Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

• Nattawut Yotapan,
• Chayan Charoenpakdee,
• Pawinee Wathanathavorn,
• Boonsong Ditmangklo,
• Hans-Achim Wagenknecht and
• Tirayut Vilaivan

Beilstein J. Org. Chem. 2014, 10, 2166–2174, doi:10.3762/bjoc.10.224

• maxima (647 nm) compared to the single-stranded PNA (656 nm) as well as a small fluorescence increase (1.36 fold at 643 nm) (Figure 3a,b). The blue-shifted fluorescence maxima and increased quantum yields of Nile red suggest that the Nile red chromophore in complementary PNA–DNA duplexes was placed in a

• chromophore and gives rise to the observed blue shifts and the fluorescence increase. In addition, a larger increase in fluorescence was also observed with DNA targets that can form a bulge in the vicinity of the Nile red label. We propose that the Nile red label is buried within the looped out structure of

Photorelease of phosphates: Mild methods for protecting phosphate derivatives

• Sanjeewa N. Senadheera,
• Abraham L. Yousef and
• Richard S. Givens

Beilstein J. Org. Chem. 2014, 10, 2038–2054, doi:10.3762/bjoc.10.212

• application in both organic chemistry and biochemistry. The reagents are generally described as “caged” compounds or photoremovable protecting groups (PPGs) in which the attached chromophore masks the biological activity of a substrate. Irradiation releases the substrate, allowing it to return to its normal

• organic chemistry and biochemistry, but they are particularly important for mechanistic studies in biochemistry and biophysics [6][8][9][10][11]. Most PPG candidates require sufficiently high energy excited states for heterolysis of a carbon–oxygen or carbon–heteroatom bond that binds the chromophore to a

• photo-Favorskii rearrangement concomitant with ligand release. The combination of these features shifts and extends the chromophore, exhibiting a more intense, broader absorption band closer to the visible region, making the PPG more accessible for photodeprotection. Thus, elaborating the two motifs by

Bis(β-lactosyl)-[60]fullerene as novel class of glycolipids useful for the detection and the decontamination of biological toxins of the Ricinus communis family

• Hirofumi Dohi,
• Takeru Kanazawa,
• Akihiro Saito,
• Keita Sato,
• Hirotaka Uzawa,
• Yasuo Seto and
• Yoshihiro Nishida

Beilstein J. Org. Chem. 2014, 10, 1504–1512, doi:10.3762/bjoc.10.155

• protein band in SDS-PAGE. The amounts were calibrated with standard samples with known concentrations. Though Bradford and Lowry methods might be useful for this kind of protein assays, the strong UV–vis absorbance of the C60 chromophore interfered with these established methodologies. Therefore, we

Homochiral BINOL-based macrocycles with π-electron-rich, electron-withdrawing or extended spacing units as receptors for C₆₀

• Marco Caricato,
• Silvia Díez González,
• Idoia Arandia Ariño and
• Dario Pasini

Beilstein J. Org. Chem. 2014, 10, 1308–1316, doi:10.3762/bjoc.10.132

• , Supporting Information File 1) show the major absorption band centered around 230 nm, typical of the binaphthyl chromophore [41]. Circular dichroism spectroscopy of the same macrocycles show the exciton couplet typical of binaphthyl moieties (Figure 3), corresponding to the maximum absorption band in the UV

• ], 3a [28], 4a [28] and p-toluenesulfonic acid 4-dimethylaminopyridinium salt (PTSA-DMAP) [45] were prepared according to literature procedures. THF (Na, benzophenone) and CH2Cl2 (CaH2) were dried before use. Analytical thin-layer chromatography was performed on silica gel, chromophore loaded, and with

Synthesis of a sucrose dimer with enone tether; a study on its functionalization

• Zbigniew Pakulski,
• Norbert Gajda,
• Magdalena Jawiczuk,
• Jadwiga Frelek,
• Piotr Cmoch and
• Sławomir Jarosz

Beilstein J. Org. Chem. 2014, 10, 1246–1254, doi:10.3762/bjoc.10.124

• dimolybdenum methodology offers the hard proof of the absolute configuration of the vic-diols [27][28][29]. In this methodology, dimolybdenum tetraacetate acts as auxiliary chromophore allowing the application of electronic circular dichroism (ECD) to (otherwise in ECD non-observable) vic-diols. Mo2(OAc)4 when

Heronapyrrole D: A case of co-inspiration of natural product biosynthesis, total synthesis and biodiscovery

• Jens Schmidt,
• Zeinab Khalil,
• Robert J. Capon and
• Christian B. W. Stark

Beilstein J. Org. Chem. 2014, 10, 1228–1232, doi:10.3762/bjoc.10.121

• (2-nitropyrrole) chromophore. HPLC–HRMS–ESI(+) analysis established a molecular formula (C19H30N2NaO5, Δmmu −0.2) for this unidentified heronapyrrole, consistent with that predicted for heronapyrrole D. Although semi-preparative HPLC fractionation returned a pure sample of this new heronapyrrole, the

The Ugi four-component reaction as a concise modular synthetic tool for photo-induced electron transfer donor-anthraquinone dyads

• Sarah Bay,
• Gamall Makhloufi,
• Christoph Janiak and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2014, 10, 1006–1016, doi:10.3762/bjoc.10.100

• the carbazole dyads 8e and 8f. Eventually, the absorption characteristics of phenothiazine dyads can be more easily red-shifted and, therefore, charge separation by PET should be accessible with visible light by fine-tuning the donor chromophore towards lower HOMO–LUMO gaps. Conclusion The Ugi four

First synthesis of meso-substituted pyrrolo[1,2-a]quinoxalinoporphyrins

• Dileep Kumar Singh and
• Mahendra Nath

Beilstein J. Org. Chem. 2014, 10, 808–813, doi:10.3762/bjoc.10.76

• demonstrated the features of both porphyrin and pyrene or fluorene subunits and suggest that there is no significant interaction between the attached chromophore and the porphyrin ring in the ground state. The fluorescence spectra of porphyrins 4f, 4g, 4h, 5 and 6 were recorded in CHCl3 at the excitation

One-pot three-component synthesis and photophysical characteristics of novel triene merocyanines

• Christian Muschelknautz,
• Robin Visse,
• Jan Nordmann and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2014, 10, 599–612, doi:10.3762/bjoc.10.51

• spectrometry and by combustion analysis. The appearance of only a single set of signals in the NMR spectra indicates that the process is highly stereoselective. The occurrence of deep-colored products indicates the presence of a chromophore with extended π-electron conjugation where the terminal acceptor and

• triene chromophore largely contribute to shorter wavelength absorption bands, the tosyl moiety does not display any coefficient density in the FMOs and, therefore, qualifies as a favorable electronic innocent bridge for ligating other chromophores to this novel class of merocyanines. Conclusion In

• display broad absorption bands and computations suggest, that novel types of panchromatic absorbing bichromophores should be readily available by ligating the second chromophore via the electronically nonperturbing N-sulfonyl moiety. Synthetic, photophysical, and computational studies addressing

The chemistry of amine radical cations produced by visible light photoredox catalysis

• Jie Hu,
• Jiang Wang,
• Theresa H. Nguyen and
• Nan Zheng

Beilstein J. Org. Chem. 2013, 9, 1977–2001, doi:10.3762/bjoc.9.234

• driven not only by its green characteristics (i.e. using visible light), but also more importantly by its unique ability to achieve unconventional bond formation. Like most organic compounds, amines do not absorb visible light efficiently, unless they have a chromophore (e.g., conjugated π-bond systems

Self-assembly of 2,3-dihydroxycholestane steroids into supramolecular organogels as a soft template for the in-situ generation of silicate nanomaterials

• Valeria C. Edelsztein,
• Andrea S. Mac Cormack,
• Matías Ciarlantini and
• Pablo H. Di Chenna

Beilstein J. Org. Chem. 2013, 9, 1826–1836, doi:10.3762/bjoc.9.213

• to n-hexane and dichloromethane xerogels. This is indicative of a more compact assembly in this polar solvent. Due to the lack of a chromophore in 1, it was not possible to use circular dichroism to prove the helicoidal nature of the fibrillar network, but images suggest that, at least in

Zinc–gold cooperative catalysis for the direct alkynylation of benzofurans

• Yifan Li and
• Jérôme Waser

Beilstein J. Org. Chem. 2013, 9, 1763–1767, doi:10.3762/bjoc.9.204

• ) [32]. Although the yield was still moderate, this was one of the first examples of direct alkynylation of a marketed drug. It also gave access in a single step to an interesting furocoumarin derivative with an extended chromophore, which could be important for phototherapy. Mechanistically, the

New core-pyrene π structure organophotocatalysts usable as highly efficient photoinitiators

• Sofia Telitel,
• Frédéric Dumur,
• Thomas Faury,
• Bernadette Graff,
• Mohamad-Ali Tehfe,
• Didier Gigmes,
• Jean-Pierre Fouassier and
• Jacques Lalevée

Beilstein J. Org. Chem. 2013, 9, 877–890, doi:10.3762/bjoc.9.101

• than the starting structure Py_1 (Figure 7, curve b). This highlights the interest of the present approach associated with the modification of the Py chromophore. CP can also be initiated in the presence of the sulfonium salt TH, e.g., with Py_3, Py_8, Py_9, Py_10 and Py_11 (Figure 6B). The conversions

Polymerization of novel methacrylated anthraquinone dyes

• Christian Dollendorf,
• Susanne Katharina Kreth,
• Soo Whan Choi and
• Helmut Ritter

Beilstein J. Org. Chem. 2013, 9, 453–459, doi:10.3762/bjoc.9.48

• absorption maxima (416, 636 and 684 nm), which can be found in the violet and red color ranges. A combination of these two colors appears purple, the complementary color to green. Methacrylation of 1 does not change the chromophore and therefore the absorption maxima. The change in the absorption behavior of

• )phenylamino)anthraquinone (5). In order to introduce polymerizable functionalities, 5 was treated with methacrylic chloride to give 1,4-bis(4-((2-methacryloxyethyl)oxy)phenylamino)anthraquinone (6) (Scheme 1, step c). The obtained blue chromophore 6 shows absorption maxima at 408, 600 and 644 nm in the UV–vis

Glycosylation efficiencies on different solid supports using a hydrogenolysis-labile linker

• Mayeul Collot,
• Steffen Eller,
• Markus Weishaupt and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2013, 9, 97–105, doi:10.3762/bjoc.9.13

• site, which was obtained by removal of the tetrahydropyran (THP) protecting group after coupling to the solid support. A terephthalic chromophore was incorporated into the linker to facilitate the UV detection during HPLC analysis or purification. The linker was directly attached to chloro

• -functionalized resins, which resulted in an amide bond that is stable under Zemplén conditions. Linker 1 was prepared starting from chromophore fragment 7 and masked amine 12 (Scheme 3, Supporting Information File 1). Fragment 7 was synthesized starting from aminopentanol 3 and acyl chloride 4. Following the

• in the automated solid-phase oligosaccharide synthesis. A linker that can be cleaved by hydrogenolysis and incorporates a chromophore to facilitate LC–MS analysis and purification was developed and served as example for glycosylation studies involving different solid supports. Cleavage of this linker

An improved synthesis of a fluorophosphonate–polyethylene glycol–biotin probe and its use against competitive substrates

• Hao Xu,
• Hairat Sabit,
• Gordon L. Amidon and
• H. D. Hollis Showalter

Beilstein J. Org. Chem. 2013, 9, 89–96, doi:10.3762/bjoc.9.12

• an alternative and more expeditious synthesis. This was driven by several concerns of the original route including (a) a poor overall yield, (b) challenges in the chromatographic purification of some intermediates due to their hydrophilicity and lack of a UV chromophore, and (c) generating and then

• studies. Due to the absence of a UV chromophore, the purity of FP–PEG–biotin 1 could not be determined by HPLC. TLC analysis was also problematic due to its reactivity with the highly polar solvent mixture required to move it up a plate. Nevertheless, we deem 1 to be of high purity due to the cleanliness

• group (in place of the TBS of the original synthesis) onto the PEG moiety to facilitate the early stages of the synthesis by providing a UV-active chromophore for easy detection; (b) introduction of a high yielding two-step iodination process, which avoids chromatography; and (c) reversing the sequence

A chemist and biologist talk to each other about caged neurotransmitters

• Graham C.R. Ellis-Davies

Beilstein J. Org. Chem. 2013, 9, 64–73, doi:10.3762/bjoc.9.8

• isolation. Thus, to solve the biological problem provided by the biologist (Hess), a newer caging chromophore [18] had to be synthesized by a chemist (Carpenter). Thus, chemists came to play a crucial role in the caged compound field. Chemistry at the service of biology is not unusual or unique, as the

• nitroindolinyl-caged transmitters [26][27][32][36]. Because of this problem, chemists have resorted to inserting a spacer unit between the caging chromophore and the substrate [7][55][56][57][58][59]. This strategy has been very successful in creating some highly stable caged compounds, but sometimes at the

• of uncaging involves two completely distinct properties [80]. First, we must consider how well a molecule absorbs light, through the molar extinction coefficient, ε. This property measures how effectively a chromophore absorbs photons. Thus, fluorescein (ε = 80,000/M/cm) absorbs light much better

Polar reactions of acyclic conjugated bisallenes

• Reiner Stamm and
• Henning Hopf

Beilstein J. Org. Chem. 2013, 9, 36–48, doi:10.3762/bjoc.9.5

• valuable for structure assignment; they clearly show that the products obtained possess a conjugated triene chromophore. The formation of the monochlorides very likely proceeds via the carbocationic intermediates 49/50 and 52/53 (R = CH3). For the generation of the aromatic isomers of the substrate we

• of a diene chromophore (see Supporting Information File 1). Repeating the bromine addition experiment with the fully substituted bisallene derivative 11 also leads to bromine addition as demonstrated by GC–MS analysis of the raw product mixture, but all attempts to separate at least the major adducts

• importance are its amide bands (3515 and 1679 cm−1) in the IR spectrum and the absorption maximum at 284 nm in the electronic spectrum (triene chromophore). The central double bond of the triene system is trans-configured (3J = 15.2 Hz) [35]. The main product is the β-lactam derivate 71. Since this primary

Acylsulfonamide safety-catch linker: promise and limitations for solid–phase oligosaccharide synthesis

• Jian Yin,
• Steffen Eller,
• Mayeul Collot and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2012, 8, 2067–2071, doi:10.3762/bjoc.8.232

• linker 1 [13][14] (Figure 1) has been developed, which can be readily cleaved from the resin by basic methanolysis. The released chromophore-containing part, such as aromatic benzyl ether protecting groups, facilitates the purification of the synthetic oligosaccharides by HPLC. Final deprotection of the

Flow photochemistry: Old light through new windows

• Jonathan P. Knowles,
• Luke D. Elliott and
• Kevin I. Booker-Milburn

Beilstein J. Org. Chem. 2012, 8, 2025–2052, doi:10.3762/bjoc.8.229

• up the photolysis of a strongly absorbing chromophore. Here, a thin film of the substrate solution flows down a glass plate or tube in close proximity to the light source. The short path length leads to very efficient irradiation. The downside is that residence time is short and often the solution

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

• ratiometric or switch-on responses even for the paramagnetic metal ions [17][18][19]. The first luminescence chemodosimeter for Hg2+ was developed by Czarnik et al. and was based on the Hg2+-mediated desulfurization of anthracene-thioamide chromophore [20][21]. Following this pioneering report, several other

Cyclodextrin nanosponge-sensitized enantiodifferentiating photoisomerization of cyclooctene and 1,3-cyclooctadiene

• Wenting Liang,
• Cheng Yang,
• Masaki Nishijima,
• Gaku Fukuhara,
• Tadashi Mori,
• Andrea Mele,
• Franca Castiglione,
• Fabrizio Caldera,
• Francesco Trotta and
• Yoshihisa Inoue

Beilstein J. Org. Chem. 2012, 8, 1305–1311, doi:10.3762/bjoc.8.149

• mechanism, we examined the solvent effects on the chromophore conformation of CDNS by circular dichroism spectroscopy and also on the CDNS-sensitized photoisomerization. Indeed, the ICD intensity was enhanced upon the addition of ethanol to an aqueous solution of CDNS (Figure 2b), which encouraged us to

Partial thioamide scan on the lipopeptaibiotic trichogin GA IV. Effects on folding and bioactivity

• Marta De Zotti,
• Barbara Biondi,
• Cristina Peggion,
• Matteo De Poli,
• Haleh Fathi,
• Simona Oancea,
• Claudio Toniolo and
• Fernando Formaggio

Beilstein J. Org. Chem. 2012, 8, 1161–1171, doi:10.3762/bjoc.8.129

• nm) and near-UV (400–250 nm) CD spectra of the three peptides, recorded in 2,2,2-trifluoroethanol (TFE) solution, are illustrated in Figure 3. In the near-UV region, in which the peptide chromophore is known not to absorb, both ψ[CS-NH]2 and ψ[CS-NH]9 display two well-separated Cotton effects at

• intense maximum (265 nm) and an extremely weak maximum (320 nm) found in the corresponding region of the UV absorption spectra (not shown) of our peptides in the same solvent. We assign the two bands to the π→π* and n→π* transitions, respectively, of thioamide chromophore [29][30][32][33][34][35][36][40

• ][41][43]. We attribute the overall much less intense CD spectrum of ψ[CS-NH]5 in this region primarily to a thioamide chromophore positioned in this peptide between the two achiral Gly5 and Gly6 residues, i.e., it is significantly far apart from the nearest chiral center (the Leu7 α-carbon). In the

Control over molecular motion using the cis–trans photoisomerization of the azo group

• Estíbaliz Merino and
• María Ribagorda

Beilstein J. Org. Chem. 2012, 8, 1071–1090, doi:10.3762/bjoc.8.119

• , azobenzene and glutamate derivative (MAG) was used as a photochromic agonist of an ionotropic glutamate receptor (iGluR) (Figure 5a) [89][90][91]. The chromophore consists of a terminal maleimide unit, which is associated covalently to the protein via a cysteine residue, a central azobenzene unit and a

Recent advances towards azobenzene-based light-driven real-time information-transmitting materials

• Jaume García-Amorós and
• Dolores Velasco

Beilstein J. Org. Chem. 2012, 8, 1003–1017, doi:10.3762/bjoc.8.113

• -chromophore and the thermal cis-to-trans isomerisation, the kinetics and mechanism are also discussed as a key point for reaching azoderivatives endowed with fast thermal back-isomerisation kinetics. Keywords: kinetics; light-controlled materials; molecular switches; photochromic switches; push–pull

• similar behaviour: relaxation times of 33 min and 306 ms in toluene and ethanol, respectively [59]. The differential kinetic behaviour detected for azophenols 11–13 in toluene and ethanol clearly evidences that the intermolecular interactions established between both the chromophore and the solvent