Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations

• Laura Abella,
• Gerard Novell-Leruth,
• Josep M. Ricart,
• Josep M. Poblet and
• Antonio Rodríguez-Fortea

Beilstein J. Org. Chem. 2024, 20, 92–100, doi:10.3762/bjoc.20.10

• nanotubular-shaped fullerene inside the peapod. Kinetic analysis with the variable-temperature (VT) SMART-TEM method for the aforementioned C60 dimerization has also been reported by these authors [9]. They concluded that the SWCNT, which accumulates energy by the interaction with the electron beam, activates

• analyzed the interaction between C60 and the nanotube within the peapod. Next, we have found that some dimeric C60–C60 fullerene structures inside the carbon nanotube are thermodynamically favorable. Experiments indicate that, besides C60 sensitization via a singlet excited state, the [2 + 2] cycloaddition

• the subsequent irreversible C–C fusions occurring in phase 2 are proposed with the help of accelerated Car–Parrinello MD simulations. Results and Discussion Nanotube-C60 interaction: stabilization of the peapod First, we estimated the size of the stabilizing interaction that holds the peapod, that is

Optimizing reaction conditions for the light-driven hydrogen evolution in a loop photoreactor

• Pengcheng Li,
• Daniel Kowalczyk,
• Johannes Liessem,
• Mohamed M. Elnagar,
• Dariusz Mitoraj,
• Radim Beranek and
• Dirk Ziegenbalg

Beilstein J. Org. Chem. 2024, 20, 74–91, doi:10.3762/bjoc.20.9

• check if there are any interactions between the studied parameters. After the insignificant parameter interaction terms were removed from the quadratic model, the interaction of photocatalyst loading and stirring speed has a “Prob>F” value of 0.0279, which means this interaction term also significantly

• affects the maximum hydrogen generation rate. The interaction effect was summarized in the modified quadratic model, which has a difference between R2adj and R2pred of 0.0863. Moreover, an ANOVA showed that the p-value of the linear and modified quadratic model is lower than 0.0001, which confirms that

• actual experimental hydrogen generation rate could be achieved. No significant difference between the prediction accuracy of the two models is observable. The only difference between the two models is that the modified model considers the interaction of parameters. Therefore, to validate the model from

Preparing a liquid crystalline dispersion of carbon nanotubes with high aspect ratio

• Keiko Kojima,
• Nodoka Kosugi,
• Hirokuni Jintoku,
• Kazufumi Kobashi and
• Toshiya Okazaki

Beilstein J. Org. Chem. 2024, 20, 52–58, doi:10.3762/bjoc.20.7

• beneath the thick bundles form mesh-like structures. The shear force exerted by the bar may not sufficiently align the DWCNTs located near the substrate. Thus, optimizing the interaction between the DWCNTs and substrate is necessary to improve the alignment. To further investigate the low alignment, the

Using the phospha-Michael reaction for making phosphonium phenolate zwitterions

• Matthias R. Steiner,
• Max Schmallegger,
• Larissa Donner,
• Johann A. Hlina,
• Christoph Marschner,
• Judith Baumgartner and
• Christian Slugovc

Beilstein J. Org. Chem. 2024, 20, 41–51, doi:10.3762/bjoc.20.6

• O1–C15 and O1–C16 distances are in 2a 3.128(3) and 3.162.3(3) Å and in 2f 3.098(4) and 3.019(4) Å, suggesting a weak hydrogen bonding interaction between O1 and the protons of the methylene groups [43]. The P1–O1 distances of 2.750(1) Å in 2a and 2.693(3) Å in 2f suggest an electrostatic interaction

• lines) and in methanol (dotted lines); the inset shows a photograph of a vial containing a solution of 2a in chloroform; right: proposed hydrogen bonding interaction in 2b in CHCl3. Conversion of 1 (initial c = 0.25 mM) toward 2a, 2b, or 2d in the presence of the respective Michael acceptors (initial c

Identification of the p-coumaric acid biosynthetic gene cluster in Kutzneria albida: insights into the diazotization-dependent deamination pathway

• Seiji Kawai,
• Akito Yamada,
• Yohei Katsuyama and
• Yasuo Ohnishi

Beilstein J. Org. Chem. 2024, 20, 1–11, doi:10.3762/bjoc.20.1

• CmaA2 and CmaA3 for CmaA1) is a matter of interest. The fact that AvaA1 and CmaA1 recognized CmaA3 and AvaA3, respectively, as partner ACP suggests that there are some important residues conserved between AvaA3 and CmaA3 for the ligase–ACP interaction. Indeed, two amino acid residues (Trp38 and His41 of

• protein–protein interaction between the carrier protein and AMP-dependent ligase and (ii) the chain length control of highly reducing type II PKSs. Experimental Strains, chemicals, and enzymes E. coli JM109 was used for DNA manipulation, and E. coli BL21(DE3) was used for expressing recombinant proteins

1-Butyl-3-methylimidazolium tetrafluoroborate as suitable solvent for BF₃: the case of alkyne hydration. Chemistry vs electrochemistry

• Marta David,
• Elisa Galli,
• Richard C. D. Brown,
• Marta Feroci,
• Fabrizio Vetica and
• Martina Bortolami

Beilstein J. Org. Chem. 2023, 19, 1966–1981, doi:10.3762/bjoc.19.147

• ‒ hydrolysis in a 1:1 in volume IL/water solution kept at 45 °C for 24 h) [105]. It should be noted that the same treatment carried out on 1-methyl-3-octylimidazolium tetrafluoroborate (OMIm-BF4) evidenced a much higher extent of BF4‒ hydrolysis. This is probably due to the weaker interaction between cation

• and anion of the IL as the length of the side alkyl chain increases, which makes the BF4‒/water interaction more effective. Although Saihara and co-workers demonstrated that BF4‒ hydrolysis generates HF, which reacts with the surrounding glass container yielding SiF62‒ (signal at −130 ppm in 19F NMR

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• be a potential mechanism of GAG particular sequence recognition by proteins. Keywords: glycosaminoglycan; molecular docking; protein–glycosaminoglycan interaction specificity; RS-REMD; umbrella sampling; Introduction Glycosaminoglycans (GAGs) are long linear periodic anionic polydisperse

• , computational approaches could be efficiently used to gain insight into protein–GAG interactions that take place at single-molecule levels [32]. More than a complementary tool, computational approaches provide a better understanding of the role of individual interaction partners (including GAGs, solvent, and

• simulations were set up. First, hybrid GAGs (Figure 1) were prepared and docked using RS-REMD to find the pose in the binding site with the lowest interaction energy. Then, the GAG was pulled away from the binding site until it was shifted 40 Å from the starting position. Afterwards, the GAG was pulled in

Anion–π catalysis on carbon allotropes

• M. Ángeles Gutiérrez López,
• Mei-Ling Tan,
• Giacomo Renno,
• Augustina Jozeliūnaitė,
• J. Jonathan Nué-Martinez,
• Javier Lopez-Andarias,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2023, 19, 1881–1894, doi:10.3762/bjoc.19.140

• activity of fullerene 8 with A/D8/9 = 2.6 (Figure 3) leaves little room to improve, and the interaction between convex aromatic surfaces is not favorable. Taken together, anion–π catalysis on multiwalled carbon nanotubes (53, A/D = 7.3) is better than on single-walled carbon nanotubes (49, A/D = 2.0) and

Aromatic systems with two and three pyridine-2,6-dicarbazolyl-3,5-dicarbonitrile fragments as electron-transporting organic semiconductors exhibiting long-lived emissions

• Karolis Leitonas,
• Brigita Vigante,
• Dmytro Volyniuk,
• Audrius Bucinskas,
• Pavels Dimitrijevs,
• Sindija Lapcinska,
• Pavel Arsenyan and
• Juozas Vidas Grazulevicius

Beilstein J. Org. Chem. 2023, 19, 1867–1880, doi:10.3762/bjoc.19.139

• )-4-(4-bromophenyl)pyridine-3,5-carbonitrile (4) was obtained by the interaction of 3,6-di-tert-butyl-9H-carbazole with compound 3 in THF/DMF solution. The ethynylphenyl-substituted pyridine 5 was synthesized by Sonogashira coupling of 4 with ethynyltrimethylsilane in the presence of PdCl2(PPh3)2 and

Thienothiophene-based organic light-emitting diode: synthesis, photophysical properties and application

• Recep Isci and
• Turan Ozturk

Beilstein J. Org. Chem. 2023, 19, 1849–1857, doi:10.3762/bjoc.19.137

• for organic electronic applications [12][35]. Dimesitylboron (DMB), with its unoccupied p-orbital, is an electron-acceptor organoboron compound used in several donor–acceptor systems to provide the system with pull–push interaction [36][37]. In this work, we have designed and synthesized a D–π–A model

• -TPA (8) exhibited a mono-exponential profile having a 3.20 ns fluorescence decay pattern (Figure S1 in Supporting Information File 1), demonstrating a strong pull–push interaction in steady-state time resolved fluorescence performance. OLED application An OLED was fabricated using a standard

Recent advancements in iodide/phosphine-mediated photoredox radical reactions

• Tinglan Liu,
• Yu Zhou,
• Junhong Tang and
• Chengming Wang

Beilstein J. Org. Chem. 2023, 19, 1785–1803, doi:10.3762/bjoc.19.131

• a wide range of transformations [7][8]. Moreover, they proposed a plausible mechanism for the aforementioned conversions (Scheme 2). Initially, an NaI/PPh3 complex I was formed through a cation–π interaction. Subsequently, the combination of complex I with N-(cyclohexanecarbonyloxy)phthalimide

• radicals for alkenylation, was primarily facilitated by the electrostatic interaction between NaI and Katritzky salts 7. This innovative approach not only expanded the scope of photoredox cross-coupling reactions but also offered valuable insights into the role of NaI in facilitating these transformations

• . An EDA complex was formed through non-covalent interaction between the redox ester 10 and n-Bu4NI (Scheme 7). Subsequently, upon the photoexcitation, radical pairs I were generated via a SET process, accompanied by the liberation of CO2 and the phthalimide anion. The recombination of the alkyl

Charge carrier transport in perylene-based and pyrene-based columnar liquid crystals

• Alessandro L. Alves,
• Simone V. Bernardino,
• Carlos H. Stadtlober,
• Edivandro Girotto,
• Giliandro Farias,
• Rodney M. do Nascimento,
• Sergio F. Curcio,
• Thiago Cazati,
• Marta E. R. Dotto,
• Juliana Eccher,
• Leonardo N. Furini,
• Hugo Gallardo,
• Harald Bock and
• Ivan H. Bechtold

Beilstein J. Org. Chem. 2023, 19, 1755–1765, doi:10.3762/bjoc.19.128

• derivatives are among the most investigated due to their easy functionalization, high chemical and thermal stability, strong photoluminescence, and n-type semiconductor character. They tend to adopt columnar organization due to the strong π–π interaction of the rigid cores, providing a path for the efficient

• previously observed for another perylene-based ColLC compound, indicating the strong molecular interaction between neighboring molecules inside the columnar structure [33]. Due to the high temperature of the Iso phase for 2, the PL intensity almost vanished. However, a slight increase could also be observed

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

• phenolic hydroxy group and the azomethine nitrogen was identified in the solid state and seems to be maintained in solution. Moreover, the presence of the electron-withdrawing nitro substituent makes this interaction stronger. However, the contact should probably not subsist for the nitro compound under

• ), it becomes possible to calculate the contribution of each type of intermolecular interaction to the whole profile [44]. In our case, results show that the sum of π···π and C–H···π contacts comprises almost 20% of the Hirshfeld surface for both compounds. The curvedness maps were also plotted over the

• Hirshfeld surfaces and evidence the strong flatness of the structures (Figures S2B and S3B in Supporting Information File 1). Important contributions of hydrogen bonds (O···H/H···O) can also be found, especially for hdz-NO2. Besides the interaction maps, crystal structures themselves may be used to

Quinoxaline derivatives as attractive electron-transporting materials

• Zeeshan Abid,
• Liaqat Ali,
• Sughra Gulzar,
• Faiza Wahad,
• Raja Shahid Ashraf and
• Christian B. Nielsen

Beilstein J. Org. Chem. 2023, 19, 1694–1712, doi:10.3762/bjoc.19.124

• , resulting in an efficiency of 18% and marking a significant advancement in OSC research [27]. Zhou and co-workers synthesized Y6-type NFA acceptors, Qx12 and Qx13, by substituting Y6’s benzothiadiazole ring with a Qx moiety. Qx13 exhibited a stronger π–π interaction compared to Qx12, which facilitated

• study raises a concern regarding the performance of dyes with tert-butyl substituted DPQ acceptors, either containing benzene (Qx74) or thiophene (Qx75) as a π-conjugation linker and their benzotriazole analogue. While the incorporation of the Qx enhances the interaction between the donor and acceptor

A deep-red fluorophore based on naphthothiadiazole as emitter with hybridized local and charge transfer and ambipolar transporting properties for electroluminescent devices

• Suangsiri Arunlimsawat,
• Patteera Funchien,
• Pongsakorn Chasing,
• Atthapon Saenubol,
• Taweesak Sudyoadsuk and
• Vinich Promarak

Beilstein J. Org. Chem. 2023, 19, 1664–1676, doi:10.3762/bjoc.19.122

• intermolecular steric interaction [53]. The weak AIE characteristic of TPECNz in the aggregate state could be attributed to the competition between the twisted ICT and AIE properties in the molecule [57][58]. The thermal properties of TPECNz were studied by thermogravimetric analysis (TGA) and differential

Tying a knot between crown ethers and porphyrins

• Maksym Matviyishyn and
• Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

• complexes, the fragment originating from the porphyrinoid could form hydrogen bonds with a carboxyl group, while the crown ether cavity would allow interaction with the protonated amine group of an amino acid molecule. The choice of macrocycle size could enable the recognition of different biomolecules

Cyclodextrins permeabilize DPPC liposome membranes: a focus on cholesterol content, cyclodextrin type, and concentration

• Ghenwa Nasr,
• Hélène Greige-Gerges,
• Sophie Fourmentin,
• Abdelhamid Elaissari and
• Nathalie Khreich

Beilstein J. Org. Chem. 2023, 19, 1570–1579, doi:10.3762/bjoc.19.115

• from 25 to 55%. The remaining β-CD derivatives showed a lower effect at 25 and 50% CHOL. Discussion The CD–membrane interaction was broadly studied in the past few decades. The ability of CDs to induce membrane permeabilization was also proved in numerous reports. This effect was dose dependent which

• increase in the fluidity of DPPC liposomes through the interaction of HP-β-CD with the polar head group region and the acyl chains of DPPC [24]. Although the complex between HP-β-CD and CHOL has been previously characterized [25], this complex seems to be unstable. Thus, a better interaction would occur

• where γ-CD always exhibited low vesicle leakage [29]. Actually, γ-CD was found to be less lipid specific than the remaining native CDs (α-CD and β-CD) [8], which implies that the interaction of γ-CD with DPPC would be not favorable. Considering its large cavity in comparison to α and β-CD, γ-CD is not

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

• also found that the stoichiometry of the formed complexes depends on the size of the amine molecule. The automated interaction sites screening (aISS) made it possible to generate molecular ensembles of complexes. The geometry of the ensembles was first optimized with the r2scan-3c functional and

• of non-covalent interactions within various types of supramolecular complexes [17]. One such method is HFLD [18], which can be considered a dispersion-corrected HF approach where the dispersion interaction between fragments is added at the DLPNO-CC level. The HFLD method demonstrates comparable

• performance to HF in terms of total interaction energies while maintaining the accuracy of DLPNO CCSD(T) [19]. This method proves very accurate in quantifying non-covalent interactions, such as those found in hydrogen-bonded systems, among others. Despite the relatively small cavity in the structure of

Unraveling the role of prenyl side-chain interactions in stabilizing the secondary carbocation in the biosynthesis of variexenol B

• Moe Nakano,
• Rintaro Gemma and
• Hajime Sato

Beilstein J. Org. Chem. 2023, 19, 1503–1510, doi:10.3762/bjoc.19.107

• possibility of through-space interactions with prenyl side chains using DFT calculations. Our calculations show that (i) the unstable secondary carbocation is stabilized by the cation–π interaction from prenyl side chains, thereby lowering the activation energy, (ii) the four-membered ring formation is

• completed through bridging from the exomethylene group, and (iii) the annulation from the exomethylene group proceeds in a barrier-free manner. Keywords: biosynthesis; carbocation; cation–π interaction; DFT; terpene; Introduction Terpene/terpenoids are most abundant natural products in nature, more than

• as the C–H–π interaction between the carbocation intermediate and the Phe residue of terpene cyclase in the biosynthesis of sesterfisherol [21], and the intricated rearrangement reaction mechanism promoted by the equilibrium state of the homoallyl cation and the cyclopropylcarbinyl cation in the

N-Sulfenylsuccinimide/phthalimide: an alternative sulfenylating reagent in organic transformations

• Fatemeh Doraghi,
• Seyedeh Pegah Aledavoud,
• Mehdi Ghanbarlou,
• Bagher Larijani and
• Mohammad Mahdavi

Beilstein J. Org. Chem. 2023, 19, 1471–1502, doi:10.3762/bjoc.19.106

• sulfur atom to Fe3+ to generate Fe2+ and radical cation I. Subsequent cleavage of the N–S bond led to cation II and radical III. Interaction of III with Fe2+ regenerated the Fe3+ species and IV. At the same time, electrophilic addition of II to alkene 9 yielded intermediate V, which was subjected to the

• activated the N–S bond in II, which reacted with I to obtain IV, followed by C–S reductive elimination to give the thiolated product 30 or 31. On the other hand, the interaction of I with Cu(OAc)2 activated the N–S bond in III to afford IV, which was subjected to C–N reductive elimination to deliver the

• dihydropyrazoles 54 as products (Scheme 22) [59]. A credible pathway for the production of isoxazole 53 is illustrated in Scheme 23. The interaction of 1 with BF3·Et2O resulted in intermediate I that is in balance with I’. Cleavage of the N–S bond of I afforded cationic species PhS+ II, which activated the double

Functions of enzyme domains in 2-methylisoborneol biosynthesis and enzymatic synthesis of non-natural analogs

• Binbin Gu,
• Lin-Fu Liang and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 1452–1459, doi:10.3762/bjoc.19.104

• needs a covalent bond between the two domains A and B, as indicated by a similar precipitation of domain B alone and domain B in the presence of domain A. In these experiments, the N-terminal His-tags at both domains A and B may influence protein–protein interaction with the consequence that the mixture

• of the individually expressed domains shows a similarly rapid precipitation as domain B alone. However, some interaction between the individually expressed domains A and B can be concluded from their reduced productivity in comparison to domain B alone. Enzymatic synthesis of non-natural analogs of 2

Visible-light-induced nickel-catalyzed α-hydroxytrifluoroethylation of alkyl carboxylic acids: Access to trifluoromethyl alkyl acyloins

• Feng Chen,
• Xiu-Hua Xu,
• Zeng-Hao Chen,
• Yue Chen and
• Feng-Ling Qing

Beilstein J. Org. Chem. 2023, 19, 1372–1378, doi:10.3762/bjoc.19.98

• -difluoroethoxyphthalimide as the fluoroalkylating reagent failed to afford the desired product. According to our previous work [39] and literature precedent [27][35][38], a possible mechanism is proposed in Figure 2. The interaction between 2 and HE generates an electron donor–acceptor (EDA) complex A, which undergoes a

Synthesis of ether lipids: natural compounds and analogues

• Marco Antônio G. B. Gomes,
• Alicia Bauduin,
• Chloé Le Roux,
• Romain Fouinneteau,
• Wilfried Berthe,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96

• with biomembranes via supramolecular interactions with the lipids and proteins that are embedded in these membranes. We can hypothesis that their mechanism of action occurs via a direct interaction with membrane proteins or by a modification of the biophysical properties of the membranes. It must be

• was selectively alkylated on the primary alcohol to produce 20.2 via the use of dibutyltin oxide as selective reagent for the alkylation of diols [109]. For this reaction, CsF was added to increase the reactivity of the alkyl bromide, likely by a combined effect that includes the interaction of the

Cyanothioacetamides as a synthetic platform for the synthesis of aminopyrazole derivatives

• Valeriy O. Filimonov,
• Alexandra I. Topchiy,
• Vladimir G. Ilkin,
• Tetyana V. Beryozkina and
• Vasiliy A. Bakulev

Beilstein J. Org. Chem. 2023, 19, 1191–1197, doi:10.3762/bjoc.19.87

• -enethioamides with hydrazine and its derivatives, the interaction proceeds with the participation of cyano- and enamine groups, not affecting the thiocarbamoyl group, and leads to the formation of 4-thiocarbamoylpyrazoles. A synthesis method has been developed and a series of 1-substituted-4-thiocarbamoyl

•  1D). Results and Discussion Considering that the construction of the pyrazole cycle can be carried out by the interaction of hydrazine with 1,3-bielectrophilic reagents, we paid attention to the structure of 2-cyanothioacetamides 1 and 3-amino-2-cyanoprop-2-enethioamides 2 [22] which combine in one

• molecule cyano- and thioamide groups, as well as a fragment of enamine, each in principle being capable of interaction with hydrazine (3a) (Figure 2). First, we have studied the reaction of thioamides 1a–c with hydrazine (3a). It was found that the reaction proceeds smoothly in ethanol at 80 °C to form 3,5

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

• -hole bond is the non-covalent inter- or intramolecular interaction between the σ-hole of a group IV–VII atom with the electron-rich site of Lewis bases such as anions, hydrides, or even π electrons [24][30]. Halogen bonding is a subset of this bonding classification, represented by the generic bonding

• negative electrostatic potential (VS,min) of the acceptor [46][48][51][52], but also by other factors [53][54][55][56][57] including hydrogen bonding [31][48], solvent polarity [47][58], the Lewis basicity of the acceptor [46][50] and by sterics [46]. As with any interatomic interaction, the energy of a

• halogen bond lengths and their interaction energies [66][67][68][69][70][71]. Comparing the VS,max of select iodine-containing molecules shows that the electrostatic potential for molecular iodine (I-1) was 0.049 e, significantly greater than that of iodobenzene (I-2, 0.027 e) [70][72], though identical