Adaptive experimentation and optimization in organic chemistry

• Artur M. Schweidtmann and
• Philippe Schwaller

Beilstein J. Org. Chem. 2025, 21, 2367–2368, doi:10.3762/bjoc.21.180

• ]. However, the contributions in the thematic issue also reveal an important insight: while automation and AI are powerful tools, human chemical intuition remains invaluable. The work of Borup et al. on pKa prediction illustrates how machine learning can complement rather than replace expert knowledge [12

Thiadiazino-indole, thiadiazino-carbazole and benzothiadiazino-carbazole dioxides: synthesis, physicochemical and early ADME characterization of representatives of new tri-, tetra- and pentacyclic ring systems and their intermediates

• Gyöngyvér Pusztai,
• László Poszávácz,
• Anna Vincze,
• András Marton,
• Ahmed Qasim Abdulhussein,
• Judit Halász,
• András Dancsó,
• Gyula Simig,
• György Tibor Balogh and
• Balázs Volk

Beilstein J. Org. Chem. 2025, 21, 2220–2233, doi:10.3762/bjoc.21.169

• physicochemical and early ADME characterization study, in the framework of which logP, pKa and logk values were calculated. Following that, kinetic solubility and in vitro gastrointestinal membrane-specific permeability measurements were carried out to assess the lead-likeness of the compounds. Subsequently, the

• surface area (TPSA) values fell in a desirable range (40–90 Å2) (see the extended table on physicochemical parameters in Supporting Information File 1, Table S1). Based on their pKa values, all compounds are non-ionizable or slightly basic. Kinetic solubility was considered good above 30 µM, moderate

Aryl iodane-induced cascade arylation–1,2-silyl shift–heterocyclization of propargylsilanes under copper catalysis

• Rasma Kroņkalne,
• Rūdolfs Beļaunieks,
• Armands Sebris,
• Anatoly Mishnev and
• Māris Turks

Beilstein J. Org. Chem. 2025, 21, 1984–1994, doi:10.3762/bjoc.21.154

• -butyldimethylsilyl)hex-5-yn-1-yl)-N-phenylaniline (15). Thus, acylamides were found to have optimal pKa and nucleophilicity to react according to our desired pathway (Scheme 4). For the heterocyclization mechanism under arylating conditions, we propose a Cu(I/III) catalyzed pathway (Scheme 5). Firstly, the copper(I

Photoswitches beyond azobenzene: a beginner’s guide

• Michela Marcon,
• Christoph Haag and
• Burkhard König

Beilstein J. Org. Chem. 2025, 21, 1808–1853, doi:10.3762/bjoc.21.143

pH-Controlled isomerization kinetics of ortho-disubstituted benzamidines: E/Z isomerism and axial chirality

• Ryota Kimura,
• Satoshi Ichikawa and
• Akira Katsuyama

Beilstein J. Org. Chem. 2025, 21, 1568–1576, doi:10.3762/bjoc.21.120

• –N rotation and C–N/C–C rotation by adjusting the pH of the solvent and the pKa of the amidine. Herein, we report our findings on the structural properties of an ortho-disubstituted benzamidine. Similar to DiBA, an ortho-disubstituted benzamidine has two types of stereoisomers: E/Z isomers arising

• calculated pKa values of the amidines are also shown in Table 1. As a result, the C–N isomerization was accelerated by an electron-withdrawing chloro substituent, and electron-donating substituents (Me, OMe and NMe2 groups) decreased the isomerization rate. Figure 7a illustrates the effect of the electronic

• the rotational barrier of the C–N/C–C concerted rotation is higher than that of C–N rotation. This finding is consistent with the calculated pKa of 10.6 for amidine 1, indicating that racemization is minimal under the conditions where most of the amidine remains in its protonated form. As pH was

Azobenzene protonation as a tool for temperature sensing

• Antti Siiskonen,
• Sami Vesamäki and
• Arri Priimagi

Beilstein J. Org. Chem. 2025, 21, 1528–1534, doi:10.3762/bjoc.21.115

• spectral changes caused by azobenzene protonation is a well-established concept, with methyl orange-based pH indicators dating back to the late 1800s [22]. Early studies primarily focused on characterizing these spectral changes, determining pKa values, and elucidating the protonation mechanism of

Substituent effects in N-acetylated phenylazopyrazole photoswitches

• Radek Tovtik,
• Dennis Marzin,
• Pia Weigel,
• Stefano Crespi and
• Nadja A. Simeth

Beilstein J. Org. Chem. 2025, 21, 830–838, doi:10.3762/bjoc.21.66

• classical azobenzenes. Heterocyclic rings offer, for example, enhanced polarity, electron pairs for metal coordination [27], better water-solubility, and variable pKa [28][29]. Special attention has been given to 5-membered N-heterocyclic azobenzenes, which not only maintain the azobenzenes properties but

Origami with small molecules: exploiting the C–F bond as a conformational tool

• Patrick Ryan,
• Ramsha Iftikhar and
• Luke Hunter

Beilstein J. Org. Chem. 2025, 21, 680–716, doi:10.3762/bjoc.21.54

• sugar and phosphorus, e.g., 82, Figure 10) are of interest as non-hydrolysable isosteres, but a better match in terms of pKa and C–C–P angle is achieved with mono- or difluorophosphonates (e.g., 83–85, Figure 10) [143][144]. In the case of the monofluorophosphonates, conformational effects can also be

• including protein kinase A (PKA). Fluorination was investigated as a strategy for altering the conformation of the central seven-membered nitrogen heterocycle, and hence possibly improving the selectivity for PKCε. A variety of fluorination patterns were investigated (100–103, Figure 11), which were found

• to induce subtly different conformations of the seven-membered ring through an interplay of the conformational influences I–III (Figure 11) and sterics. Promisingly, these different shapes were found to successfully alter the PKCε/PKA selectivity, with one analogue (100) displaying higher potency and

Recent advances in allylation of chiral secondary alkylcopper species

• Minjae Kim,
• Gwanggyun Kim,
• Doyoon Kim,
• Jun Hee Lee and
• Seung Hwan Cho

Beilstein J. Org. Chem. 2025, 21, 639–658, doi:10.3762/bjoc.21.51

• phosphoramidite ligands significantly advanced this field, with contributions from numerous research groups including Hartwig, Helmchen, Carreira, Alexakis, and You [19]. In general, soft nucleophiles that typically possess conjugate acids with pKa values less than 25 have been utilized in most Pd and Ir

• nucleophiles 5 that have conjugate acids with pKa values greater than 25 such as organolithium, organomagnesium, organozinc, and organozirconium reagents. This crucial distinction effectively expanded the scope of allylic substitution reactions beyond traditional boundaries. The evolution of copper-catalyzed

Total synthesis of (±)-simonsol C using dearomatization as key reaction under acidic conditions

• Xiao-Yang Bi,
• Xiao-Shuai Yang,
• Shan-Shan Chen,
• Jia-Jun Sui,
• Zhao-Nan Cai,
• Yong-Ming Chuan and
• Hong-Bo Qin

Beilstein J. Org. Chem. 2025, 21, 601–606, doi:10.3762/bjoc.21.47

• DIPEA, affording compound 17 with an 89% yield [11]. For the following alkylation step with tert-butyl bromoacetate, three bases were tested: potassium carbonate, cesium carbonate, and sodium hydride. Considering the targeted alkylation of a phenolic hydroxy group and the pKa requirements of this

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