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

• conformers (II, VI, and VII), and with a rotatable C–C(F) bond that generates different conformers (I). The μ values for all herbicides were computed through theoretical calculations (see computational details section) and are presented in Table 2 along with their respective experimental log P data

Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties

• Anka Utama Putra,
• Deniz Çakmaz,
• Nurgül Seferoğlu,
• Alberto Barsella and
• Zeynel Seferoğlu

Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189

• little effect on the shift for dye 3 (6 nm). In case of the Schiff bases 8–11, similar bathochromic shifts were observed. In addition, experimentally, there was no solvatochromic behavior observed for dyes 7 and 12 as was predicted by theoretical calculations. Based on theoretical calculations, the main

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• with significant Stokes shifts (+60 nm) and quantum yields of 10–32% (Table 1). Theoretical calculations To get insight into the electronic and optical properties of the 2-amino-6-chloro-substituted NDIs, we carried out computational investigations by using the Gaussian 09 program suite [32]. In

One-pot synthesis of oxazolidinones and five-membered cyclic carbonates from epoxides and chlorosulfonyl isocyanate: theoretical evidence for an asynchronous concerted pathway

• Esra Demir,
• Ozlem Sari,
• Yasin Çetinkaya,
• Ufuk Atmaca,
• Safiye Sağ Erdem and
• Murat Çelik

Beilstein J. Org. Chem. 2020, 16, 1805–1819, doi:10.3762/bjoc.16.148

• reaction of CSI with epoxides in different solvents under mild conditions and compared the reaction mechanism with previously proposed mechanisms using theoretical calculations. Keshava Murthy and Dhar [41] postulated a mechanism involving a zwitterionic intermediate. C–O bond cleavage in this unstable and

Recent synthesis of thietanes

• Jiaxi Xu

Beilstein J. Org. Chem. 2020, 16, 1357–1410, doi:10.3762/bjoc.16.116

• diradicals as intermediates. To explain the regioselectivity, theoretical calculations were performed with thiochalcone and acrylonitrile as model substrates. For the frontier molecular orbital treatment, the largest coefficients in both HOMO and LUMO of thiochalcone existed on the sulfur atom, while the

Highly selective Diels–Alder and Heck arylation reactions in a divergent synthesis of isoindolo- and pyrrolo-fused polycyclic indoles from 2-formylpyrrole

• Carlos H. Escalante,
• Eder I. Martínez-Mora,
• Carlos Espinoza-Hicks,
• Alejandro A. Camacho-Dávila,
• Fernando R. Ramos-Morales,
• Francisco Delgado and
• Joaquín Tamariz

Beilstein J. Org. Chem. 2020, 16, 1320–1334, doi:10.3762/bjoc.16.113

• ]. Theoretical calculations The Diels–Alder reaction of vinylpyrroles 8b, 8c and 8g with maleimides 7b and 7c resulted in a highly diastereoselective cycloaddition leading to the mixture of endo/exo cycloadducts 9/10, where the endo product 9 was the major one (Scheme 3 and Table 2). Considering the synthetic

• pyrrolizine-containing polycycles, including isoindolo[2,1-a]indole-based tetrahydro and fully aromatic pentacycles. These findings reveal the synthetic value of 2-formylpyrrole (13a) for the diastereo- and regioselective construction of isoindolo- and pyrrolo-fused polycyclic indoles. Theoretical

• calculations suggest that the greater stability of the endo TSs in the Diels–Alder cycloadditions is associated with NCIs between the N-substituents of both cycloaddends. These interactions are also involved in the case of pyrrolo[2,1-a]isoindole 18a with dienophile 7c. Fused aza-hetero polycyclic frames and

Development of fluorinated benzils and bisbenzils as room-temperature phosphorescent molecules

• Shigeyuki Yamada,
• Takuya Higashida,
• Yizhou Wang,
• Masato Morita,
• Takuya Hosokai,
• Kaveendra Maduwantha,
• Kaveenga Rasika Koswattage and
• Tsutomu Konno

Beilstein J. Org. Chem. 2020, 16, 1154–1162, doi:10.3762/bjoc.16.102

• corresponding bis-oxidized bisbenzil derivatives. Based on theoretical calculations, the selective formation of the fluorinated analogues stemmed from the slight modulation of the charge distribution at the alkyne moiety of the reactant induced by the electron-withdrawing fluorine atoms. Evaluation of the

Synthesis and properties of quinazoline-based versatile exciplex-forming compounds

• Rasa Keruckiene,
• Simona Vekteryte,
• Ervinas Urbonas,
• Matas Guzauskas,
• Eigirdas Skuodis,
• Dmytro Volyniuk and
• Juozas V. Grazulevicius

Beilstein J. Org. Chem. 2020, 16, 1142–1153, doi:10.3762/bjoc.16.101

• compounds, based on theoretical calculations and experimental measurements, as well as the electrochemical and thermal properties, are discussed. The synthesized compounds form glasses with glass-transition temperatures ranging from 116 °C to 123 °C. The ionization potentials estimated by cyclic voltammetry

• [15]. Theoretical calculations and electrochemical properties DFT calculations were employed to gain insight into the structure–property relationships of the quinazoline-based derivatives 1–3. The compounds have phenyl spacers between the donor and acceptor units (Figure 2). Therefore, the dihedral

• results of theoretical calculations which revealed that the HOMO and LUMO orbitals of the carbazole-substituted quinazoline compound 1 overlap. Photophysical and electronic properties Figure 4 shows the theoretical UV spectra and experimental absorption spectra of dilute THF solutions of compounds 1–3

Aryl-substituted acridanes as hosts for TADF-based OLEDs

• Naveen Masimukku,
• Dalius Gudeika,
• Oleksandr Bezvikonnyi,
• Ihor Syvorotka,
• Rasa Keruckiene,
• Dmytro Volyniuk and
• Juozas V. Grazulevicius

Beilstein J. Org. Chem. 2020, 16, 989–1000, doi:10.3762/bjoc.16.88

• . Theoretical calculations The optimized structures of 3–6 were obtained by density functional theory (DFT) calculations at the B3LYP/6-31G(d,p) level of theory (Figure 1). The dihedral angles between the acridanyl and phenyl moieties in compound 3 (37.0 and 36.3°) are comparable with the dihedral angles

• earlier [34]. 1H NMR and 13C NMR spectra were obtained using a Varian Unity Inova (300 MHz (1H) and 75 MHz (13C)). Absorption and photoluminescence (PL) spectra of dilute solutions and of the films were recorded as described previously [35]. Theoretical calculations were carried out using Gaussian 16 [29

Synthesis and properties of tetrathiafulvalenes bearing 6-aryl-1,4-dithiafulvenes

• Aya Yoshimura,
• Hitoshi Kimura,
• Kohei Kagawa,
• Mayuka Yoshioka,
• Toshiki Itou,
• Dhananjayan Vasu,
• Takashi Shirahata,
• Hideki Yorimitsu and
• Yohji Misaki

Beilstein J. Org. Chem. 2020, 16, 974–981, doi:10.3762/bjoc.16.86

• ; one was the palladium-catalyzed C–H arylation of TTF with bromide 12 (Scheme 2a) and the other was the Vilsmeier–Haack reaction of 1a, followed by triethyl phosphite-mediated cross coupling with 11 (Scheme 2b). Theoretical calculations The DFT calculations of compounds 1a, 3a, and 4 have been carried

One-pot synthesis of dicyclopenta-fused peropyrene via a fourfold alkyne annulation

• Ji Ma,
• Yubin Fu,
• Junzhi Liu and
• Xinliang Feng

Beilstein J. Org. Chem. 2020, 16, 791–797, doi:10.3762/bjoc.16.72

• exhibits a narrow energy gap (1.78 eV) and a lower LUMO energy level than the parent peropyrene without the fusion of the five-membered rings. In addition, the effects of the peri-fused pentagons on the aromaticity and molecular orbitals of 1 were evaluated by theoretical calculations. This work presents

• -diphenylethyne, Pd2(dba)3, P(o-tol)3, KOAc, LiCl, DMF, 130 °C, microwave, 6 h, 5%. Supporting Information Supporting Information File 276: Experimental details, synthetic procedures, single crystal X-ray data for 1, detailed theoretical calculations, and analytical data for the compounds. Acknowledgements We

Direct borylation of terrylene and quaterrylene

• Haruka Kano,
• Keiji Uehara,
• Kyohei Matsuo,
• Hironobu Hayashi,
• Hiroko Yamada and
• Naoki Aratani

Beilstein J. Org. Chem. 2020, 16, 621–627, doi:10.3762/bjoc.16.58

• photophysical properties of TB4 are also unchanged by the substituents because the carbon atoms at 2,5,10,13-positions have less coefficients on its HOMO and LUMO, estimated by theoretical calculations. Finally, the same borylation reaction was applied for quaterrylene, resulting in the formation of soluble

Regioselectively α- and β-alkynylated BODIPY dyes via gold(I)-catalyzed direct C–H functionalization and their photophysical properties

• Takahide Shimada,
• Shigeki Mori,
• Masatoshi Ishida and
• Hiroyuki Furuta

Beilstein J. Org. Chem. 2020, 16, 587–595, doi:10.3762/bjoc.16.53

• estimated to be 2.30, 2,14, 2.35, and 2.21 V, respectively, which is consistent with the calculated HOMO–LUMO energy gaps (vide infra, Figure S24, Supporting Information File 1). Theoretical calculations To gain insight into the substitution effect on the electronic properties of the BODIPY derivatives

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

• Panagiotis S. Gritzapis,
• Panayiotis C. Varras,
• Nikolaos-Panagiotis Andreou,
• Katerina R. Katsani,
• Konstantinos Dafnopoulos,
• George Psomas,
• Zisis V. Peitsinis,
• Alexandros E. Koumbis and
• Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

• ∙1010 s−1, which is a very large value, indicating a fast N−O bond dissociation for compound 12. Equations 1–3 are described in the theoretical calculations section. As soon as the two radicals (amidinyl and p-chlorocarbamoyloxyl) are formed, the second radical starts to decarboxylate according to the

• chemical reaction below (Scheme 3). The activation free energy for the decarboxylation reaction is only 1.09 kcal/mol and by using Equation 4 (see theoretical calculations section) we find a rate constant kr = 9.87∙1011 s−1, characterizing the reaction as an ultrafast one, with a corresponding life-time of

• factor of 1.43 [11]. Theoretical calculations Calculations for the photodegradation of carbamates The structures, properties and the basic photochemistry of compounds 11 and 12 was studied using the density functional theory (DFT) method [86][87][88][89] and the functional B3PW91 along with the 6-31 G(d

Pigmentosins from Gibellula sp. as antibiofilm agents and a new glycosylated asperfuran from Cordyceps javanica

• Soleiman E. Helaly,
• Wilawan Kuephadungphan,
• Patima Phainuphong,
• Mahmoud A. A. Ibrahim,
• Kanoksri Tasanathai,
• Suchada Mongkolsamrit,
• Janet Jennifer Luangsa-ard,
• Souwalak Phongpaichit,
• Vatcharin Rukachaisirikul and
• Marc Stadler

Beilstein J. Org. Chem. 2019, 15, 2968–2981, doi:10.3762/bjoc.15.293

• File 1. ECD theoretical calculations TDDFT-ECD was used to perform theoretical ECD calculations. Conformational searches for the investigated compounds were first performed with a MMFF94S force field and an energy window of 10 kcal/mol using Omega2 software [54][55]. Each resulting conformer was then

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

• scaffold, the theoretical calculations at the PBE0-D3/6-31G** level indicate that an insertion of electron-poor fluorine atoms in the ortho-position of the aryl ring (4pzH-F1 and 4pzH-F2) leads to an increase in the half-life from ca. 1000 days in 4pzH to 2000 days in 4pzH-F1 and to 4000 days in 4pzH-F2

• above, theoretical calculations indicate that the addition of ortho-fluoro atoms leads to higher Z-isomer stability, whereas the opposite effect is found upon chlorine ortho-substitution (Table 1). The insertion of one and two electron-donating OMe and Pyr groups systematically improve the Z-isomer

• compared to E to allow for efficient Z–E photoswitching. Theoretical calculations indicate that the family of ortho-substituted 4pzH-X photoswitches provide a weak n–π* transition, with oscillator strengths f < 0.020. In contrast, 4pzMe-X derivatives show a relatively intense n–π* excitation, with f

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

• bioimaging experiments and proved to be stable under constant light irradiation for more than 4 hours (see Figure S4 in Supporting Information File 1). Theoretical calculations were then performed for a better comprehension of the photophysical data obtained for BTD-4APTEG by means of the time-dependent

• affinity for the plasma membrane as depicted in the imaging (qualitative and quantitative) experiments. Theoretical calculations were found to be in accordance with the experimental data and helped to understand the ICT stabilizing process of the designed fluorophore. The developed green emitter was

• ) 156.4, 155.8, 144.1, 130.9, 129.2, 126.4, 123.3, 120.1, 111.9. 71.50, 71.47, 70.2, 69.9, 69.3, 38.9; HRMS (ESI-Q-TOF) calcd. for C18H23N4O3S+, 375.1485; found, 375.1460. Theoretical calculations. All DFT calculations were performed using the Gaussian 09 suite of programs [64]. Geometry optimizations

AgNTf₂-catalyzed formal [3 + 2] cycloaddition of ynamides with unprotected isoxazol-5-amines: efficient access to functionalized 5-amino-1H-pyrrole-3-carboxamide derivatives

• Ziping Cao,
• Jiekun Zhu,
• Li Liu,
• Yuanling Pang,
• Laijin Tian,
• Xuejun Sun and
• Xin Meng

Beilstein J. Org. Chem. 2019, 15, 2623–2630, doi:10.3762/bjoc.15.255

• carbene pathway presumed by mechanistic studies and theoretical calculations. Following our ongoing interest in the alkyne chemistry [36][37][38], we recently envisaged that the reaction of ynamides with isoxazoles could proceed under silver catalysis conditions, involving the generation of α-imino silver

Anion-driven encapsulation of cationic guests inside pyridine[4]arene dimers

• Anniina Kiesilä,
• Jani O. Moilanen,
• Anneli Kruve,
• Christoph A. Schalley,
• Perdita Barran and
• Elina Kalenius

Beilstein J. Org. Chem. 2019, 15, 2486–2492, doi:10.3762/bjoc.15.241

• the pyridine[4]arene dimer, and all mass spectrometric data and theoretical calculations show undoubtedly that the cation is located inside the cavity of the dimer in the gas phase. It is an interesting fact, that the binding properties of pyridine[4]arene differ from earlier reports [7][8]. However

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

• Ronja Driller,
• Daniel Garbe,
• Norbert Mehlmer,
• Monika Fuchs,
• Keren Raz,
• Dan Thomas Major,
• Thomas Brück and
• Bernhard Loll

Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228

• followed by a 1,5-hydride shift. The sequential 1,2-hydride shift (C to E) route was initially suggested by theoretical calculations, which supported the overall mechanism [33][34], and this was verified via isotope labeling [34]. Such series of two 1,2-hydride shifts have previously been demonstrated

• in terpene biosynthesis. The enzyme could be understood as passive catalyst, essentially chaperoning the intermediates during the reaction cascade. It is clear that much of terpene biosynthesis can be understood by this concept. “Inherent reactivity” largely relies on theoretical calculations

Fluorinated azobenzenes as supramolecular halogen-bonding building blocks

• Esther Nieland,
• Oliver Weingart and
• Bernd M. Schmidt

Beilstein J. Org. Chem. 2019, 15, 2013–2019, doi:10.3762/bjoc.15.197

• boxes [35]. Therefore, we herein present a comprehensive investigation of the photochemistry of highly fluorinated azobenzenes. Our efforts are supported by theoretical calculations, showing that these azobenzenes are suitable for the use as building blocks in supramolecular architectures. Results and

Tautomerism as primary signaling mechanism in metal sensing: the case of amide group

• Vera Deneva,
• Georgi Dobrikov,
• Aurelien Crochet,
• Daniela Nedeltcheva,
• Katharina M. Fromm and
• Liudmil Antonov

Beilstein J. Org. Chem. 2019, 15, 1898–1906, doi:10.3762/bjoc.15.185

• , based on 4-(phenyldiazenyl)naphthalen-1-ol. According to the theoretical calculations the enol form stabilization could be achieved through a strong intramolecular hydrogen bond formed between the tautomeric hydroxy group and the carbonyl group from the tautomeric backbone. However, intermolecular

• still not appear even after 1024 scans. Theoretical calculations Quantum-chemical calculations were performed using the Gaussian 09 D.01 program suite [17]. The M06-2X functional [18][19] was used with the 6-31++G** basis set for the calculations. This fitted hybrid meta-GGA functional with 54% HF

Synthesis, photophysical and electrochemical properties of pyridine, pyrazine and triazine-based (D–π–)₂A fluorescent dyes

• Keiichi Imato,
• Toshiaki Enoki,
• Koji Uenaka and
• Yousuke Ooyama

Beilstein J. Org. Chem. 2019, 15, 1712–1721, doi:10.3762/bjoc.15.167

• due to the increase in the electron-withdrawing ability of the azine ring in the order of pyridyl < pyrazyl < triazyl, resulting in a decrease in the energy gap between the HOMO and the LUMO. Theoretical calculations In order to examine the HOMO and LUMO distributions of OUY-2, OUK-2 and OUJ-2, the

Superelectrophilic carbocations: preparation and reactions of a substrate with six ionizable groups

• Sean H. Kennedy,
• Makafui Gasonoo and
• Douglas A. Klumpp

Beilstein J. Org. Chem. 2019, 15, 1515–1520, doi:10.3762/bjoc.15.153

• electrophiles based on the triarylmethyl cation scaffold (3–5, Scheme 1) [11][12]. These systems utilized pyridyl rings to produce increasing amounts of positive charge adjacent to the carbocation center. Both theoretical calculations and experimental results indicated that the carbocation center undergoes a

• position and deprotonation of the para-carbon to complete the arylation step. For the cyclization product 11, theoretical calculations indicate that cyclization requires deprotonation at the pyridinium ring [11]. Thus, either the tetracation 15 or the pentacation 16 is the likely precursor to the pyrido

Selenophene-containing heterotriacenes by a C–Se coupling/cyclization reaction

• Pierre-Olivier Schwartz,
• Sebastian Förtsch,
• Astrid Vogt,
• Elena Mena-Osteritz and
• Peter Bäuerle

Beilstein J. Org. Chem. 2019, 15, 1379–1393, doi:10.3762/bjoc.15.138

• (Figure 2b), because a completely flat geometry of the isolated molecule DST 3 (in the gas phase) was obtained from theoretical calculations (vide infra). Molecules of DST 3 order in a typical herringbone fashion, where the terminal hydrogen atoms form hydrogen bond-like C–H heteroatom interactions (2.819

• the crystal structure analysis. The analysis of the theoretical calculations gave also insight into the electronic properties of the heterotriacene series. The energies of the calculated frontier orbitals and electronic transitions are summarized in Table 3. In this respect, the energy of the HOMO

• to the planar π-conjugated system. Gaussian deconvolution of the experimental spectra exemplarily shown for DDT 1 (Figure 6, right) evidenced the coexistence of two electronic transitions under the absorption curve in correlation with the theoretical calculations (vide infra). The absorption maxima