Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• the DNA/RNA conjugate NDI-GCP2 showed also aggregation along the ds-polynucleotide and AFM and DLS demonstrated that NDI-GCP2 has pronounced ds-DNA condensation ability. Keywords: AFM; circular dichroism; DNA/RNA recognition; fluorescence; guanidinio-carbonyl-pyrrole; naphthalene diimide

• monitoring, fluorescence is still the most popular method [8][9][10][11]. However, many new techniques or established ones with increased sensitivity are constantly improved or developed to report complementary to fluorescence. For instance, circular dichroism (CD) spectropolarimetry, highly sensitive to

Muyocopronones A and B: azaphilones from the endophytic fungus Muyocopron laterale

• Ken-ichi Nakashima,
• Junko Tomida,
• Tomoe Tsuboi,
• Yoshiaki Kawamura and
• Makoto Inoue

Beilstein J. Org. Chem. 2020, 16, 2100–2107, doi:10.3762/bjoc.16.177

• configurations were determined using the modified Mosher’s method and through comparisons of experimental and calculated electronic circular dichroism data. In addition, muyocopronone B (2) was found to exhibit a weak antibacterial activity against some Gram-positive bacteria. Keywords: azaphilones; endophytic

• wavelength around 360 nm corresponding to 7S and 7R [22][23][24]. Therefore, positive Cotton effects at 325 and 355 nm in the electronic circular dichroism (ECD) spectrum of 1 indicated that the absolute configuration of the C-7 position was S (Figure 3). Furthermore, the coupling constant between H-10/H-11

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• )-polynucleotides. The DNA/RNA binding-induced circular dichroism (ICD) response of NDI at 450–550 nm strongly depended on the length and rigidity of the linker to the amino acid unit, which controls the orientation of the NDI unit inside within the intercalative binding site. The ICD selectivity also depends on

• the type of polynucleotide, thus the studied NDI dyes act as dual fluorimetric/ICD probes for sensing the difference between here used GC-DNA, AT-DNA and AU-RNA. Keywords: amino acid–fluorophore conjugate; circular dichroism; DNA/RNA recognition; fluorescence; intercalation; naphthalene diimide

• cations and water molecules from the DNA/RNA grooves [44][45] by side arms interacting with the grooves and thereby supporting the binding. Circular dichroism experiments CD spectroscopy is an ideal method to get insight into the changes of the polynucleotide secondary structure upon binding of small

pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide

• Goutam Ghosh and
• Gustavo Fernández

Beilstein J. Org. Chem. 2020, 16, 2017–2025, doi:10.3762/bjoc.16.168

• fractal-like morphologies, as verified by circular dichroism (CD), Fourier-transform infrared (FTIR) spectroscopy, thioflavin T (ThT) fluorescence spectroscopy assay, and atomic force microscopy (AFM). Upon changing the pH value (using pH 5.5 and 13.0), PEP-1 forms different types of secondary structures

Copper catalysis with redox-active ligands

• Agnideep Das,
• Yufeng Ren,
• Cheriehan Hessin and
• Marine Desage-El Murr

Beilstein J. Org. Chem. 2020, 16, 858–870, doi:10.3762/bjoc.16.77

• precursors affords both enantiomers Δ-10 (from CuClO4) and Λ-10 from (Cu(CH3CN)4PF6). UV–vis and circular dichroism spectroscopic studies evidence that the helical chirality exhibited by these two catalysts could be reversed by redox stimuli. These complexes could perform enantioselective Michael addition

Synthesis and circularly polarized luminescence properties of BINOL-derived bisbenzofuro[2,3-b:3’,2’-e]pyridines (BBZFPys)

• Ryo Takishima,
• Yuji Nishii,
• Tomoaki Hinoue,
• Yoshitane Imai and
• Masahiro Miura

Beilstein J. Org. Chem. 2020, 16, 325–336, doi:10.3762/bjoc.16.32

• -shifted than 4a despite such a sterically demanding group usually disturbs intermolecular stacking interactions. Subsequently, the chiroptical properties of the synthesized compounds were evaluated (Figure 2 and Figure 3, Table 2). The circular dichroism (CD) spectra in CHCl3 solutions showed apparent

Absolute configurations of talaromycones A and B, α-diversonolic ester, and aspergillusone B from endophytic Talaromyces sp. ECN211

• Ken-ichi Nakashima,
• Junko Tomida,
• Takao Hirai,
• Yoshiaki Kawamura and
• Makoto Inoue

Beilstein J. Org. Chem. 2020, 16, 290–296, doi:10.3762/bjoc.16.28

• planar structures of 1 and 2 were elucidated by extensive spectroscopic analyses. Furthermore, the absolute configurations of 1–4 were determined by single-crystal X-ray diffraction and electronic circular dichroism spectroscopy (ECD). In addition, the crystallographic data for 5 were updated for the

• been omitted for clarity. b) Electronic circular dichroism spectra of 1 (black solid line) and 2 (red dashed line). a) ORTEP drawing of 3, with thermal ellipsoids indicating 50% probability. b) Electronic circular dichroism spectra of 3 (black solid line) and 4 (red dashed line). a) ORTEP drawing of 5

• , with thermal ellipsoids indicating 50% probability. b) Electronic circular dichroism spectrum of 5. 1H (400 MHz) and 13C (100 MHz) NMR data for 1 and 2 in CDCl3. Supporting Information Supporting Information File 265: A phytogenic tree for ECN211 and related species and NMR spectra of 1 and 2

Reversible photoswitching of the DNA-binding properties of styrylquinolizinium derivatives through photochromic [2 + 2] cycloaddition and cycloreversion

• Sarah Kölsch,
• Heiko Ihmels,
• Jochen Mattay,
• Norbert Sewald and
• Brian O. Patrick

Beilstein J. Org. Chem. 2020, 16, 111–124, doi:10.3762/bjoc.16.13

• –d were further investigated by circular dichroism (CD) and flow linear dichroism (LD) spectroscopy [74][75] in phosphate buffer at different ligand-to-DNA ratios (LDR). The mixtures of compounds 3a–d with ct DNA showed clear induced circular dichroism (ICD) and LD bands in the absorption region of

Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides

• Sabrina Müller,
• Jannik Paulus,
• Jochen Mattay,
• Heiko Ihmels,
• Veronica I. Dodero and
• Norbert Sewald

Beilstein J. Org. Chem. 2020, 16, 60–70, doi:10.3762/bjoc.16.8

• derivatives was proven by CD titration experiments. The resulting induced circular dichroism (ICD) bands of the bound ligands, together with the photometric determination of the dsDNA melting temperature, revealed a significant stabilization of the DNA upon association with the ligand. The (Z)-azobenzene

• photoswitchable polyamides From a pool of new azobenzene-containing polyamides, we present the most promising photoswitchable representatives containing six or eight Im/Py units (P1, P2, and P3, Scheme 1). Their binding capability to dsDNA was analyzed by titration and temperature-dependent circular dichroism

• % P1; 67% P2; after 1 d: 76% P3). Analysis of polyamide–DNA interaction by induced circular dichroism CD spectroscopic analysis is suitable for the characterization of DNA minor groove binders, providing semiquantitative information about binding affinity and thermal stability of the target dsDNA [47

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