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

Two antibacterial and PPARα/γ-agonistic unsaturated keto fatty acids from a coral-associated actinomycete of the genus Micrococcus

• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku,
• Nobuyasu Matsuura,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 297–304, doi:10.3762/bjoc.16.29

• concentrated to give 27.5 mg of semipure material. Final purification was achieved by preparative HPLC (Cosmosil Cholester, Nacalai Tesque Inc., 10 × 250 mm, 4 mL/min, UV detection at 290 nm) with an isocratic elution of MeCN/0.1% HCO2H (63:37) to afford 1 (3.7 mg, tR 14.2 min) and 2 (2.4 mg, tR 15.7 min). (6E

Understanding the role of active site residues in CotB2 catalysis using a cluster model

• Keren Raz,
• Ronja Driller,
• Thomas Brück,
• Bernhard Loll and
• Dan T. Major

Beilstein J. Org. Chem. 2020, 16, 50–59, doi:10.3762/bjoc.16.7

• decade, numerous interdisciplinary studies have addressed the chemical mechanism of CotB2 catalysis utilizing different detection and analysis methods. Meguro and co-workers [41] established the chemical mechanism for the formation of cyclooctatin using isotope labeling experiments (Scheme 1). Recently

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

• metabolite profiles using analytical HPLC coupled with diode array detection and mass spectrometry (HPLC–DAD–MS) revealed that the production of pigmentosin B (2) was apparently specific for Gibellula sp., while the glycoasperfuran 3 was specific for C. javanica. Keywords: antibiofilm agents; natural

• 100% solvent B for 5 min, with a flow rate of 20 mL/min. Thereby, UV detection was performed at 210, 280, and 354 nm. Fractions were collected and pooled according to the observed peaks. The separation yielded two fractions including compound 1 (5.4 mg) and 2 (2.4 mg) at retention times tR 43–44 and

Chemical synthesis of tripeptide thioesters for the biotechnological incorporation into the myxobacterial secondary metabolite argyrin via mutasynthesis

• David C. B. Siebert,
• Roman Sommer,
• Domen Pogorevc,
• Michael Hoffmann,
• Silke C. Wenzel,
• Rolf Müller and
• Alexander Titz

Beilstein J. Org. Chem. 2019, 15, 2922–2929, doi:10.3762/bjoc.15.286

• phosphopantetheinyl arm of the peptide carrier protein (CP). Analysis of mutasynthon 14 obtained via the convergent synthetic route by HPLC on a HILIC stationary phase and UV detection (A) and mass spectrometry (B). Synthesis of tripeptide thioesters. Reagents and conditions: (a) SOCl2, EtOH, 78 °C; (b) IBCF, NMM

Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering

• Eric J. N. Helfrich,
• Geng-Min Lin,
• Christopher A. Voigt and
• Jon Clardy

Beilstein J. Org. Chem. 2019, 15, 2889–2906, doi:10.3762/bjoc.15.283

• NRPSs), bacterial TCs show only little overall sequence similarity [1]. The lack of conservation in primary sequence has slowed down our understanding of terpene cyclization and, as a result, hampered the development of efficient genome mining platforms for the detection of bacterial terpene BGCs

• , remain to be explored [152]. One major bottleneck in these studies is the lack of high-throughput screening tools for terpenoid production and characterization. Most terpenoids do not have any chromogenic groups and their detection still relies on liquid chromatography–mass spectrometry setups, limiting

Preparation of anthracene-based tetraperimidine hexafluorophosphate and selective recognition of chromium(III) ions

• Qing-Xiang Liu,
• Feng Yang,
• Zhi-Xiang Zhao,
• Shao-Cong Yu and
• Yue Ding

Beilstein J. Org. Chem. 2019, 15, 2847–2855, doi:10.3762/bjoc.15.278

• ; chromium(III) ion; tetraperimidine; Introduction Fluorescent chemosensors are an attractive and efficient tool for the detection of metal ions in environmental and biological science because of their high sensitivity, selectivity, and simple usage [1][2][3][4][5][6][7][8]. Among metal ions, the detection

• autoimmune and cardiovascular diseases [11]. On the other hand, the excessive incorporation of chromium(III) is toxic to humans, and can cause cancer through the oxidation of DNA and some proteins [12][13][14]. Therefore, the detection of chromium(III) has a vital practical significance for human health

• monitoring. In recent years, some fluorescent chemosensors for the detection of chromium(III) have been developed [15][16][17][18][19][20][21][22][23]. Generally, chemosensors with fluorescence enhancement are more efficient than fluorescence turn-off chemosensors [24][25][26][27][28][29] because the

Design, synthesis and investigation of water-soluble hemi-indigo photoswitches for bioapplications

• Daria V. Berdnikova

Beilstein J. Org. Chem. 2019, 15, 2822–2829, doi:10.3762/bjoc.15.275

• aqueous media possessing valuable properties for bioapplications. Experimental Materials and equipment Reagents and solvents were obtained from commercial sources (Acros, Merck, Fischer) and used as received. Reactions were monitored on POLYGRAM® SIL G/UV254 (Macherey-Nagel) TLC plates with detection by

Skeletocutins M–Q: biologically active compounds from the fruiting bodies of the basidiomycete Skeletocutis sp. collected in Africa

• Tian Cheng,
• Clara Chepkirui,
• Cony Decock,
• Josphat C. Matasyoh and
• Marc Stadler

Beilstein J. Org. Chem. 2019, 15, 2782–2789, doi:10.3762/bjoc.15.270

• of secondary metabolites for later comparison with herbarium specimens of other species by HPLC–diode array detection (HPLC–DAD)–MS. Surprisingly, we detected further members of the skeletocutin family that were not present in the cultures. The current paper is dedicated to the description of their

• , solvent A: H2O + 0.1% formic acid, solvent B: acetonitrile + 0.1% formic acid, elution gradient: 5% solvent B for 0.5 min, increasing solvent B to 100% within 19.5 min, 100% solvent B for 5 min, flow rate: 0.6 mL/min, UV–vis detection at λ = 200–600 nm) and ESI–TOF–MS analysis (maXis™ system, Bruker, scan

• ), respectively, were used as mobile phases (elution gradient: 50% solvent B, increasing solvent B to 100% within 60 min, 100% solvent B for 5 min, flow rate: 40 mL/min, UV–vis detection at 210, 254, and 350 nm). Eight fractions (F1–F8) were collected, in accordance with the observed signals. F1 was further