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

• band observed in the SDS-PAGE gel of each homolog is consistent with the expected monomer molecular masses of approximately 21 kDa, several other bands appear (Figure 2A). The banding patterns of each of the homologs are similar to those of Vs NnlA. These higher molecular weight bands are likely not

• 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

Switchable molecular tweezers: design and applications

• Pablo Msellem,
• Maksym Dekthiarenko,
• Nihal Hadj Seyd and
• Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

• protecting arms to move away from the salen complex thereby exposing the catalytic site. This triple-layer catalyst was applied in the control of a ring-opening polymerization reaction. The open state achieved full monomer conversion, while the closed state exhibited minimal activity (7% conversion after 100

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• by Alphafold [36] Monomer v2.0 for the monomer of CMA1 (A0A1S4E5V9) were trimmed to only include the N-terminal domain (residues 33–159), with all B-factors reset to 15 Å2, to be subsequently used as a search model to solve the structure of CMA1-Nter by molecular replacement using PHASER [37

Beyond n-dopants for organic semiconductors: use of bibenzo[d]imidazoles in UV-promoted dehalogenation reactions of organic halides

• Kan Tang,
• Megan R. Brown,
• Chad Risko,
• Melissa K. Gish,
• Garry Rumbles,
• Phuc H. Pham,
• Oana R. Luca,
• Stephen Barlow and
• Seth R. Marder

Beilstein J. Org. Chem. 2023, 19, 1912–1922, doi:10.3762/bjoc.19.142

• depopulations of the bibenzoimidazole-based HOMO, which, as well as π-character also has significant C–σ-bonding character associated with the inter-monomer bond, suggesting that excitation should weaken the bond (in a similar way to oxidation associated with removal of an electron from the same orbital). To

• amplitude at 654 nm decays with a 1 ps lifetime. The isosbestic point in Figure 4a is consistent with a clean transformation such as monomer formation. The corresponding monomeric radicals are calculated using TD-DFT (M06/6-31G(d,p)) (Figure 4e) to have absorptions at similar energies to those seen in the

• states absorb at similar wavelengths to the monomer radicals (see Supporting Information File 1, Figure S12). However, ISC is typically much slower than 1 ps in organic molecules, especially so for those lacking heavy atoms [45]. Conclusion Dimeric reductants of the (Y-DMBI)2 type can accomplish the

Anion–π catalysis on carbon allotropes

• M. Ángeles Gutiérrez López,
• Mei-Ling Tan,
• Giacomo Renno,
• Augustina Jozeliūnaitė,
• J. Jonathan Nué-Martinez,
• Javier Lopez-Andarias,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2023, 19, 1881–1894, doi:10.3762/bjoc.19.140

• /23 = 4.6 of the respective monomer 22, which was already best among fullerene monomers. In computational simulations, the positive maximum of the MEP surface next to the amine base was the same for dimer 37 (+13.9 kJ mol−1) and monomer 22 (+13.8 kJ mol−1), supporting that the dramatic increase in

• activity did not originate from a change in intrinsic anion–π interactions. The computed polarizability of dimer 37 (α = 1499 a.u.) was almost twice as high as that of monomer 22 (α = 903 a.u.), confirming that powerful induced anion–π interactions account for the high catalytic activity. Twenty

• dimer 37 decreased by 20%. This complementary decrease supported the formation of complex 41 with decreased electron deficiency. Control experiments with fullerene monomer 22 gave unchanged catalytic activity with intercalators 38 or 40, which suggested that complexes 42 and 43 do not form. The

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

• . An example of a synthetic spectrum generated from an experimental spectrum is shown in Figure 3. A total of 8000 synthetic spectra were randomly produced (2000 for each monomer category) out of the experimental spectra of set 1. They were shuffled to avoid training batches composed of a unique

• ) activation functions for each layer. Two dropout layers are interleaved after the first and second hidden layers with a dropout setting of 25% to avoid over-fitting issues. The training objective is a classification task between the 4 monomer categories with a cross-entropy loss function. To account for the

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

• Y and central bond are pseudo-equatorial and pseudo-axial, respectively. However, this folding is generally much less pronounced than in 1H derivatives (see below, Figure 4, and Table S2 in Supporting Information File 1) presumably since in the dimers both 2-substituents (Y and the other monomer

• , whereby the dimer is in equilibrium with a small concentration of the corresponding odd-electron monomer, which can then rapidly react with an acceptor such as an organic semiconductor (SC) through an exergonic electron transfer (ET), has been observed for the reactions of several relatively weakly bonded

• endergonic dimer-to-SC ET; subsequent rapid cleavage of the odd-electron dimer cation affords the stable monomer cation and an odd-electron monomer, the latter then undergoing an exergonic ET to another SC molecule. The “ET-first” mechanism occurs in parallel with the “cleavage-first” mechanism for many of

Tying a knot between crown ethers and porphyrins

• Maksym Matviyishyn and
• Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

• the two monomers were expected for tetra-crowned 1-Zn, where four potassium cations cooperatively clasp each monomer together. In such a case, K+ cations would ideally hover between the macrocyclic pockets of the crown ether moieties of each 1-Zn monomer. Incorporation of other metals, e.g., Cu(II

Radical chemistry in polymer science: an overview and recent advances

• Zixiao Wang,
• Feichen Cui,
• Yang Sui and
• Jiajun Yan

Beilstein J. Org. Chem. 2023, 19, 1580–1603, doi:10.3762/bjoc.19.116

• an initiator molecule; M represents a monomer molecule; Pi represents a polymer chain with i repeating units; S represents a solvent molecule; and a dot indicates free radical species. These reactions are classified into four elementary steps: initiation, propagation, termination, and transfer. The

• initiation step includes Equation 1 and Equation 2, when the thermal initiator decomposes into two small-molecule radical species and the first monomer adds to the growing chain to form the first repeating unit. The propagation step is depicted in Equation 3 when monomers take turns to undergo radical

• , which can be the monomer (Equation 6), the solvent (Equation 7), the polymer itself (Equation 8), or a chain-transfer agent intentionally added to tune the molecular weight or to introduce chain-end functionalities. When chain transfer happens, the originally growing chain halts while a new chain

Construction of hexabenzocoronene-based chiral nanographenes

• Ranran Li,
• Di Wang,
• Shengtao Li and
• Peng An

Beilstein J. Org. Chem. 2023, 19, 736–751, doi:10.3762/bjoc.19.54

• hexaphenylbenzene 68 in an 85% yield. Then the Scholl cyclodehydrogenation of compound 68 was carried out in DDQ/TfOH to afford NG 69 in a 64% yield. By the selective dimerization of azopine-containing, HBC-monomer 69, the novel BINOL-like, atropisomeric chiral oxa-nanographene 70 was obtained in high yield

Synthesis, structure, and properties of switchable cross-conjugated 1,4-diaryl-1,3-butadiynes based on 1,8-bis(dimethylamino)naphthalene

• Semyon V. Tsybulin,
• Ekaterina A. Filatova,
• Alexander F. Pozharskii,
• Valery A. Ozeryanskii and
• Anna V. Gulevskaya

Beilstein J. Org. Chem. 2023, 19, 674–686, doi:10.3762/bjoc.19.49

• formally symmetrical structure of diynes 5, naphthalene rings A and B of molecules 5b and 5d differ in their structural parameters. At the same time, the monomer fragments of the nitro derivative 5e are identical. In the case of 5e, the naphthalene rings lie in parallel planes, while in crystals of 5b and

• DMAN fragments do not participate in nonvalent interactions and do not form short contacts. The recurring motif in the crystals is the coordination of the benzene meta proton by the nitrogen atom of the C≡N group. The structural parameters of both monomer fragments of nitro derivative 5e are identical

• nitro group. There are two types of independent non-equivalent dications, marked in blue and green, and two types of BF4− anions, marked in red and yellow, in the crystal structure of salt 11c (Figure S68 in Supporting Information File 1). Monomer fragments in both are identical (Table 2, Figure 5). The

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

• basic and neutral conditions at which intramolecular stacking was less pronounced. At acidic conditions, the monomer signal (400 nm) was dominant (Figure 1). The emission of the excimer did not exclusively depend on the degree of overlapping of chromophores. Earlier theoretical examinations favored a

• DNA/RNA polynucleotides [37]. The monomer fluorescence emission at 400 nm was not changed except for titration with poly dGdC–poly dGdC where a small emission increase of emission at 400 nm was observed. At ratios of an excess of polynucleotide over compound (r[compound]/[polynucleotide] < 0.3

• polynucleotide secondary structure. Concurrently, no monomer fluorescence signal at 400 nm changed, except a small increase upon poly dGdC–poly dGdC addition. Negligible thermal stabilization (Table S1, Figures S6–S8, Supporting Information File 1) did not support the classical intercalation of phenanthridine

Investigation of cationic ring-opening polymerization of 2-oxazolines in the “green” solvent dihydrolevoglucosenone

• Solomiia Borova and
• Robert Luxenhofer

Beilstein J. Org. Chem. 2023, 19, 217–230, doi:10.3762/bjoc.19.21

• of view [28]. Accordingly, Hoogenboom et al. investigated the CROP of 2-alkyl-2-oxazoline in sulfolane and investigated its effect on monomer distribution and self-assembly of the performed copolymer [30][31][32]. However, the degradability of sulfolane into acidic components, its relatively high

• further optimizations can overcome these limitations remains to be seen. Experimental Materials and methods All substances were purchased from Sigma-Aldrich (Steinheim, Germany) and were used as received unless otherwise stated. The monomer 2-n-butyl-2-oxazoline (BuOx) was prepared following the procedure

• -oxazolines was performed as follows: 1.0 equiv of the initiator was placed into a dried and argon-flushed flask and dissolved in a respective amount of solvent. Once the monomer was added, the reaction mixture was placed into a preheated (up to the investigated temperature) oil bath and incubated till the

B–N/B–H Transborylation: borane-catalysed nitrile hydroboration

• Filip Meger,
• Alexander C. W. Kwok,
• Franziska Gilch,
• Dominic R. Willcox,
• Alex J. Hendy,
• Kieran Nicholson,
• Andrew D. Bage,
• Thomas Langer,
• Thomas A. Hunt and
• Stephen P. Thomas

Beilstein J. Org. Chem. 2022, 18, 1332–1337, doi:10.3762/bjoc.18.138

• (83%). This catalytic protocol was applied to the reduction of other aliphatic nitriles to their corresponding amine hydrochloride salts, such as cyclopropyl-bearing (1b, 72%) and branched aliphatic nitriles (1c, 91%). Hexane-1,6-diamine dihydrochloride (1d), a monomer of nylon 6,6 [1], was generated

Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions

• Michael Keppler,
• Sandra Moser,
• Henning J. Jessen,
• Christoph Held and
• Jennifer N. Andexer

Beilstein J. Org. Chem. 2022, 18, 1278–1288, doi:10.3762/bjoc.18.134

• model enzymes for PPK1 and PPK2 [9][10]. From a structure perspective, PPK1 enzymes form tetramers in solution with a mass of approximately 80 kDa for the monomer (Figure 2b). Although not being an integral membrane protein, the enzyme is described to be membrane-associated [11][12][13]. The phosphate

• , clearly demonstrating the necessity of the residues for catalysis [14]. PPK2-I enzymes are of lower molecular weight than their PPK1 counterparts, with an approximate molecular mass of 40 kDa for a monomer (Figure 2c) [5]. They form dimers or tetramers in solution and are not purified from membrane

• range from three to several thousands. Comparison of PPK1 and PPK2 enzymes. a) Reaction scheme; b) structure of the EcPPK1 monomer (PDB 1XDO) [13]; c) structure of the SmPPK2 monomer (PDB 3CZQ) [10]; d) proposed mechanism of PPK1 with phosphate transfer via a phosphor enzyme intermediate; e) PPK2

Mechanochemical bottom-up synthesis of phosphorus-linked, heptazine-based carbon nitrides using sodium phosphide

• Blaine G. Fiss,
• Georgia Douglas,
• Michael Ferguson,
• Jorge Becerra,
• Jesus Valdez,
• Trong-On Do,
• Tomislav Friščić and
• Audrey Moores

Beilstein J. Org. Chem. 2022, 18, 1203–1209, doi:10.3762/bjoc.18.125

• calculated 31P chemical shifts at 37.7 ppm (P1) and 23.3 ppm (P2), respectively, while that of the paddlewheel monomer is at 11.2 ppm (P3). The calculated shifts demonstrate phosphorus environments in the mechanochemically synthesized material are distinct to those calculated in ab initio predicted models of

Synthesis of protected precursors of chitin oligosaccharides by electrochemical polyglycosylation of thioglycosides

• Md Azadur Rahman,
• Kana Kuroda,
• Hirofumi Endo,
• Norihiko Sasaki,
• Tomoaki Hamada,
• Hiraku Sakai and
• Toshiki Nokami

Beilstein J. Org. Chem. 2022, 18, 1133–1139, doi:10.3762/bjoc.18.117

• thioglycosides as monomer is described. Oligosaccharides up to the hexasaccharide were synthesized under optimized reaction conditions. Further, a modified method enabled the synthesis of oligosaccharides up to the octasaccharide by repeating electrolysis with additional monomers. The mechanism of the

• electrochemical polyglycosylation is also discussed, based on the oxidation potential of the monomer and oligosaccharides. Keywords: electrochemical glycosylation; glucosamine; oligosaccharide; oxidation potential; polyglycosylation; Introduction Chitin oligosaccharides are partial structures of chitin, which

• one of a few examples of chemical synthesis of chitin oligosaccharides through polyglycosylation of a glucosamine monosaccharide [6]. Recently, we have reported electrochemical polyglycosylation using a glucosamine derivative as a monomer [7]. This is another example of polyglycosylation of a

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

• to the Boc side chain protections. For the submonomer solution-phase synthesis of monomer 1 and oligomers 2–5, modifications from the standard synthesis conditions were required, notably for the substitution reaction. Thus, the first substitution reaction between benzyl bromoacetate and N-Boc-N

• -methylhydrazine (3.0 equiv) was conducted in water at a concentration of 2.5 M at room temperature (rt) for overnight to afford monomer 1a in 88% yield after SiO2 chromatography [41]. Standard substitution conditions in EtOAc or THF as solvent in the presence of triethylamine did not allow full conversion of the

• ]. Conformational analysis and self-assembling properties The 1H NMR analysis of monomer 1 in various solvents including CDCl3, CD3CN, C6D6, CD3OD, D2O, and DMSO-d6 showed two sets of resonances in proportions varying from 75:25 to 90:10 (Table 3). These two sets of signals were characterized as the backbone cis

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

• . synthesized the conjugated polymer F8Py (compound 6 in Figure 5), in which the incorporation of the pyridine co-monomer provides a lone pair of electrons for binding Lewis acids [37]. The formation of acid–base adducts accurately regulated the band gap of the luminescent polymer. The PL spectra in solution

Structural basis for endoperoxide-forming oxygenases

• Takahiro Mori and
• Ikuro Abe

Beilstein J. Org. Chem. 2022, 18, 707–721, doi:10.3762/bjoc.18.71

• mammalian COXs revealed that COX-1 and COX-2 are both glycosylated by post-translational modifications [46][47][48][49][50][51]. These enzymes form homodimers, and the overall structures of COX-1 and COX-2 superimpose well, with root mean square values of ≈0.9 Å. Each COX monomer contains three domains

Syntheses of novel pyridine-based low-molecular-weight luminogens possessing aggregation-induced emission enhancement (AIEE) properties

• Masayori Hagimori,
• Tatsusada Yoshida,
• Yasuhisa Nishimura,
• Yukiko Ogawa and
• Keitaro Tanaka

Beilstein J. Org. Chem. 2022, 18, 580–587, doi:10.3762/bjoc.18.60

• in AIEE. To compare the electronic natures of the compounds with and without AIEE, we performed TD-DFT calculations on each monomer of 3a, 4a, and 4e. The graphical representations of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) for the ground-state

• geometries of each monomer are shown in Figure 5. The dihedral angles between the pyrimidine and maleimide rings, the amine linkage, were nearly zero degrees for 4a and 4e in all three solvents, adopting a highly planar structure as well as compound 3a. The HOMO and LUMO were distributed on the entire

• discrepancy between the calculated and observed Exmax values for compounds 4a and 4e suggests that aggregation occurs in water, and such behavior cannot be reproduced using the monomer model (non-aggregated form). Conclusion To discover low-molecular-weight AIEE-based luminogens, we synthesized pyrido[1,2-a

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

• , trihydroxy nucleoside 14b was protected with TBDPS to carry out the synthesis of the target nucleoside monomer 9b through a chemical pathway. However, the poor yield of this reaction compelled us to abandon the route as high solubility of the TBDPS-protected dihydroxy nucleoside in aqueous phase withstood

Stepwise PEG synthesis featuring deprotection and coupling in one pot

• Logan Mikesell,
• Dhananjani N. A. M. Eriyagama,
• Yipeng Yin,
• Bao-Yuan Lu and
• Shiyue Fang

Beilstein J. Org. Chem. 2021, 17, 2976–2982, doi:10.3762/bjoc.17.207

• phenethyl group was chosen for the development of the one-pot PEG elongation approach for PEG synthesis although other groups that meet the two criteria can be used as well. Using the phenethyl group for protection, the monomer 2 was chosen for the stepwise PEG synthesis. The simplest method for its

• synthesis would be to react (PEG)4, which is commercially available and inexpensive, with styrene to give 6 [32], and tosylation of 6 to give the monomer (Scheme 3). However, the reported conditions for the synthesis of 6 without using an expensive catalyst gave low yields. We did not test the conditions

• under basic conditions to give 7. Removal of the DMTr group of 7 under acidic conditions gave 6, which was tosylated to give 2. This route is longer than the other two, but the products of all the steps are easy to purify, and it is our preferred route. With the monomer 2 in hand, the stepwise synthesis

Cryogels: recent applications in 3D-bioprinting, injectable cryogels, drug delivery, and wound healing

• Luke O. Jones,
• Leah Williams,
• Tasmin Boam,
• Martin Kalmet,
• Chidubem Oguike and
• Fiona L. Hatton

Beilstein J. Org. Chem. 2021, 17, 2553–2569, doi:10.3762/bjoc.17.171

• properties Cryogels are macroporous hydrogels with interconnected porosity, with high swelling capacities and large surface areas. Ultimately, many of the final cryogel properties are dependent on the choice of polymer/monomer composition used. However, other factors such as crosslinking, pore size, wall

• crosslinking (ratio of monomer to crosslinking agent), while the degree of crosslinking is tuned in physically crosslinked cryogels by varying the number of freeze–thaw cycles. Pore size, wall thickness, and wall density are of significant importance for cryogels properties [16]. Thicker walls and higher wall

• densities typically result in improved mechanical properties and are influenced by the concentration of monomer or precursors used as well as the type of crosslinking in the cryogel. Moreover, the processing conditions used when synthesising cryogels have a vast effect on the internal structure. An

Exfoliated black phosphorous-mediated CuAAC chemistry for organic and macromolecular synthesis under white LED and near-IR irradiation

• Azra Kocaarslan,
• Zafer Eroglu,
• Önder Metin and
• Yusuf Yagci

Beilstein J. Org. Chem. 2021, 17, 2477–2487, doi:10.3762/bjoc.17.164

• ) Diazido monomer, bisphenol A di(3-azido-2-hydroxypropan-1-ol) (Az-3) was synthesized according to a described method [46]. Az-3 was obtained as light yellowish viscous oil and was directly used without further purification, yield 98%. 1H NMR (500 MHz, CDCl3) δ 7.15 (m, 4H), 6.82 (m, 4H), 4.16 (m, 2H), 4.0