Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria

• Kara A. Strickland,
• Brenda Martinez Rodriguez,
• Ashley A. Holland,
• Shelby Wagner,
• Michelle Luna-Alva,
• David E. Graham and
• Jonathan D. Caranto

Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75

• contaminants but are either undissociated higher oligomer states or are oligomers whose formation is induced by SDS treatment, which has been observed for other proteins [29][30]. To characterize these oligomer states of native protein, analytical size exclusion chromatography data were collected (Figure 2B

• ). As previously reported, Vs NnlA exhibited two major peaks, a lower molecular weight peak consistent with a dimer and a second peak consistent with a large oligomer [21]. By contrast, the chromatograms of the purified Ps, Mr, Ms, and Pd NnlA were dominated by a single peak ranging in molecular mass

• from 35.9 to 49.0 kDa, masses consistent with dimers (Table S2 in Supporting Information File 1). The higher oligomer peak was absent in all of these samples. As observed for Vs NnlA, there is no evidence for a significant population of monomer in any of these samples. From these data we conclude that

Biphenylene-containing polycyclic conjugated compounds

• Cagatay Dengiz

Beilstein J. Org. Chem. 2023, 19, 1895–1911, doi:10.3762/bjoc.19.141

• 12 topologies (Figure 2) [26][27][28][29][30]. In [N]phenylene structures, the presence of a formally antiaromatic four-membered ring leads to the localization of π-electrons on the benzene rings [31]. Despite this phenomenon, the oligomer series demonstrates a decreasing band gap, indicating the

First series of N-alkylamino peptoid homooligomers: solution phase synthesis and conformational investigation

• Maxime Pypec,
• Laurent Jouffret,
• Claude Taillefumier and
• Olivier Roy

Beilstein J. Org. Chem. 2022, 18, 845–854, doi:10.3762/bjoc.18.85

• /trans ratio, at least in CDCl3 and CD3OD. This suggests that the same may be true for longer oligomers. As the oligomer elongates, shoulders that may represent different rotamers in small proportions appear in the NMR spectra, but one isomer remains present predominantly. More specifically, in the case

• hydrogen bonds within an assembly, and that this is dependent on the size of the oligomers. Also, the region of the spectra corresponding to the C=O stretching (1800–1600 cm−1) show a band at 1743 cm−1 corresponding to C=O stretching of the ester and a band at 1648 cm−1 which increases with the oligomer

Post-synthesis from Lewis acid–base interaction: an alternative way to generate light and harvest triplet excitons

• Hengjia Liu and
• Guohua Xie

Beilstein J. Org. Chem. 2022, 18, 825–836, doi:10.3762/bjoc.18.83

• with BF3, BBr3, and AlCl3, respectively, mixed in the low bandgap conjugated polymer materials. This is ascribed to the formation of Lewis acid–base adducts [34]. Fluorescent materials as electron donors Hancock et al. compared the PL and EL spectra of the π-conjugated heterocyclic oligomer 6,6’-bis(2

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

• hydrolases is an interesting option to produce long COS from shorter oligomers [241]. After cleaving the glycosidic linkage, the enzyme remains attached to the new reducing end of the oligomer, releasing the cleaved part. Subsequently, the oligomer is transferred to another COS acceptor, forming a new

• , ranging from tri- to hexasaccharide, was obtained via iterative electrochemical assembly [266]. A solid-phase automated approach delivered β(1–6)-glucosamine hexasaccharide 87a and dodecasaccharide 87b (Scheme 13A) [267]. β(1–3)-Oligomer 90 was prepared as chitin mimetics (Scheme 13B). Despite the subtle

Recent advances in the application of isoindigo derivatives in materials chemistry

• Andrei V. Bogdanov and
• Vladimir F. Mironov

Beilstein J. Org. Chem. 2021, 17, 1533–1564, doi:10.3762/bjoc.17.111

• the introduction of aromatic substituents of variable nature into the oligomer structure. By the example of pyrene derivatives 7 and 8, the dependence of the binding type of the aromatic fragment to the isoindigo core was revealed. The synthetic procedure for the preparation of these monoisoindigoid

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

• duplex greatly influences its ability to resist 3'-exonucleases. Their work showed that a single or double (S)- or (R)-GNA substitution at the 3' end of a dT20 oligomer with a natural phosphodiester backbone greatly increases the oligonucleotide’s ability to resist SVPDE. Furthermore, when moving the

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

• ionization and ion mobility), CD spectroscopy and atomic force microscopy, the authors were able to obtain detailed information about the size and secondary structure associated with some of the soluble intermediates. These included: large β-sheet oligomers formed immediately after solubilization (oligomer

• O1); a small oligomer that forms transiently during the early stages of the lag phase (oligomer O2) and 4 spectroscopically distinct forms of oligomers that appear during the later stages of aggregation and apparently coexist with the proto-fibrillar species (oligomers O3–O6, Figure 10). It is worth

• characterize and quantify the relative populations of monomeric, octameric, and higher oligomer species that populate the pathway from the native PrP state to fibril formation. The equilibrium constants between states were also analysed as a function of both temperature and pressure, allowing to determine the

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

• photodimerization [55][56][57], photocleavage [58][59], and cis–trans photoisomerization [60][61][62][63][64][65]. While it had been well-established to access oligomer formation and gelation, a light-switchable particle size has remained a challenge until realized through the mentioned electrostatic self-assembly

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

• , meaning that the complex associates and dissociates in vivo, or permanent, meaning that the interaction is very stable and that the complex is only stable as an oligomer. Obligate interactions are normally permanent, while non-obligate interactions can be either [57]. The majority of proteins are found in

• tryptophan, the equilibrium between the monomer and the oligomer formation is shifted towards the latter [75][76]. Examples of PPIs within higher-order protein complexes PPIs are responsible for the assembly of large protein complexes, such as capsid proteins in viruses and protein containers. This section

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

• Jennifer Frommer and
• Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

• oligonucleotides has become a major tool for RNA structure and function studies. Reporter groups or specific functional entities are required to be attached at a pre-defined site of the oligomer. An attractive strategy is the incorporation of suitably functionalized building blocks that allow post-synthetic

Design and synthesis of multivalent α-1,2-trimannose-linked bioerodible microparticles for applications in immune response studies of Leishmania major infection

• Chelsea L. Rintelmann,
• Tara Grinnage-Pulley,
• Kathleen Ross,
• Daniel E. K. Kabotso,
• Angela Toepp,
• Anne Cowell,
• Christine Petersen,
• Balaji Narasimhan and
• Nicola Pohl

Beilstein J. Org. Chem. 2019, 15, 623–632, doi:10.3762/bjoc.15.58

• recognition. To allow for both surface functionalization of this glycan to the bioerodible microparticles and conjugation of the fluorophore, two amine handles would be necessary (Figure 3). The design would also benefit from the development of a more efficient synthesis of the mannose oligomer sidechain

Unexpected loss of stereoselectivity in glycosylation reactions during the synthesis of chondroitin sulfate oligosaccharides

• Teresa Mena-Barragán,
• José L. de Paz and
• Pedro M. Nieto

Beilstein J. Org. Chem. 2019, 15, 137–144, doi:10.3762/bjoc.15.14

• oligosaccharides in order to improve the glycosylation efficiency [20][21]. In this approach, glucose instead of GlcA residues were employed in the oligosaccharide assembly and final oxidation and derivatization was carried out at the oligomer stage. Syndecan-1 glycopeptide containing a CS type A sequence was also

MoO₃ on zeolites MCM-22, MCM-56 and 2D-MFI as catalysts for 1-octene metathesis

• Hynek Balcar,
• Martin Kubů,
• Naděžda Žilková and
• Mariya Shamzhy

Beilstein J. Org. Chem. 2018, 14, 2931–2939, doi:10.3762/bjoc.14.272

• the reaction. In later stages when most of 1-octene was isomerized to 3- and 4-octenes only little increase in oligomer amounts was observed. Conclusion 3D and 2D zeolites of MWW (MCM-22 and MCM-56) and MFI topologies were used for the first time as supports for the preparation of highly active

Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• ≈25 °C for the according hybridization with DNA was observed [40]. In addition, the cationic dimer 11 was shown to bind more tightly to native RNA and DNA strands in the presence of magnesium chloride [40]. For the cationic T-oligomer 18, Letsinger and co-workers reported a strongly reduced absorbance

• was then converted into a reactive carbodiimide 24 and coupled to a terminal amino group of the solid phase 25 (Scheme 2). This coupling furnished solid phase-attached intermediate 26, which was Fmoc-deprotected to the amine 27. Iterative repetition of this coupling-deprotection cycle gave oligomer 28

• protecting group to yield the free 5'-amine 34. Subsequent iterative coupling–deprotection cycles resulted in the formation of the guanidinium-linked oligomer 35. After basic guanidine and purine deprotection and concomitant cleavage from the solid support, final acidic deprotection furnished A5T

Preparation of trinucleotide phosphoramidites as synthons for the synthesis of gene libraries

• Ruth Suchsland,
• Bettina Appel and
• Sabine Müller

Beilstein J. Org. Chem. 2018, 14, 397–406, doi:10.3762/bjoc.14.28

• -phosphonate and the release of the oligomer with the free 3'-OH group leaving all other protecting groups intact. This strategy has been shown to be compatible with phosphoramidite chemistry and β-cyanoethyl protection of the internucleotide phosphates [33]. A more recent report describes the preparation of a

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• investigated in water and in buffer solution. The compounds bind to single-stranded templates and the strength of binding is solvent-dependent. In water solution compounds 3 and 5 both self-assemble on T10 oligomer according to canonical base–base pairing while in buffered solution only 5 effectively binds to

Chemical systems, chemical contiguity and the emergence of life

• Terrence P. Kee and
• Pierre-Alain Monnard

Beilstein J. Org. Chem. 2017, 13, 1551–1563, doi:10.3762/bjoc.13.155

• , which are potential functional catalysts, can also be synthesized from simple amino acids [40]. Indeed, dipeptides can catalyse RNA oligomer formation in the eutectic phase of water/ice [41], underscoring another possible chemical contiguity within the geochemical context. The ubiquity of polyphosphate

Synthesis of oligonucleotides on a soluble support

• Harri Lönnberg

Beilstein J. Org. Chem. 2017, 13, 1368–1387, doi:10.3762/bjoc.13.134

• was interpreted as an indication of a side product formation. Evidently, the MSNT activation had resulted in displacement of O6 by the 3-nitro-1,2,4-triazol-1-yl group [38]. The oligomer was released from the support and deprotected by successive treatments with syn-pyridine-2-carbaldoxime and

• oligomer could be isolated in pure deprotected form. No base modification reactions were now detected. The phosphotriester approach based on hydroxybenzotriazole activation has more recently applied to the synthesis of short ODNs on a branched tetrakis-O-[4-(azidomethyl)phenyl]pentaerythritol-derived

• ´), was assembled. Release and deprotection of the oligomer by conventional ammonolysis were accompanied by precipitation of the support. The pentamer, homogeneous by HPLC, was obtained in a 43% yield. Besides precipitation, extraction offers a possible approach for the separation of the soluble-supported

Cyclodextrins tethered with oligolactides – green synthesis and structural assessment

• Cristian Peptu,
• Mihaela Balan-Porcarasu,
• Alena Šišková,
• Ľudovít Škultéty and
• Jaroslav Mosnáček

Beilstein J. Org. Chem. 2017, 13, 779–792, doi:10.3762/bjoc.13.77

• polymers with different core and similar number of arms. The modification of CDs with a reduced amount of monomer units results in CD-oligomer materials which still keep an important property of the starting CDs, like their inclusion ability [16]. The CD-oligoester conjugate, compounds with a relatively

• oligomers with odd number of monomer units could be observed as well. These oligomer species with odd number of lactates resulted from intramolecular and/or intermolecular transesterification reactions and are in lower amount, when compared with the oligomers containing even number of monomers. This

• chromatographic peaks corresponding to free CD and to modified CD in ELSD chromatograms. However, this estimation was made under the reserve that CD-LA mixtures eluted after 8 min may contain also PLA oligomer species initiated by the presence of residual water in the reaction system. We chose "off line

Fluorescent carbon dots from mono- and polysaccharides: synthesis, properties and applications

• Stephen Hill and
• M. Carmen Galan

Beilstein J. Org. Chem. 2017, 13, 675–693, doi:10.3762/bjoc.13.67

• of nanoparticle formation. Trapping of the iminium electrophile could allow oligomer formation and dehydration, leading to the formation of the sp3-enriched nanocrystalline core. In the second phase of the reaction, following the loss of bulk water, further carbonisation occurs and aromaticity is

NMR reaction monitoring in flow synthesis

• M. Victoria Gomez and
• Antonio de la Hoz

Beilstein J. Org. Chem. 2017, 13, 285–300, doi:10.3762/bjoc.13.31

• and Sons. Flowsheet of the experimental setup used to study the reaction kinetics of the oligomer formation in mixtures of acetaldehyde (AA) and water (A) (Flow rates VAA 254 μL min−1 and VW 748 μL min−1). Reproduced with permission from reference [46]. Copyright 2014 The American Chemical Society

Extrusion – back to the future: Using an established technique to reform automated chemical synthesis

• Deborah E. Crawford

Beilstein J. Org. Chem. 2017, 13, 65–75, doi:10.3762/bjoc.13.9

• by initially forming a dimer from multifunctional monomers, which then forms a trimer, then oligomer and finally a polymer (Figure 4) [24]. Kim and Hyun report the synthesis of polyurethane, discussing the associated numerical simulation they conducted to determine the dependency of shear rate on

• segments. Representative diagram explaining the process involved in step growth polymerisation, which involves the formation of a dimer, then trimer followed by oligomer synthesis. Taken from [24]. Comparison of choline chloride/D-fructose DES prepared via twin screw extrusion (left) and conventional

A versatile route to polythiophenes with functional pendant groups using alkyne chemistry

• Xiao Huang,
• Li Yang,
• Rikard Emanuelsson,
• Jonas Bergquist,
• Maria Strømme,
• Martin Sjödin and
• Adolf Gogoll

Beilstein J. Org. Chem. 2016, 12, 2682–2688, doi:10.3762/bjoc.12.265

• starting points for future new functionalized EDOT monomers and following polymer or oligomer research. CVs of electrochemical polymerization of (a) pyEDOT 3 and (b) EDOT in MeCN solution with 0.1 M TEAPF6, glassy carbon electrode, 0.1 V s−1. Insets show the structure and voltammograms for the monomers