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

• the SDS-PAGE. This approach also accounts for the protein-level identification; the exact modification site remains unknown. Here we show an example of the most used and commercially available rhodamine-derived dye (TAMRA-azide, Figure 6A). The bioorthogonal reaction between probe-labeled proteins and

Photoredox catalysis harvesting multiple photon or electrochemical energies

• Mattia Lepori,
• Simon Schmid and
• Joshua P. Barham

Beilstein J. Org. Chem. 2023, 19, 1055–1145, doi:10.3762/bjoc.19.81

• enabling controlled bond activations [45]. Regarding the reductive C–C arylation, the application of the xanthene dye rhodamine 6G (Rh-6G) as a catalyst for the reduction of heteroarenes bearing two or three bromine atoms (e.g., 6) under irradiation with green light (λ = 530 nm) gave monosubstituted

• while the C(sp2)–Br bond remained untouched. Subsequent irradiation with blue light gave the sequentially substituted products 9c and 9d. As with PDI, the xanthene dye rhodamine 6G (Rh-6G) can undergo reductive quenching upon excitation with green or blue light (Figure 5C). Considering that Rh-6G

Inline purification in continuous flow synthesis – opportunities and challenges

• Jorge García-Lacuna and
• Marcus Baumann

Beilstein J. Org. Chem. 2022, 18, 1720–1740, doi:10.3762/bjoc.18.182

• concentration of less than 1% within four hours, and water-soluble monomers. In addition, the integration of this setup into an inline synthesis step starting from block copolymer solutions, and rhodamine encapsulation produced micelles without affecting the particle size is also demonstrated. The growing

Microelectrode arrays, electrosynthesis, and the optimization of signaling on an inert, stable surface

• Kendra Drayton-White,
• Siyue Liu,
• Yu-Chia Chang,
• Sakashi Uppal and
• Kevin D. Moeller

Beilstein J. Org. Chem. 2022, 18, 1488–1498, doi:10.3762/bjoc.18.156

• peptides were placed on the array along with a fluorescent dye (LRSC, lissamine rhodamine) that was used to make sure the placement chemistry was working. The array used was coated with the borate ester diblock copolymer (Figure 2), and the peptides were attached to this polymer through a PEG-6 linker in

Polymer and small molecule mechanochemistry: closer than ever

• José G. Hernández

Beilstein J. Org. Chem. 2022, 18, 1225–1235, doi:10.3762/bjoc.18.128

• remediation, the degradation of dye pollutants (e.g., rhodamine) has been accomplished using BaTiO3 as a mechanophore in solution with ultrasonication [52] or under solvent-free ball milling reaction conditions [56]. These reports complement recent studies on piezocatalysis, such as on chain-growth

Heteroleptic metallosupramolecular aggregates/complexation for supramolecular catalysis

• Prodip Howlader and
• Michael Schmittel

Beilstein J. Org. Chem. 2022, 18, 597–630, doi:10.3762/bjoc.18.62

• into the Pt8 cage 25a = (22)4(19)2(NO3)8 [65]. Counter anion exchange from NO3− to PF6− made the cages soluble in acetonitrile. All three cages formed spherical supramolecular nano-aggregates in a water/acetonitrile (9:1) mixture and showed increased emission in the aggregated state [66]. Rhodamine B

Cryogels: recent applications in 3D-bioprinting, injectable cryogels, drug delivery, and wound healing

• Luke O. Jones,
• Leah Williams,
• Tasmin Boam,
• Martin Kalmet,
• Chidubem Oguike and
• Fiona L. Hatton

Beilstein J. Org. Chem. 2021, 17, 2553–2569, doi:10.3762/bjoc.17.171

Constrained thermoresponsive polymers – new insights into fundamentals and applications

• Patricia Flemming,
• Alexander S. Münch,
• Andreas Fery and
• Petra Uhlmann

Beilstein J. Org. Chem. 2021, 17, 2123–2163, doi:10.3762/bjoc.17.138

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

Recent advances in the application of isoindigo derivatives in materials chemistry

• Andrei V. Bogdanov and
• Vladimir F. Mironov

Beilstein J. Org. Chem. 2021, 17, 1533–1564, doi:10.3762/bjoc.17.111

• terminal substituent was also revealed since a similar OSC based on the rhodamine derivative 9b showed an efficiency of only 0.66% (Table 1). It is important to note that the replacement of the thienylphenylene spacer in structure 9a by the acceptor indan-3-dicyanoethylidene-1-one-2-ylidene fragment in

Photoinduced post-modification of graphitic carbon nitride-embedded hydrogels: synthesis of 'hydrophobic hydrogels' and pore substructuring

• Cansu Esen and
• Baris Kumru

Beilstein J. Org. Chem. 2021, 17, 1323–1334, doi:10.3762/bjoc.17.92

• % aqueous solution, Merck), magnesium chloride (MgCl2, 99%, Merck), melamine (99%, Sigma-Aldrich), poly(ethylene glycol) dimethacrylate (PEGDMA, Mn 550, Sigma-Aldrich), poly(ethylene glycol) methyl ether methacrylate (PEGMEMA, Mn 300, Sigma-Aldrich), potassium chloride (KCl, 99%, Merck), rhodamine B (RhB

• in 20 mL distilled water refreshed repeatedly every 2 hours for 3 times and then left in a fume hood for drying overnight. This procedure was repeated for each substructuring monomer categorized as acidic AA (10 mol % MBA), cationic AAM (10 mol % MBA), and neutral PEGMEMA (10 mol % PEGDMA). Rhodamine

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

• conditions and the kinetics of the selected reaction can lead to drastic changes in the PSTY. de Sá et al. combined external and internal numbering up in meso- and microchemical reactors of various sizes (Figure 3e). Photocatalytic degradations of methylene blue, rhodamine B, and phenol with TiO2 were

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

• ]. This binding model 10 can be applied to cell-surface GAGs to enhance the cellular uptake efficiency. The peptide 9, with rhodamine B attached, successfully enters into the living cells while the control peptide 11 with a simple guanidinium group shows a negligible uptake efficiency. In addition, the

Mechanochemical green synthesis of hyper-crosslinked cyclodextrin polymers

• Alberto Rubin Pedrazzo,
• Fabrizio Caldera,
• Marco Zanetti,
• Silvia Lucia Appleton,
• Nilesh Kumar Dhakar and
• Francesco Trotta

Beilstein J. Org. Chem. 2020, 16, 1554–1563, doi:10.3762/bjoc.16.127

• , and rhodamine B) and the still reactive imidazoyl carbonyl group of the NS. Keywords: β-cyclodextrin; ball-milling; crosslinking; green chemistry; mechanochemistry; nanosponges; Introduction The research in the fields of nanomedicine and nanotechnology has nowadays become predominant

• nanosponges with selected organic dyes that are used as probe molecules with different structures (methyl red, rhodamine B, and fluorescein). The simple functionalization of the cyclodextrin NS, in this case via reactive imidazole moieties, is particularly interesting for a variety of applications. For

• anhydrous environment as in this case with organic dyes. The choice fell on three common, well known and widely investigated organic dyes, i.e., fluorescein, methyl red, and rhodamine B. They have a slightly different structures (and color), and also different surface charges but share a reactive

Synthesis of new fluorescent molecules having an aggregation-induced emission property derived from 4-fluoroisoxazoles

• Kazuyuki Sato,
• Akira Kawasaki,
• Yukiko Karuo,
• Atsushi Tarui,
• Kentaro Kawai and
• Masaaki Omote

Beilstein J. Org. Chem. 2020, 16, 1411–1417, doi:10.3762/bjoc.16.117

• light ray and the structures often include fluorescein, rhodamine, or 7-amino-4-methylcoumarin (7-AMC) scaffolds as fluorophores. These fluorophores usually exhibit strong fluorescence in dilute solutions, but most of their emissions are partially or completely quenched in the solid state or in highly

Photocatalysis with organic dyes: facile access to reactive intermediates for synthesis

• Stephanie G. E. Amos,
• Marion Garreau,
• Luca Buzzetti and
• Jerome Waser

Beilstein J. Org. Chem. 2020, 16, 1163–1187, doi:10.3762/bjoc.16.103

• . Other organic dyes, including several acridinium salts, have been successfully applied in organophotocatalytic decarboxylation protocols. For example, rhodamine 6G (OD14, E(PC+*/PC) ≈ 1.2 V) [42] was used for the photocatalytic decarboxylative azidation of cyclic amino acids and rose bengal (OD15) [43

• porphyrin [75] and rhodamine 6G (OD14) [76]. Aryl radicals from aryl halides. Aryl halides are generally more difficult to reduce than aryl diazonium salts (Ered < −1.2 V) [77][78]. However, they are more available and bench-stable. Their reduction potential is dependent on the substitution pattern and on

• heteroarylated to give the desired dehalogenated products 13.3 or arylheteroarenes 13.4. Other organic dyes, such as dicyanoanthracene (OD5) and rhodamine 6G (OD14), have been successfully used in similar conPET strategies for the aryl radical-mediated derivatization of aryl bromides [82][83]. A similar double

Synthesis of novel multifunctional carbazole-based molecules and their thermal, electrochemical and optical properties

• Nuray Altinolcek,
• Ahmet Battal,
• Mustafa Tavasli,
• William J. Peveler,
• Holly A. Yu and
• Peter J. Skabara

Beilstein J. Org. Chem. 2020, 16, 1066–1074, doi:10.3762/bjoc.16.93

• . This indicates that the excited state dipole moment is much greater than the ground state dipole moment. Quantum yields The relative fluorescent quantum yields (ϕFL) of compounds 7a and 7b were determined in dichloromethane by using rhodamine B (ϕFL = 49% at λexc=355 nm) in ethanol as reference [45

Cation-induced ring-opening and oxidation reaction of photoreluctant spirooxazine–quinolizinium conjugates

• Phil M. Pithan,
• Sören Steup and
• Heiko Ihmels

Beilstein J. Org. Chem. 2020, 16, 904–916, doi:10.3762/bjoc.16.82

• Information File 1). The compound 3a is essentially nonfluorescent in solution. The addition of 3.0 equiv of Cu2+, however, led to the development of a new, broad emission band at λfl = 628 nm (Φfl = 0.12 relative to rhodamine 6G [72], Figure 3B and Table 1). As supported by the corresponding excitation

• yields of the derivatives 3a, 3b, and 4a were determined relative to coumarin 307 (Φfl = 0.58 in MeCN) [72] or rhodamine 6G (Φfl = 0.95 in EtOH) [71], according to the established procedures [88][89]. Synthesis Synthesis of the quinolizinium–spirooxazine conjugates 3a and 3b (E)-2-(2-(1,3,3

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

• distributes in literature but is wrong because protons do not exist alone and data related to pH-values relate only to aqueous solutions. Ring opening by rhodamine B lactone quantitatively probed formation conjugate acid by formation of rhodamine B [5]. We interpret the term conjugate acid as a species in

A new approach to silicon rhodamines by Suzuki–Miyaura coupling – scope and limitations

• Thines Kanagasundaram,
• Antje Timmermann,
• Carsten S. Kramer and
• Klaus Kopka

Beilstein J. Org. Chem. 2019, 15, 2569–2576, doi:10.3762/bjoc.15.250

• pharmacokinetic or -dynamic properties of the tumor tracers, silicon rhodamines are relatively small and already examined as fluorophores for the optical imaging of tumors. Using silicon rhodamine SiR700 a more enhanced tumor-to-background ratio in optical imaging could be achieved compared to the cyanine based

• dyes Cy5.5 and Alexa Fluor® 680 [23]. Moreover, silicon rhodamines demonstrated in in vivo imaging experiments excellent fluorescence properties and biostabilities [23] as well as exhibited high quantum efficiencies with high tolerance to photobleaching [24]. A silicon rhodamine antibody conjugate

• could also be successfully applied for optical imaging of a xenograft tumor (human malignant meningioma) in a mouse model [24]. Again, in direct comparison with the cyanine dye Cy5.5, the silicon rhodamine conjugate showed no fading indicating that silicon rhodamine dyes are more suitable for long time

Synthesis of a dihalogenated pyridinyl silicon rhodamine for mitochondrial imaging by a halogen dance rearrangement

• Jessica Matthias,
• Thines Kanagasundaram,
• Klaus Kopka and
• Carsten S. Kramer

Beilstein J. Org. Chem. 2019, 15, 2333–2343, doi:10.3762/bjoc.15.226

• .15.226 Abstract Background: Since their first synthesis, silicon xanthenes and the subsequently developed silicon rhodamines (SiR) gained a lot of attention as attractive fluorescence dyes offering a broad field of application. We aimed for the synthesis of a fluorinable pyridinyl silicon rhodamine for

• the use in multimodal (PET/OI) medical imaging of mitochondria in cancerous cells. Results: A dihalogenated fluorinatable pyridinyl rhodamine could be successfully synthesized with the high yield of 85% by application of a halogen dance (HD) rearrangement. The near-infrared dye shows a quantum yield

• features with their optical properties and control the latter by rational dye design [15][24][25][26]. These investigations led to new silicon rhodamine dyes with enhanced and fine-tuned properties (quantum yield, lifetime, brightness, absorption and emission maxima). A recent review compared the

Synthesis and properties of sulfur-functionalized triarylmethylium, acridinium and triangulenium dyes

• Marco Santella,
• Eduardo Della Pia,
• Jakob Kryger Sørensen and
• Bo W. Laursen

Beilstein J. Org. Chem. 2019, 15, 2133–2141, doi:10.3762/bjoc.15.210

• bichromophoric behavior has been studied in detail for the dialkylamino-substituted xanthenium/rhodamine system [45][46], and is also the likely reason for these compounds being non-fluorescent. The three sulfur-substituted trioxatriangulenium dyes 6, 8, and 9 all display a first absorption band around 480 nm

• = 0.3) than the corresponding dialkylamino-substituted analogues. Structures of some representative triangulenium dyes. a) Rhodamine/fluorescine-like derivatives with donor groups in para-positions (2, 6, and 10) to the formal cation center (12c). b) Derivatives without donor groups. Examples of various

Naphthalene diimides with improved solubility for visible light photoredox catalysis

• Barbara Reiß and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2019, 15, 2043–2051, doi:10.3762/bjoc.15.201

• sustainability further, organic compounds, mainly eosin Y [25], rhodamine 6G [26], 9-mesityl-10-methylacridinium perchlorate [27], 1,2,3,5-tetrakis(carbazol-9-yl)-4,6-dicyanobenzenes [28] and N-phenylphenothiazines [29] were applied as important alternative photoredox catalysts [30][31]. These studies

• cNDI 2 [48][49]. Hence, the photoredox properties of the new cNDI 2–6 are comparable to those of eosin Y and rhodamine 6G as other organic photoredox catalysts. Photoredox catalysis with NDI 1 and cNDI 6 The α-alkylation of 1-octanal (12) by diethyl 2-bromomalonate (13) yielding product 14 (Scheme 2

• and cNDI 2 (in CH2Cl2) in comparison to other organic photoredox catalyst X, in particular eosin Y (EY), rhodamine 6G (Rh6G) and 9-mesityl-10-methylacridinium perchlorate (MesAcr) 1,2,3,5-tetrakis(carbazol-9-yl)-4,6-dicyanobenzenes (4CzIPN) and N-phenylphenothiazine (Ptz). Photoredox catalytic

Complexation of a guanidinium-modified calixarene with diverse dyes and investigation of the corresponding photophysical response

• Yu-Ying Wang,
• Yong Kong,
• Zhe Zheng,
• Wen-Chao Geng,
• Zi-Yi Zhao,
• Hongwei Sun and
• Dong-Sheng Guo

Beilstein J. Org. Chem. 2019, 15, 1394–1406, doi:10.3762/bjoc.15.139

• azocalix[4]arene with rhodamine 123 as the reporter pair [16]. Consequently, with regard to bioimaging, the study of the complexation between macrocycles and two-photon probes is meaningful as two-photon excitation microscopy exhibits several distinct advantages including a deeper tissue penetration

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

• of the commercially available rhodamine dye, TAMRA (555ex/580em), to the dendrimer would allow for standard immunofluorescence assays, to track the microparticle following cellular uptake and intracellular processing. TAMRA’s high photostability, low pH sensitivity and ease of incorporation through