Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry

• Maria-Paula Schröder,
• Isabel P.-M. Pfeiffer and
• Silja Mordhorst

Beilstein J. Org. Chem. 2024, 20, 1652–1670, doi:10.3762/bjoc.20.147

• of toxic agents such as MeI, TFA, or sodium cyanoborohydride can be harmful to both health and environment. Additionally, the need for constant protection and deprotection steps is time-consuming and results in low atomic economy, while also increasing the use of solvents, energy, and chemicals

New triazinephosphonate dopants for Nafion proton exchange membranes (PEM)

• Fátima C. Teixeira,
• António P. S. Teixeira and
• C. M. Rangel

Beilstein J. Org. Chem. 2024, 20, 1623–1634, doi:10.3762/bjoc.20.145

• . Romão Ramalho, 59, 7000-671 Évora, Portugal 10.3762/bjoc.20.145 Abstract A new paradigm for energy is underway demanding decarbonized energy systems. Some of them rely on emerging electrochemical devices, crucial in hydrogen technologies, including fuel cells, CO2 and water electrolysers, whose

• Decarbonized energy sources are the new paradigm in a world with increasing energy demands, primarily powered by fossil fuels, being proposed as a key strategy for restricting the detrimental effects of climate change. Vast efforts are being made to fulfil this crucial challenge of the 21st century. Clean

• , renewable, and environmental-friendly technological processes are being considered using electrochemical devices which convert chemical to electric energy and/or vice versa that, when associated to renewable energy sources, can promote sustainable energy systems [1][2][3][4]. Among them are included proton

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

• XGBoost. They trained on experimental pKa values in 39 solvents from the “internet Bond-energy Databank” (iBonD). Thus, they could predict the lowest pKa value for a wide range of molecules that contain bonds such as N–H, O–H, C–H, S–H, and P–H. However, they reported a scarcity of non-aqueous pKa values

• identify the lowest-energy conformer. We then conduct re-optimization in ORCA (v. 5.0.4) [22][23], using the dispersion D4-corrected DFT functional CAM-B3LYP [24][25], the Karlsruhe [26][27] triple-ζ basis set, def2-TZVPPD, and the conductor-like polarizable continuum model (CPCM) [28] as the implicit

• methods are evaluated as single-point calculations or optimization and frequency calculations. For comprehensive details, refer to Supporting Information File 1, section “Benchmark study - computational methods”. Hereafter, we check the geometries for imaginary frequencies and use the total thermal energy

Supramolecular assemblies of amphiphilic donor–acceptor Stenhouse adducts as macroscopic soft scaffolds

• Ka-Lung Hung,
• Leong-Hung Cheung,
• Yikun Ren,
• Ming-Hin Chau,
• Yan-Yi Lam,
• Takashi Kajitani and
• Franco King-Chi Leung

Beilstein J. Org. Chem. 2024, 20, 1590–1603, doi:10.3762/bjoc.20.142

• Abstract In the design of photoharvesting and photoresponsive supramolecular systems in aqueous medium, the fabrication of amphiphilic photoswitches enables a noninvasive functional response through photoirradiation. Although most aqueous supramolecular assemblies are driven by high-energy and biodamaging

• ; visible light; Introduction Solar energy is of paramount importance to life on the earth for various reasons, such as maintenance of a stable temperature and enabling photosynthesis as the basis of the food chain. Inspired by the natural photosynthetic processes, synthetic molecules were designed and

• functionalized with photoresponsive and photoabsorbing functional motifs, serving as the counterpart of natural photosystems. This allowed to construct smart materials that harvest light energy, e.g., solar cells, photosensitizers, and photochromic materials [1][2][3][4]. Supramolecular assemblies are commonly

Divergent role of PIDA and PIFA in the AlX₃ (X = Cl, Br) halogenation of 2-naphthol: a mechanistic study

• Kevin A. Juárez-Ornelas,
• Manuel Solís-Hernández,
• Pedro Navarro-Santos,
• J. Oscar C. Jiménez-Halla and
• César R. Solorio-Alvarado

Beilstein J. Org. Chem. 2024, 20, 1580–1589, doi:10.3762/bjoc.20.141

• reported by our group, was elucidated via quantum chemical calculations using density functional theory. The chlorination mechanism using PIFA and AlCl3 demonstrated a better experimental and theoretical yield compared to using PIDA. Additionally, the lowest-energy chlorinating species was characterized by

• energy than our proposed species. The reaction mechanisms are described in detail in this work and were found to be in excellent agreement with the experimental yield. These initial results confirmed that our proposed mechanism was energetically favored and therefore more plausible compared to

• points along the potential surface energy of the possible chlorination and bromination pathways studied in this work, Br and I atoms were treated with the revised version of the LANL2DZ basis set and effective core potential, referred to as LANL08(d), providing d-type polarization functions. Meanwhile

Regio- and stereochemical stability induced by anomeric and gauche effects in difluorinated pyrrolidines

• Ana Flávia Candida Silva,
• Francisco A. Martins and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2024, 20, 1572–1579, doi:10.3762/bjoc.20.140

• crystallographic data using the 3-fluoropyrrolidinium cation and 3-fluoropyrrolidine. Subsequently, we explored the relative energy of all favored conformations of all different stereoisomers of 2,3-, 2,4-, and 3,4-difluoropyrrolidines at the B3LYP-D3BJ/6-311++G** level. A generalized anomeric effect, arising from

• pyrrolidinium salt [11] with the CCSD/DGTZVP geometry of the pyrrolidinium cation (with an exclusively axial C–F bond) and the energy of 3-fluoropyrrolidine conformations. Various combinations of DFT methods (B3LYP-D3BJ, ωB97XD, and PBEPBE) and basis sets (DGTZVP and 6-311++G**) were evaluated. The selection of

• these functionals was based on whether or not they included dispersion terms that could influence the absolute energy. These functionals are widely used and have demonstrated strong performance in numerous evaluations and validations across the literature. Similarly, for the basis sets, a comparison was

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

• Science and Advanced Chemical Energy Research Center, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan 10.3762/bjoc.20.139 Abstract An electrocatalytic hydrogenation of

Primary amine-catalyzed enantioselective 1,4-Michael addition reaction of pyrazolin-5-ones to α,β-unsaturated ketones

• Pooja Goyal,
• Akhil K. Dubey,
• Raghunath Chowdhury and
• Amey Wadawale

Beilstein J. Org. Chem. 2024, 20, 1518–1526, doi:10.3762/bjoc.20.136

• ent-3aa-ent-3na, 1H, 13C NMR spectra of 3aa–na, 1H NMR of ent-3aa–ent-3na and their HPLC traces and single crystal data of ent-3ba. Acknowledgements The authors are thankful to Ms. Ketki Lele for her help in some preliminary experiments. Funding The authors thank the Department of Atomic Energy (DAE

Electrophotochemical metal-catalyzed synthesis of alkylnitriles from simple aliphatic carboxylic acids

• Yukang Wang,
• Yan Yao and
• Niankai Fu

Beilstein J. Org. Chem. 2024, 20, 1497–1503, doi:10.3762/bjoc.20.133

• electrophotochemical transition metal catalysis [26][27][28][29][30][31] as a unique and powerful synthetic platform for radical decarboxylative functionalization of aliphatic carboxylic acids [32][33][34][35][36][37]. In particular, the commonly required high activation energy for radical decarboxylation was provided

Photoswitchable glycoligands targeting Pseudomonas aeruginosa LecA

• Yu Fan,
• Ahmed El Rhaz,
• Stéphane Maisonneuve,
• Emilie Gillon,
• Maha Fatthalla,
• Franck Le Bideau,
• Guillaume Laurent,
• Samir Messaoudi,
• Anne Imberty and
• Juan Xie

Beilstein J. Org. Chem. 2024, 20, 1486–1496, doi:10.3762/bjoc.20.132

• rather similar Kd values. In order to rationalize this difference in binding mechanism, molecular models were obtained for selected low-energy conformations of E- and Z-isomers of a “model” scaffold of the para-azobenzene derivative in the binding site of LecA (Figure 5), by simple superpositioning of

• enthalpy (ΔH), and stoichiometry (n). Values for free energy change (ΔG) and entropy contributions (TΔS) were derived from the equation ΔG = ΔH − TΔS = − RT ln Kd (with T = 298.15 K and R = 8.314 J mol−1K−1). General procedure I for the O-alkylation with BrCH2CH2NHBoc: A solution of glycosyl azobenzene

• represents a ΔG value of −30 kJ/mol, corresponding to a Kd of approx 5 μM in the experimental conditions. (B) Manual docking of scaffold for compound 3 with selected low energy conformations of the E-isomer (yellow sticks) and Z-isomer (cyan sticks) superimposed on conserved position of galactose in all LecA

Selectfluor and alcohol-mediated synthesis of bicyclic oxyfluorination compounds by Wagner–Meerwein rearrangement

• Ziya Dağalan,
• Muhammed Hanifi Çelikoğlu,
• Saffet Çelik,
• Ramazan Koçak and
• Bilal Nişancı

Beilstein J. Org. Chem. 2024, 20, 1462–1467, doi:10.3762/bjoc.20.129

• ] and many more (Figure 1). On the other hand, with unusual geometry and high reactivity norbornadiene and benzonorbornadiene derivative bicyclic compounds attract great attention by researchers with their use as building blocks in different application areas such as polymers, solar energy storage

Predicting bond dissociation energies of cyclic hypervalent halogen reagents using DFT calculations and graph attention network model

• Yingbo Shao,
• Zhiyuan Ren,
• Zhihui Han,
• Li Chen,
• Yao Li and
• Xiao-Song Xue

Beilstein J. Org. Chem. 2024, 20, 1444–1452, doi:10.3762/bjoc.20.127

• ][45][46][47] have highlighted the critical role of bond dissociation energy (BDE) in understanding the group transfer capabilities and chemical stability of hypervalent iodine(III) reagents. In this context, detailed knowledge of the BDE of hypervalent bromine(III) and chlorine(III) reagents is

• iodine [61][62][63][64][65][66][67][68][69][70][71][72][73][74][75][76] and the computational database of organic species by Paton and co-workers [77], geometry optimizations and single point energy calculations for homolytic BDEs are both performed using M06-2X/def2-TZVPP [78][79][80] in the gas phase

• stabilize cyclic hypervalent bromine(III) and chlorine(III) reagents. In addition, we also calculated the heterolytic BDEs of cyclic hypervalent halogen reagents [46][47] to comprehensively examine the strength of chemical bonds (Table 2). Geometry optimizations and single point energy calculations for

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

• halogen-bond formation by the linear combination of the % p-orbital character on the halogen and energy of the σ-hole on the halogen-bond donor. Keywords: aryl halide; diarylhalonium; halogen; halogen bond; non-covalent interaction; Introduction Halogen bonding has emerged as an important attractive

• that, for a set of monovalent iodine-based halogen-bond donors, a linear combination of σ-hole and σ* energy provides a superior predictive ability than σ-hole alone [26]. In this work we compare a set of both monovalent and nominally hypervalent halogen-bond donors in which the central halogen atom is

• Cl, Br, I, and At. We have used density functional theory (DFT) to uncover periodic trends in the orbitals used by the central halogen atom in forming covalent and non-covalent interactions and how this impacts the interatomic distance and energy of halogen-bond interactions (Scheme 1c). Results and

Generation of alkyl and acyl radicals by visible-light photoredox catalysis: direct activation of C–O bonds in organic transformations

• Mithu Roy,
• Bitan Sardar,
• Itu Mallick and
• Dipankar Srimani

Beilstein J. Org. Chem. 2024, 20, 1348–1375, doi:10.3762/bjoc.20.119

• heightened by the current energy crisis and the adverse impacts of industrialization. The development of green and energy-efficient methods in organic chemistry that use renewable sources of starting materials is considered highly sustainable [1][2][3]. Radical reactions have profound applications in organic

• synthesis [4][5][6][7][8][9]. In the context of sustainable catalysis, visible-light-mediated chemistry is becoming a prominent viable option for radical transformations in the synthesis of biologically useful compounds due to the energy efficiency and environmental friendliness [10][11]. Recently, the

• catalysis In recent times, visible-light-mediated photoredox chemistry has evolved as a unique tool for various organic transformations. In contrast to traditional catalysis, the photochemical process uses an electron or energy transfer mechanism to form reactive intermediates. Typically, a photocatalyst is

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

• hyperconjugation via bending the exocyclic methyl group such that the formal p-orbital at C3 no longer aligns with the C2–C7 bond results in the 6/6/6-tricyclic C3 tertiary cation B2+, which is 13.0 kcal mol−1 higher in energy. In principle, either A2+ or B2+ could be deprotonated to form products. A similar

• energy profile is seen for protonation-induced cyclization of 1, although the 6/6/6-tricyclic C3 tertiary cation is 7.1 kcal mol−1 higher in energy than its preceding intermediate (Figure 2C). A lower energy conformer of 1 exists, but we have been unable to find the corresponding cation A1b+, which

• [22]. An X-ray structure of 9 allowed us to solve its absolute configuration and measure the C2–C7 distance to be 3.31 Å. This distance matches reasonably well with the calculated distance, 3.36 Å, of the lowest energy conformer of 9. Calculation of the proposed 6,7-epoxy derivative of 2, which was

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

• Diels–Alder reactions and can be used repeatedly without significant degradation. These materials also allow the reaction to be completed in less time, with less energy consumption and higher yields. Keywords: biobased solvent; epoxyisoindoles; furanics; green chemistry; intramolecular Diels–Alder

Diameter-selective extraction of single-walled carbon nanotubes by interlocking with Cu-tethered square nanobrackets

• Guoqing Cheng and
• Naoki Komatsu

Beilstein J. Org. Chem. 2024, 20, 1298–1307, doi:10.3762/bjoc.20.113

• mechanically interlocking cyclic molecules are reported not to be removed with washing [11][22][23][24]. In addition, these Raman signals of 1b shift to higher frequencies at e- and i-SWNTs, similarly to our previous report [11], probably due to the structural change of Cu-nanobrackets 1b, or the energy

• binding energy between SWNTs and the host molecules is calculated by the GFN2-xTB method, because the number of atoms is too large to use DFT methods. The binding energy Ebind is calculated by the following equation: The Ehost, ESWNTs and Ecomplex are the electronic energies of the host molecules, SWNTs

• p-SWNTs. Red and black characters indicate metallic and semiconducting SWNTs, respectively. (a, b) Enriched (n,m)-SWNTs are shown in orange. (a) Binding energy between SWNTs of various (n,m)-structures with Cu-nanobrackets 1a and 1b; GFN2-xTB-optimized structures of (b) 1a@(9,4)-SWNT and (c) 1b

Synthesis of indano[60]fullerene thioketone and its application in organic solar cells

• Yong-Chang Zhai,
• Shimon Oiwa,
• Shinobu Aoyagi,
• Shohei Ohno,
• Tsubasa Mikie,
• Jun-Zhuo Wang,
• Hirofumi Amada,
• Koki Yamanaka,
• Kazuhira Miwa,
• Naoyuki Imai,
• Takeshi Igarashi,
• Itaru Osaka and
• Yutaka Matsuo

Beilstein J. Org. Chem. 2024, 20, 1270–1277, doi:10.3762/bjoc.20.109

• transporters [9][10]. Organic photovoltaic (OPV) and perovskite solar cell (PSC) technologies have proven to be promising candidates for the sustainable use of solar energy, with power conversion efficiency (PCE) improving to 17% for OPVs and over 25% for PSCs in just a few years [11]. Functionalized fullerene

• derivatives with an emphasis on tuning solubility and energy levels. Meanwhile, less attention has been devoted to improving the thermal stability of fullerene derivatives. One well-known example is [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), which is recognized for its excellent solubility in solution

• bond length may have caused the higher reactivity and lower degradation temperature of t-Bu-FIDS compared with t-Bu-FIDO. Electron-accepting ability is one of the most important properties for fullerene derivatives, and it is typically described in terms of the energy level of the lowest unoccupied

Synthesis and optical properties of bis- and tris-alkynyl-2-trifluoromethylquinolines

• Stefan Jopp,
• Franziska Spruner von Mertz,
• Peter Ehlers,
• Alexander Villinger and
• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 1246–1255, doi:10.3762/bjoc.20.107

• different fine structures. However, TD-DFT calculations using the long-range correlated CAM-B3LYP/6-311G(d,p) level of theory reveal that the lowest energy band for all three derivatives 6a, 9a and 12a originate mainly from a HOMO→LUMO transition with some admixture of HOMO−1→LUMO+1 and HOMO−1→LUMO

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

• catalyst in the sulfonylation/arylation of styrenes and as a triplet sensitizer in energy transfer catalysis. The singlet lifetime is sufficiently long to exploit the exceptional excited state reduction potential for the activation of 4-cyanopyridine. Photoinduced electron transfer generating the radical

• increased when the triplet efficiently reacts in a catalytic cycle such that turnover numbers exceeding 4400 are achievable with this organocatalyst. Keywords: energy transfer; laser spectroscopy; organocatalyst; photoredox; time-resolved spectroscopy; Introduction The emergence of photoredox chemistry in

• lifetimes, limiting their use in collision-based electron/energy transfer reactions unless high substrate concentrations are used [29][30]. In contrast, triplet states populated via intersystem crossing (ISC) have much longer lifetimes and can efficiently react at lower substrate concentrations [30

Competing electrophilic substitution and oxidative polymerization of arylamines with selenium dioxide

• Vishnu Selladurai and
• Selvakumar Karuthapandi

Beilstein J. Org. Chem. 2024, 20, 1221–1235, doi:10.3762/bjoc.20.105

• comparing the relative energy of the frontier molecular orbitals of arylamines with SeO2 could be a convenient measure to understand the differences in polymerization tendency. The relative energy of the frontier molecular orbitals of arylamines and SeO2 is shown in Figure 7. In an oxidative polymerization

• process, an electron is transferred from the HOMO of an arylamine donor to the LUMO of the SeO2 acceptor. The computed HOMO–LUMO energy difference (∆E) between arylamines and SeO2 decreased in the following order: o-anisidine − SeO2 > aniline − SeO2 > methyl anthranilate − SeO2. It revealed that the HOMO

• of methyl anthranilate was relatively buried, with a large energy gap (mismatch) between the donor and acceptor orbitals, which slowed down the oxidative polymerization process and allowed the alternative reaction pathway, electrophilic substitution of SeO2 on the aryl ring. This result was further

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

• seven-membered ring and the remaining four 5-7 bicyclic compounds with the carbocation on the five-membered ring. The variations in energy within the groups of carbocations (i.e., 6-6 and two kinds of 5-7 bicyclic carbocations) can be ascribed to intramolecular repulsion interactions, as seen from non

• derived from germecrene A. Keywords: carbocation; germacrene A; hedycaryol; stability trend; terpenes; Introduction Terpenoids form a large and highly diverse group of natural products with a wide range of usage in the pharmaceutical, cosmetic, agricultural, food, and energy industry. Among their

• several significant processes, terpenoids play an indispensable role in cell-wall and membrane biosynthesis, sensing, plant defense, electron transport, or conversion of light into chemical energy [1][2]. Based on the number of hydrocarbon units, terpenes are classified into various families like

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

Kinetically stabilized 1,3-diarylisobenzofurans and the possibility of preparing large, persistent isoacenofurans with unusually small HOMO–LUMO gaps

• Qian Liu and
• Glen P. Miller

Beilstein J. Org. Chem. 2024, 20, 1099–1110, doi:10.3762/bjoc.20.97

• the molecule’s entire π-system including the 1,3-diphenyl substituents. This extensive delocalization of orbital density significantly raises the HOMO energy level and lowers the LUMO energy level compared to parent isobenzofuran (1). Conversely, both the HOMO and LUMO orbitals for compound 3 with 1,3

• -dimesityl substituents show reduced orbital density on the mesityl substituents compared to the phenyl substituents of 2. Likewise, 3 possesses a lower energy HOMO orbital and a higher energy LUMO orbital compared to 2. The π-systems for compounds 23, 24 and 25 with 2’,4’,6’-triethylphenyl, 2’,4’,6

Mild and efficient synthesis and base-promoted rearrangement of novel isoxazolo[4,5-b]pyridines

• Vladislav V. Nikol’skiy,
• Mikhail E. Minyaev,
• Maxim A. Bastrakov and
• Alexey M. Starosotnikov

Beilstein J. Org. Chem. 2024, 20, 1069–1075, doi:10.3762/bjoc.20.94

• fields of chemistry and materials science. These compounds are widespread in medicinal chemistry [1][2][3], production of high-energy-density compounds [4][5][6][7], and many others. In particular, isoxazolo[4,5-b]pyridines are of considerable interest due to their remarkable variety of biological