption band, whose shape and shift matched its DNA-bound form. The association of the released monomer 3b with DNA was also clearly

Carbazole-functionalized hyper-cross-linked polymers for CO₂ uptake based on Friedel–Crafts polymerization on 9-phenylcarbazole

• Dandan Fang,
• Xiaodong Li,
• Meishuai Zou,
• Xiaoyan Guo and
• Aijuan Zhang

Beilstein J. Org. Chem. 2019, 15, 2856–2863, doi:10.3762/bjoc.15.279

• polymers (HCPs), a series of 9-phenylcarbazole (9-PCz) HCPs (P1–P11) has been made by changing the molar ratio of cross-linker to monomer, the reaction temperature T1, the used amount of catalyst and the concentration of reactants. Fourier transform infrared spectroscopy was utilized to characterize the

• structure of the obtained polymers. The TG analysis of the HCPs showed good thermal stability. More importantly, a comparative study on the porosity revealed that: the molar ratio of cross-linker to monomer was the main influence factor of the BET specific surface area. Increasing the reaction temperature

• outstanding porous properties. Studies of the effects on porosity of HCPs are significant, but almost all investigations focused on the role of monomer length and geometry on the porosity [6][19][20][21][22][23][24][25][26][27][28][29][30][31][32]. Researchers have synthesized a series of carbazole-based

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

• analogue of the formula [Fe{C5H4COO(CH2)3 C≡}2]2 in a ratio of approximately 4:1. Related NMR spectra can be found in Supporting Information File 1 (Figures S9 and S10). Separation of the monomer 2b could be achieved with column chromatography on silica gel with a yield of 53%. The ring-closed dimer

• remained in a mixture with excess monomer. Single crystals of compound 2b suitable for X-ray diffraction analysis could be obtained at room temperature from a DCM or CDCl3 solution layered with hexane, respectively. An ORTEP drawing of 2b is shown in Figure 6. The ferrocenophane crystallises in the

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

• , 12-mer long sequences are a suitable starting point for our preliminary tests. An overview of all the sequences of this study can be found in Table 1 and Table 2. Contrary to the previous synthetic approach of azobenzene-containing PNAs [35][36][41], in which the preformed monomer building block was

• , the large separation between the n → π* bands of the trans and the cis-forms (Δλ = 69 nm; Figure S24, Supporting Information File 1) did not lead to the quasi-quantitative conversion for the cis-isomer, as for the photoswitchable PNA monomer 1 and the molecular transducer [43][46]. This slightly lower

• cis-form did not show any decomposition under these conditions (Figure S27C, Supporting Information File 1), unlike when the oF4Azo was grafted onto a pyrrole scaffold [48]. Next, we explored if the inclusion of oF4Azo as monomer surrogate within the PNA sequence could affect its hybridization to a