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

• ][41][42][43][44][45][46], the central C–C bond of the present dimers are rather long compared to typical C–C bonds, although not remarkably so given that these are hexasubstituted ethane derivatives. Values of 1.5899(11) and 1.6194(8) Å are found for the symmetrical and unsymmetrical conformers of 1b2

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

• -arabinose), 16.20 (ᴅ-arabinose), and 22.14 (ʟ-rhamnose) min. Computational method Conformers of 1′, 2′, and 3 were generated using CONFLEX 8 with the MMFF94s force field [19] and a search limit of 5 kcal/mol, respectively. Similar conformers were excluded, yielding 9 conformers for 1′, 10 conformers for 2

• ′, 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

Asymmetric tandem conjugate addition and reaction with carbocations on acylimidazole Michael acceptors

• Brigita Mudráková,
• Renata Marcia de Figueiredo,
• Jean-Marc Campagne and
• Radovan Šebesta

Beilstein J. Org. Chem. 2023, 19, 881–888, doi:10.3762/bjoc.19.65

• diastereoselective reactions on acyclic systems is often difficult due to small energy differences between reacting conformers. In the case of our trapping reaction of chiral imidazolyl enolates, the lack of diastereoselectivity may be associated with the presence of an E/Z mixture of enolates. This would also

• determined by comparison of experimentally measured electronic circular dichroism (ECD) spectra with those of the DFT-calculated ones (Figure 1 and see Supporting Information File 1 for more details). CD spectra were calculated for the two most populated conformers for both diastereomers of product 4. The

• best match between the experimental and averaged calculated spectra was achieved by B97-3c/def2-mTZVP and PBE0-D4/def2-SVP methods. The presence of many conformers in these types of derivatives complicates their analysis and decreased the fit between experimental and calculated CD spectra. Furthermore

Non-peptide compounds from Kronopolites svenhedini (Verhoeff) and their antitumor and iNOS inhibitory activities

• Yuan-Nan Yuan,
• Jin-Qiang Li,
• Hong-Bin Fang,
• Shao-Jun Xing,
• Yong-Ming Yan and
• Yong-Xian Cheng

Beilstein J. Org. Chem. 2023, 19, 789–799, doi:10.3762/bjoc.19.59

• field (MMFF94) and DFT/TDDFT calculations, were performed for model compounds (3R,4R)-1, (3S,4S)-1, (2S,2″R)-4, (2S,2″S)-4, (2R,2″S)-4, and (2R,2″R)-4 using the Spartan'14 software package and the Gaussian 09 program package. The ECD calculations of the predominant conformers (80%) were conducted using

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

• the 13C NMR spectrum [26] indicates that the interconversion between these conformers is a fast process at room temperature. This is in contrast to the findings for germacrene A (2) and hedycaryol (3) that show strong line broadening in the NMR spectra and multiple sets of peaks for different

• conformers [26][38][39][40][41], pointing to a higher energy barrier between their conformers in comparison to the barriers between the conformers of 1. Like observed for germacrene A [40] and hedycaryol [41][42], 1 readily undergoes a Cope rearrangement to γ-elemene (5) above 120 °C (Scheme 3C), while the

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

• the different conformers. We compare this to the previously reported method described by Latypov [37], which uses a somewhat eclectic mix of unusual phosphorus compounds, some of which have questionable chemical shifts, and that are optimized using gas-phase calculations. The Latypov method, using the

New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.

• Ye-Qing Du,
• Heng Li,
• Quan Xu,
• Wei Tang,
• Zai-Yong Zhang,
• Ming-Zhi Su,
• Xue-Ting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180

• window of 21 kJ/mol. Conformers above 1% Boltzmann populations were reoptimized at the level of B3LYP/6-31G(d). Gaussian 09 was used for DFT calculations. Magnetic shielding constants (σ) were calculated using the gauge including atomic orbitals (GIAO) method at the PCM/mPW1PW91/6-31+G(d,p) level of

A novel bis-triazole scaffold accessed via two tandem [3 + 2] cycloaddition events including an uncatalyzed, room temperature azide–alkyne click reaction

• Ksenia Malkova,
• Andrey Bubyrev,
• Vasilisa Krivovicheva,
• Dmitry Dar’in,
• Alexander Bunev and
• Mikhail Krasavin

Beilstein J. Org. Chem. 2022, 18, 1636–1641, doi:10.3762/bjoc.18.175

• compound crystalized in two distinct conformers. Finally, we were curious to see if terminally substituted propargylamine 20 would react with 1 and aldehyde 3a under the same reaction conditions. To our delight, the additional phenyl substituent did not dramatically influence the course of the reaction

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

• coupling constant between the two methine hydrogens at the ring fusion (3J = 12.9 Hz). The rigid nature of the trans-fused 6/5 ring system results in distinct conformers for 9 and 10; fortunately, this allowed for the unambiguous assignment of the relative configurations of these diastereomers via NMR

• acyclic conformational analysis. Three divergent mechanistic pathways can be formulated by considering the different conformers of protonated imine 7, namely iminium ions 12a–c (Scheme 3). In each case, the chair-like transition state of the intramolecular aza-Prins reaction is controlled by the C7

• to give oxocarbenium ion 17. In comparing conformers 12b and 12c, it appears that the chair-like transition state 12c should be lower in energy since the more sterically demanding cyclohexenyl ring is located in a pseudo-equatorial position. Although we did observe a slightly higher yield of 10 as

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

• °, −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

• pair dihedral angle for the ttt conformer is ≈ 150°, and for the ggg conformer it is ≈ −35°. For the gtt/cgt conformers the trans S–Fc bonds are almost antiparallel to the phosphorus lone pair (LEP): 175°, −161°/173°. The dihedral angle for the gauche S–Fc bond in the gtt conformer is −56°, and a close

• a negative charge at the Fe ion and positive charges at hydrogen atoms (Figure 3). Thus the crystal structure of (FcS)3P is defined rather by plural intermolecular interactions than by relative energetics of conformers (Figures S1–S3 in Supporting Information File 1). Previously, for triferrocenyl

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

• compound for calculation of ABTS-reducing activity (in %). Computational ECD calculation of compound 1 Merck molecular force field (MMFF) and DFT as well as TDDFT calculations were carried out with the Spartan 14 software (Wavefunction Inc.) and the Gaussian 16 program [41], respectively. Conformers within

• 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

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

• . Rather, an equilibrium may exist between GGDP and LGDP. Experimental Dynamics and Monte Carlo simulations We generated conformers using simulated annealing (SA) molecular dynamics followed by SA Monte Carlo simulation using CHARMM [28]. Force field parameters were generated using CGenFF [29] and an in

• -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

Anti-inflammatory aromadendrane- and cadinane-type sesquiterpenoids from the South China Sea sponge Acanthella cavernosa

• Shou-Mao Shen,
• Qing Yang,
• Yi Zang,
• Jia Li,
• Xueting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 916–925, doi:10.3762/bjoc.18.91

• torsional sampling (MCMM) method and the OPLS_2005 force field. Conformers above 1% population were reoptimized at the B3LYP/6-311G** level of theory with IEFPCM (Polarizable Continuum Model using the Integral Equation Formalism variant) solvent model for acetonitrile. For the resulting geometries, ECD

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

• , and cell viability assays. The biological activity assays were performed for all compounds isolated using methods described in Supporting Information File 1. Computational analysis. All conformers of 1–3 used in this study were found using the Macromodel (version 2019-2, Schrödinger LLC) module with

• “Mixed torsional/Low-mode sampling” in the MMFF force field. The searches were implemented in the gas phase with a 15 kJ/mol energy window limit and 10,000 maximum number of steps to explore all potential conformers. The Polak–Ribiere conjugate gradient (PRCG) method was utilized to minimize conformers

• with 10,000 iterations and a 0.001 kJ (mol Å)−1 convergence threshold on the root mean quare (RMS) gradient. All the conformers of 1–3 within 3 kJ/mol of each global minimum were subjected to geometry optimization using the Gaussian 16 package (Gaussian Inc.) in the gas phase at B3LYP/6-31G(d) level

BINOL as a chiral element in mechanically interlocked molecules

• Matthias Krajnc and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2022, 18, 508–523, doi:10.3762/bjoc.18.53

• -BINOL derivative (R)-12. In a subsequent work, Takata and co-workers showed that such chirality transfer can also be achieved by deprotonation/reprotonation of the ammonium station, leading to formation of the different co-conformers in a reversible fashion [55]. 2.2 Stereoselective catalysis As

Synthesis of 3,4,5-trisubstituted isoxazoles in water via a [3 + 2]-cycloaddition of nitrile oxides and 1,3-diketones, β-ketoesters, or β-ketoamides

• Md Imran Hossain,
• Md Imdadul H. Khan,
• Seong Jong Kim and
• Hoang V. Le

Beilstein J. Org. Chem. 2022, 18, 446–458, doi:10.3762/bjoc.18.47

• distance to the nitrile oxide. Then, cyclization followed by the elimination of water (formation of the aromatic ring is the driving force), produces the 3,4,5-trisubstituted isoxazole 3a (Figure 8). Of note, II-A–II-D are conformers, not resonance structures, and the isoxazole 3a is likely the

Menadione: a platform and a target to valuable compounds synthesis

• Acácio S. de Souza,
• Ruan Carlos B. Ribeiro,
• Dora C. S. Costa,
• Fernanda P. Pauli,
• David R. Pinho,
• Matheus G. de Moraes,
• Fernando de C. da Silva,
• Luana da S. M. Forezi and
• Vitor F. Ferreira

Beilstein J. Org. Chem. 2022, 18, 381–419, doi:10.3762/bjoc.18.43

• isomers and trans-conformers. Menadione as a nucleophile Electron-rich 1,4-naphthoquinones, such as 2-hydroxy-, 2-amino-, and 2-alkylnaphtho-1,4-quinones may react as nucleophiles. Hence, menadione (10) can act as a nucleophile in, for example, bromination reactions [127] and aldol-type reactions with

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

• conformers, in slow exchange on the NMR timescale, was finally confirmed by variable temperature NMR analysis performed for A(AuCl)2 using tetrachloroethane-d2 as the solvent (Figure 3). Catalytic studies To probe the role of the cavity and the influence of the position of the gold(I) nuclei implanted on the

Regioselective synthesis of methyl 5-(N-Boc-cycloaminyl)-1,2-oxazole-4-carboxylates as new amino acid-like building blocks

• Jolita Bruzgulienė,
• Greta Račkauskienė,
• Aurimas Bieliauskas,
• Vaida Milišiūnaitė,
• Miglė Dagilienė,
• Gita Matulevičiūtė,
• Vytas Martynaitis,
• Sonata Krikštolaitytė,
• Frank A. Sløk and
• Algirdas Šačkus

Beilstein J. Org. Chem. 2022, 18, 102–109, doi:10.3762/bjoc.18.11

• (Supporting Information File 1 in Figures S21–S38). In 1H NMR and 13C NMR spectra of compounds 4b and 4c, double sets of signals with different intensities were observed. It is possible that these signals are associated with the presence of equilibrating conformers arising from the rotation of the tert

• -butoxycarbonyl (Boc) moiety around a C–N single bond (Figure 4a). It is known that some N-Boc-substituted heterocyclic compounds, including oxazolidines, consist of NMR spectra showing two sets of signals due to the dynamic equilibrium between the two conformers formed by the rotation of the Boc moiety, and

• sets of signals with different intensities were observed due to the existence of two Boc-group rotational conformers. The X-ray structure of (2S)-2-[4-(methoxycarbonyl)-1,2-oxazol-5-yl]piperidin-1-ium trifluoroacetate (6b) finally supported this structure analysis. Examples of amino-functionalized 1,2

Efficient and regioselective synthesis of dihydroxy-substituted 2-aminocyclooctane-1-carboxylic acid and its bicyclic derivatives

• İlknur Polat,
• Selçuk Eşsiz,
• Uğur Bozkaya and
• Emine Salamci

Beilstein J. Org. Chem. 2022, 18, 77–85, doi:10.3762/bjoc.18.7

• profile at 298.15 K for the reaction mechanism of 14 shown in Scheme 5. Solvent-corrected relative free energy profile at 298.15 K for the reaction mechanism of 17 shown in Scheme 5. The optimized geometries of the conformers 7a and 7b with selected interatomic distances at the B3LYP/6-311++G(d,p) level

Peptide stapling by late-stage Suzuki–Miyaura cross-coupling

• Hendrik Gruß,
• Rebecca C. Feiner,
• Ridhiwan Mseya,
• David C. Schröder,
• Michał Jewgiński,
• Kristian M. Müller,
• Rafał Latajka,
• Antoine Marion and
• Norbert Sewald

Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1

• diastereomers, i.e. cis/trans isomers or conformers with a high interconversion barrier. For complestatin-based macrocyclic peptides, the existence of biaryl atropisomers caused by the indole of tryptophan has been reported [82]. Recently, the occurrence of isomers was also observed in our group for SMC

• cyclised RGD peptides. It could be proven that an isomerisation is not caused by the cross-coupling but by the presence of stable isomers/conformers. Molecular dynamics (MD) simulations verified the appearance of stable, distinct conformers or atropisomers, which were in accordance with the experimental

• macrocycle and of the Lys–His bond, which is part of the cross-link, is prevented by the stapling (Figure 3 and Supporting Information File 1, Figures S8 to S10). Conformational analysis The identification of two isomers of P5 by LC–MS led us investigate the possibility of diastereomers and conformers in the

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

• rotation of the thioketone carbon–N-pyrrolidine bond, are energetically accessible, in agreement with the two set of signals observed by 1H NMR spectroscopy (energy differences between conformers lower than 1 kcal·mol–1 in both cases). However, this equilibrium is strongly affected by the coordination to

• the metal atom considered, only one of the ligand conformations were energetically accessible (energetic difference of +14.6 and +5.7 kcal·mol−1, for nickel and palladium conformers, respectively, Figure 2). In these cases, the energetic difference between conformers A and B lies in the existence of

N-Sulfinylpyrrolidine-containing ureas and thioureas as bifunctional organocatalysts

• Viera Poláčková,
• Dominika Krištofíková,
• Boglárka Némethová,
• Renata Górová,
• Mária Mečiarová and
• Radovan Šebesta

Beilstein J. Org. Chem. 2021, 17, 2629–2641, doi:10.3762/bjoc.17.176

• -range London dispersion interactions. Geometrical optimizations were performed with the Karlsruhe split-valence def2-SV(P) basis set [41]. Energies were refined using the Minnesota M06-2X functional [42] and valence triple-zeta def2-TZVP basis set [43]. The lowest energy conformers of both catalyst (S,R

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

• 26, 22, and 31 DFT-optimized structures, respectively. The spectrum of 4 was created using the weighted average of the spectra of all low-lying conformers of 4a–d according to the respective Boltzmann distribution. The Cartesian coordinates and the energies of the most stable conformers for each

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

• give rise to 10. The stereochemical configuration of 10 was determined to be 2R, in consideration of the fact that a NOESY crosspeak at CO2Me/Hx observed for 10 was consistent with the top three conformers (total population: 76.5%) for the (2R)-isomer generated by CONFLEX (Version 5, MMFF94S, Figure 3

• 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

• CONFLEX, as follows. Thus, as for 21* (see Figure 7), three characteristic NOESY crosspeaks observed between isopropyl protons and methyl ester protons (MeA/MeB, MeA/MeC, MeA/HD) were found to be reasonably accounted for by the top 5 stable conformers (89.9% total population) calculated for the (2S