Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity

• Jamshid Amiri Moghaddam,
• Huijuan Guo,
• Karsten Willing,
• Thomas Wichard and
• Christine Beemelmanns

Beilstein J. Org. Chem. 2022, 18, 722–731, doi:10.3762/bjoc.18.72

• farnesylation of 8-HQA; B) calculated MS2 fragmentation pattern of farnesylated 8-HQA; C) extracted ion chromatogram (EIC) for m/z 394.2376 (tR 18.03 min, red arrow) of enriched UbiA-297 protein fractions, cell-membrane fraction containing UbiA-297 (Maribacter sp. MS6), denaturated enriched UbiA-297 (negative

• , and point mutated UbiA-297 (R145A) from Maribacter sp. MS6; E and F) HRMS and MS2 spectrum showing fragmentation of prenylated 8-HQA (m/z 394.2367, tR 18.03 min). Supporting Information Supporting Information File 176: Sequence analysis and copies of MS/MS and NMR spectra. Acknowledgements We would

Amamistatins isolated from Nocardia altamirensis

• Till Steinmetz,
• Wolf Hiller and
• Markus Nett

Beilstein J. Org. Chem. 2022, 18, 360–367, doi:10.3762/bjoc.18.40

• : R1 = H, R2 = H, R3 = H; 4: R1 = H, R2 = OH, R3 = H; 5: R1 = CHO, R2 = OH, R3 = OH. 1H,1H COSY and selected 1H,13C HMBC correlations in compounds 1 and 6. MS–MS fragmentation of amamistatins (1–5). Proposed biosynthesis of amamistatins isolated in this study. 1H and 13C NMR spectroscopic data for

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

• /succinic acid module (Scheme 1, paths E1 and E2). The third elimination product, C15-ketene (structure in square brackets, Scheme 1) was not observed, but a pentadecenoate anion, appearing at m/z 239, warranted the existence of fragmentation path E3 and also the chain length of the acyl unit. Hydration of

• acquired on a quadrupole time-of-flight mass spectrometer in the negative ion mode. MS/MS fragmentation pathway for compound 1. 1H and 13C NMR data for tenacibactin K (1) in DMSO-d6. 1H and 13C NMR data for tenacibactins L (2) and M (3) in DMSO-d6. Cytotoxicity data of compounds 1–3. Supporting

Adjusting the length of supramolecular polymer bottlebrushes by top-down approaches

• Tobias Klein,
• Franka V. Gruschwitz,
• Maren T. Kuchenbrod,
• Ivo Nischang,
• Stephanie Hoeppener and
• Johannes C. Brendel

Beilstein J. Org. Chem. 2021, 17, 2621–2628, doi:10.3762/bjoc.17.175

• interest. While ultrasonication (US) represents a standard but rather harsh fragmentation technique, we additionally introduced dual asymmetric centrifugation (DAC) as an excellent alternative top-down method for effective, more controlled, and adaptable preparation of polymer nanostructures [24][25][26

• ][27][28]. Both methods are applied for fragmentation of initially µm-long SPBs based on BTU–PEO and BTP–PEO conjugates. The resulting nanofibers were characterized in detail by cryogenic transmission electron microscopy (cryoTEM), as well as by asymmetrical flow field-flow fractionation measurements

• comparably mild treatment already caused a significant fragmentation of the µm-long fibers, resulting in structures of 50–200 nm length according to the cryoTEM images after 10 min of treatment (Figure 2). An average fiber length of 92 ± 51 nm and 74 ± 39 nm for BTU DAC (10 min, 1,000 rpm) and BTP DAC (10

Constrained thermoresponsive polymers – new insights into fundamentals and applications

• Patricia Flemming,
• Alexander S. Münch,
• Andreas Fery and
• Petra Uhlmann

Beilstein J. Org. Chem. 2021, 17, 2123–2163, doi:10.3762/bjoc.17.138

Methodologies for the synthesis of quaternary carbon centers via hydroalkylation of unactivated olefins: twenty years of advances

• Thiago S. Silva and
• Fernando Coelho

Beilstein J. Org. Chem. 2021, 17, 1565–1590, doi:10.3762/bjoc.17.112

• substituted hydrazones obviated their generation in situ, and as ethanol was identified as a better solvent in the initial coupling step, no solvent exchange was necessary in the fragmentation step of the hydrazide intermediate. The addition of triethylamine and heating the reaction to 80 °C for 1 hour were

Icilio Guareschi and his amazing “1897 reaction”

• Gian Cesare Tron,
• Alberto Minassi,
• Giovanni Sorba,
• Mara Fausone and
• Giovanni Appendino

Beilstein J. Org. Chem. 2021, 17, 1335–1351, doi:10.3762/bjoc.17.93

• carbonyl derivative. Guareschi found that the fragmentation was quantitative when an ethanolic solution of the imide was treated with magnesium hydroxide, poorly soluble but sufficient to ionize the cyanopyridone. It should be pointed out that the identification of gaseous compounds was not at all trivial

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

• the marine bacteria. To separate algal and bacterial metabolism, single colonies of Roseovarius sp. MS2 and Maribacter sp. MS6 were deposited onto glass slides and analysed with AP-SMALDI-HRMS/MS. Using spectral similarity matching based on the fragmentation pattern obtained from AP-SMALDI-HRMS/MS

• , choline). MS/MS experiments were performed with AP-SMALDI-HRMS to match the fragmentation pattern between the standard ectoine and bacteria monoculture profile. Fragmentation spectra of ectoine were acquired from the bacterial isolate Roseovarius sp. MS2 and an ectoine standard. To perform a measurement

• covered with the DHB matrix, following the standard ectoine procedure. Samples were analysed in positive ion mode, with the number of laser shots per spot set to 30 (approximately 1.2 μJ shot−1). All-ion fragmentation (AIF) mode was set as follows: molecular ion of ectoine at m/z 143.1; isolation window m

Prins cyclization-mediated stereoselective synthesis of tetrahydropyrans and dihydropyrans: an inspection of twenty years

• Asha Budakoti,
• Pradip Kumar Mondal,
• Prachi Verma and
• Jagadish Khamrai

Beilstein J. Org. Chem. 2021, 17, 932–963, doi:10.3762/bjoc.17.77

• -trimethylsilylalkenyl cation 242 formed by the Grob-type fragmentation (Scheme 57), which was trapped by the subsequent attack of the halide anion, leading to the formation of Prins product 244. On the basis of theoretical calculations, the authors could conclude factors controlling the alkyne Prins cyclization over

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

• compounds, structural suggestions were made based on their mass spectrometric fragmentation pattern and confirmed by the synthesis of reference compounds. The results of the feeding experiments allowed to conclude on the substrate tolerance of DMSP degrading enzymes in marine bacteria. Keywords: Allium

• fragmentation pattern of the mass spectrum (Figure 3A). The molecular ion together with its isotope pattern pointed to two sulfur atoms, while the fragment ion at m/z = 64 ([S2]+) pointed to a disulfide. The fragment ions at m/z = 59 ([C2O2H3]+) and 161 ([M − OMe]+) indicated a methyl ester, and the series of m

• . The analysis of the fragmentation pattern (Figure 3B) suggested that 27 could be methyl 3-(methylsulfonyl)propanoate, an oxidation product of 23. This hypothesis was confirmed by the chemical oxidation of 23, yielding methyl 3-(methylsulfonyl)propanoate with an identical mass spectrum and retention

Amino- and polyaminophthalazin-1(2H)-ones: synthesis, coordination properties, and biological activity

• Zbigniew Malinowski,
• Emilia Fornal,
• Agata Sumara,
• Renata Kontek,
• Karol Bukowski,
• Beata Pasternak,
• Dariusz Sroczyński,
• Joachim Kusz,
• Magdalena Małecka and
• Monika Nowak

Beilstein J. Org. Chem. 2021, 17, 558–568, doi:10.3762/bjoc.17.50

• 63Cu2+/65Cu2+ ion complex containing two ligands L2. However, a significant amount of unchanged ligand was also visible. For the ion at m/z = 719.5 Da, tandem spectra were recorded. The first fragmentation gave ions at m/z = 329.3 Da (L2 + H+) and 391.4 Da (ligand L2 and copper). The further

• fragmentation of the ion at m/z = 391.4 Da gave rise to an ion series: 362.4 Da (probably after elimination of HCO), 311.4 Da, 286.3 Da (100%), and 235.4 Da. We did not observe in the tandem spectra the signal after the elimination of copper alone. Similarly, the ESIMS spectrum of an equimolar mixture of

• compound 7 (L3) and CuCl2 showed the presence of two types of complexes containing one and two phthalazinone ligands: [(L3)Cu(II)Cl]+ and [(L3)2Cu2(II)Cl3]+. The most abundant peak at m/z = 422.3 Da corresponded to the complex [(L3)Cu(II)Cl]+. The MS/MS fragmentation of the ions at m/z = 422.3 Da for 63Cu

Coupling biocatalysis with high-energy flow reactions for the synthesis of carbamates and β-amino acid derivatives

• Alexander Leslie,
• Thomas S. Moody,
• Megan Smyth,
• Scott Wharry and
• Marcus Baumann

Beilstein J. Org. Chem. 2021, 17, 379–384, doi:10.3762/bjoc.17.33

• interesting case concerned the use of 3-oxocyclobutanecarboxylic acid (1m), which yielded the desired carbamate product 3m along with the carbamoyl-urea species 3m’. This observation parallels recent reports [25] proposing a fragmentation of the desired carbamate followed by a combination of the resulting

Insight into functionalized-macrocycles-guided supramolecular photocatalysis

• Minzan Zuo,
• Krishnasamy Velmurugan,
• Kaiya Wang,
• Xueqi Tian and
• Xiao-Yu Hu

Beilstein J. Org. Chem. 2021, 17, 139–155, doi:10.3762/bjoc.17.15

• occur within the CB[8] cavity via host–guest interactions, and thus predominantly produced the syn- instead of the anti-dimers. An alternative approach introduced by An et al. is about the 2:1 CB[7]–perylene diimide (PDI) host–guest-assisted reversible addition–fragmentation chain transfer (RAFT

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• incorporated deuterium can then be localised through protease-generated peptide fragments or fragmentation within the mass spectrometer. The rate of hydrogen-to-deuterium exchange provides insight into the solvent accessibility. HDXMS provides information on the conformation of the protein, PPIs, and even

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification

• Steffen Lippold,
• Arnoud H. de Ru,
• Jan Nouta,
• Peter A. van Veelen,
• Magnus Palmblad,
• Manfred Wuhrer and
• Noortje de Haan

Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253

• digest from affinity-purified immunoglobulins G and A was analyzed on a nano-reversed-phase liquid chromatography–tandem mass spectrometry platform with a high-resolution mass analyzer and higher-energy collisional dissociation fragmentation. Initial glycopeptide identification based on MS/MS data was

• ]. Advances in MS technologies tremendously enhanced the detection and informative fragmentation of glycopeptides in the past years [9]. The large amount of highly complex data acquired using these technologies shifted the major bottleneck in glycopeptide analysis to the data processing steps. Next to the

• glycopeptide identification by GlycopeptideGraphMS. In MS/MS scoring approaches such as Byonic, the definition of a threshold for the automated assignment of glycopeptides is generally a challenge as the scores depend largely on the fragmentation method, the peptide characteristics (e.g., peptide length or

All-carbon [3 + 2] cycloaddition in natural product synthesis

• Zhuo Wang and
• Junyang Liu

Beilstein J. Org. Chem. 2020, 16, 3015–3031, doi:10.3762/bjoc.16.251

• fragmentation to afford alkene 72 in 61% yield. Marcfortine B (8) was synthesized from alkene 72 in seven steps. The enantioselective synthesis of marcfortine C (9) commenced with a catalytic asymmetric cyano-substituted TMM cycloaddition of oxindole 73 and TMM donor 75 with Pd(dba)2/74 as catalyst to give a

• complex B (Scheme 11B). A facile migration–fragmentation process of complex B eliminates a ketone through fragmentation and produces metal-carbene intermediate C. The freshly prepared metal-carbene C is equilibrated to stabilized 1,3-dipole D. D undergoes a diastereoselective [3 + 2] cycloaddition to give

Ultrasound-assisted Strecker synthesis of novel 2-(hetero)aryl-2-(arylamino)acetonitrile derivatives

• Emese Gal,
• Luiza Gaina,
• Hermina Petkes,
• Alexandra Pop,
• Castelia Cristea,
• Gabriel Barta,
• Dan Cristian Vodnar and
• Luminiţa Silaghi-Dumitrescu

Beilstein J. Org. Chem. 2020, 16, 2929–2936, doi:10.3762/bjoc.16.242

• frequencies between 20 and 100 kHz were reported in the literature as optimal to enhance the nucleation and fragmentation rates, but the exact optimal frequency is probably reactor and system specific [8]. The exciting properties of the heterocyclic phenothiazine core displaying tunable chemical, redox

On the mass spectrometric fragmentations of the bacterial sesterterpenes sestermobaraenes A–C

• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2020, 16, 2807–2819, doi:10.3762/bjoc.16.231

• investigation of the electron impact mass spectrometry (EIMS) fragmentation reactions of these sesterterpene hydrocarbons. Keywords: isotopes; mass spectrometry; reaction mechanisms; sesterterpenes; Streptomyces mobaraensis; Introduction The sestermobaraenes A–F (1–6) and sestermobaraol (7) are a series of

• reaction proceeds in reverse order of a thermal reaction promoted by the thermal conditions of the gaschromatographic analysis) [14]. The fragmentation reactions of structurally simple compounds such as fatty acid methyl esters have been well investigated by isotopic labelling experiments [15][16] and the

• complicated cases, as was exemplified for the side products of bacterial 2-methylisoborneol synthases [22], but in general the structural complexity of terpenes does not allow for such approaches. Nevertheless, more knowledge about the MS fragmentation reactions of terpenes is desirable, but represents a

3-Acetoxy-fatty acid isoprenyl esters from androconia of the ithomiine butterfly Ithomia salapia

• Florian Mann,
• Daiane Szczerbowski,
• Lisa de Silva,
• Melanie McClure,
• Marianne Elias and
• Stefan Schulz

Beilstein J. Org. Chem. 2020, 16, 2776–2787, doi:10.3762/bjoc.16.228

• explained by the different stabilization of the respective ions (Figure 3). The abundance of m/z 68 is higher in isoprenyl esters due to the more stable allyl radical cation (Figure 3A). In contrast, prenyl ester fragmentation produces a stabilized allyl cation m/z 69 (Figure 3B), while isoprenyl esters

• 68 (A), m/z 69 (B), and m/z 280 (C). Mass spectra and fragmentation of A: isoprenyl (3-methyl-3-butenyl) 9-octadenoate (9) and B: prenyl (3-methyl-2-butenyl) 9-octadecenoate (10). Red arrows show characteristics in the mass spectra differentiating prenyl and isoprenyl esters. Mass spectra and

• fragmentation of A: isoprenyl 3-acetoxyoctadecanoate (11); B: isoprenyl (Z)-3-acetoxy-13-octadecenoate (12). Separation of the enantiomers of methyl (Z)-3-hydroxy-13-octadecenoate (25) on a β-6-TBDMS hydrodex gas chromatographic phase. A) Natural extract; B) synthetic rac-25; C) synthetic (R)-25; X: methyl 3

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

• used to counteract the need for complementary analytic techniques. One of the examples of this is tandem mass spectrometry, where the glycan fragmentation is controlled to obtain the identification of the glycosylation sites and a complete description of the glycan structure compositions, including

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

• tool has been particularly upgraded for MS spectrum annotation by adding an intuitive interface with additional features. The upgraded version can depict bond fragmentation, repeating structural unit anomeric groups, adduct ions, different types of glycosidic linkages etc. These advanced features make

• different fragmentation modes [54]. Glycano. Glycano (available at http://glycano.cs.uct.ac.za) is a software tool for drawing glycans. This tool is based on JavaScript, which can be used without the requirement of any server or browser dependency. The interactive interface allows sketching via the drag-and

Photosensitized direct C–H fluorination and trifluoromethylation in organic synthesis

• Shahboz Yakubov and
• Joshua P. Barham

Beilstein J. Org. Chem. 2020, 16, 2151–2192, doi:10.3762/bjoc.16.183

• ][119][120][121][122]. There are many approaches to photosensitized fluorination that do not involve direct C–H activation, which are reviewed elsewhere [123][124][125], such as C–C bond fragmentation/C–F bond formation [126], aminofluorination of cyclopropanes [127] and decarboxylative fluorination

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

• to identify and measure with GlypNirO. Because there are often multiple potential sites of O-glycosylation within a tryptic peptide and site-specific assignment is challenging with CID or HCD fragmentation information, we used peptide-centric analysis of the plasma O-glycoproteome. Comparing peptide

A complementary approach to conjugated N-acyliminium formation through photoredox-catalyzed intermolecular radical addition to allenamides and allencarbamates

• Olusesan K. Koleoso,
• Matthew Turner,
• Felix Plasser and
• Marc C. Kimber

Beilstein J. Org. Chem. 2020, 16, 1983–1990, doi:10.3762/bjoc.16.165

• product, with only a complex mixture, as identified by 1H NMR, being isolated. Significantly, in the 1H NMR spectra of this complex mixture we observed complete fragmentation of the sulfonamide unit. Two chiral allenamides (24 and 25) were exposed to the photoredox conditions with 2,4-dimethylaniline, and

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

• of 45 °C. MS data were acquired over a range from 100–3000 m/z in positive mode. Auto MS/MS fragmentation was achieved with rising collision energy (35–50 keV over a gradient from 500–2000 m/z) with a frequency of 4 Hz for all ions over a threshold of 100. UHPLC started with 90% H2O containing 0.1