Synthesis of the biologically important dideuterium-labelled adenosine triphosphate analogue ApppI(d₂)

• Petri A. Turhanen

Beilstein J. Org. Chem. 2022, 18, 1466–1470, doi:10.3762/bjoc.18.153

• available, and in fact only few papers describe corresponding synthetic methods [19][20][21][22]. It is well known that labelled compounds (such as those with 2H and 13C labels) can be used as internal standards for the quantitative measurements of the equal compound without label, e.g., straight from the

The stereochemical course of 2-methylisoborneol biosynthesis

• Binbin Gu,
• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 818–824, doi:10.3762/bjoc.18.82

• Supporting Information File 1). All compounds were identified from their EI mass spectra and retention indices in comparison to synthetic standards [29]. The substrate (R)-2-Me-LPP gave high yields of compound 1 (62% of total enzyme products in GC), besides 2-methylenebornane (10, 21%) and small amounts of 2

Sesquiterpenes from the soil-derived fungus Trichoderma citrinoviride PSU-SPSF346

• Wiriya Yaosanit,
• Vatcharin Rukachaisirikul,
• Souwalak Phongpaichit,
• Sita Preedanon and
• Jariya Sakayaroj

Beilstein J. Org. Chem. 2022, 18, 479–485, doi:10.3762/bjoc.18.50

• , 321.1309; found, 321.1320. Antimicrobial assay Antimicrobial activity was evaluated according to the Clinical and Laboratory Standards Institute [16]. Vancomycin was used as a positive control for S. aureus and methicillin-resistant S. aureus and exhibited MIC values of 0.25 and 1.0 μg/mL, respectively

Tenacibactins K–M, cytotoxic siderophores from a coral-associated gliding bacterium of the genus Tenacibaculum

• Yasuhiro Igarashi,
• Yiwei Ge,
• Tao Zhou,
• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku and
• Agus Trianto

Beilstein J. Org. Chem. 2022, 18, 110–119, doi:10.3762/bjoc.18.12

• solvent protons (DMSO-d6: δH 2.50; CDCl3/CD3OD: δH 7.27) and carbons (DMSO-d6: δC 39.5; CDCl3/CD3OD: δC 77.0) as internal standards. HR–ESITOFMS spectra were measured on a Bruker compact qTOF mass spectrometer. Negative ion mode MS/MS experiments were operated on the same instrument under a multiple

Efficient synthesis of ethyl 2-(oxazolin-2-yl)alkanoates via ethoxycarbonylketene-induced electrophilic ring expansion of aziridines

• Yelong Lei and
• Jiaxi Xu

Beilstein J. Org. Chem. 2022, 18, 70–76, doi:10.3762/bjoc.18.6

• were conducted on a CEM discovery SP microwave reactor. The plates were visualized under UV light, as well as other TLC stains. 1H, 13C, and 31P NMR spectra were recorded on a Bruker 400 MHz spectrometer in CDCl3 with solvent peaks as internal standards, for 31P NMR, 85% H3PO4 as an external standard

Unsaturated fatty acids and a prenylated tryptophan derivative from a rare actinomycete of the genus Couchioplanes

• Shun Saito,
• Kanji Indo,
• Naoya Oku,
• Hisayuki Komaki,
• Masashi Kawasaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2939–2949, doi:10.3762/bjoc.17.203

• 13C NMR data, and high-resolution ESIMS data were presented. While an S-configuration was assigned for phialomustin B based on its positive specific rotation ([α]D25 +55.5, c 1.5, CHCl3) in comparison with those of synthetic standards [26], opposite negative signs in CHCl3 and MeOH ([α]D27 –12, c

First total synthesis of hoshinoamide A

• Haipin Zhou,
• Zihan Rui,
• Yiming Yang,
• Shengtao Xu,
• Yutian Shao and
• Long Liu

Beilstein J. Org. Chem. 2021, 17, 2924–2931, doi:10.3762/bjoc.17.201

• procedures. 1H NMR spectra were obtained using a Bruker AVANCE AV 400 spectrometer at a frequency of 400 MHz, respectively in CDCl3, CD3OD or D2O. Chemical shifts are reported in parts per million (ppm) and coupling constants in Hertz (Hz). The residual solvent peaks were used as internal standards. 1H NMR

Cryogels: recent applications in 3D-bioprinting, injectable cryogels, drug delivery, and wound healing

• Luke O. Jones,
• Leah Williams,
• Tasmin Boam,
• Martin Kalmet,
• Chidubem Oguike and
• Fiona L. Hatton

Beilstein J. Org. Chem. 2021, 17, 2553–2569, doi:10.3762/bjoc.17.171

• systems, progress can be made in achieving stable print structures for the ultra-high standards set by the human body. 5.2. Injectable cryogels Implantable biomaterials are proposed as a viable solution when dealing with issues relating to either the delivery or recruitment of cells. Currently the methods

Exfoliated black phosphorous-mediated CuAAC chemistry for organic and macromolecular synthesis under white LED and near-IR irradiation

• Azra Kocaarslan,
• Zafer Eroglu,
• Önder Metin and
• Yusuf Yagci

Beilstein J. Org. Chem. 2021, 17, 2477–2487, doi:10.3762/bjoc.17.164

• detector was calibrated with polystyrene standards having narrow molecular-weight distributions. The data were analyzed using Eco-SEC analysis software. A Hitachi HT7700 (TEM) with EXALENS (120 kV) working at a high-resolution (HR) mode was used to obtain transmission electron microscopy (TEM) images, high

Isolation and characterization of new phenolic siderophores with antimicrobial properties from Pseudomonas sp. UIAU-6B

• Emmanuel T. Oluwabusola,
• Olusoji O. Adebisi,
• Fernando Reyes,
• Kojo S. Acquah,
• Mercedes De La Cruz,
• Larry L. Mweetwa,
• Joy E. Rajakulendran,
• Digby F. Warner,
• Deng Hai,
• Rainer Ebel and
• Marcel Jaspars

Beilstein J. Org. Chem. 2021, 17, 2390–2398, doi:10.3762/bjoc.17.156

• compounds 1–5 was assigned as ʟ, based on the derivatization with Marfey’s reagent of compound 2 and 4 hydrolysates, which represented the two distinctive structural scaffolds and chemical shifts followed by HPLC analysis of the derivatized amino acid residuals in the hydrolysate and threonine standards

• shown in Figure S47 (Supporting Information File 1). Retention times (min) for the derivatized (ʟ-FDAA) threonine standards and for the observed peaks in the HPLC trace of each ʟ-FDAA-derivatized hydrolysis product under the reported conditions were as follows: retention times of standards: ʟ-Thr: 19.62

Nomimicins B–D, new tetronate-class polyketides from a marine-derived actinomycete of the genus Actinomadura

• Zhiwei Zhang,
• Tao Zhou,
• Taehui Yang,
• Keisuke Fukaya,
• Enjuro Harunari,
• Shun Saito,
• Katsuhisa Yamada,
• Chiaki Imada,
• Daisuke Urabe and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2194–2202, doi:10.3762/bjoc.17.141

• Spectrum 100, respectively. All NMR experiments were performed on a Bruker AVANCE 500 spectrometer in CD3OD using the residual solvent proton (δΗ 3.31) and carbon (δC 49.2) signals as internal standards. HRESITOFMS were recorded on a Bruker micrOTOF focus mass spectrometer. An Agilent HP1200 system

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

• ][260]. The automated solid-phase approach required only two BBs with the amino group protected either with the N-TCA 79 or with the N-Cbz group 80 (Scheme 12). Compounds 81–85 served as standards to explore the conformational space of COS with different PA. NMR analysis and MD simulations revealed the

Volatile emission and biosynthesis in endophytic fungi colonizing black poplar leaves

• Christin Walther,
• Pamela Baumann,
• Katrin Luck,
• Beate Rothe,
• Peter H. W. Biedermann,
• Jonathan Gershenzon,
• Tobias G. Köllner and
• Sybille B. Unsicker

Beilstein J. Org. Chem. 2021, 17, 1698–1711, doi:10.3762/bjoc.17.118

• volatiles were identified by comparing their mass spectra with those of authentic standards or reference spectra from databases (Wiley, Version 8, National Institute of Standards and Technology (NIST, Version 11)) using GCMS SOLUTION v.4.20 (Shimadzu). In addition, non-isothermal Kovats retention indices

• with a gradient of 60 °C min−1 and a hold of 2 min. Compounds were identified by comparing their retention times and mass spectra to those of authentic standards, or by reference spectra in the Wiley and NIST libraries. Sequence analysis and phylogenetic tree construction For the estimation of a

Electron-rich triarylphosphines as nucleophilic catalysts for oxa-Michael reactions

• Susanne M. Fischer,
• Simon Renner,
• A. Daniel Boese and
• Christian Slugovc

Beilstein J. Org. Chem. 2021, 17, 1689–1697, doi:10.3762/bjoc.17.117

• from MZ-Gel SD plus, 500 A and 100 A, linear 5 µ; UV detector (SPD-20A) and RI detector (RID-20A)) using THF as eluent. Poly(styrene) standards in the range of 350 to 17800 g/mol purchased from Polymer Standard Service were used for calibration. Computational details All calculations were run with the

• –Currier repeat units; right: size exclusion chromatograms (in THF, relative to poly(styrene) standards) of poly4 prepared with 5 mol % TPP, MMTPP or TMTPP using a reaction time of 24 h and a reaction temperature of 23 °C (dashed lines) or 80 °C (full lines). Left: Oxidation stability of the phosphines

A new glance at the chemosphere of macroalgal–bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry

• Marine Vallet,
• Filip Kaftan,
• Veit Grabe,
• Fatemeh Ghaderiardakani,
• Simona Fenizia,
• Aleš Svatoš,
• Georg Pohnert and
• Thomas Wichard

Beilstein J. Org. Chem. 2021, 17, 1313–1322, doi:10.3762/bjoc.17.91

• similarity with standards. Using combined imaging mass spectrometry and confocal laser scanning microscopy, we then linked the chemical and microscopic observations that characterise the symbiotic association (cLSM). Results and Discussion Comparative metabolomics using AP-SMALDI-HRMS identifies metabolites

• class (Figure 1c). Among the statistically significant features in all datasets (Table S1, Supporting Information File 1), six metabolites were identified, which were annotated using spectral similarity with analytical standards. For example, the features m/z 104.1064 and m/z 143.0815 were selected

• chemical formula based on exact mass. We also used spectral similarity matching of data acquired from analytical standards. Choline was identified from the molecular peak m/z 104.1064 for [M]+ (calculated m/z as 104.1069 ± 4.8 ppm for C5H14NO) in the profiles of axenic U. mutabilis (Figure 2a). This small

Microwave-assisted multicomponent reactions in heterocyclic chemistry and mechanistic aspects

• Shivani Gulati,
• Stephy Elza John and
• Nagula Shankaraiah

Beilstein J. Org. Chem. 2021, 17, 819–865, doi:10.3762/bjoc.17.71

• seems to be compromised imposing restrictions on using microwaves at a scale-up level. However, the batch process and continuous flow process seem to provide an entry into scale-up standards with safety. The microwave reactors serving the purpose of batch and parallel approach are designed in various

Designed whole-cell-catalysis-assisted synthesis of 9,11-secosterols

• Marek Kõllo,
• Marje Kasari,
• Villu Kasari,
• Tõnis Pehk,
• Ivar Järving,
• Margus Lopp,
• Arvi Jõers and
• Tõnis Kanger

Beilstein J. Org. Chem. 2021, 17, 581–588, doi:10.3762/bjoc.17.52

• solvent signals were used (CDCl3: δ = 7.26 for 1H NMR, δ = 77.2 for 13C NMR or CD3OD: δ = 3.31 for 1H NMR, δ = 49.0 for 13C NMR) as internal standards. Optical rotations were obtained by using an Anton Paar GWB Polarimeter MCP500. High-resolution mass spectra were recorded with an Agilent Technologies

Breakdown of 3-(allylsulfonio)propanoates in bacteria from the Roseobacter group yields garlic oil constituents

• Anuj Kumar Chhalodia and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2021, 17, 569–580, doi:10.3762/bjoc.17.51

• °C min−1 to 320 °C and operated in the splitless mode (60 s valve time); carrier gas (He): 1.2 mL min−1. The retention indices were determined from n-alkane standards (C8–C32) [42]. General synthetic methods All chemicals were purchased from TCI (Deutschland) or Sigma-Aldrich Chemie (Germany), and

Identification of volatiles from six marine Celeribacter strains

• Anuj Kumar Chhalodia,
• Jan Rinkel,
• Dorota Konvalinkova,
• Jörn Petersen and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2021, 17, 420–430, doi:10.3762/bjoc.17.38

• mass spectra to library spectra and of retention indices [38] to tabulated literature data (Table 1), or by a direct comparison to authentic standards. The structures of the identified compounds are shown in Figure 2. While the headspace extracts from C. marinus, C. neptunius and C. manganoxidans were

Ring-closing metathesis of prochiral oxaenediynes to racemic 4-alkenyl-2-alkynyl-3,6-dihydro-2H-pyrans

• Viola Kolaříková,
• Markéta Rybáčková,
• Martin Svoboda and
• Jaroslav Kvíčala

Beilstein J. Org. Chem. 2020, 16, 2757–2768, doi:10.3762/bjoc.16.226

• internal standards. Chemical shifts are given in parts per million and coupling constants in hertz. Mass spectra (ESI, APCI) and HRMS spectra were measured with a hybrid LTQ Obitrap XL instrument (Thermo Fisher Scientific). All reactions were performed in a dry inert atmosphere (Ar) in oven-dried flasks

Synthesis of purines and adenines containing the hexafluoroisopropyl group

• Viacheslav Petrov,
• Rebecca J. Dooley,
• Alexander A. Marchione,
• Elizabeth L. Diaz,
• Brittany S. Clem and
• William Marshall

Beilstein J. Org. Chem. 2020, 16, 2739–2748, doi:10.3762/bjoc.16.224

• -temperature operation. The sample temperature was calibrated against neat ethylene glycol and neat methanol standards. Selective inversion experiments at subambient temperature effected the selective inversion with iBURP shapes [25]. The spin–lattice relaxation time T1 for each site was determined with

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

• Bruker AVANCE II 500 MHz NMR spectrometer in DMSO-d6 supplemented with a trace amount of trifluoroacetic acid using the signals of the residual solvent protons (δH 2.49) and carbon atoms (δC 39.5) as internal standards for compounds 1–5, or in CDCl3 using the signals of the residual solvent protons (δH

• 7.27) and carbon atoms (δC 77.0) as internal standards for other compounds. HRESITOFMS spectra were recorded on a Bruker micrOTOF focus mass spectrometer. An Agilent HP1200 system equipped with a diode array detector was used for analysis and purification. Microorganism The coral sample Mycedium sp

A heterobimetallic tetrahedron from a linear platinum(II)-bis(acetylide) metalloligand

• Matthias Hardy,
• Marianne Engeser and
• Arne Lützen

Beilstein J. Org. Chem. 2020, 16, 2701–2708, doi:10.3762/bjoc.16.220

• 31P). In order to measure 19F and 31P NMR spectra, the NMR tube was equipped with a coaxial insert containing the external standards. 1H NMR data are reported as follows: chemical shift (δ) in ppm, multiplicity (dt = doublet of triplets, m = multiplet), coupling constant (J) in Hertz (Hz), integral

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

• Benjamin P. Kellman,
• Yujie Zhang,
• Emma Logomasini,
• Eric Meinhardt,
• Karla P. Godinez-Macias,
• Austin W. T. Chiang,
• James T. Sorrentino,
• Chenguang Liang,
• Bokan Bao,
• Yusen Zhou,
• Sachiko Akase,
• Isami Sogabe,
• Thukaa Kouka,
• Elizabeth A. Winzeler,
• Iain B. H. Wilson,
• Matthew P. Campbell,
• Sriram Neelamegham,
• Frederick J. Krambeck,
• Kiyoko F. Aoki-Kinoshita and
• Nathan E. Lewis

Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215

• compliance with FAIR standards. Here, we present Linear Code for Reaction Rules (LiCoRR), version 1.0, an unambiguous representation for describing glycosylation reactions in both literature and code. Keywords: glycoinformatics; linear code; systems glycobiology; Introduction Glycans are predominantly

• adaptations made to accommodate reaction rule representation, the discordance between various implementations, and proposed a consensus for future representations called LiCoRR. The adoption of a common reaction rule representation would increase FAIR (Findable, Accessible, Interoperable, Reusable) standards

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

• definitions match dictionary standards as well as output multiple helper tools to aid the processes of refinement and model building [24]. Most importantly, Privateer already contains methods that allow the extraction of carbohydrate atomistic definitions to create abstract definitions of glycans in memory