Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages

• Keith G. Andrews

Beilstein J. Org. Chem. 2025, 21, 421–443, doi:10.3762/bjoc.21.30

• a size-selective space [105][126][129][130][132][134]. A key advantage is that these capsules have been made on multi-hundred-gram scales and can be recycled [132]. Additionally, control of structural or bound water by the capsule [105] and properties such as a lowered pKa inside [125] demonstrate a

• hydrophobic [160] products have been popular, including hydrolyses, ring openings, and rearrangements [22]. These reaction classes have been discussed [24][25][140]. Cavity-directed changes in ion-localization [161][162] and pKa are effective [37][107][163][164], and size-selectivity [36][165][166][167] and

• the cage framework to polarize adjacent aryl–hydrogen bonds in the ligands by enough to coordinate and activate substrates (Figure 5E) [190]. Here, the use of bulky counteranions reinforces the cationic cage interior, which is enhanced further by use of lower polarity solvents, and the pKa of confined

Synthesis of extended fluorinated tripeptides based on the tetrahydropyridazine scaffold

• Thierry Milcent,
• Pascal Retailleau,
• Benoit Crousse and
• Sandrine Ongeri

Beilstein J. Org. Chem. 2024, 20, 3174–3181, doi:10.3762/bjoc.20.262

• groups (CF3 or CF2H) in organic molecules can modulate their physicochemical (pKa, lipophilicity), structural (additional hydrophobic and hydrogen-bond interactions), and biological properties (metabolic stability, membrane permeability) [14][15]. Alongside the very well-known CF3 group, the CF2H group

Surprising acidity for the methylene of 1,3-indenocorannulenes?

• Shi Liu,
• Märt Lõkov,
• Sofja Tshepelevitsh,
• Ivo Leito,
• Kim K. Baldridge and
• Jay S. Siegel

Beilstein J. Org. Chem. 2024, 20, 3144–3150, doi:10.3762/bjoc.20.260

• of the first acidity constant (pKa) for BFC (27.6 in CH3CN) and FIC (27.8 in CH3CN) shows the methylene protons to be significantly more acidic than those in related cyclopentadiene (32 in CH3CN), indene (34 in CH3CN), or fluorene (37 in CH3CN) and comparable to the methine of 9

• -perfluorophenylfluorene (28.14 in CH3CN). This work reports quantitative pKa values of BFC and FIC, places those values in a broadened context of CpH-cognate hydrocarbon acidity and presents a Clar–Loschmidt graph perspective to help understand the “surprises”. Keywords: acidity; aromatic hydrocarbon; Clar sextet

• ; Loschmidt group element; molecular graph; Introduction A classic textbook tetrad linking hydrocarbon acidity to aromatic stabilization energy comprises cyclopentadiene (CpH), indene (InH), fluorene (FlH), and diphenylmethane (DPMH) [1][2], with pKa values in DMSO equal to 18 [3], 20.1 [3], 22.6 [3], and

Synthesis of fluorinated acid-functionalized, electron-rich nickel porphyrins

• Mike Brockmann,
• Jonas Lobbel,
• Lara Unterriker and
• Rainer Herges

Beilstein J. Org. Chem. 2024, 20, 2954–2958, doi:10.3762/bjoc.20.248

• –CH2–(CF2)n–COOCH3) with triflate as leaving group in terminal position are easily accessible and versatile building blocks for attaching long chain acids (pKa 0–1) to substrates in Williamson ether-type reactions. Keywords: acid-functionalized porphyrin; electron-rich porphyrin; nickel porphyrin

• -triflated, perfluoroalkylated carboxylic acids 16, 17, and 18 are easily accessible and versatile building blocks for connecting long chain acids (pKa range between 0 and 1) to substrates in Williamson ether-type reactions. Synthesis of the starting materials 16, 17, and 18 for the subsequent Williamson

gem-Difluorovinyl and trifluorovinyl Michael acceptors in the synthesis of α,β-unsaturated fluorinated and nonfluorinated amides

• Monika Bilska-Markowska,
• Marcin Kaźmierczak,
• Wojciech Jankowski and
• Marcin Hoffmann

Beilstein J. Org. Chem. 2024, 20, 2946–2953, doi:10.3762/bjoc.20.247

• , such a reaction pathway was absent for derivatives 11a–d, where the alpha-positioned proton exhibited a low pKa, favouring an easy elimination reaction. This is supported by the higher yields of products 12a–d compared to their 11a–d counterparts. The exclusive formation of E isomers in compounds 11a–d

Structure and thermal stability of phosphorus-iodonium ylids

• Andrew Greener,
• Stephen P. Argent,
• Coby J. Clarke and
• Miriam L. O’Duill

Beilstein J. Org. Chem. 2024, 20, 2931–2939, doi:10.3762/bjoc.20.245

• Information File 1, Figure S6), the Kamlet–Taft hydrogen bond acceptor ability (β) (Supporting Information File 1, Figure S7) [37], the pKa of the conjugate acid HX (Figure S8), or the anion’s position (axial vs equatorial). The main stabilising factor we identified was the torsion angle φ between the

Investigation of a bimetallic terbium(III)/copper(II) chemosensor for the detection of aqueous hydrogen sulfide

• Parvathy Mini,
• Michael R. Grace,
• Genevieve H. Dennison and
• Kellie L. Tuck

Beilstein J. Org. Chem. 2024, 20, 2818–2826, doi:10.3762/bjoc.20.237

• ). It was interesting to note that neither of the sulfur-containing compounds caused a remarkable increase in luminescence, especially lipoic acid and glutathione which contain an –S–S (pKa = 4.7) and –SH (pKa = 9.65) group respectively similar to HS−(aq) (pKa = 6.9). This demonstrates that the sensors

C–C Coupling in sterically demanding porphyrin environments

• Liam Cribbin,
• Brendan Twamley,
• Nicolae Buga,
• John E. O’ Brien,
• Raphael Bühler,
• Roland A. Fischer and
• Mathias O. Senge

Beilstein J. Org. Chem. 2024, 20, 2784–2798, doi:10.3762/bjoc.20.234

• stability than boronic acids and other employed esters as the four methyl groups protect the boron center from attack of water [44][45], preventing protodeboronation from the hydrolysis route. However, protodeboronation can be complex when it comes to pKa considerations, for example, 3,5

• -dinitrophenylboronic acid has a marginally lower pKa than pentafluorophenyl boronic acid [46]; however, it undergoes protodeboronation, several orders of magnitude slower [47]. The synthesis of porphyrin 31 with a benzothiophene moiety, proved challenging (Table 1, entries 14–19). Use of a microwave-assisted procedure

HFIP as a versatile solvent in resorcin[n]arene synthesis

• Hormoz Khosravi,
• Valeria Stevens and
• Raúl Hernández Sánchez

Beilstein J. Org. Chem. 2024, 20, 2469–2475, doi:10.3762/bjoc.20.211

• ][75]. Variations in catalyst nature between a Brønsted and Lewis acid, and the acid’s pKa (Table 1, entries 6–8) did not improve the yield compared to HCl (Table 1, entry 4). Last, further exploration of the conditions using HFIP/HCl revealed that the reaction progress achieves its maximum conversion

Facile preparation of fluorine-containing 2,3-epoxypropanoates and their epoxy ring-opening reactions with various nucleophiles

• Yutaro Miyashita,
• Sae Someya,
• Tomoko Kawasaki-Takasuka,
• Tomohiro Agou and
• Takashi Yamazaki

Beilstein J. Org. Chem. 2024, 20, 2421–2433, doi:10.3762/bjoc.20.206

• decreased the chemical yields as well as the diastereomeric ratios (Table 3, entries 1–4). The higher pKa values of the carbonyl α-proton of 4 (for example, the pKa values of the protons of X-CH2C(O)Ph in DMSO were reported to be 17.1 (X: PhS) [45] and 20.3 (X: Ph2N) [46]) would result in the contamination

• , allowing to isolate the acyclic hydroxyester anti-9e in 76% yield. Smooth conversion to the dihydrofuran syn-7e was observed from this intermediary compound anti-9e by refluxing the crude solution in AcOEt. Different from these outcomes, other possible nucleophilic candidates like acetylacetone (pKa value

pKalculator: A pK_a predictor for C–H bonds

• Rasmus M. Borup,
• Nicolai Ree and
• Jan H. Jensen

Beilstein J. Org. Chem. 2024, 20, 1614–1622, doi:10.3762/bjoc.20.144

• Rasmus M. Borup Nicolai Ree Jan H. Jensen Department of Chemistry, University of Copenhagen, Copenhagen, DK-2100, Denmark 10.3762/bjoc.20.144 Abstract Determining the pKa values of various C–H sites in organic molecules offers valuable insights for synthetic chemists in predicting reaction sites

• . As molecular complexity increases, this task becomes more challenging. This paper introduces pKalculator, a quantum chemistry (QM)-based workflow for automatic computations of C–H pKa values, which is used to generate a training dataset for a machine learning (ML) model. The QM workflow is

• benchmarked against 695 experimentally determined C–H pKa values in DMSO. The ML model is trained on a diverse dataset of 775 molecules with 3910 C–H sites. Our ML model predicts C–H pKa values with a mean absolute error (MAE) and a root mean squared error (RMSE) of 1.24 and 2.15 pKa units, respectively

Electrocatalytic hydrogenation of cyanoarenes, nitroarenes, quinolines, and pyridines under mild conditions with a proton-exchange membrane reactor

• Koichi Mitsudo,
• Atsushi Osaki,
• Haruka Inoue,
• Eisuke Sato,
• Naoki Shida,
• Mahito Atobe and
• Seiji Suga

Beilstein J. Org. Chem. 2024, 20, 1560–1571, doi:10.3762/bjoc.20.139

• of 3a. Based on this hypothesis, we examined the reduction of 1a in the presence of several acids (Table 2). First, electrochemical reduction was performed with 0.2 or 1.0 equiv of acetic acid, but the yield of 3a did not decrease, suggesting that 2a could not be trapped by acetic acid (pKa = 4.75

• ). To ensure the capture of 2a, we performed reduction with phosphoric acid (pKa = 2.12). Although the generation of 3a was suppressed, only a trace amount of 2a was obtained, and almost 1a was recovered (Table 2, entry 4). This was probably because the presence of water inhibited the reaction

• . Therefore, it was necessary to perform the reaction under anhydrous conditions. Hence, we used ethyl phosphate (mono- and di-mixture) (pKa = 1.42), which reacts easily under anhydrous conditions. As expected, the generation of 3a was suppressed and 2a was selectively obtained (Table 2, entry 5). With the

Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A

• Maksim V. Kvach,
• Stefan Harjes,
• Harikrishnan M. Kurup,
• Geoffrey B. Jameson,
• Elena Harjes and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2024, 20, 1088–1098, doi:10.3762/bjoc.20.96

• observed that the β-anomer of charge-neutral nucleoside Vb exhibited similar inhibition of hCDA as the control dZ (IIc). Presence of a negative charge in nucleoside Va led to lack of inhibition at pH 7.4. We assumed that protonation of Va might result in some inhibition of hCDA. However, the pKa of Va was

Novel route to enhance the thermo-optical performance of bicyclic diene photoswitches for solar thermal batteries

• Akanksha Ashok Sangolkar,
• Rama Krishna Kadiyam and
• Ravinder Pawar

Beilstein J. Org. Chem. 2024, 20, 1053–1068, doi:10.3762/bjoc.20.93

• TBR barrier were accounted at the (8,8)-CASPT2/6-311++G** level. These calculations performed in the presence of solvents were modelled using the continuum solvation model density (SMD) solvation model. The pure implicit SMD solvation model has poor reliability to predict the pKa values, and therefore

Auxiliary strategy for the general and practical synthesis of diaryliodonium(III) salts with diverse organocarboxylate counterions

• Naoki Miyamoto,
• Daichi Koseki,
• Kohei Sumida,
• Elghareeb E. Elboray,
• Naoko Takenaga,
• Ravi Kumar and
• Toshifumi Dohi

Beilstein J. Org. Chem. 2024, 20, 1020–1028, doi:10.3762/bjoc.20.90

• a cartridge filled with powdered oxone® for in situ generation of bis(trifluoroacetoxyiodo)arenes and their reaction with electron-rich arene or arylboronic acid [19] (Scheme 1B). Carboxylic acids, such as acetic acid and benzoic acid, characterized by substantial difference in pKa values when

Three-component N-alkenylation of azoles with alkynes and iodine(III) electrophile: synthesis of multisubstituted N-vinylazoles

• Jun Kikuchi,
• Roi Nakajima and
• Naohiko Yoshikai

Beilstein J. Org. Chem. 2024, 20, 891–897, doi:10.3762/bjoc.20.79

• ) resulted in 4aa as the major adduct, accompanied by the tetrazole adducts 4ja and 4ja’ (the ratio 4aa/4ja/4ja’ = 71:21:8; Scheme 3b). Superficially, these results appear correlated with the acidity of the corresponding azoles (pKa value: pyrazole, 19.8; 1,2,3-triazole, 13.9; tetrazole, 8.2), with the

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