Hyper-reticulated calixarene polymers: a new example of entirely synthetic nanosponge materials

• Alberto Spinella,
• Marco Russo,
• Antonella Di Vincenzo,
• Delia Chillura Martino and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2018, 14, 1498–1507, doi:10.3762/bjoc.14.127

• varied though maintaining a fixed chromophore moiety. The results obtained, expressed in terms of percent of guest absorbed, are summarized in Table 1. As we can notice, the parent p-nitroaniline (1) is absorbed fairly well by CaNSs under neutral conditions, up to an extent comparable with the one

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• presence of the complementary DNA target as a result of the restricted rotation of the TO chromophore upon its intercalation into the base stack (Figure 19). Considering the bulkiness of the TO dye, it is quite likely that the opposite nucleobase was forced away from the duplex and so did not directly

Synthesis and spectroscopic properties of β-meso directly linked porphyrin–corrole hybrid compounds

• Baris Temelli and
• Hilal Kalkan

Beilstein J. Org. Chem. 2018, 14, 187–193, doi:10.3762/bjoc.14.13

• obtaining multiporphyrin arrays [7][8][9] that could stabilize only metal ions in a bivalent state. To overcome this limitation, porphyrin conjugates with different chromophore groups such as fullerene [10][11][12], BODIPY [13][14][15], corrole [16][17][18][19][20][21][22][23], phthalocyanine [24][25][26

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• match tC and/or tCO. To this end we developed the nitro-version of tC, 7-nitro-1,3-diaza-2-oxophenothiazine (tCnitro) (Scheme 3) [14][38][45]. From UV–vis spectroscopy we showed that it, as do tC and tCO, forms stable, B-form duplexes and stacks firmly inside the DNA. It is a non-emissive chromophore

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• chromophore also absorbs in this range, the deconvolution of all contributions is not trivial (see interpretation of results in the chapters of the corresponding methods); b) monitoring changes in polarization spectra at λ > 300 nm for ligands that have corresponding chromophores. This is the most common used

• (ECD) will be discussed first as the most common technique with the least pitfalls. Thus it is most often appropriate for the characterization of the systems of interest. Then, LD follows as a complementary method used to reveal the mutual orientation of the ligand chromophore with respect to the DNA

• that at least the chromophoric portions that are associated with the observed transitions of the compound are not intercalated (inserted between the base pairs, thus being perpendicular to the DNA chiral axis). Instead, the direction of the chromophore transition moment (e.g., the chromophore long axis

Halogen-containing thiazole orange analogues – new fluorogenic DNA stains

• Aleksey A. Vasilev,
• Meglena I. Kandinska,
• Stanimir S. Stoyanov,
• Stanislava B. Yordanova,
• David Sucunza,
• Juan J. Vaquero,
• Obis D. Castaño,
• Stanislav Baluschev and
• Silvia E. Angelova

Beilstein J. Org. Chem. 2017, 13, 2902–2914, doi:10.3762/bjoc.13.283

• atoms (connected directly to the chromophore or as side groups) on the molar absorptivity and the fluorescence intensity of a series of new TO analogues. Photophysical properties of a series of TO analogues that have fluoro- or trifluoromethyl groups connected to the heterocyclic end groups of the

• (Experimental part) with ethanol as the reaction medium. It is worth noting that replacement of the methanol with the environmentally more benign and less harmful ethanol significantly decreases the formation of blue-colored self-condensation byproducts (probably a chromophore constructed from quinolone and

• quinoline moiety of the chromophore leads to a bathochromic shift of the longest wavelength absorption maximum in all new compounds when compared to TO. The presence of a benzyl substituent in compounds 5a–d doesn’t have significant effect on the maxima position, slightly shifting the transition further

The photodecarboxylative addition of carboxylates to phthalimides as a key-step in the synthesis of biologically active 3-arylmethylene-2,3-dihydro-1H-isoindolin-1-ones

• Ommid Anamimoghadam,
• Saira Mumtaz,
• Anke Nietsch,
• Gaetano Saya,
• Cherie A. Motti,
• Jun Wang,
• Peter C. Junk,
• Ashfaq Mahmood Qureshi and
• Michael Oelgemöller

Beilstein J. Org. Chem. 2017, 13, 2833–2841, doi:10.3762/bjoc.13.275

• [41], followed by amination [42] furnishes the desired target compounds. The amino group is introduced in the final step as it would otherwise interfere with the desired photoreaction. In fact, amines are very potent electron donors and are easily oxidized by the excited phthalimide chromophore [43

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

• Marco Russo,
• Daniele La Corte,
• Annalisa Pisciotta,
• Serena Riela,
• Rosa Alduina and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2751–2763, doi:10.3762/bjoc.13.271

• values for p-nitroanilines are affected by an induced circular dichroism effect due to the interaction between the dipole moments of the polarized chromophore guest moiety and of the cyclodextrin cavity. Therefore, these parameters provide an estimation of the time-averaged tilt angle between the

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• , or oligothymidine, T10, respectively, as template strands were investigated in water. Due to the nearly complete insolubility of the chromophore–nucleobase conjugates in water it is possible to follow this self-assembly simply by UV–vis absorption spectroscopy (Figure 5). Only those chromophore

• –nucleoside conjugates that are bound and assembled along the (dA)10 or T10 template are kept soluble in aqueous media. A higher concentrated stock solution of each chromophore–nucleobase conjugate was prepared in DMSO and added as aliquots to an aqueous solution (2.5 μM) of the (dA)10 or T10 template. The

• chromophore conjugate and allows more efficient self-assembly, whereas the carbonyl group of 3 induces a more rigid conformation that interferes with self-assembly. To gain more insight about self-assembly of 3 and 5, additional titration experiments were done with the double-stranded template (dA)10-T10 that

Structure–property relationships and third-order nonlinearities in diketopyrrolopyrrole based D–π–A–π–D molecules

• Jan Podlesný,
• Lenka Dokládalová,
• Oldřich Pytela,
• Adam Urbanec,
• Milan Klikar,
• Numan Almonasy,
• Tomáš Mikysek,
• Jaroslav Jedryka,
• Iwan V. Kityk and
• Filip Bureš

Beilstein J. Org. Chem. 2017, 13, 2374–2384, doi:10.3762/bjoc.13.235

• , respectively. Commercially available 4-(N,N-dimethylamino)phenylboronic, 4-methoxyphenylboronic, and 2-thienylboronic acids completed with tributyl(5-methoxythiophen-2-yl)stannane, prepared from 2-methoxythiophene [33], were used. Chromophore 4a was also attempted by Suzuki–Miyaura reaction using the

• (ΔλmaxA = 32 nm). However, chromophore 2b with a 4-methoxyphenyl donor possesses almost identical absorption maxima as thiophen-2-yl derivative 3b (λmaxA = 605 nm), implying their similar electron-releasing abilities. A combination of both methoxy and thiophene auxiliary donors as in 4b shifted its

• as follows: Generally largest THG responses were recorded for chromophores with extended π-system in series b. Chromophore 1b bearing a strong N,N-dimethylamino donor and an extended π-system showed the highest third-order NLO response of 130 pm2/V2. However, a comparison of electron donors is less

Synthesis and application of trifluoroethoxy-substituted phthalocyanines and subphthalocyanines

• Satoru Mori and
• Norio Shibata

Beilstein J. Org. Chem. 2017, 13, 2273–2296, doi:10.3762/bjoc.13.224

• conjugation. The electronic interaction between the covalently connected chromophore unit leads to important changes in the absorption spectra and so these dimers are expected to serve as attractive building blocks for the construction of multicomponent photoinduced electron transfer supramolecular systems

Remarkable functions of sn-3 hydroxy and phosphocholine groups in 1,2-diacyl-sn-glycerolipids to induce clockwise (+)-helicity around the 1,2-diacyl moiety: Evidence from conformation analysis by ¹H NMR spectroscopy

• Yoshihiro Nishida,
• Mengfei Yuan,
• Kazuo Fukuda,
• Kaito Fujisawa,
• Hirofumi Dohi and
• Hirotaka Uzawa

Beilstein J. Org. Chem. 2017, 13, 1999–2009, doi:10.3762/bjoc.13.196

• representative model for the 1,2-diacyl-sn-glycerols, as categorized in Scheme 1. Although the exciton chirality CD methodology is not applicable for these 1,2-diacyl-sn-glycerolipids without an appropriate UV/CD chromophore, 1H NMR spectroscopy will permit the precise determination of their helical

p-tert-Butylthiacalix[4]arenes functionalized by N-(4’-nitrophenyl)acetamide and N,N-diethylacetamide fragments: synthesis and binding of anionic guests

• Alena A. Vavilova and
• Ivan I. Stoikov

Beilstein J. Org. Chem. 2017, 13, 1940–1949, doi:10.3762/bjoc.13.188

• p-tert-butylthiacalix[4]arene 4 is also of interest because this fragment contains a polar NH group able to interact with anionic substrates and a chromophore fragment necessary for the spectrophotometric detection of the complex formation. In this regard, the alkylation of monosubstituted

Theoretical simulation of the infrared signature of mechanically stressed polymer solids

• Matthew S. Sammon,
• Milan Ončák and
• Martin K. Beyer

Beilstein J. Org. Chem. 2017, 13, 1710–1716, doi:10.3762/bjoc.13.165

• Hessian matrix in redundant internal coordinates under the influence of an external mechanical force [75][80]. So far, most studies on infrared spectroscopy of stressed polymers focused on polypropylene [30]. Lacking a pronounced infrared chromophore, however, the spectrum is relatively complicated

Correlation of surface pressure and hue of planarizable push–pull chromophores at the air/water interface

• Frederik Neuhaus,
• Fabio Zobi,
• Gerald Brezesinski,
• Marta Dal Molin,
• Stefan Matile and
• Andreas Zumbuehl

Beilstein J. Org. Chem. 2017, 13, 1099–1105, doi:10.3762/bjoc.13.109

• observed hue of the monolayer starting at 18 mN/m. Although the measured areas per molecule are not fully quantitative [23], a value of 38 Å2 can be assumed for the flipper chromophore in the condensed state. Upon expansion, the hue relaxes back to the initial range. Compared to compression the hue

Cycloheximide congeners produced by Streptomyces sp. SC0581 and photoinduced interconversion between (E)- and (Z)-2,3-dehydroanhydrocycloheximides

• Li Yang,
• Ping Wu,
• Jinghua Xue,
• Huitong Tan,
• Zheng Zhang and
• Xiaoyi Wei

Beilstein J. Org. Chem. 2017, 13, 1039–1049, doi:10.3762/bjoc.13.103

• intensities) at 36 h (Figure 5), whereas no changes were detected for the solutions kept in the dark (Figure 5), confirming the interconversion is a photoinduced geometrical isomerization. Compounds 2 and 3 possess a chiral 6-ethylidene-2-cyclohexenone chromophore. To the best of our knowledge, Z/E

• photoisomerizations of compounds with this kind of chromophore had been rarely reported. For better understanding the insights into this reaction, we conducted theoretical investigation using the truncated structures 2a and 3a (Figure 1). At first, the lowest-energy geometries of 2a and 3a in MeOH in the ground (S0

• Φ of these geometries are presented in Table 2. Compound 4 has a structure similar to 2 except for replacement of the C2–C3 double bond by a single bond. Its geometrical isomerization was not observed in the present study, but (E)-2-ethylidenecyclohexanone, which has a similar chromophore to that of

Energy down converting organic fluorophore functionalized mesoporous silica hybrids for monolith-coated light emitting diodes

• Markus Börgardts and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2017, 13, 768–778, doi:10.3762/bjoc.13.76

• , stable structures like silica-based materials, in particular mesoporous silica, offer favorable properties [4][10]. Eventually, organic–inorganic hybrid materials can be easily accessed by covalent ligation of the functional guest chromophore to a silica host matrix [11][12]. As a consequence the

• inherent robustness and stability of the rigid inorganic silica material can be combined with the functionality and tunability of the organic chromophore. In addition, these mesoporous materials possess defined pore structures in which the organic dye can be homogeneously distributed [13]. Thereby

Novel β-cyclodextrin–eosin conjugates

• Gábor Benkovics,
• Damien Afonso,
• András Darcsi,
• Szabolcs Béni,
• Sabrina Conoci,
• Éva Fenyvesi,
• Lajos Szente,
• Milo Malanga and
• Salvatore Sortino

Beilstein J. Org. Chem. 2017, 13, 543–551, doi:10.3762/bjoc.13.52

• -cyclodextrin–EoY conjugate retains both the fluorescence properties and the capability to photogenerate singlet oxygen of the unbound chromophore. In contrast, the corresponding β-cyclodextrin–EoB conjugate did not show either relevant emission or photosensitizing activity probably due to aggregation in

Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications

• Srikala Pangannaya,
• Neethu Padinchare Purayil,
• Shweta Dabhi,
• Venu Mankad,
• Prafulla K. Jha,
• Satyam Shinde and
• Darshak R. Trivedi

Beilstein J. Org. Chem. 2017, 13, 222–238, doi:10.3762/bjoc.13.25

• position of the imine linkage connecting the conjugated naphthyl group. The pyridine ring possessing –CN and –NO2 functionalities in R1 and R2 reflect their identity as a signaling unit/chromophore. In total, the nature and position of binding site and signaling unit play the key role in the chromogenic

Interactions between photoacidic 3-hydroxynaphtho[1,2-b]quinolizinium and cucurbit[7]uril: Influence on acidity in the ground and excited state

• Jonas Becher,
• Daria V. Berdnikova,
• Darinka Dzubiel,
• Heiko Ihmels and
• Phil M. Pithan

Beilstein J. Org. Chem. 2017, 13, 203–212, doi:10.3762/bjoc.13.23

• appropriately sized CB[n]. To test this hypothesis we synthesized 3-hydroxynaphtho[1,2-b]quinolizinium (2, Figure 1) and studied its prototropic equilibria in the ground and excited state along with the influence of CB[7] on its acidity. We chose the naphthoquinolizinium chromophore because of its positive

• ]. Notably, the chromophore of the oxyanion-substituted quinolizinium derivative 2cB resembles the well-established solvatochromic pyridinium-N-phenolate betaine dyes that are employed as polarity probes [53]. Correspondingly, the derivative 2cB shows a similar positive solvatochromism, i.e., a blue shift of

Effects of solvent additive on “s-shaped” curves in solution-processed small molecule solar cells

• John A. Love,
• Shu-Hua Chou,
• Ye Huang,
• Guilllermo C. Bazan and
• Thuc-Quyen Nguyen

Beilstein J. Org. Chem. 2016, 12, 2543–2555, doi:10.3762/bjoc.12.249

• , National Taiwan University, Taipei, 10617, Taiwan 10.3762/bjoc.12.249 Abstract A novel molecular chromophore, p-SIDT(FBTThCA8)2, is introduced as an electron-donor material for bulk heterojunction (BHJ) solar cells with broad absorption and near ideal energy levels for the use in combination with common

• , with peak absorption at 650 nm. The red-shifted absorption of p-SIDT(FBTThCA8)2 with respect to p-SIDT(FBTTh2)2, whose absorption onset in the solid state occurs at 670 nm, is further confirmation that the addition of electron-withdrawing endgroups reduces the bandgap of the chromophore. Importantly

High performance p-type molecular electron donors for OPV applications via alkylthiophene catenation chromophore extension

• Paul B. Geraghty,
• Calvin Lee,
• Jegadesan Subbiah,
• Wallace W. H. Wong,
• James L. Banal,
• Mohammed A. Jameel,
• Trevor A. Smith and
• David J. Jones

Beilstein J. Org. Chem. 2016, 12, 2298–2314, doi:10.3762/bjoc.12.223

• ), quinquethiophene) were synthesised to examine the influence of chromophore extension on the device performance and stability for OPV applications. The BTxR (x = 4, butyl, and x = 8, octyl) series of materials were synthesised by varying the oligothiophene π-bridge alkyl substituent to examine structure–property

• relationships in OPV device performance. The devices assembled using electron donors with an extended chromophore (BQR and BPR) are shown to be more thermally stable than the BTR containing devices, with un-optimized efficiencies up to 9.0% PCE. BQR has been incorporated as a secondary donor in ternary blend

• route to facilitate translation to printing programs? Structure–property relationships: Can we modify the BTR chromophore length or alkyl side-chain length thereby improving device thermal stability and device performance? We report here a simplified synthetic route to a series of BTR analogues (Figure

Synthesis and properties of fluorescent 4′-azulenyl-functionalized 2,2′:6′,2″-terpyridines

• Adrian E. Ion,
• Liliana Cristian,
• Mariana Voicescu,
• Masroor Bangesh,
• Augustin M. Madalan,
• Daniela Bala,
• Constantin Mihailciuc and
• Simona Nica

Beilstein J. Org. Chem. 2016, 12, 1812–1825, doi:10.3762/bjoc.12.171

• spectroscopy in dichloromethane solution. The 2,2′:6′,2″-terpyridine moiety is an excellent chromophore with an absorption maximum at 279 in dichloromethane solution [8]. Upon 4′-substitution with a phenyl group the longest-wavelength absorption is not affected, only the fluorescence emission is shifted

A flow reactor setup for photochemistry of biphasic gas/liquid reactions

• Josef Schachtner,
• Patrick Bayer and
• Axel Jacobi von Wangelin

Beilstein J. Org. Chem. 2016, 12, 1798–1811, doi:10.3762/bjoc.12.170

• other (e.g., choice of chromophore vs wavelength of light vs type of (transparent) reactor walls, concentration of reagents vs residence time for complete conversion vs length of reactor vs flow rate, etc.). The awareness of such multidimensional interdependencies is a prerequisite for the expedient

• the need for filters and allows high quantum yields by the correct matching of lamp emission and chromophore absorption bands (Figure 4 and Figure 5). The absence of UV emission bands regarding the used red and warm white LEDs enhances the selectivity of many organic reactions by suppression of