Synthetic strategies for the fluorescent labeling of epichlorohydrin-branched cyclodextrin polymers

• Milo Malanga,
• Mihály Bálint,
• István Puskás,
• Kata Tuza,
• Tamás Sohajda,
• László Jicsinszky,
• Lajos Szente and
• Éva Fenyvesi

Beilstein J. Org. Chem. 2014, 10, 3007–3018, doi:10.3762/bjoc.10.319

• polymer leads to compounds with enhanced spectroscopic properties, but it has been rarely described. Zohrehvand and Evans reported the synthesis, characterization and fluorescence studies of a water-soluble 2-naphthol-containing β-CD-epichlorohydrin copolymer [16], but in this case the fluorophore is

• polymers and the approaches are based on the introduction of a dedicated anchoring group for the fluorophore (functionalization) into the CD scaffold. The general scheme for the two synthetic approaches is shown in Scheme 1. The first strategy is based on the post-branching functionalization (Scheme 1

• determination of the molecular weight is in progress, we have to find the proper solvent as in water unreliable values were obtained. The following modification of the methylated polymer is the introduction of the dedicated anchoring group for the fluorophore, which is in the specific case a tosyl moiety

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

• bromide was introduced as a part of a heterogenic two-chromophore system, to take advantage of very efficient FRET energy transfer process (77%) from fluorescein to the RNA-intercalated phenanthridinium fluorophore (Figure 8, left) [83]. The resulting fluorescent dye exhibited improved ds-RNA-marker

A small azide-modified thiazole-based reporter molecule for fluorescence and mass spectrometric detection

• Stefanie Wolfram,
• Hendryk Würfel,
• Stefanie H. Habenicht,
• Christine Lembke,
• Phillipp Richter,
• Eckhard Birckner,
• Rainer Beckert and
• Georg Pohnert

Beilstein J. Org. Chem. 2014, 10, 2470–2479, doi:10.3762/bjoc.10.258

• to minimize the structural complexity of the fluorophores to achieve higher atom economy and reduce the interaction with biomacromolecules. In this context it was critical to realize that the thiazole moiety itself can also act as a fluorophore, especially the class of 4-hydroxythiazoles [4][5]. 4

• ]. ABPP probes contain two structural units: (1) a reactive group that reacts with the protein target and (2) a reporter unit for detection which could be, e.g., a fluorophore, a MS-tag, biotin or a combination of these [16][17]. For in vivo or in situ applications the alkyne (or azide) modified reactive

• group is usually applied to living organisms and after cell lysis the reporter is introduced by CuAAC [16]. Fluorophore tagged proteins can then be visualized by gel electrophoresis [17]. Besides fluorescence detection, mass spectrometry (MS) is also suited for the monitoring of tagged biological

Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2014, 10, 2307–2321, doi:10.3762/bjoc.10.240

• . Schematic illustrations (experiments A–F) of the specific DNA duplex formation at artificial lipid bilayers forming structures of various membrane-bound nucleic acid–dye complexes. A) Covalent bound Cy5-fluorophore and intercalated SG with DNA duplex were irradiated simultaneously at 635 nm and 470 nm. B

Multichromophoric sugar for fluorescence photoswitching

• Stéphane Maisonneuve,
• Rémi Métivier,
• Pei Yu,
• Keitaro Nakatani and
• Juan Xie

Beilstein J. Org. Chem. 2014, 10, 1471–1481, doi:10.3762/bjoc.10.151

• photo resistance. Keywords: click chemistry; energy transfer; fluorophore; monosaccharide; photochromism; Introduction The development of functional nanomaterials is nowadays a very attractive field of fundamental and applied research. The chemical functions at the molecular level yield properties

• function. Actually, fluorescence allows the possibility to reach high sensitivity and very low detection levels, down to the single molecule limit, whereas absorption spectroscopy requires a high number of active molecules [2]. If structural and spectral features of the fluorophore and the photochromic

• colorless form (state A), the absence of FRET would keep the fluorescence alive, showing that the combination of these two functional molecules leads to a photon-driven fluorescence switch. Previously, we have synthesized a fluorescent-photochromic dyad (1, Figure 2) combining a DCM fluorophore (4

Molecular recognition of surface-immobilized carbohydrates by a synthetic lectin

• Melanie Rauschenberg,
• Eva-Corrina Fritz,
• Christian Schulz,
• Tobias Kaufmann and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2014, 10, 1354–1364, doi:10.3762/bjoc.10.138

• Information File 1). Successful incorporation of the fluorophore was also evident in the UV–vis spectrum of the precursor FITC-labeled Cys-His-Cys (see Figure S1 in the Supporting Information File 1). We note that if prepared directly by air oxidation from Cys-His-Cys, HisHis as well as FITC-HisHis consist of

Direct and indirect single electron transfer (SET)-photochemical approaches for the preparation of novel phthalimide and naphthalimide-based lariat-type crown ethers

• Dae Won Cho,
• Patrick S. Mariano and
• Ung Chan Yoon

Beilstein J. Org. Chem. 2014, 10, 514–527, doi:10.3762/bjoc.10.47

• substances that signal guest-binding by interrupting the SET-quenching of the excited states of the fluorophore moieties that are appended to the host (Scheme 15). We expected that metal cation binding to 72–74 would be assisted by the oxygen, nitrogen, and sulfur donors within the pendant side chain. As a

• consequence, it would be accompanied concomitantly by a dislocation of the side chain moiety and a reduction in intramolecular SET quenching of the singlet excited naphthalene fluorophore by the strong electron donating sulfur and nitrogen atoms. In the studies, it was observed that fluorescence of these and

Advancements in the mechanistic understanding of the copper-catalyzed azide–alkyne cycloaddition

• Regina Berg and
• Bernd F. Straub

Beilstein J. Org. Chem. 2013, 9, 2715–2750, doi:10.3762/bjoc.9.308

• mechanistic proposals: computational and experimental evidence The groups of Fokin and Finn have tested different heterocyclic chelating ligands for CuAAC by fluorescence quenching in the reaction of dansyl azide fluorophore and dabsyl alkyne, and carried out kinetic measurements with a bis

Flow synthesis of a versatile fructosamine mimic and quenching studies of a fructose transport probe

• Matthew B. Plutschack,
• D. Tyler McQuade,
• Giulio Valenti and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2013, 9, 2022–2027, doi:10.3762/bjoc.9.238

• . Without easy access to NBDM, the use of this compound in biological experiments would supersede the investigation of its fluorescent properties. Fluorescence: Fluorescence in biological systems is often complicated by fluorophore quenching. Alexa fluorophores can be quenched by certain amino acids and NBD

Synthesis and spectroscopic properties of 4-amino-1,8-naphthalimide derivatives involving the carboxylic group: a new molecular probe for ZnO nanoparticles with unusual fluorescence features

• Laura Bekere,
• David Gachet,
• Vladimir Lokshin,
• Wladimir Marine and
• Vladimir Khodorkovsky

Beilstein J. Org. Chem. 2013, 9, 1311–1318, doi:10.3762/bjoc.9.147

• (3H)-yl)benzoic acid (4) was found to be a sensitive molecular probe for ZnO nanoparticles. We investigated in detail one- and two-photon absorption properties of this fluorophore. In nonpolar solvents, the acid 4 absorbs at about 400 nm and fluoresces at 500 nm with a fluorescence lifetime of about 7

• previously unknown methyl 4-(6-piperidinyl-1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl)benzoate and the corresponding acid. The phenyl moiety can serve as a rigid spacer, while the carboxylic group can function as an anchor for grafting the fluorophore to metal oxide surfaces. This approach to the

• grafting. Conclusion Derivative 4 involving both the fluorophore moiety and the carboxylic group capable of binding the ZnO surface can serve as an efficient molecular probe owing to the high sensitivity to the polarity of the surroundings. Derivative 2 can also be used when fluorescence detection at

Design and synthesis of tag-free photoprobes for the identification of the molecular target for CCG-1423, a novel inhibitor of the Rho/MKL1/SRF signaling pathway

• Jessica L. Bell,
• Andrew J. Haak,
• Susan M. Wade,
• Yihan Sun,
• Richard R. Neubig and
• Scott D. Larsen

Beilstein J. Org. Chem. 2013, 9, 966–973, doi:10.3762/bjoc.9.111

• isolation and/or visualization (e.g., biotin or fluorophore) via click chemistry. This technology has been highly successful in profiling enzyme activity in living cells and even in whole organisms [21]. In ABPP, covalent linkage by the reactive functionality is usually dependent upon a particular enzymatic

Superstructures of fluorescent cyclodextrin via click-reaction

• Arkadius Maciollek,
• Helmut Ritter and
• Rainer Beckert

Beilstein J. Org. Chem. 2013, 9, 827–831, doi:10.3762/bjoc.9.94

• , Humboldtstr. 10, 07743 Jena, Germany 10.3762/bjoc.9.94 Abstract Mono-(6-azido-6-deoxy)-β-cyclodextrin (CD) was covalently attached to an alkyne-modified 5-methyl-2-(pyridin-2-yl)thiazol-4-ol yielding a fluorophore containing CD in a click-type reaction. Intermolecular complexes were formed by poly(host–guest

• used as potentially biological markers, as molecular sensors, or for chiral recognition in aqueous solution [11][12][13]. Thus, in this present paper we describe the spectroscopic and structural behavior of a “CD-Click-Fluorophore” in the absence and presence of a competitive guest in water. Results

• exclusion of the fluorophore moiety from the hydrophobic cavity of CD. This exchange causes a change in the HOMO–LUMO gap [14][15]. Figure 3 shows the fluorescence spectra of 3 in aqueous solution. Upon addition of potassium adamantane-1-carboxylate the maximum wavelength changes from 417 to 442 nm and the

Spin state switching in iron coordination compounds

• Philipp Gütlich,
• Ana B. Gaspar and
• Yann Garcia

Beilstein J. Org. Chem. 2013, 9, 342–391, doi:10.3762/bjoc.9.39

Hydrophobic analogues of rhodamine B and rhodamine 101: potent fluorescent probes of mitochondria in living C. elegans

• Laurie F. Mottram,
• Safiyyah Forbes,
• Brian D. Ackley and
• Blake R. Peterson

Beilstein J. Org. Chem. 2012, 8, 2156–2165, doi:10.3762/bjoc.8.243

• differences exist between the calculated and measured values, the relative trends illustrate how structural modifications of these compounds are likely to affect fluorophore solubility and cellular permeability. Imaging of fluorophores in vivo by confocal microscopy To visualize the absorption and

• variety of fluorophore concentrations revealed that most cells of living C. elegans accumulate the fluorophores rhodamine 6G (7), HRB 9, and HR101 10 after treatment for 2 h (Figure 5). Under these conditions, the more polar rhodamine 101 (8) was observed to be excluded from some cells and tissues

• volume, 5 mM phosphate, pH 7.4) to provide 5 mM solutions of the fluorophore. Samples were shaken for 24 h at 25 °C to equilibrate. The top and bottom 1 mL fractions were isolated and centrifuged at 15,000 rpm (no precipitate was observed for any of the samples). Aliquots of these fractions were diluted

Synthesis of trifunctional cyclo-β-tripeptide templates

• Frank Stein,
• Tahir Mehmood,
• Tilman Plass,
• Javid H. Zaidi and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2012, 8, 1576–1583, doi:10.3762/bjoc.8.180

• . Aggregation by stacking of the functionalized peptide rings will further provide a higher density of organized recognition motifs and labels. As a proof-of-concept, the successive coupling of a fluorophore 5(6)-tetramethylcarboxyrhodamine 5 (TAMRA-COOH) and a cell-penetrating peptide to the template 4 is

• enzymatic degradation, and their ability to form intermolecular staples by backbone hydrogen bonding. This might be of special advantage to target or imitate multivalent and/or cooperative processes. As an initial effort, we equipped the cyclic β-tripeptide with a fluorophore and a protected cell

A simple and efficient dual optical signaling chemodosimeter for toxic Hg(II)

• Sabir H. Mashraqui,
• Sapna A. Tripathi,
• Sushil S. Ghorpade and
• Smita R. Britto

Beilstein J. Org. Chem. 2012, 8, 1352–1357, doi:10.3762/bjoc.8.155

• photostable fluorophore [52], has been designed to function as metal ion and anion sensor [53][54][55][56][57]. In contrast to moderately fluorescent acridone, its thione analog is poorly emissive presumably on account of the intersystem crossing process of the C=S bonding [58]. Keeping this in mind, we have

Multistep organic synthesis of modular photosystems

• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2012, 8, 897–904, doi:10.3762/bjoc.8.102

• acid 28. Hydrazide deprotection in NDI 29 and in situ hydrazone formation with benzaldehyde 30 gave propagator 3. In contrast to propagator 3, propagator 4 is constructed around a yellow, core-substituted cNDI fluorophore. Nevertheless, the synthesis of this target molecule also starts with NDA 13

Investigation of the network of preferred interactions in an artificial coiled-coil association using the peptide array technique

• Raheleh Rezaei Araghi,
• Carsten C. Mahrenholz,
• Rudolf Volkmer and
• Beate Koksch

Beilstein J. Org. Chem. 2012, 8, 640–649, doi:10.3762/bjoc.8.71

• three β- and two γ-amino acids, was synthesized by standard solid-phase peptide synthesis and labeled at the N-terminus with the fluorophore 5(6)-tetramethylrhodamine (TAMRA). As described above, the chimera has a modified pentad (β- and γ-amino acids) at the center of its 31-residue sequence (positions

A novel high-yield synthesis of aminoacyl p-nitroanilines and aminoacyl 7-amino-4-methylcoumarins: Important synthons for the synthesis of chromogenic/fluorogenic protease substrates

• Xinghua Wu,
• Yu Chen,
• Herve Aloysius and
• Longqin Hu

Beilstein J. Org. Chem. 2011, 7, 1030–1035, doi:10.3762/bjoc.7.117

• acid/peptide conjugates liberates the free chromophore or fluorophore, allowing the convenient determination of the rate of enzyme catalysis with a UV or fluorescence spectrophotometer. p-Nitroaniline (pNA) is one of the most commonly used chromogenic reagents. The synthesis of peptide-pNAs usually

Fluorometric recognition of both dihydrogen phosphate and iodide by a new flexible anthracene linked benzimidazolium-based receptor

• Kumaresh Ghosh and
• Debasis Kar

Beilstein J. Org. Chem. 2011, 7, 254–264, doi:10.3762/bjoc.7.34

• of 1 with H2PO4− in the gas phase [34]. In the complex, benzimidazolium protons (C+–H) and amide protons are cooperatively involved in hydrogen bonding with H2PO4−. Anthracene, being a fluorophore in 1, has the advantage of being considered as a flat hydrophobic fluorophore probe for sensing of

An easy assembled fluorescent sensor for dicarboxylates and acidic amino acids

• Xiao-bo Zhou,
• Yuk-Wang Yip,
• Wing-Hong Chan and
• Albert W. M. Lee

Beilstein J. Org. Chem. 2011, 7, 75–81, doi:10.3762/bjoc.7.11

• (i.e., chromophore or fluorophore) as sensing probes for dicarboxylates [8][9][10][11][12][13]. Additionally, chiral recognition of carboxylates has been actively explored in the sensor field [14][15][16]. By using cholic acid as the molecular scaffold for the construction of sensing probes, we have

• -trimethylbenzene with sodium azide in DMSO afforded the corresponding bis-azide. Transformation of the crude bis-azide into bis-isothiocyanate 3 was achieved by treatment with triphenylphosphine in the presence of CS2. The “fluorophore–spacer–receptor” sensing motif for carboxylate was incorporated into the

Donor-acceptor substituted phenylethynyltriphenylenes – excited state intramolecular charge transfer, solvatochromic absorption and fluorescence emission

• Ritesh Nandy and
• Sethuraman Sankararaman

Beilstein J. Org. Chem. 2010, 6, 992–1001, doi:10.3762/bjoc.6.112

• state rendering its fluorescence emission sensitive to environment and solvent polarity [20][21][22]. Pyrene is a prototypical example of a fluorophore and its monomer emission occurs around 380 nm. It has been shifted to as high as 600 nm by multiple substitution by groups that extend the conjugation

• transfer quenching of fluorescence. Correlation of Stokes shifts with solvent polarity Solvent induced spectral shifts are often interpreted in terms of the Lippert–Mataga [43][44][45] equation, which describes Stokes shifts in terms of the change in the dipole moment of the fluorophore and the dependence

• of the energy of the dipole on the dielectric constant and refractive index of the solvent. The Lippert–Mataga equation accounts for the general solvent effect and does not account for specific solvent–fluorophore interactions, for example, through hydrogen bonding etc. The Lippert–Mataga plot for 1c

Chromo- and fluorophoric water-soluble polymers and silica particles by nucleophilic substitution reaction of poly(vinyl amine)

• Katja Hofmann,
• Ingolf Kahle,
• Frank Simon and
• Stefan Spange

Beilstein J. Org. Chem. 2010, 6, No. 79, doi:10.3762/bjoc.6.79

• polymers [2][3][4]. In general, there are two approaches for the synthesis of fluorescent polymers: First, the polymerization of a monomer that contains a fluorescent chromophore is possible. However, in some cases the new fluorophore-carrying polymer [1][5] is accompanied by a non-adequate effort

• with the thiolated RGD peptide cyclo(Arg-Gly_Asp-Phe-Lys(mpa))(c(RGDFK)-SH) leads to a fluorescent sensor for imaging tumor cells [37]. In this paper we report our current studies on the functionalization of PVAm with carbonitrile 1 to introduce a chromophore as well as a fluorophore into the polymer

• NMR spectroscopy. Figure 1 compares the solid state 13C NMR spectra of pure PVAm, fluorophore-functionalized PVAm 1-P and the model compound 1-M. It can be seen that the signals observed for 1-M and pure PVAm are also visible in the 13C-{1H}-CP-MAS NMR spectrum of 1-P. This is an excellent evidence

Synthetic incorporation of Nile Blue into DNA using 2′-deoxyriboside substitutes: Representative comparison of (R)- and (S)-aminopropanediol as an acyclic linker

• Daniel Lachmann,
• Sina Berndl,
• Otto S. Wolfbeis and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2010, 6, No. 13, doi:10.3762/bjoc.6.13

• explore how important the chirality of the 3-amino-1,2-propanediol linker is with respect to the optical properties of an attached fluorophore. We chose Nile Blue as the fluorescent probe for these experiments since the redox properties of this phenoxazinium label exhibit a potential sufficient for

• - and L-threoninol [39][40][41][42] the chirality of the 3-amino-1,2-glycol linker as a substitute for the 2′-deoxyriboside in our studies had no influence on the optical properties of the attached fluorophore. In order to image this result we worked out molecular models for the duplex DNA1A (R

Synthesis of indolo[3,2-b]carbazole-based new colorimetric receptor for anions: A unique color change for fluoride ions

• Ajit Kumar Mahapatra,
• Giridhari Hazra and
• Prithidipa Sahoo

Beilstein J. Org. Chem. 2010, 6, No. 12, doi:10.3762/bjoc.6.12

• occurs by forming the anion of receptor 1; the excited state was modified considerably leading to the quenching of fluorescence. A commonly accepted mechanism for the quenching phenomenon involves an inversion between the strongly emissive ππ* and the poorly emissive nπ* states of this fluorophore. Such