Identification and removal of a cryptic impurity in pomalidomide-PEG based PROTAC

• Bingnan Wang,
• Yong Lu and
• Chuo Chen

Beilstein J. Org. Chem. 2025, 21, 407–411, doi:10.3762/bjoc.21.28

• product on HPLC even for the reaction of diethylene glycolamine and 1. Capping the free hydroxy group with a methyl group improved the separation on HPLC marginally. However, incorporating a clickable propargyl group greatly benefited separation. Similar to the alcohol, amino-PEG5-acid also reacted with 1

Cyclodextrin-based rotaxanes for polymer materials: challenge on simultaneous realization of inexpensive production and defined structures

• Yosuke Akae

Beilstein J. Org. Chem. 2024, 20, 3026–3049, doi:10.3762/bjoc.20.252

• from the chiral nature of the CD molecule, and its behavior fits well with the theoretical consideration. As comprehensively described [32], CD-based rotaxanes are typically synthesized by two methods: (1) the end-capping method (route a1, a2) in which the formation of a pseudorotaxane structure first

• proceeds through the formation of CD and an axle molecule, followed by the end-capping of the axle end; (2) the slipping method (route b) involving threading a dumbbell molecule comprising bulky axle-end groups through CD. As the latter is likely to produce a pseudorotaxane framework, the end-capping

• methods are more popular than the slipping method. However, this end-capping method must fulfill the following seven points to appropriately realize a rotaxane framework, and this causes several complexities (Figure 3): (1) The axle molecule must form a stable inclusion complex with CD, (2) the axle

Applications of microscopy and small angle scattering techniques for the characterisation of supramolecular gels

• Connor R. M. MacDonald and
• Emily R. Draper

Beilstein J. Org. Chem. 2024, 20, 2608–2634, doi:10.3762/bjoc.20.220

• -assembly across length scales using a combination of SANS and cryo-TEM, as well as other characterisation techniques. To investigate how the change in capping group changed the self-assembly of diphenylalanine, indole-FF, and carbazole-FF (F = phenylalanine) were characterised by SAXS. While both indole-FF

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• and precise results from MD simulation. It is also worth to note that, to generate the input files for MD, some modifications on the .pdb file of the protein are required. For instance, capping the protein termini with non-charged groups and replacing original hydrogens to guarantee compatibility with

Synthesis and characterization of water-soluble C₆₀–peptide conjugates

• Yue Ma,
• Lorenzo Persi and
• Yoko Yamakoshi

Beilstein J. Org. Chem. 2024, 20, 777–786, doi:10.3762/bjoc.20.71

• Synthesis of oligopeptides on resin 1a–c The oligopeptides on resin 1a–c were synthesized via a general SPPS protocol. The first addition of Fmoc-AA(PG)-OH to the 2-chlorotrityl resin was performed in the presence of DIPEA (2 equiv) in CH2Cl2, followed by capping with a CH2Cl2/MeOH/DIPEA (18:2:1, v/v

Green and sustainable approaches for the Friedel–Crafts reaction between aldehydes and indoles

• Periklis X. Kolagkis,
• Eirini M. Galathri and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2024, 20, 379–426, doi:10.3762/bjoc.20.36

• requires large amounts of capping agents to combat, Pratihar and his research group offered the alternative of iron oxalates for the nanocatalysis of BIMs, which, after thermal decomposition form Fe(ox)-Fe3O4 oxides [108]. Metal oxalates in general are more stable nanoparticles than their oxide

Long oligodeoxynucleotides: chemical synthesis, isolation via catching-by-polymerization, verification via sequencing, and gene expression demonstration

• Yipeng Yin,
• Reed Arneson,
• Alexander Apostle,
• Adikari M. D. N. Eriyagama,
• Komal Chillar,
• Emma Burke,
• Martina Jahfetson,
• Yinan Yuan and
• Shiyue Fang

Beilstein J. Org. Chem. 2023, 19, 1957–1965, doi:10.3762/bjoc.19.146

• File 1 for details). To block any hydroxy groups on the surface of CPG that were not capped, including those resulted from mechanical breakage of CPG, before commencing a synthesis, the CPG was subjected to typical capping conditions for 20 minutes. To reduce steric hindrance within the pores of CPG

• the formation of 2,6-diaminopurine from a capping-modified guanine base during ammonium hydroxide ODN deprotection and subsequent reading as dA during PCR [26][27][28]. The dT-to-dC substitution could have been resulted from amination of dT to give 5-methyl-dC, which is recognized as dC in PCR as well

• as sequencing [26]. Single-nucleotide deletion could be a result of failure sequences that were not capped in the capping step or incomplete detritylation. Plasmids of two colonies containing the GFP gene assembled from the 399 and 401 bp fragments were also submitted for Sanger sequencing. No error

Active-metal template clipping synthesis of novel [2]rotaxanes

• Cătălin C. Anghel,
• Teodor A. Cucuiet,
• Niculina D. Hădade and
• Ion Grosu

Beilstein J. Org. Chem. 2023, 19, 1776–1784, doi:10.3762/bjoc.19.130

• , reported by Sauvage in 1983 [14], the synthetic strategies employed to access MIMs, including catenanes, rotaxanes and molecular knots, have grown in number and complexity of the obtained structures [15]. Thus, currently, synthesis of rotaxanes is usually performed through clipping, capping, snaping or

Quinoxaline derivatives as attractive electron-transporting materials

• Zeeshan Abid,
• Liaqat Ali,
• Sughra Gulzar,
• Faiza Wahad,
• Raja Shahid Ashraf and
• Christian B. Nielsen

Beilstein J. Org. Chem. 2023, 19, 1694–1712, doi:10.3762/bjoc.19.124

• enhanced electron hopping and reduced geminate recombination. Qx12 and Qx13 achieved remarkable PCEs of 13.31% and 16.64%, respectively, with PBDB-TF donor in OSC devices [28]. Zhu et al. reported a modification in Qx13 by incorporating an imide-functionalized Qx moiety in its core and end-capping groups

Linker, loading, and reaction scale influence automated glycan assembly

• Marlene C. S. Dal Colle,
• Manuel G. Ricardo,
• Nives Hribernik,
• José Danglad-Flores,
• Peter H. Seeberger and
• Martina Delbianco

Beilstein J. Org. Chem. 2023, 19, 1015–1020, doi:10.3762/bjoc.19.77

• (BBs) [1][2]. Iterative cycles of glycosylation, capping, and selective deprotection afford the support-bound glycan with a programmable sequence (Figure 1A). The protected glycan is then cleaved from the solid support and subjected to post-AGA deprotection steps to reveal the target glycan. AGA is

CuAAC-inspired synthesis of 1,2,3-triazole-bridged porphyrin conjugates: an overview

• Dileep Kumar Singh

Beilstein J. Org. Chem. 2023, 19, 349–379, doi:10.3762/bjoc.19.29

• rigid 1,2,3-triazole linker between the porphyrin and the capping group using the CuAAC click reaction (Scheme 29). Capped porphyrin 142 was synthesized in similar yields under both aqueous (method A) and anhydrous (method B) conditions. Method A produced capped porphyrin 142 in 19% yield by clicking

• % yield using Cu(MeCN)4PF6 and triethylamine in anhydrous DMF. This ‘capped’ porphyrin was designed so that the rigid triazole linkers prevent the capping group from collapsing onto the porphyrin. Gilday et al. [60] also synthesized porphyrin 142 and studied its anion-binding properties and found that it

BINOL as a chiral element in mechanically interlocked molecules

• Matthias Krajnc and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2022, 18, 508–523, doi:10.3762/bjoc.18.53

• containing electron-rich hydroquinone or 1,5-dioxynaphthalene units (macrocycles 15/21/23), together with suitable dicationic bis-bipyridinium precursors (16/19). Self-assembly of the corresponding pseudorotaxanes by π–π stacking, following by capping with dibromo-p-xylene 17 gave rise to a series of chiral

• -capping. The resulting compounds were treated with chloroacetic anhydride and then with thiazole. After anion exchange the chiral thiazolium salts (R)-35a/b, which differ in the chain length of the axle, were obtained in 9%/42% overall yield (see Figure 8a). For comparison, a rotaxane containing a BINOL

• -based axle and an achiral macrocycle was also synthesized. This design was chosen to investigate the difference between a covalently and a mechanically linked chiral unit with regard to the chiral induction in asymmetric catalysis. By acylative end-capping, followed by introduction of the thiazole unit

Synthesis and bioactivity of pyrrole-conjugated phosphopeptides

• Qiuxin Zhang,
• Weiyi Tan and
• Bing Xu

Beilstein J. Org. Chem. 2022, 18, 159–166, doi:10.3762/bjoc.18.17

• ., Nap-ffpy (1)) [36][61][62][63][64][65][66]. Considering naphthyl is an aromatic group, we decided to explore other aromatic N-terminal capping groups, such as heteroaromatic, N-terminal capping groups of phosphopeptides for EISA because they receive little exploration [67]. Our previous studies have

• shown nucleobases, as the heteroaromatic groups, are able to act as the N-capping group for EISA of phosphopeptides [67]. In this study, we chose to examine a different type of heteroaromatic group, pyrroles, because pyrrole is adaptable for solid-phase synthesis [68] so that it is feasible to conjugate

• . According to this rationale, replacing the Nap capping group in 1 with a dipyrrole or a tripyrrole segment at the N-terminal generates 2a and 2b. Introducing two or three glycine residues between the pyrrole segment and the self-assembling segment produces 2c–h, which would help to understand the role of a

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

• capping step [279] permitted to drastically improve overall yields and to simplify the purification (Figure 6). The 100mer 93 was obtained with a calculated average stepwise yield of 98.75% (Scheme 14). Long α-mannosides have the advantageous feature of being highly soluble due to the high flexibility of

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

Simulating the enzymes of ganglioside biosynthesis with Glycologue

• Andrew G. McDonald and
• Gavin P. Davey

Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64

• acting as a wildcard character. Double branches are used to form symmetric core structures, such as the trimannosyl core of N-glycans, or O-linked glycan cores based on GalNAc (Equation 3): Capping of branches and linearly extended chains is achieved through termination, of which sialylation is a typical

Synthesis and physicochemical evaluation of fluorinated lipopeptide precursors of ligands for microbubble targeting

• Masayori Hagimori,
• Estefanía E. Mendoza-Ortega and
• Marie Pierre Krafft

Beilstein J. Org. Chem. 2021, 17, 511–518, doi:10.3762/bjoc.17.45

• for capping the unreacted amino acids and the mixture was shaken for 5 min. In a similar manner, each of the peptide chains was elongated by coupling Fmoc-Ser(t-Bu)-OH (3 equiv), Fmoc-Gly-OH (3 equiv) and Fmoc-Lys(Boc)-OH (3 equiv) to the Rink Amide AM resin. After introducing Fmoc-Lys(Fmoc)-OH as the

• capping the reaction with 25% of acetic anhydride in DCM (2 mL), the column was washed with DCM (3 × 2 mL), DMF (3 × 2 mL), and methanol (3 × 2 mL), and dried overnight. A solution of 2.5 mL of TFA/TIS/H2O 94:2.5:2.5 (v/v/v) was added to the column for cleaving the compound from the resin, and the

Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders

• David Straßburger,
• Svenja Herziger,
• Katharina Huth,
• Moritz Urschbach,
• Rainer Haag and
• Pol Besenius

Beilstein J. Org. Chem. 2021, 17, 97–104, doi:10.3762/bjoc.17.10

• acid as capping reagent for the synthesized oligopeptide on the resin. To maintain orthogonal functionalities a resin-bound diamine was deployed as starting point to start off the oligopeptide synthesis. A low loading of the resin (0.16 mmol/g) was important to prevent crosslinking during the reaction

• with trimesic acid. The coupling steps were performed using HBTU, HOBt, DIPEA in DMF with Fmoc derivatives of ʟ-phenylalanine and ε-aminohexanoic acid while the final capping was achieved using HATU, HOAt, DIPEA in NMP (Scheme 1). After cleavage from the resin the hetero-trifunctional peptide was

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

• the further capping of the pseudorotaxanes to construct rotaxanes. Keywords: host–guest chemistry; pillar[4]arene[1]quinones; pillararenes; pseudorotaxanes; supramolecular chemistry; Introduction Relying on the research of basic science, supramolecular chemistry has become an important mean for

• between H and G were weak and that there was a complexation competition with solvent molecules. Furthermore, the addition of G did not change the maximum UV–vis absorption wavelength of H. The bromine atoms at the periphery of the guest molecule provide convenience for the further capping of the

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

• (“ & ”, “ ~ ”, “or”) and structural ambiguity (“ ... ”, “ _ ”, “ | ”, “ * ”), all of which were used to specify constraints. For example, a constraint “Ma6 & Ma3” means the reaction will happen only if both Ma6 and Ma3 appear in the glycan; as an N-glycan, these are the terminal mannoses capping the chitobiose core

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

• containing glycans that were previously unreported and inconsistent with glycan biosynthetic pathways. In particular, the model contained oligosaccharide chains with Man-(1→3)-GlcNAc and GlcNAc-(1→3)-GlcNAc linkages, β-galactosyl motifs capping oligomannose-type glycans and hybrid-type glycans containing

• terminal Man-(1→3)-GlcNAc [14]. Moreover, the proposed model contained systematic errors in the anomer annotations and carbohydrate stereochemistry. To this day, there is still no experimental evidence reported for these types of linkages and capping in an identical context. The new version of Privateer

Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition

• Sivaraman Balasubramaniam,
• Sajith Vijayan,
• Liam V. Goldman,
• Xavier A. May,
• Kyra Dodson,
• Sweta Adhikari,
• Fatima Rivas,
• Davita L. Watkins and
• Shana V. Stoddard

Beilstein J. Org. Chem. 2020, 16, 628–637, doi:10.3762/bjoc.16.59

• that of panobinostat [12]. In developing such analogues, the hydroxamate tails and indole capping moiety were maintained as both are essential to binding at the active site of HDAC2 and HDAC8. Results suggested that TOI1, TOI2, and TOI4 [12] would be inhibitors exhibiting similar potency as that of

Automated glycan assembly of arabinomannan oligosaccharides from Mycobacterium tuberculosis

• Alonso Pardo-Vargas,
• Priya Bharate,
• Martina Delbianco and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2019, 15, 2936–2940, doi:10.3762/bjoc.15.288

• the understanding of these polysaccharides and the development of novel therapeutical and diagnostic agents. Automated glycan assembly (AGA) was employed to prepare the core structure of AM from MTB, containing α-(1,6)-Man, α-(1,5)-Ara, and α-(1,2)-Man linkages. The introduction of a capping step

• after each glycosylation and further optimized reaction conditions allowed for the synthesis of a series of oligosaccharides, ranging from hexa- to branched dodecasaccharides. Keywords: arabinomannan; automated glycan assembly; capping; Introduction Bacterial infections caused by MTB killed 1.7

• incubation and reaction temperatures (from −20 °C to 0 °C) was introduced (procedure B). Capping after each glycosylation prevented the formation of undesired side products [26] and improved the isolated yield of 5 to 53%, with no detectable deletion sequences (Table 1). The inclusion of a capping step in

An improved, scalable synthesis of Notum inhibitor LP-922056 using 1-chloro-1,2-benziodoxol-3-one as a superior electrophilic chlorinating agent

• Nicky J. Willis,
• Elliott D. Bayle,
• George Papageorgiou,
• David Steadman,
• Benjamin N. Atkinson,
• William Mahy and
• Paul V. Fish

Beilstein J. Org. Chem. 2019, 15, 2790–2797, doi:10.3762/bjoc.15.271

• . Pharmacokinetic studies in mouse showed CNS penetration of 1 is very low with a brain/plasma concentration ratio of just 0.01. A small library of amides 17 were prepared from acid 1 to explore if 1 could be modified to deliver a CNS penetrant tool by capping off the acid as an amide. Although significant Notum

• brain tissue. Amide analogues of 1 to explore CNS penetration and future opportunities With a peripherally restricted control in hand, we elected to explore if 1 could be modified to deliver a CNS penetrant tool by capping off the acid as an amide. A small library of amides 17 were prepared from acid 1

• tool by capping off the acid as an amide. Although significant Notum inhibition activity could be achieved, none of these amides demonstrated the required combination of metabolic stability along with cell permeability without evidence of P-gp mediated efflux. The identification of a suitable analogue

Reversible end-to-end assembly of selectively functionalized gold nanorods by light-responsive arylazopyrazole–cyclodextrin interaction

• Maximilian Niehues,
• Patricia Tegeder and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2019, 15, 1407–1415, doi:10.3762/bjoc.15.140

• of gold nanorods (AuNR) by thiolated cyclodextrin (CD) host molecules. As a result of the complete removal of the precursor capping agent cetyltrimethylammonium bromide (CTAB) by a tetraethylene glycol derivative, competitive binding to the host cavity was prevented, and reversible, light-responsive

• advantage of the different ligand exchange kinetics of CTAB on the ends and the side of the particles [14][15]. CTAB serves as a capping agent in AuNR synthesis by the seed-mediated growth process and is essential for the anisotropic growth. Due to the different crystallographic environments on the particle

• potential and therefore about the capping agent (Figure 1a). CTAB-functionalized AuNR have a highly positive surface charge (+55 mV) due to the formation of CTAB double layers. The intermediate state [tCD]AuNR shows a decreased surface charge (+42 mV) indicating a reduction of the CTAB surface coverage. It