Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

• -bonding (Figure 6) [94]. A significant bottleneck for triple helix formation is the requirement for cytosine protonation to form the natural C+•G–C triplet. Because of the low pKa of cytosine (≈4.5), formation of the C+•G–C triplet is unfavorable at physiological pH, which severely destabilizes the

• pseudoisocytosine (J, Figure 6) in triplex-forming oligonucleotides, alleviating the problem of unfavorable cytosine protonation [95][96]. Nielsen and co-workers replaced Cs with Js in the Hoogsteen strand of their original design of bis-PNAs in 1995 [34]. While J demonstrated weaker binding than C at pH 5, J

• cationic RNA binding compounds, perhaps, because the protonation event is coupled with the Hoogsteen hydrogen bond formation. As a result, the partially protonated M strengthens the triple helix without compromising the sequence specificity of recognition [28][30][31]. As discussed above, guanidine groups

Methodologies for the synthesis of quaternary carbon centers via hydroalkylation of unactivated olefins: twenty years of advances

• Thiago S. Silva and
• Fernando Coelho

Beilstein J. Org. Chem. 2021, 17, 1565–1590, doi:10.3762/bjoc.17.112

• the protonation of a Pd(II) enolate intermediate by a proton source (HCl) generated at the cyclization step. The catalytic cycle begins with the enolic carbon of A attacking the complexed metal–olefin double bond in a turnover-limiting 6-endo-trig cyclization step (Scheme 3). The formed alkylpalladium

• (II) intermediate (B) then undergoes a sequence of reversible hydride β-eliminations [30] until the formation of the Pd(II) enolate (F), which, after protonation, irreversibly furnishes the product 2 and regenerates the Pd(II) catalyst. The lack of the usually kinetically favored 5-exo-trig

• product was also compatible with the reaction conditions. Alkylated phenols 61 were obtained after protonation/isomerization of the generated enolate intermediate (Scheme 24B). In 2018, the same authors continued to explore the synthetic opportunities offered by the enolate generated in MHAT radical

Breaking paracyclophane: the unexpected formation of non-symmetric disubstituted nitro[2.2]metaparacyclophanes

• Suraj Patel,
• Tyson N. Dais,
• Paul G. Plieger and
• Gareth J. Rowlands

Beilstein J. Org. Chem. 2021, 17, 1518–1526, doi:10.3762/bjoc.17.109

• , protonation might not be the key step, and the highly oxidizing nature of nitration conditions that can lead to the formation of a cationic intermediate via a radical cation might control this reaction [68]. A possible mechanism for the formation of 5 and 6 starts with protonation of 1 give the Wheland

• observed (Figure 6). As with the oxidation, we assume that the lower deck blocks approach from one face. Protonation of the adduct also occurs anti to the para ring. We suspect that this second addition favors the trans product over the cis rather than the para ring influencing the approach of the proton

One-step synthesis of imidazoles from Asmic (anisylsulfanylmethyl isocyanide)

• Louis G. Mueller,
• Allen Chao,
• Embarek AlWedi and
• Fraser F. Fleming

Beilstein J. Org. Chem. 2021, 17, 1499–1502, doi:10.3762/bjoc.17.106

• in 93% yield (Table 1, entry 6). Presumably the cyclization of 6 is followed by protonation at the former isocyanide carbon by HMDS (the emerging C-2 of the imidazole) with the reformed LiHMDS deprotonating C-4 to form the imidazole ring. Identifying LiHMDS as the optimal base allowed the scope of

Synthesis of 1-indolyl-3,5,8-substituted γ-carbolines: one-pot solvent-free protocol and biological evaluation

• Premansh Dudhe,
• Mena Asha Krishnan,
• Kratika Yadav,
• Diptendu Roy,
• Krishnan Venkatasubbaiah,
• Biswarup Pathak and
• Venkatesh Chelvam

Beilstein J. Org. Chem. 2021, 17, 1453–1463, doi:10.3762/bjoc.17.101

• in determining ring closure either via path a or path b. In path a, the protonation of the imine nitrogen in 7a by the conjugate acid (+ BH) leads to an electrophilic aromatic substitution at the 3-position of the indole unit to form a carbon–carbon bond in the intermediate 8. A further proton

• moderately polar dichloromethane and then highly polar DMSO (Table 2, Figure 3). The fluorescence quenching of 3ac in methanol is attributed to the partial protonation of the carboline unit's nitrogen atoms facilitated by polar-protic solvents [33]. The fluorescence lifetimes were measured by time-correlated

Photoinduced post-modification of graphitic carbon nitride-embedded hydrogels: synthesis of 'hydrophobic hydrogels' and pore substructuring

• Cansu Esen and
• Baris Kumru

Beilstein J. Org. Chem. 2021, 17, 1323–1334, doi:10.3762/bjoc.17.92

• due to amine groups' protonation on the polymer backbone via electrostatic attraction, and it responded to monovalent electrolyte with a higher ESR. With the increased pH, HGCM-PAA eventuated with enhanced ESR results arising from the dissociation of carboxylic acid groups. Swelling in saltwater

A comprehensive review of flow chemistry techniques tailored to the flavours and fragrances industries

• Guido Gambacorta,
• James S. Sharley and
• Ian R. Baxendale

Beilstein J. Org. Chem. 2021, 17, 1181–1312, doi:10.3762/bjoc.17.90

Synthetic accesses to biguanide compounds

• Oleksandr Grytsai,
• Cyril Ronco and
• Rachid Benhida

Beilstein J. Org. Chem. 2021, 17, 1001–1040, doi:10.3762/bjoc.17.82

• (pKaH = 13.6) [2]. Moreover, due to the stability of the monocation they display significantly lower second dissociation constants (pKa2H ≈ 3.0). X-ray crystallographic studies and modelling studies have shown that the first protonation occurs mainly on the N4 nitrogen atom, weakening substantially the

• intramolecular H-bond character. The second protonation rather takes place on the N3 nitrogen atom, causing planar character disruption and preventing H-bonding (Figure 2) [1]. Biguanide derivatives often display low melting points (mp = 136 °C for simple biguanide). However, above 130 °C, a concomitant thermal

• 1888 it was discovered that heating a mixture of cyanoguanidine and amine hydrochloride in a polar solvent (mainly alcohols) led to the formation of biguanide. Indeed, proton exchanges at high temperatures may lead to the activation of cyanoguanidine by protonation, and the subsequent attack of the

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

•  18). A sequence of reactions involving elimination of a proton from 83, treatment of 84 with an alkoxide, and protonation of the resulting enolate delivered thermodynamically favored equatorial ester 80 and 81. The highly diastereoselective Brønsted superacid-catalyzed Prins cyclization of

Microwave-assisted multicomponent reactions in heterocyclic chemistry and mechanistic aspects

• Shivani Gulati,
• Stephy Elza John and
• Nagula Shankaraiah

Beilstein J. Org. Chem. 2021, 17, 819–865, doi:10.3762/bjoc.17.71

• -proliferative activity against tumor cell lines leading to the discovery of new lead compounds (Scheme 6). A tentative mechanism in Scheme 7 depicts the formation of iminium ion A from the reaction between 19 and 20 after the intramolecular protonation by carboxylic acid. The A conformer stabilized by

• the allene intermediate D. Finally, an intramolecular 6π-electrocyclization and tautomerism results in the desired products 143a. The authors proposed a mechanism for azepinoindoles (Scheme 59) [128] wherein acid-catalyzed protonation of arylglyoxal monohydrate followed by dehydration and addition of

Synthesis of β-triazolylenones via metal-free desulfonylative alkylation of N-tosyl-1,2,3-triazoles

• Soumyaranjan Pati,
• Renata G. Almeida,
• Eufrânio N. da Silva Júnior and
• Irishi N. N. Namboothiri

Beilstein J. Org. Chem. 2021, 17, 762–770, doi:10.3762/bjoc.17.66

• , triazoles 1b and 1c containing electron donating 4-tolyl and 4-methoxyphenyl groups did not deliver the products 3b and 3c, respectively, even after prolonged reaction time. This is attributable to the greater reactivity of their corresponding triazolyl anion which preferred protonation over Michael

α,γ-Dioxygenated amides via tandem Brook rearrangement/radical oxygenation reactions and their application to syntheses of γ-lactams

• Mikhail K. Klychnikov,
• Radek Pohl,
• Ivana Císařová and
• Ullrich Jahn

Beilstein J. Org. Chem. 2021, 17, 688–704, doi:10.3762/bjoc.17.58

• equilibrium (Table 4, entries 7 and 11 vs entries 1 and 9). Attempts to influence the diastereomeric ratio of the cyclization products by irreversible stoichiometric deprotonation of the lactams 12d,f,i by LDA at −78 °C and subsequent protonation by methanol did not lead to substantial changes of the initial

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

• the data for 1,3-di-alkyltetrazolium-5-aminide salts as described in the literature [25][26][28][32][33][34][35]. First of all, it should be mentioned that the formation of the salt from the corresponding mesoionic compound followed by protonation of the endocyclic N atom in all cases presented in

• ), showing that the largest negative charge and the deepest minimum of MESP of 8a are located near the exocyclic atom N5, and hence it is the most preferable protonation site in 8a. The TD-tHCTHhyb/6-311+G(2d,p) calculated UV–vis spectra of compound 8a in n-hexane, THF, chloroform, methanol, and water are

• of a hydrogen bond between the exocyclic N5 atom and the solvent is taken into account (model structure in Figure 4b). For the methanol and water solutions, the agreement between the calculated and experimental spectra is observed only when the protonation of the N5 atom is taken into account (model

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

• , and triflate 45f, which was isolated after basic workup of the reaction (59% yield) [63]. Hence, protonation of 44 led to dialkoxysulfonium triflate 47 along with the release of alcohol 9g. The subsequent formation of the excellent sultine leaving group 46 (assumed to be as good of a leaving group as

• , Pittman, et al. investigated the protonation of a variety of trifluoromethyl ketones in a superacid [35][91]. Trifluoromethyl ketone protonation was observed by NMR spectroscopy at −60 °C in a superacidic FSO3H–SbF5–SO2 solution (Scheme 34). The 19F chemical shift variation for the generated oxygen

• ] (Scheme 38). In these reactions, oxygen-stabilized α-(trifluoromethyl)carbenium ions 142 are supposed to be generated by protonation or Lewis acid activation of the starting ketones. Klumpp et al. explored the reactivity of CF3-substituted superelectrophiles (defined as multiply charged cationic

Hydrazides in the reaction with hydroxypyrrolines: less nucleophilicity – more diversity

• Dmitrii A. Shabalin,
• Evgeniya E. Ivanova,
• Igor A. Ushakov,
• Elena Yu. Schmidt and
• Boris A. Trofimov

Beilstein J. Org. Chem. 2021, 17, 319–324, doi:10.3762/bjoc.17.29

• traces of the 1,4-dihydropyridazine 4af were detected following the two-step, one-pot protocol (Scheme 3). Apparently, the basic pyridine nitrogen atoms of intermediate 3af deactivate the acid catalyst, whilst the use of 3.4 equiv of TFA causes the full protonation of the pyridine rings thus making them

• (Scheme 4). A proposed mechanism for the recyclization of hydroxypyrrolines 1 with hydrazides 2 is shown in Scheme 5. The protonation of the starting hydroxypyrroline 1 with TFA leads to the formation of cation A, which reacts with hydrazide 2 to give the pyrrolidine derivative B. The latter undergoes a

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

• -fluoropyrroles 142 (Scheme 62) [113]. The reaction involved the gem-difluorocyclopropyl ketones 143 and nitriles 144. It was proposed that the protonation of the ketone with triflic acid led to a partial ring opening of the gem-difluorocyclopropyl ketone to generate a carbocation-like center that was stabilized

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

•  4. Cycle I starts with the excitation of the photoacid by irradiation at λ = 300 nm with the aim to achieve the protonation of the hydroxyflavylium molecule, and the subsequent opening to the Cc form. After keeping the assemblies in the dark and addition of HCl, assemblies as in state C should

Novel library synthesis of 3,4-disubstituted pyridin-2(1H)-ones via cleavage of pyridine-2-oxy-7-azabenzotriazole ethers under ionic hydrogenation conditions at room temperature

• Romain Pierre,
• Anne Brethon,
• Sylvain A. Jacques,
• Aurélie Blond,
• Sandrine Chambon,
• Sandrine Talano,
• Catherine Raffin,
• Branislav Musicki,
• Claire Bouix-Peter,
• Loic Tomas,
• Gilles Ouvry,
• Rémy Morgentin,
• Laurent F. Hennequin and
• Craig S. Harris

Beilstein J. Org. Chem. 2021, 17, 156–165, doi:10.3762/bjoc.17.16

• ). No product was observed via direct SNAr using KOH (Table 1, entry 1) [3]. Acidic conditions (Table 1, entries 2–5) [4], where we can expect protonation thus activation of the pyridine ring towards nucleophilic attack, resulted in only traces of product along with hydrolysis of the amide moiety at C-3

• protonation and activation of the pyridine towards SNAr with HOAt (Table 4). Exploration of the C-4 amine vector As we moved forwards in the program, we were eager to develop our understanding of SARs (structure–activity relationships) from the C-4 vector. Although we could have adopted the same methodology

• the C-2–OAt ether presumably due to the lower basicity of 26 compared to 8, therefore, activation via protonation of the pyridine was not occurring. With a view to capitalize on our knowledge acquired so far on this scaffold, we decided to force the transformation to the OBt ether by SNAr under basic

Direct synthesis of anomeric tetrazolyl iminosugars from sugar-derived lactams

• Michał M. Więcław and
• Bartłomiej Furman

Beilstein J. Org. Chem. 2021, 17, 115–123, doi:10.3762/bjoc.17.12

• proton donor in the reaction mixture. Intriguingly, this behavior is inconsistent with the generally accepted mechanism of this transformation, which assumes the hydrolysis of TMSN3 to HN3 and activation of the imine species by protonation. Scheme 7 presents our proposal for the possible course of the

Synthesis of aryl 2-bromo-2-chloro-1,1-difluoroethyl ethers through the base-mediated reaction between phenols and halothane

• Yukiko Karuo,
• Ayaka Kametani,
• Atsushi Tarui,
• Kazuyuki Sato,
• Kentaro Kawai and
• Masaaki Omote

Beilstein J. Org. Chem. 2021, 17, 89–96, doi:10.3762/bjoc.17.9

• carbon atom is a reasonable process to forward the reaction with the generation of carbanion 6. Finally, the protonation of 6 by 1 or other acidic compounds, such as water molecules present in the reaction medium, would provide 2. Conclusion We exploited the reaction of various phenols with halothane to

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

• assembly pathway rather than the equilibration at a given solvent composition. Apparently, hydrophobic interactions dominate the self-assembly, mitigating the repulsion of the charged carboxylate groups (partial protonation of the carboxylate moieties can also not be ruled out as a result of the

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

• reactivity of compounds 9. Its protonation makes the formation of a key cyclization intermediate 11 difficult. It is known that the [n]helicenes with at least one five-membered heteroaromatic ring need n ≥ 6 to become intrinsically chiral [9][10]. High-performance liquid chromatography on chiral stationary

Synthesis of tetrafluorinated piperidines from nitrones via a visible-light-promoted annelation reaction

• Vyacheslav I. Supranovich,
• Igor A. Dmitriev and
• Alexander D. Dilman

Beilstein J. Org. Chem. 2020, 16, 3104–3108, doi:10.3762/bjoc.16.260

• substitution could be catalyzed by iodide anions accumulating in the reaction mixture. Finally, the deoxygenation of the N-oxide fragment may proceed via consecutive protonation and electron-transfer steps [28]. Conclusion In summary, a one-step method for the synthesis of tetrafluorinated piperidines starting

Pentannulation of N-heterocycles by a tandem gold-catalyzed [3,3]-rearrangement/Nazarov reaction of propargyl ester derivatives: a computational study on the crucial role of the nitrogen atom

• Giovanna Zanella,
• Martina Petrović,
• Dina Scarpi,
• Ernesto G. Occhiato and
• Enrique Gómez-Bengoa

Beilstein J. Org. Chem. 2020, 16, 3059–3068, doi:10.3762/bjoc.16.255

• suggested that the presence of water can catalyze this reaction (proton-transport catalysis strategy) through a two-step deprotonation/protonation process [11][21][41][42][44], but in our study, preliminary calculations in the presence of water did not improve the results in Figure 5. Therefore, we focused

• protonation/deprotonation sequence. Finally, although we did not study in detail the acetate hydrolysis from XV to 15, we could confirm the higher stability (by more than 6 kcal⋅mol−1) of 15 relative to the enone isomer arising from XII, in agreement again with the experimental results. Experimental

Synthesis of imidazo[1,5-a]pyridines via cyclocondensation of 2-(aminomethyl)pyridines with electrophilically activated nitroalkanes

• Dmitrii A. Aksenov,
• Nikolai A. Arutiunov,
• Vladimir V. Maliuga,
• Alexander V. Aksenov and
• Michael Rubin

Beilstein J. Org. Chem. 2020, 16, 2903–2910, doi:10.3762/bjoc.16.239

• , entries 2 and 3). To the contrary, an attempt to carry out the reaction in 80% PPA provided a conversion of only 6% even at 140 °C (Table 1, entry 4), whereas no reaction was observed in 100% orthophosphoric acid (Table 1, entry 5). Evidently, under acidic conditions, protonation of the primary amino