Synthesis, structure, ionochromic and cytotoxic properties of new 2-(indolin-2-yl)-1,3-tropolones

• Yurii A. Sayapin,
• Eugeny A. Gusakov,
• Inna O. Tupaeva,
• Alexander D. Dubonosov,
• Igor V. Dorogan,
• Valery V. Tkachev,
• Anna S. Goncharova,
• Gennady V. Shilov,
• Natalia S. Kuznetsova,
• Svetlana Y. Filippova,
• Tatyana A. Krasnikova,
• Yanis A. Boumber,
• Alexey Y. Maksimov,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2025, 21, 358–368, doi:10.3762/bjoc.21.26

• ://www.ccdc.cam.ac.uk/data_request/cif. Computational methods Quantum chemical calculations were performed using the Gaussian 09 software package [34] with hybrid functional PBE0 [35][36] and 6-311+G (d,p) basis set. Solvent effects were modeled by using polarizable continuum model (PCM) [37] within the integral

Antibiofilm and cytotoxic metabolites from the entomopathogenic fungus Samsoniella aurantia

• Rita Toshe,
• Syeda J. Khalid,
• Blondelle Matio Kemkuignou,
• Esteban Charria-Girón,
• Paul Eckhardt,
• Birthe Sandargo,
• Kunlapat Nuchthien,
• J. Jennifer Luangsa-ard,
• Till Opatz,
• Hedda Schrey,
• Sherif S. Ebada and
• Marc Stadler

Beilstein J. Org. Chem. 2025, 21, 327–339, doi:10.3762/bjoc.21.23

• on forces and step size. The IEFPCM solvent model [33] was used to simulate the solvent effects of methanol and frequency calculations were used to determine the conformers as minima. Conformers 4.5 kcal/mol above the lowest energy conformer and double conformers were discarded. Time-dependent DFT

Machine learning-guided strategies for reaction conditions design and optimization

• Lung-Yi Chen and
• Yi-Pei Li

Beilstein J. Org. Chem. 2024, 20, 2476–2492, doi:10.3762/bjoc.20.212

• solvent effects may complicate the results [122]. Therefore, reaction-level DFT-based descriptors are not widely used for reaction featurization. A more popular alternative is the differential reaction fingerprint (DRFP) developed by Probst et al. [123], which converts a reaction SMILES sequence into a

Hypervalent iodine-mediated cyclization of bishomoallylamides to prolinols

• Smaher E. Butt,
• Konrad Kepski,
• Jean-Marc Sotiropoulos and
• Wesley J. Moran

Beilstein J. Org. Chem. 2024, 20, 2455–2460, doi:10.3762/bjoc.20.209

• previous report on N-alkenylamide cyclizations. B) An overview of the present work. Calculated mechanism for the cyclization of amide 3a optimized at the B3LYP/ 6-31+G(d,p) level of theory with SDDall used for iodine. Solvent effects were considered using the CPCM model. All ΔG values are in kcal·mol−1

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

• values as Gibbs free energy at 298 K and 1 atm. All our calculations were performed in the gas phase. Then, the solvent effects were included according to the polarizable continuum model via the solvent model density (SMD) option considering Truhlar’s model [36][37][38][39][40] and MeCN as the solvent

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

• yields and the desired stereoselectivity [59][60][61]. The viscous nature of the aminofuranes usually requires the use of toxic solvents such as toluene, and in some studies, solvents such as DMSO, which are difficult to remove from the reaction medium [62][63][64]. Although solvent effects are of little

Structure–property relationships in dicyanopyrazinoquinoxalines and their hydrogen-bonding-capable dihydropyrazinoquinoxalinedione derivatives

• Tural N. Akhmedov,
• Ajeet Kumar,
• Daken J. Starkenburg,
• Kyle J. Chesney,
• Khalil A. Abboud,
• Novruz G. Akhmedov,
• Jiangeng Xue and
• Ronald K. Castellano

Beilstein J. Org. Chem. 2024, 20, 1037–1052, doi:10.3762/bjoc.20.92

• and aromatic groups as strong donors in the backbone; the dione groups in the case of DPQDs diminish the acceptor properties of the aza π-system. It is worth mentioning that ICT is significantly influenced by solvent polarity and the comprehensive study of solvent effects is not within the scope of

Ligand effects, solvent cooperation, and large kinetic solvent deuterium isotope effects in gold(I)-catalyzed intramolecular alkene hydroamination

• Ruichen Lan,
• Brock Yager,
• Yoonsun Jee,
• Cynthia S. Day and
• Amanda C. Jones

Beilstein J. Org. Chem. 2024, 20, 479–496, doi:10.3762/bjoc.20.43

• mechanism in Scheme 2). Solvent effects: Michon and co-workers reported the beneficial assistance of water on enantioselective hydroamination, with the perchlorate being the best performing counterion. They propose that the anion is acting as a salting-in agent to contribute to better solvation of catalyst

• here. Previous discussions of solvent effects focus on the ability to support or disrupt substrate metal interactions. Acetonitrile was shown to coordinate to gold more strongly than C–C multiple bonds, thus highly disfavoring the necessary π-coordination to initiate reactivity, and acetonitrile

• deviating from classic π-activation. Solvent effects that subtly impact solubility and proton transfer processes are likely to mask the impact of individual mechanistic steps involving gold and are not adequate to distinguish between the contrasting mechanisms under consideration here (Scheme 1 vs Scheme 2

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

• intermediate was not viable under such mild conditions. The initially proposed ionic pathway (Figure 5, left) was abandoned as solvent effects had little influence on the reaction rate, and since no Wagner–Meerwein rearrangement products were detected with bicyclic olefin precursors. Radical-based pathways

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• , and then did TD-DFT calculations at the same level of theory. Solvent effects were modeled using the SMD implicit water solvation. The obtained vertical transitions corresponding to absorption maxima at pH 7.0 are 260 and 372 nm (Phen-Py-1), and 270 and 397 nm (Phen-Py-2). At pH 5.0 vertical

• package [55], with the water solvent effects modeled through the implicit SMD solvation [56]. The choice of such computational setup was prompted by its success in reproducing various features of different organic [57][58], organometallic [59], and protein systems [60], being particularly accurate for

Naphthalimide-phenothiazine dyads: effect of conformational flexibility and matching of the energy of the charge-transfer state and the localized triplet excited state on the thermally activated delayed fluorescence

• Kaiyue Ye,
• Liyuan Cao,
• Davita M. E. van Raamsdonk,
• Zhijia Wang,
• Jianzhang Zhao,
• Daniel Escudero and
• Denis Jacquemin

Beilstein J. Org. Chem. 2022, 18, 1435–1453, doi:10.3762/bjoc.18.149

• ) using the same functional and basis sets as in the ground-state optimizations [61]. TDA-TD-DFT is preferred over standard (or “full”) TD-DFT as the former is often more reliable for triplet excited states. Solvent effects were included using the polarizable continuum model (PCM) [62][63][64]. The above

A Streptomyces P450 enzyme dimerizes isoflavones from plants

• Run-Zhou Liu,
• Shanchong Chen and
• Lihan Zhang

Beilstein J. Org. Chem. 2022, 18, 1107–1115, doi:10.3762/bjoc.18.113

• conformers were chosen for ECD calculations in methanol at the B3LYP/6-311+G (d,p) level. Solvent effects were taken into consideration using the self-consistent reaction field (SCRF) method with the polarizable continuum model (PCM). The ECD spectrum was generated by the SpecDis program [42] using a

Morita–Baylis–Hillman reaction of 3-formyl-9H-pyrido[3,4-b]indoles and fluorescence studies of the products

• Nisha Devi and
• Virender Singh

Beilstein J. Org. Chem. 2022, 18, 926–934, doi:10.3762/bjoc.18.92

• exhibit excellent fluorescence characteristics. Different parameters like contact time, concentration, solvent effects and substituent effects were examined for obtaining the optimal results. It was observed that the MBH derivatives exhibited excellent fluorescence characteristics at a concentration of 5

Comparative study of thermally activated delayed fluorescent properties of donor–acceptor and donor–acceptor–donor architectures based on phenoxazine and dibenzo[a,j]phenazine

• Saika Izumi,
• Prasannamani Govindharaj,
• Anna Drewniak,
• Paola Zimmermann Crocomo,
• Satoshi Minakata,
• Leonardo Evaristo de Sousa,
• Piotr de Silva,
• Przemyslaw Data and
• Youhei Takeda

Beilstein J. Org. Chem. 2022, 18, 459–468, doi:10.3762/bjoc.18.48

• collected in Table S1 (Supporting Information File 1). The Tamm–Dancoff (TDA) approximation was used in all excited state calculations and solvent effects were included by means of the polarizable continuum model (PCM) associated with a perturbative state specific solvation method using toluene as solvent

Iridium-catalyzed hydroacylation reactions of C1-substituted oxabenzonorbornadienes with salicylaldehyde: an experimental and computational study

• Angel Ho,
• Austin Pounder,
• Krish Valluru,
• Leanne D. Chen and
• William Tam

Beilstein J. Org. Chem. 2022, 18, 251–261, doi:10.3762/bjoc.18.30

• local minima have only real frequencies, while transition-state structures were characterized by exactly one imaginary frequency. Solvent effects (solvent = 1,4-dioxane) were taken into account using the polarized continuum model (PCM) of Tomasi and co-workers [72] and were involved in all geometry

Electron-rich triarylphosphines as nucleophilic catalysts for oxa-Michael reactions

• Susanne M. Fischer,
• Simon Renner,
• A. Daniel Boese and
• Christian Slugovc

Beilstein J. Org. Chem. 2021, 17, 1689–1697, doi:10.3762/bjoc.17.117

• calculations, temperature effects (298 K) and zero-point energies have been approximated by the rigid-rotor-harmonic oscillator (RRHO) approximation. The zero-point energies have been scaled by a factor of 1.0030 (B3LYP/def2-TZVPPD) and 1.0302 (PBE/def2-SVPD) to account for anharmonic effects [52]. Solvent

• effects of chloroform have been considered for calculation of the Gibbs free energy (ΔG) of zwitterion formation and were calculated by the conductor-like screening model (COSMO) [53][54] with a dielectric constant of 4.8 and a radius of 3.17. Our best estimate for the calculation of zwitterion energies

The synthesis of chiral β-naphthyl-β-sulfanyl ketones via enantioselective sulfa-Michael reaction in the presence of a bifunctional cinchona/sulfonamide organocatalyst

• Deniz Tözendemir and
• Cihangir Tanyeli

Beilstein J. Org. Chem. 2021, 17, 494–503, doi:10.3762/bjoc.17.43

• ). The solvent effects on the SMA of the chalcone derivatives and naphthalene-1-thiol are summarized in Figure 2. This behavior might be related to the better stabilization of the transition state of the substrates containing electron-withdrawing substituents or halogen atoms with THF, or vice versa. In

Conformational preferences of fluorine-containing agrochemicals and their implications for lipophilicity prediction

• Daniela Rodrigues Silva,
• Joyce K. Daré and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2020, 16, 2469–2476, doi:10.3762/bjoc.16.200

• . Solvent effects were accounted for by geometry optimization using the integral equation formalism variant of the polarizable continuum model (IEFPCM) [35]. Insights into the intramolecular interactions governing conformational preferences were obtained through the natural bond orbital (NBO) analysis [19

One-pot synthesis of isosorbide from cellulose or lignocellulosic biomass: a challenge?

• Isaline Bonnin,
• Raphaël Mereau,
• Thierry Tassaing and
• Karine De Oliveira Vigier

Beilstein J. Org. Chem. 2020, 16, 1713–1721, doi:10.3762/bjoc.16.143

• particular, in situ kinetic studies by spectroscopic methods [31] correlated to computational chemistry approaches [32] might reveal specific interaction between reactants and catalysts as well as solvent effects at work in such a complex system that should provide an understanding of the underlying reason

Suzuki–Miyaura cross coupling is not an informative reaction to demonstrate the performance of new solvents

• James Sherwood

Beilstein J. Org. Chem. 2020, 16, 1001–1005, doi:10.3762/bjoc.16.89

• ][22], and excels in a variety of reaction media. On the evidence of this study, it can be concluded that the Suzuki–Miyaura reaction is not an informative case study for solvent effects and cannot reliably validate the benefits of one particular solvent. This is because catalysts and conditions can be

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

• rearrangements proceed via isopolar transition states and, therefore solvent effects are rather small. For this reason and due to the complete lack of enantioselectivity, at this stage, we did not investigate other solvents with the catalysts collected in Figure 1. In order to gain further insight into the

• . As mentioned above, the Ireland–Claisen rearrangement, as a pericyclic reaction, is expected to be rather insensitive to solvent effects. However, minor improvements in reaction time have been noted in some cases [39]. Therefore, with the aim of improving the reaction course, we evaluated several

A combinatorial approach to improving the performance of azoarene photoswitches

• Joaquin Calbo,
• Aditya R. Thawani,
• Rosina S. L. Gibson,
• Andrew J. P. White and
• Matthew J. Fuchter

Beilstein J. Org. Chem. 2019, 15, 2753–2764, doi:10.3762/bjoc.15.266

• ground state geometries of both Z- and E-isomers were computed under the time-dependent density functional theory (TDDFT) approach [41][42]. The 20 lowest-lying singlet excited states were calculated in all conformers at the TD-PBE0/6-31G** level of theory in the gas phase. Solvent effects in

Plasma membrane imaging with a fluorescent benzothiadiazole derivative

• Pedro H. P. R. Carvalho,
• Jose R. Correa,
• Karen L. R. Paiva,
• Daniel F. S. Machado,
• Jackson D. Scholten and
• Brenno A. D. Neto

Beilstein J. Org. Chem. 2019, 15, 2644–2654, doi:10.3762/bjoc.15.257

• for the calculated properties of the designed structure (Figure 4). The UV–vis absorption spectra of BTD-4APTEG calculated at the PBE1PBE/6-311+G(2d,p)//CAM-B3LYP/6-311+G(d) are shown in Figure 4B and solvent effects were also accounted using the IEF-PCM formalism [51]. The theoretical absorption

• were carried out with the long-range corrected density functional CAM-B3LYP with 6-31G(d) Pople’s split basis set. Harmonic frequency calculations were performed to verify that a genuine energetic minimum was achieved. Solvent effects on the BTD-4APTEG geometries were assessed using the polarizable

• the performance of different density functionals: B3LYP, CAM-B3LYP, LC-ωPBE, M06, M06-2X, and PBE1PBE. It was employed the 6-311+G(2d,p) basis set to simulate the excitation spectra of the BTDs. To comprise the solvent effects, the implicit PCM treatment was also included in the TD-DFT calculations

Probing of local polarity in poly(methyl methacrylate) with the charge transfer transition in Nile red

• Aydan Yadigarli,
• Qimeng Song,
• Sergey I. Druzhinin and
• Holger Schönherr

Beilstein J. Org. Chem. 2019, 15, 2552–2562, doi:10.3762/bjoc.15.248

• stained with NR [19]. Recently, the phase of the microcapsules and their energy release were analyzed by monitoring the color of NR fluorescence in an energy storage microsystem [22]. Although NR solvent effects are a useful tool in biology and technology, an adequate description and characterization of

Small anion-assisted electrochemical potential splitting in a new series of bistriarylamine derivatives: organic mixed valency across a urea bridge and zwitterionization

• Keishiro Tahara,
• Tetsufumi Nakakita,
• Alyona A. Starikova,
• Takashi Ikeda,
• Masaaki Abe and
• Jun-ichi Kikuchi

Beilstein J. Org. Chem. 2019, 15, 2277–2286, doi:10.3762/bjoc.15.220

• potential splitting should be smaller in case of compound 1a because of the separated redox units (N···N 13.13 Å for 1a+ in the DFT-optimized structure). Unfortunately, no investigations of solvent effects were performed with 1b due to the low solubility in polar solvents including MeCN/CH2Cl2 mixed