Control over size, shape, and photonics of self-assembled organic nanocrystals

• Chen Shahar,
• Yaron Tidhar,
• Yunmin Jung,
• Haim Weissman,
• Sidney R. Cohen,
• Ronit Bitton,
• Iddo Pinkas,
• Gilad Haran and
• Boris Rybtchinski

Beilstein J. Org. Chem. 2021, 17, 42–51, doi:10.3762/bjoc.17.5

• applicability of organic nanocrystals. Experimental General information The 1H and 13C NMR spectra were recorded at 20 °C on a 300 MHz NMR spectrometer (Bruker). Electrospray ionization (ESI) mass spectrometry was performed using a Micromass Platform instrument. UV–vis absorption and fluorescence measurements

The fluorescence of a mercury probe based on osthol

• Guangyan Luo,
• Zhishu Zeng,
• Lin Zhang,
• Zhu Tao and
• Qianjun Zhang

Beilstein J. Org. Chem. 2021, 17, 22–27, doi:10.3762/bjoc.17.3

• fluorescence, UV–vis spectrophotometry, mass spectrometry, and 1H NMR spectroscopy, and the recognition mechanism is discussed. The results showed that OST and Hg2+ can form a complex with a stoichiometric ratio of 1:1. The binding constant was 1.552 × 105 L∙mol−1, having a highly efficient and specific

• irreversible nerve damage. Therefore, it is very important to develop a highly sensitive and selective method for mercury detection. At present, the detection of mercury mainly includes atomic absorption and atomic emission spectrometry [4], inductively coupled plasma mass spectrometry [5][6], and capillary

• UV absorption intensity was achieved at n(Hg2+)/n((OST) + (Hg2+)) = 0.5 at 325 nm, indicating that the binding ratio of the OST probe to Hg2+ was 1:1. Combined with mass spectrometry data (Figure 5), the fragment peak of ESIMS at m/z 892.5422 corresponded to [OST2–Hg2]+ (calculated as 892.5429

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

• proteins and other biological molecules, all of which have their own biological role and chemical interactions. Characterisation methods that can be employed to study PPIs can be divided into four categories: atomic resolution methods, mass spectrometry methods, biophysical methods, and computational

• (or any other organic molecule [19]) structure. A resolution of up to 0.6 Å (RNA-binding protein FUS, residues 37–42, EMD-0699, PDB: 6KJ4 [20]) were obtained when using this method. Nannenga and Gonen gave a detailed account on MicroED [21]. As another category, mass spectrometry methods are used to

• determine the amino acid sequences at the PPIs site. Examples include protein painting [22] and chemical cross-linking [23], hydrogen–deuterium exchange mass spectrometry (HDXMS) [24], and fast photochemical oxidation of proteins [25]. In protein painting, small-molecular dyes are introduced to protein

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

• 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

• quantification. Keywords: bioinformatics; cysteine oxidation; glycoproteomics; immunoglobulins; mass spectrometry; Introduction Protein glycosylation mainly occurs in the form of N- and O-glycosylation. N-Glycans are attached to Asn within an amino acid consensus sequence (Asn-Xxx-Ser/Thr, Xxx ≠ Pro) and O

Naphthalonitriles featuring efficient emission in solution and in the solid state

• Sidharth Thulaseedharan Nair Sailaja,
• Iván Maisuls,
• Jutta Kösters,
• Alexander Hepp,
• Andreas Faust,
• Jens Voskuhl and
• Cristian A. Strassert

Beilstein J. Org. Chem. 2020, 16, 2960–2970, doi:10.3762/bjoc.16.246

• characterized by nuclear magnetic resonance spectroscopy (NMR, Supporting Information File 1, Figures S1–S24) as well as exact electrospray mass spectrometry (EM–ESIMS, Supporting Information File 1, Figures S25–S30) and appear as white to faint yellow solids. Only the dimethylamino-substituted product shows a

Construction of pillar[4]arene[1]quinone–1,10-dibromodecane pseudorotaxanes in solution and in the solid state

• Xinru Sheng,
• Errui Li and
• Feihe Huang

Beilstein J. Org. Chem. 2020, 16, 2954–2959, doi:10.3762/bjoc.16.245

• . Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) was conducted to investigate the complexation properties. However, no signal related to the complex but only peaks of H were found, implying weak host–guest interactions between H and G (Figures S3 and S4

• , Supporting Information File 1). A Job plot based on the proton NMR data was made to determine the complexation stoichiometry between H and G. The formation signified a 1:1 binding stoichiometry in chloroform-d at room temperature (Figures S5 and S6, Supporting Information File 1). Combined with the mass

• spectrometry results, we believed that the differences between the stoichiometric ratio of the complexation in the solid state and in solution could be owing to the competitive role of solvent molecules in the combination of H and G. The association constant (Ka) calculated by the nonlinear curve fitting

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

• enzymatic conversion of the correspondingly 13C-labelled isoprenyl diphosphate precursors with the sestermobaraene synthase from Streptomyces mobaraensis. The main compounds sestermobaraenes A, B, and C were analysed by gas chromatography–mass spectrometry (GC–MS), allowing for a deep mechanistic

• 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

• water, simple alcohols. These volatile compounds can efficiently be trapped by specialised methods including the closed-loop stripping apparatus (CLSA) [4] technique or solid-phase microextraction (SPME) [5][6], and then analysed by gas chromatography–mass spectrometry (GC–MS) [7]. Through these and

Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• moderate yields (16–38%), mainly because of severe difficulties to completely remove the copper ions that apparently bind tightly to the compounds. The new compounds 4a–e were identified and fully characterized with NMR spectroscopy (1H, 13C, COSY, HSQC, HMBC), mass spectrometry, and elemental analysis

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

• species in regions where they co-occur. Furthermore, the occurrence of positional isomers of unsaturated fatty acid derivatives indicates activity of two different desaturases within these butterflies, Δ9 and Δ11, which has not been reported before in male Lepidoptera. Keywords: fatty acid esters; mass

• spectrometry; mimicry; pheromones; pyrrolizidine alkaloids; Introduction The Neotropical butterfly tribe Ithomiini (Nymphalidae: Danainae) is very diverse and species-rich, with over 390 species and 50 genera [1][2] and extensively involved in Müllerian mimetic interactions [3]. Ithomiines are well suited for

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

• mixture of 2a,b was washed with cold hexane on a ceramic filter to give a material with a 2a,b ratio of 95:5. Recrystallization of this sample from hexane gave the isomer 2b (purity 99%, by NMR), and this sample was used for an X-ray diffraction experiment. The reaction conditions, mass spectrometry, and

• reaction conditions, mass spectrometry, and NMR data are given in Table 1 and Table 3. Reaction of 5-azabenzimidazole (4) and 1 A mixture of 1.2 g (0.01 mol) of 5-azabenzimidazole (4), 2 g (0.06 mol) of 1, and 15 mL of DMSO was agitated at ambient temperature for 24 h. The precipitated sulfur was filtered

• acetate gradient, 100 mL/min, cartridge SNAP 340 g). The structure of each isomer was determined by X-ray diffraction. The reaction conditions, mass spectrometry, and NMR data are given in Table 1 and Table 3. Reaction of adenine (5) and 2-fluoroadenine (6), respectively, and 1 A mixture of 0.01 mol of

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• obtained through nucleophilic substitution reactions between BImNs (N = 4, 10, 12, 14) and 3. All synthesized compounds were characterized by NMR spectroscopy and high-resolution mass spectrometry. Self-assembly properties of PBImNs in aqueous buffer The self-assembly properties of the four PBImN

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

• diastereomers. The new complexes were characterized by NMR and UV–vis spectroscopy and ESI mass spectrometry. Using GFN2-xTB we generated energy-minimized models of the diastereomers of this cage that further corroborated the results from analytical findings. Keywords: cage compounds; heterobimetallic

• , 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

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

• Rules Linear Code was first used to represent reaction rules in 2009. A reaction network, specifying glycans with condensed IUPAC and Linear Code, was trained on mass spectrometry abundance to learn biosynthetic enzyme activities [10]. Their reaction rules table contained four features: enzyme, reactant

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

• -heterotetracenes and -hexacene were clearly identified, fully characterized, and their structures confirmed by 1H and 13C NMR spectroscopy and high-resolution mass spectrometry (HRMS) via matrix-assisted laser desorption/ionization (MALDI) (Supporting Information File 1, Figures S1–S5). In the 1H NMR spectra, the

Particle size effect in the mechanically assisted synthesis of β-cyclodextrin mesitylene sulfonate

• Stéphane Menuel,
• Sébastien Saitzek,
• Eric Monflier and
• Frédéric Hapiot

Beilstein J. Org. Chem. 2020, 16, 2598–2606, doi:10.3762/bjoc.16.211

• preparation of the investigated compound. Acknowledgements We thank N. Kania for BET analysis, J. Ternel for NMR experiments and J. Hachani for MALDI–TOF mass spectrometry. We are grateful to Dr. A. Fadel and Dr. A. Addad for their contribution in setting up the SEM measurements. Funding The SEM facility in

Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

• Henrik Hupatz,
• Marius Gaedke,
• Hendrik V. Schröder,
• Julia Beerhues,
• Arto Valkonen,
• Fabian Klautzsch,
• Sebastian Müller,
• Felix Witte,
• Kari Rissanen,
• Biprajit Sarkar and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2020, 16, 2576–2588, doi:10.3762/bjoc.16.209

• supports the mechanically interlocked structure for NDIRot in analogy to similar structures investigated by tandem mass spectrometry earlier [35][40]. Cyclic voltammograms of NDIRot show two reversible reductions E1/2red1 and E1/2red2 independent of the used solvent (pure DCE or DCE/CH3CN 1:1, Figure S11

Water-soluble host–guest complexes between fullerenes and a sugar-functionalized tribenzotriquinacene assembling to microspheres

• Si-Yuan Liu,
• Xin-Rui Wang,
• Man-Ping Li,
• Wen-Rong Xu and
• Dietmar Kuck

Beilstein J. Org. Chem. 2020, 16, 2551–2561, doi:10.3762/bjoc.16.207

• fully characterized by 1H and 13C NMR spectroscopy and mass spectrometry (see Supporting Information File 1) and the data were found to be consistent with the proposed structures. For the hexakis-propargyl ether TBTQ-(OP)6, the signals at δ = 2.53 ppm in the 1H NMR spectrum and at δ = 78.98 and 76.07

• detail by NMR spectroscopy and mass spectrometry. The host–guest complexation of TBTQ-(OG)6 with C60 and C70 takes place in a 1:1 molar ratio in both cases and with association constants of Ka = (1.50 ± 0.10) × 105 M−1 and Ka = (2.20 ± 0.16) × 105 M−1, respectively. It is suggested that the formation of

• 474: 1H NMR, 13C NMR spectroscopy, and mass spectrometry of all new compounds, and the xyz coordinates (in Å) of the complex of TBTQ-(OG)6 with C60. Acknowledgements We acknowledge Prof. Xiang-Feng Chen for his help in the mass spectrometry testing. Funding The following sources of funding are

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

• complexity of glycans in glycoproteins have been, and currently remain, significant challenges in structural biology. These aspects present unique problems to the two most prolific techniques: X-ray crystallography and cryo-electron microscopy. At the same time, advances in mass spectrometry have made it

• alternative glycan composition exists in the form of, e.g., mass spectrometry data [14]. Harnessing glycomics and glycoproteomics results to inform glycan model building Current methods used to obtain accurate atomistic descriptions of molecules fall short in dealing with the heterogeneity of glycoproteins

• . However, there are other methods that have been proven to successfully tackle the challenges posed by glycan heterogeneity, with mass spectrometry emerging as the one with the most relevance due to the ability to elucidate the complete composition descriptions of individual oligosaccharide chains on

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

• this tool ideal for integrated use with various glycoinformatics software and also for applications in glycoproteomics, glycomics and mass spectrometry (MS). One of the illustrations involves combined use with the gpAnnotate application, dedicated to score and annotate MS/MS glycopeptide spectrums in

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

• ; doublet, d; doublet-doublet, dd; doublet-triplet, dt; triplet, t; multiplet, m. High-resolution mass spectra (HRMS) were recorded at Gazi University Faculty of Pharmacy using electron ionization (EI) mass spectrometry (Waters-LCT-Premier-XE-LTOF (TOF-MS) instruments; in m/z (rel. %). Elemental analysis

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

• . CarbArrayART: Status: Development (available for testing upon request). Description: CarbArrayART is a software in development for the storage, processing and presentation of microarray data [38][39]. It is based on the GRITS Toolbox (classically used for mass spectrometry data) [40]. Features of CarbArrayART

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

• Queensland, St. Lucia, QLD 4072, Australia 10.3762/bjoc.16.180 Abstract Mass spectrometry glycoproteomics is rapidly maturing, allowing unprecedented insights into the diversity and functions of protein glycosylation. However, quantitative glycoproteomics remains challenging. We developed GlypNirO, an

• statistical workflows. We used GlypNirO to analyse a published plasma glycoproteome dataset and identified changes in site-specific N- and O-glycosylation occupancy and structure associated with hepatocellular carcinoma as putative biomarkers of disease. Keywords: glycoproteomics; mass spectrometry; N

• diseased states [8]. The current state-of-the art technology for the characterisation, identification, and quantification of the glycome or glycoproteome is liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) [9]. Popular and powerful glycoproteomic workflows typically involve standard

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

• of m/z 400–2000 was used, with an acquisition speed of 1 Hz, and the mass spectrometry was set at the following conditions: 2.75 kV electrospray ionization capillary voltage, 15 V cone voltage, 120 °C ion source temperature, 300 °C desolvation temperature, 800 L/h desolvation gas flow. A lockspray

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

• Avance 400 spectrometer. The chemical shifts are reported in ppm and refer to the residual proton signal of the solvent as internal standard. Signal multiplicities are denoted as s (singlet), d (doublet), t (triplet), and m (multiplet). High-resolution ESI-TOF mass spectrometry was carried out on a

pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide

• Goutam Ghosh and
• Gustavo Fernández

Beilstein J. Org. Chem. 2020, 16, 2017–2025, doi:10.3762/bjoc.16.168

• of the peptide (Figure S2, Supporting Information File 1). The identity of the peptide was confirmed by MALDI–TOF mass spectrometry (Figure S3, Supporting Information File 1). The yield of the purified PEP-1 was 42%. Self-assembly and secondary-structure formation CD, FTIR spectroscopy, and ThT