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

• monosaccharides show striking differences across platforms even though the appropriate colours to be used are strictly defined (https://www.ncbi.nlm.nih.gov/glycans/snfg.html#tab2). The colour discrepancy observed here means that some of the tools do not conform to SNFG standards. For some purposes, this

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• internal standard, and analyzed. Calibration standards were prepared by gravimetric serial dilution from commercial stock standard solutions of B at 1000 mg L−1. The wavelength used for B determination was 249.772 nm whereas for Ge the line at 209.426 nm was used. The operating conditions were optimized to

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

• for assessment. With large cohorts of CE-LIF data, peak picking and peak area calculations still remain a problem for fast and accurate quantitation, despite the presence of internal and external standards to reduce misalignment for the qualitative analysis. The peak picking and area calculation

• qualitatively curate large cohort CE-LIF glycomics data. For glycan identification, a previously reported method based on internal triple standards is used. For determining the glycan relative quantities our method uses a clustering algorithm to ‘divide and conquer’ highly heterogeneous electropherograms into

• -throughput analysis [9]. In CE-LIF, released and fluorescently labelled glycans migrate over a capillary and are identified by comparison to the standardized migration time with external or internal oligosaccharide standards. In order to achieve standardized migration time in a high-throughput manner

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

• far exceeds the related tetrapeptide analogues with arginine or lysine residues. As a result, the gene transfection efficiency of 13 is better than that of polyethylenimine (PEI) with a large number of charges, which is one of the current standards in gene transfection. The uptake takes place through

• ][58] has been suggested to further improve the standards set by the CAPA [59]. Standard high-throughput (HT) screening has been used regularly to facilitate studies on cellular uptake [60]. In standard assays, a single macroscopic parameter, usually the fluorescence intensity, is automatically

Et₃N/DMSO-supported one-pot synthesis of highly fluorescent β-carboline-linked benzothiophenones via sulfur insertion and estimation of the photophysical properties

• Dharmender Singh,
• Vipin Kumar and
• Virender Singh

Beilstein J. Org. Chem. 2020, 16, 1740–1753, doi:10.3762/bjoc.16.146

• , β-carbolines are also used as fluorescence standards. Recently, a novel β-carboline-based fluorescent chemosensor was developed by Batra and co-workers for the quantitative analysis of fluoride ions (F−) at ppb level [19]. Sulfur-containing organic compounds are broadly associated with numerous

Models of necessity

• Timothy Clark and
• Martin G. Hicks

Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137

• big data in chemistry. This would require sufficient measurements under the same conditions with varying parameters, a homogeneous spread of measured properties over chemical space, and adequate standards for data measurement and reporting. None of these exists in chemistry at present. Melting points

• to recognize the role of models and to agree on unified, parsimonious model standards. This will not affect the everyday language of chemistry but may help understand the unique basis of chemical language. Representation of clozapine to emphasize the quantum mechanical characteristics of the molecule

Activated carbon as catalyst support: precursors, preparation, modification and characterization

• Melanie Iwanow,
• Tobias Gärtner,
• Volker Sieber and
• Burkhard König

Beilstein J. Org. Chem. 2020, 16, 1188–1202, doi:10.3762/bjoc.16.104

• determined by using ASTM standards. A defined amount of sample is weighed in a porcelain basin, heated in a muffle furnace to a given final temperature and for a certain time. After cooling to room temperature in a desiccator, the sample is reweighed. The ash content is calculated using the following

A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium

• Shun Saito,
• Kota Atsumi,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Naoya Oku,
• Md. Rokon Ul Karim,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97

• ) was added and then diluted with MeCN/0.2% HCO2H aqueous solution (100 μL, 50:50). The Marfey’s derivatives of the hydrolysate and standards were analyzed by LC–MS using a Cosmosil 5C18-AR-II column eluted with MeCN/0.1% HCO2H aqueous solution at a flow rate of 1.0 mL/min, monitoring at 340 nm with a

• linear gradient of MeCN from 15% to 85% over 30 min. Retention times for the amino acid standards were 20.1 min for ʟ-Pro-ʟ-FDLA, 21.1 min for ᴅ-Pro-ʟ-FDLA, while the ʟ-FDLA-hydrolysate of 1 gave a peak at 20.1 min (Figure S8 in Supporting Information File 1). (R)- and (S)-PGME amides of 1 (5a and 5b) To

Copper-based fluorinated reagents for the synthesis of CF₂R-containing molecules (R ≠ F)

• Louise Ruyet and
• Tatiana Besset

Beilstein J. Org. Chem. 2020, 16, 1051–1065, doi:10.3762/bjoc.16.92

• trifluoromethoxybenzene as internal standards. b90 °C, 72 h. c80 °C, 24 h. d80 °C, 48 h. e90 °C, 48 h. In situ generation of CuCF2CF3 species from a cyclic-protected hexafluoroacetone and KCu(Ot-Bu)2. 19F NMR yields were determined using benzotrifluoride (BTF) as the internal standard. Pentafluoroethylation of bromo- and

Efficient synthesis of dipeptide analogues of α-fluorinated β-aminophosphonates

• Marcin Kaźmierczak and
• Henryk Koroniak

Beilstein J. Org. Chem. 2020, 16, 756–762, doi:10.3762/bjoc.16.69

• were expressed in parts per million downfield from tetramethylsilane (TMS) as an internal standard (δ = 0) in CDCl3 or CD3CN. 13C NMR chemical shifts were expressed in parts per million downfield from CDCl3 (δ = 77.0) or CD3CN (δ = 1.39) as internal standards. 19F NMR chemical shifts were expressed in

Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0

• Bernd Strehmel,
• Christian Schmitz,
• Ceren Kütahya,
• Yulian Pang,
• Anke Drewitz and
• Heinz Mustroph

Beilstein J. Org. Chem. 2020, 16, 415–444, doi:10.3762/bjoc.16.40

• applications related to Chemistry 4.0 standards. These were mainly photopolymer coatings, which can be found for applications in the graphic industry or to protect selected substrates. The huge release of heat on demand upon turning ON or OFF the NIR light source enables them for photothermal treatment in

Formal preparation of regioregular and alternating thiophene–thiophene copolymers bearing different substituents

• Atsunori Mori,
• Keisuke Fujita,
• Chihiro Kubota,
• Toyoko Suzuki,
• Kentaro Okano,
• Takuya Matsumoto,
• Takashi Nishino and
• Masaki Horie

Beilstein J. Org. Chem. 2020, 16, 317–324, doi:10.3762/bjoc.16.31

• MHz), 19F NMR (376 MHz), and 13C{1H} NMR (100 MHz) spectra were measured on a JEOL ECZ400 spectrometer as a CDCl3 solution, unless otherwise noted. The chemical shifts were expressed in ppm with CHCl3 (7.26 ppm for 1H), C6F6 (−164.9 ppm for 19F), or CDCl3 (77.16 ppm for 13C) as internal standards. IR

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

• Shimadzu UV-1800 and a Perkin-Elmer Spectrum 100 spectrophotometer, respectively. NMR spectra were obtained on a Bruker AVANCE 500 spectrometer in CDCl3 using the signals of the residual solvent (δH 7.26) and (δC 77.0) as internal standards. HRESIMS-TOF was recorded on a Bruker micrOTOF focus

A review of asymmetric synthetic organic electrochemistry and electrocatalysis: concepts, applications, recent developments and future directions

• Munmun Ghosh,
• Valmik S. Shinde and
• Magnus Rueping

Beilstein J. Org. Chem. 2019, 15, 2710–2746, doi:10.3762/bjoc.15.264

• organic chemists towards reaching targets selectively from readily available starting materials using low cost, nontoxic reagents and solvents while maintaining high atom and step economy and minimizing waste production with respect to safety standards, electroorganic chemistry (EOC) stands out as a

Nanangenines: drimane sesquiterpenoids as the dominant metabolite cohort of a novel Australian fungus, Aspergillus nanangensis

• Heather J. Lacey,
• Cameron L. M. Gilchrist,
• Andrew Crombie,
• John A. Kalaitzis,
• Daniel Vuong,
• Peter J. Rutledge,
• Peter Turner,
• John I. Pitt,
• Ernest Lacey,
• Yit-Heng Chooi and
• Andrew M. Piggott

Beilstein J. Org. Chem. 2019, 15, 2631–2643, doi:10.3762/bjoc.15.256

• library (>7,100 standards) also failed to provide a single known secondary metabolite, further suggesting the strain was a hitherto unaccounted species of Aspergillus. A. nanangensis was cultivated separately on jasmine rice and pearl barley for 21 days, which resulted in confluent and thick mycelial

Isolation and biosynthesis of an unsaturated fatty acid with unusual methylation pattern from a coral-associated bacterium Microbulbifer sp.

• Amit Raj Sharma,
• Enjuro Harunari,
• Tao Zhou,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2019, 15, 2327–2332, doi:10.3762/bjoc.15.225

• was recorded on a Shimadzu UV-1800 spectrophotometer. The IR spectrum was measured on a Perkin-Elmer Spectrum 100. NMR spectra were obtained on a Bruker AVANCE 500 spectrometer in CDCl3 using the signals of the residual solvent proton (δH 7.26) and carbon (δH 77.0) as internal standards. HR-ESI-TOFMS

Analysis of sesquiterpene hydrocarbons in grape berry exocarp (Vitis vinifera L.) using in vivo-labeling and comprehensive two-dimensional gas chromatography–mass spectrometry (GC×GC–MS)

• Philipp P. Könen and
• Matthias Wüst

Beilstein J. Org. Chem. 2019, 15, 1945–1961, doi:10.3762/bjoc.15.190

• ) coupled to a time-of-flight mass spectrometer (TOF–MS) after headspace-solid phase microextraction (HS-SPME). The identification of structurally complex natural compounds, such as sesquiterpenes from fruits and vegetables, is often reported as “tentative”, as authentic standards are not commercially

• advantages of multidimensional gas chromatography with those of in vivo labeling. In vivo labeling makes it possible to identify compounds for which authentic standards are not commercially available, which applies to the majority of compounds found in plant foods [18]. We performed feeding experiments on

Steroid diversification by multicomponent reactions

• Leslie Reguera,
• Cecilia I. Attorresi,
• Javier A. Ramírez and
• Daniel G. Rivera

Beilstein J. Org. Chem. 2019, 15, 1236–1256, doi:10.3762/bjoc.15.121

• fractions; such compounds are too complex for analysis at a molecular level, so it is important to synthesize analytical standards for their study. In this context, Schulze et al. optimized a multicomponent cyclocondensation reaction [50][51] between 5α-cholestan-3-one (43), aromatic aldehydes and 2

Mechanochemical amorphization of chitin: impact of apparatus material on performance and contamination

• Thomas Di Nardo and
• Audrey Moores

Beilstein J. Org. Chem. 2019, 15, 1217–1225, doi:10.3762/bjoc.15.119

• iCap 6500 Duo Series spectrometer. The samples were digested in aqua regia (5 mL) for 2 hours at 90 °C. The samples were then diluted to total volume of 50 mL with DI water and run against standards of the elements of interest. Kinetic energy calculation Kinetic energy of the ball determined by using

Mechanistic investigations on multiproduct β-himachalene synthase from Cryptosporangium arvum

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2019, 15, 1008–1019, doi:10.3762/bjoc.15.99

• comparison with commercially available standards (Figures S6–S9, Supporting Information File 1). The non-enzymatic degradation of GPP as a background reaction to 15 resulted in a substantial loss of stereoinformation for this compound (7% ee). Also the cyclised products 10, 11 and 13 where not obtained in

Mechanochemical synthesis of poly(trimethylene carbonate)s: an example of rate acceleration

• Sora Park and
• Jeung Gon Kim

Beilstein J. Org. Chem. 2019, 15, 963–970, doi:10.3762/bjoc.15.93

• HPLC grade, Fisher) at 40 °C at 1.0 mL/min and calibrated using 14 monodisperse polystyrene standards (Alfa Aesar). The temperature was recorded using a Fluke VT04 Visual IR thermometer. Synthesis of trimethylene carbonate. 1,3-Propanediol (4.72 mL, 0.657 mol) and ethyl chloroformate (12.5 mL, 0.131

Synthesis of polydicyclopentadiene using the Cp₂TiCl₂/Et₂AlCl catalytic system and thin-layer oxidation of the polymer in air

• Zhargolma B. Bazarova,
• Ludmila S. Soroka,
• Alex A. Lyapkov,
• Мekhman S. Yusubov and
• Francis Verpoort

Beilstein J. Org. Chem. 2019, 15, 733–745, doi:10.3762/bjoc.15.69

• -permeation chromatography on the instrument Agilent Technologies 1260 Infinity with a refractive index detector, GPC/SEC – styrogel column, length 300 mm, internal diameter 7.5 mm, eluent (CHCl3) rate 1 mL/s, calibration according to the polystyrene standards known molecular weight. Thermal analysis was

Synthesis and SAR of the antistaphylococcal natural product nematophin from Xenorhabdus nematophila

• Frank Wesche,
• Hélène Adihou,
• Thomas A. Wichelhaus and
• Helge B. Bode

Beilstein J. Org. Chem. 2019, 15, 535–541, doi:10.3762/bjoc.15.47

• fascinating small and bioactive amide. Results and Discussion We first synthesized 1 and 1-methylnematophin (3) as standards to confirm preliminary results. We then initiated the synthesis of derivatives 2, and 4–12. Briefly, the appropriate α-keto carboxylic acid was coupled to the respective amine. Amide

A novel and efficient synthesis of phenanthrene derivatives via palladium/norbornadiene-catalyzed domino one-pot reaction

• Yue Zhong,
• Wen-Yu Wu,
• Shao-Peng Yu,
• Tian-Yuan Fan,
• Hai-Tao Yu,
• Nian-Guang Li,
• Zhi-Hao Shi,
• Yu-Ping Tang and
• Jin-Ao Duan

Beilstein J. Org. Chem. 2019, 15, 291–298, doi:10.3762/bjoc.15.26

• were monitored through UV light. Flash chromatography was carried out on silica gel 300–400 mesh. 1H and 13C NMR spectra were recorded in CDCl3 at 500 and 126 MHz, respectively, using the solvents as internal standards. High-resolution mass spectra were taken on Waters Synapt MS. The peak patterns are

Asymmetric synthesis of a high added value chiral amine using immobilized ω-transaminases

• Antonella Petri,
• Valeria Colonna and
• Oreste Piccolo

Beilstein J. Org. Chem. 2019, 15, 60–66, doi:10.3762/bjoc.15.6

• °C. The eluent was H2O/CH3CN/DEA 70:30:0.1. Authentic standards were analyzed before analysis of the reaction mixtures. The enantiomeric excesses were determined after derivatization. An aliquot (50 mg) of the crude sample and 100 mg K2CO3 were added to a 15 mL volumetric flask and dissolved in 1 mL