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

• metabolic enzymes. In addition, it has been shown to irreversibly inhibit isocitrate lyase 1 (ICL1) from Mycobacterium tuberculosis [40], and key metabolic protein for these pathogens [41]. Isocitrate lyases convert isocitrate to glyoxylate and succinate. Deprotonation of 3NP (pKa = 9.0) results in the

• transition analog of carboxylate groups, resulting in nitro compounds also acting as tight-binding reversible inhibitors [42]. Deprotonation of NNG also results in formation of the corresponding nitronate, albeit with a pKa of 6.6 [24], far lower than that for 3-NP (Scheme 2). Therefore, a much larger

Advancements in hydrochlorination of alkenes

• Daniel S. Müller

Beilstein J. Org. Chem. 2024, 20, 787–814, doi:10.3762/bjoc.20.72

• ) [78]. Another advantage of the MH HAT process is that the α-C–H bond in the corresponding radical is comparatively stable, whereas a carbocation has superacidic α-C–H bonds with a pKa of ≈ −17 [79]. Therefore, polar hydrochlorination reactions are in competition with elimination reactions which is not

Synthesis of 2,2-difluoro-1,3-diketone and 2,2-difluoro-1,3-ketoester derivatives using fluorine gas

• Alexander S. Hampton,
• David R. W. Hodgson,
• Graham McDougald,
• Linhua Wang and
• Graham Sandford

Beilstein J. Org. Chem. 2024, 20, 460–469, doi:10.3762/bjoc.20.41

• estimated from pKa differences between acidic species and potential base species. The pKa(MeCN) for dibenzoylmethane (1a) can be estimated from pKa(DMSO) [50], where pKa(MeCN) = pKa(DMSO) + 12.9 = 13.4 + 12.9 = 26.3. Mayr and co-workers have shown the 2-fluoro-substituted species to be only slightly less

• this base that accelerates enolization of 2a–i-keto to allow difluorination to occur. The fluoride ion is a relatively strong base (pKa(MeCN) of HF is ≈25 based on pKa(DMSO) [55][56]), especially when formed in situ under anhydrous conditions, where solvation of fluoride ion is not possible. Since the

• pKa(MeCN) of 1a-keto is ≈26.3, and we expect a pKa(MeCN) of 2a-keto to be similar in value [51][52], we suggest fluoride ion may be sufficiently basic to cause significant acceleration of the deprotonation of 2a–i-keto and allow formation of 2a–i-enolates, which then react rapidly with fluorine gas

Facile approach to N,O,S-heteropentacycles via condensation of sterically crowded 3H-phenoxazin-3-one with ortho-substituted anilines

• Eugeny Ivakhnenko,
• Vasily Malay,
• Pavel Knyazev,
• Nikita Merezhko,
• Nadezhda Makarova,
• Oleg Demidov,
• Gennady Borodkin,
• Andrey Starikov and
• Vladimir Minkin

Beilstein J. Org. Chem. 2024, 20, 336–345, doi:10.3762/bjoc.20.34

• conditions. The reactions proceed readily in refluxing acidified (pKa = 1–5) ethanol solutions of the amine hydrochlorides to give 2-monosubstituted derivatives of 3H-phenoxazin-3-ones in a moderate yield [10][17]. In the present work, we intended to explore the reaction of 3H-phenoxazin-3-ones with aromatic

Additive-controlled chemoselective inter-/intramolecular hydroamination via electrochemical PCET process

• Kazuhiro Okamoto,
• Naoki Shida and
• Mahito Atobe

Beilstein J. Org. Chem. 2024, 20, 264–271, doi:10.3762/bjoc.20.27

• , entry 3); thus, the phosphate base plays a crucial role in N-alkylation, while its basicity is insufficient to promote aza-Michael addition (pKa of the conjugate acid of the phosphate base is 1.72 in H2O) [12]. Furthermore, N-alkylation proceeded in a divided cell (anodic chamber); thus, the possibility

• current (Figure 2B, blue line). We considered that the inter- and intramolecular chemoselectivities were derived from the pKa of the proton sources. The pre-organization of the amide substrate and phosphate bases is an important process in PCET [13]. Recently, Gschwind et al. published a detailed NMR

• spectroscopic analysis of a PCET-mediated hydroamination reaction, which indicated that the pKa of the proton source (PhSH or PhOH in the study) determines the size of the hydrogen bond complex. PhSH as the more acidic additive (pKa = 6.62 in H2O) provided better results in the PCET-induced intramolecular

Substitution reactions in the acenaphthene analog of quino[7,8-h]quinoline and an unusual synthesis of the corresponding acenaphthylenes by tele-elimination

• Ekaterina V. Kolupaeva,
• Narek A. Dzhangiryan,
• Alexander F. Pozharskii,
• Oleg P. Demidov and
• Valery A. Ozeryanskii

Beilstein J. Org. Chem. 2024, 20, 243–253, doi:10.3762/bjoc.20.24

• forced to strongly repel each other in space, can lead to a sharp increase in basicity [8]. Thus, quino[7,8-h]quinoline (3), first obtained in the Staab group [9], already exceeds in basicity not only quinoline itself, but also 1,8-bis(dimethylamino)naphthalene (1, “proton sponge”) (Scheme 1; pKa values

• comparison, in the protonated cation of the starting diazine 5 in CD3CN, the chemical shift of the “acidic” proton is observed at 18.02 ppm [15]. Next, we evaluated the pKa value of base 14 by a competitive method in acetonitrile (NMR transprotonation involving an equivalent amount of "proton sponge" 1 as a

• reference compound) [6]. Additionally, we measured the basicity of unsubstituted compound 5 in acetonitrile for the first time by the same method and the results are given in Figure 7; the pKa values for compounds 1 and 3 are taken from references [24][25]. As can be seen, although diazine 14 turned out to

Aldiminium and 1,2,3-triazolium dithiocarboxylate zwitterions derived from cyclic (alkyl)(amino) and mesoionic carbenes

• Nedra Touj,
• François Mazars,
• Guillermo Zaragoza and
• Lionel Delaude

Beilstein J. Org. Chem. 2023, 19, 1947–1956, doi:10.3762/bjoc.19.145

• acetonitrile (Scheme 4). However, all our attempts to purify compounds 6c–f by recrystallization or column chromatography remained unsuccessful. Several studies have shown that metal alkoxides, such as potassium tert-butoxide (pKa = 22), were basic enough to deprotonate 1,2,3-triazolium salts (pKa ≈ 22–23

• ) depending on the nature of their aliphatic or aromatic substituents, and that the use of the stronger base KN(SiMe3)2 (pKa = 26) was not always mandatory [25][69][70]. Grubbs, Bertrand et al. also noticed that treating 1-benzyl-3-methyl-4-phenyl-1H-1,2,3-triazolium iodide with KOt-Bu did not afford the

Selectivity control towards CO versus H₂ for photo-driven CO₂ reduction with a novel Co(II) catalyst

• Lisa-Lou Gracia,
• Philip Henkel,
• Olaf Fuhr and
• Claudia Bizzarri

Beilstein J. Org. Chem. 2023, 19, 1766–1775, doi:10.3762/bjoc.19.129

• solvents and with water, it has been used in a large variety of (electro)chemical reactions [53]. The hydroxy group of this alcohol has a pKa of 9.3 [54][55], so we can expect that it is a suitable proton donor for this kind of reaction. We performed the photocatalytic CO2 reduction by dissolving in 5 mL 1

Effects of the aldehyde-derived ring substituent on the properties of two new bioinspired trimethoxybenzoylhydrazones: methyl vs nitro groups

• Dayanne Martins,
• Roberta Lamosa,
• Talis Uelisson da Silva,
• Carolina B. P. Ligiero,
• Sérgio de Paula Machado,
• Daphne S. Cukierman and
• Nicolás A. Rey

Beilstein J. Org. Chem. 2023, 19, 1713–1727, doi:10.3762/bjoc.19.125

• physiological conditions since the presence of this substituent significantly affects the pKa of the phenol: an apparent value of 5.68 ± 0.02 was obtained. This also impacts the basicity of the azomethine nitrogen and, as a consequence, increases the hydrazone’s susceptibility to hydrolysis. Nevertheless, both

• electron-donating group decreases the compound’s hydrolysis rate and therefore improves its suitability for uses demanding physiological-like conditions. On the other hand, the presence of the –NO2 group has a very pronounced effect on the pKa of the phenol moiety and, to a lesser extent, on the stability

• apparent pKa of 5.68 ± 0.02 was obtained. This is quite lower than the pKa of 2-nitrophenol (around 7.2), but a similar experiment by us demonstrated that it is higher than the one of the precursor 2-hydroxy-3-nitrobenzaldehyde (4.80 ± 0.04), since the aldehyde group has a stronger electron-withdrawing

Morpholine-mediated defluorinative cycloaddition of gem-difluoroalkenes and organic azides

• Tzu-Yu Huang,
• Mario Djugovski,
• Sweta Adhikari,
• Destinee L. Manning and
• Sudeshna Roy

Beilstein J. Org. Chem. 2023, 19, 1545–1554, doi:10.3762/bjoc.19.111

• solvent (morpholine) or molarity of the reaction did not improve the yield (same or within 5%, see Supporting Information File 1, Table S1). We believe that LiHMDS gave the best results primarily because it is more miscible, resulting in a homogenous reaction mixture. LiHMDS being a strong base (pKa

• ≈ 25.8) [34], facilitates the direct deprotonation of morpholine as opposed to acting as a scavenger base. Due to the significant difference in pKa values between the conjugate acids of morpholine (pKa of the conjugate acid is 8.3) [35] and LiHMDS, we posit that LiHMDS directly deprotonates morpholine

• 13). Among the liquid bases that were screened, N,N-diisopropylethylamine (pKa ≈ 9) gave the product in 38% yield, whereas NaHMDS afforded a 24% yield. Since LiHMDS gave the best yield thus far, we wanted to examine if Li+ ions play a role in the reaction. When the reaction was carried out with a

Complexes of resorcin[4]arene with secondary amines: synthesis, solvent influence on “in-out” structure, and theoretical calculations of non-covalent interactions

• Waldemar Iwanek

Beilstein J. Org. Chem. 2023, 19, 1525–1536, doi:10.3762/bjoc.19.109

• . The highly ionic structure of these complexes makes them insoluble in non-polar solvents such as CHCl3. To explain the opposite arrangement of the amine molecules in the 1:2 complexes, the pKa of the protons of the hydroxy groups in R[4]A not involved in the formation of hydrogen bonds was calculated

• . The calculations following Equation 1 were performed using the CREST/GFN2-xTB/ALBP(H2O) program [27], which automatically calculates the pKa of the indicated protons. The obtained results are shown in Figure 5. with kdiss = ΔG(aq)/ln(10) RT and c1 = −1656.6999511, c2 = 23.18499947, c3 = −0.11103000

• groups’ protons not involved in the formation of hydrogen bonds in the R[4]A molecule was calculated with the CREST program using the “pKa” command. General method for the synthesis of R[4]A complexes with sec-amines: 0.2 g (0.225 mmol) of R[4]A was weighed into a round-bottomed flask and dissolved in 20

Enabling artificial photosynthesis systems with molecular recycling: A review of photo- and electrochemical methods for regenerating organic sacrificial electron donors

• Grace A. Lowe

Beilstein J. Org. Chem. 2023, 19, 1198–1215, doi:10.3762/bjoc.19.88

• quenched by a substrate or catalyst and then reduced by the sacrificial donor (oxidative quenching pathway). In the presence of protons, proton donors, or oxidized donor species with a low pKa, a proton-coupled electron transfer (PCET) can take place [14][15]. PCET reactions are important in artificial

• rather than just electrons, as well as by carefully matching the oxidation potential of the donor to the redox potentials of the system. However, one must also carefully calculate the pKa values of the system and choose a donor to match [17][45][49]. Measuring or calculating the redox potentials of

Exploring the role of halogen bonding in iodonium ylides: insights into unexpected reactivity and reaction control

• Carlee A. Montgomery and
• Graham K. Murphy

Beilstein J. Org. Chem. 2023, 19, 1171–1190, doi:10.3762/bjoc.19.86

• cycloaddition reactions that occur without transition metal catalysts, the unexpected initiation of single electron transfer (SET) processes or photochemical transformations, and even proton transfers that appear to defy pKa limitations. The reaction pathways followed by iodonium ylides and Lewis basic reaction

• insertion reactions could occur (Scheme 10) [100]. Systematic evaluation of acidic compounds showed that carboxylic acids (pKa ≈ 5; 85–99% yield) and thiophenols (pKa ≈ 7; 50f, 59%) were especially viable, whereas electron-rich phenols (pKa ≈ 10; 50d, <15% yield) were not. Though electron-poor phenols (pKa

• ≈ 8; 50e, 64–74% yield) were suitable, they were unreactive in the presence of a carboxylic acid (50c). If these insertions proceed via initial protonation of the iodonium ylide to produce 51 (Figure 11), its high acidity (pKa ≈ 0) [131][132] would suggest that only strong acids should undergo this

Clauson–Kaas pyrrole synthesis using diverse catalysts: a transition from conventional to greener approach

• Dileep Kumar Singh and
• Rajesh Kumar

Beilstein J. Org. Chem. 2023, 19, 928–955, doi:10.3762/bjoc.19.71

• chose nicotinamide as the catalyst for this study because it has a pKa of 3.43 and could act as a chemical antioxidant. In some cases, aminophenol hydrochloride is the only form of the corresponding aminophenol that can be isolated, so use of aminophenol hydrochloride as the starting material is also an

• of amine nucleophiles were examined in this method. As a result, it was found that nucleophiles with low pKa values, such as sulfonamides, reacted very well, while reactions with nucleophiles with high pKa values, such as benzylamine, did not work well. Compared with other classical methods, this

Eschenmoser coupling reactions starting from primary thioamides. When do they work and when not?

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

Beilstein J. Org. Chem. 2023, 19, 808–819, doi:10.3762/bjoc.19.61

• 70–95%). The presence of a base and the type of solvent seems to be an important factor for the reaction course. In toluene, ionic liquid or in refluxing ethanol without a base [16][19][20] or in the presence of weakly basic pyridine [17][18][21] (pKa = 5.23 in water, 3.4 in DMSO, 3.3 in DMF, and

• 5.44 in MeOH) [22] the formation of thiazole/thiazol-4-one (XI/XIII) is clearly preferred, whereas reactions in common chlorinated solvents (CH2Cl2, CHCl3) containing either an equivalent of strong base (methoxide) or excess of medium base in heterogeneous system (e.g., carbonate with pKa = 9.93 in

• where TEA behaves as a stronger base, the presence of benzonitrile was proved in the 1H NMR spectrum of the crude reaction mixture. On the other hand, the addition of 3 equivalents of a mild base (solid KHCO3; pKa = 6.35 in water [30]) into the DMF solution or MeCN suspension of salt 6a leads to the

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

• aryl fragment, the less intense the long-wavelength maximum. Conjugation between the aryl substituent and the DMAN fragment in salts 11 is indirectly supported by the fact that the basicity of monomer 6b with the donor methoxy group (pKa = 8.2, measured in DMSO by the 1H NMR transprotonation approach

• [40]) is almost an order of magnitude higher than that of monomer 6e with the acceptor nitro group (pKa = 7.3). The absorption maxima of 2,7-dialkynyl derivatives of DMAN 9 were observed at 402–465 nm, regularly shifting to the red region when passing from compound 9b bearing terminal methoxy groups

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

• monocations, protonated at the phenanthridine nitrogen atom. These structures correspond to pH values of pH 7 and pH 5, respectively, in accordance with experiments conducted here. Taking the experimental pKa value of the isolated phenanthridine, pKa = 4.65 [31] our calculated pKa of methylphenanthridine is

• pKa = 6.3. We assumed that this value would not change much in the prepared conjugates, which confirms that both Phen-Py-1 and Phen-Py-2 are monoprotonated at pH 5. We submitted all four systems to molecular dynamics simulations and performed clustering analysis on the obtained structures. The most

Synthesis and reactivity of azole-based iodazinium salts

• Thomas J. Kuczmera,
• Annalena Dietz,
• Andreas Boelke and
• Boris J. Nachtsheim

Beilstein J. Org. Chem. 2023, 19, 317–324, doi:10.3762/bjoc.19.27

• result obtained when using the stabilized salt 12 (Scheme 2b) [44]. Here, no counter-ion exchange to chloride was observed. The favored counter ion is determined by the pKa value of the corresponding acids but not by halogen bonding due to the steric hindrance at the iodines’ σ-holes. The reaction of

Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives

• Martin Kalník,
• Sergej Šesták,
• Juraj Kóňa,
• Maroš Bella and
• Monika Poláková

Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24

• geometries of the resulting inhibitor:dGMII complexes (for 10, 20, 28–30 and DIM) were optimized at the hybrid QM/MM level (BP86/LACVP*:OPLS2005). Based on the previous pKa calculations [22] of DIM, 30 and 31 bound at the active site of dGMII (their pKa = 4.9–5.4 at pH 6 of Golgi), all imino-ᴅ-lyxitol

• derivatives in this study were modeled in the neutral form (despite their pKa values in aqueous solution may be higher than 7). Superimposing the binding pose of the most potent inhibitor 29 in the active site of dGMII on the bound swainsonine in the X-ray complex (PDB ID: 3BLB) [23][39] (Figure 2) showed

Insight into oral amphiphilic cyclodextrin nanoparticles for colorectal cancer: comprehensive mathematical model of drug release kinetic studies and antitumoral efficacy in 3D spheroid colon tumors

• Sedat Ünal,
• Gamze Varan,
• Juan M. Benito,
• Yeşim Aktaş and
• Erem Bilensoy

Beilstein J. Org. Chem. 2023, 19, 139–157, doi:10.3762/bjoc.19.14

• pH. Preliminary studies have evidenced pKa values in the 8.3 range for non-amphiphilic surrogates of these cationic CDs, supporting the cationic character of the resulting NPs [20]. We hypothesized that these polycationic CD NPs, which we designed in our previous studies, could protect the active and

Reductive opening of a cyclopropane ring in the Ni(II) coordination environment: a route to functionalized dehydroalanine and cysteine derivatives

• Oleg A. Levitskiy,
• Olga I. Aglamazova,
• Yuri K. Grishin and
• Tatiana V. Magdesieva

Beilstein J. Org. Chem. 2022, 18, 1166–1176, doi:10.3762/bjoc.18.121

• electrolysis of complex 3 can be protonated using acetic acid (pKa in DMSO = 12.3 [53]), in contrast to their counterparts formed from complex 4. In the latter case, a stronger protonating agent is required, e.g., PhNEt2·HCl (pKa in DMSO = 2.45 for PhN+HMe2 [53]). The pKa value of 6 determined in DMSO solution

Cs₂CO₃-Promoted reaction of tertiary bromopropargylic alcohols and phenols in DMF: a novel approach to α-phenoxyketones

• Ol'ga G. Volostnykh,
• Olesya A. Shemyakina,
• Anton V. Stepanov and
• Igor' A. Ushakov

Beilstein J. Org. Chem. 2022, 18, 420–428, doi:10.3762/bjoc.18.44

• acidic than phenols 2a–c,f–i (pKa values: 9.99 [25][26] phenol (2a), 9.40 [27] α-naphthol (2b), 9.57 [27] β-naphthol (2c), 7.18 [25][26] p-nitrophenol (2d), 7.23 [25][26] o-nitrophenol (2e), 10.28 [25][26] p-cresol (2f), 10.27 [25][26] p-methoxyphenol (2g), 9.36 [25][26] p-bromophenol (2h), 10.19 eugenol

A resorcin[4]arene hexameric capsule as a supramolecular catalyst in elimination and isomerization reactions

• Tommaso Lorenzetto,
• Fabrizio Fabris and
• Alessandro Scarso

Beilstein J. Org. Chem. 2022, 18, 337–349, doi:10.3762/bjoc.18.38

• evidence of the importance of an accessible cavity for the activation of the reaction after alcohol protonation. It is known that 16 behaves as a weakly acidic assembly with pKa of about 5.5 [42], while the resorcinol moiety presents a pKa of 9.15. This enhanced acidity is likely to promote the protonation

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

• was observed after warming the reaction mixture to −50 °C and stirring at the temperature for less than two hours. Because LDA has a short shelf life, and has to be stored at low temperature, we were curious if KHMDS (pKa of conjugate acid, 26), which is a much weaker base than LDA (pKa of conjugate

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

• ), as functional groups on the polymer chains can have weak acidic characteristics if they release protons, or weak basic characteristics if they accept protons, in response to changes in pH. This can come about from even small variations in solution pH, depending on the degree of ionisation and pKa