Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

Understanding X-ray-induced isomerisation in photoswitchable surfactant assemblies

• Beatrice E. Jones,
• Camille Blayo,
• Jake L. Greenfield,
• Matthew J. Fuchter,
• Nathan Cowieson and
• Rachel C. Evans

Beilstein J. Org. Chem. 2024, 20, 2005–2015, doi:10.3762/bjoc.20.176

• brilliance of synchrotron X-ray sources enables the mechanisms of structural changes in PS to be studied, using in-situ light irradiation with time-resolved data collection. For example, Tribet and co-workers used this approach to explore the kinetics of micellisation and dissolution of cationic Azo-PS, both

• that ensure the Z-rich PSS can be measured appropriately. To address this, here we investigate the effects of light- and X-ray irradiation on PS assemblies to further understand the parameters which influence X-ray-induced Z–E isomerisation. Two different cationic PS molecules are studied, based on the

Harnessing the versatility of hydrazones through electrosynthetic oxidative transformations

• Aurélie Claraz

Beilstein J. Org. Chem. 2024, 20, 1988–2004, doi:10.3762/bjoc.20.175

• the electrolysis was a four-electron oxidative process. Based on this study, the authors proposed the initial anodic oxidation of hydrazone 44 through the loss of two electrons and one proton to form cation 47. Subsequent nucleophilic addition of the azaarene led to new highly acidic cationic species

• iodonium through a two-electron process. Subsequent reaction with the hydrazone and deprotonation formed the N-iodo hydrazone intermediate 80, triggering the reaction with the amine 78 through cationic species 81. Final cyclization delivered the desired pyrazole 79 (Scheme 15) [60]. The group of D. Tang

• ) atom were well tolerated and the best result was obtained with a morpholine ring. Based on cyclic voltammetry studies, the transformation initiated with the anodic oxidation of hydrazone 101 to form highly electrophilic radical cationic species 104. Subsequent addition of azide 102 and desilylation

Development of a flow photochemical process for a π-Lewis acidic metal-catalyzed cyclization/radical addition sequence: in situ-generated 2-benzopyrylium as photoredox catalyst and reactive intermediate

• Masahiro Terada,
• Zen Iwasaki,
• Ryohei Yazaki,
• Shigenobu Umemiya and
• Jun Kikuchi

Beilstein J. Org. Chem. 2024, 20, 1973–1980, doi:10.3762/bjoc.20.173

• catalytic cycles). In catalytic cycle I, the key cationic components, 2-benzopyrylium intermediates A, are generated in situ by the activation of the alkyne moiety of ortho-carbonyl alkynylbenzene derivatives 1 in the presence of the π-Lewis acidic metal catalyst [M]X [AgNTf2 or Cu(NTf2)2] and subsequent

• ) generates, e.g., key cationic components, 2-benzopyrylium intermediates A without light irradiation, it is necessary to ensure that the reaction time of catalytic cycle I is not affected by the timescale of the flow reaction. Therefore, we adopted a dual syringe system in which two solutions are mixed

• -isochromene derivatives in higher yields than the batch reaction system, even with the amount of the π-Lewis acidic metal catalyst reduced by half. In the present sequential transformation, the key cationic species, 2-benzopyrylium intermediates, were generated in situ through the AgNTf2-catalyzed

Novel oxidative routes to N-arylpyridoindazolium salts

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

Beilstein J. Org. Chem. 2024, 20, 1906–1913, doi:10.3762/bjoc.20.166

• electrode in MeCN solution using Bu4NBF4 as a supporting electrolyte. Oxidation of the salts occurs at high positive potentials (>2 V vs Ag/AgCl, KCl(sat.), Figure 1a), in accordance with the cationic nature of the heterocycle. In the negative potential range, an irreversible peak can be observed in the

Benzylic C(sp³)–H fluorination

• Alexander P. Atkins,
• Alice C. Dean and
• Alastair J. J. Lennox

Beilstein J. Org. Chem. 2024, 20, 1527–1547, doi:10.3762/bjoc.20.137

• that can undergo facile α-proton elimination facilitated by the strongly electron-withdrawing thiocyanate group. Subsequent anodic oxidation affords a cationic species that can be trapped by fluoride to afford the product. This reaction was demonstrated on four substrates in yields of 47–71%. The

• , and secondly, to improve the electrophilicity of the phthalide cationic intermediate generated by the SET/PT/SET sequence. Model substrate 18 could be fluorinated in excellent yield, but the yields decreased upon variation of the substrate. A poor selectivity for primary and secondary benzylic

A comparison of structure, bonding and non-covalent interactions of aryl halide and diarylhalonium halogen-bond donors

• Nicole Javaly,
• Theresa M. McCormick and
• David R. Stuart

Beilstein J. Org. Chem. 2024, 20, 1428–1435, doi:10.3762/bjoc.20.125

• Nicole Javaly Theresa M. McCormick David R. Stuart Department of Chemistry, Portland State University, 1719 SW 10th Ave, Portland OR 97201, United States 10.3762/bjoc.20.125 Abstract Halogen bonding permeates many areas of chemistry. A wide range of halogen-bond donors including neutral, cationic

• , monovalent, and hypervalent have been developed and studied. In this work we used density functional theory (DFT), natural bond orbital (NBO) theory, and quantum theory of atoms in molecules (QTAIM) to analyze aryl halogen-bond donors that are neutral, cationic, monovalent and hypervalent and in each series

• of cationic monovalent halogen-bond donors 37–40 with chloride as the imidazolium iodide is a well-established core of halogen-bonding catalysts [34][35] (Scheme 3). In general, we observed that more exergonic association of the halogen-bond donors with chloride were associated with closer X---Cl

Hypervalent iodine-catalyzed amide and alkene coupling enabled by lithium salt activation

• Akanksha Chhikara,
• Fan Wu,
• Navdeep Kaur,
• Prabagar Baskaran,
• Alex M. Nguyen,
• Zhichang Yin,
• Anthony H. Pham and
• Wei Li

Beilstein J. Org. Chem. 2024, 20, 1405–1411, doi:10.3762/bjoc.20.122

• , which then partitions into an ion pair suitable for olefin activation, followed by the addition of the bifunctional anionic carbamate (Scheme 1c). Our hypothesis here aims to directly access the reactivity of the cationic hypervalent iodine catalyst through an initial activation first, which we reason

• will then enable soft nucleophiles such as unadorned amides to readily participate in the ensuing olefin addition. In this regard, we wondered if the hypervalent iodine with difluoro ligands could undergo salt metathesis with lithium salts such as LiBF4 or LiPF6 to afford the more reactive cationic

• hypervalent iodine catalyst. The cationic hypervalent iodine catalyst could then activate the olefin to allow the addition of bifunctional nucleophiles such as an amide to achieve an overall olefin oxyamination process. We have previously reported a series of iodide-catalyzed processes, in which the

Computation-guided scaffold exploration of 2E,6E-1,10-trans/cis-eunicellanes

• Zining Li,
• Sana Jindani,
• Volga Kojasoy,
• Teresa Ortega,
• Erin M. Marshall,
• Khalil A. Abboud,
• Sandra Loesgen,
• Dean J. Tantillo and
• Jeffrey D. Rudolf

Beilstein J. Org. Chem. 2024, 20, 1320–1326, doi:10.3762/bjoc.20.115

• chemically-induced cationic cyclization mechanisms, we performed quantum chemical calculations [mPW1PW91/6–31+G(d/p)/SMD(chloroform)] [13][14][15][16][17][18][19][20] to obtain the relative free energies of the cationic intermediates and transition states that interconvert them, as well as the relative free

• energies of the neutral products. In the cyclization of 2, protonation at C6, results in a C7 tertiary cationic intermediate (A2+) where C2 is only 1.65 Å away from C7 (Figure 2B); this structure can be viewed as protonated 5 or 6 with a strongly hyperconjugated C2–C7 bond [21]. Reducing this

• epoxide 9, but the similar reaction with 2 yields gersemienol 8. Isolation yields are provided. (B and C) Results of DFT calculations on the protonation-induced cyclizations of 1 and 2. The energies of the cationic intermediates (italicized values) are not on the same energy scale as for the substrates

Sustainable tandem acylation/Diels–Alder reaction toward versatile tricyclic epoxyisoindole-7-carboxylic acids in renewable green solvents

• Ayhan Yıldırım

Beilstein J. Org. Chem. 2024, 20, 1308–1319, doi:10.3762/bjoc.20.114

• and Discussion In this study, the course of the reaction was first investigated in aqueous micellar media using cetyltrimethylammonium bromide (CTAB), a cationic surfactant. The aminofuran and maleic anhydride shown in Table 1 were reacted with 10% CTAB in the same molar ratios. However, contrary to

Mechanistic investigations of polyaza[7]helicene in photoredox and energy transfer catalysis

• Johannes Rocker,
• Till J. B. Zähringer,
• Matthias Schmitz,
• Till Opatz and
• Christoph Kerzig

Beilstein J. Org. Chem. 2024, 20, 1236–1245, doi:10.3762/bjoc.20.106

• ][13][14][15]. Most of the established organic catalysts (acridinium salts [16][17][18][19], cyanoarenes [8][20][21][22], quinones [23][24], etc.) [10][25] are cationic or electron-deficient and tend to act as excited state oxidants in a reductive quenching cycle. Only recently, more reducing catalyst

Stability trends in carbocation intermediates stemming from germacrene A and hedycaryol

• Naziha Tarannam,
• Prashant Kumar Gupta,
• Shani Zev and
• Dan Thomas Major

Beilstein J. Org. Chem. 2024, 20, 1189–1197, doi:10.3762/bjoc.20.101

• C6 position of the C6–C7 double bond leads to 4 distinct 6-6 bicyclic cationic stereoisomers (A–D, Figure 1). Reprotonation at the C3-position of the C2–C3 double bond forms 6-6 bicyclic compounds that are not observed in nature for eudesmanes as they proceed via a secondary carbocation [16

Manganese-catalyzed C–C and C–N bond formation with alcohols via borrowing hydrogen or hydrogen auto-transfer

• Mohd Farhan Ansari,
• Atul Kumar Maurya,
• Abhishek Kumar and
• Saravanakumar Elangovan

Beilstein J. Org. Chem. 2024, 20, 1111–1166, doi:10.3762/bjoc.20.98

• regeneration of the active catalyst Mn23-a (Scheme 61). Later, Srimani and co-workers studied the C-3 alkylation of indoles with various primary and secondary alcohols using Mn24 (5 mol %) and KOH (0.6 equiv) under neat conditions for 36 h at 130 °C (Scheme 62) [90]. The same cationic complex was used for the

Light on the sustainable preparation of aryl-cored dibromides

• Fabrizio Roncaglia,
• Alberto Ughetti,
• Nicola Porcelli,
• Biagio Anderlini,
• Andrea Severini and
• Luca Rigamonti

Beilstein J. Org. Chem. 2024, 20, 1076–1087, doi:10.3762/bjoc.20.95

• follows a different mechanism, producing the ortho and para-bromoarenes through Ar-SE, that involves cationic intermediates. In this case, a catalytic amount of iodine [21][22] or FeCl3 [23] is added to enhance the electrophilicity of bromine. While widely employed and capable of producing reliable

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

• (TFE, Scheme 2B) [21]. Our group previously reported the synthesis of diaryliodonium(III) salts by combining hypervalent iodine(III) reagents with electron-rich arenes in fluoroalcohol solvents, such as TFE or 1,1,1,3,3,3-hexafluoro-2-propanol [21][22]. These solvents stabilize the cationic

Spin and charge interactions between nanographene host and ferrocene

• Akira Suzuki,
• Yuya Miyake,
• Ryoga Shibata and
• Kazuyuki Takai

Beilstein J. Org. Chem. 2024, 20, 1011–1019, doi:10.3762/bjoc.20.89

• diamagnetic molecule (S = 0, no spin magnetism) compared with other metallocenes [17]. However, FeCp2 is easily oxidized to a monovalent cation, the electronic structure of which is magnetic (S = 1/2). Electron spin resonance (ESR) spectroscopy revealed the spin magnetism of cationic FeCp2 accommodated in

Enantioselective synthesis of β-aryl-γ-lactam derivatives via Heck–Matsuda desymmetrization of N-protected 2,5-dihydro-1H-pyrroles

• Arnaldo G. de Oliveira Jr.,
• Martí F. Wang,
• Rafaela C. Carmona,
• Danilo M. Lustosa,
• Sergei A. Gorbatov and
• Carlos R. D. Correia

Beilstein J. Org. Chem. 2024, 20, 940–949, doi:10.3762/bjoc.20.84

• all other lactams as R was done by analogy. The assignment of the absolute stereochemistry allowed us to propose a rationale for the Heck–Matsuda reaction (Scheme 7). Upon activation of the catalyst (I), oxidative addition of aryldiazonium salt and subsequent nitrogen release generates the cationic

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

• this conjecture, the present reaction is proposed to involve reversible complexation between the alkyne and the cationic iodine(III) electrophile and subsequent trans-addition of the azole nucleophile, the latter step being coupled with concomitant deprotonation of the N–H bond by the triflate anion

Confirmation of the stereochemistry of spiroviolene

• Yao Kong,
• Yuanning Liu,
• Kaibiao Wang,
• Tao Wang,
• Chen Wang,
• Ben Ai,
• Hongli Jia,
• Guohui Pan,
• Min Yin and
• Zhengren Xu

Beilstein J. Org. Chem. 2024, 20, 852–858, doi:10.3762/bjoc.20.77

• deoxyconidiogenol (4, Scheme 1A) by several terpene cyclases from fungus (PcCS, PchDS, PrDS) [15][16], which involves a 1,11-10,14 cyclization of GGPP, followed by 1,2-alkyl shift and a 2,10-cyclization, to give the key C3 cationic intermediate IM-1. A key 1,2-hydride shift from C2 to C3, which was observed in the

• isotope labeling experiments [6], followed by a 2,7-cyclization, afforded C6 cationic intermediate IM-3 with cyclopiane skeleton. Quench of the cation IM-3 with water would give 4, while upon two 1,2-alkyl shifts of IM-3, followed by deprotonation of cation IM-4, would give spiroviolene (1). On the other

Advancements in hydrochlorination of alkenes

• Daniel S. Müller

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

• ) could be prevented when switching to BCl3 (10 mol %). Interestingly, toluene (94), which is generated as a byproduct of the Grob fragmentation, must react more sluggishly with the generated cationic intermediates compared to chloride, as no alkylations of toluene were reported. In 2017, the Snyder group

• concerning the polar hydrochlorinations the activation energy for an anti-Markovnikov addition is at least by 30 kJ mol−1 higher than for normal addition. Therefore, the formation of the anti-Markovnikov product via purely cationic intermediates is never observed. The only report for the formation of the

• yield). Metal hydride hydrogen atom transfer reactions vs cationic reactions; BDE (bond-dissociation energy). Mechanism for the cobalt hydride hydrogen atom transfer reaction reported by Carreira. Proposed mechanism for anti-Markovnikov hydrochlorination by Nicewicz. Mechanism for anti-Markovnikov

Synthesis and characterization of water-soluble C₆₀–peptide conjugates

• Yue Ma,
• Lorenzo Persi and
• Yoko Yamakoshi

Beilstein J. Org. Chem. 2024, 20, 777–786, doi:10.3762/bjoc.20.71

• ) showed much smaller aggregation (dotted green line, ≈12 nm), providing a transparent solution, while C60–oligo-Arg (5c) remained insoluble over the tested pH value range (4.0–9.2). This was presumably due to the strong cation–π interactions between the cationic Arg moieties and the aromatic C60, which is

SOMOphilic alkyne vs radical-polar crossover approaches: The full story of the azido-alkynylation of alkenes

• Julien Borrel and
• Jerome Waser

Beilstein J. Org. Chem. 2024, 20, 701–713, doi:10.3762/bjoc.20.64

• since the formation of a stabilized carbocation might be required for the reaction to occur. Xu [41] and Molander [42] previously reported the quenching of similar cationic species by alkynyl-BF3K salts. Boronate 5a was therefore selected as nucleophilic alkyne. Gratifyingly, using Cu(dap)2Cl in DCE

Palladium-catalyzed three-component radical-polar crossover carboamination of 1,3-dienes or allenes with diazo esters and amines

• Geng-Xin Liu,
• Xiao-Ting Jie,
• Ge-Jun Niu,
• Li-Sheng Yang,
• Xing-Lin Li,
• Jian Luo and
• Wen-Hao Hu

Beilstein J. Org. Chem. 2024, 20, 661–671, doi:10.3762/bjoc.20.59

• (TEMPO) and the corresponding radical-trapping product A could be confirmed by HRMS of both reaction mixtures, unambiguously supporting radical mechanisms (Scheme 4a). The reaction with styrene was conducted under standard conditions, but no product X could be detected, indicating the cationic

Enhanced reactivity of Li⁺@C₆₀ toward thermal [2 + 2] cycloaddition by encapsulated Li⁺ Lewis acid

• Hiroshi Ueno,
• Yu Yamazaki,
• Hiroshi Okada,
• Fuminori Misaizu,
• Ken Kokubo and
• Hidehiro Sakurai

Beilstein J. Org. Chem. 2024, 20, 653–660, doi:10.3762/bjoc.20.58

• member of the emerging ion-endohedral fullerene family, have attracted significant attention owing to the distinctive ionic properties originating from the ion pair structure consisting of a cationic endohedral fullerene core and an external counter anion. Despite being a relatively recent addition, Li

Recent developments in the engineered biosynthesis of fungal meroterpenoids

• Zhiyang Quan and
• Takayoshi Awakawa

Beilstein J. Org. Chem. 2024, 20, 578–588, doi:10.3762/bjoc.20.50

• cationic intermediates, leading to the terpenoid structure of each product [6][7]. Particular attention has been paid to the biosynthesis of the compounds derived from farnesyl-DMOA (5) composed of 3,5-dimethylorsellinic acid (DMOA, 4) and the C15 terpenoid moiety due to their structural diversity (Figure

• -6-6-5-membered andrastin E (9) (Figure 2) [8]. Like Trt1, AusL and AdrI create the common cation intermediate from 6, but they deprotonate the cationic intermediate from H-1' and H-11, respectively [12]. The differences in the structural bases of Trt1, AusL, and AdrI are quite intriguing, in that