Applications of microscopy and small angle scattering techniques for the characterisation of supramolecular gels

• Connor R. M. MacDonald and
• Emily R. Draper

Beilstein J. Org. Chem. 2024, 20, 2608–2634, doi:10.3762/bjoc.20.220

• structures. Some of the key features and capabilities of these techniques are summarised in Table 1. CLSM is a fluorescence microscopy technique capable of acquiring high-resolution optical images at selected depths of the sample. This is achieved by exciting compounds with laser light and, by using a

• pinhole to select focal planes, allows fluorescence at various depths to be focused and imaged. The resulting 2D focal plane images can be stacked to yield a 3D fluorescence image of high resolution, allowing complex morphologies to be visualised (Figure 2) [11]. While CLSM provides in situ 3D imaging

• attached to the molecules themselves or is interacting with them. Introducing fluorescent dyes to self-assembling systems affects their chemical and mechanical stability as the hydrophobic features can destabilise the self-assembled network [18]. This reliance on fluorescence labels or dyes leading to a

Anion-dependent ion-pairing assemblies of triazatriangulenium cation that interferes with stacking structures

• Yohei Haketa,
• Takuma Matsuda and
• Hiromitsu Maeda

Beilstein J. Org. Chem. 2024, 20, 2567–2576, doi:10.3762/bjoc.20.215

• desorption ionization time-of-flight mass spectrometry (MALDI–TOF MS). The synthesized ion pairs showed similar electronic properties in solution state. In CH3CN, 2+-BF4− exhibited UV–vis absorptions at 273, 350, and 524 nm and fluorescence emission at 607 nm upon excitation at 524 nm. The absorption band at

• spectra were referenced to residual solvent. UV–visible absorption spectra were recorded on a Hitachi U-4500 spectrometer. Fluorescence spectra were recorded on a Hitachi F-4500 fluorescence spectrometer. MALDI–TOF MS was recorded on a Shimadzu Axima-CFRplus. TLC analyses were carried out on aluminum

Photoredox-catalyzed intramolecular nucleophilic amidation of alkenes with β-lactams

• Valentina Giraldi,
• Giandomenico Magagnano,
• Daria Giacomini,
• Pier Giorgio Cozzi and
• Andrea Gualandi

Beilstein J. Org. Chem. 2024, 20, 2461–2468, doi:10.3762/bjoc.20.210

• the cis-isomer. The optimal PC for the reaction was acridinium salt IV (Table 1, entry 1), while the Fukuzumi catalyst (I), commonly employed by Nicewicz et al., was less effective (Table 1, entry 9). 3CzClIPN, an organic dye belonging to the class of thermally activated delayed fluorescence (TADF

Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers

• Andreas Wiest and
• Pavel Kielkowski

Beilstein J. Org. Chem. 2024, 20, 2323–2341, doi:10.3762/bjoc.20.199

• -PAGE) and visualized by in-gel fluorescence scanning (Figure 6A). In this approach the tag is a suitable fluorophore. Previously, during an introduction period of a chemical proteomics workflow of activity-based protein profiling (ABPP), the resulting fluorescent bands might be simply cut out from the

• gel and subjected to MS analysis to identify the labeled proteins [77][78]. The in-gel analysis is often used for target validation with corresponding protein mutants or knockout cell lines, with loss of the identified probe–protein interaction leading to disappearance of the fluorescence band from

• the TAMRA-azide yields a mixture of labeled and unlabeled proteins. The proteins are then separated on SDS-PAGE by their molecular weight and fluorescence of the labeled proteins is recorded (Figure 6A). Due to the high sensitivity of fluorescence read-out, this allows to identify protein labeling

Cell-free protein synthesis with technical additives – expanding the parameter space of in vitro gene expression

• Tabea Bartsch,
• Stephan Lütz and
• Katrin Rosenthal

Beilstein J. Org. Chem. 2024, 20, 2242–2253, doi:10.3762/bjoc.20.192

• workflows [45]) and performance evaluation. This is convenient because product formation and even concentration can be easily quantified measuring the fluorescence intensity. To take advantage of this, fusion proteins with sfGFP can be constructed for CFPS performance evaluation [46]. Therefore, sfGFP was

• increase the synthesis yield, but the general influence of all additives will be investigated. Figure 1 shows the results of sfGFP synthesis with different technical additives. All values were normalized in relation to the fluorescence intensity of the reference with 2% PEG-8000. Macromolecular crowding is

• , as it provides a simple and robust readout, the fluorescence signal. As a result, the composition of the CFPS solution is optimized for the synthesis of GFP. In addition, larger and more complex enzymes are usually more difficult to synthesize with CFPS [56], although there are exceptions, such as

Metal-free double azide addition to strained alkynes of an octadehydrodibenzo[12]annulene derivative with electron-withdrawing substituents

• Naoki Takeda,
• Shuichi Akasaka,
• Susumu Kawauchi and
• Tsuyoshi Michinobu

Beilstein J. Org. Chem. 2024, 20, 2234–2241, doi:10.3762/bjoc.20.191

• addition. Thus, compound 6a shows an ultraviolet absorption peak at 249 nm (λmax) and no absorption in the visible region was observed. When excited at 249 nm, an emission band at 513 nm (λem) appeared in the spectrum with a fluorescence quantum yield (Φ) of 7.0%. The absorption and fluorescence spectra

• the double benzyl azide adduct of DBA-OHex was 21900 cm−1 and larger than that of 6a (20700 cm−1), the Φ was 4.3%. This result suggested that replacing the hexyloxy substituents with electron-withdrawing ones enhanced the fluorescence intensity by approximately 1.6 times. Crosslinker application Using

• previously reported electron-donating hexyloxy substituents. The addition pattern was experimentally investigated by 2D NMR, which was also supported by DFT calculations. The bistriazole product displayed fluorescence in the visible range with a fluorescence quantum yield of 7.0%. Finally, the developed

Novel truxene-based dipyrromethanes (DPMs): synthesis, spectroscopic characterization and photophysical properties

• Shakeel Alvi and
• Rashid Ali

Beilstein J. Org. Chem. 2024, 20, 2163–2170, doi:10.3762/bjoc.20.186

• –80%) along with their preliminary photophysical (absorption, emission and time resolved fluorescence lifetime) properties. The condensation reaction for assembling the required DPMs were catalyzed with trifluoroacetic acid (TFA) at 0 °C to room temperature (rt), and the stable dipyrromethanes were

• derivatives were successfully characterized and their structures were established by means of the 1H and 13C NMR spectroscopy, besides further confirmation by mass spectrometry (see Supporting Information File 1). The UV–vis absorption, emission and time-resolved fluorescence spectra Emission and absorption

• these compounds were found ranged from 350 to 508 nm, with a small shoulder in each case, which displays vibronic features (Figure 2). Exact values of the fluorescence maxima for these compounds are as follows: 12 (406.78, 428.93, and 457.04), 14 (406.42, 429.65, and 458.53), and 15 (406.42, 429.65, and

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• networks (NN), that allows the user to predict protein-glycan binding. Taking a glycan structure as input, this model is able to predict the strength of the interaction based on the relative fluorescence units (RFUs) measured in the Consortium for Functional Glycomics glycan arrays and extrapolating these

Cage-like microstructures via sequential Ugi reactions in aqueous emulsions

• Rita S. Alqubelat,
• Yaroslava A. Menzorova and
• Maxim A. Mironov

Beilstein J. Org. Chem. 2024, 20, 2078–2083, doi:10.3762/bjoc.20.179

• , which was monitored through the disappearance of isocyanide in the reaction medium using a color reaction [19]. Then the emulsion was applied to the glass surface and evaporated at a temperature of 50 °C. The resulting samples were analyzed using fluorescence microscopy at a wavelength of 490 nm. After

A new platform for the synthesis of diketopyrrolopyrrole derivatives via nucleophilic aromatic substitution reactions

• Vitor A. S. Almodovar and
• Augusto C. Tomé

Beilstein J. Org. Chem. 2024, 20, 1933–1939, doi:10.3762/bjoc.20.169

• region [3][4]. In turn, N-substituted DPP derivatives are soluble in common organic solvents, exhibit large molar extinction coefficients, Stokes shifts in the range of 10–70 nm and high fluorescence quantum yields [5][6][7]. Due to their outstanding photophysical properties, DPP-based dyes have been

• consistently displayed the protonated molecular ion [M + H]+ as the base peak. The UV–vis and fluorescence spectra of DPP derivatives 3a–f, 4a, 4d and 4f in DMF are presented in Figure 1, and their photophysical properties are summarized in Table 1. These compounds are highly fluorescent, and their UV–vis

• fluorescence quantum yields, ranging from 0.66 to 0.83, confirming their potential applications in fluorescence imaging, sensors, and optoelectronic devices. A comprehensive discussion of the potential uses of these fluorescent substances in areas such as materials science, biology, or chemistry may provide a

The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)

• Cristina Martini,
• Muhammad Idham Darussalam Mardjan and
• Andrea Basso

Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162

• on biological activities or photophysical properties (i.e., fluorescence) of GBB adducts. Another advantage is that, by replacing the amidine component (classically 2-aminopyridines) with other heterocycles, different scaffolds are obtained, and this is extremely efficient in diversity-oriented

• proof of concept, one of the GBB adducts was transformed into a N,C-palladacycle and was investigated as a potential catalyst for carbon–carbon bond-forming reactions. Furthermore, the authors studied in detail the fluorescence properties of the GBB adducts, that will be discussed in chapter 5. As

• economy (water was the only byproduct) and thermal stability as well as remarkable fluorescence properties. Multicomponent reaction can be also employed to prepare crystalline porous materials namely covalent organic frameworks (COFs). The structural diversity and functionality of COFs were assembled from

Synthesis and characterization of 1,2,3,4-naphthalene and anthracene diimides

• Adam D. Bass,
• Daniela Castellanos,
• Xavier A. Calicdan and
• Dennis D. Cao

Beilstein J. Org. Chem. 2024, 20, 1767–1772, doi:10.3762/bjoc.20.155

• has low fluorescence intensity (Φ = 0.006) [20], 7-Hex emits more efficiently with Φ = 0.41. Interestingly, 7-Ph has nearly no emission intensity, as evidenced by the low signal-to-noise ratio in the data and a near-zero quantum yield when excited at 400 nm. This fluorescence quenching is likely

Supramolecular assemblies of amphiphilic donor–acceptor Stenhouse adducts as macroscopic soft scaffolds

• Ka-Lung Hung,
• Leong-Hung Cheung,
• Yikun Ren,
• Ming-Hin Chau,
• Yan-Yi Lam,
• Takashi Kajitani and
• Franco King-Chi Leung

Beilstein J. Org. Chem. 2024, 20, 1590–1603, doi:10.3762/bjoc.20.142

• (150 mM) before white-light irradiation and (b) DA11, (d) DA7, and (f) DA6 after white-light irradiation for 60 min. Macroscopic soft DAn scaffolds fabricated by the shear-flow method. Images taken during fluorescence microscopy. Photographs of freshly prepared (a) DA11, (c) DA10, (e) DA7, and (g) DA6

• , merged image of bright field and fluorescence with hBM-MSCs after 3 days of incubation. Fluorescence images of live cells in (b) DA11, (d) DA10, (f) DA7, and (h) DA6 after 3 days of incubation to observe the cell affinity on the hydrogel surface. Scale bar: 200 μm, applied for all panels. The large

Generation of alkyl and acyl radicals by visible-light photoredox catalysis: direct activation of C–O bonds in organic transformations

• Mithu Roy,
• Bitan Sardar,
• Itu Mallick and
• Dipankar Srimani

Beilstein J. Org. Chem. 2024, 20, 1348–1375, doi:10.3762/bjoc.20.119

• was applicable to various carboxylic acids with electron-donating as well as electron-withdrawing substituents but unfortunately, aliphatic acids were not effective in this reaction. In addition, several control experiments, such as fluorescence quenching and Stern–Volmer studies, were done to analyze

Domino reactions of chromones with activated carbonyl compounds

• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 1256–1269, doi:10.3762/bjoc.20.108

• chromone 9a and for the diene containing a methoxy group (R4 = OMe). The products proved to be interesting, due to their blue fluorescence. 3-Formylchromones Dimethyl acetone-1,3-dicarboxylate The reaction of 3 with 3-formylchromones 10a–d afforded benzophenones 19a–d in moderate to good yields (Scheme 5

Synthesis and optical properties of bis- and tris-alkynyl-2-trifluoromethylquinolines

• Stefan Jopp,
• Franziska Spruner von Mertz,
• Peter Ehlers,
• Alexander Villinger and
• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 1246–1255, doi:10.3762/bjoc.20.107

• steady state absorption and fluorescence spectroscopy which give insights of the influence of the substitution pattern and of the type of substituents on the optical properties. Keywords: alkynes; catalysis; fluorescence; heterocycles; palladium; Introduction Quinoline is a well-known core structure

• –10°. Optical properties Steady-state absorption and fluorescence measurements were carried out. Compounds 6a, 9a, and 12a were selected to study the impact of the position of the alkynyl group on the optical properties. Comparison of the absorption and emission features of 12a, 12b and 12c gives

• and applied to palladium-catalysed Sonogashira reactions. Optimised reaction conditions allow the synthesis of various bis- or tris-alkynylated products in one step. Products were generally obtained in high yields and intensive fluorescence. The photophysical properties of selected compounds were

Mechanistic investigations of polyaza[7]helicene in photoredox and energy transfer catalysis

• Johannes Rocker,
• Till J. B. Zähringer,
• Matthias Schmitz,
• Till Opatz and
• Christoph Kerzig

Beilstein J. Org. Chem. 2024, 20, 1236–1245, doi:10.3762/bjoc.20.106

• potentials of Aza-H and the substrates and initial steady-state fluorescence quenching experiments (Scheme 1, left), but detailed mechanistic insights and direct evidence of the transient radical ions could not be obtained yet [45]. Figure 1A illustrates the absorption and emission spectra of Aza-H in MeCN

• radical ions of polyazahelicenes. The moderate fluorescence quantum yield of 48% (in MeCN) [46] implies that a non-emissive triplet-excited state (at room temperature) could also be generated via intersystem crossing, potentially initiating electron transfer reaction sequences. 77 K emission measurements

• were thus carried out and they showed short-lived fluorescence and long-lived emission (phosphorescence) that was assigned to the triplet state of Aza-H with an energy of 2.32 eV (Figure 1A). Quantum mechanical computations of the Aza-H triplet state yielded a triplet energy of 2.17 eV (adiabatic

Kinetically stabilized 1,3-diarylisobenzofurans and the possibility of preparing large, persistent isoacenofurans with unusually small HOMO–LUMO gaps

• Qian Liu and
• Glen P. Miller

Beilstein J. Org. Chem. 2024, 20, 1099–1110, doi:10.3762/bjoc.20.97

• isobenzofurans 2, 3 and 23 were studied by UV–vis and fluorescence spectroscopies (Figure 5). Compound 2 is devoid of ortho groups on its 1,3-diphenyl substituents and shows the longest wavelengths of absorption (λmax = 415 nm) and emission (emission λmax = 484 nm) in this series, consistent with a more highly

• -filled cuvette. Fluorescence spectra were measured on a FS5 spectrofluorometer (150 W CW Ozone-free xenon arc lamp) from Edinburgh Instruments. 1,3-Dimesitylisobenzofuran (3) To a round bottom flask was added 1,2-phenylenebis(mesitylmethanone) (21, 0.10 g, 0.27 mmol), zinc dust (0.70 g, 11 mmol) and 10

• ) level of theory using Spartan ’20 [8]. A structural rendering of 1,3-dimesitylisobenzofuran showing the requirement for non-planar mesityl groups in order to avoid steric repulsion between ortho-methyl groups and the nearest benzo hydrogen atoms. UV–vis (top) and fluorescence (middle) spectra for 10−6 M

Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A

• Maksim V. Kvach,
• Stefan Harjes,
• Harikrishnan M. Kurup,
• Geoffrey B. Jameson,
• Elena Harjes and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2024, 20, 1088–1098, doi:10.3762/bjoc.20.96

• individual α- and β-anomers of nucleoside Va as inhibitors of A3. This real-time NMR-based assay is a direct assay: it uses only A3 enzymes and ODNs in a buffer, unlike many fluorescence-based assays where a secondary enzyme and a fluorescently modified oligonucleotide are used [72]. The NMR-based assay

Novel analogues of a nonnucleoside SARS-CoV-2 RdRp inhibitor as potential antivirotics

• Luca Julianna Tóth,
• Kateřina Krejčová,
• Milan Dejmek,
• Eva Žilecká,
• Blanka Klepetářová,
• Lenka Poštová Slavětínská,
• Evžen Bouřa and
• Radim Nencka

Beilstein J. Org. Chem. 2024, 20, 1029–1036, doi:10.3762/bjoc.20.91

• simplified structural derivatives, the applied routes were optimized for maximal efficacy of the synthetic work. Regarding the inhibitory activity, six of the novel compounds showed inhibition in the fluorescence-based primer extension assay. The two simplified molecules were the most promising inhibitors

Auxiliary strategy for the general and practical synthesis of diaryliodonium(III) salts with diverse organocarboxylate counterions

• Naoki Miyamoto,
• Daichi Koseki,
• Kohei Sumida,
• Elghareeb E. Elboray,
• Naoko Takenaga,
• Ravi Kumar and
• Toshifumi Dohi

Beilstein J. Org. Chem. 2024, 20, 1020–1028, doi:10.3762/bjoc.20.90

• benzoate in 70% yield (Scheme 6A). Furthermore, iodonium salt 7aj with an umbelliferone-3-carboxylate counterion displayed extremely weak blue fluorescence emission under 365 nm UV light compared to free carboxylic acid 6j. This unique property was utilized for tracing the counterion exchange process of

• the diaryliodonium(III) salt by irradiating with 365 nm UV light. The counterion exchange in umbelliferone carboxylate salt 7aj with trifluoroacetic acid was rapid, and after 30 s, the completion of the reaction was confirmed by the emergence of strong blue fluorescence emission due to the liberation

• of the fluorescent-labeling carboxylic acid 6j (see Supporting Information File 1, Figure S1). Thus, this post-fluorescence iodonium salt can be used for visual indication of the ligand exchange process, elucidating the arylation mechanism of diaryliodonium(III) salts for their further applications

Synthesis and properties of 6-alkynyl-5-aryluracils

• Ruben Manuel Figueira de Abreu,
• Till Brockmann,
• Alexander Villinger,
• Peter Ehlers and
• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 898–911, doi:10.3762/bjoc.20.80

• of different functional groups was tested. The influence of different functional groups on the physical properties was studied by ultraviolet–visible (UV–vis) and fluorescence spectroscopy, providing new insights into the potential applications of uracil-based structures. Keywords: catalysis; cross

• -coupling; fluorescence; heterocycles; regioselectivity; Introduction Organic life is a complex interplay of many different building blocks. One of these building blocks is uracil. Discovered for the first time in 1901 by Alberto Ascoli, it is now known to be one of the four nucleobases of RNA [1]. It

• . Applications and tolerance to a wide range of functional groups have been tested. Furthermore, their physical properties were analyzed by ultraviolet–visible and fluorescence spectroscopy. Results and Discussion Synthesis The synthetic strategy for the desired compounds is based on a four-step sequence

Methodology for awakening the potential secondary metabolic capacity in actinomycetes

• Shun Saito and
• Midori A. Arai

Beilstein J. Org. Chem. 2024, 20, 753–766, doi:10.3762/bjoc.20.69

• et al. applied a fluorescence-based DNA cleavage assay coupled with HiTES to Streptomyces clavuligerus and identified the steroid 11α-hydroxyprogesterone (14) as an effective elicitor and characterized 10 cryptic enediyne-derived natural products, designated clavulynes A (15) and B–J with unusual

Isolation and structure determination of a new analog of polycavernosides from marine Okeania sp. cyanobacterium

• Kairi Umeda,
• Naoaki Kurisawa,
• Ghulam Jeelani,
• Tomoyoshi Nozaki,
• Kiyotake Suenaga and
• Arihiro Iwasaki

Beilstein J. Org. Chem. 2024, 20, 645–652, doi:10.3762/bjoc.20.57

• in 100 mL phosphate-buffered saline) was added to each well. The plates were incubated for an additional 3 h. The plates were read in a SpectraMax Gemini XS microplate fluorescence scanner (Molecular Devices) using an excitation wavelength of 536 nm and an emission wavelength of 588 nm. WI-38 cells

Synthesis of photo- and ionochromic N-acylated 2-(aminomethylene)benzo[b]thiophene-3(2Н)-ones with a terminal phenanthroline group

• Vladimir P. Rybalkin,
• Sofiya Yu. Zmeeva,
• Lidiya L. Popova,
• Irina V. Dubonosova,
• Olga Yu. Karlutova,
• Oleg P. Demidov,
• Alexander D. Dubonosov and
• Vladimir A. Bren

Beilstein J. Org. Chem. 2024, 20, 552–560, doi:10.3762/bjoc.20.47

• light and H+ or sequential addition of Fe2+ and AcO− ions. Keywords: fluorescence; molecular switches; N→O acyl rearrangement; naked eye effect; photochromism; Introduction Photochromism is defined as the reversible transformation of a molecular entity between different forms, having different

• -Acylated compounds 2a–c in solutions exhibited fluorescence in the region of 465–468 nm, and the excitation emission spectra agreed well with the absorption spectra (Figure 1). Compounds 2a–c in solutions demonstrated a typical negative photochromism [1][16] when irradiated with visible light of 436 nm

• (Figure 2). A decrease in the long-wavelength absorption was accompanied by a simultaneous increase in the shorter-wavelength absorption in the spectral region around 370 nm. During this process, a gradual diminishment of the initial fluorescence intensity at 465–468 nm up to zero was observed. The