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

Synthesis and characterization of bis(4-amino-2-bromo-6-methoxy)azobenzene derivatives

• David Martínez-López,
• Amirhossein Babalhavaeji,
• Diego Sampedro and
• G. Andrew Woolley

Beilstein J. Org. Chem. 2019, 15, 3000–3008, doi:10.3762/bjoc.15.296

• conditions (pH < 1). While the low pKa makes the azonium form unsuitable, the neutral versions of these compounds undergo trans-to-cis photoisomerization with blue-green light and exhibit slow (τ1/2 ≈ 10 min) thermal reversion and so may find applications under physiological conditions. Keywords: azobenzene

• azobenzenes – have recently been found to exhibit photoswitching properties suitable for in vivo use [8][9][10]. Typically, the formation of azonium ions from aminoazobenzenes occurs at pH < 3.5 [11][12], however, the pKa of the trans-azonium ion 1 is ca. 7.5 in aqueous solution (Figure 1) [9][10]. The

• elevated pKa of 1 has been attributed to resonance stabilization of the azonium cation together with intramolecular H-bonding between the azonium proton and methoxy groups in ortho-position to the azo double bond [10]. Since the azonium ion 1 forms under physiological conditions, i.e., at neutral pH value

Why do thioureas and squaramides slow down the Ireland–Claisen rearrangement?

• Dominika Krištofíková,
• Juraj Filo,
• Mária Mečiarová and
• Radovan Šebesta

Beilstein J. Org. Chem. 2019, 15, 2948–2957, doi:10.3762/bjoc.15.290

• demanding ones, e.g., C6, C9 or C11. In addition, the acidity of the hydrogen-bond-donating moiety also ranges over a rather large area from pKa (H2O) 1 for phosphoric acid C10 to pKa (DMSO) 28 of diols C7 and C8. However, neither steric factors, nor the acidity of the H-bond-donor moiety seemed to play a

A green, economical synthesis of β-ketonitriles and trifunctionalized building blocks from esters and lactones

• Daniel P. Pienaar,
• Kamogelo R. Butsi,
• Amanda L. Rousseau and
• Dean Brady

Beilstein J. Org. Chem. 2019, 15, 2930–2935, doi:10.3762/bjoc.15.287

• solubility of both the KOt-Bu base and the acetonitrile derived KCH2CN salt. This effectively accelerates the generation of the latter and as such, its reaction with the lactone (or ester) carbonyl carbon. By increasing the solubility of the conjugate base salt, the pKa of acetonitrile in the ethereal

Photoreversible stretching of a BAPTA chelator marshalling Ca²⁺-binding in aqueous media

• Aurélien Ducrot,
• Arnaud Tron,
• Robin Bofinger,
• Ingrid Sanz Beguer,
• Jean-Luc Pozzo and
• Nathan D. McClenaghan

Beilstein J. Org. Chem. 2019, 15, 2801–2811, doi:10.3762/bjoc.15.273

• over Mg2+ ions, and relative insensitivity to pH in biological media due to the relatively low pKa of the electron-poor aniline nitrogens [1]. BAPTA-type molecules complex Ca2+ in an octacoordinated fashion, involving the two aniline functions, the two central ether oxygens and the four carboxylates

An improved, scalable synthesis of Notum inhibitor LP-922056 using 1-chloro-1,2-benziodoxol-3-one as a superior electrophilic chlorinating agent

• Nicky J. Willis,
• Elliott D. Bayle,
• George Papageorgiou,
• David Steadman,
• Benjamin N. Atkinson,
• William Mahy and
• Paul V. Fish

Beilstein J. Org. Chem. 2019, 15, 2790–2797, doi:10.3762/bjoc.15.271

• by activation with HBTU and then subsequent reaction with the amine 18 (Scheme 4). These amides 17 were designed to have molecular properties (mw, cLogP, tPSA, HBD, pKa) consistent with CNS drug-like space [20]. Although significant Notum inhibition activity could be achieved (IC50 < 100 nM), none of

1,5-Phosphonium betaines from N-triflylpropiolamides, triphenylphosphane, and active methylene compounds

• Vito A. Fiore,
• Chiara Freisler and
• Gerhard Maas

Beilstein J. Org. Chem. 2019, 15, 2603–2611, doi:10.3762/bjoc.15.253

• -indanedione (2c), malononitrile (2e), 4-cyanomethyl-2,3,5,6-tetrafluorobenzonitrile (2f) were successfully applied as active methylene compounds; all of them have pKa values between 4.70 (2b, in dioxane/H2O 3:1 [20]) and ≈15.80, reported for 2-(pentafluorophenyl)acetonitrile in DMSO [21], the value for 2f

• was obtained from 1,1,1,5,5,5-hexafluoropropane-2,4-dione (pKa 2.30 in DMSO) and dimedone (pKa 11.42 in DMSO). Figure 1 also shows that 3-aryl- as well as various 3-alkyl-substituted propiolamides 1 furnish betaines 3 in high yields. A separate case was observed for 3-trimethylsilylpropiolamide 1f

1,2,3-Triazolium macrocycles in supramolecular chemistry

• Mastaneh Safarnejad Shad,
• Pulikkal Veettil Santhini and
• Wim Dehaen

Beilstein J. Org. Chem. 2019, 15, 2142–2155, doi:10.3762/bjoc.15.211

• also determined the dissociation constant pKa of this acid−base switchable MIM system by an indicator method which could make a quantitative and precise estimation of its dynamics with environmental acidity change. By combining NMR spectroscopic data and quantum chemistry calculations, a motion

Enantioselective PCCP Brønsted acid-catalyzed aza-Piancatelli rearrangement

• Gabrielle R. Hammersley,
• Meghan F. Nichol,
• Helena C. Steffens,
• Jose M. Delgado,
• Gesine K. Veits and
• Javier Read de Alaniz

Beilstein J. Org. Chem. 2019, 15, 1569–1574, doi:10.3762/bjoc.15.160

• (Figure 1) [38]. First, the pKa values measured in acetonitrile (MeCN) are lower than chiral phosphoric acids (Brønsted acid pKa = 8.85 vs chiral phosphoric acids pKa = 12–14) [38]. Given the enhanced acidity, we reasoned that this type of chiral Brønsted acid catalyst could facilitate the dehydration

Host–guest interactions between p-sulfonatocalix[4]arene and p-sulfonatothiacalix[4]arene and group IA, IIA and f-block metal cations: a DFT/SMD study

• Valya K. Nikolova,
• Cristina V. Kirkova,
• Silvia E. Angelova and
• Todor M. Dudev

Beilstein J. Org. Chem. 2019, 15, 1321–1330, doi:10.3762/bjoc.15.131

• descriptors of the group IA, IIA and f-block metal cations binding to the host calixarene systems have been evaluated and the factors that affect the interactions in the gas phase and in water medium have been unraveled. Available data on the experimental pKa values [31][33][34] imply that in acidic water

Synthesis of non-racemic 4-nitro-2-sulfonylbutan-1-ones via Ni(II)-catalyzed asymmetric Michael reaction of β-ketosulfones

• Alexander N. Reznikov,
• Anastasiya E. Sibiryakova,
• Marat R. Baimuratov,
• Eugene V. Golovin,
• Victor B. Rybakov and
• Yuri N. Klimochkin

Beilstein J. Org. Chem. 2019, 15, 1289–1297, doi:10.3762/bjoc.15.127

• ) complexes [56]. The above considerations lead to the use of β-ketosulfones in the Ni(II)-catalyzed reaction, since the proposed mechanism [47], that involves the formation of cyclic Ni enolate, and the high CH acidity of ketosulfones (pKa 9.8–10.5 [4]). The formation of the key intermediate can be provided

Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection

• Shahien Shahsavari,
• Dhananjani N. A. M. Eriyagama,
• Bhaskar Halami,
• Vagarshak Begoyan,
• Marina Tanasova,
• Jinsen Chen and
• Shiyue Fang

Beilstein J. Org. Chem. 2019, 15, 1116–1128, doi:10.3762/bjoc.15.108

• linkers for ODN synthesis [40][41]. Due to the low acidity of H-2 (pKa ≈31) in the Dmoc function, these groups and linkers were expected to be stable under ODN synthesis conditions. However, once the dithioketal in the group is oxidized, the acidity of H-2 (pKa ≈12) is drastically increased [42][43

• ]. Considering that the widely used Fmoc protecting group, of which the H-9 has a pKa of ≈22 [42], can be readily removed with a weak base such as piperidine, we hypothesized that the oxidized Dmoc groups and linkers could be cleaved under weakly basic and non-nucleophilic conditions via β-elimination. Indeed

Selective benzylic C–H monooxygenation mediated by iodine oxides

• Kelsey B. LaMartina,
• Haley K. Kuck,
• Linda S. Oglesbee,
• Asma Al-Odaini and
• Nicholas C. Boaz

Beilstein J. Org. Chem. 2019, 15, 602–609, doi:10.3762/bjoc.15.55

• -methylpyridine (89.7 versus 87.2 kcal/mol, respectively) [56]. Moreover, the electron withdrawing nature of the pyrimidine nitrogen atoms will affect the pKa of the adjacent secondary benzylic C–H bonds. The hydrogen atom abstraction from this position would then be influenced by the pKa of the C–H bond via a

Syntheses and chemical properties of β-nicotinamide riboside and its analogues and derivatives

• Mikhail V. Makarov and
• Marie E. Migaud

Beilstein J. Org. Chem. 2019, 15, 401–430, doi:10.3762/bjoc.15.36

• +, NMN and NAD+ are readily hydrolyzed to Nam, with their rapid decomposition particularly promoted by heat and basic aqueous solutions (pH ≥ 8). Under non-buffered conditions, the hydrolysis of the glycosidic bond leads to the release of Nam, which possesses a pKa at 3.35 [47]. The release of Nam

Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

• Ferran Planas,
• Michael J. McLeish and
• Fahmi Himo

Beilstein J. Org. Chem. 2019, 15, 145–159, doi:10.3762/bjoc.15.15

• same manner. Of course, while the relative stability of the TC form may slow down the BFDC reaction, it is conceivable that it may also play a beneficial role. As the pKa of the C2 proton decreases, the activity of the ThDP cofactor increases [62]. However, concomitantly, the thiazolium ring becomes

A convenient and practical synthesis of β-diketones bearing linear perfluorinated alkyl groups and a 2-thienyl moiety

• Ilya V. Taydakov,
• Yuliya M. Kreshchenova and
• Ekaterina P. Dolotova

Beilstein J. Org. Chem. 2018, 14, 3106–3111, doi:10.3762/bjoc.14.290

• developed two new mild protocols for the regeneration of diketones (Scheme 3). A vigorously stirred or shaken two-phase mixture of EtOAc and an aqueous solution of the reagent were used, and a finely ground solid Cu chelate was added to it in small portions. The choice of the reagent depends on the pKa of

1,8-Bis(dimethylamino)naphthyl-2-ketimines: Inside vs outside protonation

• A. S. Antonov,
• A. F. Pozharskii,
• P. M. Tolstoy,
• A. Filarowski and
• O. V. Khoroshilova

Beilstein J. Org. Chem. 2018, 14, 2940–2948, doi:10.3762/bjoc.14.273

• rotation of the NH2+ fragment in dications. Keywords: hydrogen bond; imine; NMR; proton sponge; superbase; Introduction It is well known that the extremely high basicity of 1,8-bis(dimethylamino)naphthalene (1, DMAN; pKa = 12.1 in H2O [1][2], 18.62 in MeCN [3], 7.5 in DMSO [4]) and its derivatives

• sponge moiety: for example, the basicity of benzophenone imine (pKa = 6.82) and even that of cyclohexanone imine (pKa = 9.15) [12] is much lower than that of DMAN (pKa = 12.1) [1][2]. Moreover, as it was already mentioned in the introduction, this is the third known example of a DMAN derivative with a

An overview on recent advances in the synthesis of sulfonated organic materials, sulfonated silica materials, and sulfonated carbon materials and their catalytic applications in chemical processes

• Hashem Sharghi,
• Pezhman Shiri and
• Mahdi Aberi

Beilstein J. Org. Chem. 2018, 14, 2745–2770, doi:10.3762/bjoc.14.253

• commercial strong acids with pKa-values of −1.9 and −2.8, respectively, which are regularly used as simplest and more usable catalysts in chemical reactions. MSA is almost completely ionized at a concentration of 0.1 M in an aqueous solution. The oxidative stability of organic compounds and metal ions in MSA

Learning from B₁₂ enzymes: biomimetic and bioinspired catalysts for eco-friendly organic synthesis

• Keishiro Tahara,
• Ling Pan,
• Toshikazu Ono and
• Yoshio Hisaeda

Beilstein J. Org. Chem. 2018, 14, 2553–2567, doi:10.3762/bjoc.14.232

• constant of 14 [11]. It is slightly basic, with a pKa lower than 1 for the Co–H complex [12]. The “supernucleophilic” cob(I)alamin is found in many enzymes such as methionine synthetases, adenosyltransferases, and reductive dehalogenases. In addition, the reactivity of cob(I)alamin has been investigated