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

• parallel triple helices and limits their applications in biological systems. Two obvious strategies to solve this problem are to modify the cytosine heterocycle to either 1) increase the pKa or 2) create neutral analogues of protonated cytosine. In the latter strategy, Ono et. al. introduced

• subtle modulation of the pKa and better π-stacking [99]. Several other research groups have further increased the pKa value by removing electronegative substituents from C arriving at derivatives of 2-aminopyridine (M, Figure 6) as more basic nucleobases that improve binding of triplex-forming

Chemical synthesis of C6-tetrazole ᴅ-mannose building blocks and access to a bioisostere of mannuronic acid 1-phosphate

• Eleni Dimitriou and
• Gavin J. Miller

Beilstein J. Org. Chem. 2021, 17, 1527–1532, doi:10.3762/bjoc.17.110

• has a similar pKa to a carboxylate yet provides enhanced hydrogen bonding capability and alternative prospects for permeability due to a larger hydrophobic region enabling improved lipophilic contacts. These alternative properties and a prospect for their inclusion within new alginate fragments led us

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

• showed traces of [2.2]metaparacyclophane (3). A quick investigation of the strengths of acids required to cause rearrangement revealed that both triflic acid (pKa = −14) and perchloric acid (pKa = −10) were sufficiently strong to cause rearrangement while nitric (−1.3), sulfuric (−3.0), and acetic acids

• (4.8) were all too weak. While these results seem to make sense, when we compare the pKa values, they do not explain why a mixture of nitric and sulfuric acids causes rearrangement. It is possible that we are comparing the wrong values. pKa measures acidity in water. Under our reaction conditions it

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

• represented as the major tautomer 1b with the conjugated system –C=N–C=N– and the numbering of the different atoms will be established as depicted in Figure 1. Biguanides are relatively strong bases, with pKa1H ≈ 11.5 (pKa of the conjugate acid of biguanide); however, significantly less basic than guanidine

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

• additive having a similar pKa value to that of H2SO3 that is likely to be present in liquid SO2 (Table 2, entries 3 and 8) [55]. Thus, the previously considered probable contributory effect of H2SO3 can be ruled out. Further, in combination with polar aprotic Lewis basic solvents (MeCN, THF) [67] sulfur

Synthesis of (Z)-3-[amino(phenyl)methylidene]-1,3-dihydro-2H-indol-2-ones using an Eschenmoser coupling reaction

• Lukáš Marek,
• Lukáš Kolman,
• Jiří Váňa,
• Jan Svoboda and
• Jiří Hanusek

Beilstein J. Org. Chem. 2021, 17, 527–539, doi:10.3762/bjoc.17.47

• , like DMSO or DMF or in polar protic solvents like alcohols. For carbon acids the ΔpKa is 12.9 between ACN and DMSO but the ΔpKa is only −1.5 between DMF and DMSO [34]. A change of the solvent from acetonitrile to DMF should therefore decrease the pKa by ca. 11 units. In polar protic solvents (e.g., in

• substituent (4-OCH3; entry 2 in Table 3) enhances the yield to 88%. From these observations it is clear that the influence of R4 is much stronger than the influence of the substituent R1 (cf. entries 1 and 10–13 or entries 6 and 14–17 in Table 3). The attached EWG substituent R4 lowers the pKa (and thus also

• . This result is in accordance with the relatively low nucleofugality of diethyl phosphate which is roughly quantified by the pKa = 1.39 of its conjugated acid [43]. We have also examined an addition of 20% of tetrabutylammonium bromide as a nucleophilic catalyst which could transform the phosphate 1g in

1,2,3-Triazoles as leaving groups: S_NAr reactions of 2,6-bistriazolylpurines with O- and C-nucleophiles

• Dace Cīrule,
• Irina Novosjolova,
• Ērika Bizdēna and
• Māris Turks

Beilstein J. Org. Chem. 2021, 17, 410–419, doi:10.3762/bjoc.17.37

• deprotonated acetylacetone and diphenylmethane. Even there are reports on SNAr reactions of acetylacetone with purines and pyrimidines [56][80], in our hands only polymerization of acetylacetone was observed. On the other hand, the diphenylmethane anion (pKa 32; DMSO [81]) apparently is too basic and

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

• amount of the moderately acidic (S)-TRIP (pKa = 3–4 in DMSO [113][114]) in dichloromethane afforded the chiral α-(trifluoromethyl)aminoaryl derivatives 177 in an excellent yield and enantiomeric excess (Scheme 42). The authors proposed that hemiacetal 175 and amine 176 react under the reaction conditions

Regioselective chemoenzymatic syntheses of ferulate conjugates as chromogenic substrates for feruloyl esterases

• Olga Gherbovet,
• Fernando Ferreira,
• Apolline Clément,
• Mélanie Ragon,
• Julien Durand,
• Sophie Bozonnet,
• Michael J. O'Donohue and
• Régis Fauré

Beilstein J. Org. Chem. 2021, 17, 325–333, doi:10.3762/bjoc.17.30

• stability over a wide pH value range (up to pH 9.0), irrespective of the temperature. This is because in compound 12, the ferulate moiety is not directly linked to the good leaving group 4NTC (pKa = 6.61 [40]). Instead, it is bonded to the linker with a pKa value that can be compared either to that of

• glycerol (pKa = 13.61) or ʟ-arabinose (pKa = 11.31) [41], meaning that it is a poor leaving group. Moreover, our observations regarding the linker stability are consistent with the known stability of the ester linkages under basic conditions. The usefulness of 4NTC–linker–Fe (12) for the characterization

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

• poly(allylamine) at pH 7.0. At this pH value, both the polyelectrolyte and also the photoacid are protonated [81][82]. Upon irradiation, the pKa of the photoacid decreases to pKa = −2.6 leading to deprotonation [82]. In addition to the electrostatic self-assembly of the photoacid and the

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

• –Cl amide product 14. Closer inspection of the reaction progression by UV-LC–MS revealed the expected product 14 is formed first and is slowly transformed to 15 overnight. We postulated that the acidic HOAt (pKa = 3.76) liberated from the coupling reaction must be protonating thus activating the basic

• obtained for the 3-(2-(dimethylamino)ethyl)aniline analogue 24j was due to the fact the 2-Cl-Py did not transform to the OAt ether in situ and the subsequent hydrolysis step was very sluggish. We postulate that the presence of the more basic N,N,-dimethylaminoethyl side chain (pKa ≈11) must prevent

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

• ], producing two different modes of binding: pH-dependent and salt-dependent binding mechanisms. In a pH-dependent binding mechanism, an overall proton is either released or taken up during the protein interaction due to the binding-induced pKa shift of acidic or basic amino acids present at the complex

Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties

• Anka Utama Putra,
• Deniz Çakmaz,
• Nurgül Seferoğlu,
• Alberto Barsella and
• Zeynel Seferoğlu

Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189

• pKa determination of 8 in aqueous solution The pH value of aqueous systems is important to maintain the physiological stability, both inside and outside a living organism. The hydroxide anion plays a special and critical role in the ecosystem. Therefore, the necessity to develop new pH sensors is

• was accompanied by darkening purple color shifts of the solutions with increased pH value. However, the slight increase in the fluorescence was hardly noticeable below 365 nm UV light as is shown in Figure 8. The pKa of 8 was calculated by using a spectrophotometric method and was 8.22 ± 0.03 (Figure

• stated earlier for the UV–vis absorption study at room temperature (25 °C). All photographs were taken using a SONY RX100 pocket camera with ISO values of 200 and variable aperture at “Program Auto” mode. pKa Determination of dye 8 The solubility of dye 8 in deionized water was investigated by studying

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• GCP moiety by itself does not interact with DNA/RNA but, if combined with oligomers [15][16] or attached to the aryl moiety containing at least two aromatic rings [17], it will ensure efficient DNA/RNA binding. Moreover, due to the weakly acidic pKa = 6 of GCP, interactions and consequently

Photosensitized direct C–H fluorination and trifluoromethylation in organic synthesis

• Shahboz Yakubov and
• Joshua P. Barham

Beilstein J. Org. Chem. 2020, 16, 2151–2192, doi:10.3762/bjoc.16.183

• a positive impact on the biological absorption and distribution. Moreover, C–H/C–F substitution strongly decreases the basicity of neighboring amines (and lowers the pKa by a similar increment) due to the σ-inductive effect of F. This results in i) a higher oral bioavailability [19], ii) a potential

Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups

• Benjamin Jeffries,
• Zhong Wang,
• Robert I. Troup,
• Anaïs Goupille,
• Jean-Yves Le Questel,
• Charlene Fallan,
• James S. Scott,
• Elisabetta Chiarparin,
• Jérôme Graton and
• Bruno Linclau

Beilstein J. Org. Chem. 2020, 16, 2141–2150, doi:10.3762/bjoc.16.182

• ]. Apart from a slight shape/volume alteration caused by the significant change in bond angles and the deletion of two hydrogen atoms, this bioisosteric modification also usually results in improved metabolic stability, increased rigidity and, due to its electron-withdrawing nature, pKa modulation of

• -position (5), the introduction of the oxetanyl group leading to 6 induces a significant pKa(H) decrease. While the reduction in logP is still observed, the larger proportion of unprotonated substrate leads to a logD7.4 increase. Aliphatic fluorination can also be employed to decrease lipophilicities [6][19

Azo-dimethylaminopyridine-functionalized Ni(II)-porphyrin as a photoswitchable nucleophilic catalyst

• Jannis Ludwig,
• Julian Helberg,
• Hendrik Zipse and
• Rainer Herges

Beilstein J. Org. Chem. 2020, 16, 2119–2126, doi:10.3762/bjoc.16.179

• , spiropyranes, and stilbenes [2]. Diarylethenes were reported in the context of photoswitchable catalysis as inhibitors of the Karstedt´s catalyst [3] and for pKa modulation in acid–base-controlled processes [4]. Molecular motors for stereodivergent anion binding catalysis [5], azopeptides for the acetylation

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• ]. Firstly, in comparison to simple guanidinium cations 2 (pKa 12.5) and ammonium cations 3 (pKa 10.5), the Schmuck cation has a lower pKa value of 7 to 8 due to the increased acidity of acylguanidiniums, which favors the formation of stronger hydrogen-bonded ion pairs (Figure 1, magenta part). Secondly, the

• an endosomal pathway. The low pKa value of the four GCP moieties could result in an improved buffering capacity, which could facilitate endosomal escape by the proton-sponge effect [28]. Significant inhibition of DNA transfection by bafilomycin (a macrolide antibiotic that can block the endosomal

Design, synthesis and application of carbazole macrocycles in anion sensors

• Alo Rüütel,
• Ville Yrjänä,
• Sandip A. Kadam,
• Indrek Saar,
• Mihkel Ilisson,
• Astrid Darnell,
• Kristjan Haav,
• Tõiv Haljasorg,
• Lauri Toom,
• Johan Bobacka and
• Ivo Leito

Beilstein J. Org. Chem. 2020, 16, 1901–1914, doi:10.3762/bjoc.16.157

• increase between pH 2.8 and 6.8 due to the deprotonation of acetic acid (pKa = 4.76) [34], which should result in a decrease in the measured potentials. The measured potentials were then expected to remain constant after pH 6.8 since the activity of acetate should no longer appreciably change with the

Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines

• Vladimir Kubyshkin

Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151

• trifluoromethyl- or a difluoromethylene group. This orientation of the substituents explains the observed trends in the pKa values, lipophilicity, and the kinetics of the amide bond rotation. The study also provides a set of evidences that the transition state of the amide-bond rotation in peptidyl-prolyl favors

• compounds 5 and 6 follow generally similar chiral bias to 3 and 4. The pKa data for the free amino acids shows that there is an identical reduction of the pKa values from fluorination (Figure 10B and C). It was then found that neither the side-chain conformation markers (J coupling at 2-CH) nor the trans

Facile synthesis of 7-alkyl-1,2,3,4-tetrahydro-1,8-naphthyridines as arginine mimetics using a Horner–Wadsworth–Emmons-based approach

• Rhys A. Lippa,
• John A. Murphy and
• Tim N. Barrett

Beilstein J. Org. Chem. 2020, 16, 1617–1626, doi:10.3762/bjoc.16.134

• ; Introduction Tetrahydronaphthyridines are prominent in peptidomimetic pharmaceuticals as arginine mimetics and they are widely used in Arg–Gly–Asp (RGD) peptide mimetics such as αv integrin inhibitors [1]. Tetrahydronaphthyridines represent less basic but more permeable alternatives to arginine (pKa ≈ 7 versus

• 1). This may be due the disparity in the pKa between the base and tetrahydro-1,8-naphthyridine (based on 2-aminopyridine, the pKa of the saturated ring nitrogen is expected to be ≈28) [20]. Similarly, nitrogen-centred bases (Table 1, entries 2 and 3) gave moderate conversions to phosphoramidate 13

• due to a close match of the pKa of tetrahydronaphthyridine 11 and the pKaH of the base; s-BuLi also gave reasonable conversion to the product (Table 1, entry 4) albeit contaminated with some impurities. This could likely be attributed to the thermal instability of the base and/or lithiated

The McKenna reaction – avoiding side reactions in phosphonate deprotection

• Katarzyna Justyna,
• Joanna Małolepsza,
• Damian Kusy,
• Waldemar Maniukiewicz and
• Katarzyna M. Błażewska

Beilstein J. Org. Chem. 2020, 16, 1436–1446, doi:10.3762/bjoc.16.119

• excess Et3N makes compound 12 more susceptible to N-alkylation. The reason for this observation might be the significantly higher basicity of Et3N (pKa 10.65) compared to 12, as approximated based on the pKas of representative amines resembling the structure of compound 12, Me3N (pKa 9.76) and

• allyldimethylamine (pKa 8.72), respectively [44]. This effect was reinforced by the higher nucleophilicity of the nitrogen atom in 12 compared with Et3N, as we deduced by comparison of model tertiary amines: Me3N (in MeCN: N 23.05, sN 0.45) and Et3N (in MeCN: N 17.10, sN 0.52) [45][46]. On the other hand, the lower

Disposable cartridge concept for the on-demand synthesis of turbo Grignards, Knochel–Hauser amides, and magnesium alkoxides

• Mateo Berton,
• Kevin Sheehan,
• Andrea Adamo and
• D. Tyler McQuade

Beilstein J. Org. Chem. 2020, 16, 1343–1356, doi:10.3762/bjoc.16.115

• ⋅LiCl solution, in the collection flask, away from a heat source. System scope: Bis(trimethylsilyl)amine (HMDS), diphenylamine (Ph2NH), aniline (PhNH2), and 2,2,6,6-tetramethylpiperidine (TMPH) were selected as substrates. Ph2NH, HMDS, and PhNH2 due to their lower pKa (25, 30, and 31, respectively, in

• DMSO) [59] and TMPH due to its broad application in synthesis (Knochel–Hauser base, pKa = 37 in DMSO) [47][59][60][61][62][63][64][65][66][67][68][69]. Excellent yields were obtained: HMDSMgCl⋅LiCl 1.15 M (98%), Ph2NMgCl⋅LiCl 1.16 M (97%), and PhNHMgCl⋅LiCl (1.15 M, 96%, Table 4, entries 1–3). For TMPH

The charge-assisted hydrogen-bonded organic framework (CAHOF) self-assembled from the conjugated acid of tetrakis(4-aminophenyl)methane and 2,6-naphthalenedisulfonate as a new class of recyclable Brønsted acid catalysts

• Svetlana A. Kuznetsova,
• Alexander S. Gak,
• Yulia V. Nelyubina,
• Vladimir A. Larionov,
• Han Li,
• Michael North,
• Vladimir P. Zhereb,
• Alexander F. Smol'yakov,
• Artem O. Dmitrienko,
• Michael G. Medvedev,
• Igor S. Gerasimov,
• Ashot S. Saghyan and
• Yuri N. Belokon

Beilstein J. Org. Chem. 2020, 16, 1124–1134, doi:10.3762/bjoc.16.99

• NDS and of one equivalent of TAPM at ambient temperature immediately produced F-1 as a white precipitate (Scheme 1). The pKa (in water) of NDS is expected to be −11 to −10, by analogy with the pKa of polystyrene sulfonic acids [12]. The four pKas of the conjugated acids of TAPM were calculated (see

• water and dichloromethane. The methanol and dichloromethane mixture did not need to be considered as F-1 was not soluble in this mixture. For the other two solvent mixtures, the four ammonium groups of the protonated form of TAPM had pKa values in water (according to the calculations discussed above

• × 10−2 M in water. Assuming that the average pKa value of the ammonium groups of the protonated form of TAPM was around 4.0, the pH value of the solution would be between 4 and 5. It is therefore most likely that F-1 operated via the general acid catalysis mechanism in this solvent mixture. As the pKa

Efficient synthesis of piperazinyl amides of 18β-glycyrrhetinic acid

• Dong Cai,
• ZhiHua Zhang,
• Yufan Meng,
• KaiLi Zhu,
• LiYi Chen,
• ChangXiang Yu,
• ChangWei Yu,
• ZiYi Fu,
• DianShen Yang and
• YiXia Gong

Beilstein J. Org. Chem. 2020, 16, 798–808, doi:10.3762/bjoc.16.73

• factor is that the acidity of chloroacetic acid (pKa = 2.87) was stronger than that of acetic acid (pKa = 4.76). The procedure for the generation of byproduct 11 was similar to N-Boc-deprotection using trifluoroacetic acid. The effective synthesis of compound 10 was then explored (Table 3). In our