Pigmentosins from Gibellula sp. as antibiofilm agents and a new glycosylated asperfuran from Cordyceps javanica

• Soleiman E. Helaly,
• Wilawan Kuephadungphan,
• Patima Phainuphong,
• Mahmoud A. A. Ibrahim,
• Kanoksri Tasanathai,
• Suchada Mongkolsamrit,
• Janet Jennifer Luangsa-ard,
• Souwalak Phongpaichit,
• Vatcharin Rukachaisirikul and
• Marc Stadler

Beilstein J. Org. Chem. 2019, 15, 2968–2981, doi:10.3762/bjoc.15.293

• ) were not elucidated previously. Therefore, electronic circular dichroism (ECD) measurements combined with time-dependent density functional theory (TDDFT) calculations of ECD data of compound 1 in MeOH at the B3LYP/6-311+G* level of theory were carried out. The CD spectrum of 1 showed strong Cotton

Influence of the cis/trans configuration on the supramolecular aggregation of aryltriazoles

• Sara Tejera,
• Giada Caniglia,
• Rosa L. Dorta,
• Andrea Favero,
• Javier González-Platas and
• Jesús T. Vázquez

Beilstein J. Org. Chem. 2019, 15, 2881–2888, doi:10.3762/bjoc.15.282

• stabilization of the supramolecular aggregation of bis(4-bromophenyl)triazoles. The trans or cis spatial disposition of the triazole rings is highly important for gelation, with the cis configuration having higher propensity. Keywords: circular dichroism; cis/trans configuration; gels; triazole; X-ray

• hydroxymethyl group in position 6 in the gg rotamer, likely linked through hydrogen bonds. Electronic circular dichroism (ECD) is a powerful technique to study supramolecular systems [20][21], since many interactions responsible for the presence of CD Cotton effects occur through space, such as the well-known

Isolation of fungi using the diffusion chamber device FIND technology

• Benjamin Libor,
• Henrik Harms,
• Stefan Kehraus,
• Ekaterina Egereva,
• Max Crüsemann and
• Gabriele M. König

Beilstein J. Org. Chem. 2019, 15, 2191–2203, doi:10.3762/bjoc.15.216

• together with the NOESY correlation between H3-14 and H3-15 the relative configurations of C-2, C-6 and C-7 could thus be delineated as 2S*, 6S* and 7S*, respectively. The absolute configurations of C-2, C-6 and C-7 were determined by comparison of our experimental with simulated circular dichroism (CD

α-Photooxygenation of chiral aldehydes with singlet oxygen

• Dominika J. Walaszek,
• Magdalena Jawiczuk,
• Jakub Durka,
• Olga Drapała and
• Dorota Gryko

Beilstein J. Org. Chem. 2019, 15, 2076–2084, doi:10.3762/bjoc.15.205

• by electronic circular dichroism spectroscopy’). Functionalization of 3,4-diphenylbutanal (1) at the α-position can lead to four stereoisomers, but photooxygenation catalyzed by secondary amines 16, 17 and 18 furnished only two of them. The diastereoisomeric ratio was always close to 2:1, the same as

• ). Additional experiments indicated that acetonitrile required in the first step has a negative effect on the subsequent α-photooxygenation reaction (for details see Supporting Information File 1). Determination of the absolute configuration of the product by electronic circular dichroism spectroscopy Despite

• anti’-6 obtained from the reaction with diarylprolinol silyl ether (R)-18 (Table 1, entry 5) were analyzed using electronic circular dichroism spectroscopy (ECD) and TD-DFT methods. So-called in situ methodology with dimolybdenum tetraacetate (19) acting as auxiliary chromophores which proved a very

Bipolenins K–N: New sesquiterpenoids from the fungal plant pathogen Bipolaris sorokiniana

• Chin-Soon Phan,
• Hang Li,
• Simon Kessler,
• Peter S. Solomon,
• Andrew M. Piggott and
• Yit-Heng Chooi

Beilstein J. Org. Chem. 2019, 15, 2020–2028, doi:10.3762/bjoc.15.198

• -13 were α-oriented. The absolute configuration of 1 was determined to be 1R,3R,6S,7R,13S by comparison of the experimental electronic circular dichroism (ECD) spectrum with time-dependent density functional theory (TDDFT)-calculated ECD spectra of the two possible enantiomers of 1 (Figure 4

Complexation of chiral amines by resorcin[4]arene sulfonic acids in polar media – circular dichroism and diffusion studies of chirality transfer and solvent dependence

• Bartosz Setner and
• Agnieszka Szumna

Beilstein J. Org. Chem. 2019, 15, 1913–1924, doi:10.3762/bjoc.15.187

• chemistry. In the present study we demonstrate that resorcin[4]arene sulfonic acid (RSA) interacts with chiral amines (amino acid derivatives and aminocavitands) to form inclusion complexes and capsules based on electrostatic interactions. The complexes were characterized by circular dichroism and DOSY NMR

• aromatic analytes afford strongly induced circular dichroism (ICD) signals in the near-UV and visible regions [18]. Endo-functionalized molecular tubes, first reported by the Glass group [19], were used by the Jiang group for molecular recognition and chiroptical sensing of epoxides in water. The absolute

• configurations and ee values were simultaneously determined by circular dichroism spectroscopy [20]. Recently, dyn[4]arene, first described by the Leclaire and co-authors [21], was demonstrated to bind various lysine derivatives which leads to distinct ICD outputs in buffered aqueous solution [22]. Even a larger

Synthesis, enantioseparation and photophysical properties of planar-chiral pillar[5]arene derivatives bearing fluorophore fragments

• Guojuan Li,
• Chunying Fan,
• Guo Cheng,
• Wanhua Wu and
• Cheng Yang

Beilstein J. Org. Chem. 2019, 15, 1601–1611, doi:10.3762/bjoc.15.164

• due to the bulky chromophore introduced, and the resolution of the enantiomers was achieved due to the bulky size of the fluorophores. The absolute configuration of the enantiomers was determined by circular dichroism (CD) spectra. The solvent-induced aggregation behavior was investigated with the

• : aggregation; circular dichroism; chirality; click chemistry; macrocycles; pillar[5]arenes; Introduction Planar-chiral compounds are structurally appealing and potentially applicable in various functional materials such as chiral discriminators [1][2], chiral polymers, supramolecular sensors [3] and chiral

• ). These results demonstrated that the bulky substituents DPA or perylene effectively prevent the ring rotations, and therefore making the separation of Rp and Sp conformers possible. Figure 3d and e show the circular dichroism (CD) and UV–vis spectra of each fraction for P5A-DPA. The CD signals of both

Efficient resolution of racemic crown-shaped cyclotriveratrylene derivatives and isolation and characterization of the intermediate saddle isomer

• Sven Götz,
• Andreas Schneider and
• Arne Lützen

Beilstein J. Org. Chem. 2019, 15, 1339–1346, doi:10.3762/bjoc.15.133

• phase (Figure 1). This simple procedure was successfully used for the semi-preparative separation of 156 mg of (rac)-1. It was possible to separate more than 25 mg substance per injection giving both enantiomers of 1 in an enantiomeric excess of >99%. Electronic circular dichroism spectra (ECD) were

6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288

• attributed to the conformational restriction of the sugar [62][64]. The Gibbs free energy of duplex formation corresponded well with the observed Tm values. CD spectroscopy Circular dichroism of ON1–7 paired with DNA or RNA was recorded to further analyze their helical conformation and to compare it with

A self-assembled photoresponsive gel consisting of chiral nanofibers

• Lei Zou,
• Dan Han,
• Zhiyi Yuan,
• Dongdong Chang and
• Xiang Ma

Beilstein J. Org. Chem. 2018, 14, 1994–2001, doi:10.3762/bjoc.14.174

• absorption spectroscopy, circular dichroism, scanning electron microscopy and rheological techniques. This work provides a new method for facile synthesis of chiro-optical gels. Keywords: chirality; nanostructure; organogel; photoresponse; self-assembly; Introduction Supramolecular gels [1][2] immobilized

• compound 3. These two azobenzene moieties within the molecule are close and the dimerization of the UPy moiety results in a more crowded structure. The circular dichroism (CD) spectrum was then measured to trace the different states of aggregation in solution of compound 3 in different solvents. Benzene

Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae

• Bimal Koirala,
• Robert A. Hillman,
• Erin K. Tiwold,
• Michael A. Bertucci and
• Yftah Tal-Gan

Beilstein J. Org. Chem. 2018, 14, 1769–1777, doi:10.3762/bjoc.14.151

• scaffold had on its conformation. We utilized circular dichroism (CD) spectroscopy to evaluate the main structural motifs of the different analogs. Since only conserved modifications were introduced to the CSP1 sequence, we did not expect significant changes to the overall structural characteristics

• absorbance of ortho-nitrophenol (ONP). Abs550 is the scatter from cell debris, which, when multiplied by 1.75 approximates the scatter observed at 420 nm. t is the duration of incubation with ONPG in minutes, v is volume of lysate in milliliters, and Abs600 reflects cell density. Circular dichroism (CD

Design and biological characterization of novel cell-penetrating peptides preferentially targeting cell nuclei and subnuclear regions

• Anja Gronewold,
• Mareike Horn and
• Ines Neundorf

Beilstein J. Org. Chem. 2018, 14, 1378–1388, doi:10.3762/bjoc.14.116

• in triplicate. Cells treated with medium only served as negative control and their fluorescent signal was subtracted from all other samples in each set of experiment. Circular dichroism spectra of the novel peptides solved in 10 mM phosphate buffer (pH 7) (A), or phosphate buffer with the addition of

Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• single base mismatch in the center of the DNA strand. Two base mismatches in the center of the DNA counterstrand led to a complete loss of hybridization [64]. In addition to these thermal denaturation experiments, Bruice et al. also reported circular dichroism (CD) spectroscopic studies to obtain further

One hundred years of benzotropone chemistry

• Arif Dastan,
• Haydar Kilic and
• Nurullah Saracoglu

Beilstein J. Org. Chem. 2018, 14, 1120–1180, doi:10.3762/bjoc.14.98

• circular dichroism (CD) measurements, respectively (Scheme 36) [151]. In conjunction with the efficient preparation of 5H-benzo[7]annulen[1,2-b]naphthalenes as key intermediates to the naturally occurring red pigment radermachol (226), condensation of the anion of the isobenzofuranone 222 with 2,3

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

• fluorescein dyes to target mouse major satellite DNA using thermal denaturation, gel-shift electrophoresis, circular dichroism and fluorescence spectroscopy [89][90]. Some of these fluorescent probes were found to detect target sequences in mouse living cell lines and the nuclear substructures formed by

• , DNA-melting experiments, and circular dichroism (CD) analysis revealed these conjugates are high affinity sequence specific DNA groove binders and could successfully recognize a C·C mismatch in a DNA duplex. Recently, the binding mechanism of the anticancer drug cytarabine with calf thymus DNA (ct-DNA

• appropriate curvature helps them to bind with specific DNA sequence [129]. A series of arylimidamide analogues were synthesized and their binding affinities towards DNA minor groove was studied by Wilson et al. via fluorescence displacement titration, circular dichroism, DNase I footprinting, biosensor

Synthesis and in vitro biochemical evaluation of oxime bond-linked daunorubicin–GnRH-III conjugates developed for targeted drug delivery

• Sabine Schuster,
• Beáta Biri-Kovács,
• Bálint Szeder,
• Viktor Farkas,
• László Buday,
• Zsuzsanna Szabó,
• Gábor Halmos and
• Gábor Mező

Beilstein J. Org. Chem. 2018, 14, 756–771, doi:10.3762/bjoc.14.64

• formaldehyde (e.g., from the softeners of the plastic tubes) not only during the reaction steps (cleavage, ligation) but also under the HPLC purification conditions which has a high impact on the yield [35]. Secondary structure determination by electronic circular dichroism spectroscopy ECD spectra of GnRH-III

• , 3 µm) (Hesperia, CA) using a linear gradient from 2–70% B in 25 min (eluent A: ddH2O, 0.1% HCOOH; eluent B: 80% ACN, 0.1% HCOOH at a flow rate of 0.2 mL/min). Spectra were recorded in positive ion mode in the 100–2500 m/z range. Electronic circular dichroism spectroscopy Electronic circular

• dichroism (ECD) spectra were recorded on a Jasco J-810 (Jasco International Co., Ltd., Tokyo, Japan) spectropolarimeter at 25 °C in quartz cells of 0.02 cm path length, under constant nitrogen flush. The instrument was calibrated with 0.06% (w/v) ammonium-D-camphor-10-sulfonate (Katayama Chemical, Japan) in

Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

• Françoise Debart,
• Christelle Dupouy and
• Jean-Jacques Vasseur

Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32

• the 5’-end) prone to form a G-quadruplex structure (Scheme 7). Circular dichroism studies have indicated that TBANB adopts a random coil structure while after reduction caused by chemical (Na2S2O4) or enzymatic (nitroreductase with NADH) stimuli, the formation of a G-quadruplex structure was evidenced

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

• conformations depending on conditions. Z-DNA, a GC-repeat rich, thermodynamically less preferred, left-handed helical conformation that is favored by cytosine methylation is known to form in vivo under negative supercoiling or high salt concentrations [64][65][66][67][68]. Circular dichroism is traditionally

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

• compatible conditions and are extensively time consuming. Therefore, in search for faster methods which can be applied to conditions that are at least similar to the naturally occurring ones, a set of polarization spectroscopy methods has shown highly promising results. Electronic circular dichroism (ECD) is

• between nucleic acids and small ligands. This tutorial aims to help researchers entering the research field to organize experiments accurately and to interpret the obtained data reliably. Keywords: circular dichroism; emission-based dichroism; groove binding; intercalation; linear dichroism; non-covalent

• interactions; nucleic acids recognition; vibrational circular dichroism; Review 1. Introduction Many biological molecules are chiral and chromophoric among which the most important examples include proteins and nucleic acids. Moreover, the chiral constituents of natural biopolymers are homochiral, e.g

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

Recent progress in the racemic and enantioselective synthesis of monofluoroalkene-based dipeptide isosteres

• Myriam Drouin and
• Jean-François Paquin

Beilstein J. Org. Chem. 2017, 13, 2637–2658, doi:10.3762/bjoc.13.262

• important for the activity (Table 6). Conformational studies of the fluorinated peptide using circular dichroism also showed that the incorporation of the monofluoroalkene did not perturb the formation of the secondary structure of the peptide, which was a α-helix. Dory and co-workers wanted to study 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

• chromophores [19][20][21]. This helical twist was evidenced by circular dichroism, in particular a strong bisignate Cotton effect for the DNA-templated pyrene assemblies [19][20]. Figure 1 shows selected examples of pyrene-modified nucleic acids and nucleosides. On the other hand, pyrene–nucleobase conjugates

Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

• Vladimir Kubyshkin and
• Nediljko Budisa

Beilstein J. Org. Chem. 2017, 13, 2442–2457, doi:10.3762/bjoc.13.241

• 8c was also prepared for comparison (Scheme 5A). Measured circular dichroism (CD) spectra for the hexapeptides 8a–c (Figure 5, top) demonstrate strong negative bands at 204 nm and weak positive bands at 227 nm, which indicate a polyproline-II fold. Remarkably, this spectral shape was observed for all

• the midpoint and the top of the logD projection peak. Experimental logD values were compared to the calculated ones (Equation 5). Circular dichroism spectra were recorded in a 1 mm quartz cell at 298 K in methanol (HPLC grade) or aqueous potassium phosphate buffer (50 mM, pH 7.01 at 297 K). The

• solvent dielectric constant, ε. The trans/cis ratios were determined from the 1H and 19F NMR spectra at 298 K. Solvent set: C6D6, CDCl3, CD2Cl2, CD3OD, CD3CN, D2O. For details see Table S1 in Supporting Information File 1. Mean residue molar circular dichroism (Δε) of peptides 8–10 in methanol (left) and

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

• among α-glycosyl 1,2-diacyl-sn-glycerols in the solution state [16]. Probably, the two gauche conformers, namely gt(+) and gg(−), are stabilized in a manner so as to permit stacking interactions between the 1,2-diacyl chains. In our previously reported circular dichroism (CD) studies [17][18], helical

• > 3JH1proS,H2 Hz). This rule is maintained among 1,2-diacetyl-, 1,2-dipalmitoyl-, and 1,2-dibenzoyl-sn-glycerols and substituents at the sn-3 position. The validity of this rule is confirmed in a comparative analysis using circular dichroism (CD) spectroscopy [17][18]. The current study applies these

2-Methyl-2,4-pentanediol (MPD) boosts as detergent-substitute the performance of ß-barrel hybrid catalyst for phenylacetylene polymerization

• Julia Kinzel,
• Daniel F. Sauer,
• Marco Bocola,
• Marcus Arlt,
• Tayebeh Mirzaei Garakani,
• Andreas Thiel,
• Klaus Beckerle,
• Tino Polen,
• Jun Okuda and
• Ulrich Schwaneberg

Beilstein J. Org. Chem. 2017, 13, 1498–1506, doi:10.3762/bjoc.13.148

• FhuA ΔCVFtev (see MD simulation results, Figure 2C and D), ensuring the long-term stability of the protein (Figure S1, Supporting Information File 1). The aforementioned features are consistent with results from circular dichroism (CD) spectroscopy (Figure S1, Supporting Information File 1), showing

• the transmembrane region could not be achieved, leading to an incomplete coverage of the hydrophobic belt. D) Water molecules in the first solvation sphere (<5 Å) are partly covering the hydrophobic belt of FhuA ΔCVFtev using 126 MPD molecules. MPD, 2-methyl-2,4-pentanediol. Circular dichroism spectra