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

• 0.2–0.8 °C in the thermal stability of RNA/DNA hybrid duplexes for each AM1 modification [11][78]. NMR structural studies have shown that the AM1 modification is well tolerated in an RNA duplex, with little effect on the global structure [79]. Furthermore, siRNA duplexes with amide modifications at

• increase in silencing activity for AM1-modified siRNAs with amide linkages at specific sites [75]. Structural insight into this observation was obtained using the crystal structure of the complex between Bacillus halodurans RNase H and the r(GAC ACC UGA UAM1UC) - d(GAA TCA GGT GTC) hybrid duplex [73

• modification has been attractive in antisense therapeutics as these altered oligonucleotides can form a hybrid duplex with unmodified RNA, which is recognized by RNase H [89][90]. While the thermal stability of PS2-modified RNA duplexes slightly decreases compared to the unmodified duplex, there is an increase

A chromatography-free and aqueous waste-free process for thioamide preparation with Lawesson’s reagent

• Ke Wu,
• Yichen Ling,
• An Ding,
• Liqun Jin,
• Nan Sun,
• Baoxiang Hu,
• Zhenlu Shen and
• Xinquan Hu

Beilstein J. Org. Chem. 2021, 17, 805–812, doi:10.3762/bjoc.17.69

• incomparable chelating ability towards selected transition metals, and the corresponding complexes were applied in various areas such as chemical-sensor materials, tunable redox-potential complexes, polymer hybrid luminescence materials, building blocks for multinuclear complexes, and as catalysts for cross

[2 + 1] Cycloaddition reactions of fullerene C₆₀ based on diazo compounds

• Yuliya N. Biglova

Beilstein J. Org. Chem. 2021, 17, 630–670, doi:10.3762/bjoc.17.55

• . For example, fullerene-containing materials are used as electron-withdrawing components and buffer layers in the development and design of photoconductors [41][42], supercapacitors [43][44], field effect transistors (FET) [45][46], organic light-emitting diodes (OLEDs) [47][48] and organic or hybrid

Synthetic strategies of phosphonodepsipeptides

• Jiaxi Xu

Beilstein J. Org. Chem. 2021, 17, 461–484, doi:10.3762/bjoc.17.41

• not require the preparation of 1-aminoalkylphosphonic acid or 1-aminoalkylphosphonous acid derivatives first as starting materials (Scheme 28) [42]. Similarly, phosphinopeptides [45][46], phosphinodepsipeptides [47], and hybrid sulfonophosphinopeptides [48][49] were prepared from amino amides and 2

Mesoionic tetrazolium-5-aminides: Synthesis, molecular and crystal structures, UV–vis spectra, and DFT calculations

• Vladislav A. Budevich,
• Sergei V. Voitekhovich,
• Alexander V. Zuraev,
• Vadim E. Matulis,
• Vitaly E. Matulis,
• Alexander S. Lyakhov,
• Ludmila S. Ivashkevich and
• Oleg A. Ivashkevich

Beilstein J. Org. Chem. 2021, 17, 385–395, doi:10.3762/bjoc.17.34

• –vis spectra and charge transfer were carried out within density functional theory for ground states and time-dependent density functional theory (TD-DFT) for excited states using the τ-dependent hybrid tHCTHhyb functional [37] with the 6-311+G(2d,p) basis set [38]. The chosen functional allows to

The preparation and properties of 1,1-difluorocyclopropane derivatives

• Kymbat S. Adekenova,
• Peter B. Wyatt and
• Sergazy M. Adekenov

Beilstein J. Org. Chem. 2021, 17, 245–272, doi:10.3762/bjoc.17.25

Insight into functionalized-macrocycles-guided supramolecular photocatalysis

• Minzan Zuo,
• Krishnasamy Velmurugan,
• Kaiya Wang,
• Xueqi Tian and
• Xiao-Yu Hu

Beilstein J. Org. Chem. 2021, 17, 139–155, doi:10.3762/bjoc.17.15

• with various macrocyclic hosts as well as on the role of macrocyclic-hosts-assisted hybrid materials in energy transfer. To keep the clarity of this review, the macrocycles are categorized into the most commonly used supramolecular hosts, including crown ethers, cyclodextrins, cucurbiturils

• , calixarenes, and pillararenes. This minireview not only summarizes the role that macrocycles play in photocatalytic reactions but also clarifies the photocatalytic mechanisms. Finally, the future research efforts and new pathways to apply macrocycles and supramolecular hybrid materials in photocatalysis are

• -dependent selective arrangement of one or two substrates within the cavity for photocatalysis. Therefore, this review will focus on: i) the role of the supramolecular system in mediating the photocatalytic selectivity, yield, and the rate of the photocatalytic products and ii) macrocycle-assisted hybrid

Synthesis, crystal structures and properties of carbazole-based [6]helicenes fused with an azine ring

• Daria I. Tonkoglazova,
• Anna V. Gulevskaya,
• Konstantin A. Chistyakov and
• Olga I. Askalepova

Beilstein J. Org. Chem. 2021, 17, 11–21, doi:10.3762/bjoc.17.2

• , we synthesized carbazole-based [6]helicenes fused with an azine ring (quinoxaline, pyrazine or pyridine ones). Scheme 2 represents the current work. We envisaged that combining the carbazole unit with the readily available azine building block would result in the formation of donor–acceptor hybrid

• quinoxaline-fused hybrid 10a is intermediate (52.8° and 50.5°). Comparing the sum of the inner helix torsion angles of the helicenes 10a–c and 12 reveals the same patterns. Evidently, the repulsive interaction of the H(14) and H(g) atoms of 10c is the main reason for the observed extra twisting, whereas

Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities

• Heiko T. Kiesewalter,
• Carlos N. Lozano-Andrade,
• Mikael L. Strube and
• Ákos T. Kovács

Beilstein J. Org. Chem. 2020, 16, 2983–2998, doi:10.3762/bjoc.16.248

• synthesised by NRPS gene clusters (surfactin, plipastatin, and bacillibactin) and one by a hybrid NRPS–PKS gene cluster (bacillaene, Figure 1). The well-studied biosurfactant surfactin, encoded by the srfAA-AD gene cluster, reduces the surface tension needed for swarming and sliding motility [38][39]. The

• incubated at 30 °C with continuous shaking (548 cpm, 2 mm), and the OD600 was measured in 15 min intervals over 24 h. All graphical visualisations were prepared using ggplot2 [79]. Overview of the NRPs surfactin, plipastatin, bacillibactin, and iturin as well as the hybrid NRP-PK bacillaene produced by

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

• temperature than the other ones. Most notably, the representative DNA denaturation analysis with ligand 4e and different quadruplex forms clearly reveals a significant selectivity. Hence, the hybrid antiparallel G4-DNA 22AG as well as the parallel quadruplex-forming KRAS sequence are stabilized to a

Ring-closing metathesis of prochiral oxaenediynes to racemic 4-alkenyl-2-alkynyl-3,6-dihydro-2H-pyrans

• Viola Kolaříková,
• Markéta Rybáčková,
• Martin Svoboda and
• Jaroslav Kvíčala

Beilstein J. Org. Chem. 2020, 16, 2757–2768, doi:10.3762/bjoc.16.226

• internal standards. Chemical shifts are given in parts per million and coupling constants in hertz. Mass spectra (ESI, APCI) and HRMS spectra were measured with a hybrid LTQ Obitrap XL instrument (Thermo Fisher Scientific). All reactions were performed in a dry inert atmosphere (Ar) in oven-dried flasks

Encrypting messages with artificial bacterial receptors

• Pragati Kishore Prasad,
• Naama Lahav-Mankovski,
• Leila Motiei and
• David Margulies

Beilstein J. Org. Chem. 2020, 16, 2749–2756, doi:10.3762/bjoc.16.225

• during bacterial growth. The emission spectra of the bacterial samples labeled with the three DNA-based receptors were recorded using black flat-bottom 384-well microplates (Corning) and a BioTek synergy H4 hybrid multiwell plate reader. The fluorescence responses were measured using excitation

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

Palladium nanoparticles supported on chitin-based nanomaterials as heterogeneous catalysts for the Heck coupling reaction

• Tony Jin,
• Malickah Hicks,
• Davis Kurdyla,
• Sabahudin Hrapovic,
• Edmond Lam and
• Audrey Moores

Beilstein J. Org. Chem. 2020, 16, 2477–2483, doi:10.3762/bjoc.16.201

• parameters were performed on PdCl2 and either ChNC or ChsNC, but with no H2 reductant. In this case, the solution color remained yellow, indicating that using either ChNC or ChsNC alone cannot fully reduce PdCl2. The resulting hybrid materials are noted PdNP@ChNC and PdNP@ChsNC, respectively. Dihydrogen was

Catalytic trifluoromethylation of iodoarenes by use of 2-trifluoromethylated benzimidazoline as trifluoromethylating reagent

• Tatsuhiro Uchikura,
• Nanami Kamiyama,
• Taisuke Ishikawa and
• Takahiko Akiyama

Beilstein J. Org. Chem. 2020, 16, 2442–2447, doi:10.3762/bjoc.16.198

• diamine ligandsa. Supporting Information Supporting Information File 480: Details of screening experiments, synthetic procedures and characterization data of new compounds, and copies of spectra. Funding JSPS KAKENHI Grant Numbers JP17H03060, JP20H00380, and JP20H04826 (Hybrid Catalysis)

Recent developments in enantioselective photocatalysis

• Callum Prentice,
• James Morrisson,
• Andrew D. Smith and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2020, 16, 2363–2441, doi:10.3762/bjoc.16.197

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• ][21][22][23]. More specifically, we investigate how core α(1-3)-linked fucose (Fuc) and β(1-2)-linked xylose (Xyl) affect the structure and dynamics of plants N-glycoforms [23] and of hybrid constructs with mammalian N-glycoforms [24]. At first glance plants protein N-glycosylation [23] is quite

• refer to N-glycans as either “plant” or “hybrid” separately. Nevertheless, it is important to underline that some of these motifs, such as β(1-2) xylosylation and difucosylated core are also found in invertebrate N- glycosylation [30]. Finally, we discuss these findings within a framework where the

• position of the deoxy-C6 of the fucose in LeX relative to LeA. Hybrid N-glycans. To understand how characteristic plant N-glycan motifs can affect the structure of mammalian N-glycoforms, we have designed and analysed the dynamics of a set of hybrid systems. In particular, we were interested in the effect

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• mechanism studies using computational chemistry methods. The probable reaction mechanisms were studied by hybrid DFT QM/MM molecular dynamics simulations [11] where the possible transition state (TS) structures were localized. The observation of the possible TS structure opens the opportunities for the in

Et₃N/DMSO-supported one-pot synthesis of highly fluorescent β-carboline-linked benzothiophenones via sulfur insertion and estimation of the photophysical properties

• Dharmender Singh,
• Vipin Kumar and
• Virender Singh

Beilstein J. Org. Chem. 2020, 16, 1740–1753, doi:10.3762/bjoc.16.146

• hybrid containing the benzothiophene moiety (Figure 1) [57][58]. The present study was inspired by the recent findings of Nguyen and co-workers [59][60][61]. As a part of our ongoing project [62][63], we devised a simple and efficient one-pot practical approach for the construction of β-carboline

Microwave-assisted efficient one-pot synthesis of N²-(tetrazol-5-yl)-6-aryl/heteroaryl-5,6-dihydro-1,3,5-triazine-2,4-diamines

• Moustafa Sherief Moustafa,
• Ramadan Ahmed Mekheimer,
• Saleh Mohammed Al-Mousawi,
• Mohamed Abd-Elmonem,
• Hesham El-Zorba,
• Afaf Mohamed Abdel Hameed,
• Tahany Mahmoud Mohamed and
• Kamal Usef Sadek

Beilstein J. Org. Chem. 2020, 16, 1706–1712, doi:10.3762/bjoc.16.142

• specific biological target such as a receptor or an enzyme. A promising strategy that overcomes the classical one-target, one-molecule approach is the design of stable chemical hybrid molecules which are a combination of two biologically active scaffolds acting at different targets [20][21][22][23][24

NHC-catalyzed enantioselective synthesis of β-trifluoromethyl-β-hydroxyamides

• Alyn T. Davies,
• Mark D. Greenhalgh,
• Alexandra M. Z. Slawin and
• Andrew D. Smith

Beilstein J. Org. Chem. 2020, 16, 1572–1578, doi:10.3762/bjoc.16.129

• stereogenic trifluoromethyl centers is through enantioselective addition of enolates or their equivalents to prochiral trifluoromethyl ketones (Figure 1A). Within this area, a common catalytic approach has utilized aliphatic ketones as enolate equivalents using prolinamide, cinchona, or hybrid catalysts that

Five-component, one-pot synthesis of an electroactive rotaxane comprising a bisferrocene macrocycle

• Natalie Lagesse,
• Luca Pisciottani,
• Maxime Douarre,
• Pascale Godard,
• Brice Kauffmann,
• Vicente Martí-Centelles and
• Nathan D. McClenaghan

Beilstein J. Org. Chem. 2020, 16, 1564–1571, doi:10.3762/bjoc.16.128

• Rigaku FRX® high flux rotating anode with a Pilatus 200K hybrid pixel detector. Using Olex2 [27], the structure was solved with the ShelXT [28] structure solution program using Intrinsic Phasing and refined with the ShelXL [29] refinement package using the full least-squares correlation matrix. The non

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

• conjugated porous polymers (CPPs) [3][10][171], covalent organic frameworks (COFs) [172][173][174][175], and hybrid materials, such as metal–organic frameworks (MOFs) [1][176][177]. MOFs, for example, have three distinct origins of photocatalysis; (i) semiconducting metal cluster nodes, (ii) photocatalytic

In silico rationalisation of selectivity and reactivity in Pd-catalysed C–H activation reactions

• Liwei Cao,
• Mikhail Kabeshov,
• Steven V. Ley and
• Alexei A. Lapkin

Beilstein J. Org. Chem. 2020, 16, 1465–1475, doi:10.3762/bjoc.16.122

• modern supercomputer clusters [19]. The structures were generated by the Python module developed in house and explained in detail elsewhere [20]. Electronic energies were evaluated using Becke’s three-parameter hybrid B3LYP functional, while the molecular orbitals are expanded in triple-zeta all electron

Synthesis and properties of quinazoline-based versatile exciplex-forming compounds

• Rasa Keruckiene,
• Simona Vekteryte,
• Ervinas Urbonas,
• Matas Guzauskas,
• Eigirdas Skuodis,
• Dmytro Volyniuk and
• Juozas V. Grazulevicius

Beilstein J. Org. Chem. 2020, 16, 1142–1153, doi:10.3762/bjoc.16.101

• . The potentials were calibrated against the standard ferrocene/ferrocenium (Fc/Fc+) redox system [24]. The ground-state geometries were optimized by using the B3LYP (Becke three parameters hybrid functional with Lee–Yang–Perdew correlation) [25] functional at the 6-31G (d, p) level of theory in vacuum