Benzoimidazolium-derived dimeric and hydride n-dopants for organic electron-transport materials: impact of substitution on structures, electrochemistry, and reactivity

• Swagat K. Mohapatra,
• Khaled Al Kurdi,
• Samik Jhulki,
• Georgii Bogdanov,
• John Bacsa,
• Maxwell Conte,
• Tatiana V. Timofeeva,
• Seth R. Marder and
• Stephen Barlow

Beilstein J. Org. Chem. 2023, 19, 1651–1663, doi:10.3762/bjoc.19.121

• that the sample represents neither solely a high-symmetry conformer, nor a mixture of rapidly exchanging lower symmetry conformers. In the case of 1b2 all the proton resonances are rather broad, and variable-temperature experiments (see Supporting Information File 1, Figure S2) showed further

• reported Y = ferrocenyl derivative, 1c2 [14], or the molecule in the structure 22 [35], all three of which also have Ci symmetry. The other conformer present, although also staggered, has no crystallographic, or even approximate molecular, symmetry and is characterized by a Y–C–C–Y torsion angle of 60.3

• mostly somewhat folded towards a puckered envelope conformation, generally with the Y group in a pseudo-axial position and the 1,3-methyl groups and the central C–C bond in pseudo-equatorial positions, although for one of the monomers in the unsymmetrical conformer in the structure of (N-DMBI)2, 1b2, the

Sulfur-containing spiroketals from Breynia disticha and evaluations of their anti-inflammatory effect

• Ken-ichi Nakashima,
• Naohito Abe,
• Masayoshi Oyama,
• Hiroko Murata and
• Makoto Inoue

Beilstein J. Org. Chem. 2023, 19, 1604–1614, doi:10.3762/bjoc.19.117

• ′, and 24 conformers for 3. The geometry of each conformer was optimized using DFT calculations at the B3LYP/6-31G(d) level of theory [20][21] with the conductor-like polarizable continuum model (CPCM) solvent model (MeOH) and Gibbs free energy was calculated subsequent frequency calculations. Time

• -dependent (TD)-DFT calculations at the B3LYP/6-31+G(d,p) level with CPCM solvent model (MeOH) [22] were performed for the optimized conformers. The resulting ECD spectra calculated for each conformer were averaged using Boltzmann populations evaluated at 300 K from Gibbs free energy calculated from the

CuAAC-inspired synthesis of 1,2,3-triazole-bridged porphyrin conjugates: an overview

• Dileep Kumar Singh

Beilstein J. Org. Chem. 2023, 19, 349–379, doi:10.3762/bjoc.19.29

• porphyrin subunits and was more efficient in DMSO as compared to chloroform. Also, a clear evidence of a folded conformer was found by electrostatic and CH–π interactions, which was also, confirmed by density functional theory (DFT) calculations. In another report, meso-triazole-bridged porphyrin-carborane

Germacrene B – a central intermediate in sesquiterpene biosynthesis

• Houchao Xu and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 186–203, doi:10.3762/bjoc.19.18

• main product [36]. Based on molecular mechanics calculations, four conformers 1a–d have been described for 1 (Scheme 3B) [37]. The calculations revealed all four conformers are of similar stability, with 1a being the most stable conformer. The fact that 1 shows a defined set of fifteen sharp signals in

A novel spirocyclic scaffold accessed via tandem Claisen rearrangement/intramolecular oxa-Michael addition

• Anastasia Vepreva,
• Alexander Yanovich,
• Dmitry Dar’in,
• Grigory Kantin,
• Alexander Bunev and
• Mikhail Krasavin

Beilstein J. Org. Chem. 2022, 18, 1649–1655, doi:10.3762/bjoc.18.177

• rationalized by the greater steric repulsion in the conformer of the respective oxyanion leading to the anti diastereomer compared to that from which the major, syn diastereomer is formed (Scheme 5). Notably, a compound analogous to 5a was synthesized with thiophenol in 78% yield. However, it turned out to be

Synthesis of (−)-halichonic acid and (−)-halichonic acid B

• Keith P. Reber and
• Emma L. Niner

Beilstein J. Org. Chem. 2022, 18, 1629–1635, doi:10.3762/bjoc.18.174

• -stereogenic center, which bears a methyl group, the electrophilic site (the iminium ion), and two possible nucleophilic sites (a prenyl group and a trisubstituted alkene within a cyclohexene ring). In conformer 12a, the prenyl group occupies a pseudo-axial position, the methyl group occupies a pseudo

• -equatorial position, and the trisubstituted alkene within the six-membered ring serves as the nucleophile. It is important to note that in this chair-like conformer, the ethyl ester group at C2 assumes a pseudo-equatorial position. Although an alternative boat-like conformer is also possible (which would

• of the 3-azabicyclo[3.3.1]nonane ring system. In any case, this aza-Prins reaction is by far the preferred mode of cyclization of iminium ion 12 based on the isolated yield of 8 (64%), ultimately leading to the carbon skeleton found in the natural product halichonic acid ((+)-1). In conformer 12b

Comparison of crystal structure and DFT calculations of triferrocenyl trithiophosphite’s conformance

• Ruslan P. Shekurov,
• Mikhail N. Khrizanforov,
• Ilya A. Bezkishko,
• Tatiana P. Gerasimova,
• Almaz A. Zagidullin,
• Daut R. Islamov and
• Vasili A. Miluykov

Beilstein J. Org. Chem. 2022, 18, 1499–1504, doi:10.3762/bjoc.18.157

• trithiophosphite have been considered quantum-chemically (Figure 2, Table 1): trans-trans-trans (ttt), gauche-trans-trans (gtt), gauche-gauche-trans (ggt), and gauche-gauche-gauche (ggg). During optimization the ggt conformer adopted a cis-gauche-trans conformation with Fc(C)–S–P lone pair dihedral angles of 8

• °, −60°, and 173°, respectively (Table 1). The lowest energy has been predicted for the gtt conformer, nevertheless the energy differences between the gtt and cgt conformers are negligible (0.23 kcal/mol). Interestingly, the cgt conformation has been found previously for tricymantrenyl trithiophosphite

• [19]. The highest relative energy is predicted for the ggg conformer (1.7 kcal/mol). The ferrocene adopts an almost eclipsed conformation in all the models with the dihedral angle between two Cp rings of ≈ 10°. Our previous work indicated that Cp can rotate at room temperature [20]. The Fc(C)–S–P lone

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

• the 2 kJ/mol energy window were generated and optimized using DFT calculations at the B3LYP/6-31+G (d,p) level. Frequency calculations were performed at the same level to confirm that each optimized conformer was true minimum and to estimate the relative thermal free energy (ΔG) at 298.15 K. The two

Understanding the competing pathways leading to hydropyrene and isoelisabethatriene

• Shani Zev,
• Marion Ringel,
• Ronja Driller,
• Bernhard Loll,
• Thomas Brück and
• Dan T. Major

Beilstein J. Org. Chem. 2022, 18, 972–978, doi:10.3762/bjoc.18.97

• -house code which modifies parameters for cations from existing parameters for neutral molecules. For each intermediate in the reaction mechanism (path HP and IE) we created 100 conformers which were subsequently clustered (a cluster width of 1.0 Å was used). For each unique conformer we performed QM

• calculations and then chose the lowest energy conformer as representative of each carbocation intermediate in the mechanism. Hence, each intermediate state is represented by a single conformer, which is the lowest energy conformer found. Quantum chemistry calculations Optimizations and subsequent frequency

Terpenoids from Glechoma hederacea var. longituba and their biological activities

• Dong Hyun Kim,
• Song Lim Ham,
• Zahra Khan,
• Sun Yeou Kim,
• Sang Un Choi,
• Chung Sub Kim and
• Kang Ro Lee

Beilstein J. Org. Chem. 2022, 18, 555–566, doi:10.3762/bjoc.18.58

• , H-3b/H-2b; H-6/H-3b/H3-15 suggested that H-6, H3-14, and H3-15 were positioned in the same orientation. To confirm the relative configuration of C-8 in 2 was determined using a DP4+ statistical analysis [13]. The DP4+ protocol was applied to the simulated 13C NMR chemical shifts of the conformer 2a

• based on the Boltzmann populations of each conformer in the associated Gibbs free energy (Supporting Information File 1, Figure S45). The ECD spectra were Boltzmann-weighted and generated using SpecDis software (Version 1.71) [23] with a σ/γ value of 0.30 eV. The chemical shift values were calculated

Chemistry of polyhalogenated nitrobutadienes, 17: Efficient synthesis of persubstituted chloroquinolinyl-1H-pyrazoles and evaluation of their antimalarial, anti-SARS-CoV-2, antibacterial, and cytotoxic activities

• Viktor A. Zapol’skii,
• Isabell Berneburg,
• Ursula Bilitewski,
• Melissa Dillenberger,
• Katja Becker,
• Stefan Jungwirth,
• Aditya Shekhar,
• Bastian Krueger and
• Dieter E. Kaufmann

Beilstein J. Org. Chem. 2022, 18, 524–532, doi:10.3762/bjoc.18.54

• imidoacetal D. Due to free rotation of the (O,N,N)C–C(NO2) axis the suitable conformer E can be formed. Thus, the less hindered NH group of intermediate E interacts with the C3 position giving an intramolecular, five-membered addition product F. Upon elimination of HCl from F by means of the second equivalent

Unexpected chiral vicinal tetrasubstituted diamines via borylcopper-mediated homocoupling of isatin imines

• Marco Manenti,
• Leonardo Lo Presti,
• Giorgio Molteni and
• Alessandra Silvani

Beilstein J. Org. Chem. 2022, 18, 303–308, doi:10.3762/bjoc.18.34

• . Interestingly, the molecule does not bear any pseudo-mirror plane, that is, the observed conformer is asymmetric (C1) in itself, regardless the configuration of the two sulfinamide substituents. This peculiarity is likely due to the hindered rotation across the newly formed C–C bond, joining the two oxindole

• conformer. Aiming to generalize the discovered transformation, a brief scope of the reaction with respect to the N-tert-butanesulfinyl imine substrate was next performed (Figure 2). The protecting group R1 on the oxindole nitrogen atom was found to have a moderate effect on the reactivity, with R1 = Bn

• ) and one sulfinamide oxygen (O4). Atom numbering as in Figure 1. The asymmetry of such interactions reflects the intrinsic asymmetry of the solid-state conformer. Supporting Information Supporting Information File 42: Experimental part, NMR spectra and christallographic data of compound 2a.

Diametric calix[6]arene-based phosphine gold(I) cavitands

• Gabriele Giovanardi,
• Andrea Secchi,
• Arturo Arduini and
• Gianpiero Cera

Beilstein J. Org. Chem. 2022, 18, 190–196, doi:10.3762/bjoc.18.21

• high symmetrical geometry. Finally, a single broad peak for the four methoxy groups ($) appears at 2.96 ppm. In analogy with parental diureido and dithioureido calix[6]arenes, we were able to observe the presence of a second minor cone conformer, in a ≈4:1 ratio, highlighted by the presence of a second

Biological properties and conformational studies of amphiphilic Pd(II) and Ni(II) complexes bearing functionalized aroylaminocarbo-N-thioylpyrrolinate units

• Samet Poyraz,
• Samet Belveren,
• Sabriye Aydınoğlu,
• Mahmut Ulger,
• Abel de Cózar,
• Maria de Gracia Retamosa,
• Jose M. Sansano and
• H. Ali Döndaş

Beilstein J. Org. Chem. 2021, 17, 2812–2821, doi:10.3762/bjoc.17.192

• ligand rotamers were considered during the optimization process. Only one enantiomer was selected for running the calculations for simplicity. The obtained results are gathered in Figure 1 and Figure 2. These calculations show that for ligands L1 and L3, conformer A and conformer B, resulting from a free

• nickel or palladium atoms. As far as the L1-Ni complex was concerned, this fluxional equilibrium disappeared due to metal coordination. In this case, complexes involving conformer B were highly energetic due to steric repulsion between the CO2Me substituents of the pyrrolidine ring. Thus, only one set of

• signals in NMR spectra (corresponding to conformer A) would be observed. For L1-Pd complexes, the aggregate included two energetically accessible rotamers at room temperature (energetic difference of +2.2 kcal·mol−1, Figure 1). Therefore, the duplicated set of signals in the 1H NMR was justified. We

Synthesis and investigation on optical and electrochemical properties of 2,4-diaryl-9-chloro-5,6,7,8-tetrahydroacridines

• Najeh Tka,
• Mohamed Adnene Hadj Ayed,
• Mourad Ben Braiek,
• Mahjoub Jabli and
• Peter Langer

Beilstein J. Org. Chem. 2021, 17, 2450–2461, doi:10.3762/bjoc.17.162

• value, while the calculated LUMO energy was less negative. This can be explained by the fact that the calculations were achieved based on an equilibrium conformer. Conclusion In conclusion, we developed a convenient synthesis of novel 2,4-diaryl-9-chloro-5,6,7,8-tetrahydroacridines starting from

• a PGSTAT30 Autolab potentiostat. Theoretical calculations The theoretical studies were realized in vacuum with the Gaussian 09 program [70]. The geometry of the equilibrium conformer at the ground state was first found at AM1 level. Then, further optimization through density functional theory (DFT

Nomimicins B–D, new tetronate-class polyketides from a marine-derived actinomycete of the genus Actinomadura

• Zhiwei Zhang,
• Tao Zhou,
• Taehui Yang,
• Keisuke Fukaya,
• Enjuro Harunari,
• Shun Saito,
• Katsuhisa Yamada,
• Chiaki Imada,
• Daisuke Urabe and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2194–2202, doi:10.3762/bjoc.17.141

• Minimum (MCMM) method with PRCG energy minimization by the OPLS3e force field to obtain 56 conformational isomers within 10.0 kcal/mol from the minimum energy conformer. Geometries of the conformers were then optimized at the M06-2X/6-31G(d) level of theory with the SMD solvation model. Frequency

• of theory, affording 24 conformers within 3.0 kcal/mol from the minimum Gibbs free energy. The ECD spectrum of each conformer was simulated by the TDDFT calculation of 25 excited states at the ωB97X-D/def2-TZVP-PCM level of theory. The spectrum of structure 4a was created by the weighted average of

2,4-Bis(arylethynyl)-9-chloro-5,6,7,8-tetrahydroacridines: synthesis and photophysical properties

• Najeh Tka,
• Mohamed Adnene Hadj Ayed,
• Mourad Ben Braiek,
• Mahjoub Jabli,
• Noureddine Chaaben,
• Kamel Alimi,
• Stefan Jopp and
• Peter Langer

Beilstein J. Org. Chem. 2021, 17, 1629–1640, doi:10.3762/bjoc.17.115

• equilibrium conformer at ground state was first found at AM1 level. Then, further optimizations through density functional theory (DFT) approach [73] at the restricted Becke3–Lee–Yang–Parr hybrid functional (B3LYP) with standard basis set 6-31G were carried out. Experimental procedure and spectroscopic data

Synthesis of 10-O-aryl-substituted berberine derivatives by Chan–Evans–Lam coupling and investigation of their DNA-binding properties

• Peter Jonas Wickhorst,
• Mathilda Blachnik,
• Denisa Lagumdzija and
• Heiko Ihmels

Beilstein J. Org. Chem. 2021, 17, 991–1000, doi:10.3762/bjoc.17.81

• shift of the equilibrium between the [3 + 1] conformer, related to the shoulder at 255 nm [59], and the basket-type conformation of 22AG, assigned to the positive signal at 290 nm and the weak negative band at 260 nm [60][61] in favor of the latter. Hence, these observations showed that the ligands bind

Microwave-assisted multicomponent reactions in heterocyclic chemistry and mechanistic aspects

• Shivani Gulati,
• Stephy Elza John and
• Nagula Shankaraiah

Beilstein J. Org. Chem. 2021, 17, 819–865, doi:10.3762/bjoc.17.71

• -proliferative activity against tumor cell lines leading to the discovery of new lead compounds (Scheme 6). A tentative mechanism in Scheme 7 depicts the formation of iminium ion A from the reaction between 19 and 20 after the intramolecular protonation by carboxylic acid. The A conformer stabilized by

Menthyl esterification allows chiral resolution for the synthesis of artificial glutamate analogs

• Kenji Morokuma,
• Shuntaro Tsukamoto,
• Kyosuke Mori,
• Kei Miyako,
• Ryuichi Sakai,
• Raku Irie and
• Masato Oikawa

Beilstein J. Org. Chem. 2021, 17, 540–550, doi:10.3762/bjoc.17.48

• in the top five conformers (total population: 94.4%, data not shown, see below for detailed discussions). Although the characteristic NOESY crosspeak shown in Scheme 4 seemed to be attributable to the second conformer of the (2S)-isomer (29.4% population, data not shown), the other conformers were

• )-isomers 10 and 21, these three conditions match to define the stable conformer (see Figure 3 and Figure 8). However, the situation is different for the (S)-isomers 10* and 21* because there is no conformation that simultaneously fulfills these three conditions in these compounds. Thus, in 21*, to avoid a

• steric repulsion with the large ring C with the TFA group, the isopropyl group takes a conformation proximal to the methyl ester (see Figure 7). For 10*, with smaller size of the ring C, a conformer in which the isopropyl group and the methyl ester are separated also seems to be energetically

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

• provides a higher stability to the trans-conformer, while the S-Flp increases the stability of the cis-amide. The relative stabilization is usually about 1–2 kJ⋅mol−1 when measured for the typical model compounds. Dfp exhibits a relatively weak destabilization of the trans-amide [16][52]. These energetic

Direct synthesis of anomeric tetrazolyl iminosugars from sugar-derived lactams

• Michał M. Więcław and
• Bartłomiej Furman

Beilstein J. Org. Chem. 2021, 17, 115–123, doi:10.3762/bjoc.17.12

• of the product as a chair (1C4, 4C1) or a skew-boat (1S3, 3S1) conformer, of which the former is favored, as it proceeds via the lower-energetic chair-like transition state. The favored path of action will result in addition syn or anti to the substituent in position 5, depending on the starting

• conformer. Therefore, once the ground conformer of the oxocarbenium ion is established, this logic may be used to predict the reaction’s stereochemistry. The same principle may be successfully applied to reactions of iminium cations. We have previously shown that in the case of glucose- and galactose

Chiral anion recognition using calix[4]arene-based ureido receptors in a 1,3-alternate conformation

• Tereza Horáčková,
• Jan Budka,
• Vaclav Eigner,
• Wen-Sheng Chung,
• Petra Cuřínová and
• Pavel Lhoták

Beilstein J. Org. Chem. 2020, 16, 2999–3007, doi:10.3762/bjoc.16.249

• different conformations. Although the overwhelming majority of calixarene-based receptors makes use of the cone conformer A (Figure 1), the corresponding diureidocalix[4]arenes in the 1,3-alternate conformation B showed [42][43] surprisingly good complexation abilities towards selected anions. Especially

• for chiral anion recognition, contrary to the cone receptor, a design based on the 1,3-alternate conformer enables the introduction of chiral units into the phenolic functions of the inverted aromatic moieties nearby the ureido cavity responsible for the binding, as in C. This design can be

• exemplified by our previously published receptors C1 based on a calix[4]arene moiety or by C2 using thiacalix[4]arene as the core scaffold [44][45]. Moreover, the introduction of the tert-butyl groups into the 1,3-alternate conformer should lead to the overall increase rigidity of the molecule, possibly

Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• 22AG that are formed in the K+-containing buffer solution [59]. In particular, the decrease of the positive shoulder around 270 nm shows the disappearance of the (3 + 1) conformer, to which this band is assigned [59], in favor of the basket-type antiparallel quadruplex structure, which is identified by

Vicinal difluorination as a C=C surrogate: an analog of piperine with enhanced solubility, photostability, and acetylcholinesterase inhibitory activity

• Yuvixza Lizarme-Salas,
• Alexandra Daryl Ariawan,
• Ranjala Ratnayake,
• Hendrik Luesch,
• Angela Finch and
• Luke Hunter

Beilstein J. Org. Chem. 2020, 16, 2663–2670, doi:10.3762/bjoc.16.216

• seem to dominate the conformer population distribution of 2 in chloroform solution, because the weight-averaged calculated J-values of 2a–c match the experimentally-measured J-values quite well (Figure 2). But none of the structures 2a–c are a close conformational match with piperine (1). A noteworthy

• approximate rotamers I and IV, respectively (Figure 1). The unexpectedly high relative energy that was calculated for compound 2f might be partially attributable to the fact that it features only a single F···H contact within 2.50 Å. The calculations suggest that the conformer 2f is not significantly

• this might increase the accessibility of conformer 2f. We reasoned that comparing the biological activities of 1 vs 2 might shed light on this possibility (vide infra). Photostability A limitation of piperine (1) as a drug lead is its instability under UV light. The conjugated system of 1 is well-known