Nocarimidazoles C and D, antimicrobial alkanoylimidazoles from a coral-derived actinomycete Kocuria sp.: application of ¹J_C,H coupling constants for the unequivocal determination of substituted imidazoles and stereochemical diversity of anteisoalkyl chains in microbial metabolites

• Md. Rokon Ul Karim,
• Enjuro Harunari,
• Amit Raj Sharma,
• Naoya Oku,
• Kazuaki Akasaka,
• Daisuke Urabe,
• Mada Triandala Sibero and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 2719–2727, doi:10.3762/bjoc.16.222

• purification was achieved by preparative HPLC (Cosmosil AR-II, Nacalai Tesque Inc., 10 × 250 mm, 4 mL/min, UV detection at 254 nm) with an isocratic elution of MeCN/0.1% HCO2H (42:58) to afford nocarimidazole C (1, 2.4 mg, tR 8.45 min), nocarimidazole D (2, 3.2 mg, tR 14.9 min), nocarimidazole A (3, 3.8 mg, tR

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes

• Lena Reinke,
• Julia Bartl,
• Marcus Koch and
• Stefan Kubik

Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219

• /bjoc.16.219 Abstract Gold nanoparticles covered with a mixture of ligands of which one type contains solubilizing triethylene glycol residues and the other peripheral zinc(II)–dipicolylamine (DPA) complexes allowed the optical detection of hydrogenphosphate, diphosphate, and triphosphate anions in

• )–dipicolylamine complexes beyond 25% had a negative impact on the limit of detection and the optical response. Transmission electron microscopy provided evidence that the changes of the nanoparticle properties observed in the presence of the phosphates were due to a nanoparticle crosslinking, consistent with the

• conformational reorganization of the linker connecting the chromophore with the surface. The likely most frequently used strategy of analyte detection relies on the color change of AuNP solutions resulting from analyte-induced nanoparticle crosslinking. Depending on whether soluble or insoluble aggregates are

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• formed to another carbohydrate unit. Crucially, the linkage detection in Privateer does not rely at all on metadata present in the structure file. Instead, linkages are identified based on the perceived chemistry of the input model: which atoms are close enough – but not too close – to be plausibly

• , glycoprotein models deposited in the PDB feature flaws ranging from minor irregularities to gross modelling errors [14][17][41][64]. The automated validation of minor irregularities was already possible with automated tools such as pdb-care [37], CARP [65], and Privateer [24]. However, the automated detection

• of gross modelling errors is currently a challenge due to the lack of publicly available tools. Our newly developed computational bridge between structural biology and glycomics databases makes the detection of gross modelling errors easier, as demonstrated by the following examples. Example 1 – 2H6O

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• . If a signal broadens beyond detection and thus disappears from the spectrum, be it due to aggregation or intermediate exchange kinetics, it is also impossible to trace its trajectory and determine the chemical shift perturbation. In the case of a bifunctional GCP ligand binding to survivin [46], the

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• information, coupled with the emergence of new platforms and technologies, has benefitted glycoscience to the point of enabling the detection and high-resolution determination and representation of complex glycans [1]. Increasing numbers of carbohydrate sequences have accumulated throughout extensive work in

Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties

• Anka Utama Putra,
• Deniz Çakmaz,
• Nurgül Seferoğlu,
• Alberto Barsella and
• Zeynel Seferoğlu

Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189

• excitation leads to a red-shifted emission which is viable for the detection of various substrates in biological tissues and samples [28][29][30]. Recently, there was an increasingly growing interest in studies regarding push-pull organic molecules comprising of the dicyanomethylene group as a strong

• light indicated that the dye was deprotonated. Indeed, the addition of only 5 equiv of TFA regenerated the light yellow color of the solution indicative for the reversed protonation of 12. All dyes, except 8, showed this reversibility. Furthermore, the limits of detection (LOD) and quantification (LOQ

Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• utilizes a different mechanism of binding the ligands to the surface. Choosing an appropriate surface often depends on the type of glycoconjugates to be printed, as well as the GBP and detection wavelengths used. For example, a nitrocellulose surface has an intrinsic high background when scanned at 488 nm

• wavelength, thus making the surface incompatible with detection reagents which rely on this wavelength. While it is possible to use nitrocellulose slides at 488 nm wavelength with lower detector sensitivity (PMT setting) and lower scan power (laser power), it might be more advisable to check other

• placed on slide (≈70 μL), and a coverslip is placed on top to spread the sample evenly across the array surface of the slide and helps to prevent evaporation during the assay. Detailed protocols for either method of microarray experiment and that cover different types of samples and detection methods are

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• assumed to not quantitatively affect detection. These results were concatenated into the final output file, where columns are the different samples and rows are the different peptide and glycoforms that have been analysed. The protein name of each glycosylated protein detected in the analysis was also

Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations

• Ian Walsh,
• Matthew S. F. Choo,
• Sim Lyn Chiin,
• Amelia Mak,
• Shi Jie Tay,
• Pauline M. Rudd,
• Yang Yuansheng,
• Andre Choo,
• Ho Ying Swan and
• Terry Nguyen-Khuong

Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176

• to facilitate better peak picking and quantitation with electropherograms that were composed of heterogeneous peak shapes in our glycan analysis. Peak detection and quantitation of non-Gaussian peaks using Riemann approximation Quantitation of sets of electropherograms that were similar (i.e

• µm i.d. uncoated bare fused capillary, HR-NCHO separation gel buffer (Sciex). The applied electric field strength was 1500 V/cm with the cathode at the injection side and the anode at the detection side (reversed polarity). Samples were electrokinetically injected using 1kV for 5 s. For migration

Isolation and structure determination of a tetrameric sulfonyl dilithio methandiide in solution based on crystal structure analysis and ⁶Li/¹³C NMR spectroscopic data

• Jürgen Vollhardt,
• Hans Jörg Lindner and
• Hans-Joachim Gais

Beilstein J. Org. Chem. 2020, 16, 2057–2063, doi:10.3762/bjoc.16.172

• dynamics were poor solubility and problems to locate the 13C signals of the dianionic C atoms or the detection of only broad ones. Knowledge of the solution structure of dilithio methandiides would be, however, highly desirable in order to obtain a more complete understanding of the reactivity and

• coordination chemistry in general, and of the dianionic C atom in particular. During the structural investigation of 2a it was observed that the Li2O-free methandiide is in contrast to (2a)6·Li2O·(THF)6 readily soluble in THF. 6Li and 13C NMR spectroscopy of 2a had led to the detection of an aggregate, a

• Li2 (δ = 1.17 pm) [15][51][52][53]. Essential for the success of the NMR spectroscopic investigation of 2a was the 13C,6Li labelling of the dilithio methandiide. It allowed the detection of the otherwise low intensity signals of the dianionic carbon atoms of the aggregates and the attainment of

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

• sensitivity to particular target, read-out accuracy, limits of detection, and selectivity at biorelevant conditions. Experimental All solvents were purchased from commercial sources and used as received. Solvents for spectroscopic studies were of spectroscopic grade. Polynucleotides poly(dA-dT)2, poly(AU

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• ), here exemplified by asparagusic acid. A persistent challenge in this evolution is the simultaneous and quantitative detection of cytosolic delivery and cytotoxicity in a high-throughput format. Here, we show that the combination of the HaloTag-based chloroalkane penetration assay (CAPA) with automated

• unorthodox COC chemistry covering ETPs [52], diselenolanes [53], and benzopolysulfanes [54], the activity gradually increased. The Achilles heel of much research on new transporters for cellular uptake, from CPPs and Schmuck cations to CPDs and COCs, is the quantitative detection of the delivery in the

• with the HC CAPA. To quantify the impact of the HC CAPA on the detection of the cytosolic delivery, the newly introduced peptide-based COC 23 was evaluated for the transport of a model protein with the new analytical improvements. With a CP50 value of 7.3 ± 0.5 μM with the mitochondrial mask, complex

Design, synthesis and application of carbazole macrocycles in anion sensors

• Alo Rüütel,
• Ville Yrjänä,
• Sandip A. Kadam,
• Indrek Saar,
• Mihkel Ilisson,
• Astrid Darnell,
• Kristjan Haav,
• Tõiv Haljasorg,
• Lauri Toom,
• Johan Bobacka and
• Ivo Leito

Beilstein J. Org. Chem. 2020, 16, 1901–1914, doi:10.3762/bjoc.16.157

• directed our efforts towards sensing carboxylates. The detection of these analytes is important in a number of areas and there is an obvious lack of easy-to-use sensing methods. Carboxylates are challenging analytes for two reasons. Firstly, binding is mainly achieved through either ion–ion interactions or

• transport phenomena and this semicircle was attributed to slow ion transfer kinetics at the ISM interfaces. Potentiometric calibrations in sodium acetate solutions were used to determine the linear ranges (R2 ≥ 0.999), slopes, and detection limits of the sensors (Table 2). Examples of the calibration curves

• variations in the position of the plug as a result of handling the reference electrode while setting up the measurements. This flow of chloride resulted in narrower linear ranges, lower slopes, and poorer detection limits due to the mixed responses to acetate and chloride. The degree of deviation from the

Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines

• Vladimir Kubyshkin

Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151

• [49][50]. The presence of a fluorine-rich group in the structure is also beneficial for the NMR studies based on the detection of the 19F nucleus [51][52][53]. Limited attention has been given to the polarity effects in the proline analogues though. Few studies reported peptides containing proline

Synthesis of 3-substituted isoxazolidin-4-ols using hydroboration–oxidation reactions of 4,5-unsubstituted 2,3-dihydroisoxazoles

• Lívia Dikošová,
• Júlia Laceková,
• Ondrej Záborský and
• Róbert Fischer

Beilstein J. Org. Chem. 2020, 16, 1313–1319, doi:10.3762/bjoc.16.112

• identified as a readily oxidizable polar component by permanganate detection even at room temperature. The prior attempts to cleave the Troc group by zinc dust in acetic acid [42] failed due to the reduction of the N–O bond. Conclusion In summary, we have developed a new synthetic approach towards 3

Synthesis and properties of quinazoline-based versatile exciplex-forming compounds

• Rasa Keruckiene,
• Simona Vekteryte,
• Ervinas Urbonas,
• Matas Guzauskas,
• Eigirdas Skuodis,
• Dmytro Volyniuk and
• Juozas V. Grazulevicius

Beilstein J. Org. Chem. 2020, 16, 1142–1153, doi:10.3762/bjoc.16.101

• 6.2 V could be attributed to energy barriers due to the high ionization potential (6.08 eV) of compound 1 (Figure 7e, inset). A relatively high maximum brightness of 3030 cd/m2 was achieved. Taking into account the rare detection of versatile exciplex-forming properties of compound 1 both with a donor

A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA

• Ekaterina A. Bryushkova,
• Erik R. Gandalipov and
• Julia V. Nuzhina

Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100

• types of compounds. It is most promising to develop simple and effective biosensors for the use in situations where traditional methods are not available due to their complexity and laboriousness. In this project, a novel smart deoxyribozyme-based fluorescent sensor for the detection of androgen

• mRNA molecule of the androgen receptor. The constructed sensor is easy to use, has high efficiency and selectivity for the RNA target, and can be reconstructed for the detection of various nucleic acid sequences due to its modular structure. Thus, similar biosensors may be useful for the differential

• electrode, covered by immobilizing enzyme glucose oxidase, for the detection of glucose [1]. A biosensor means a small molecular device that traditionally consists of a bioreceptor (enzyme, cell, aptamer, oligonucleotide, antibody, and other) for the specific recognition of the target molecule and a

Fluorinated phenylalanines: synthesis and pharmaceutical applications

• Laila F. Awad and
• Mohammed Salah Ayoup

Beilstein J. Org. Chem. 2020, 16, 1022–1050, doi:10.3762/bjoc.16.91

• , compared to, for example, magnetic resonance imaging (MRI). PET is particularly well-suited to differentiate neoplastic tissue from non-specific changes induced by chemotherapy treatments [85]. PET is particularly used for the early detection of tumors and metastases, and is an established tool for the

• used in PET due to its relatively long half-life (109 min). In this section we highlight two selected 18FPhe derivatives which are used for PET tumor detection. 4-Borono-2-[18F]fluoro-ᴅ,ʟ-phenylalanine ([18F]FBPA, 70), is a fluorinated derivative of the parent compound designed for boron neutron

Recent applications of porphyrins as photocatalysts in organic synthesis: batch and continuous flow approaches

• Rodrigo Costa e Silva,
• Luely Oliveira da Silva,
• Aloisio de Andrade Bartolomeu,
• Timothy John Brocksom and
• Kleber Thiago de Oliveira

Beilstein J. Org. Chem. 2020, 16, 917–955, doi:10.3762/bjoc.16.83

• the same authors using 2 mol % of a Ru complex as photocatalyst (44–88%) [24]. The mechanism proposed by the authors was supported by the detection of some reaction intermediates, and suggest that TPP works in both energy transfer and photoredox catalysis (Scheme 2). Subsequently, Gryko’s group

Cation-induced ring-opening and oxidation reaction of photoreluctant spirooxazine–quinolizinium conjugates

• Phil M. Pithan,
• Sören Steup and
• Heiko Ihmels

Beilstein J. Org. Chem. 2020, 16, 904–916, doi:10.3762/bjoc.16.82

• formation of the respective oxidation product caused the development of a broad absorption band between 425 nm and 500 nm and a new emission band at λfl = 628 nm, so that it may be employed as a selective chemosensor or chemodosimeter for the colorimetric and fluorimetric detection of Cu2+ and Fe3

• for the development of photochromic chemosensors that allow the colorimetric or fluorimetric detection of particular analytes [5][29][35][36][37][38][39][40][41]. Furthermore, studies of such spiro derivatives [16][42][43], specifically spiroindolinonaphthoxazines [44][45][46][47], have shown that the

• cations also caused a fluorimetric response due to the developing orange emission at λfl = 628 nm so that 3a may be employed as a selective chemosensor or chemodosimeter for the colorimetric and fluorimetric detection of Cu2+ and Fe3+, respectively. As shown by NMR spectroscopic and mass spectrometric

Bipyrrole boomerangs via Pd-mediated tandem cyclization–oxygenation. Controlling reaction selectivity and electronic properties

• Liliia Moshniaha,
• Marika Żyła-Karwowska,
• Joanna Cybińska,
• Piotr J. Chmielewski,
• Ludovic Favereau and
• Marcin Stępień

Beilstein J. Org. Chem. 2020, 16, 895–903, doi:10.3762/bjoc.16.81

• by means of chiral HPLC with CD detection, leading to enantioenriched samples of some boomerangs. The enantiomers of cR2O were found to racemize very fast, thus it was not possible to separate them. The cR3X systems, which contain a 7-membered ring, showed a remarkably diverse behavior. Enantiomers

Aldehydes as powerful initiators for photochemical transformations

• Maria A. Theodoropoulou,
• Nikolaos F. Nikitas and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2020, 16, 833–857, doi:10.3762/bjoc.16.76

• . Moreover, the excited 4-anisaldehyde (98) underwent energy transfer over the addition to the double bond of the alkene, as no Paterno–Büchi cycloadducts were observed. Furthermore, the detection of the photolysis products of the alkyl halides mentioned above indicated the presence of triplet state 4

Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition

• Sivaraman Balasubramaniam,
• Sajith Vijayan,
• Liam V. Goldman,
• Xavier A. May,
• Kyra Dodson,
• Sweta Adhikari,
• Fatima Rivas,
• Davita L. Watkins and
• Shana V. Stoddard

Beilstein J. Org. Chem. 2020, 16, 628–637, doi:10.3762/bjoc.16.59

• dimethylformamide (DMF) were degassed in 20 L drums and passed through two sequential purification columns (activated alumina; molecular sieves for DMF) under a positive argon atmosphere. Thin-layer chromatography (TLC) was performed on SiO2-60 F254 aluminum plates with visualization by ultraviolet (UV) detection

A systematic review on silica-, carbon-, and magnetic materials-supported copper species as efficient heterogeneous nanocatalysts in “click” reactions

• Pezhman Shiri and
• Jasem Aboonajmi

Beilstein J. Org. Chem. 2020, 16, 551–586, doi:10.3762/bjoc.16.52

• delivery [93], and cancer detection [94]. In this regard, various functionalized MNPs were employed in diverse organic reactions, including Suzuki–Miyaura reactions, Sonogashira reactions, Ullmann coupling, hydrogenation reactions, oxidation reactions, hydroformylation reactions, and “click” reactions [89

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

• column, n-hexane/2-propanol 90:10, 1.0 mL/min, 40 °C; (S)-1: tR = 17.9 min, (R)-1: tR = 6.83 min, UV detection at 250.0 nm. Preparation of 2 To a 20 mL two-necked round-bottomed flask were added 1 (796 mg, 2.0 mmol) and Cs2CO3 (978 mg, 6.0 mmol). 2,6-Difluoropyridine (0.55 mL, 6.0 mmol) and DMF (10 mL

• ), 19F NMR (376 MHz, CDCl3) δ 69.06; HRMS–APCI (m/z): [M + H]+ calcd for C38H35F2N2O2, 589.2644; found, 589.2661. The enantiomeric purity was confirmed by HPLC analysis: CHIRAL ART Cellulose-SB column, n-hexane/chloroform 95:5, 1.0 mL/min, 40 °C; (S)-2: tR = 9.86 min, (R)-2: tR = 21.29 min, UV detection

• /chloroform 95:5, 1.0 mL/min, 40 °C; (S)-3a: tR = 7.25 min, (R)-3a: tR = 14.12 min, UV detection at 250.0 nm. Compound 3b: Synthesized similarly to 3a using 4-tert-butylphenol. Purified by silica gel column chromatography (eluent: hexane/EtOAc 4:1) and GPC to give the title compound as white solid; (S)-3b