Synthesis of bis-spirocyclic derivatives of 3-azabicyclo[3.1.0]hexane via cyclopropene cycloadditions to the stable azomethine ylide derived from Ruhemann's purple

• Alexander S. Filatov,
• Olesya V. Khoroshilova,
• Anna G. Larina,
• Vitali M. Boitsov and
• Alexander V. Stepakov

Beilstein J. Org. Chem. 2022, 18, 769–780, doi:10.3762/bjoc.18.77

• using density functional theory (DFT) methods at the M11/cc-pVDZ level of theory. The cycloaddition reactions have been found to be HOMOcyclopropene–LUMOylide controlled while the transition-state energies for the reaction of 3-methyl-3-phenylcyclopropene with PRP are fully consistent with the

• experimentally observed stereoselectivity. Keywords: azomethine ylides; cycloaddition; cyclopropenes; DFT calculations; spiro heterocycles; Introduction Spiro compounds (molecules containing at least two rings with only one common atom) are an important class of both synthetic and naturally occurring

• ). Based on these observations, we concluded that electronic properties of the substituent at the C3 position of a cyclopropene ring have a major impact on the reactivity. A more detailed discussion of this issue is presented in the section devoted to the DFT (density functional theory) computational study

An isoxazole strategy for the synthesis of 4-oxo-1,4-dihydropyridine-3-carboxylates

• Timur O. Zanakhov,
• Ekaterina E. Galenko,
• Mikhail S. Novikov and
• Alexander F. Khlebnikov

Beilstein J. Org. Chem. 2022, 18, 738–745, doi:10.3762/bjoc.18.74

• intermediate 3, as shown for the reaction of isoxazole 1g (Scheme 2). Taking into account that compounds 2 can potentially exist in pyridone and pyridole tautomeric forms, we performed calculations at the DFT B3LYP-D3/6-311+G(d,p) level of theory with SMD solvent model to evaluate this tautomeric equilibrium

Structural basis for endoperoxide-forming oxygenases

• Takahiro Mori and
• Ikuro Abe

Beilstein J. Org. Chem. 2022, 18, 707–721, doi:10.3762/bjoc.18.71

• molecular dynamics analyses, as well as DFT calculations of the FtmOx1 reaction, suggested a modified mechanism [72][73][74]. In this mechanism, the tyrosyl radical at Tyr224 is generated by the Fe(IV)=O species, which abstracts a hydrogen atom at C21 to form an endoperoxide ring through the reaction with

Heteroleptic metallosupramolecular aggregates/complexation for supramolecular catalysis

• Prodip Howlader and
• Michael Schmittel

Beilstein J. Org. Chem. 2022, 18, 597–630, doi:10.3762/bjoc.18.62

• cooperative effect resulting from an additional η2-binding of the second copper(I) at the acetylene unit at which the second click reaction would take place. In case of distance mismatch, it is the formation of this copper–alkyne η2-complex that compensates for the build-up of strain as demonstrated by DFT

Syntheses of novel pyridine-based low-molecular-weight luminogens possessing aggregation-induced emission enhancement (AIEE) properties

• Masayori Hagimori,
• Tatsusada Yoshida,
• Yasuhisa Nishimura,
• Yukiko Ogawa and
• Keitaro Tanaka

Beilstein J. Org. Chem. 2022, 18, 580–587, doi:10.3762/bjoc.18.60

• -induced emission enhancement (AIEE) properties in aqueous media. Compounds 4a and 4e, bearing electron-withdrawing groups (Br and CF3, respectively) showed 7.0 and 15 times fluorescence enhancement. Time-dependent density functional theory (TD-DFT) calculations were performed to gain better insight into

• the electronic nature of the compounds with and without AIEE properties. Keywords: acceptor–donor–acceptor; AIEE; low molecular weight; one-pot reaction; ((pyridin-2-yl)amino)maleimide; TD-DFT calculation; Introduction Fluorescent compounds have attracted considerable attention as functional

• in AIEE. To compare the electronic natures of the compounds with and without AIEE, we performed TD-DFT calculations on each monomer of 3a, 4a, and 4e. The graphical representations of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) for the ground-state

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

• theory (DFT) studies suggested that the excellent stereoselectivities of the catenane are a direct result of the cooperative interaction of both phosphoric acid groups, enabled by the mechanical bond. Follow-up studies showed that such acid–acid interactions are also relevant for monophosphoric acid

• for the non-interlocked mixture, see Figure 15). DFT calculations showed that the reaction takes place by cooperative action of the Li phosphate macrocycle and the amine thread, enabled by the mechanical bond. The Li phosphate acts as a Lewis acid to activate the malonic acid diethyl ester, which is

Substituent effect on TADF properties of 2-modified 4,6-bis(3,6-di-tert-butyl-9-carbazolyl)-5-methylpyrimidines

• Irina Fiodorova,
• Tomas Serevičius,
• Rokas Skaisgiris,
• Saulius Juršėnas and
• Sigitas Tumkevicius

Beilstein J. Org. Chem. 2022, 18, 497–507, doi:10.3762/bjoc.18.52

• confirm the structures of the synthesized compounds (see Figures S1–S27 in Supporting Information File 1). DFT analysis To assess the structural and electronic properties of the chromophores tCbz-mPYR and 1–6, quantum chemical calculations were performed. DFT analysis revealed that all studied compounds

• the similar molecular structures, the studied chromophores showed somewhat different electronic properties, mainly due to the variation of the acceptor structure. The DFT computed spatial distribution of frontier molecular orbitals (FMOs) of compounds tCbz-mPYR and 1–6 is presented in Figure 2. A

• spectra were rather similar for all compounds, described with, typical for tCbz units, vibronic progression-having peaks bellow ≈340 nm [41]. Molar absorption coefficients were in the range of 19700–34200 M−1 cm−1, being in line with DFT predicted S0→S1 oscillator strengths and LUMO energies. The

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

• the efficacy of introducing two electronic donors on the acceptor unit. The calculations employed density functional theory (DFT) with the long-range corrected ωPBE functional and the 6-31G(d,p) basis set. Tuning of the range separation parameter was performed for both molecules [20] with the results

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

• electron-withdrawing groups inactivates the iridium catalyst, perhaps by chelation with the carbonyl and the bridging oxygen atom. Computational Computational details All density functional theory (DFT) calculations in this study were carried out with the Gaussian 16, C.01 suite of programs [68]. Geometry

• calculated from the optimized structures by single-point calculations by adding thermochemical corrections to the electronic energy. Optimized structures are illustrated using CYLview [73]. In order to further understand the iridium-catalyzed hydroacylation reaction, we carried out DFT calculations on the

• diminished product yields. Using DFT calculations, we investigated the [Ir(COD)OH]2-catalyzed hydroacylation reactions of C1-substituted OBDs. From these results, we found the reductive elimination step is the rate-determining step and the origin of regioselectivity for the catalytic cycle. Moreover, we

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

• -functional theory (DFT) computations were used to explain the reaction mechanism for the ring opening of the epoxide and the formation of five-membered lactones. The stereochemistry of the synthesized compounds was determined by 1D and 2D NMR spectroscopy. The configuration of methyl 6-hydroxy-9-oxo-8

• -oxabicyclo[5.2.1]decan-10-yl)carbamate was confirmed by X-ray diffraction. Keywords: aminocyclitol; azidolysis; bicyclic β-lactam; bicyclic lactone; cyclic β-amino acids; DFT; Introduction Cyclic β-amino acids have for the past few decades aroused widespread synthetic interest owing to their diverse

• , which is a typical transesterification reaction. To explain the formation of lactone 10, we performed a series of DFT computations using the Gaussian 16 software [29]. For this purpose, we performed geometry optimizations using the B3LYP functional [30][31][32][33]. Vibrational frequencies were computed

1,2-Naphthoquinone-4-sulfonic acid salts in organic synthesis

• Ruan Carlos B. Ribeiro,
• Patricia G. Ferreira,
• Amanda de A. Borges,
• Luana da S. M. Forezi,
• Fernando de Carvalho da Silva and
• Vitor F. Ferreira

Beilstein J. Org. Chem. 2022, 18, 53–69, doi:10.3762/bjoc.18.5

• equilibrium between A and B using semiempirical calculations (AM1 and PM3) and DFT (B3LYP/6-31G(d)) in the gas phase and water, where it was observed that in the gas phase B is the most stable, while in water A is formed, which is in agreement with the experimental results reported in the literature. There

The enzyme mechanism of patchoulol synthase

• Houchao Xu,
• Bernd Goldfuss,
• Gregor Schnakenburg and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 13–24, doi:10.3762/bjoc.18.2

• reactivated by protonation for further cyclisation steps, while previously discussed intra- and intermolecular hydrogen transfers are not supported. Furthermore, the isolation of the new natural product (2S,3S,7S,10R)-guaia-1,11-dien-10-ol from patchouli oil is reported. Keywords: biosynthesis; DFT

• contradictory. For this reason, we have reinvestigated the enzyme mechanism of PTS in isotopic labelling experiments through methods recently developed in our laboratory that make use of 13C and 2H-substituted terpene precursors, and by DFT calculations. The general strategy in these experiments is to use

• experiments and the DFT calculations were not only carried out in a way to gain support for one mechanism, but also to disprove some of the earlier reports in order to resolve the contradictions in the literature. Results and Discussion Absolute configurations of patchoulol and pogostol In order to

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

• -helicity in water. Investigation of several derivatives by means of density functional theory (DFT) geometry optimisations indicated that substitution at indole C6 tends to induce more significant deformation of the peptide chain compared to substitution at indole C7. Moreover, introduction of an

• in i + 4-position of the linear axin CBD sequence aAxWt were substituted by tryptophan and lysine, respectively, to have a higher analogy to the lysine modified SMC stapled peptides. Following the indications of DFT calculations, stapled peptide P5 was synthesised by modification of lysine in the i

• experimentally. Conclusion In conclusion, suitable reaction conditions were found for the synthesis of stapled peptides by an intramolecular late-stage SMC on resin. The peptide sequences are based on the CBD of axin. Optimisation of the cross-link, guided by DFT geometry optimisation, finally resulted in SMC

DABCO-promoted photocatalytic C–H functionalization of aldehydes

• Bruno Maia da Silva Santos,
• Mariana dos Santos Dupim,
• Cauê Paula de Souza,
• Thiago Messias Cardozo and
• Fernanda Gadini Finelli

Beilstein J. Org. Chem. 2021, 17, 2959–2967, doi:10.3762/bjoc.17.205

• , in a similar fashion of previous reports [31][32]. However, addition of bromide from external sources led to diminished yields (Supporting Information File 1, Table S6). Also, DFT calculations demonstrated that a HAT reaction between bromine radical and isovaleraldehyde is a barrierless reaction

• results do not support this is the operating mechanism and further investigations are underway to determine a plausible path for the reaction in the absence of bicyclic amine catalysts (see Supporting Information File 1, chapter 8 for details). The HAT step with 1 was investigated by DFT calculations at

• the DFT/M06-2X/cc-pVTZ level with DABCO and quinuclidine. The energy profiles include the separated reagent molecules (Reac. ∞), the reactants complex (RC), the transition state (TS), the products complex (PC) and the separated products (Prod. ∞). Figure 3 show the calculated Gibbs free energies for

Effect of a twin-emitter design strategy on a previously reported thermally activated delayed fluorescence organic light-emitting diode

• Ettore Crovini,
• Zhen Zhang,
• Yu Kusakabe,
• Yongxia Ren,
• Yoshimasa Wada,
• Bilal A. Naqvi,
• Prakhar Sahay,
• Tomas Matulaitis,
• Stefan Diesing,
• Ifor D. W. Samuel,
• Wolfgang Brütting,
• Katsuaki Suzuki,
• Hironori Kaji,
• Stefan Bräse and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2021, 17, 2894–2905, doi:10.3762/bjoc.17.197

• DICzTRZ were determined by a combination of NMR spectroscopy, mass spectrometry, and IR spectroscopy. Theoretical calculations Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations in the gas phase at the PBE0/6-31G(d,p) level reveal the potential of DICzTRZ as a TADF material. The

• nature of the S1 and T1 states and their corresponding energies were then obtained using the Tamm–Dancoff approximation [27] to TD-DFT (TDA-DFT). DICzTRZ possesses a ΔEST of 0.19 eV, comparable to 0.22 eV obtained for ICzTRZ at the same level of theory. We can observe a slightly stabilized S1 energy of

• stabilized compared to that predicted from DFT (EHOMO: −5.03 eV); however, the less positive oxidation potentials in DICzTRZ versus ICzTRZ does align with the predictions obtained by DFT. The UV–vis absorption spectrum of DICzTRZ, while slightly red-shifted and with higher molar absorptivity (as was the case

Iron-catalyzed domino coupling reactions of π-systems

• Austin Pounder and
• William Tam

Beilstein J. Org. Chem. 2021, 17, 2848–2893, doi:10.3762/bjoc.17.196

• theory (DFT) mechanistic study. The authors proposed a radical-polar crossover mechanism. First, a SET from Fe(II) to the alkyl diacyl peroxide generates the alkyl acyloxy radical which decarboxylates to afford the alkyl radical 165. Addition of the radical across the alkene affords the benzylic radical

• observed generating spiro succinimidetetrahydropyridine derivatives 172. To understand the chemoselectivity of the reaction, the authors performed a DFT mechanistic study. After the iminyl radical is generated it will undergo a 1,5-HAT to form the more stable alkyl radical which will add across the alkene

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

• , C. tropicalis, and C. glabrata standard strains. A deep conformational survey was monitored using DFT calculations with the aim to explain the importance of the final conformation in the biological experimental results. Keywords: antituberculosis; bidentate ligands; DFT; nickel; palladium

• results of its corresponding nickel(II) [18] and palladium(II) [19][20] complexes with the analogous tests obtained in the case of having a benzylic substituent at the same position. Also, DFT calculations are run in order to study the conformational analysis of the synthetized complexes. Results and

• 62.50–125 μg/mL (Table 2) when compared to reference drugs. the L3-Ni complex has the highest activity against Candida glabrata. DFT calculations of complexes The survey of relationship between structure of the complex and activity (SAR) moved us to design DFT calculations. The difference of the

Recent advances in the asymmetric phosphoric acid-catalyzed synthesis of axially chiral compounds

• Alemayehu Gashaw Woldegiorgis and
• Xufeng Lin

Beilstein J. Org. Chem. 2021, 17, 2729–2764, doi:10.3762/bjoc.17.185

• provide easy access to the privileged NOBIN (2-amino-2’-hydroxy-1,1’-binaphthyl) structures 41. The additional insights into the origins of enantiocontrol were described by DFT calculations. Owing to the presence of axially chiral indole-based biaryl scaffolds such as naphthylindoles and phenylindoles in

• excellent enantioselectivity when either CAT 1 (93–97% ee) or CPA 7 (93–96% ee) was used as catalyst (Scheme 21). The authors described that, BINOL-derived CPAs and pThr-type CPA scaffolds were found to be effective for atroposelective cyclodehydrations. Both the DFT and catalyst correlation studies showed

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

• influence on the catalytic reactions. Under ball-milling conditions, the Michael adducts were obtained in good yields but with slightly lower enantiomeric purities than in solution. DFT calculations elucidated its mode of action and confirmed a dual activation mode, which combines enamine activation of

• have evaluated the suitability of these catalysts under solvent-free conditions. With the help of DFT calculations, we elucidated the mode of action of these catalysts. Results and Discussion Synthesis of catalysts We have started the synthesis of the catalysts from Boc-protected (S)-prolinol (1), from

• 8f in 76 and 79% yield with comparable diastereoselectivity and enantioselectivity (Table 4, entries 8 and 9). DFT calculations of catalyst structure and reaction stereo-course To understand the catalyst operation, we have conducted DFT calculations of its structure and reaction course. All

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

• and their optical and electrochemical properties investigation by the use of UV–vis and emission spectroscopy, CV measurements as well as DFT calculations. Results and Discussion Synthesis. At the beginning of this study, we synthesized 2,4-dibromo-9-chloro-5,6,7,8-tetrahydroacridine (2) by refluxing

• further study the electronic properties, DFT calculations were carried out on the fully ground state at the restricted B3LYPlevel with 6-31G(d) basis set using dichloromethane as a continuum solvent model. The optimized chemical structures of 4a–d are given in Figure 7 with selected geometrical parameters

• 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

Synthesis of 5-arylacetylenyl-1,2,4-oxadiazoles and their transformations under superelectrophilic activation conditions

• Andrey I. Puzanov,
• Dmitry S. Ryabukhin,
• Anna S. Zalivatskaya,
• Dmitriy N. Zakusilo,
• Darya S. Mikson,
• Irina A. Boyarskaya and
• Aleksander V. Vasilyev

Beilstein J. Org. Chem. 2021, 17, 2417–2424, doi:10.3762/bjoc.17.158

• bond of these oxadiazoles quantitatively resulted in E/Z-vinyl triflates. The reactions of the cationic intermediates have been studied by DFT calculations and the reaction mechanisms are discussed. Keywords: acetylene-oxadiazoles; Friedel–Crafts reaction; hydroarylation; superelectrophilic activation

• ], it was shown by means of NMR spectroscopy and DFT calculation that the protonation of these oxadiazoles in Brønsted superacids TfOH and FSO3H gave reactive N,C-diprotonated species. The protonation of oxadiazoles 1 takes place at the nitrogen N4 and the α-carbon of the side chain C=C bond. One would

• expect the formation of similar dications at the protonation of acetylenyloxadiazoles 3 in Brønsted superacids (see Table 1). Table 1 contains data on DFT calculations of cations Aa–d (N-protonated forms) and Ba–d (N,C-diprotonated forms) derived at the protonation of oxadiazoles 3a–d. Charge

Halides as versatile anions in asymmetric anion-binding organocatalysis

• Lukas Schifferer,
• Martin Stinglhamer,
• Kirandeep Kaur and
• Olga García Macheño

Beilstein J. Org. Chem. 2021, 17, 2270–2286, doi:10.3762/bjoc.17.145

• example highlighting the importance of sidechain catalyst design was given by Jacobsen et al. in the tail-to-head cyclization of neryl chloride and derivatives 59 (Scheme 13) [17]. Mechanistic studies and DFT calculations revealed that an extended π-system in the sidechain of the bidentate urea catalyst

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

• functional theory (DFT) calculation of the ECD spectrum for 4, for which the absolute configuration was established by the modified Mosher’s method in our previous work [15]. Since the acyltetronic acid exists as a mixture of keto–enol tautomers, the calculation was carried out using the four possible

• 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

Sustainable manganese catalysis for late-stage C–H functionalization of bioactive structural motifs

• Jongwoo Son

Beilstein J. Org. Chem. 2021, 17, 1733–1751, doi:10.3762/bjoc.17.122

• . Additionally, difluorination was observed with negligible amounts because the monofluorinated product is rendered more electronically deficient by the first fluorine atom. Based on an analysis by DFT calculations, the postulated reaction pathway of manganese-catalyzed C–H fluorination is described in Figure 1

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

• radical cations of the phosphines under investigation were calculated by density functional theory (DFT), namely B3LYP-def2-TZVPPD. According to criterion introduced by Stewart et al. postulating air stability of phosphines when the SOMO energy is higher than −10 eV, the three derivatives should be air

• activity of differently substituted triarylphosphines in the oxa-Michael addition of alcohols to electron-deficient olefins was investigated. In general, the activity increases with increasing methoxy-substitution in the order TPP < MMTPP < TMTPP. The activity order was rationalized based on DFT