Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities

• Heiko T. Kiesewalter,
• Carlos N. Lozano-Andrade,
• Mikael L. Strube and
• Ákos T. Kovács

Beilstein J. Org. Chem. 2020, 16, 2983–2998, doi:10.3762/bjoc.16.248

• surfactin mutant. A similar but smaller correlation with two bacillaene mutant-treated communities was detectable as well. These results imply a negative impact of either surfactin or bacillaene on the four ASVs. Interestingly, the vector-based analysis suggests that, depending on the ASVs, the genus

• diversity was estimated with the Shannon diversity index in the R package phyloseq [76]. The beta diversity was determined by dissimilarities among the samples with the Bray–Curtis distance and visualised in a nMDS with the R package vegan [78]. The correlation of individual ASVs on the overall bacterial

• correlation. Abundance ratios for each genus and replicate (points) in the control community compared to the WT-treated (A) and to the sfp-treated community (B). Red-box plots highlight the statistical significance, which is defined as P ≤ 0.05 (*), P ≤ 0.01 (**), and P ≤ 0.001 (***). The relative abundance

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

• Jennifer Frommer and
• Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

• the evaluation. The H3’-signal was easily assigned owing to its HMBC correlation with C5’, which is missing for all of the other protons. Its distinct multiplicity in the two spectra in Figure 1 already indicates a different coupling environment in the two isomers. The merged signal of H2’ and 3’-OH

• in Figure 1A reveals a HMBC correlation of both protons with C4’, but only H2’ shows a correlation with C1’. In Figure 1B, the OH signal shows a correlation with C1’, and, very importantly, not with C4’, which in combination with the distinct multiplicity of H3’ clearly indicates that the spectrum in

• measurements. A) The merged 1H signal at 5.17 ppm results from the H2’ and an OH group, since the H3’ can be clearly identified through the HMBC correlation with C5’. The zoomed region shows the HMBC correlation of the OH group with C4’, which together with the weaker signal between H2’ and C1’ identifies this

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

• -11/H-14, H-12/H-13) were defined by the analysis of the COSY spectrum (Figure 2). Meanwhile, HMBC correlations from the two methyl protons (H-13 and H-14) to well-resolved C-11, and C-12, along with a correlation from H-14 to C-10, allowed to assemble an anteisomethyl terminus from C-10 to C-14. The

• correlation from H-2 to C-6 established the linkage between the chain part and the imidazole ring (Figure 2). The remaining question was whether the amino group is bound to C-2 or C-5 in the imidazole ring. A literature survey suggested a diagnostic use of 1JC,H coupling constants [23]. In imidazole and ʟ

• of one doublet methyl and one methine signal. Two aliphatic fragments, H-7/H-8/H-9 and H-14/H-15, were identified from COSY correlation data. These fragments were then joined into a nonbranching linear alkyl chain by HMBC correlations from H-15 to C-13 and H-8 to C-10, though H-11/C-11 and H-12/C-12

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

• , correlation of the proton. Low- and high-resolution electrospray ionization mass spectrometry (ESIMS) spectra were recorded on a Bruker Daltonic LTQ Orbitrap XL. The UV–vis spectrum was recorded on a Specord 200 spectrometer (Analytik Jena AG) at ambient temperature. 4-Ethynylaniline (1) [50], trans-[Pt(PBu3

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

• to better control the properties. Future work will aim at establishing this correlation. In addition, the substrate scope of the mixed monolayer-protected AuNPs will be extended by introducing other receptor motifs. An attractive option would be the use of Schmuck’s guanidiniocarbonylpyrrole moiety

Synthesis and characterization of S,N-heterotetracenes

• Astrid Vogt,
• Florian Henne,
• Christoph Wetzel,
• Elena Mena-Osteritz and
• Peter Bäuerle

Beilstein J. Org. Chem. 2020, 16, 2636–2644, doi:10.3762/bjoc.16.214

• precursors and amines [11][12], the series of S,N-heteroacenes has been systematically extended from pentamer SN5 [13][14] up to a stable and still soluble S,N-heterotridecacene SN13 [7][15][16][17]. Correlation of, e.g., absorption or redox potentials vs conjugated chain length led to interesting structure

Anion exchange resins in phosphate form as versatile carriers for the reactions catalyzed by nucleoside phosphorylases

• Julia N. Artsemyeva,
• Ekaterina A. Remeeva,
• Tatiana N. Buravskaya,
• Irina D. Konstantinova,
• Roman S. Esipov,
• Anatoly I. Miroshnikov,
• Natalia M. Litvinko and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2020, 16, 2607–2622, doi:10.3762/bjoc.16.212

• : 87.90 (C1′), 73.48 (C2′), 70.61 (C3′), 85.86 (C4′), 61.63 (C5′); furfuryl fragment: 141.81 (correlation with the proton resonance at 7.56 ppm), 110.43 (correlation with the proton resonance at 6.38 ppm), 106.63 (correlation with the proton resonance at 6.25 ppm), the C1-ipso at 152.87 and the CH2

Synthesis of 4-substituted azopyridine-functionalized Ni(II)-porphyrins as molecular spin switches

• Jannis Ludwig,
• Tobias Moje,
• Fynn Röhricht and
• Rainer Herges

Beilstein J. Org. Chem. 2020, 16, 2589–2597, doi:10.3762/bjoc.16.210

• state. 4-Substituted pyridines exhibit a distinguished correlation between basicity and coordination strength as axial ligands with Ni-porphyrins [12]. Hence, Hammet σ values might be used to predict and to systematically optimize the performance of the spin switch. In previous studies we have shown

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• but this shows no correlation to the effect of glycosylation, for example, Pro6, Ala7 (Figure S1 and S2 in Supporting Information File 1), and finally, the conformational preference seen for glycosylation in solution aligns with the preference seen for both bound antigens, for example, Asp3 and Thr4

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

• the ligand needs to dissociate again from the protein in order to be detected. Therefore, strong (nM or better) binders are not suitable for these experiments. No information about the binding site(s) on the protein is obtained. Magnetization transfer via NOE depends on a molecule’s correlation

Conformational preferences of fluorine-containing agrochemicals and their implications for lipophilicity prediction

• Daniela Rodrigues Silva,
• Joyce K. Daré and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2020, 16, 2469–2476, doi:10.3762/bjoc.16.200

• organic molecule, as above mentioned. Therefore, this work also seeks to assess a correlation between calculated μ values and experimental log P measures, in order to unveil the dependence of lipophilicity with molecular conformation. Results and Discussion Conformational analysis of penoxsulam Given the

• known in the literature [23] and, accordingly, it differs from the energy minimum conformations computed in this work. However, a conformational search in the gas phase, as performed herein, is necessary to fully understand the intramolecular interactions and to establish the correlation between μ and

• log P, since this physicochemical property does not depend on the geometry of penoxsulam inside a biological receptor. Effect of molecular conformation on log P Herein, we aim at evaluating the correlation of molecular conformation with lipophilicity, described in terms of the n-octanol/water

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

• with different polarities and showed absorption in the visible region and green-red emission with low quantum yields. The absorption and the emission maxima were shifted bathocromically by increasing the solvent’s polarity. However, there was no correlation with the polarity parameters of the solvents

• absorption maxima (λabsmax), oscillator strengths (f), and relevant transitions and their contributions (w) are given in Table 1 and Table S1 in Supporting Information File 1). The shifts of the absorption maxima of the dyes were little dependent on the solvent polarity and there was no obvious correlation

• all dyes 3–7 and 8–12 were recorded in the same solvents of various polarities that were used in the UV–vis studies, and the results are summarized in Table 1 and Table S1 (Supporting Information File 1). All dyes showed fluorescence properties and there was no direct correlation of the increase of

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

• 0.1 equiv of 1). Supporting Information Supporting Information File 426: Methods for UV–vis and fluorescence measurements, UV–vis and fluorescence spectra of Dex-1b, Dex-1c, and 1 in DMSO, FTIR spectra of PBA-BODIPY 1, dextran and Dex-1a–d; MTT assay and correlation coefficient of Dex-1b

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

• Dashboard (GLAD) is a tool to visualize, analyze, compare and mine glycan array data. The tool allows users to visualize glycan array data alongside the structures using bar charts, heatmaps, calendar heatmaps, force directed graphs and correlation plots. In addition, the tool also couples some data mining

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

• for Ka and n given in Table 1 all have satisfactory correlation coefficients (>0.999). Thermal melting curves for DNA, RNA, and their complexes with the studied compound were determined as previously described [37] by following the absorption change at 260 nm as a function of temperature. The

Regioselective cobalt(II)-catalyzed [2 + 3] cycloaddition reaction of fluoroalkylated alkynes with 2-formylphenylboronic acids: easy access to 2-fluoroalkylated indenols

• Tatsuya Kumon,
• Miroku Shimada,
• Jianyan Wu,
• Shigeyuki Yamada and
• Tsutomu Konno

Beilstein J. Org. Chem. 2020, 16, 2193–2200, doi:10.3762/bjoc.16.184

• out based on NMR techniques, as shown in Scheme 4 [36]. A strong correlation between the carbonyl carbon atom and Ha was obtained, whereas the cross-peak between the carbonyl carbon atom and Hb was not observed, strongly indicating that the indanone 5aA possessed a CF3 group at the 3-position. On the

Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups

• Benjamin Jeffries,
• Zhong Wang,
• Robert I. Troup,
• Anaïs Goupille,
• Jean-Yves Le Questel,
• Charlene Fallan,
• James S. Scott,
• Elisabetta Chiarparin,
• Jérôme Graton and
• Bruno Linclau

Beilstein J. Org. Chem. 2020, 16, 2141–2150, doi:10.3762/bjoc.16.182

• ]. We have previously used the SMD implicit solvation model with the MN15 functional in theoretical lipophilicity predictions of linear fluorohydrins [27][28], which gave an excellent correlation with the experimental values (r2 = 0.957), although the absolute values were much higher (a slope of >2 was

• to have essentially the same lipophilicities. The correlation with the experimental values shows a coefficient of determination value of 0.776 (Figure 10A), which is worse than many of the investigated fragment-based clogP methods (see above), for which such clustering is not observed. When these

• values are combined with the full available set of fluorohydrins calculated with the MN15 functional (Figure 10B), the correlation is now reduced from r2 = 0.957 to 0.860. Interestingly, the theoretical and experimental values, while much different in absolute value and in relative difference, correspond

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

• , migration time is generally calculated by correlation with internal standards that bracket the time of elution of the glycans of interest [10]. This process is used to calculate a glucose unit (GU) which helps to align the datasets so that the GU of each glycan can be used to identify the glycan through

• average total abundance. If peaks <1% are not considered it might seem insignificant but it affects the relative abundance of other peaks to an extent of 3.8% in total. Supporting Information File 1, Figure S1 shows the correlation between clustering + HappyTools and the automated software quantitative

• FA1/FA2G2S1/A2 only (red box peak not picked by 32 Karat), (H) M5 peaks only (red box peak not picked by 32 Karat, and (I) when FA1/FA2G2S1/A2 and M5 peak areas were combined there was excellent correlation between both approaches suggesting 32 Karat integrates the two peaks as a whole. The clustering

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

• ) for C1B (δ = 51.4 ppm) due to 6Li,13C spin coupling. The 6Li NMR spectrum of 2a-I at −103 °C displayed three signals split by 6Li,13C spin coupling. Selective 6Li{13C} double resonance and two-dimensional double quantum based shift correlation experiments had served to establish the 6Li–13C

• the tetramer (2a)4·(THF)6 in the crystal. Although the lithium oxygen bonds of 2a-I evaded a direct detection by NMR spectroscopy, the 13C,6Li shift correlation experiments of 2a-I had shown two 6Li signals, lacking correlation with 13C signals [15]. Thus, there is good reason to believe that the

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

• ][41][42]. Values for Ks and n given in Table 3 all have satisfactory correlation coefficients (>0.999). Thermal melting curves for DNA, RNA, and their complexes with the studied compounds (Table 2) were determined as previously described [39][61] by following the absorption change at 260 nm as a

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

• (Figure 11a). This very poor correlation for the transient transfection of the HaloTags on the Golgi contrasted sharply with an r2 value of 0.983 obtained with the stable HGM cells with the HaloTags expressed on the mitochondria. The difference between the two plots in Figure 11a and Figure 8a was

• signal from the Golgi apparatus without an initial cell selection was tested next (Figure 10a, yellow only). With this Golgi mask without cell selection, the correlation of the fluorescence of the GFP and 26, with an r2 value of 0.549, was even worse than the r2 value of 0.626 for the whole-cell mask

• , yellow only). The application of both the cell selection and the Golgi mask to the analysis finally improved the correlation of the GFP and the 26 emission to r2 = 0.816 (Figure 11d). This value was slowly approaching the precision realized without further effort using the stable cell line HGM (Figure 8b

Pauson–Khand reaction of fluorinated compounds

• Jorge Escorihuela,
• Daniel M. Sedgwick,
• Alberto Llobat,
• Mercedes Medio-Simón,
• Pablo Barrio and
• Santos Fustero

Beilstein J. Org. Chem. 2020, 16, 1662–1682, doi:10.3762/bjoc.16.138

• carbons, which also showed a correlation with the regioselectivity. In 2016, León and Fernández reported the first intermolecular PKR of internal alkynylboronic esters with norbornadiene [81]. For this purpose, terminal alkynes were converted into their corresponding alkynylboronic pinacol esters, and

Fluorohydration of alkynes via I(I)/I(III) catalysis

• Jessica Neufeld,
• Constantin G. Daniliuc and
• Ryan Gilmour

Beilstein J. Org. Chem. 2020, 16, 1627–1635, doi:10.3762/bjoc.16.135

• 3–5). In addition, a nearly linear correlation between the equivalents of added H2O and the product yield was observed (Table 2 insert). Cognisant that H2O is likely being introduced to the reaction via the HF source, and to prevent reproducibility issues due to variation of the H2O content, 1.0

Synthesis of new dihydroberberine and tetrahydroberberine analogues and evaluation of their antiproliferative activity on NCI-H1975 cells

• Giacomo Mari,
• Lucia De Crescentini,
• Serena Benedetti,
• Francesco Palma,
• Stefania Santeusanio and
• Fabio Mantellini

Beilstein J. Org. Chem. 2020, 16, 1606–1616, doi:10.3762/bjoc.16.133

• of 13a-C, 13-C and 15-C (signals highlighted in green, Figure 3). It is noteworthy that in the reduction process of the DHBER 2 precursors, a single diastereoisomer of the corresponding THBERs 3 is produced according to 1H and 13C NMR data. In particular, the NOE correlation between C13−H and C13a−H

• . 1H,1H-COSY spectrum of DHBER 2a [65]. Detail of the hydrazone signal in the HMBC spectrum of THBER 3a. Comparison between 1H NMR spectra of DHBER 2a and of THBER 3a. NOE correlation between C13−H and C13a−H of THBER 3a. Effects of 25 µM hydrazono-DHBERs 2a–n (A) and hydrazono-THBERs 3a–g,i–n [70] (B

Antibacterial scalarane from Doriprismatica stellata nudibranchs (Gastropoda, Nudibranchia), egg ribbons, and their dietary sponge Spongia cf. agaricina (Demospongiae, Dictyoceratida)

• Cora Hertzer,
• Stefan Kehraus,
• Nils Böhringer,
• Fontje Kaligis,
• Robert Bara,
• Dirk Erpenbeck,
• Gert Wörheide,
• Till F. Schäberle,
• Heike Wägele and
• Gabriele M. König

Beilstein J. Org. Chem. 2020, 16, 1596–1605, doi:10.3762/bjoc.16.132

• correlation between the methylene protons H2-22 (δ −0.06 brt, J = 4.8 Hz, δ 0.43 dd, J = 3.9, 9.2 Hz), and the methine proton H-3 (δ 0.55 m), based on HMBC cross peaks between the protons H2-22 and the carbon atoms C-2 (δ 19.0), C-5 (δ 53.2) and C-21 (δ 23.3). The entire assignment of all NMR data is given in