Ligand effects, solvent cooperation, and large kinetic solvent deuterium isotope effects in gold(I)-catalyzed intramolecular alkene hydroamination

• Ruichen Lan,
• Brock Yager,
• Yoonsun Jee,
• Cynthia S. Day and
• Amanda C. Jones

Beilstein J. Org. Chem. 2024, 20, 479–496, doi:10.3762/bjoc.20.43

Discovery of unguisin J, a new cyclic peptide from Aspergillus heteromorphus CBS 117.55, and phylogeny-based bioinformatic analysis of UngA NRPS domains

• Sharmila Neupane,
• Marcelo Rodrigues de Amorim and
• Elizabeth Skellam

Beilstein J. Org. Chem. 2024, 20, 321–330, doi:10.3762/bjoc.20.32

• ]+ at m/z 773.4338, calculated for C41H57N8O7+, m/z 773.4345, Δ 0.9 ppm; [M + Na]+ at m/z 795.4162, calculated for C41H56N8O7Na+, m/z 795.4164, Δ 0.3 ppm) and NMR data analysis, corresponding to eighteen indices of hydrogen deficiency. Its UV spectrum exhibited absorption maxima at λmax 219 and 279 nm

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• would be significantly smaller. Data analysis and its graphical representation were done with the R-package [49] and VMD [50]. Results In total, 14 US simulations were performed to investigate the specificity of GAG–protein interactions, capabilities of US simulations to dissociate and reassociate

GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data

• Thomas Barillot,
• Baptiste Schindler,
• Baptiste Moge,
• Elisa Fadda,
• Franck Lépine and
• Isabelle Compagnon

Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134

• appealing candidates to address this challenge. They have been used for mass spectrometry data analysis since the 2000’s [6] and the idea of using them on vibrational spectra goes back to the early 90’s [7]. Support vector machines (SVM) and decision tree ensemble methods were benchmarked on infrared

• single spectrum is arbitrarily chosen by the operator and serves as reference for all future analyses. The latest MS–IR developments brought the data collection down to few seconds [5]. This is a considerable step towards high throughput carbohydrate analysis, which must be accompanied by fast data

• analysis, thus excluding manual interpretation. Besides, in the prospective of deploying the technology beyond the molecular spectroscopy community, it is essential to develop an automated, reliable, and robust strategy for the analysis of the spectroscopic data. Machine learning methods appear to be

Benzoimidazolium-derived dimeric and hydride n-dopants for organic electron-transport materials: impact of substitution on structures, electrochemistry, and reactivity

• Swagat K. Mohapatra,
• Khaled Al Kurdi,
• Samik Jhulki,
• Georgii Bogdanov,
• John Bacsa,
• Maxwell Conte,
• Tatiana V. Timofeeva,
• Seth R. Marder and
• Stephen Barlow

Beilstein J. Org. Chem. 2023, 19, 1651–1663, doi:10.3762/bjoc.19.121

• (DOE) under Contract No. DE-AC36-08GO28308; specifically, some of the data analysis was carried out as part of a Laboratory Directed Research and Development (LDRD) Program at NREL. The views expressed in the article do not necessarily represent the views of the DOE or the U.S. Government. The U.S

Unravelling a trichloroacetic acid-catalyzed cascade access to benzo[f]chromeno[2,3-h]quinoxalinoporphyrins

• Chandra Sekhar Tekuri,
• Pargat Singh and
• Mahendra Nath

Beilstein J. Org. Chem. 2023, 19, 1216–1224, doi:10.3762/bjoc.19.89

• . After workup and chromatographic purification, the isolated product was characterized based on spectral data analysis as copper(II) benzo[f]quinoxalinoporphyrin intermediate 17. Further, porphyrin 17 reacted with benzaldehyde and dimedone in chloroform containing 20 mol% trichloroacetic acid at 65 °C to

• copper(II) porphyrins 3–8. Finally, the structures of all newly synthesized benzo[f]chromeno[2,3-h]quinoxalinoporphyrins 3–16 and benzo[f]quinoxalinoporphyrin 17 were assigned on the basis of IR, 1H and 13C NMR, and HRMS data analysis. Photophysical characteristics The UV–vis spectra of the newly

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• calorimetry (ITC) titrations were performed on a Malvern PEAQ-ITC microcalorimeter (MicroCal, Inc.,Northampton, MA, USA). MicroCal PEAQ-ITC analysis software, supplied by the manufacturer, was used for data analysis. Polynucleotides were purchased as noted: calf thymus (ct)-DNA, poly dAdT–poly dAdT, poly dGdC

Synthesis and characterisation of new antimalarial fluorinated triazolopyrazine compounds

• Kah Yean Lum,
• Jonathan M. White,
• Daniel J. G. Johnson,
• Vicky M. Avery and
• Rohan A. Davis

Beilstein J. Org. Chem. 2023, 19, 107–114, doi:10.3762/bjoc.19.11

• ) triazolopyrazine scaffold (Series 4). The structures of all analogues were fully characterised by NMR, UV and MS data analysis; three triazolopyrazines were confirmed by X-ray crystal structure analysis. The inhibitory activity of all compounds against the growth of the malaria parasite Plasmodium falciparum (3D7

Using UHPLC–MS profiling for the discovery of new sponge-derived metabolites and anthelmintic screening of the NatureBank bromotyrosine library

• Sasha Hayes,
• Aya C. Taki,
• Kah Yean Lum,
• Joseph J. Byrne,
• Merrick G. Ekins,
• Robin B. Gasser and
• Rohan A. Davis

Beilstein J. Org. Chem. 2022, 18, 1544–1552, doi:10.3762/bjoc.18.164

• marine natural product, ianthesine E (2). The chemical structure of the new compound was determined following detailed spectroscopic and spectrometric data analysis. These two compounds (1 and 2) along with seven previously reported marine bromotyrosine alkaloids from the NatureBank open access library

• -scale extraction and isolation work. Small-scale (300 mg) extraction of the abundant 39 sponge samples followed by UHPLC–MS and data analysis led to the prioritisation of several extracts for follow-up large-scale chemical investigations (see Figure S1 in Supporting Information File 1 for all UHPLC–MS

Enantioselective total synthesis of putative dihydrorosefuran, a monoterpene with an unique 2,5-dihydrofuran structure

• Irene Torres-García,
• Josefa L. López-Martínez,
• Rocío López-Domene,
• Manuel Muñoz-Dorado,
• Ignacio Rodríguez-García and
• Miriam Álvarez-Corral

Beilstein J. Org. Chem. 2022, 18, 1264–1269, doi:10.3762/bjoc.18.132

• cyclization is a simple and efficient strategy for the preparation of the 2,5-dihydrofuran moiety present in many natural products. In fact, we have achieved the total synthesis of the 2,5-dihydrofuran structure 1. After systematic data analysis of our prepared compound and those in the literature, it can be

Terpenoids from Glechoma hederacea var. longituba and their biological activities

• Dong Hyun Kim,
• Song Lim Ham,
• Zahra Khan,
• Sun Yeou Kim,
• Sang Un Choi,
• Chung Sub Kim and
• Kang Ro Lee

Beilstein J. Org. Chem. 2022, 18, 555–566, doi:10.3762/bjoc.18.58

• reported literature and NOESY data analysis. Comparison with 1H NMR of 1β,10α;4α,5β-diepoxy-8α-isobutoxy-glechomanolide (8α-DIG) and 1β,10α;4α,5β-diepoxy-8β-isobutoxy-glechomanolide (8β-DIG) of reference [8], the two epimers similar to 1 showed a significant difference in the chemical shift of H-5 (8α, δH

Regioselective synthesis of methyl 5-(N-Boc-cycloaminyl)-1,2-oxazole-4-carboxylates as new amino acid-like building blocks

• Jolita Bruzgulienė,
• Greta Račkauskienė,
• Aurimas Bieliauskas,
• Vaida Milišiūnaitė,
• Miglė Dagilienė,
• Gita Matulevičiūtė,
• Vytas Martynaitis,
• Sonata Krikštolaitytė,
• Frank A. Sløk and
• Algirdas Šačkus

Beilstein J. Org. Chem. 2022, 18, 102–109, doi:10.3762/bjoc.18.11

• structural assignment of regiospecific compound 4a was readily deduced via detailed spectral data analysis. The IR spectrum of 4a contained characteristic absorption bands such as 1723 (C=O, ester), and 1687 (C=O, Boc) cm−1. The 1H NMR spectrum of compound 4a revealed a characteristic resonance for the Boc

Chemical and chemoenzymatic routes to bridged homoarabinofuranosylpyrimidines: Bicyclic AZT analogues

• Sandeep Kumar,
• Jyotirmoy Maity,
• Banty Kumar,
• Sumit Kumar and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2022, 18, 95–101, doi:10.3762/bjoc.18.10

• established on the basis of 1H,1H-COSY and NOESY NMR spectral data analysis of nucleoside 9a (Figure 2). Herein, cross peaks were observed in the NOESY spectrum of compound 9a due to the spatial interaction of the C6′ methylene protons resonating at δ 3.41 with the C3′ proton resonating at δ 4.73 and the C5

• , 13C NMR, 1H,1H-COSY NMR, 1H,13C-HETCOR NMR, NOESY NMR and HRMS) data analysis. The structures of known compounds 11 and 17 were further confirmed by comparison of their physical and spectral data with those reported in literature [28]. Conclusion The efficiency of Lipozyme® TL IM was discovered for

GlycoBioinformatics

• Kiyoko F. Aoki-Kinoshita,
• Frédérique Lisacek,
• Niclas Karlsson,
• Daniel Kolarich and
• Nicolle H. Packer

Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184

• MS data analysis tools for glycoproteomic characterization and quantification. The article by Walsh et al. [11], on the other hand, addresses the problems of an irreproducible retention time and peak integration in antibody glycomic analysis using CE, thus allowing small quantitative differences to

In-depth characterization of self-healing polymers based on π–π interactions

• Josefine Meurer,
• Julian Hniopek,
• Johannes Ahner,
• Michael Schmitt,
• Jürgen Popp,
• Stefan Zechel,
• Kalina Peneva and
• Martin D. Hager

Beilstein J. Org. Chem. 2021, 17, 2496–2504, doi:10.3762/bjoc.17.166

• controlled program was developed, which mainly uses the well-established data analysis library pandas as well as the SciPy and NumPy libraries for linear algebra, integration and interpolation. Polymer synthesis The polymer synthesis was adapted from literature [23] and is reported briefly in the following

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

• (100% water, 0.1% FA) and B (100% acetonitrile, 0.1% FA), with a linear gradient elution mode 10 to 65% CH3CN for 50 min and 65–100% CH3CN over 20 min at a flow rate of 1.0 mL/min and monitored by a diode array HPLC detector at 340 nm. The HPLC traces were aligned and visualized using data analysis as

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

Analogs of the carotane antibiotic fulvoferruginin from submerged cultures of a Thai Marasmius sp.

• Birthe Sandargo,
• Leon Kaysan,
• Rémy B. Teponno,
• Christian Richter,
• Benjarong Thongbai,
• Frank Surup and
• Marc Stadler

Beilstein J. Org. Chem. 2021, 17, 1385–1391, doi:10.3762/bjoc.17.97

• like hercynolactone. However, NMR data analysis disclosed that the position C-9 (δC 70.8) is hydroxylated. The ROESY spectrum indicates H-9 (δH 4.88) to be cofacial with H-5 and H-13. Thus, fulvoferruginin F could also be named 9-hydroxyhercynolactone [9]. Assessing the bioactivity of the

Antiviral therapy in shrimp through plant virus VLP containing VP28 dsRNA against WSSV

• Santiago Ramos-Carreño,
• Ivone Giffard-Mena,
• Jose N. Zamudio-Ocadiz,
• Alfredo Nuñez-Rivera,
• Ricardo Valencia-Yañez,
• Jaime Ruiz-Garcia,
• Maria Teresa Viana and
• Ruben D. Cadena-Nava

Beilstein J. Org. Chem. 2021, 17, 1360–1373, doi:10.3762/bjoc.17.95

• data analysis indicates that VLP-dsRNAvp28 by oral therapy reduces the mortality rate by reducing the WSSV infection. Mejía-Ruiz et al. [28] reported that antiviral protection provided by a single IM administration of dsRNAvp28 is short-lived, 10 to 20 days post-treatment (dpt), with 63% and 87

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

• statistical analysis were uploaded and are freely accessible in the Max Planck repository Edmond (https://dx.doi.org/10.17617/3.4v). Significant features analysis and metabolite identification Data analysis was conducted in MetaboAnalyst 4.0 [48] to perform univariate and multivariate statistical tests and

Multiswitchable photoacid–hydroxyflavylium–polyelectrolyte nano-assemblies

• Alexander Zika and
• Franziska Gröhn

Beilstein J. Org. Chem. 2021, 17, 166–185, doi:10.3762/bjoc.17.17

• experiment, one initial injection of 15 μL to saturate the titration cell wall was followed by 35 injections of 7.5 μL each. The time span between subsequent injections was 100 s. All experiments were conducted at 25 °C. Data analysis was performed with the modified model described and implemented in the

• MicroCal ITC data analysis software for Origin 7.0. Top: pelargonidin cation (Flavy) and network of chemical reactions; bottom: corresponding UV–vis spectra of the different states of Flavy. Characterization of Flavy: a) 1H NMR spectrum at pH 7.0 (form A) before and after irradiation; b) 13C NMR spectrum

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

• painting. However, even though HDXMS is a very reproducible and straightforward method (albeit the experiment has to be carefully and properly performed), data analysis, even with recent software automation, is the major limitation as the interpretation requires a certain level of expertise. Biophysical

• ., the protein–protein interface. Limitations of this approach include the possibility of having no protease cleavage regions in the interface region and the size of the probes used [22]. These limitations can be overcome by using HDXMS. Even though HDX dates back to the 1950s [26], advances in data

• analysis software and automation in liquid chromatography–mass spectrometry over the past decade made HDXMS an increasingly attractive tool for biochemists. In HDXMS, changes in the mass associated with the isotopic exchange between amide hydrogen atoms and surrounding deuterated solvent are measured. The

Chemical constituents of Chaenomeles sinensis twigs and their biological activity

• Joon Min Cha,
• Dong Hyun Kim,
• Lalita Subedi,
• Zahra Khan,
• Sang Un Choi,
• Sun Yeou Kim and
• Chung Sub Kim

Beilstein J. Org. Chem. 2020, 16, 3078–3085, doi:10.3762/bjoc.16.257

• together with 11 known phytochemicals through chromatographic methods. The chemical structure of the new isolate 1 was determined by conventional 1D and 2D NMR data analysis, ECD experiment, hydrolysis followed by a modified Mosher’s method, and LC–MS analysis. The characterized compounds’ biological

• a new megastigmane-type norsesquiterpenoid glycoside 1 along with 11 known compounds (2–12, Figure 1). The structure of the new compound 1 was established on the basis of spectroscopic and spectrometric data analysis, and chiral derivatization coupled with NMR or LC–MS experiments. All isolated

• . sinensis twigs and their structures were characterized by intensive 1D and 2D NMR data analysis, ECD experiment, modified Mosher’s method, and LC–MS analysis. The 12 phytochemicals were evaluated for their anticancer, antineuroinflammatory, and neurotrophic effects and the active compounds 8–11 could be

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

• complex, reflecting the high structural diversity of peptide and glycan portions. The use of glycopeptide-centered glycoproteomics by mass spectrometry is rapidly evolving in many research areas, leading to a demand in reliable data analysis tools. In recent years, several bioinformatic tools were

• automated processing of several IgA glycopeptides. Finally, this study presents a semiautomated workflow for reliable glycoproteomic data analysis by the combination of software packages for MS/MS- and MS1-based glycopeptide identification as well as the integration of analyte quality control and

• high complexity of glycosylation itself, data analysis is further complicated by interfering background signals from biological matrices and isomeric and near-isobaric ambiguities resulting from combinations of monosaccharides, adducts, amino acids, and amino acid modifications [10][11]. Efforts have

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

• approach by investigating the in-silico binding of a peptide and glycopeptide epitope of the glycoprotein Mucin 1 (MUC1) binding with the antibody AR20.5. To study the binding, we performed molecular dynamics simulations using OpenMM and then used the Galaxy platform for data analysis. The same analysis

• of the analyses was carried out using Galaxy, the popular open web-based platform for bioinformatics and computational data analysis, which enables the creation of repeatable analysis pipelines (workflows). There are several well-known molecular dynamics analysis packages (MDAnalysis [37], Bio3D [38