Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers

• Andreas Wiest and
• Pavel Kielkowski

Beilstein J. Org. Chem. 2024, 20, 2323–2341, doi:10.3762/bjoc.20.199

• action on a molecular level. To search elusive, often labile, and low-abundant conjugates between proteins and active compounds, chemical proteomics introduces a feasible strategy that allows to enrich and detect these conjugates. Recent advances in mass spectrometry techniques and search algorithms

• identification rates and may help to identify otherwise difficult to find interactions between active compounds and proteins, which may result from unperturbed conditions, and thus are of high physiological relevance. Keywords: chemical proteomics; diagnostic ions; mass spectrometry; target identification

• disease [2][3]. In parallel, mass spectrometry (MS) has been crucial in many areas centered around the characterization of NPs [4]. First to annotate their often complex structures using diverse fragmentation techniques [4]. Nowadays, MS is applied for the identification of NPs’ cellular protein targets

Deuterated reagents in multicomponent reactions to afford deuterium-labeled products

• Kevin Schofield,
• Shayna Maddern,
• Yueteng Zhang,
• Grace E. Mastin,
• Rachel Knight,
• Wei Wang,
• James Galligan and
• Christopher Hulme

Beilstein J. Org. Chem. 2024, 20, 2270–2279, doi:10.3762/bjoc.20.195

• . Optimization of deuterated Leuckart–Wallach reactiona. Microsomal stability package of deuterated and non-deuterated dihydropyridines. Supporting Information Supporting Information File 86: Experimental and analytical data and copies of NMR spectra. Acknowledgements We thank the UA mass spectrometry and NMR

Novel truxene-based dipyrromethanes (DPMs): synthesis, spectroscopic characterization and photophysical properties

• Shakeel Alvi and
• Rashid Ali

Beilstein J. Org. Chem. 2024, 20, 2163–2170, doi:10.3762/bjoc.20.186

• derivatives were successfully characterized and their structures were established by means of the 1H and 13C NMR spectroscopy, besides further confirmation by mass spectrometry (see Supporting Information File 1). The UV–vis absorption, emission and time-resolved fluorescence spectra Emission and absorption

A facile three-component route to powerful 5-aryldeazaalloxazine photocatalysts

• Ivana Weisheitelová,
• Radek Cibulka,
• Marek Sikorski and
• Tetiana Pavlovska

Beilstein J. Org. Chem. 2024, 20, 1831–1838, doi:10.3762/bjoc.20.161

• unexpected structure of product 6 was confirmed by 1H, 13C NMR and mass spectrometry. The main feature of the 1H NMR spectrum of compound 6 is the absence of the signals of the aromatic aldehyde moiety and the appearance of the singlet of the 5-CH methyne group at 9.56 ppm and the singlets of the protons of

• source in this reaction, a deuterium labelling experiment was conducted (Scheme 2C). Indeed, the deazaalloxazine derivative 6-d with quantitative incorporation of deuterium in C(5) position, was isolated and confirmed by 1H NMR analysis and mass spectrometry (for more details on possible reaction

Ugi bisamides based on pyrrolyl-β-chlorovinylaldehyde and their unusual transformations

• Alexander V. Tsygankov,
• Vladyslav O. Vereshchak,
• Tetiana O. Savluk,
• Serhiy M. Desenko,
• Valeriia V. Ananieva,
• Oleksandr V. Buravov,
• Yana I. Sakhno,
• Svitlana V. Shishkina and
• Valentyn A. Chebanov

Beilstein J. Org. Chem. 2024, 20, 1773–1784, doi:10.3762/bjoc.20.156

• stirring for three hours (Scheme 3, conditions A). However, the results of this attempted post-Ugi transformation were quite unexpected: Instead of acid 11, we isolated the amide of the unsaturated derivative of pyruvic acid 10a according to the 1H and 13C NMR spectra and mass spectrometry data. In order

• conventional thermal heating, amide 10a was isolated, albeit in a lower yield and accompanied with tar formation. In addition to the 1H, 13C NMR spectra and mass spectrometry data, the structure of compound 10d was established by X-ray diffraction analysis (Figure 3). It was also found that the substituents at

Oxidation of benzylic alcohols to carbonyls using N-heterocyclic stabilized λ³-iodanes

• Thomas J. Kuczmera,
• Pim Puylaert and
• Boris J. Nachtsheim

Beilstein J. Org. Chem. 2024, 20, 1677–1683, doi:10.3762/bjoc.20.149

• detected as a side reaction via mass spectrometry. Vinyl alcohols were also studied, giving carvone (4v) in 74% yield without oxidation of the double bonds. Finally, other heterocyclic benzylic alcohols were investigated, which led to undesired chlorinations in the case of benzimidazoles 3w and 3x and

Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty

• Weimao Zhong and
• Vinayak Agarwal

Beilstein J. Org. Chem. 2024, 20, 1635–1651, doi:10.3762/bjoc.20.146

• known parabens (2, 5, 6, and 11), five new ones (7–10, and 12) were identified. Their structures were elucidated by high-resolution mass spectrometry (HRMS) and 1D and 2D nuclear magnetic resonance (NMR). The configuration in 8 and 10 remained undetermined. Antimicrobial activities of compounds 2 and 5

• Microbulbifer bacteria and is not limited to Microbulbifer strains isolated from either coral or sponge microbiomes. Imaging mass spectrometry demonstrated that bulbiferamides are excreted by Microbulbifer bacterial colonies into the extracellular media. Based on the characteristic mass spectrometric

New triazinephosphonate dopants for Nafion proton exchange membranes (PEM)

• Fátima C. Teixeira,
• António P. S. Teixeira and
• C. M. Rangel

Beilstein J. Org. Chem. 2024, 20, 1623–1634, doi:10.3762/bjoc.20.145

• characterization of the dopants was carried out by Fourier-transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). 1H, 13C and 31P NMR characterization was done using different one- and two-dimensional techniques, and were obtained on a Bruker Avance III HD

Hypervalent iodine-catalyzed amide and alkene coupling enabled by lithium salt activation

• Akanksha Chhikara,
• Fan Wu,
• Navdeep Kaur,
• Prabagar Baskaran,
• Alex M. Nguyen,
• Zhichang Yin,
• Anthony H. Pham and
• Wei Li

Beilstein J. Org. Chem. 2024, 20, 1405–1411, doi:10.3762/bjoc.20.122

• . Acknowledgements We thank Dr. Yong W. Kim (University of Toledo) for NMR assistance. Mr. Babatunde Obadawo (University of Toledo) is acknowledged for collecting the high-resolution mass spectrometry data. We acknowledge Dr. Navdeep Kaur’s Ph. D. for her contributions in her Ph. D. thesis titled “Selective

Synthesis of 1,2,3-triazoles containing an allomaltol moiety from substituted pyrano[2,3-d]isoxazolones via base-promoted Boulton–Katritzky rearrangement

• Constantine V. Milyutin,
• Andrey N. Komogortsev and
• Boris V. Lichitsky

Beilstein J. Org. Chem. 2024, 20, 1334–1340, doi:10.3762/bjoc.20.117

• spectroscopy and high-resolution mass spectrometry. Moreover, X-ray analysis was used for confirmation of structure of compound 4g (Figure 1). A plausible mechanism of the studied rearrangement is presented in Scheme 5. At first, anion A is generated from starting hydrazone 3 under action of base. Next

• obtained the recyclized product 6a (Scheme 6), whose structure was confirmed by 1H, 13C NMR spectroscopy, high-resolution mass spectrometry and X-ray analysis. Based on the aforementioned reaction we have synthesized a set of pyrazolylisoxazoles 6 (Scheme 7). The proposed mechanism of investigated

Computation-guided scaffold exploration of 2E,6E-1,10-trans/cis-eunicellanes

• Zining Li,
• Sana Jindani,
• Volga Kojasoy,
• Teresa Ortega,
• Erin M. Marshall,
• Khalil A. Abboud,
• Sandra Loesgen,
• Dean J. Tantillo and
• Jeffrey D. Rudolf

Beilstein J. Org. Chem. 2024, 20, 1320–1326, doi:10.3762/bjoc.20.115

• crystallographic information. Acknowledgements We acknowledge the University of Florida Center for Nuclear Magnetic Resonance Spectroscopy and Ion Ghiviriga for excellent NMR support. We acknowledge the University of Florida Mass Spectrometry Research and Education Center (MSREC), which is supported by the NIH

Diameter-selective extraction of single-walled carbon nanotubes by interlocking with Cu-tethered square nanobrackets

• Guoqing Cheng and
• Naoki Komatsu

Beilstein J. Org. Chem. 2024, 20, 1298–1307, doi:10.3762/bjoc.20.113

• extraction, the square Cu-nanobrackets 1b were successfully obtained by the reaction between the nanobracket 4b and copper(II) acetylacetonate in THF at room temperature. The product was characterized as 1b by MALDI-TOF mass spectrometry (Figure 1a), absorption (Figure 1b) and Raman (Figure 2c

Synthesis of indano[60]fullerene thioketone and its application in organic solar cells

• Yong-Chang Zhai,
• Shimon Oiwa,
• Shinobu Aoyagi,
• Shohei Ohno,
• Tsubasa Mikie,
• Jun-Zhuo Wang,
• Hirofumi Amada,
• Koki Yamanaka,
• Kazuhira Miwa,
• Naoyuki Imai,
• Takeshi Igarashi,
• Itaru Osaka and
• Yutaka Matsuo

Beilstein J. Org. Chem. 2024, 20, 1270–1277, doi:10.3762/bjoc.20.109

• amount of Lawesson's reagent was increased to 3 equiv (Table 1, entry 5), the signal of thioketone was observed for the first time by high-performance liquid chromatography (HPLC) and MALDI time-of-flight mass spectrometry. Subsequently, a conversion of 99% was achieved by further increasing the amount

Mechanistic investigations of polyaza[7]helicene in photoredox and energy transfer catalysis

• Johannes Rocker,
• Till J. B. Zähringer,
• Matthias Schmitz,
• Till Opatz and
• Christoph Kerzig

Beilstein J. Org. Chem. 2024, 20, 1236–1245, doi:10.3762/bjoc.20.106

• , Supporting Information File 1) [76]. A reaction course plot in the absence of 4CP and TsNa revealed rapid decomposition of the photocatalyst, presumably in a [2 + 2]-photocycloaddition with the styrene component as observed in mass spectrometry (see Figure S17 and Figure S18 in Supporting Information File 1

• reported similar efficiencies for the formation of both isomers starting from the perpendicular triplet state (Figure 5E) [35][83]. In contrast to styrene substrates, mass spectrometry shows no addition products of catalyst and stilbene. Hence, the photocatalyst is not consumed by side reactions

Competing electrophilic substitution and oxidative polymerization of arylamines with selenium dioxide

• Vishnu Selladurai and
• Selvakumar Karuthapandi

Beilstein J. Org. Chem. 2024, 20, 1221–1235, doi:10.3762/bjoc.20.105

• from through solvent (acetonitrile) oxidation was isolated as a colorless solid (vide infra). It was characterized by FTIR, 1H NMR, and mass spectrometry. The FTIR and mass spectrometry data were in accordance with the literature report [48][49]. Interestingly, the mass spectrum of the oxide 3 showed a

Cofactor-independent C–C bond cleavage reactions catalyzed by the AlpJ family of oxygenases in atypical angucycline biosynthesis

• Jinmin Gao,
• Liyuan Li,
• Shijie Shen,
• Guomin Ai,
• Bin Wang,
• Fang Guo,
• Tongjian Yang,
• Hui Han,
• Zhengren Xu,
• Guohui Pan and
• Keqiang Fan

Beilstein J. Org. Chem. 2024, 20, 1198–1206, doi:10.3762/bjoc.20.102

• the spontaneous formation of a limited quantity of 1 derived from 8, we detected the generation of products, including the previously characterized benzofluorene intermediate 4 and benzofluorene dimer 5, alongside a novel compound, designated as 10 (Figure 1, trace d). High-resolution mass

• spectrometry (HRMS) analysis of 10 ([M − H]− calcd for C18H12O5, 307.0612; found, 307.0607, Figure S4, Supporting Information File 1) suggested a possible identity as hydroquinone–kinobscurinone [11]. However, attempts to elucidate the chemical structure of 10 were not successful due to the inherent

Two-fold addition reaction of silylene to C₆₀: structural and electronic properties of a bis-adduct

• Masahiro Kako,
• Masato Kai,
• Masanori Yasui,
• Michio Yamada,
• Yutaka Maeda and
• Takeshi Akasaka

Beilstein J. Org. Chem. 2024, 20, 1179–1188, doi:10.3762/bjoc.20.100

• perpendicularly. Unfortunately, the matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry of 3 afforded no molecular ion peak expected for adducts derived from Dip2Si and C60 while a base peak at m/z 720 due to C60 was observed probably because of the low stability of radical

Kinetically stabilized 1,3-diarylisobenzofurans and the possibility of preparing large, persistent isoacenofurans with unusually small HOMO–LUMO gaps

• Qian Liu and
• Glen P. Miller

Beilstein J. Org. Chem. 2024, 20, 1099–1110, doi:10.3762/bjoc.20.97

• spectroscopy. After 51 hours of reaction in boiling CH2Cl2, Diels–Alder adduct 27 was observed in 22% yield. Compound 27 was identified by 1H NMR and 13C NMR spectroscopies as well as high-resolution ESI mass spectrometry. Although the lack of reactivity observed for 3 and 23 limited our kinetic analysis, we

Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A

• Maksim V. Kvach,
• Stefan Harjes,
• Harikrishnan M. Kurup,
• Geoffrey B. Jameson,
• Elena Harjes and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2024, 20, 1088–1098, doi:10.3762/bjoc.20.96

• the enzymatic assays and the synthesis of nucleosides and modified ODNs, assignment of 1H, 13C, 31P NMR and IR spectra and results of HRESIMS experiments for new compounds synthesised as well as RP-HPLC profiles and HRESIMS spectra of ODNs. Acknowledgements NMR and mass spectrometry facilities at

Structure–property relationships in dicyanopyrazinoquinoxalines and their hydrogen-bonding-capable dihydropyrazinoquinoxalinedione derivatives

• Tural N. Akhmedov,
• Ajeet Kumar,
• Daken J. Starkenburg,
• Kyle J. Chesney,
• Khalil A. Abboud,
• Novruz G. Akhmedov,
• Jiangeng Xue and
• Ronald K. Castellano

Beilstein J. Org. Chem. 2024, 20, 1037–1052, doi:10.3762/bjoc.20.92

• temperatures of 21 and 7 °C, respectively, from their corresponding DCPQ comparators. To complement the TGA studies, the thermal stability of compound 4b was evaluated through its exposure to air inside a 200 °C oven for one week. Structural evaluation by 2D NMR and mass spectrometry confirmed no decomposition

• .: CHE-1057411; R.K.C./J.X.: CHE-1507561). K.A.A. wishes to acknowledge the NSF and the University of Florida for funding of the purchase of the X-ray equipment. The mass spectrometry data has been generated by the Mass Spectrometry Research and Education Center at the University of Florida which is

A Diels–Alder probe for discovery of natural products containing furan moieties

• Alyssa S. Eggly,
• Namuunzul Otgontseren,
• Carson B. Roberts,
• Amir Y. Alwali,
• Haylie E. Hennigan and
• Elizabeth I. Parkinson

Beilstein J. Org. Chem. 2024, 20, 1001–1010, doi:10.3762/bjoc.20.88

• easily identifiable on liquid chromatography–mass spectrometry (LC–MS). The molecular probe, which undergoes this reaction with a variety of furans, was designed with both a UV-tag and a mass tag to enable easy identification. The probe has been tested with a variety of purified furans, including natural

• supernatant. There are two main types of molecular probes based on their detection methods: imaging and UV–vis (Figure 2A). An imaging probe contains a mass spectrometry (MS) tag, oftentimes a halogen with a distinct isotopic ratio such as chlorine or bromine. A UV–vis probe contains a UV-tag, such as an

Ortho-ester-substituted diaryliodonium salts enabled regioselective arylocyclization of naphthols toward 3,4-benzocoumarins

• Ke Jiang,
• Cheng Pan,
• Limin Wang,
• Hao-Yang Wang and
• Jianwei Han

Beilstein J. Org. Chem. 2024, 20, 841–851, doi:10.3762/bjoc.20.76

• Technology, 130 Meilong Road, Shanghai 200237, P. R. China National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, The Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China 10.3762/bjoc.20.76 Abstract Cyclic annulation involving diaryliodonium

Synthesis of new representatives of A₃B-type carboranylporphyrins based on meso-tetra(pentafluorophenyl)porphyrin transformations

• Victoria M. Alpatova,
• Evgeny G. Rys,
• Elena G. Kononova and
• Valentina A. Ol'shevskaya

Beilstein J. Org. Chem. 2024, 20, 767–776, doi:10.3762/bjoc.20.70

• carborane A3B-porphyrin were also synthesized based on the amino-substituted A3B-porphyrin. The structures of the prepared carboranylporphyrins were determined by UV–vis, IR, 1H, 19F, 11B NMR spectroscopic data and MALDI mass spectrometry. Keywords: bioconjugation; carboranes; fluorine; porphyrin; SNAr

• azide substituent in porphyrin 2 with SnCl2·2H2O in MeOH resulted in the formation of porphyrin amino-derivative 3 in 82% yield (Scheme 1). The molecular structures of compounds 2 and 3 were confirmed by a combination of NMR spectroscopy and mass spectrometry. Having synthesized porphyrins 2 and 3 we

• easily converted into hydrophilic charged entities by the protonation of the unsubstituted amino functionalities in their structure providing improved bioconjugation. Spectroscopic data All porphyrin conjugates were structurally characterized by IR, UV–vis, NMR spectroscopy, and mass spectrometry. The IR

Substrate specificity of a ketosynthase domain involved in bacillaene biosynthesis

• Zhiyong Yin and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2024, 20, 734–740, doi:10.3762/bjoc.20.67

• is still important. Previous approaches to determine KS domain specificities have involved mass spectrometry (MS)-based methods [22][23], MS analysis of trypsin-digested proteins [24], and radiochemical assays [25]. Here, we report on a new method using 13C-labelled substrate surrogates in

Production of non-natural 5-methylorsellinate-derived meroterpenoids in Aspergillus oryzae

• Jia Tang,
• Yixiang Zhang and
• Yudai Matsuda

Beilstein J. Org. Chem. 2024, 20, 638–644, doi:10.3762/bjoc.20.56

• four enzymes in the Aspergillus oryzae NSARU1 strain [19]. Consequently, the A. oryzae transformant yielded two metabolites 1 and 2, which were absent in the host strain (Figure 2B, traces i and ii). Although we were unable to isolate compounds 1 and 2 because of their instability, high-resolution mass

• spectrometry (HRMS) analysis revealed the molecular formula of 1 to be C25H36O5, corresponding to the 4-desmethyl form of (6R,10′R)-epoxyfarnesyl-DMOA methyl ester (Figure 2C). Furthermore, the molecular formula of 2 was determined to be C25H38O6, indicating that 2 is formed by the hydrolysis of the epoxide