Double-headed nucleosides: Synthesis and applications

• Vineet Verma,
• Jyotirmoy Maity,
• Vipin K. Maikhuri,
• Ritika Sharma,
• Himal K. Ganguly and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98

• followed by their duplex formation studies against complimentary oligonucleotide strands had described a very selective zipper-interaction [35], whereas a relative stabilization was observed due to stacking of these additional nucleobases across the minor groove [31]. The biological activity of the acyclic

• duplexes. The introduction of two double-headed nucleosides in two complementary DNA sequences forming a DNA-zipper motif showed a stabilization of the duplex and increased base–base stacking interactions. Nielsen and co-workers [30][31][65] synthesized double-headed nucleosides 5′-(S)-C-(thymine-1-yl

• the second nucleobase thymine through Mitsunobu reaction followed by deprotection steps in the presence of TBAF and methanolic ammonia (Scheme 28) [30][65]. The nucleoside monomer 118 was phosphitylated and then incorporated into oligodeoxynucleotides but stabilization in the secondary structures due

Synthesis of 10-O-aryl-substituted berberine derivatives by Chan–Evans–Lam coupling and investigation of their DNA-binding properties

• Peter Jonas Wickhorst,
• Mathilda Blachnik,
• Denisa Lagumdzija and
• Heiko Ihmels

Beilstein J. Org. Chem. 2021, 17, 991–1000, doi:10.3762/bjoc.17.81

• as CD and LD spectroscopy. Fluorimetric DNA melting analysis with different types of quadruplex DNA revealed a moderate stabilization of the telomeric quadruplex-forming oligonucleotide sequence G3(TTAG3)3. The derivatives showed a moderate affinity towards quadruplex DNA (Kb = 5–9 × 105 M−1) and ct

• forms, the effect of thermally induced unfolding of dye-labeled, quadruplex-forming oligonucleotides in the presence of the ligands was studied. In general, the binding of the ligand to the G4-DNA leads to a stabilization and thus to an increasing melting temperature of the DNA (Table 2). This effect of

• quadruplex structures. Although the ∆Tm values do not necessarily correlate directly with the binding affinity [23], as they only refer to the stabilization at elevated temperatures, the data show that these ligands do not bind extremely strong to G4-DNA. Nevertheless, as these screening experiments revealed

Metal-free glycosylation with glycosyl fluorides in liquid SO₂

• Krista Gulbe,
• Jevgeņija Lugiņina,
• Edijs Jansons,
• Artis Kinens and
• Māris Turks

Beilstein J. Org. Chem. 2021, 17, 964–976, doi:10.3762/bjoc.17.78

• halosulfites may dissociate. Thus, we proposed that a plausible formation of the fluorosulfite species and stabilization of the oxocarbenium ion intermediate could facilitate the glycosylation with glycosyl fluorides as glycosyl donors in liquid SO2 without the need of external promoter. Results and Discussion

• stabilization of the oxocarbenium ion intermediate in a form of a dioxolenium ion by the remote protecting group in C3 or C6 position could be the reason for such a good α-selectivity in liquid SO2 [75]. Within this study, several experiments were also carried out to test the reactivity of peracylated manno

Prins cyclization-mediated stereoselective synthesis of tetrahydropyrans and dihydropyrans: an inspection of twenty years

• Asha Budakoti,
• Pradip Kumar Mondal,
• Prachi Verma and
• Jagadish Khamrai

Beilstein J. Org. Chem. 2021, 17, 932–963, doi:10.3762/bjoc.17.77

• and co-workers explained the formation of all-cis-2,4,6-trisubstituted THPs with the help of density functional theory (DFT) and stated that in the presence of an external nucleophile, the stabilization of the carbocation intermediate is favored through hyperconjugation [28]. The vacant p-orbital 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

• increased thermal stability when binding to either DNA or RNA complements with Tm increases of +1 to +8 and +2 to +10 °C, respectively [127][128][130][131][132][133][134]. The higher stabilization of RNA can be attributed to the preorganization of LNA nucleosides towards formation of A-form duplexes [128

• revealed that thermal stabilization may be attributed to nonconventional hydrogen bonds in the backbone [195][196][197]. Gene silencing by RNAi has also been explored with siRNA containing FANA residues [198]. These studies have shown that FANA is accommodated in the sense strand and 5'-end and 3'-termini

• modified with 4'-fluoro modifications have more labile glycosidic linkages under similar conditions [203][204]. Rosenberg attributed this contrast to the electronegativity differences between the groups and the effect this would have on the stabilization of the resulting oxocarbenium ion [202]. Oligomers

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

• ]. It is noteworthy that most of the phospholipid-stabilized MBs investigated in research and preclinical development are stabilized by a fluorocarbon (FC) gas [11][31][34]. FCs are known to contribute to MB stabilization through an osmotic effect [31]. In addition, FCs were also found to act as co

The synthesis of chiral β-naphthyl-β-sulfanyl ketones via enantioselective sulfa-Michael reaction in the presence of a bifunctional cinchona/sulfonamide organocatalyst

• Deniz Tözendemir and
• Cihangir Tanyeli

Beilstein J. Org. Chem. 2021, 17, 494–503, doi:10.3762/bjoc.17.43

• ). The solvent effects on the SMA of the chalcone derivatives and naphthalene-1-thiol are summarized in Figure 2. This behavior might be related to the better stabilization of the transition state of the substrates containing electron-withdrawing substituents or halogen atoms with THF, or vice versa. In

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

• thermodynamic stabilization of proteins [29][30][31]. The regulation of the proline content in proteins is an evolutionary strategy for environmental adaptation in extremophilic organisms. Proline is of a higher abundance in the proteomes of thermophilic organisms (organisms living at a high temperature) and of

• modifications of proline residues are sparse. The most common among them is hydroxylation at position 4 by molecular oxygen, which is mediated by prolyl-4-hydroxylase [34]. This process has a remarkable relevance in the stabilization of collagen in higher organisms [35]. The experimental expression of the

• the conformations. However, R-Flp stabilizes the C4-exo-pucker, while S-Flp stabilizes the C4-endo system [51]. It is believed that Dfp has no conformational preference akin to proline [52]. The stabilization of the puckers is one of the most prominent features of fluoroprolines that justifies their

Synthesis of trifluoromethyl ketones by nucleophilic trifluoromethylation of esters under a fluoroform/KHMDS/triglyme system

• Yamato Fujihira,
• Yumeng Liang,
• Makoto Ono,
• Kazuki Hirano,
• Takumi Kagawa and
• Norio Shibata

Beilstein J. Org. Chem. 2021, 17, 431–438, doi:10.3762/bjoc.17.39

• success of our DMF-free systems lies in the generation of sterically demanding cationic species, [P4-t-Bu]H+ or glyme capsulized K+, resulting in the stabilization of CF3− from HCF3 by ion separation. The sterically demanding [P4-t-Bu]H+ or encapsulation of K+ by glymes effectively inhibits the contact of

CF₃-substituted carbocations: underexploited intermediates with great potential in modern synthetic chemistry

• Anthony J. Fernandes,
• Armen Panossian,
• Bastien Michelet,
• Agnès Martin-Mingot,
• Frédéric R. Leroux and
• Sébastien Thibaudeau

Beilstein J. Org. Chem. 2021, 17, 343–378, doi:10.3762/bjoc.17.32

• very small π-electron density calculated in the 2pC orbital of CF3CH2+ (0.04 electrons) led the authors to conclude that “there is no hyperconjugative stabilization by the CF3 group”. The presence of this attractive interaction should, however, not be discarded. Indeed, the quantitative PMO analysis at

• spectroscopic evidence for the complete ionization of several α-(trifluoromethyl) alcohol precursors 9a–c in a superacidic FSO3H–SbF5–SO2 medium. They also brought experimental 19F NMR variation values up to Δδ = +24.8 ppm (Scheme 3). This suggests a partial stabilization of the cationic center by

• partial stabilization of the cationic center by the phenyl groups. Similarly, Laali et al. observed significant 19F NMR downfield chemical shifts upon the formation of α-(trifluoromethyl)pyrenylcarbenium- and α-(trifluoromethyl)anthracenylcarbenium ions 12a–d from the corresponding carbinols 11a–d (Scheme

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

• disrotation at C2 and C3 during stereomutation in 1,1-difluorocyclopropanes [85]. An important feature in the fluorinated system was the stabilization of the intermediate 2,2-difluorotrimethylene radicals due to the conjugation of the radical centers with the σ*-orbital of C–F bond, which can be represented

• opening was attributed to the stabilization of the developing cationic center by the +M effect of the fluorine atoms. The formation of the 2,2-difluorohomoallyl cation or 3,3-difluorocyclobutyl cation did not occur as a result of the strong destabilization by the −I effect of the fluorine atoms [96]. On

• . Such selectivity is caused by the possibility of the resonance stabilization of the biradical that is formed. If other reagents are absent, the biradical can rearrange and recombine, leading to isomerization of the starting material as was observed in the case of 1,1-difluoro-2,3-dialkylcyclopropanes

Exploring the possibility of using fluorine-involved non-conjugated electron-withdrawing groups for thermally activated delayed fluorescence emitters by TD-DFT calculation

• Dongyang Chen and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2021, 17, 210–223, doi:10.3762/bjoc.17.21

• to the greatest stabilization of the HOMO level at −5.89 eV. 2CzTRZ, and 2CzBP possess destabilized HOMO levels of −5.69 and −5.60 eV, respectively. The LUMOs of 2CzBN, 2CzTRZ and 2CzBP are each located on the bridging benzene ring and the electron-acceptor groups. The LUMO levels for 2CzBN, 2CzTRZ

Au(III) complexes with tetradentate-cyclam-based ligands

• Ann Christin Reiersølmoen,
• Thomas N. Solvi and
• Anne Fiksdahl

Beilstein J. Org. Chem. 2021, 17, 186–192, doi:10.3762/bjoc.17.18

• immediate color change into dark red/brown took place after addition of complex 6b-Au(III), indicating a low stabilization of the coordinated diphenyl ligand and a fast release of Au. The de-coordination resulted in full conversion within 15 min in both reactions (Table 1, entries 3 and 6), compared to 24

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

• BODIPY and the zinc porphyrin. The excited zinc porphyrin further transferred the electron to the fullerene, yielding a charge-separated state, with a long lifetime of 23 µs, indicating the charge stabilization of the supramolecular assembly. Thus, an artificial photocatalytic system that can mimic the

Supramolecular polymers with reversed viscosity/temperature profile for application in motor oils

• Jan-Erik Ostwaldt,
• Christoph Hirschhäuser,
• Stefan K. Maier,
• Carsten Schmuck and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2021, 17, 105–114, doi:10.3762/bjoc.17.11

• precoordinating effect to favor the cyclic form at lower temperatures. Thus, the alkylene-bridged monomer A shows no effect in terms of viscosity improvement. In contrast, the gem-dimethyl unit in monomer B leads to sufficient stabilization of the cyclic form at lower temperatures. This allows a ring–chain

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

• (THF renders the system more dynamic, lowering the activation barrier for a molecular reorganization [38][49]), resulting in long rigid fibers that interact (Figure 3E), leading to larger ordered arrays and templating the further assembly process. This, together with the better stabilization of the

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

• contributing to the emissive singlet state cannot be entirely ruled out; besides the obvious lack of solvent stabilization in frozen matrices, a TICT suppression at 77 K can also account for the blue-shifted emission in the frozen glassy matrix. However, further transient-absorption experiments and TD-DFT

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

• with one representative ligand from the series that such berberine–adenine conjugates exhibit a selective binding, specifically a selectivity to quadruplex DNA in competition with duplex DNA, and a preferential thermal stabilization of the G4-DNA forms 22AG and KRAS. Notably, the experimental data do

• ligands 4a–d and 22AG as well as for ligands 4a,b and a2 with log Kb values between 5.1 (4d and 22AG) and 5.9 (4a and 22AG). Thermal DNA denaturation analysis In addition, the thermal stabilization of the G4-DNA 22AG and a2 upon the binding of the ligands 4a–e was investigated by thermal DNA denaturation

• the two dyes. With this assay, the thermodynamic stabilization or destabilization of the quadruplex structure upon the complexation of the ligand is indicated by the shift of the melting temperature ΔTm. The analysis revealed an increasing stabilization of the quadruplex F21T toward dissociation with

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

• explained by the different stabilization of the respective ions (Figure 3). The abundance of m/z 68 is higher in isoprenyl esters due to the more stable allyl radical cation (Figure 3A). In contrast, prenyl ester fragmentation produces a stabilized allyl cation m/z 69 (Figure 3B), while isoprenyl esters

Selective and reversible 1,3-dipolar cycloaddition of 6-aryl-1,5-diazabicyclo[3.1.0]hexanes with 1,3-diphenylprop-2-en-1-ones under microwave irradiation

• Alexander P. Molchanov,
• Mariia M. Efremova,
• Mariya A. Kryukova and
• Mikhail A. Kuznetsov

Beilstein J. Org. Chem. 2020, 16, 2679–2686, doi:10.3762/bjoc.16.218

• pyrazolines 4a and 4b. At the same time, the reaction of DABCH 1b with chalcone 2a also gives adducts 3m and 3a and the same pyrazolines 4a and 4b. As it was marked in the literature, the reactions were expected to occur in ionic liquids more selectively than in organic solvents owing to the stabilization of

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

• potentials are shifted to lower values in pure DCE due to decreased charge stabilization. As expected, all TTF macrocycles display two reversible oxidation processes (E1/2ox1, TTF→TTF•+ and E1/2ox2, TTF•+→TTF2+). E1/2ox1 and E1/2ox2 of the free exTTFC8 and exTTFC7 crown ethers are anodically shifted compared

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• able to affect the structural transition and suppresses the formation of amyloid fibril formation [25]. The solution structure of O-glycosylated prion peptide was not shifted significantly, with only minor shifts seen in the vicinity of the glycosylation site. Yet there is a stabilization of the β

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• combination of two or more GCP moieties with variable linkers enables the construction of multivalent ligands geared towards a specific spot on protein surface, which by design can lead to either stabilization [42][43][44][45] or inhibition [46] of a given protein–protein interaction. The inhibition of the

• stabilization of the ligand by additional crystal contacts to neighboring proteins [6][18][20][21][22][26][27][28]. For some supramolecular ligands, like sulfonatocalix[8]arene or phosphonatocalix[6]arene, the tendency to bridge two protein interfaces that do not usually interact in solution goes so far that

• domain (p53TD). 15N-HSQC titrations of the ligand showed sequential binding of the ligand at both edges of the tetramer interface for both the wild-type protein and its R337H mutant. Binding of the calixarene to p53TD-R337H resulted in a significant stabilization of the tetramer interface, which was

Conformational preferences of fluorine-containing agrochemicals and their implications for lipophilicity prediction

• Daniela Rodrigues Silva,
• Joyce K. Daré and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2020, 16, 2469–2476, doi:10.3762/bjoc.16.200

• term overcomes the stabilization from hyperconjugation interactions (ΔENL), and classical electrostatic and steric interactions are the main factors governing conformational preferences of penoxsulam (I). It is worth mentioning that the structure of penoxsulam in the biological environment is already

Reactions of 3-aryl-1-(trifluoromethyl)prop-2-yn-1-iminium salts with 1,3-dienes and styrenes

• Thomas Schneider,
• Michael Keim,
• Bianca Seitz and
• Gerhard Maas

Beilstein J. Org. Chem. 2020, 16, 2064–2072, doi:10.3762/bjoc.16.173

• of 1a and 2,3-dimethylbutadiene (DMBD), the regioselectivity of which is as expected for a highly asynchronous transition state with effective stabilization of the positive charge or a two-step ionic process (vide infra). The high electrophilic power of the 1-CF3-substituted propyn-1-iminium ion