Impact of multivalent charge presentation on peptide–nanoparticle aggregation

• Daniel Schöne,
• Boris Schade,
• Christoph Böttcher and
• Beate Koksch

Beilstein J. Org. Chem. 2015, 11, 792–803, doi:10.3762/bjoc.11.89

• included in this study by adding one, two, or three heptad repeats containing alanine in their f-positions (R2A3, R2A4 and R2A5); these were based on the sequence of R2A2 (Figure 1). Secondary and quaternary structure of the model peptides Circular dichroism (CD) spectroscopy and analytical

TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy

• Dnyaneshwar B. Gophane and
• Snorri Th. Sigurdsson

Beilstein J. Org. Chem. 2015, 11, 219–227, doi:10.3762/bjoc.11.24

• in the melting temperature, while UA destabilized the duplex by more than 10 °C. Circular dichroism (CD) measurements indicated that all three labels were accommodated in B-DNA duplex. The mobility of the spin label TA varied with different base-pairing partners in duplex DNA, with the TA•T pair

• gel electrophoresis. The incorporation of TA, UA and UC into DNA was confirmed by MALDI–TOF mass spectrometry (Table S1, Supporting Information File 1). Circular dichroism measurements showed that the incorporation of TA, UA and UC does not alter the B-DNA conformation of DNA duplexes containing these

A comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR)

• Darinka Dzubiel,
• Heiko Ihmels,
• Mohamed M. A. Mahmoud and
• Laura Thomas

Beilstein J. Org. Chem. 2014, 10, 2963–2974, doi:10.3762/bjoc.10.314

• of 1 nm, a recording speed of 1 nm s−1 and a time per data point of 0.5 s. For the temperature dependent circular dichroism (CD) experiments, solutions of the ILPR-quadruplex a2 (20 μM) and the ligand (20 μM) were prepared in potassium phosphate buffer (95 mM, pH 7.0) and measured after an

Trogopterins A–C: Three new neolignans from feces of Trogopterus xanthipes

• Soyoon Baek,
• Xuikui Xia,
• Byung Sun Min,
• Chanil Park and
• Sang Hee Shim

Beilstein J. Org. Chem. 2014, 10, 2955–2962, doi:10.3762/bjoc.10.313

• comparing the circular dichroism (CD) data to those of previously reported neoligans containing a dihydrobenzofuran skeleton [17]. The CD of compound 1 showed positive cotton effects at 255 and 327 nm along with a negative cotton effect at 234 nm. These features were very similar to those of neolignans [17

• with a Jasco P1000 digital polarimeter. UV spectra were recorded by a Hewlett Packard 8453 UV–vis spectrometer. CD spectra were obtained with a Jasco J-715 circular dichroism spectrophotometer. 1D and 2D NMR were performed on a VNS 600 MHz spectrometer operating at 600 MHz for protons and 150 MHz for

Preparation of neuroprotective condensed 1,4-benzoxazepines by regio- and diastereoselective domino Knoevenagel–[1,5]-hydride shift cyclization reaction

• László Tóth,
• Yan Fu,
• Hai Yan Zhang,
• Attila Mándi,
• Katalin E. Kövér,
• Tünde-Zita Illyés,
• Attila Kiss-Szikszai,
• Balázs Balogh,
• Tibor Kurtán,
• Sándor Antus and
• Péter Mátyus

Beilstein J. Org. Chem. 2014, 10, 2594–2602, doi:10.3762/bjoc.10.272

• performed on a Jasco HPLC system with Chiralpak IA column (5 μm, 150 × 4.6 mm, hexane/dichloromethane 80:20 or 70:30 eluents, 1 mL min−1 flow rate) and HPLC-ECD spectra were recorded in stopped-flow mode on a JASCO J-810 electronic circular dichroism spectropolarimeter equipped with a 10 mm HPLC flow cell

Reversibly locked thionucleobase pairs in DNA to study base flipping enzymes

• Christine Beuck and
• Elmar Weinhold

Beilstein J. Org. Chem. 2014, 10, 2293–2306, doi:10.3762/bjoc.10.239

• 1I6S-Et-S4U2 and 1G6S-Et-S4U2 clearly confirms the shift of the thio-nucleobase absorption band over 300 nm towards lower wavelengths as it is typical for S-alkylated thio-nucleobases (Figure 2c and Figure 3c). Circular dichroism [53] spectroscopy is sensitive to the overall global conformation of

Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

• Marijana Radić Stojković,
• Marko Škugor,
• Łukasz Dudek,
• Jarosław Grolik,
• Julita Eilmes and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2175–2185, doi:10.3762/bjoc.10.225

• recognition; circular dichroism; DBTAA-adenine conjugate; ds-DNA/RNA; minor groove binding; nucleic acids; Introduction The majority of natural and artificial applications involving small molecule-DNA/RNA recognition depend on several non-covalent binding modes. Typical examples are double-stranded (ds) DNA

• due to the extensive broadening and decreasing of proton signals, which eventually merged with the baseline (details about unsuccessful NMR experiments see [11]). Circular dichroism (CD) experiments CD spectropolarimetry offers unique possibilities for the investigation of small molecule–DNA/RNA

Multicomponent reactions in nucleoside chemistry

• Mariola Koszytkowska-Stawińska and
• Włodzimierz Buchowicz

Beilstein J. Org. Chem. 2014, 10, 1706–1732, doi:10.3762/bjoc.10.179

• %. The diastereoisomers were separated and their absolute configuration was determined using X-ray crystallography and circular dichroism spectroscopy. The stereochemical outcome of the synthesis of compounds 79 and 80 was suggested to result from some internal asymmetric induction of the chiral residue

Clicked and long spaced galactosyl- and lactosylcalix[4]arenes: new multivalent galectin-3 ligands

• Silvia Bernardi,
• Paola Fezzardi,
• Gabriele Rispoli,
• Stefania E. Sestito,
• Francesco Peri,
• Francesco Sansone and
• Alessandro Casnati

Beilstein J. Org. Chem. 2014, 10, 1672–1680, doi:10.3762/bjoc.10.175

• -tagged full-length Gal-3 was expressed in E. coli BL21 and purified on IMAC (immobilized metal ion affinity chromatography) columns. Purified protein was characterized by SDS-PAGE electrophoresis, circular dichroism (CD), and MS/MS analysis upon digestion on trypsin gel (see Figure S15, Supporting

• /glycocalixarene binding experiments), 1H NMR spectra of selected intermediates, and final glycocalixarenes 1–4 together with electrophoresis gel, circular dichroism spectrum and thermal unfolding of purified Gal-3. Supporting Information File 610: Experimental part. Acknowledgements The authors gratefully

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

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

• oxidized with osmium tetroxide to a diol. Absolute configurations of the allylic alcohol as well as the diol were determined by circular dichroism (CD) spectroscopy using the in situ dimolybdenum methodology. Keywords: CD-spectroscopy; Cotton effect; multivalent glycosystems; osmylation; stereoselective

• circular dichroism spectroscopy (CD) using the in situ dimolybdenum methodology (see next chapter). Next steps of the synthesis consisted of the protection of the C6–OH as benzyl ether (to 12) and osmylation of the double bond. The cis-dihydroxylation provided, as single stereoisomer, a diol to which

• surprising. The assignment of the configuration of this diol was further confirmed also by the CD methodology; this is discussed in the next chapter. Determination of the absolute configuration of 11 and 13 It is widely acceptable that the circular dichroism (CD) spectroscopy utilizing the in situ

cis–trans Isomerization of silybins A and B

• Michaela Novotná,
• Radek Gažák,
• David Biedermann,
• Florent Di Meo,
• Petr Marhol,
• Marek Kuzma,
• Lucie Bednárová,
• Kateřina Fuksová,
• Patrick Trouillas and
• Vladimír Křen

Beilstein J. Org. Chem. 2014, 10, 1047–1063, doi:10.3762/bjoc.10.105

• optically pure compounds was determined by using NMR and comparing their electronic circular dichroism data with model compounds of known absolute configurations. Mechanisms for cis–trans-isomerization of silybin are proposed and supported by quantum mechanical calculations. Keywords: 2,3-cis-silybin

• -cis-10,11-trans-isomer 12 and a minor 23-O-acetyl-2,3-trans-10,11-cis-isomer 13 (Scheme 3). Surprisingly, the absolute configuration at C-2, C-3 of compound 13 was the opposite of 1a (2S,3S vs 2R,3R), which was confirmed by a comparison of their electronic circular dichroism (ECD) data. Formation of

A new building block for DNA network formation by self-assembly and polymerase chain reaction

• Holger Bußkamp,
• Sascha Keller,
• Marta Robotta,
• Malte Drescher and
• Andreas Marx

Beilstein J. Org. Chem. 2014, 10, 1037–1046, doi:10.3762/bjoc.10.104

• circular dichroism (CD) spectroscopy. The CD spectra of Y-shaped bDNA ODN I bound to oligonucleotides 8–11, respectively, show dichroic peaks similar to those of unmodified DNA duplexes, indicating that bDNA maintain the B-DNA form (see Supporting Information File 1). As the Y-shaped bDNA is able to

Decandrinin, an unprecedented C₉-spiro-fused 7,8-seco-ent-abietane from the Godavari mangrove Ceriops decandra

• Hui Wang,
• Min-Yi Li,
• Félix Zongwe Katele,
• Tirumani Satyanandamurty,
• Jun Wu and
• Gerhard Bringmann

Beilstein J. Org. Chem. 2014, 10, 276–281, doi:10.3762/bjoc.10.23

• , Ceriops decandra, collected in the estuary of Godavari, Andhra Pradesh. The constitution and the relative configuration of 1 were determined by HRMS (ESI) and extensive NMR investigations, and the absolute configuration by circular dichroism (CD) and optical-rotatory dispersion (ORD) spectroscopy in

• combination with quantum-chemical calculations. Decandrinin is the first 7,8-seco-ent-abietane. Keywords: abietane; absolute configuration; Ceriops decandra; circular dichroism; decandrinin; Rhizophoraceae; Introduction Ceriops decandra is a mangrove of the family Rhizophoraceae. It is widely distributed

• NMR investigations, and by circular dichroism (CD) and optical-rotatory dispersion (ORD) spectroscopy in combination with quantum-chemical calculations. Results and Discussion Decandrinin (1) was obtained as a colorless solid. Its molecular formula was established as C20H28O4 by HRMS (ESI) (m/z

Charge-transfer interaction mediated organogels from 18β-glycyrrhetinic acid appended pyrene

• Jun Hu,
• Jindan Wu,
• Qian Wang and
• Yong Ju

Beilstein J. Org. Chem. 2013, 9, 2877–2885, doi:10.3762/bjoc.9.324

• in the formation of CT gels is demonstrated through the formation of gels in a variety of solvents. Thermal stability, stoichiometry, scanning electron microscopy (SEM), optical micrographs, and circular dichroism (CD) are performed on these CT gels to investigate their thermal and assembly

• reported to aggregate in both forms, right-handed and left-handed helices in equal proportions [57][58]. Therefore, circular dichroism (CD) was used to investigate the chirality of these CT gels and sol. The results showed a strong negative signal around 430 nm and a positive signal around 550 nm

• Finnigan TSQ spectrometer in positive mode; circular dichroism spectra were performed on JASCO J-815 CD spectrometer; scanning electron microscopy (SEM) images were performed on a Variable Pressure Tescan Vega3 SBU; optical micrographs were performed on a Olympus CKX41 microscope. Samples for optical

Synthesis of enantiomerically pure (2S,3S)-5,5,5-trifluoroisoleucine and (2R,3S)-5,5,5-trifluoro-allo-isoleucine

• Holger Erdbrink,
• Elisabeth K. Nyakatura,
• Susanne Huhmann,
• Ulla I. M. Gerling,
• Dieter Lentz,
• Beate Koksch and
• Constantin Czekelius

Beilstein J. Org. Chem. 2013, 9, 2009–2014, doi:10.3762/bjoc.9.236

• peptide (KX), its α-helix propensity can be calculated from circular dichroism (CD) spectroscopy [8][9]. Therefore, 5-F3Ile was converted into its Fmoc analogue and subsequently used in solid-phase synthesis of K-5-F3Ile applying standard Fmoc-based chemistry (see Supporting Information File 1) [30]. The

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

Molecular assembly of amino acid interlinked, topologically symmetric, π-complementary donor–acceptor–donor triads

• M. B. Avinash,
• K. V. Sandeepa and
• T. Govindaraju

Beilstein J. Org. Chem. 2013, 9, 1565–1571, doi:10.3762/bjoc.9.178

• ). In order to gain further insights into the nature of molecular interactions, 1, 2 and 3 were subjected to circular dichroism (CD) spectroscopic studies. The CD spectra of 1 in DMSO show positive excitonic cotton effects, indicating a P-type helical assembly (Figure 3a). However, with increase in the

• -21G basis set) to get additional insights about their conformations (Figure 5a, 5b). After careful evaluation of absorption, fluorescence, circular dichroism, NMR as well as PXRD data, the plausible molecular stacking model depicting the charge-transfer complexation under enhanced hydrophobic forces

Linkage of α-cyclodextrin-terminated poly(dimethylsiloxanes) by inclusion of quasi bifunctional ferrocene

• Helmut Ritter,
• Berit Knudsen and
• Valerij Durnev

Beilstein J. Org. Chem. 2013, 9, 1278–1284, doi:10.3762/bjoc.9.144

• by circular dichroism spectroscopy [8] and thermogravimetric analysis [9]. In addition, the complex of ferrocene and α-CD could be detected in the gas phase by mass spectrometry [10]. Recently, there have been many reports focusing on the use of α-CD in aqueous solution as a mobile phase for optical

Inclusion of the insecticide fenitrothion in dimethylated-β-cyclodextrin: unusual guest disorder in the solid state and efficient retardation of the hydrolysis rate of the complexed guest in alkaline solution

• Dyanne L. Cruickshank,
• Natalia M. Rougier,
• Raquel V. Vico,
• Susan A. Bourne,
• Elba I. Buján,
• Mino R. Caira and
• Rita H. de Rossi

Beilstein J. Org. Chem. 2013, 9, 106–117, doi:10.3762/bjoc.9.14

• shift was noted and the change in absorbance was not large enough for an accurate determination of the binding constant. The induced circular dichroism (ICD) spectrum of DIMEB and 1 is shown in Figure 9a, where the spectrum recorded for β-CD and TRIMEB with 1 is also shown for comparison. It can be seen

• that the native β-CD and DIMEB show a negative and a positive peak (Figure 9a). The negative peaks appear at 320 and 324 nm and the positive ones at 260 and 265 nm for β-CD and DIMEB, respectively. The positive peak in the circular dichroism spectrum is slightly displaced from the maximum of the UV–vis

• DIMEB·1 structure, viewed along [100] (left) and [010] (right). The symmetry related molecules are distinguished by the reverse green and black host and guest molecules. For clarity, only guest molecules A and B are shown and the hydrogen atoms have been omitted. Induced circular dichroism (a) and UV

Multivalent display of the antimicrobial peptides BP100 and BP143

• Imma Güell,
• Rafael Ferre,
• Kasper K. Sørensen,
• Esther Badosa,
• Iteng Ng-Choi,
• Emilio Montesinos,
• Eduard Bardají,
• Lidia Feliu,
• Knud J. Jensen and
• Marta Planas

Beilstein J. Org. Chem. 2012, 8, 2106–2117, doi:10.3762/bjoc.8.237

• were significantly more active against both pathogens and were able to kill 99.99% of all cells within 30–90 min at 2.5 μM. Circular dichroism We investigated the secondary structures of carbopeptides 1 and 3 by analyzing their CD spectra at 100 μM in (i) 10 mM sodium phosphate buffer at pH 7.4; (ii

• (Bruker Daltonics). High-resolution mass spectrometry (HRMS) was recorded on a Bruker MicroToF-Q MALDI instrument by using a hybrid quadrupole time-of-flight mass spectrometer (University of Zaragoza). Circular dichroism (CD) measurements were obtained using a Jasco spectropolarimeter (J-810, Easton, MD

• , Madrid, Spain) as a positive control. The percentage of hemolysis (H) was calculated by using the following equation: H = 100 × [(Op−Ob)/(Om−Ob)], where Op was the density for a given compound concentration, Ob for the buffer, and Om for the melittin positive control. Circular dichroism spectroscopy

Dimerization of a cell-penetrating peptide leads to enhanced cellular uptake and drug delivery

• Jan Hoyer,
• Ulrich Schatzschneider,
• Michaela Schulz-Siegmund and
• Ines Neundorf

Beilstein J. Org. Chem. 2012, 8, 1788–1797, doi:10.3762/bjoc.8.204

• -butyloxycarbonyl (Boc). Indeed, we did not observe concomitant deprotection of lysine side chains, which was favored by the fact that Mtt groups situated at the N-terminus are even more acid-sensitive than Nε-Mtt groups [25]. The structural analysis of the (sC18)2 conjugates by circular dichroism spectroscopy did

• analytical RP-HPLC. For the peptide sequences see Table 1. Circular dichroism spectroscopy Circular dichroism spectra were recorded on a Jasco spectropolarimeter J 715 at 20 °C in 10 mM phosphate buffer (pH 7.0) with or without addition of 50% trifluoroethanol, respectively. The concentration of the peptides

• triplicate with n = 2. Error bars represent the standard deviation. Chromatogram and ESI-MS of purified Cym2-GFL-(sC18)2. The gradient was 10→60% acetonitrile in water over 45 min. Circular dichroism spectra of the (sC18)2 conjugates. Spectra were acquired in 10 mM phosphate buffer with or without 50

Antifreeze glycopeptide diastereomers

• Lilly Nagel,
• Carsten Budke,
• Axel Dreyer,
• Thomas Koop and
• Norbert Sewald

Beilstein J. Org. Chem. 2012, 8, 1657–1667, doi:10.3762/bjoc.8.190

• replacement of L-threonine by its allo-L-diastereomer. Both glycopeptides were analyzed regarding their conformational properties, by circular dichroism (CD), and their ability to inhibit ice recrystallization in microphysical experiments. Keywords: bioorganic chemistry; circular dichroism; glycopeptides

Organocatalytic asymmetric addition of malonates to unsaturated 1,4-diketones

• Sergei Žari,
• Tiiu Kailas,
• Marina Kudrjashova,
• Mario Öeren,
• Ivar Järving,
• Toomas Tamm,
• Margus Lopp and
• Tõnis Kanger

Beilstein J. Org. Chem. 2012, 8, 1452–1457, doi:10.3762/bjoc.8.165

• configuration of the product 3a was determined by a comparison of the experimental and calculated vibrational circular dichroism (VCD) spectra. DFT calculations (method B3PW91/6-311G**) of a series of conformers of compound 3a with R-configuration were performed. Calculations of harmonic vibrational frequencies

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

• substrates, including some pharmaceuticals [25], enzymes [26], pollutants [27], polymers [28], agrochemicals [29], and metal ions [30]. The complexation behavior of 1Z and 2ZZ with CDNSs was examined by means of circular dichroism spectroscopy, showing negative induced circular dichroism (ICD) at the 1La

• the steric hindrance in the network polymer and/or the less efficient complexation inside the nanoparticle of CDNS would be responsible. The circular dichroism spectral changes observed for the more cross-linked CDNSs 4 and 5 upon binding 1Z or 2ZZ were too small to allow quantitative evaluation of

• units with pH was examined by circular dichroism spectroscopy. As shown in Figure 2a, increasing the solution pH caused a significant enhancement of the negative ICD of CDNS 3. This seems reasonable, as the ionization of the carboxylic acid moieties on the PM units (pKa1 = 2.93 for pyromellitic acid